Biology [Fifth edition.] 9781260169621, 1260169626

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BIOLOGY, FIFTH EDITION Published by McGraw-Hill Education, 2 Penn Plaza, New York, NY 10121. Copyright © 2020 by McGraw-Hill Education. All rights reserved. Printed in the United States of America. Previous editions © 2017, 2014, and 2011. No part of this publication may be reproduced or distributed in any form or by any means, or stored in a database or retrieval system, without the prior written consent of McGraw-Hill Education, including, but not limited to, in any network or other electronic storage or transmission, or broadcast for distance learning. Some ancillaries, including electronic and print components, may not be available to customers outside the United States. This book is printed on acid-free paper. 1 2 3 4 5 6 7 8 9  LWI/LWI  21 20 19 ISBN 978-1-260-16962-1 MHID 1-260-16962-6 Portfolio Manager: Andrew Urban Product Developer: Elizabeth M. Sievers Marketing Manager: Kelly Brown Content Project Managers: Jessica Portz/Brent Dela Cruz/Sandra Schnee Buyer: Laura M. Fuller Design: David W. Hash Content Licensing Specialist: Lori Hancock Cover Image: ©BlueOrange Studio/Shutterstock Compositor: MPS Limited ©soponyono/Shutterstock All credits appearing on page are considered to be an extension of the copyright page. Library of Congress Cataloging-in-Publication Data Brooker, Robert J., author.   Biology / Robert J. Brooker, University of Minnesota - Twin Cities,   Eric P. Widmaier, Boston University, Linda E. Graham, University of   Wisconsin - Madison, Peter D. Stiling, University of South Florida.   Fifth edition. | New York, NY : McGraw-Hill Education, [2020] |   Includes index.   LCCN 2018023793 | ISBN 9781260169621   LCSH: Biology—Textbooks.   LCC QH308.2 .B564445 2020 | DDC 570—dc23 LC record   available at https://lccn.loc.gov/2018023793

The Internet addresses listed in the text were accurate at the time of publication. The inclusion of a website does not indicate an endorsement by the authors or McGraw-Hill Education, and McGraw-Hill Education does not guarantee the accuracy of the information presented at these sites.

mheducation.com/highered

Brief Contents About the Authors  iv Acknowledgements  v A Modern Vision for Learning: Emphasizing Core Concepts and Core Skills vi Preparing Students for Careers in Biololgy with NEW Cutting-Edge Content x Strengthening Problem-Solving Skills and Key Concept Development with Connect® xiii Contents  xvii 1 An Introduction to Biology  1

28 Protists 581 29 Fungi 605 30 Microbiomes: Microbial Systems On and Around Us  622 31 Plants and the Conquest of Land  641 32 The Evolution and Diversity of Modern Gymnosperms

Unit I Chemistry 23

Unit VI Flowering Plants 759

2 The Chemical Basis of Life I: Atoms, Molecules,

and Water  24 3 The Chemical Basis of Life II: Organic Molecules  45

Unit II Cell 68

4 Evolutionary Origin of Cells and Their General Features  69 5 Membrane Structure, Synthesis, and Transport  106 6 An Introduction to Energy, Enzymes, and Metabolism  127 7 Cellular Respiration and Fermentation  145 8 Photosynthesis 164 9 Cell Communication  183 10 Multicellularity 202

Unit III Genetics 219

11 Nucleic Acid Structure, DNA Replication, and

Chromosome Structure  220 12 Gene Expression at the Molecular Level I: Production of mRNA and Proteins  243 13 Gene Expression at the Molecular Level II: Non-coding RNAs 266 14 Gene Expression at the Molecular Level III: Gene Regulation 282 15 Mutation, DNA Repair, and Cancer  304 16 The Eukaryotic Cell Cycle, Mitosis, and Meiosis  323 17 Mendelian Patterns of Inheritance  348 18 Epigenetics, Linkage, and Extranuclear Inheritance  373 19 Genetics of Viruses and Bacteria  391 20 Developmental Genetics  413 21 Genetic Technologies and Genomics  434

Unit IV Evolution 457

22 An Introduction to Evolution  458 23 Population Genetics  477 24 Origin of Species and Macroevolution  496 25 Taxonomy and Systematics  516 26 History of Life on Earth and Human Evolution 

Unit V Diversity 560 27 Archaea and Bacteria 

561

and Angiosperms  664 33 An Introduction to Animal Diversity  686 34 The Invertebrates  701 35 The Vertebrates  734

36 An Introduction to Flowering Plant Form and Function 760 37 Flowering Plants: Behavior  782 38 Flowering Plants: Nutrition  801 39 Flowering Plants: Transport  818 40 Flowering Plants: Reproduction  839

Unit VII Animals 858

41 Animal Bodies and Homeostasis  859 42 Neuroscience I: Cells of the Nervous System  881 43 Neuroscience II: Evolution, Structure, and Function of the Nervous System  904 44 Neuroscience III: Sensory Systems  925 45 Muscular-Skeletal Systems and Locomotion  951 46 Nutrition and Animal Digestive Systems  970 47 Control of Energy Balance, Metabolic Rate, and Body Temperature 991 48 Circulatory and Respiratory Systems  1010 49 Excretory Systems  1043 50 Endocrine Systems  1058 51 Animal Reproduction and Development  1084 52 Immune Systems  1108 53 Integrated Responses of Animal Organ Systems to a Challenge to Homeostasis  1131

Unit VIII Ecology 1148

54 An Introduction to Ecology and Biomes  1149 55 Behavioral Ecology  1180 56 Population Ecology  1201 57 Species Interactions  1217 58 Communities and Ecosystems: Ecological Organization at Large Scales  1236 59 The Age of Humans  1257 60 Biodiversity and Conservation Biology  1280

535

Appendix A: Periodic Table of the Elements  A-1 Appendix B: Answer Key  A-2 Glossary  G-1 Index  I-1

iii

About the Authors Robert J. Brooker

Rob Brooker (Ph.D., Yale University) received his B.A. in biology at Wittenberg University, Springfield, Ohio, in 1978, and studied genetics while a graduate student at Yale. For his postdoctoral work at Harvard, he studied lactose permease, the product of the lacY gene of the lac operon. He continued working on transporters at the University of Minnesota, where he is a Professor in the Department of Genetics, Cell Biology, and Development and the Department of Biology Teaching and Learning. At the University of Minnesota, Dr. Brooker teaches undergraduate courses in biology, genetics, and cell biology. In addition to many other publications, he has written two undergraduate genetics texts published by McGraw-Hill: Genetics: Analysis & Principles, 6th edition, copyright 2018, and Concepts of Genetics, 3rd edition, copyright 2019.

Eric P. Widmaier Eric Widmaier received his B.A. degree in biological sciences at Northwestern University in 1979, where he performed research in animal behavior. In 1984, he earned his Ph.D. in endocrinology from the University of California at San Francisco, where he examined hormonal actions and their mechanisms in mammals. As a postdoctoral fellow at the Worcester Foundation for Experimental Research and later at The Salk Institute, he continued his focus on the cellular and molecular control of hormone secretion and action, with a particular focus on the brain. His current research focuses on the control of body mass and metabolism in mammals, the hormonal correlates of obesity, and the effects of high-fat diets on intestinal cell function. Dr. Widmaier is currently Professor of Biology at Boston University, where he teaches undergraduate human physiology and recently received the university’s highest honor for excellence in teaching. Among other publications, he is lead author of Vander’s Human Physiology: The Mechanisms of Body Function, 15th edition, published by McGraw-Hill, copyright 2019.

Linda E. Graham

Linda Graham earned an undergraduate degree from Washington University (St. Louis), a master’s degree from the University of Texas, and Ph.D. from the University of Michigan, Ann Arbor, where she also did postdoctoral research. Presently Professor of Botany at the University of Wisconsin-Madison, her research explores the evolutionary origins of algae and land-adapted plants, focusing on their cell and molecular biology as well as microbial interactions. In recent years Dr. Graham has engaged in research expeditions to remote regions of the world to study algal and plant microbiomes. She teaches undergraduate courses in microbiology and plant biology. She is the coauthor of, among other publications, Algae, 3rd edition, copyright 2016, a textbook on algal biology, and Plant Biology, 3rd edition, copyright 2015, both published by LJLM Press. iv

Left to right: Eric Widmaier, Linda Graham, Peter Stiling, and Rob Brooker

The authors are grateful for the help, support, and patience of their families, friends, and students, Deb, Dan, Nate, and Sarah Brooker, Maria, Caroline, and Richard Widmaier, Jim, Michael, Shannon, and Melissa Graham, and Jacqui, Zoe, Leah, and Jenna Stiling.

Peter D. Stiling

Peter Stiling obtained his Ph.D. from University College, Cardiff, United Kingdom. Subsequently, he became a postdoctoral fellow at Florida State University and later spent two years as a lecturer at the University of the West Indies, Trinidad. Dr. Stiling was formerly Chair of the Department of Integrative Biology at the University of South Florida (USF) at Tampa, where he is currently an Assistant Vice Provost for Strategic Initiatives and Professor of Biology. His research interests include plant-animal relationships and invasive species. He currently teaches biology to students in the USF in London summer program which he established in 2015. Dr. Stiling was elected an AAAS Fellow in 2012. He is also the author of Ecology: Global Insights and Investigations, 2nd edition, published by McGraw-Hill.

A Message from the Authors

As active teachers and writers, one of the great joys of this process for us is that we have been able to meet many more educators and students during the creation of this textbook. It is humbling to see the level of dedication our peers bring to their teaching. Likewise, it is encouraging to see the energy and enthusiasm so many students bring to their studies. We hope this book and its digital resources will serve to aid both faculty and students in meeting the challenges of this dynamic and exciting course. For us, this remains a work in progress, and we encourage you to let us know what you think of our efforts and what we can do to serve you better. Rob Brooker, Eric Widmaier, Linda Graham, Peter Stiling

Acknowledgements The lives of most science-textbook authors do not revolve around an analysis of writing techniques. Instead, we are people who understand science and are inspired by it, and we want to communicate that information to our students. Simply put, we need a lot of help to get it right. Editors are a key component who help the authors modify the content of this textbook so it is logical, easy to read, and inspiring. The editorial team for this Biology textbook has been a catalyst that kept this project rolling. The members played various roles in the editorial process. Andrew Urban  and his predecessor Justin Wyatt, Portfolio Managers (Majors Biology), have done an excellent job overseeing the 5th edition. Elizabeth Sievers, Senior Product Developer, has been the master organizer. Liz’s success at keeping us on schedule is greatly appreciated. We would also like to acknowledge our copy editor, Jane Hoover, for her thoughtful editing that has contributed to the clarity of this textbook. Another important aspect of the editorial process is the actual design, presentation, and layout of materials. It’s confusing if the text and art aren’t on the same page, or if a figure is too large or too small. We are indebted to the tireless efforts of Jessica Portz, Content Project Manager, and David Hash, Senior Designer at McGraw-Hill. Likewise, our production company, MPS Limited, did an excellent job with the paging, revision of existing art, and the creation of new art for the 5th edition. Their artistic talents, ability to size and arrange figures, and attention to the consistency of the figures have been remarkable. We would also like to acknowledge the ongoing efforts of the superb marketing staff at McGraw-Hill. Special thanks to Kelly Brown, Executive Marketing Manager, whose effort intensifies when this edition comes out.



Finally, other staff members at McGraw-Hill Higher Education have ensured that the authors and editors were provided with adequate resources to achieve the goal of producing a superior textbook. These include G. Scott Virkler, Senior Vice President, Products & Markets; Michael Ryan, Vice President, General Manager, Products & Markets; and Betsy Whalen, Vice President, Production and Technology Services.

Reviewers for Biology, 5th edition

∙∙ Lubna Abu-Niaaj  Central State University ∙∙ Joseph Covi  University of North Carolina at Wilmington ∙∙ Art Frampton  University of North Carolina at Wilmington ∙∙ Brian Gibbens  University of Minnesota ∙∙ Judyth Gulden  Tulsa Community College ∙∙ Alexander Motten  Duke University

∙∙ Melissa Schreiber  Valencia College ∙∙ Madhavi Shah  Raritan Valley Community College ∙∙ Jack Shurley  Idaho State University ∙∙ Om Singh  University of Pittsburgh at Bradford ∙∙ Michelle Turner-Edwards  Suffolk County Community College ∙∙ Ryan Udan  Missouri State University ∙∙ D. Alexander Wait  Missouri State University ∙∙ Kimberly Wallace  Texas A & M University San Antonio ∙∙ Megan Wise de Valdez  Texas A & M University San Antonio

v

A Modern Vision for Learning: Emphasizing Core Concepts and Core Skills Over the course of five editions, the ways in which biology is more of them. This approach will serve two purposes. First, the taught have dramatically changed. We have seen a shift away icon will help students to see how the various topics in this textfrom the memorization of details, which are easily forgotten, book are connected to each other by the five core concepts of and a movement toward emphasizing core concepts and critical biology. Second, the icon will allow students to appreciate the thinking skills. The previous edition of Biology strengthened skill important skills they are developing as they progress through development by adding two new features, called CoreSKILLS the text. and BioTIPS (described later), which are aimed at helping students develop effective strategies for solving problems and applying their knowledge in novel situations. In this edition, we have KEY PEDAGOGICAL FEATURES focused our pedagogy on the five core concepts of biology as OF THIS EDITION advocated by “Vision and Change” and introduced at a national conference organized by the American Association for the The author team is dedicated to producing the most engaging Advancement of Science (see www.visionandchange.org). These and current text available forSYNTHESIS, undergraduate students119who are MEMBRANE STRUCTURE, AND TRANSPORT core concepts, which are introduced in Chapter 1 (see Figure 1.4) majoring in biology. We have listened to educators and reviewed include the following: theysuch did notas rupture even and after 1Change, hour. Taken A together, results which this gene in a test tube (in vitro) using gene cloning techniques documents, Vision Call these to Action, are consistent with the hypothesis that CHIP28 functions as a chan(see Chapter 21). Starting with many copies of the gene in vitro, includes a summary of recommendations made at a national connel that allows the facilitated diffusion of water across the memthey added an enzyme transcribe the gene into mRNA that 1.  Evolution: The diversity of life evolved overtotime by processes ference organized the American Association for the Advancebrane. Many by subsequent studies confirmed this observation. Later, encodes the CHIP28 protein. This mRNA was then injected into of mutation, selection, andfrog genetic exchange. CHIP28 wasWe renamed to indicatetoitsreflect newly identified oocytes, chosen because these oocytes are large, easy to of Science. ment wantaquaporin our textbook core concepts function of allowing water to diffuse through a channel in the memandunits lack pre-existing proteinsdefine in their plasma 2. Structure and function: inject, Basic of structure the membranes and skills and provide a more learner-centered approach. To brane. In 2003, Agre was awarded the Nobel Prize in Chemistry for that allow the rapid movement of water. Following injection, the function of all living things. achieve these goals, Biology, 5th edition, has the following pedathis work. mRNA was translated into CHIP28 proteins that were inserted into the and plasmastorage: membrane The of the growth oocytes. After time 3.  Information flow, exchange, andsufficientgogical features. had been allowed for this to occur, the oocytes were placed in behavior of organisms area activated through the expression of Experimental Questions hypotonic medium. As a control, oocytes that had not been ∙∙ NEW!1.Core What observations about particular cell types in the human body Concepts: As mentioned, the five core concepts genetic information. injected with CHIP28 mRNA were also exposed to a hypotonic led to the experimental strategy of Figure 5.16?  medium. are introduced in Chapter 1 (see Figure 1.4). Throughout 4. Pathways and transformations of energy and matter: Bio2. What were the characteristics of CHIP28 that made Agre and As you can see in the data, a striking difference was observed Chaptersassociates 2 through 60, these core concepts emphasized speculate that it may transport water? are In your own logical systems grow andbetween change via that processes that are based oocytes expressed CHIP28 versus the control oocytes. words, briefly explain how they tested the hypothesis that CHIP28 by a Vision and Change icon, , placed next to headings Within minutes, oocytes thatgoverned contained the on chemical transformation pathways and are byCHIP28 the protein were has this function.  seen to swell due to the rapid uptake of water. Three to five minutes subsections andthebeneath certain figure 3. CoreSKILL » Explain how results of the experiment of legends. laws of thermodynamics. after being placed in a hypotonic medium, they actually ruptured!of particular Figure 5.16 support the proposed hypothesis. By comparison, the control oocytes did not swell as rapidly, and 5.  Systems: Living systems are interconnected and interacting. In addition to core concepts, “Vision and Change” has strongly advocated the development of core skills (also called core competencies). Transporters Bind Their Solutes and Undergo Those skills that are emphasized in this textbook are as follows: Conformational Changes

Hydrophilic pocket

∙∙ The ability to use models the andmembrane simulation chapter to the (each other side (Figure 5.17). For example, in 1995, biologist RobertModeling Brooker and colleagues proposed that a in Biology, 5e, contains a American new feature called transporter called lactose permease, which is found in the bacterium Challenge that asks students to create their own model or E. coli, has a hydrophilic pocket that binds lactose. They further prointerpret a model provided) posed that the two halves of the transporter protein come together at interface that moves in such a way that the lactose-binding site ∙∙ The ability to tap into the an interdisciplinary nature of science alternates between an outwardly accessible pocket and an inwardly

Solute

change that switches the exposure of the pocket from one side of

accessible pocket, as shown in Figure 5.17. This idea was later con∙∙ The ability to communicate and collaborate with professionals firmed by studies that determined the structure of the lactose permein other disciplines ase and related transporters. provide the principal ∙∙ The ability to understand the Transporters relationship between sciencepathway and for the cellular uptake of organic molecules, such as sugars, amino acids, and society nucleotides. In animals, they also allow cells to take up certain hor-

and neurotransmitters. In addition, many transporters play a A key goal of this textbook ismones to bring to life these five core conkey role in export. Waste products of cellular metabolism must be cepts of biology and the corereleased skills.from These and toxic skills areFor example, a cells concepts before they reach levels. transporter removesand lactic acid, a by-product highlighted in each chapter with a “Vision Change” icon, of muscle , cells during exercise. Other transporters, which are involved with ion transport, which indicates subsectionsplayand figures that focus on one or an important role in regulating internal pH and controlling

cell volume. Transporters tend to be much slower than channels. Their rate of transport is typically 100 to 1,000 ions or molecules per second.

vi

Conformational change

Let’s nowof turn our attention to a second category of transport proteins ∙∙ The ability to apply the process science known as transporters.* These transmembrane proteins bind one or ∙∙ The ability to use quantitative more solutes in a hydrophilic pocket and undergo a conformational reasoning

* Transporters are also called carriers. However, this term is misleading because transporters do not physically carry the solutes across the membrane.

For transport to occur, a solute binds in a hydrophilic pocket exposed on one side of the membrane. The transporter then undergoes a conformational change that switches the exposure of the pocket to the other side of the membrane, where the solute is then released.

Figure 5.17 Mechanism of transport by a transporter, also called a carrier.

Core Concept: Structure and Function Two structural features—a hydrophilic pocket and the ability to switch back and forth between two conformations— allow transporters to move ions and molecules across the membrane.

Transporters are named according to the number of solutes they bind and the direction in which they transport those solutes (Figure 5.18). Uniporters bind a single ion or molecule and transport it across the membrane. Symporters bind two or more ions or molecules and transport them in the same direction. Antiporters bind two or more ions or molecules and transport them in opposite directions.

into a purple pigment. The P allele is dominant because one P allele encodes enough of the functional protein—50% of the amount found in a PP homozygote—to provide a purple phenotype. Therefore, the PP homozygote and the Pp heterozygote both make enough of the purple pigment to512 yield purple flowers. CHAPTER 24 The pp homozygote cannot make any of the functional protein required for pigment synthesis, so its flowers are white. ∙∙ NEW! Core Skills: Six core skills aregene alsoevolution introduced in evolution ∙ A comparison of Hox and animal This explanation—that 50% of theparallels. functional protein is60, enough— Chapter 1 (see Section 1.6). In Chapters 2 through reveals striking Researchers havethese analyzed Hox gene is true for many dominant alleles.among In such cases, species the homozygote with sequences modern and made core skills are emphasized by a Vision and Change icon,estimates regarding two dominant alleles isthe making much more of the protein than necestiming ofof past events. Though the date is difficult to next toisheadings particular subsections, sary, ,soplaced if the amount reducedpinpoint, to 50%, as first it is Hox in the heterozygote, precisely the gene arose well over 600 mya. such as Feature andduplications beneath certain figure the individual stillInvestigations, has In plenty of this to accomplish whatevergene produced addition, geneprotein of this primordial legends. To distinguish them from theinCore Concepts, the cellular function it performs. In other cases, however, an allele may clusters of Hox genes other species. Clusters such as those be dominant the heterozygote actually than approximately found in modern likely tomore bethe present Core Skills because are highlighted in blueinsects type.were Inproduces addition, 50% of the functional protein. This increased production is due to the 600 mya. A duplication of atoHox cluster is estimated to have designator CoreSKILLS has been added certain learning phenomenon of gene regulation. The dominant occurred around 520 mya. allele is up-regulated outcomes and end-of-chapter questions that emphasize skills in the heterozygote to compensate for the lack of function of the of Hox gene origins correlate with major diversineeded the study Estimates of biology. recessivein allele. fication events in the history of animals. The Cambrian period,

unction.

at exhibit

e in determining

heritance patterns the first section of f traits affected by which is dominant lian inheritance, early demonstrate ssing the molecuow the molecular on an organism’s itance patterns of do not display a mission of these oduce the ratios of el’s observations. er, the inheritance patterns he chose ions in Mendelian

menon

del studied seven Figure 17.2). The s for these traits in a prevalent allele a wild-type allele unt and functions tered by mutation tural populations. ants, the recessive

nant and another ne products at the recessive allele is protein. In other likely to decrease a protein. These why many loss-ofuantitative look at

he recessive allele e. In this type of

∙∙

stretching from 543 to 490 mya, saw a great diversification of animal species. This diversification occurred after the Hox cluster was formed and was possibly undergoing its first duplication to produce two Hox clusters. Also, approximately 420 mya, a second duplicaGenotype PP Pp pp tion produced species with four Hox clusters. This event preceded Amount of functional the proliferation 100% of tetrapods—vertebrates 50% 0% with four limbs—that protein P produced occurred during the Devonian period, approximately 417–354 mya. Modern tetrapods four Hox clusters. Phenotype Purple have Purple WhiteThis second duplication may have been a critical event that led to the evolution of complex Only 50% of the terrestrial vertebrates with four limbs, such as amphibians, reptiles, functional proteinand mammals. is needed to produce the purple phenotype The striking correlation between the number of Hox genes and body complexity is thought have been instrumental in the evolution of animals. However, research has also shown that body complexity may not be solely dependent on the number of Hox genes. For example, the Colorless precursor Purple pigment Protein P in most tetrapods number of Hox clusters is four, whereas some fishes, molecule which do not have more complex bodies than tetrapods, have seven or eight Hox clusters. In addition, researchers have discovered that specialized body structures can be formed by influencing the regulation of Hox genes that are controlled by Hox genes. Figure 17.16 How genes giveand risethe to other traitsgenes during simple These findings indicate that changes in body complexity do not always Mendelian inheritance. In the heterozygote, the amount of protein have to be related total number of Hox genes or Hox clusters. encoded by a single dominant alleletoisthe sufficient to produce the dominant phenotype. In this example, the gene encodes an enzyme that is needed to produce a purple pigment. A plant with one or two Variation in Growth Rates Can Have a Dramatic copies of the dominant allele makes enough pigment to produce purple flowers. In aEffect pp homozygote, the complete lack of the on Phenotype functional protein (enzyme) results in white flowers. Another way that genetic variation can influence morphology is by controlling the relative growth rates different parts of the body durCore Skill: Quantitative Reasoning In aofsimple ing development. The term heterochrony dominant/recessive relationship, even though refers the to differences among species in theproduce rate or timing developmental events. The speeding heterozygote may less ofof a functional or slowingtodown of growth appears to be a common occurrence in proteinupcompared the homozygote that has two and leads to different species withbystriking morphological copiesevolution of the dominant allele, the amount made the heterozygote sufficient the dominant differences. is With regard to to yield the pace of evolution, such changes may phenotype. rapidly lead to the formation of new species. As an example, Figure 24.16 compares the progressive growth of human and chimpanzee skulls. At the fetal stage, the sizes and shapes of the skulls look fairly similar. However, after this stage, the relative growth rates of certain regions become markedly different, thereby affecting the shape and size of the adult skull. In the chimpanzee, the jaw region grows faster, adult NEW! Modeling Challenges: A growing trendgiving is thethe use of chimpanzee a much larger and longer jaw. In the human, the jaw grows more slowly, models in biology education. Students are asked to interpret and the region of the skull that surrounds the brain—the cranium— models and to create models data or humans a scenario. grows faster. Thebased result on is that adult have a smaller jaw but a largermodels craniumand thansimulations adult chimpanzees. Furthermore, using is one of the core

skills that is emphasized by “Vision and Change.” The author team has added a new feature called Modeling Challenge that asks students to create a model or to interpret a model they are given. Possible answers to the Modeling Challenges are provided in Connect.



Human

Chimpanzee

Fetus

Infant

Adult

Figure 24.16 Heterochrony. Due to heterochrony, one region of

the body may grow faster than another during development in different species. For example, the skulls of adult chimpanzees and humans have different shapes even though their fetal skull shapes are quite similar. Core Skill: Modeling The goal of this modeling challenge is to make a series of models that show the differences in limb lengths among orangutans, chimpanzees, and humans. Modeling Challenge: Search the Internet and look at photos of orangutans, chimpanzees, and humans. Even though these species look similar, one noticeable difference is the relative lengths of their limbs. Although the limbs in an early fetus look similar in all three species, the limbs in the adults show significant differences in their relative lengths. Draw models, similar to those in Figure 24.16, that show an early fetus, infant, and adult for all three species. Include an explanation of how heterochrony affects limb development.

Core Concept: Evolution The Study of the Pax6 Gene Indicates That Different Types of Eyes Evolved from One Simple Form ∙∙ Feature Investigations: The emphasis on skill development Thus farin in the this Feature section, we have focused on the rolesprovide of particular continues Investigations, which complete genes as they influence the development of species with different descriptions of experiments. These investigations begin with body structures. Explaining how a complex organ comes into background information in the text that describes the events that led to a particular study. The study is then presented as an illustration that begins with the hypothesis and then describes the experimental protocol at the experimental and conceptual levels. The illustration also includes data and the conclusions that were drawn from the data. This integrated approach

A MODERN VISION FOR LEARNING

vii

ure 16.13f–j). DNA replication does not occur between meiosis I and meiosis II. The sorting events of meiosis II are similar to those of mitosis, but the starting point is different. For a diploid cell with six chromosomes, mitosis begins with 12 chromatids that are joined as six pairs of sister chromatids (see Figure 16.8). By comparison, the two cells that begin meiosis II each have six chromatids that are joined as three pairs of sister chromatids. helps students to understand how experimentation leads to an Otherwise, the steps that occur during prophase, prometaphase, 118 CHAPTER 5 understanding of biological concepts. metaphase, anaphase, and telophase of meiosis II are analogous towater a channels mitotic division. Sister are separated during Figure 5.16 The discovery of (aquaporins) by Agre. (4): Courtesy Dr. Peterchromatids Agre anaphase II. HYPOTHESIS CHIP28 may function as a water channel. KEY MATERIALS Prior to this work, a protein called CHIP28 was identified that is abundant in red blood cells and kidney cells. The gene that encodes this protein was cloned, which means that many copies of the gene were made in a test tube. Experimental level

1

2

3

4

5 6

Conceptual level

Mitosis and Meiosis Differ in a Few Key Steps

Add an enzyme (RNA polymerase) and nucleotides to a test tube that contains many copies of the CHIP28 gene. This results in the synthesis of many copies of CHIP28 mRNA.

CHIP28 mRNA

RNA polymerase

Enzymes and nucleotides

How are the outcomes of mitosis and meiosis different? Mitosis produces two diploid daughter CHIP28cells that are genetically identical. In DNA our example shown in Figure 16.8, the starting cell had six chromo(three homologous pairs of chromosomes), and both daughter Inject the CHIP28 mRNA into somes frog eggs (oocytes). Wait several hours to allow cells time for the mRNA to be translated into received copies of the same six chromosomes. By comparison, CHIP28 protein at the ER membrane and CHIP28 protein is then moved via vesicles to the plasma meiosis reduces the number of setsCHIP28 of chromosomes. example insertedIn into the the membrane. plasma membrane. mRNA shown in Figure 16.13, the starting cell also had six chromosomes, CHIP28 protein Frog oocyte whereas theNucleus resulting fourCytosol daughter cells have Ribosomeonly three chromosomes. However, the daughter cells do not contain a random mix of Place oocytes into a hypotonic medium three chromosomes. Each haploid daughter cell contains one comand observe under a light microscope. As a control, also place oocytes that Control plete set of chromosomes, whereas the original diploid mother cell have not been injected with CHIP28 mRNA into a hypotonic medium and observe by microscopy. had two complete sets. How do we explain the different outcomes of mitosis and meiosis? Table 16.1 emphasizes the differences between certain key steps THE DATA in mitosis and meiosis that account for the different outcomes of these two processes. DNA replication Oocyte rupturing occurs prior to mitosis and meiosis I, Oocyte but not between meiosis I and II. During prophase of meiosis I, the homologs synapse to form bivalents. This explains why crossing over 3–5 minutes CHIP28 protein occurs commonly during meiosis, but rarely during mitosis. During prometaphase of mitosis and meiosis II, pairs of sister chromatids are Control CHIP28attached to bothControl poles. InCHIP28 contrast, during meiosis I, each pair of sister chromatids (within a bivalent) is attached to a single pole. BivaCONCLUSION The CHIP28 protein, now called aquaporin, allows the rapid movement of water across the membrane. lents align along the metaphase plate during metaphase of meiosis I, SOURCE Preston, G. M., Carroll, T. P., Guggino,sister W. B., and Agre, P. 1992. Appearance of water channels in Xenopus expressing red cell whereas chromatids align along the oocytes metaphase plate during CHIP28 protein. Science 256: 385–387. metaphase of mitosis and meiosis II. At anaphase of meiosis I, the homologous chromosomes separate, but the sister chromatids remain contrast, sister chromatid separation occurs ∙∙ BioTIPS: together. A featureInthat was added to the previous edition is during anaphase of mitosis and meiosis II. Taken together, the steps of mitosis aimed at helping students improve their problem-solving skills. produce two diploid cells that are genetically identical, whereas the Chapters 2steps through 60 contain solved problems cell called BioTIPS, of meiosis involve two sequential divisions that produce where “TIPS” stands for Information, and Problemfour haploid cellsTopic, that may not be genetically identical.

wo nuclei s is called omosomes a result of o not have

(see Fign meiosis similar to a diploid hromatids ure 16.8). have six romatids. etaphase, viii nalogous d during

Solving Strategy. These solved problems follow a consistent pattern in which students are given advice on how to solve problems in biology using 11 different problem-solving strategies: Make a drawing. Compare and contrast. Relate structure and function. Sort out the steps in a complicated process. Propose a hypothesis. Design an experiment. Predict the outcome. Interpret THE statistics. EUKARYOTIC CELL aCYCLE, MITOSIS,Search AND MEIOSIS 337 data. Use Make calculation. the literature.

BIO TIPS

THE QUESTION A diploid cell has 12 chromosomes, or 6 pairs. In the following diagram, in what phase of mitosis, meiosis I or meiosis II, is this cell?

MODERN VISION FOR LEARNING T A OPIC What topic in biology does this question address? The topic is cell division. More specifically, the question is asking

T OPIC What topic in biology does this question address? The topic is cell division. More specifically, the question is asking you to be able to look at a drawing and discern which phase of cell division a particular cell is in.

I NFORMATION What information do you know based on the question and your understanding of the topic? In the question, you are given a diagram of a cell at a particular phase of the cell cycle. This cell is derived from a mother cell with 6 pairs of chromosomes. From your understanding of the topic, you may remember the various phases of mitosis, meiosis I, and meiosis II, which are described in Figures 16.8 and 16.13. If so, you may initially realize that the cell is in metaphase.

P ROBLEM-SOLVING S TRATEGY Sort out the steps in a complicated process. To solve this problem, you may need to describe the steps, starting with a mother cell that has 6 pairs of chromosomes. Keep in mind that a mother cell with 6 pairs of chromosomes has 12 chromosomes during G1, which then replicate to form 12 pairs of sister chromatids during S phase. Therefore, at the beginning of M phase, this mother cell will have 12 pairs of sister chromatids. During mitosis, the 12 pairs of sister chromatids will align at metaphase. During meiosis I, 6 bivalents will align along the metaphase plate in the mother cell. During meiosis II, 6 pairs of sister chromatids will align along the metaphase plate in the two cells.

ANSWER The cell is in metaphase of meiosis II. You can tell because the chromosomes are lined up in a single row along the metaphase plate, and the cell has only 6 pairs of sister chromatids. If it were mitosis, the cell would have 12 pairs of sister chromatids. If it were in meiosis I, bivalents would be aligned along the metaphase plate.

∙∙ Formative Assessment: A trend in biology education is to spend more class time engaging students in active learning. While this is a positive approach that fosters learning, a drawback is that instructors have less time to explain the material in the textbook. When students are expected to learn textbook material on their own, it is imperative that they are regularly given formative assessment—feedback regarding their state of learning while they are engaging in the learning process. This allows students to gauge whether they are mastering the material. Formative assessment is a major feature of this textbook and is bolstered by Connect—a state-of-the art digital assignment and assessment platform. In Biology, 5th edition, formative assessment is provided in multiple ways. ∙∙ First, many figure legends have Concept Check questions that focus on key concepts of a given topic. ∙∙ Second, questions in Assess and Discuss at the end of each chapter explore students’ understanding of concepts and mastery of skills. Core Concepts and Core Skills are again addressed under the Conceptual Questions. The answers to the Concept Checks and the end-of-chapter questions are in Appendix B, so students can immediately see if they are mastering the material.

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Conceptual Questions

the same way. In another family, parents, who were also born in 1900, delay reproduction until age 33 but have triplets. Their children and grandchildren behave in the same way. Which family has the most descendants by 2000? What can you conclude?

Collaborative Questions 1279

THE AGE OF HUMANS

1. The Earth’s atmosphere consists of 78% nitrogen. Why is nitrogen a limiting nutrient? 2. Why does maximum sustainable yield occur at the midpoint of the logistic curve and not where the population is at carrying capacity? 3.

Core Skill: Science and Society In one family, parents, who were born in 1900, have twins at age 20 but then have no more children. Their children, grandchildren, and so on behave in the same way. In another family, parents, who were also born in 1900, delay reproduction until age 33 but have triplets. Their children and grandchildren behave in the same way. Which family has the most descendants by 2000? What can you conclude?

∙∙ Learning Outcomes: As advocated in Vision and Change, educational materials should have well-defined learning goals. 2. As a group, try to predict what effects an atmospheric concentration of Each sectionroles of every chapter begins with a set DNA of Learning are associated important in a variety of processes, including replica700 ppm of CO2 might have on the environment. tion, chromatin modification, translation, and key genome Outcomes. These outcomestranscription, inform students of the conceptscancer, neuro ncRNAs are a In most cell types, ncRNAs are more abundant than mRNAs. theydefense. will learn and the skills they will acquire in mastering plants that are For example, in a typical human cell, only about 20% of transcription the involves material. alsoofprovide tangible ofwith how In this ch the They production mRNAs, awhereas 80%indication is associated properties of student learning assessed.underscores The assessments in Connect making ncRNAs!will This be observation the importance of RNA in the enterprise life, and indicatesOutcomes why it deserves were developed usingofthese Learning as agreater guide in functions they role of ncRNA recognition and deeper study. Furthermore, abnormalities in ncRNAs formulating online questions, thereby linking the learning goals of the text with the assessments in Connect. 1. Discuss what might limit human population growth in the future.

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Collaborative Questions ∙∙ In Connect, a particularly robust type of formative assessment

∙∙ Unit openers: Each unit begins with a unit opener that provides an overview of the chapters within that unit. This overview allows the student to see the big picture of the unit. In addition, the unit openers draw attention to the core concepts and core skills of biology that will be emphasized in each unit.

UNIT III

1. Describe the ability of ncRNAs to bind to other molecules and macromolecules. 2. Outline the general functions of ncRNAs. 3. Define ribozyme. 4. List several examples of ncRNAs, and describe their functions.

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GENETICS

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The study of ncRNAs is a rapidly expanding field, and researchers speculate that many ncRNAs have yet to be discovered. Also, due to the relative youth thiswith field, not all researchers agree on the names Genetics is the branch of biology that of deals inheritance— ncRNAs or their primaryWe functions. Even so, some broad the transmissionof of certain characteristics from parent to offspring. begin this unit by examining structure oftothe genetic matethemes arethe beginning emerge. In this section, we will survey the rial, namely DNA, at the molecular levels.and We will general featuresand ofcellular ncRNAs, in later sections, we will discuss explore the structure and replication and see how it is specific examplesofinDNA greater detail.

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packaged into chromosomes (Chapter 11). We will then consider how segments of DNA are organized into units called genes, and ncRNAs Can tolevel Different how those genes are expressed at theBind molecular to produce Types of Molecules mRNA, proteins,The and noncoding (Chapters 12 andout 13). an In amazing array of functions is ability of RNAs ncRNAs to carry Chapter 14, we will consider how the expression of genes is regulargely related to their ability to bind to different types of molecules. lated. We will also examine how mutations alter the properties of Figure 13.1a shows four common types of molecules that are recgenes and even lead to diseases such as cancer (Chapter 15). ognized by ncRNAs. Some ncRNAs bind to DNA or another RNA In Chapter 16, we turn our attention to the mechanisms by complementary base pairing. This allows ncRNAs to affect which genes arethrough transmitted from parent to offspring, beginning processes such as DNA replication, transcription, and translation. In with a discussion of how chromosomes are sorted and transmitaddition, ncRNAs can18bind to the proteins or small molecules. ted during cell division. Chapters 17 and explore relationships between the transmission of genes and the outcome an As described in Chapter 12, RNAofmolecules, such as tRNAs, can offspring’s traits.form We will look at genetic patterns calledback Mendestem-loop structures (refer to Figure 12.14). Similar struclian inheritancetures and more complex patternsmay that bind couldto notpockets have on the surface of proteins, in other ncRNAs been predicted from Mendel’s work. or multiple stem-loops may form a binding site for a small molecule. The remaining chapters of this unit explore additional topics In some cases, a single ncRNA may contain multiple binding sites. that are of interest to biologists. In Chapter 19, we will examine Thisgenetic allowsproperties an ncRNA to facilitate the formation of a large structure some of the unique of bacteria and viruses. composed of multiple such as an ncRNA and three differChapter 20 considers the central role genesmolecules, play in the developasashown Figure 13.1bWe . ment of animalsent andproteins, plants from fertilizedinegg to an adult. end this unit by exploring genetic technologies that are used by researchers, clinicians, and biotechnologists to unlock the mysncRNAs Can Perform a Diverse Set of Functions teries of genes and provide tools and applications that benefit In21). recent decades, researchers have uncovered many examples in humans (Chapter

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which ncRNAs play a critical role in different biological processes. Let’s first consider how ncRNAs work in a general way. The common The following Core Concepts and Core functions of ncRNAs are the following. Skills will be emphasized in this unit:

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• Information: Throughout this unit, we will see how the nents, such a group of different which is descr genetic material carries theasinformation to sustain life.proteins. Much like the beams in • Structure and Function: In Chapters 11 through 15, we e cienchow the structures of DNA, RNA, genes, and will examine va/S rsity of isele na K e, Unive to ©Ele chromosomes underlie their functions. ag ; ; (12): Daniel G ©Biopho Photo ): orbis ck ry/C o; (14): © es; (16 my Sto ck ra b ag la Sto /A Man tty Im to Li ndia /Alamy Reasoning: In Chapters 17 and 18, we will consider e Pho Miguel • /GQuantitative nce , ck ): ©A ne /Scie Eulalio ook Sto ers; (18 al-on-Li rI e ut b ijv na e dic used to predict the outcome of genetic crosses. De V iacca, A zo/Work igheti/R ): methods ©Me r Van ro G e Cardo Radu S ce; (20 Piete (11): ©Pieter Van De VijverI/Science Photo Library/Corbis; (12): ©Elena Kiseleva Mau ur © tt (11): © ; (13): © ): ©Yve ce; (17): e So • Science and Society: In Chapter 21, we will examine genetic 5 ce ur cienc Source; (13): ©Mauro Giacca, Ana Eulalio, Miguel Mano; (14): ©Daniel Gage, U Sour cticut; (1 nce So wsett/S e e o a Conn ates/Sci Barry D am technologies that have many applications in our society. Connecticut; (15): ©Yvette Cardozo/Workbook Stock/Getty Images; (16): ©Biop . ugiy ci Asso CAMR/A mihiro S © Associates/Science Source; (17): ©Radu Sigheti/Reuters; (18): ©Andia/Alamy S (19): ; (21): ©Fu to • Process of Science: Every chapter in this unit has a Feature Pho (19): ©CAMR/A. Barry Dowsett/Science Source; (20): ©Medical-on-Line/Alamy Investigation that describes a pivotal experiment that Photo; (21): ©Fumihiro Sugiyama provided insights into our understanding of genetics.

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ncRNA

A MODERN VISION FOR LEARNING

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USING STUDENT USAGE DATA TO MAKE IMPROVEMENTS To help guide the revision for the 5th edition, the authors consulted student usage data and input, which were derived from thousands of SmartBook® users of the 4th edition. SmartBook “heat maps” provided a quick visual snapshot of chapter usage data and the relative difficulty students experienced in mastering the content. These data directed the authors to evaluate text content that was particularly challenging for students. These same data were also used to revise the SmartBook probes.

Below is an example of one of the heat maps from Chapter 8. The color-coding of highlighted sections indicates the various levels of difficulty students experienced in learning the material, topics highlighted in red being the most challenging for students.

∙∙ If the data indicated that the subject was more difficult than other parts of the chapter, as evidenced by a high proportion of students responding incorrectly to the SmartBook questions, the authors revised or reorganized the content to be as clear and illustrative as possible, for example, by rewriting the section or providing additional examples or revised figures to assist visual learners. ∙∙ In other cases, one or more of the SmartBook questions for a section was not as clear as it should have been or did not appropriately reflect the content in the chapter. In these cases the question, rather than the text, was edited.

Preparing Students for Careers in Biololgy with NEW Cutting-Edge Content A key purpose of a majors biology course is to prepare students for biology-related careers, including those in the health professions, teaching, and research. The author team has reflected on the direction of biology and how that direction will affect future careers that students may pursue. We are excited to announce that Biology, 5th edition, has four new chapters that reflect current trends in biology research and education. These trends are opening the doors to exciting new career options in biology.  ∙∙ Chapter 13. Gene Expression at the Molecular Level II: Non-coding RNAs. The past decade or so has seen an explosion in the discovery of different types of non-coding RNAs. This work has revealed a variety of roles of non-coding RNAs at the molecular level, as well as roles in human diseases and plant health. ∙∙ Chapter 30. Microbiomes: Microbial Systems On and Around Us. Recent research has revealed the staggering complexity and biological importance of microbiomes—assemblages of microbes that are associated with a particular host or environment. This new chapter explores how microbiomes are analyzed and describes their interactions with diverse hosts, including humans, protists, and plants.  x

∙∙ Chapter 53: Integrated Responses of Animal Organ Systems to a Challenge to Homeostasis. Systems biology has been a recent trend in biological research and education. This chapter takes systems biology to a new level by exploring how multiple organs systems respond in a coordinated way to the same threat—a challenge to homeostasis.  ∙∙ Chapter 59: The Age of Humans. We face a tug-of-war between the undesirable effects of humans on the environment and the efforts of ecologists to prevent such changes. This new chapter surveys the impacts that the growing human population has had on climate change and on the survival of native species. This material may inspire some students to pursue a career as an ecologist or environmental biologist.

With regard to the scientific content in the textbook, the author team has worked with faculty reviewers to refine this new edition and to update the content so that students are exposed to the most current material. In addition to the four new chapters and our new pedagogical additions involving Core Concepts, Core Skills, and Modeling Challenges, every chapter has been extensively edited for clarity, presentation, layout, readability, modifications of artwork, and new and challenging end-of-chapter questions. Examples of some of the key changes are summarized below.

PREPARING STUDENTS FOR CAREERS IN BIOLOLGY WITH NEW CUTTING-EDGE CONTENT

∙∙ Chapter 1. An Introduction to Biology.  Chapter 1 provides a description of the Core Concepts (see Figure 1.4) and the Core Skills (see Section 1.6) that are advocated by Vision and Change.

Chemistry Unit

∙∙ Chapter 2. The Chemical Basis of Life I: Atoms, Molecules, and Water.  The topics of pH and buffers have been placed in their own section (see Section 2.4).

Cell Unit

∙∙ Chapter 4. Evolutionary Origin of Cells and Their General Features.  This chapter now begins with a discussion of the evolutionary origin of cells (see Section 4.1). It also discusses a new topic, droplet organelles, which are organelles that are not surrounded by a membrane (see Section 4.3). ∙∙ Chapter 6. An Introduction to Energy, Enzymes, and Metabolism.  For the topic of how cells use ATP as a source of energy, a revised subsection compares the Core Concept: Information to the Core Concept: Energy and Matter.   ∙∙ Chapter 7. Cellular Respiration and Fermentation. A Modeling Challenge asks students to predict the effects of a mutation on the function of ATP synthase (see Figure 7.12). ∙∙ Chapter 10. Multicellularity.  Four figures have been revised to better depict the relative locations of cell junctions between animal cells.

Genetics Unit

∙∙ Chapter 11. Nucleic Acid Structure, DNA Replication, and Chromosome Structure.  Figure 11.8b has a Modeling Challenge that asks students to predict how the methylation of a base would affect the ability of that base to hydrogen bond with a base in the opposite strand. ∙∙ Chapter 13. NEW! Gene Expression at the Molecular Level II:  Non-coding RNAs. This new chapter begins with an overview of the general properties of non-coding RNAs and then describes specific examples in which non-coding RNAs are involved with chromatin structure, transcription, translation, protein sorting, and genome defense.   ∙∙ Chapter 16. The Eukaryotic Cell Cycle, Mitosis, and Meiosis.  The Core Concept: Evolution is highlighted in a subsection that explains how mitosis in eukaryotes evolved from binary fission in prokaryotic cells (see Figure 16.10). ∙∙ Chapter 17. Mendelian Patterns of Inheritance.  The organization of this chapter has been revised to contain the patterns of inheritance that obey Mendel’s laws.   ∙∙ Chapter 18. Epigenetics, Linkage, and Extranuclear Inheritance.  This chapter now covers inheritance patterns that violate Mendel’s laws. The topic of epigenetics has been expanded from one section in the previous edition to four sections in the 5th edition (see Sections 18.1 through 18.4). ∙∙ Chapter 19. Genetics of Viruses and Bacteria.  Discussion of the Zika virus has been added to this chapter. ∙∙ Chapter 21. Genetic Technologies and Genomics.  The use of CRISPR-Cas technology to alter genes is now discussed (see Figure 21.10).

Evolution Unit

∙∙ Chapter 22. An Introduction to Evolution. This chapter has been moved so that it is the first chapter in this unit on evolution. ∙∙ Chapter 23. Population Genetics. After learning about the Hardy-Weinberg equation, students are presented with a Modeling Challenge that asks them to propose a mathematical model that extends the Hardy-Weinberg equation to a gene that exists in three alleles (see Figure 23.2). ∙∙ Chapter 25. Taxonomy and Systematics.  The topic of taxonomy is related to the Core Concept: Evolution through an explanation of how taxonomy is based on the evolutionary relationships among different species. ∙∙ Chapter 26. History of Life on Earth and Human Evolution.  The topic of human evolution has been moved from the unit on diversity to this unit. The expanded version of this topic describes recent examples of human evolution and discusses the amount of genetic variation between different human populations (see Section 26.3).

Diversity Unit

∙∙ Chapter 27. Archaea and Bacteria. This chapter has been reorganized to provide essential background for new Chapter 30 (an exploration of microbiomes). The Core Skill: Connections is illustrated by linking electromagnetic sensing in bacteria with that in certain animals. ∙∙ Chapter 29. Fungi. An overview of fungal phylogeny has been updated to reflect new research discoveries. Coverage of plant root-fungal associations (mycorrhizae) and lichens has been moved to new Chapter 30. ∙∙ Chapter 30. NEW!  Microbiomes: Microbial Systems On and Around Us.  This new chapter integrates information about microbial diversity (Chapters 27 through  29) with material on genetic technologies that is introduced in Chapter 21 to explain the evolutionary, medical, agricultural, and environmental importance of microbial associations. ∙∙ Chapter 31. Plants and the Conquest of Land.  The diagrammatic overview of plant phylogeny has been updated to reveal challenges in understanding the pattern of plant evolution. ∙∙ Chapter 33. An Introduction to Animal Diversity. Figure 33.3, animal phylogeny, has been redrawn to reflect the idea that ctenophores, rather than sponges, are now considered to be the earliest diverging animals. Section 33.2 on animal classification has been largely revised.  ∙∙ Chapter 34. The Invertebrates.  Following the new themes introduced in Chapter 33, this chapter has been reorganized to discuss ctenophores as the earlier evolving animals, followed by sponges, cnidria, jellyfish, and other radially symmetrical animals.

Flowering Plants Unit

∙∙ Chapter 36. An Introduction to Flowering Plant Form and Function. A new chapter opener links the economic importance of plants, represented by cotton, to the significance of plant structure-function relationships.

PREPARING STUDENTS FOR CAREERS IN BIOLOLGY WITH NEW CUTTING-EDGE CONTENT

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∙∙ Chapter 37. Flowering Plants: Behavior.  A Modeling Challenge links plant responses to conditions on Earth to those experienced in space.  ∙∙ Chapter 38. Flowering Plants: Nutrition. In a  Modeling Challenge related to plant-microbe interaction process, students infer how specific mutations might affect an important nutritional feature. ∙∙ Chapter 40. Flowering Plants: Reproduction. This chapter explores intriguing parallels between the reproductive processes of animals and those of plants.

Animals Unit

∙∙ Chapter 41. Animal Bodies and Homeostasis.  A section entitled “Homeostatic Control of Internal Fluids” (Section 41.4) now follows the section “General Principles of Homeostasis,” providing students with an understanding of body fluid compartments, osmolarity, and how animal bodies exchange ions and water with their environments. These concepts are important to students’ understanding of subsequent chapters. ∙∙ Chapter 42. Neuroscience I: Cells of the Nervous System.  The Core Skill: Science and Society is featured numerous times in the unit on animals, including in  Figure 42.18 which describes the use of magnetic resonance imaging in modern medicine. ∙∙ Chapter 43. Neuroscience II: Evolution, Structure, and Function of the Nervous System. The Core Skill: Connections is also featured throughout the unit on animals, including in Figure 43.1 in which students are asked to identify the defining features of animals by referring to Chapter 33. ∙∙ Chapter 44. Neuroscience III: Sensory Systems. New research demonstrating a correlation between the types of locomotion of vertebrates and the relative sizes of their semicircular canals is described. ∙∙ Chapter 46. Nutrition and Animal Digestive Systems. A Modeling Challenge was added in which students are tasked with creating models of hypothetical alimentary canals of two species with different diets, eating patterns, and teeth. ∙∙ Chapter 47. Control of Energy Balance, Metabolic Rate, and Body Temperature.  The meaning of body mass index and its usefulness and limitations are more fully elucidated, and data on obesity statistics in the United States have been updated to reflect current trends. ∙∙ Chapter 48. Circulatory and Respiratory Systems. These topics were formerly addressed in two chapters but are now integrated into a single chapter that streamlines the presentation

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and emphasizes important connections between the two systems.  Chapter 49. Excretory Systems. The chapter has been more narrowly focused on excretory systems by moving the material on osmoregulation and body fluids earlier in the unit, to Chapter 41. Chapter 51. Animal Reproduction and Development. Formerly two chapters, this material is now covered in one chapter, which eliminated redundancy in coverage. For example, the topic of fertilization (Section 51.2) is now covered in its entirety in the same section as the topic of gametogenesis, rather than being split between two chapters. Chapter 52. Immune Systems.  Exciting new information has been added that describes the evolution of toll-like receptors and the presence of a TLR-domain in bacterial genes associated with immune defenses.  Chapter 53. NEW!  Integrated Responses of Animal Organ Systems to a Challenge to Homeostasis. This new chapter integrates material from virtually the entire unit on animals, using a classic challenge to homeostasis as an example. It includes a compelling case study of a young athlete that begins and concludes the chapter.

Ecology Unit

∙∙ Chapter 54. An Introduction to Ecology and Biomes. The section on aquatic biomes as been expanded with a new figure and explanation of the annual cycle of temperate lakes, as well as new information on tide formation and waves. ∙∙ Chapter 57. Species Interactions. This chapter has been reduced in length by the deletion of four figures and streamlined for easier understanding. ∙∙ Chapter 58. Communities and Ecosystems: Ecological Organization at Large Scales.  This chapter has been reorganized to include both community ecology and ecosystems ecology.  ∙∙ Chapter 59. NEW!  The Age of Humans.  This new chapter synthesizes information concerning the effects of humans on the natural environment. It contains discussions of human population growth (previously covered in Chapter 56), the effect of global warming on climate change (previously covered in Chapter 54), and human effects on biogeochemical cycles and biomagnification (previously covered in Chapter 59), and new information on habitat destruction, overexploitation, and invasive species. ∙∙ Chapter 60. Biodiversity and Conservation Biology. The coverage of the value of biodiversity to human welfare, detailed in Section 60.3 has been updated and expanded.

PREPARING STUDENTS FOR CAREERS IN BIOLOLGY WITH NEW CUTTING-EDGE CONTENT

Strengthening Problem-Solving Skills and Key Concept Development with Connect® Detailed Feedback in Connect®

Learning is a process of iterative development, of making mistakes, reflecting, and adjusting over time. The question and test banks in Connect® for Biology, 5th edition, are more than direct assessments; they are self-contained learning experiences that systematically build student learning over time. For many students, choosing the right answer is not necessarily based on applying content correctly; it is more a matter of increasing the statistical odds of guessing. A major fault with this approach is students don’t learn how to process the questions correctly, mostly because they are repeating and reinforcing their mistakes rather than reflecting and learning from them. To help students develop problem-solving skills, all higher-level Bloom’s questions in Connect are supported with hints, to help students focus on important information needed to answer the questions, and detailed feedback that walks students through the problem-solving process, using Socratic questions in a decision-tree framework to scaffold learning, in which each step models and reinforces the learning process. The feedback for each higher-level Bloom’s question (Apply, Analyze, Evaluate) follows a similar process: Clarify Question, Gather Content, Consider Alternatives, Choose Answer, Reflect on Process.

Rather than leaving it up to the student to work through the detailed feedback, we present a second version of the question in a stepwise format. Following the problem-solving steps, students need to answer questions about the problem-solving process, such as “What is the key concept addressed by the question?” before answering the original question. A professor can choose which version of the question to include in the assignment based on the problem-solving skills of the students.

Graphing Interactives

To help students develop analytical skills, Connect® for Biology, 5th edition, is enhanced with interactive graphing questions. Students are presented with a scientific problem and the opportunity to manipulate variables, producing different results on a graph. A series of questions follows the graphing activity to assess if the student understands and is able to interpret the data and results. 

Unpacking the Concepts

We’ve taken problem solving a step further. In each chapter, two higher-level Bloom’s questions in the question and test banks are broken down according to the steps in the detailed feedback.



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Students—study more efficiently, retain more and achieve better outcomes. Instructors—focus on what you love—teaching.

SUCCESSFUL SEMESTERS INCLUDE CONNECT

For Instructors You’re in the driver’s seat. Want to build your own course? No problem. Prefer to use our turnkey, prebuilt course? Easy. Want to make changes throughout the semester? Sure. And you’ll save time with Connect’s auto-grading too.

65%

Less Time Grading

They’ll thank you for it. Adaptive study resources like SmartBook® help your students be better prepared in less time. You can transform your class time from dull definitions to dynamic debates. Hear from your peers about the benefits of Connect at www.mheducation.com/highered/connect

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Chapter 1 An Introduction to Biology  1 1.1 Levels of Biology  2 1.2 Core Concepts of Biology  4 1.3 Biological Evolution  5 Core Concept: Evolution:  The Study of Genomes and Proteomes Provides an Evolutionary Foundation for Our Understanding of Biology  7

3.6 Proteins  56 Feature Investigation:  Anfinsen Showed That the Primary Structure of Ribonuclease Determines Its Three-Dimensional Structure  61 Core Concept: Evolution:  Proteins Contain Functional Domains 63

3.7 Nucleic Acids  64

UNIT II  Cell

1.4 Classification of Living Things  8 1.5 Biology as a Scientific Discipline  12 1.6 Core Skills of Biology  17 Feature Investigation:  Observation and Experimentation Form the Core of Biology  18

UNIT I  Chemistry ©Steve Gschmeissner/Science Source

Chapter 4 Evolutionary Origin of Cells and Their General Features  69

©Dr. Parvinder Sethi

4.1 Origin of Living Cells on Earth  69 4.2 Microscopy  75 4.3 Overview of Cell Structure and Function  78

Chapter 2

The Chemical Basis of Life I: Atoms, Molecules, and Water  24 2.1 Atoms  24 Feature Investigation:  Rutherford Determined the Modern Model of the Atom  25

2.2 Chemical Bonds and Molecules  30 2.3 Properties of Water  36 2.4 pH and Buffers  41

4.4 The Cytosol  83 4.5 The Nucleus and Endomembrane System  88 Feature Investigation:  Palade Discovered That Proteins Destined for Secretion Move Sequentially Through Organelles of the Endomembrane System  92

4.6 Semiautonomous Organelles  96 4.7 Protein Sorting to Organelles  99 4.8 Systems Biology of Cells: A Summary  102

Chapter 3

Chapter 5

The Chemical Basis of Life II: Organic Molecules  45

Membrane Structure, Synthesis, and Transport  106

3.1 The Carbon Atom  45 3.2 Formation of Organic Molecules and Macromolecules  48 3.3 Overview of the Four Major Classes of Organic Molecules Found in Living Cells  48 3.4 Carbohydrates  48 3.5 Lipids  52

Core Concepts: Information, Structure and Function:  The Characteristics of a Cell Are Largely Determined by the Proteins It Makes  81

5.1 Membrane Structure  107 Core Concept: Information:  Approximately 20–30% of All Genes Encode Transmembrane Proteins  108

5.2 Fluidity of Membranes  109 5.3 Synthesis of Membrane Components in Eukaryotic Cells 111 xvii

CONTENTS

Contents

CONTENTS

5.4 Overview of Membrane Transport  113 5.5 Transport Proteins  117 Feature Investigation:  Agre Discovered That Osmosis Occurs More Quickly in Cells with a Channel That Allows the Facilitated Diffusion of Water  117

5.6 Exocytosis and Endocytosis  122

Chapter 6 An Introduction to Energy, Enzymes, and Metabolism  127 6.1 Energy and Chemical Reactions  127 Core Concept: Information, Energy and Matter:  Genomes Encode Many Proteins That Use ATP as a Source of Energy  130

Chapter 9 Cell Communication  183 9.1 General Features of Cell Communication  183 9.2 Cellular Receptors and Their Activation  187 9.3 Signal Transduction and the Cellular Response  190 9.4 Hormonal Signaling in Multicellular Organisms  195 Core Concept: Information:  A Cell’s Response to Hormones and Other Signaling Molecules Depends on the Genes It Expresses  196

9.5 Apoptosis: Programmed Cell Death  196 Feature Investigation:  Kerr, Wyllie, and Currie Found That Hormones May Control Apoptosis  197

6.2 Enzymes and Ribozymes  131 Feature Investigation:  The Discovery of Ribozymes by Sidney Altman Revealed That RNA Molecules May Also Function as Catalysts 135

6.3 Overview of Metabolism  137 6.4 Recycling of Organic Molecules  141

Chapter 7 Cellular Respiration and Fermentation  145 7.1 Overview of Cellular Respiration  145 7.2 Glycolysis  147 Core Concept: Information:  The Overexpression of Certain Genes Causes Cancer Cells to Exhibit High Levels of Glycolysis  149



7.3 7.4 7.5 7.6

Breakdown of Pyruvate  150 Citric Acid Cycle  151 Overview of Oxidative Phosphorylation  153 A Closer Look at ATP Synthase  155

Chapter 10 Multicellularity  202 10.1 Extracellular Matrix and Cell Walls 203 Core Concepts: Evolution, Structure and Function:  Collagens Are a Family of Proteins That Give the ECM of Animals a Variety of Properties  205

10.2 Cell Junctions 208 Feature Investigation:  Loewenstein and Colleagues Followed the Transfer of Fluorescent Dyes to Determine the Size of GapJunction Channels  212

10.3 Tissues 214

UNIT III  Genetics

Feature Investigation:  Yoshida and Kinosita Demonstrated That the γ Subunit of ATP Synthase Spins  157

7.7 Connections Among Carbohydrate, Protein, and Fat Metabolism  159 7.8 Anaerobic Respiration and Fermentation  159

Chapter 8 Photosynthesis 164 8.1 Overview of Photosynthesis  164 8.2 Reactions That Harness Light Energy  167 Core Concepts: Evolution, Structure and Function:  The Cytochrome Complexes of Mitochondria and Chloroplasts Contain Evolutionarily Related Proteins  171

8.3 Molecular Features of Photosystems  172 8.4 Synthesizing Carbohydrates via the Calvin Cycle  174 Feature Investigation:  The Calvin Cycle Was Determined by Isotope-Labeling Methods  176

8.5 Variations in Photosynthesis  178 xviii CONTENTS

©Pieter Van De VijverI/Science Photo Library/Corbis

Chapter 11 Nucleic Acid Structure, DNA Replication, and Chromosome Structure  220 11.1 Biochemical Identification of the Genetic Material  220 Feature Investigation:  Avery, MacLeod, and McCarty Used Purification Methods to Reveal That DNA Is the Genetic Material 222

11.2 Nucleic Acid Structure  224 11.3 Overview of DNA Replication  228

Core Concepts: Evolution, Structure and Function:  DNA Polymerases Are a Family of Enzymes with Specialized Functions 236

11.5 Molecular Structure of Eukaryotic Chromosomes  238

14.4 Regulation of Transcription in Eukaryotes II: Changes in Chromatin Structure and DNA Methylation  296 14.5  Regulation of RNA Modification and Translation in Eukaryotes 299 Core Concepts: Evolution, Information:  Alternative Splicing Is More Prevalent in Complex Eukaryotic Species  300

Chapter 12

Chapter 15

Gene Expression at the Molecular Level I: Production of mRNA and Proteins  243 12.1 12.2 12.3 12.4

Overview of Gene Expression  244 Transcription  247 RNA Modification in Eukaryotes  249 Translation and the Genetic Code  252 Feature Investigation:  Nirenberg and Leder Found That RNA Triplets Can Promote the Binding of tRNA to Ribosomes  254

Mutation, DNA Repair, and Cancer  304 15.1 Consequences of Mutations  304 15.2 Causes of Mutations  308 Feature Investigation:  The Lederbergs Used Replica Plating to Show That Mutations Are Random Events  308

15.3 DNA Repair  312 15.4 Cancer  314

12.5 The Machinery of Translation  256

Core Concept: Evolution:  Mutations in Approximately 300 Human Genes May Promote Cancer  321

Core Concept: Evolution:  Comparisons of Small Subunit rRNAs Among Different Species Provide a Basis for Establishing Evolutionary Relationships  259

Chapter 16

12.6 The Stages of Translation  260

The Eukaryotic Cell Cycle, Mitosis, and Meiosis  323

Chapter 13 Gene Expression at the Molecular Level II: Non-coding RNAs  266 13.1 Overview of Non-coding RNAs  267 13.2 Effects of Non-coding RNAs on Chromatin Structure and Transcription  270 13.3 Effects of Non-coding RNAs on Translation and mRNA Degradation 270 Feature Investigation:  Fire and Mello Showed That DoubleStranded RNA Is More Potent Than Antisense RNA in Silencing mRNA 271

13.4 Non-coding RNAs and Protein Sorting  275 13.5 Non-coding RNAs and Genome Defense  275 13.6 Roles of Non-coding RNAs in Human Disease and Plant Health 278

Chapter 14 Gene Expression at the Molecular Level III: Gene Regulation  282 14.1 Overview of Gene Regulation  282 14.2 Regulation of Transcription in Bacteria  285 Feature Investigation:  Jacob, Monod, and Pardee Studied a Constitutive Mutant to Determine the Function of the Lac Repressor 289

14.3 Regulation of Transcription in Eukaryotes I: Roles of Transcription Factors and Mediator  294

16.1 The Eukaryotic Cell Cycle  323 Feature Investigation:  Masui and Markert’s Study of Oocyte Maturation Led to the Identification of Cyclins and CyclinDependent Kinases  328

16.2 Mitotic Cell Division  330 Core Concept: Evolution:  Mitosis in Eukaryotes Evolved from the Binary Fission That Occurs in Prokaryotic Cells  333

16.3 Meiosis  334 16.4 Sexual Reproduction  340 16.5 Variation in Chromosome Structure and Number  341

Chapter 17 Mendelian Patterns of Inheritance  348 17.1 17.2 17.3 17.4

Mendel’s Laws of Inheritance  349 The Chromosome Theory of Inheritance  355 Pedigree Analysis of Human Traits  358 Sex Chromosomes and X-Linked Inheritance Patterns  359 Feature Investigation:  Morgan’s Experiments Showed a Correlation Between a Genetic Trait and the Inheritance of a Sex Chromosome in Drosophila 361

17.5 Variations in Inheritance Patterns and Their Molecular Basis  363 Core Concept: Systems:  The Expression of a Single Gene Often Has Multiple Effects on Phenotype  364

17.6 Gene Interaction  366 17.7 Genetics and Probability  368 CONTENTS

xix

CONTENTS

11.4 Molecular Mechanism of DNA Replication  231

Chapter 18 CONTENTS

Epigenetics, Linkage, and Extranuclear Inheritance 373 18.1 18.2 18.3 18.4 18.5

Overview of Epigenetics  374 Epigenetics I: Genomic Imprinting  375 Epigenetics II: X-Chromosome Inactivation  377 Epigenetics III: Effects of Environmental Agents  379 Extranuclear Inheritance: Organelle Genomes  381

21.3 Bacterial and Archaeal Genomes  445 Feature Investigation:  Venter, Smith, and Colleagues Sequenced the First Genome in 1995  446

21.4 Eukaryotic Genomes  448 Core Concept: Evolution:  Gene Duplications Provide Additional Material for Genome Evolution, Sometimes Leading to the Formation of Gene Families  450

21.5 Repetitive Sequences and Transposable Elements  452

UNIT IV  Evolution

Core Concepts: Evolution, Information:  Chloroplast and Mitochondrial Genomes Are Relatively Small, but Contain Genes That Encode Important Proteins  381

18.6 Genes on the Same Chromosome: Linkage and Recombination 384 Feature Investigation:  Bateson and Punnett’s Cross of Sweet Peas Showed That Genes Do Not Always Assort Independently  384

Chapter 19 Genetics of Viruses and Bacteria  391 19.1 General Properties of Viruses  392 19.2 Viral Reproductive Cycles  395 Core Concept: Evolution:  Several Hypotheses Have Been Proposed to Explain the Origin of Viruses  400

19.3 Viroids and Prions  401 19.4 Genetic Properties of Bacteria  403 19.5 Gene Transfer Between Bacteria  406 Feature Investigation:  Lederberg and Tatum’s Work with E. coli Demonstrated Gene Transfer Between Bacteria and Led to the Discovery of Conjugation  406 Core Concept: Evolution:  Horizontal Gene Transfer Can Occur Within a Species or Between Different Species   411

Chapter 20 Developmental Genetics  413 20.1 General Themes in Development  413 20.2 Development in Animals I: Pattern Formation  418 Core Concept: Evolution:  A Homologous Group of Homeotic Genes Is Found in Nearly All Animals  423

20.3 Development in Animals II: Cell Differentiation  424 Feature Investigation:  Davis, Weintraub, and Lassar Identified Genes That Promote Muscle Cell Differentiation  427

20.4 Development in Plants  429

Chapter 21 Genetic Technologies and Genomics  434 21.1 Gene Cloning  434 21.2 Genomics: Techniques for Studying and Altering Genomes 440 xx CONTENTS

©Mark Dadswell/Getty Images

Chapter 22 An Introduction to Evolution  458 22.1 Overview of Evolution  459 Feature Investigation:  The Grants Observed Natural Selection in Galápagos Finches  463

22.2 Evidence of Evolutionary Change  465

22.3 The Molecular Processes That Underlie Evolution  473 Core Concept: Evolution:  Gene Duplications Produce Gene Families 473

Chapter 23 Population Genetics  477 23.1 Genes in Populations  478 Core Concept: Evolution:  Genes Are Usually Polymorphic  478

23.2 Natural Selection  482 23.3 Sexual Selection  485 Feature Investigation:  Seehausen and van Alphen Found That Male Coloration in African Cichlids Is Subject to Female Choice  487

23.4 Genetic Drift  489 23.5 Migration and Nonrandom Mating  491

Chapter 24 Origin of Species and Macroevolution  496 24.1  Identification of Species  497 24.2  Mechanisms of Speciation  502 Feature Investigation:  Podos Found That an Adaptation for Feeding May Have Promoted Reproductive Isolation in Finches  504

Core Concept: Evolution:  The Study of the Pax6 Gene Indicates That Different Types of Eyes Evolved from One Simple Form  512

Chapter 25 Taxonomy and Systematics  516 25.1 Taxonomy  517 25.2 Phylogenetic Trees  519 25.3  Cladistics  523 Feature Investigation:  Cooper and Colleagues Compared DNA Sequences from Extinct Flightless Birds and Existing Species to Propose a New Phylogenetic Tree  527

25.4 Molecular Clocks  529 25.5 Horizontal Gene Transfer  531 Core Concept: Evolution:  Due to Horizontal Gene Transfer, the “Tree of Life” Is Really a “Web of Life”  532

27.5 Ecological Roles and Biotechnology Applications  573 Feature Investigation:  Dantas and Colleagues Found That Many Bacteria Can Break Down and Consume Antibiotics as a Sole Carbon Source  574 Core Concept: Evolution:  The Evolution of Bacterial Pathogens 578

Chapter 28 Protists 581 28.1 An Introduction to Protists  581 28.2 Evolution and Relationships  584 Core Concept: Evolution:  Genome Sequences Reveal the Different Evolutionary Pathways of Trichomonas vaginalis and Giardia intestinalis  586

28.3 Nutritional and Defensive Adaptations  593 Feature Investigation:  Cook and Colleagues Demonstrated That Cellulose Helps Green Algae Avoid Chemical Degradation  594

28.4 Reproductive Adaptations  596

Chapter 26

Chapter 29

History of Life on Earth and Human Evolution  535

Fungi 605

26.1 The Fossil Record  536 26.2 History of Life on Earth  538 Core Concept: Evolution:  The Origin of Eukaryotic Cells Involved a Union Between Bacterial and Archaeal Cells  541

26.3 Human Evolution 

547

Core Concept: Evolution:  Comparing the Genomes of Humans and Chimpanzees  550

UNIT V  Diversity

29.1 Evolution and Distinctive Features of Fungi  605 29.2 Overview of Asexual and Sexual Reproduction in Fungi 609 29.3 Diversity of Fungi  611 29.4 Fungal Ecology and Biotechnology  617 Feature Investigation:  Márquez and Associates Discovered That a Three-Partner Symbiosis Allows Plants to Cope with Heat Stress 618

Chapter 30 Microbiomes: Microbial Systems On and Around Us  622 30.1 Microbiomes: Diversity of Microbes and Functions  622 30.2 Microbiomes of Physical Systems  628 30.3 Host-Associated Microbiomes  630 Feature Investigation:  Blanton, Gordon, and Associates Found That Gut Microbiomes Affect the Growth of Malnourished Children 635

©Dr. Jeremy Burgess/SPL/Science Source

Chapter 27 Archaea and Bacteria  561 27.1 27.2 27.3 27.4

Diversity and Evolution  562 Structure and Movement  566 Reproduction  571 Nutrition and Metabolism  572

30.4 Engineering Animal and Plant Microbiomes  637

Chapter 31 Plants and the Conquest of Land  641 31.1 Ancestry and Diversity of Modern Plants  641 Core Concepts: Evolution, Information:  Comparison of Plant Genomes Reveals Genetic Changes That Occurred During Plant Evolution 648 CONTENTS

xxi

CONTENTS

24.3 The Pace of Speciation  508 24.4 Evo-Devo: Evolutionary Developmental Biology  509

CONTENTS

31.2 How Land Plants Have Changed the Earth  648 31.3 Evolution of Reproductive Features in Land Plants  651 31.4 Evolutionary Importance of the Plant Embryo  655 Feature Investigation:  Browning and Gunning Demonstrated That Placental Transfer Tissues Facilitate the Movement of Organic Molecules from Gametophytes to Sporophytes  655

31.5 The Origin and Evolutionary Importance of Leaves and Seeds  658 31.6 A Summary of Plant Features  662

34.4 Lophotrochozoa: The Flatworms, Rotifers, Bryozoans, Brachiopods, Mollusks, and Annelids  705 Feature Investigation:  Fiorito and Scotto’s Experiments Showed That Invertebrates Can Exhibit Sophisticated Observational Learning Behavior  712

34.5 Ecdysozoa: The Nematodes and Arthropods  716 Core Concept: Information:  DNA Barcoding: A New Tool for Species Identification  726

34.6 Deuterostomia: The Echinoderms and Chordates  726 34.7 A Comparison of Animal Phyla  731

Chapter 32 Chapter 35

The Evolution and Diversity of Modern Gymnosperms and Angiosperms   664 32.1 Overview of Seed Plant Diversity  664 32.2 The Evolution and Diversity of Modern Gymnosperms  665 32.3 The Evolution and Diversity of Modern Angiosperms 671 Core Concept: Evolution:  Whole-Genome Duplications Influenced the Evolution of Flowering Plants  675 Feature Investigation:  Hillig and Mahlberg Analyzed Secondary Metabolites to Explore Species Diversification in the Genus Cannabis 679

32.4 The Role of Coevolution in Angiosperm Diversification 681 32.5 Human Influences on Angiosperm Diversification  683

Chapter 33

The Vertebrates  734 35.1 35.2 35.3 35.4

Vertebrates: Chordates with a Backbone  734 Cyclostomata: Jawless Fishes  737 Gnathostomes: Jawed Vertebrates  738 Tetrapods: Gnathostomes with Four Limbs  742 Feature Investigation:  Davis and Colleagues Provided a Genetic-Developmental Explanation for Limb Length in Tetrapods 743

35.5 Amniotes: Tetrapods with a Desiccation-Resistant Egg 746 35.6 Mammals: Milk-Producing Amniotes  752

UNIT VI   Flowering Plants

An Introduction to Animal Diversity  686 33.1 Characteristics of Animals  687 33.2 Animal Classification  688 Core Concept: Evolution:  Changes in Hox Gene Expression Control Body Segment Specialization 694

33.3 The Use of Molecular Data in Constructing Phylogenetic Trees for Animals  695 Feature Investigation:  Aguinaldo and Colleagues Analyzed SSU rRNA Sequences to Determine the Taxonomic Relationships of Arthropods to Other Phyla in Protostomia  697

Chapter 34 The Invertebrates  701 34.1 Ctenophores: The Earliest Animals  702 34.2 Porifera: The Sponges  702 34.3 Cnidaria: Jellyfish and Other Radially Symmetric Animals 704

xxii CONTENTS

©Linda Graham

Chapter 36 An Introduction to Flowering Plant Form and Function  760 36.1 From Seed to Seed—The Life of a Flowering Plant  760 36.2 How Plants Grow and Develop  764 36.3 The Shoot System: Stem and Leaf Adaptations  769 Feature Investigation:  Sack and Colleagues Showed That Palmate Venation Confers Tolerance of Leaf Vein Breakage 771

36.4 Root System Adaptations  777

Chapter 37 Flowering Plants: Behavior  782 37.1 Overview of Plant Behavioral Responses  782 37.2 Plant Hormones  785

40.3 Male and Female Gametophytes and Double Fertilization 848 40.4 Embryo, Seed, Fruit, and Seedling Development  851 40.5 Asexual Reproduction in Flowering Plants  855 Core Concept: Evolution:  The Evolution of Plantlet Production in Kalanchoë  855

UNIT VII  Animals

Feature Investigation:  An Experiment Performed by Briggs Revealed the Role of Auxin in Phototropism 788 Core Concept: Evolution:  Gibberellin Function Arose in a Series of Stages During Plant Evolution  790

37.3 Plant Responses to Environmental Stimuli  792

Chapter 38 Flowering Plants: Nutrition  801 38.1 Plant Nutritional Requirements  801 38.2 The Role of Soil in Plant Nutrition  805 Feature Investigation:  Hammond and Colleagues Engineered Smart Plants That Can Communicate Their Phosphate Needs 810

38.3 Biological Sources of Plant Nutrients  811 Core Concepts: Systems, Information:  Development of Legume-Rhizobia Symbioses  813

Chapter 39 Flowering Plants: Transport  818    39.1  Overview of Plant Transport  818 39.2 Uptake and Movement of Materials at the Cellular Level 819 39.3 Tissue-Level Transport  822 39.4 Long-Distance Transport  824 Feature Investigation:  Park, Cutler, and Colleagues Genetically Engineered an ABA Receptor Protein to Foster Crop Survival During Droughts  831

Chapter 40 Flowering Plants: Reproduction  839 40.1 An Overview of Flowering Plant Reproduction  839 40.2 Flower Production, Structure, and Development  843 Feature Investigation:  Liang and Mahadevan Used Time-Lapse Video and Mathematical Modeling to Explain How Flowers Bloom 846



©John Rowley/Getty Images

Chapter 41 Animal Bodies and Homeostasis  859 41.1 Organization of Animal Bodies  859 Core Concept: Information:  Organ Development and Function Are Controlled by Hox Genes  864

41.2 The Relationship Between Structure and Function  865 41.3 General Principles of Homeostasis  867 41.4 Homeostatic Control of Internal Fluids  872 Feature Investigation:  Cade and Colleagues Discovered Why Athletes’ Performances Wane on Hot Days  876

Chapter 42 Neuroscience I: Cells of the Nervous System 881 42.1 Cellular Components of Nervous Systems  882 42.2 Electrical Properties of Neurons and the Resting Membrane Potential  884 42.3 Generation and Transmission of Electrical Signals Along Neurons 888 42.4 Electrical and Chemical Communication at Synapses 892 Feature Investigation:  Otto Loewi Discovered Acetylcholine 896 Core Concepts: Evolution, Information:  The Evolution of Varied Subunit Compositions of Neurotransmitter Receptors Allowed for Precise Control of Neuronal Regulation  898

42.5 Impact on Public Health  900

CONTENTS

xxiii

CONTENTS

Core Concept: Information:  Genetic Control of Stomatal GuardCell Development  774

CONTENTS

Chapter 43

Chapter 46

Neuroscience II: Evolution, Structure, and Function of the Nervous System  904

Nutrition and Animal Digestive Systems  970

43.1 The Evolution and Development of Nervous Systems 904 43.2 Structure and Function of the Nervous Systems of Humans and Other Vertebrates  907 Core Concepts: Information, Evolution:  Many Genes Have Been Important in the Evolution and Development of the Cerebral Cortex  916

43.3 Cellular Basis of Learning and Memory  917 Feature Investigation:  Gaser and Schlaug Discovered That the Sizes of Certain Brain Structures Differ Between Musicians and Nonmusicians 920

46.1 Animal Nutrition  970 46.2 General Principles of Digestion and Absorption of Nutrients  972 46.3 Overview of Vertebrate Digestive Systems  975 46.4 Mechanisms of Digestion and Absorption in Vertebrates 980 Core Concept: Evolution:  Evolution and Genetics Explain Lactose Intolerance  981

46.5 Neural and Endocrine Control of Digestion  984 46.6 Impact on Public Health  985 Feature Investigation:  Marshall and Warren and Coworkers Demonstrated a Link Between Bacterial Infection and Ulcers  987

43.4 Impact on Public Health  922

44.1 44.2 44.3 44.4 44.5

Chapter 44

Chapter 47

Neuroscience III: Sensory Systems  925

Control of Energy Balance, Metabolic Rate, and Body Temperature  991

An Introduction to Sensation  925 Mechanoreception  927 Thermoreception and Nociception  933 Electromagnetic Reception  934 Photoreception  935 Core Concept: Evolution:  Color Vision Is an Ancient Adaptation in Animals  938

44.6 Chemoreception  942 Feature Investigation:  Buck and Axel Discovered a Family of Olfactory Receptor Proteins That Bind Specific Odor Molecules 944

47.1 Use and Storage of Energy  991 47.2 Regulation of the Absorptive and Postabsorptive States 994 Core Concept: Evolution:  A Family of GLUT Proteins Transports Glucose in All Animal Cells  995

47.3 Energy Balance and Metabolic Rate  997 Feature Investigation:  Coleman Revealed a Satiety Factor in Mammals 1000

47.4 Regulation of Body Temperature  1002 47.5 Impact on Public Health  1006

44.7 Impact on Public Health  947

Chapter 45 Muscular-Skeletal Systems and Locomotion 951 45.1 Types of Animal Skeletons  951 45.2 Skeletal Muscle Structure and the Mechanism of Force Generation  953 Core Concept: Evolution:  Myosins Are an Ancient Family of Proteins  956

45.3 Types of Skeletal Muscle Fibers and Their Functions 961 Feature Investigation:  Evans and Colleagues Activated a Gene to Produce “Marathon Mice”  962

45.4 Animal Locomotion  964 45.5 Impact on Public Health  966

xxiv CONTENTS

Chapter 48 Circulatory and Respiratory Systems  1010 48.1 Types of Circulatory Systems  1011 Core Concept: Evolution:  A Four-Chambered Heart Evolved from Simple Contractile Tubes  1012

48.2 48.3 48.4 48.5

The Composition of Blood  1014 The Vertebrate Heart and Its Function  1016 Blood Vessels  1019 Relationship Among Blood Pressure, Blood Flow, and Resistance  1022 48.6 Physical Properties of Gases  1024 48.7 Types of Respiratory Systems  1025 48.8 Structure and Function of the Mammalian Respiratory System 1028 Feature Investigation:  Fujiwara and Colleagues Demonstrated the Effectiveness of Administering Surfactant to Newborns with RDS 1031

Chapter 49 Excretory Systems  1043 49.1 Excretory Systems in Different Animal Groups  1043 49.2  Structure and Function of the Mammalian Kidney 1047 Core Concept: Evolution:  Aquaporins in Animals Are Part of an Ancient Superfamily of Channel Proteins  1053

Chapter 52 Immune Systems  1108 52.1 Types of Pathogens  1109 52.2 Innate Immunity  1109 Core Concept: Evolution:  Innate Immune Responses Require Proteins That Recognize Features of Many Pathogens  1112 Feature Investigation:  Lemaitre and Colleagues Identify an Immune Function for Toll Protein in Drosophila 1113

52.3 Adaptive Immunity  1115 52.4 Impact on Public Health  1126

Chapter 53

49.3 Impact on Public Health  1054

Chapter 50 Endocrine Systems  1058 50.1 Types of Hormones and Their Mechanisms of Action 1059 50.2 Links Between the Endocrine and Nervous Systems 1062 50.3 Hormonal Control of Metabolism and Energy Balance 1065 Feature Investigation:  Banting, Best, MacLeod, and Collip Were the First to Isolate Active Insulin  1071

50.4 Hormonal Control of Mineral Balance  1073 Core Concept: Evolution:  Hormones and Receptors Evolved as Tightly Integrated Molecular Systems  1076

50.5 Hormonal Control of Growth and Development  1077 50.6 Hormonal Control of Reproduction  1079 50.7 Impact on Public Health  1080

Integrated Responses of Animal Organ Systems to a Challenge to Homeostasis  1131 53.1 Effects of Hemorrhage on Blood Pressure and Organ Function 1132 53.2 The Rapid Phase of the Homeostatic Response to Hemorrhage 1133 Core Concept: Evolution:  Baroreceptors May Have Evolved to Minimize Increases in Blood Pressure in Vertebrates  1135 Feature Investigation:  Cowley and Colleagues Determined the Function of Baroreceptors in the Control of Blood Pressure in Mammals 1136

53.3 The Secondary Phase of the Homeostatic Response to Hemorrhage 1140 53.4 Impact on Public Health  1144

UNIT VIII  Ecology

Chapter 51 Animal Reproduction and Development  1084 51.1 Overview of Sexual and Asexual Reproduction  1084 Feature Investigation:  Paland and Lynch Provided Evidence That Sexual Reproduction May Promote the Elimination of Harmful Mutations in Populations  1086

51.2 Gametogenesis and Fertilization  1087 51.3 Human Reproductive Structure and Function  1090 51.4 Pregnancy and Birth in Mammals  1096 Core Concept: Evolution:  The Evolution of the Globin Gene Family Has Been Important for Internal Gestation in Mammals 1097

51.5 General Events of Embryonic Development  1099 51.6 Impact on Public Health  1104



©Dante Fenolio/Science Source

Chapter 54 An Introduction to Ecology and Biomes  1149 54.1 The Scale of Ecology  1150 Feature Investigation:  Callaway and Aschehoug’s Experiments Showed That the Secretion of Chemicals Gives Invasive Plants a Competitive Edge over Native Species  1150

54.2 Ecological Methods  1152

CONTENTS

xxv

CONTENTS

48.9 Mechanisms of Gas Transport in Blood  1034 4  8.10 Control of Ventilation  1036 48.11 Impact on Public Health  1037

Chapter 58

54.3 The Environment’s Effect on the Distribution of Organisms 1155

CONTENTS

Communities and Ecosystems: Ecological Organization on Large Scales  1236

Core Concept: Information:  Temperature Tolerance May Be Manipulated by Genetic Engineering  1157

54.4 Climate and Its Relationship to Biological Communities 1160 54.5 Major Biomes  1164 54.6 Biogeography  1175

58.1 58.2 58.3 58.4

Feature Investigation:  Simberloff and Wilson’s Experiments Tested the Predictions of the Equilibrium Model of Island Biogeography 1246

Chapter 55 Behavioral Ecology  1180 55.1 The Influence of Genetics and Learning on Behavior  1181 Core Concept: Evolution:  Some Behavior Results from Simple Genetic Influences  1181

58.5 Food Webs and Energy Flow  1248 58.6 Biomass Production in Ecosystems  1252

Chapter 59

55.2 Local Movement and Long-Range Migration  1184 Feature Investigation:  Tinbergen’s Experiments Showed That Digger Wasps Use Landmarks to Find Their Nests  1185

55.3 55.4 55.5 55.6 55.7

Foraging Behavior and Defense of Territory  1189 Communication  1190 Living in Groups  1192 Altruism  1193 Mating Systems  1196

Chapter 56 Population Ecology  1201 56.1 Understanding Populations  1201 56.2 Demography  1205 Feature Investigation:  Murie’s Construction of a Survivorship Curve for Dall Mountain Sheep Suggested That the Youngest and Oldest Sheep Were Most Vulnerable to Predation by Wolves 1207

56.3 How Populations Grow  1209 Core Concept: Evolution:  Hexaploidy Increases the Growth of Coast Redwood Trees  1214

Chapter 57 Species Interactions  1217 57.1 Competition  1218 Feature Investigation:  Connell’s Experiments with Barnacle Species Revealed Each Species’ Fundamental and Realized Niches  1222

57.2 Predation, Herbivory, and Parasitism  1224 57.3 Mutualism and Commensalism  1229 57.4 Bottom-Up and Top-Down Control  1231

xxvi CONTENTS

Patterns of Species Richness and Species Diversity  1236 Species Richness and Community Stability  1240 Succession: Community Change  1240 Island Biogeography  1243

The Age of Humans  1257 59.1 Human Population Growth  1257 59.2 Global Warming and Climate Change  1260 59.3 Pollution and Human Influences on Biogeochemical Cycles 1262 Feature Investigation:  Stiling and Drake’s Experiments with Elevated CO2 Showed an Increase in Plant Growth but a Decrease in Herbivore Survival 1264

59.4 59.5 59.6 59.7

Pollution and Biomagnification  1268 Habitat Destruction  1269 Overexploitation  1271 Invasive Species  1275

Chapter 60 Biodiversity and Conservation Biology  1280 60.1 Genetic, Species, and Ecosystem Diversity  1280 60.2 Biodiversity and Ecosystem Function  1281 Feature Investigation:  Ecotron Experiments Analyzed the Relationship Between Ecosystem Function and Species Richness 1282

60.3 Value of Biodiversity to Human Welfare  1285 60.4 Conservation Strategies  1287 Appendix A: Periodic Table of the Elements  A-1 Appendix B: Answer Key  A-2 Glossary  G-1 Index  I-1

CHAPTER OUTLINE

An Introduction to Biology

1.1 Levels of Biology 1.2 Core Concepts of Biology 1.3 Biological Evolution 1.4 Classification of Living Things 1.5 Biology as a Scientific Discipline 1.6 Core Skills of Biology Summary of Key Concepts Assess & Discuss

1

B

iology is the study of life. The diverse forms of life found on Earth provide biologists with an amazing array of organisms to study. In many cases, the investigation of living things leads to discoveries that no one would have imagined. For example, researchers determined that the venom from certain poisonous snakes contains a chemical that lowers blood pressure in humans. By analyzing that chemical, scientists developed drugs to treat high blood pressure (Figure 1.1). Biologists have discovered that plants can communicate with each other. For example, the beautiful umbrella thorn acacia (Vachellia tortillis), shown in Figure 1.2, emits volatile organic molecules when it is attacked by herbivores. These molecules warn other nearby acacia trees that herbivores are in the area, and those trees release toxins to protect themselves. Another interesting example of a biological discovery is a seemingly bizarre phenomenon known as zombie parasites. As you may know, zombies are fictional creatures featured in some horror and fantasy novels and movies, where they appear as dead

The giraffe, genus Giraffa.  Giraffes, which are found in Africa, are the tallest living terrestrial animals. They are members of the genus Giraffa. Until recently, biologists thought that all giraffes belonged to a single species. As discussed later in this chapter, that view may be changing as a result of analyses of genetic features of giraffes from different regions of Africa. ©Robert Muckley/Getty Images

H N N

O

C O

OCH2CH3

CH2COOH

ACE inhibitor (Lotensin)

Figure 1.1  The Brazilian arrowhead viper and an inhibitor of high blood pressure.  Derivatives of a chemical, called an angiotensinconverting enzyme (ACE) inhibitor, are found in the venom of the Brazilian arrowhead viper and are commonly used to treat high blood pressure. ©Francois Gohier/Science Source

Figure 1.2  Plant communication.  If attacked by herbivores, this acacia tree will emit molecules that will warn other acacia trees in the area. ©Mark Snodgrass/Getty Images

Table 1.1      Examples of Zombie Parasites Host

Parasite

Description

House cricket (Acheta domesticus)

Horsehair worm (Paragordius varius)

A horsehair worm larva infects a cricket and grows inside it. The cricket is terrestrial, but the adult stage of the horsehair worm is aquatic. When the larva matures into an adult, it alters the behavior of the cricket, causing it to jump into the nearest body of water! As the cricket drowns, an adult horsehair worm emerges.

Spider (Plesiometa argyra)

Wasp (Hymenoepimecis argyraphaga)

A female wasp glues an egg onto a spider’s body. After the egg develops into a larva, the larva pokes a few holes in the spider’s abdomen, which allows it to suck the spider’s blood and also to transfer chemicals into the spider, which control its behavior. The spider stops building its normal orb-shaped web and starts building a web whose geometry is strikingly different: The new web is designed to suspend the larva’s cocoon in the air, where it will be protected from predators.

Various vertebrates, including mice and rats

Protozoan (Toxoplasma gondii)

Toxoplasma gondii is a parasite whose life cycle involves more than one vertebrate host. The definitive host is the cat, which is where T. gondii becomes mature and reproduces sexually. An intermediate host can be any of a variety of vertebrates, including mice and rats, which can ingest the parasite from cat feces. In the intermediate host, the parasite develops and reproduces asexually. To escape an intermediate host, such as a mouse or rat, and move to the definitive host, T. gondii dramatically alters the host's behavior. The infected animal becomes attracted to the smell of cat urine! This makes it more likely to be eaten by a cat and thereby allows T. gondii to enter its definitive host and mature.

creatures that are able to move because of some magical force. A zombie parasite is a parasite that infects its host and is then able to control the host’s behavior. A relatively small group of researchers have begun to investigate this phenomenon, and their work has spawned a new field called neuroparasitology—the study of how parasites control the nervous systems of their hosts. During the past few decades, researchers have discovered many examples of zombie parasites. A few are described in Table 1.1. These are but a few of the many discoveries that make biology an intriguing discipline. The study of life not only reveals the fascinating characteristics of living species but also leads to the development of medicines and research tools that benefit the lives of people. To make new discoveries, biologists view life from many different perspectives: What is the composition of living things? How is life organized? How do organisms reproduce? Sometimes the questions posed by biologists are fundamental and even philosophical in nature: How did living organisms originate? Can we live forever? What is the physical basis for memory? Can we save endangered species?

1.1

Levels of Biology

Learning Outcome: 1. Explain how life can be viewed at different levels of biological complexity.

Let’s begin our journey through the wonderful world of biology by considering how life is organized. The term organism can be applied to all forms of life. Organisms maintain an internal order that is separated from the environment. The complexity of living organisms can be analyzed at different levels, starting with the smallest level of organization and progressing to levels that are physically much larger and more complex. Figure 1.3 depicts a biologist’s view of the levels of biological organization. 1. Atoms. An atom is the smallest unit of an element that has the chemical properties of the element. All matter is composed of atoms.

Future biologists will continue to make important advances. Biologists are scientific explorers looking for answers to some of life’s most enduring mysteries. Unraveling these mysteries presents exciting challenges to the best and brightest minds. The rewards of a career in biology include the excitement of forging into uncharted territory, the thrill of making discoveries that can improve the health and lives of people, and the satisfaction of trying to preserve the environment and protect endangered species. For these and many other compelling reasons, students seeking challenging and rewarding careers may wish to choose biology as a lifelong pursuit. In this chapter, we will begin by examining the levels of biology and the core concepts that are common to all forms of life. One of those core concepts is evolution, which is discussed in greater depth in Section 1.3. We then explore the general approaches that scientists follow when making new discoveries. Finally, we will consider the skills that students need to develop as they pursue careers in this exciting discipline and the ways in which this textbook fosters those skills.

2. Molecules and macromolecules.  As discussed in Unit I, atoms bond with each other to form molecules. A polymer such as a polypeptide is formed of many molecules bonded together and is called a macromolecule. Carbohydrates, proteins, and nucleic acids (DNA and RNA) are important macromolecules found in living organisms. 3. Cells.  The simplest unit of life is the cell, which we will examine in Unit II. A cell is surrounded by a membrane and contains a variety of molecules and macromolecules. Unicellular organisms are composed of one cell, whereas multicellular organisms, such as plants and animals, contain many cells. 4. Tissues.  In multicellular organisms, many cells of the same type associate with each other to form tissues. An example is muscle tissue. 5. Organs.  In complex multicellular organisms, an organ is composed of two or more types of tissue. For example, the heart is composed of several types of tissues, including muscle, nervous, and connective tissue.



AN INTRODUCTION TO BIOLOGY 3

1

Atoms

2

Molecules and macromolecules

3

5

6

4

Organs

Cells

Tissues

Organism

10

7

Biosphere

Population

9 8

Ecosystem

Community

Figure 1.3  The levels of biological organization. Concept Check:   At which level of biological organization would you place a herd of buffalo?

6. Organism.  All living things can be called organisms. Biologists classify organisms as belonging to a particular species, which is a related group of organisms that share a distinctive form and set of attributes in nature. The members of the same species are closely related genetically. In Units VI and VII, we will examine plants and animals at the level of cells, tissues, organs, and complete organisms. 7. Population.  A group of organisms of the same species that occupy the same environment is called a population. 8. Community.  A biological community is an assemblage of populations of different species. The types of species found in

a community are determined by the environment and by the interactions of species with each other. 9. Ecosystem.  Researchers may extend their work beyond living organisms and also study the physical environment. Ecologists analyze ecosystems, which are formed by interactions of a community of organisms with their physical environment. Unit VIII considers biological organization from populations to ecosystems. 10. Biosphere. The biosphere includes all of the places on the Earth where living organisms exist. Life is found in the air, in bodies of water, on the land, and in the soil.

4

CHAPTER 1

1.2 

Core Concepts of Biology

Learning Outcome: 1. Describe the core concepts of biology as advocated by “Vision and Change.”

In 2007, the American Association for the Advancement of Science initiated a series of regional conversations with more than 200 biology faculty to discuss how to improve undergraduate biology education. In 2009, using the findings of these regional conversations, the organization held a conference called “Vision and Change in

Undergraduate Biology Education.” More than 500 biology faculty, college and university administrators, representatives of professional societies, and students and postdoctoral scholars from around the country attended the conference. The proceedings led to various recommendations that can be found at http://visionandchange.org. A key outcome of “Vision and Change” was the identification of five core concepts of biology (Figure 1.4): 1. Evolution: The diversity of life evolved over time by processes of mutation, natural selection, and genetic exchange. 2. Structure and function: Basic units of structure define the function of all living things.

(a) Evolution: Biological evolution, or simply evolution, refers to a heritable change in a population of organisms from generation to generation. As a result of evolution, populations become better adapted to the environment in which they live. For example, the long snout of an anteater is an adaptation that enhances its ability to obtain food, namely ants, from hard-to-reach places. Over the course of many generations, the fossil record indicates that the long snout occurred via biological evolution in which modern anteaters evolved from populations of organisms with shorter snouts. (b) Structure and function: Biologists often say “structure determines function.” This core concept pertains to very tiny biological molecules and to very large biological structures. The feet of different birds provide a striking example. Aquatic birds have webbed feet that function as paddles for swimming. By comparison, the feet of nonaquatic birds are not webbed and are better adapted for grasping food, perching on branches, and running along the ground. The structure of a bird’s feet, webbed versus nonwebbed, is a critical feature that affects their function. (c) Information: Genetic material composed of DNA (deoxyribonucleic acid) provides a blueprint for the organization, development, and function of living things. During reproduction, a copy of this blueprint is transmitted from parents to offspring. DNA is heritable, which means that offspring inherit DNA from their parents. A key feature of reproduction is that offspring tend to have characteristics that greatly resemble those of their parent(s). As seen here, this mother dolphin and her offspring have strikingly similar features.

(d) Energy and matter: All living organisms acquire energy and matter from the environment and use them to synthesize essential molecules and maintain the organization of their cells and bodies. These sunflower plants carry out photosynthesis in which they capture light energy and acquire carbon dioxide and water, thereby allowing them to make carbohydrates. This process provides energy and organic molecules so the plants can grow and produce beautiful flowers.

(e) Systems: When the parts of an organism interact with each other or with the external environment to create novel structures and functions, the resulting characteristics are called emergent properties. For example, the human eye is composed of many different types of cells that are organized to sense incoming light and transmit signals to the brain. Our ability to see is an emergent property of this complex arrangement of different cell types. Biologists use the term systems biology to describe the study of how new properties of life arise by complex interactions of its individual parts.

Figure 1.4  Core concepts of biology, as advocated by “Vision and Change.”  These core concepts will be emphasized throughout this textbook. a: ©Lucas Leuzinger/Shutterstock; b: ©G.K. & Vikki Hart/Getty Images; c: ©Image Source/Getty Images; d: Source: Photo by Bruce Fritz, USDA-ARS; e: ©Maria Teijeiro/Getty Images



AN INTRODUCTION TO BIOLOGY

3. Information flow, exchange, and storage: The growth and behavior of organisms are activated through the expression of genetic information. 4. Pathways and transformations of energy and matter: Biological systems grow and change via processes that are based on chemical transformation pathways and are governed by the laws of thermodynamics. 5. Systems: Living systems are interconnected and interacting.

5

Ancestral limb Modification over time

A key goal of this textbook is to bring to life these five core concepts of biology. These concepts will be highlighted in each chapter with a “Vision and Change” icon, , which indicates subsections and figures that focus on one or more of these five core concepts. Bat wing

Dolphin flipper

1.3 Biological Evolution Learning Outcomes: 1. Explain two mechanisms by which evolutionary change occurs: vertical descent with mutation and horizontal gene transfer. 2. Describe how changes in genomes and proteomes underlie evolutionary changes.

Unity and diversity are two words that often are used to describe the living world. All modern forms of life display a common set of characteristics that distinguish them from nonliving objects. In this section, we will explore how this unity of common traits is rooted in the phenomenon of biological evolution, or simply evolution, which is a heritable change in a population of organisms from one generation to the next. Life on Earth is united by an evolutionary past in which modern organisms have evolved from populations of pre-existing organisms. This unity is a core concept of biology. However, evolutionary unity does not mean that organisms are exactly alike. The Earth has many different types of environments, ranging from tropical rain forests to salty oceans, hot and dry deserts, and cold mountaintops. Diverse forms of life have evolved in ways that help them prosper in the different environments the Earth has to offer. In this and the following section, we will begin to examine the unity and diversity that exists within the biological world.

Modern Forms of Life Are Connected by an Evolutionary History Life began on Earth as primitive cells about 3.5–4 billion years ago (bya). Since that time, populations of living organisms have undergone evolutionary changes that ultimately gave rise to the species we see today. Understanding the evolutionary history of species can provide key insights into the structure and function of an organism’s body, because evolutionary change frequently involves modifications of characteristics in pre-existing populations. Over long periods of time, populations may change so that structures with a particular function become modified to serve a new function. For example, the wing of a bat is used for flying, and the flipper of a dolphin is used for swimming. Evidence from

Figure 1.5  An example of a modification that has occurred as a

result of biological evolution.  The wing of a bat and the flipper of a dolphin are modifications of a limb that was used for walking in a pre-existing ancestor. Core Concepts: Evolution, Structure and Function  Via evolution, the different structures of the front limbs seen here result in functions that are best suited for these organisms.

the fossil record indicates that both structures were modified from a front limb that was used for walking in a pre-existing ancestor (Figure 1.5).

Evolutionary Change Involves Changes in the Genetic Material The example shown in Figure 1.5 represents evolution at the macroscopic level. At the molecular level, evolution involves changes in the genetic material, which is composed of DNA (deoxyribonucleic acid). DNA provides a blueprint for the organization, development, and function of living things. During reproduction, a copy of this blueprint is transmitted from parent to offspring. DNA is heritable, which means that offspring inherit DNA from their parents. As discussed in Unit III, genes, which are segments of DNA, govern the characteristics, or traits, of organisms. Most genes are transcribed into a type of RNA (ribonucleic acid) molecule called messenger RNA (mRNA), which is then translated into a polypeptide with a specific amino acid sequence. A protein is composed of one or more polypeptides. The structures and functions of proteins play a key role in determining the traits of organisms. On relatively rare occasions, changes may occur in DNA. A mutation is a heritable change in the genetic material—one that can be passed from cell to cell or from parent to offspring. Mutations can alter the properties of genes and thereby affect the characteristics of the offspring that inherit them. With regard to survival, mutations can be beneficial, detrimental, or neutral. As described next, changes in the genetic material underlie the process of evolution.

6

CHAPTER 1

Changes to the Genetic Material during Evolution May Occur in Different Ways  As a given species evolves and as new species are formed, different types of mechanisms may cause changes in the genetic material. Two common mechanisms are vertical descent with mutation and horizontal gene transfer. Let’s take a brief look at each one. Vertical Descent with Mutation  The traditional way to study evolution is to examine a progression of changes in a series of related ancestral species. Such a series is called a lineage. Figure 1.6 shows a portion of the lineage that gave rise to modern horses. This type of evolution is called vertical evolution because it occurs in a lineage. Biologists have traditionally depicted such evolutionary change in a diagram like the one shown in Figure 1.6. In this mechanism of evolution, new species evolve from pre-existing ones by the accumulation of mutations. But why would some mutations accumulate in a population and eventually change the characteristics of an entire species? One reason is that a mutation may alter the traits of organisms

in a way that increases their chances of survival and reproduction. When a mutation causes such a beneficial change, the frequency of the mutation may increase in a population from one generation to the next, a process called natural selection. This topic is discussed in Units IV and V. Evolution also involves the accumulation of neutral changes that do not benefit or harm a species, and evolution sometimes involves rare changes that may be harmful. With regard to the horses shown in Figure 1.6, the fossil record has revealed adaptive changes in various traits such as size and tooth morphology. The first horses were the size of dogs, whereas modern horses typically weigh more than a half ton. The teeth of Hyracotherium were relatively small compared with those of modern horses. Over the course of millions of years, horses' teeth have increased in size, and a complex pattern of ridges has developed on the molars. How do evolutionary biologists explain these changes in horse characteristics? They can be attributed to natural selection, in which changing global climates favored the survival and reproduction of horses with certain types of traits. Over North America, where much of horse evolution occurred, large areas changed from dense forests to grasslands.

0 Hippidium and other genera

Equus

5

Nannippus Styohipparion Neohipparion Hipparion

10 Sinohippus

Pliohippus

Megahippus

Calippus

Millions of years ago (mya)

Archaeohippus

20

Anchitherium

Merychippus Hypohippus

Parahippus

Miohippus Mesohippus

40

Figure 1.6  An example of vertical evolution: the

Paleotherium Epihippus

Propalaeotherium Orohippus

Pachynolophus

55

Hyracotherium

horse lineage.  This diagram shows the horse lineage. The highlighted branch gave rise to the modern horse (Equus), which evolved from ancestors that were much smaller. The vertical evolution shown here occurred due to the accumulation of mutations that altered the traits of the species. Concept Check:   What is the relationship between biological evolution and natural selection?



AN INTRODUCTION TO BIOLOGY

Horses with genetic variation that made them larger were more likely to escape predators and to be able to travel greater distances in search of food. The changes seen in horses’ teeth are consistent with a dietary shift from eating tender leaves to eating grasses and other types of vegetation that are more abrasive and require more chewing. Horizontal Gene Transfer  The most common way for genes to be transferred is in a vertical manner. This can involve the transfer of genetic material from a mother cell to daughter cells, or it can occur via gametes—sperm and egg—that unite to form a new organism. However, as discussed in later chapters, genes are sometimes transferred between organisms by other mechanisms. These other mechanisms are collectively known as horizontal gene transfer, which is the transfer of genetic material from one organism to another organism that is not its offspring. In some cases, horizontal gene transfer can occur between members of different species. For example, you may have heard in the news media that resistance to antibiotics among bacteria is a growing medical problem. As discussed in Chapter 19, genes that confer antibiotic resistance are sometimes transferred between different bacterial species (Figure 1.7). Genes transferred horizontally may be subject to natural selection and promote changes in an entire species. This has been an important mechanism of evolutionary change, particularly among bacterial species. In addition, during the early stages of evolution, which occurred a few billion years ago, horizontal gene transfer was an important part of the process that gave rise to all modern species. Traditionally, biologists have described evolution using diagrams that depict the vertical evolution of species on a long time scale. This type of evolutionary tree was shown earlier in Figure 1.6. For many decades, a simplistic view held that all living organisms evolved from a common ancestor, resulting in a “tree of life” that depicted the vertical evolution that gave rise to all modern species. Now that we understand the great importance of horizontal gene transfer in the evolution of life on Earth, biologists have re-evaluated the way evolution has occurred over time. Rather than a tree of life, a more appropriate way

DNA

Antibioticresistance gene Bacterial species such as Escherichia coli

DNA

Antibioticresistance gene from E. coli

Horizontal gene transfer to another species Bacterial species such as Streptococcus pneumoniae

Figure 1.7  An example of horizontal gene transfer: antibiotic

resistance.  One bacterial species may transfer a gene, such as a gene that confers resistance to an antibiotic, to another bacterial species.

7

to view the unity of living organisms is as a “web of life,” as shown in Figure 1.8, which accounts for both vertical descent and horizontal gene transfer. In a lineage in which the time scale is depicted on a vertical axis, horizontal gene transfer between different species is shown as a horizontal line.

Core Concept: Evolution The Study of Genomes and Proteomes Provides an Evolutionary Foundation for Our Understanding of Biology As we have seen, evolutionary unity is a core concept of biology. We can understand the unity of modern organisms by realizing that all living species evolved from an interrelated group of ancestors. However, from an experimental perspective, this realization presents a dilemma—we cannot take a time machine back over the course of 4 billion years to carefully study the characteristics of extinct organisms and fully appreciate the series of changes that have led to modern species. Fortunately, though, evolution has given biologists some wonderful puzzles to study, including the fossil record and the genomes of modern species. The term genome refers to the complete genetic composition of an organism or species (Figure 1.9a). The genomes of bacteria and archaea usually contain a few thousand genes, whereas those of eukaryotes may contain tens of thousands. A genome is critical to life because it performs these functions: ∙  Stores information in a stable form: The genome of every organism stores information that provides a blueprint for producing that organism's characteristics. ∙  Provides continuity from generation to generation: The genome is copied and transmitted from generation to generation. ∙ Acts as an instrument of evolutionary change: Every now and then, the genome undergoes a mutation that may alter the characteristics of an organism. In addition, a genome may acquire new genes by horizontal gene transfer. The accumulation of genome changes from generation to generation produces the evolutionary changes that alter species and produce new species. An exciting advance in biology over the past couple of decades has been the ability to analyze the DNA sequence of genomes, a technology called genomics. For example, a researcher can compare the genomes of a frog, a giraffe, and a petunia and discover intriguing similarities and differences. These comparisons help us to understand how new traits evolved. All three types of organisms have the same kinds of genes needed for the breakdown of nutrients such as sugars. In contrast, only the petunia has genes that allow it to carry out photosynthesis. Also, genomics helps us to understand evolutionary relationships. As discussed later in this chapter, researchers analyzed the genomes of giraffes across Africa and concluded that they constitute four distinct species.

8

CHAPTER 1

Bacteria

Archaea

Eukarya Fungi

Animals

Plants

Protists

KEY Vertical evolution Horizontal gene transfer Common ancestral community of primitive cells

Figure 1.8  The web of life, showing both vertical descent and horizontal gene transfer.  This diagram includes both of these important mechanisms in the evolution of life on Earth. Note: Archaea are unicellular species that are similar in cell structure to bacteria. Concept Check:   How does the concept of a tree of life differ from that of a web of life?

An extension of genome analysis is the study of the proteome, which refers to all of the proteins that a cell or organism makes. The function of most genes is to encode polypeptides that become units in proteins. As shown in Figure 1.9b, these include proteins that form a cytoskeleton and proteins that function in cell organization and as enzymes, transport proteins, cell-signaling proteins, and extracellular proteins. The genome of each species carries the information to make its proteome—the hundreds or thousands of proteins that each cell of that species makes. Proteins are largely responsible for the structures and functions of cells and organisms. The set of techniques known as proteomics allows researchers to analyze the proteome of a single species and compare the proteomes of different species. Proteomics helps us understand how the various levels of biology are related to one another, from the molecular level—at the level of protein molecules—to higher levels, such as how the functioning of proteins produces the characteristics of cells and organisms and affects the ability of populations of organisms to survive in their natural environments.

1.4  Classification of Living Things Learning Outcome: 1. Outline how organisms are classified.

As biologists study species and discover new species, they try to place them into groups based on their evolutionary history. This is a difficult task because researchers estimate that the Earth has between 5 and 50 million different species! The rationale for classification is based on vertical descent. Species with a recent common ancestor are grouped together, whereas species whose common ancestor was in the very distant past are placed into different groups. The field of biology that is concerned with the grouping and classification of species is termed taxonomy. Why is taxonomy useful? First, taxonomy allows use to appreciate the amazing diversity of life on Earth. Also, because taxonomy is based on evolution, it provides a view of the evolutionary relationships among living species, and between living and extinct species.



AN INTRODUCTION TO BIOLOGY 9

In eukaryotes, most of the genome is contained within chromosomes that are located in the cell nucleus. Gene

(a) The genome

Cytoplasm

Most genes encode mRNAs that contain the information to make proteins.

DNA

Chromosome

Cell signaling: Proteins are needed for cell signaling with other cells and with the environment.

Sets of chromosomes

Nucleus

Cytoskeleton: Proteins are involved in cell shape and movement.

Cell organization: Proteins organize the components within cells.

Enzymes: Proteins function as enzymes to synthesize and break down cellular molecules and macromolecules.

(b) The proteome

Transport proteins: Proteins facilitate the uptake and export of substances.

Extracellular proteins: Proteins hold cells together in tissues.

Extracellular fluid

Figure 1.9  Genomes and proteomes.  (a) The genome, which is composed of DNA, is the entire genetic composition of an organism. Most of the genetic material in eukaryotic cells is found in the cell nucleus. The primary function of the genome is to encode the proteome (b), which is the entire protein complement of a cell or organism. Six general categories of proteins are illustrated. Proteins are largely responsible for the structure and function of cells and organisms. Concept Check:   Biologists sometimes say that the genome is the storage unit of life, whereas the proteome is largely the functional unit of life. Explain this statement. 

The Classification of Living Organisms Allows Biologists to Appreciate the Unity and Diversity of Life Let’s first consider taxonomy on a broad scale. You may have noticed that Figure 1.8 showed three main groups of organisms. From an evolutionary perspective, all forms of life can be placed into those three large categories, or domains, called Bacteria, Archaea, and Eukarya (Figure 1.10). Bacteria and archaea are microorganisms that are also termed prokaryotic because their cell structure is relatively simple. At the molecular level, bacterial and archaeal cells show significant differences in their compositions. By comparison, organisms in the domain Eukarya are eukaryotic and have cells with internal compartments that

serve various functions. A defining distinction between prokaryotic and eukaryotic cells is that eukaryotic cells have a cell nucleus in which the genetic material is surrounded by a membrane. The organisms in domain Eukarya were once subdivided into four major categories, or kingdoms, called Protista (protists), Plantae (plants), Fungi, and Animalia (animals). However, as discussed in Chapter 25 and Unit V, this traditional view became invalid as biologists gathered new information regarding the evolutionary relationships of these organisms. We now know that the protists do not form a single kingdom but instead are divided into several broad categories called supergroups. Taxonomy involves multiple levels in which particular species are placed into progressively smaller and smaller groups whose

10

CHAPTER 1

6.2 μm

(a) Domain Bacteria: Mostly unicellular prokaryotes that inhabit many diverse environments on Earth.

3.2 μm

(b) Domain Archaea: Unicellular prokaryotes that often live in extreme environments, such as hot springs.

375.2 μm Protists: Unicellular and small multicellular organisms that are now subdivided into seven broad groups based on their evolutionary relationships.

Plants: Multicellular organisms that can carry out photosynthesis.

Fungi: Unicellular and multicellular organisms that have a cell wall but cannot carry out photosynthesis. Fungi usually survive on decaying organic material.

Animals: Multicellular organisms that usually have a nervous system and are capable of locomotion. They must eat other organisms or the products of other organisms to live.

(c) Domain Eukarya: Unicellular and multicellular organisms having cells with internal compartments that serve various functions.

Figure 1.10  The three domains of life.  Two of these domains, (a) Bacteria and (b) Archaea, consist of species with prokaryotic cells. The third domain, (c) Eukarya, comprises species that are eukaryotes. a: ©BSIP/age fotostock; b: ©Eye of Science/Science Source; c (protists): ©Jan Hinsch/Getty

Images; c (plants): ©Kent Foster/Science Source; c (fungi): ©Carl Schmidt-Luchs/Science Source; c (animals): ©Ingram Publishing/age fotostock

Core Skill: Connections  Look ahead to Figure 25.1. Are fungi more closely related to plants or animals?



AN INTRODUCTION TO BIOLOGY 11

Taxonomic group

The ocellaris clownfish is found in

Approximate time when the common ancestor for this group arose

Approximate number of modern species in this group

Domain

Eukarya

2,000 mya

> 5,000,000

Supergroup

Opisthokonta

2,000 mya

> 1,000,000

Kingdom

Animalia

600 mya

> 1,000,000

Phylum

Chordata

525 mya

50,000

Class

Actinopterygii

420 mya

30,000

Order

Perciformes

80 mya

7,000

Family

Pomacentridae

~ 40 mya

360

Genus

Amphiprion

~ 9 mya

28

Species

ocellaris

< 3 mya

1

Examples

Figure 1.11  Taxonomic classification of the ocellaris clownfish.  Concept Check:   Why is it useful to place organisms into taxonomic groupings?

members are more closely related to each other evolutionarily. Such an approach emphasizes the unity and diversity of different species. As an example, let’s consider the clownfish, a popular saltwater aquarium fish (Figure 1.11). Several species of clownfish have been identified.  One species of clownfish, which is orange with white stripes, has several common names, including ocellaris clownfish. The broadest grouping for this clownfish is the domain, namely, Eukarya, followed by progressively smaller divisions, from supergroup (Opisthokonta), to kingdom (Animalia), and eventually to species. In the animal kingdom, clownfish are part of a phylum, Chordata, the chordates, which is subdivided into classes. Clownfish are in a class called Actinopterygii, which includes all ray-finned fishes.

The common ancestor that gave rise to ray-finned fishes arose about 420 million years ago (mya). Actinopterygii is subdivided into several smaller orders. The clownfish are in the order Perciformes (bony fish). The order is, in turn, divided into families; the clownfish belong to the family of marine fish called Pomacentridae, which are often brightly colored. Families are divided into genera (singular, genus). The genus Amphiprion is composed of 28 different species; these are various types of clownfish. Therefore, the genus contains species that are very similar to each other in form and have evolved from a common (extinct) ancestor that lived relatively recently on an evolutionary time scale. Biologists use a two-part description, called binomial nomenclature, to provide each species with a unique scientific name. The

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Figure 1.12  A proposal that giraffes constitute four distinct species.  Each species has its own distinctive coat pattern. From left to right: northern giraffe (Giraffa camelopardalis), reticulated giraffe (G. reticulata), Masai giraffe (G. tippelskirchi), and southern giraffe (G. giraffa). (northern giraffe): ©NSP-RF/Alamy Stock Photo; (reticulated giraffe): ©McGraw-Hill Education; (Masai giraffe): ©iStock/Getty Images; (southern giraffe): ©Egmont Strigl/Westend61/ Getty Images

Core Skill: Process of Science  The gathering and analysis of new data suggest that giraffes, which were once thought to be a single species, constitute four different species.

scientific name of the ocellaris clownfish is Amphiprion ocellaris. The first word is the genus, and the second word is the specific epithet, or species descriptor. By convention, the genus name is capitalized, whereas the specific epithet is not. Both names are italicized. Scientific names are usually Latinized, which means they are made similar in appearance to Latin words. The origins of scientific names are typically Latin or Greek, but they can come from a variety of sources, including a person’s name.

Taxonomy Changes as Researchers Gather Evidence Regarding the Characteristics and Genetic Composition of Organisms Located in Different Places How do we judge if a gray squirrel living in Minnesota and another one living in California are members of the same species? As discussed in Chapter 24, biologists use different criteria to decide if similar organisms living in different places are the same species or different species. For example, they may analyze morphological features or study DNA samples. Science is a work in progress. As biologists gather new information and conduct experiments, their views often change. An interesting example involves the classification of giraffes, shown on the cover of this textbook. Giraffes are currently classified as a single species,  Giraffa camelopardalis, but recent studies are challenging that conclusion. In 2016, a study by Axel Janke and colleagues suggested that there are four distinct species of giraffes. This work was based on a genetic analysis of DNA samples taken from 190 giraffes across Africa. By comparing these DNA samples, the researchers concluded that giraffes should be classified as four distinct species (Figure 1.12).

While not all experts agree on this conclusion, this work illustrates how our perception of biological diversity can change as we gather more information. 

1.5 B  iology as a Scientific Discipline Learning Outcomes: 1. Explain how researchers study biology at different levels, ranging from molecules to ecosystems. 2. CoreSKILL » Distinguish between discovery-based science and hypothesis testing, and describe the steps of the scientific method.

What is science? Surprisingly, the definition of science is not easy to state. Most people have an idea of what science is, but actually articulating that idea proves difficult. In biology, we can define science as the observation, identification, experimental investigation, and theoretical explanation of natural phenomena. Science is conducted in different ways and at different levels. Some biologists study the molecules that compose life, and others try to understand how organisms survive in their natural environments. Experimentally, researchers often focus their efforts on model organisms—organisms studied by many different researchers so they can compare their results and determine scientific principles that apply more broadly to other species. Examples of model organisms include Escherichia coli (a bacterium), Saccharomyces cerevisiae (a yeast), Drosophila melanogaster (fruit fly), Caenorhabditis elegans (a nematode worm), Mus musculus (mouse), and Arabidopsis thaliana (a flowering plant). Model organisms offer experimental advantages

over other species. For example, E. coli is a very simple organism that can be easily grown in the laboratory. By limiting their work to a few model organisms, researchers can gain a deeper understanding of these species. Importantly, the discoveries made using model organisms help us to understand how biological processes work in other species, including humans. In this section, we will examine how biologists follow a standard approach, called the scientific method, to test their ideas. We will explore how scientific knowledge makes predictions that can be experimentally tested. However, not all discoveries are the result of researchers following the scientific method. Some discoveries are made simply by gathering new information. For example, as illustrated earlier, in Figure 1.1 the characterization of many living organisms has led to the development of important medicines. In this section, we will also consider how researchers often set out on “factfinding missions” aimed at uncovering new information that may eventually lead to important discoveries in biology.

Biologists Investigate Life at Different Levels of Organization In Figure 1.3, we examined the various levels of biological organization. The study of these different levels depends not only on the scientific interests of biologists but also on the tools available to them. The study of organisms in their natural environments is a branch of biology called ecology, which considers populations, communities, and ecosystems (Figure 1.13a). Some researchers examine the structures and functions of plants and animals; these subjects form the disciplines called anatomy and physiology (Figure 1.13b). With the advent of microscopy, cell biology, which is the study of cells and their interactions, became an important branch of biology in the early 1900s and remains so today (Figure 1.13c). In the 1970s, genetic tools became available for studying single genes and the proteins they encode. This genetic technology enabled researchers to study individual molecules, such as proteins, in living cells and thereby spawned the field of molecular biology. Together with biochemists and biophysicists, molecular biologists focus their efforts on the structure and function of the molecules of life ( Figure 1.13d). Such researchers want to understand how biology works at the molecular and even atomic levels. Overall, the 20th century saw a progressive increase in the number of biologists who used an approach to understanding biology called reductionism—reducing complex systems to simpler components as a way to understand how the system works. In biology, reductionists study the parts of a cell or organism as individual units. In the 1990s, the pendulum began to swing in the other direction. Scientists have invented new tools that allow them to study groups of genes (genomic techniques) and groups of proteins (proteomic techniques). Biologists now use the term systems biology to describe research aimed at understanding how emergent properties arise. This term is often applied to the study of cells. In this context, systems biology may involve the investigation of groups of genes that encode proteins with a common purpose (Figure 1.13e). For example, a systems biologist may conduct experiments that try to characterize an entire cellular process, which is driven by dozens of different proteins. However, systems biology is not new. Animal

AN INTRODUCTION TO BIOLOGY 13

Ecologists study species in their native environments.

(a) Ecology—population/ community/ecosystem levels

Cell biologists often use microscopes to learn how cells function.

(c) Cell biology—cellular levels

Anatomists and physiologists study how the structures of organisms are related to their functions. (b) Anatomy and physiology— tissue/organ/organism levels

Molecular biologists and biochemists study the molecules and macromolecules that make up cells. (d) Molecular biology— atomic/molecular levels

Systems biologists may study groups of molecules. The microarray shown in the inset determines the expression of many genes simultaneously. (e) Systems biology—all levels, shown here at the molecular level

Figure 1.13  Biological investigation at different levels of

organization. a: ©Diane Nelson; b: ©Purestock/SuperStock; c: ©Erik Isakson/Blend

Images; d: ©Northwestern, Shu-Ling Zhou/AP Images; e: ©Andrew Brookes/Corbis/ Getty Images; e (inset): ©Alfred Pasieka/Science Source

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and plant physiologists have been studying the functions of complex organ systems for centuries. Likewise, ecologists have been characterizing ecosystems for a very long time. The excitement surrounding systems biology in recent years has been the result of new experimental tools that allow biologists to study complex interactions at the molecular level.

A Hypothesis Is a Proposed Idea, Whereas a Theory Is a Broad Explanation Backed by Extensive Evidence Let’s now consider the process of science. In biology, a hypothesis is a proposed explanation for a natural phenomenon. It is a proposition based on previous observations or experimental studies. For example, with knowledge of seasonal changes, you might hypothesize that maple trees drop their leaves in the autumn because of the shortened amount of daylight. An alternative hypothesis might be that the trees drop their leaves because of lower temperatures. In biology, a hypothesis requires more work by researchers to evaluate its validity. A useful hypothesis must make predictions—expected outcomes that can be shown to be correct or incorrect. In other words, a useful hypothesis is testable. If a hypothesis is incorrect, it should be falsifiable, which means that it can be shown to be incorrect by additional observations or experimentation. Alternatively, a hypothesis may be correct, so further work will not disprove it. In such cases, we say that the researchers have failed to reject the hypothesis. Even so, in science, a hypothesis is never really proven but rather always remains provisional. Researchers accept the possibility that perhaps they have not yet conceived of the correct hypothesis. After many experiments, biologists may conclude that a hypothesis is consistent with known data, but they should never say the hypothesis is proven. By comparison, the term theory, as it is used in biology, is a broad explanation of some aspect of the natural world that is substantiated by a large body of evidence. Biological theories incorporate observations, hypothesis testing, and the laws of other disciplines such as chemistry and physics. Theories are powerful because they allow us to make many predictions about the properties of living organisms. As an example, let’s consider the theory that DNA is the genetic material and that it is organized into units called genes. An overwhelming body of evidence has substantiated this theory. Thousands of living species have been analyzed at the molecular level. All of them have been found to use DNA as their genetic material and to express genes that produce the proteins that lead to their characteristics. This theory makes many valid predictions. For example, certain types of mutations in genes are expected to affect the traits of organisms. This prediction has been confirmed experimentally. Similarly, this theory predicts that genetic material is copied and transmitted from parents to offspring. By comparing the DNA of parents and offspring, this prediction has also been confirmed. Furthermore, the theory explains the observation that offspring resemble their parents. Overall, two key attributes of a scientific theory are (1) consistency with a vast amount of known data and (2) the ability to make many correct predictions. The meaning of “theory” is sometimes muddled because the word is used in different situations. In everyday language, a theory

is often viewed as little more than a guess. For example, a person might say, “My theory is that Professor Simpson did not come to class today because he went to the beach.” However, in biology, a theory is much more than a guess. A theory is an established set of ideas that explains a vast amount of data and offers valid predictions that can be tested. Like a hypothesis, a theory can never be proven to be true. Scientists acknowledge that they do not know everything. Even so, biologists would say that theories are extremely likely to be true, based on all known information. In this regard, theories are viewed as knowledge, which is the awareness and understanding of information.

Discovery-Based Science and Hypothesis Testing Are Scientific Approaches That Help Us Understand Biology The path that leads to an important discovery is rarely a straight line. Rather, scientists ask questions, make observations, ask modified questions, and may eventually conduct experiments to test their hypotheses. The first attempts at experimentation may fail, and new experimental approaches may be needed. To suggest that scientists follow a rigid scientific method is an oversimplification of the process of science. Scientific advances often occur as scientists dig deeper and deeper into a topic that interests them. Curiosity is the key phenomenon that sparks scientific inquiry. How is biology actually conducted? As discussed next, researchers typically follow two general types of approaches: discovery-based science and hypothesis testing. Discovery-Based Science  The collection and analysis of data without the need for a preconceived hypothesis is called discoverybased science, or simply discovery science. Why is discovery-based science carried out? The information gained from discovery-based science may lead to the formation of new hypotheses and, in the long run, may have practical applications that benefit people. Researchers, for example, have identified and begun to investigate previously unknown genes within the human genome without already knowing the function of those genes. The goal is to gather additional clues that may eventually allow them to propose a hypothesis that explains a gene’s function. Discovery-based science often leads to hypothesis testing. Hypothesis Testing  In biological science, the scientific method, also known as hypothesis testing, is usually followed to formulate and test the validity of a hypothesis. This strategy may be described as a five-step method: 1. Observations are made regarding natural phenomena. 2. These observations lead to a hypothesis that tries to explain the phenomena. A useful hypothesis is one that is testable because it makes specific predictions. 3. Experimentation is conducted to determine if the predictions are correct. 4. The data from the experiment are analyzed. 5. The hypothesis is considered to be consistent with the data, or it is rejected.



AN INTRODUCTION TO BIOLOGY 15

1

OBSERVATIONS The leaves on maple trees fall in autumn when the days get colder and shorter.

2

HYPOTHESIS The shorter amount of daylight causes the leaves to fall.

3

EXPERIMENTATION Small maple trees are grown in 2 greenhouses where the only variable is the length of light.

Control group: Amount of daily light remains constant for 180 days.

5

THE DATA Number of leaves dropped per tree after 180 days

4

Experimental group: Amount of daily light becomes progressively shorter for 180 days.

CONCLUSION The hypothesis cannot be rejected.

200 A statistical analysis can determine if the control and the experimental data are significantly different. In this case, they are.

100

Control Experimental group group

The scientific method is intended to be an objective way to gather knowledge. As an example, let’s return to the question of why maple trees drop their leaves in autumn. By observing the length of daylight throughout the year and comparing that data with the time of the year when leaves fall, one hypothesis might be that leaves fall in response to a shorter amount of daylight (Figure 1.14). This hypothesis makes a prediction—exposure of maple trees to shorter periods of daylight will cause their leaves to fall. To test this prediction, researchers would design and conduct an experiment. How is hypothesis testing conducted? Although hypothesis testing may follow many paths, certain experimental features are common to this approach. First, data are often collected in two parallel ways. One set of experiments is done on the control group, while another set is conducted on the experimental group. In an ideal experiment, the control and experimental groups differ by only one factor. For example, an experiment could be conducted in which two groups of trees are observed, and the only difference between their environments is the length of light each day. To conduct such an experiment, researchers would grow small trees in a greenhouse where they could keep other factors such as temperature, water, and nutrients the same between the control and experimental groups, while providing the two groups with different amounts of light via artificial lighting. In the control group, the number of hours of light

Figure 1.14  The steps of the scientific method, also known as hypothesis testing.

Core Skill: Process of Science  In this example, the goal is to test the hypothesis that maple trees drop their leaves in the autumn due to the shorter amount of daylight. Concept Check:   What is the purpose of a control group in hypothesis testing? 

provided is kept constant each day, whereas in the experimental group, the amount of light provided each day becomes progressively shorter to mimic seasonal light changes. The researchers would then record the number of leaves dropped by the two groups of trees over a certain period of time. Another key feature of hypothesis testing is data analysis. The result of experimentation is a set of data from which a biologist tries to draw conclusions. Biology is a quantitative science. When experimentation involves control and experimental groups, a common form of analysis is to determine if the data collected from the two groups are truly different. Biologists apply statistical analyses to their data to determine if the outcomes from the control and experimental groups are likely to differ because of the single variable that is different between the two groups. When differences between the control and experimental data are statistically significant, they are not likely to have occurred as a matter of random chance. In our example in Figure 1.14, the trees in the control group dropped far fewer leaves than did those in the experimental group. A statistical analysis could determine if the data collected from the two greenhouses are significantly different from each other. If the two sets of data are found not to be significantly different, the hypothesis will be rejected. Alternatively, if the differences between the two sets of data are significant, as shown in Figure 1.14, biologists can conclude

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that the hypothesis is consistent with the data, though it is not proven. A hallmark of science is that valid experiments are repeatable, which means that similar results are obtained when an experiment is conducted on multiple occasions. For our example in Figure 1.14, the data would be valid only if the experiment was repeatable. As described next, discovery-based science and hypothesis testing are often used together to learn more about a particular scientific topic. As an example, let’s look at how both approaches led to successes in the study of the disease called cystic fibrosis.

The Study of Cystic Fibrosis Provides Examples of Discovery-Based Science and Hypothesis Testing Let’s consider how biologists made discoveries related to the disease cystic fibrosis (CF), which affects about 1 in every 3,500 Americans. Persons with CF produce abnormally thick and sticky mucus that obstructs the lungs and leads to life-threatening lung infections. The thick mucus also blocks ducts in the pancreas, which prevents the digestive enzymes this organ produces from reaching the intestine. Without these enzymes, the intestine cannot fully absorb amino acids and fats, which can cause malnutrition. Persons with this disease may also experience liver damage because the thick mucus can obstruct the liver. On average, people with CF in the United States currently live into their late 30s. Fortunately, as more advances have been made in treatment, this number has steadily increased. Because of its medical significance, many scientists are interested in CF and are conducting studies aimed at gaining greater information regarding its underlying cause. The hope is that knowing more about the disease may lead to improved treatment options, and perhaps even a cure. As described next, discovery-based science and hypothesis testing have been critical to gaining a better understanding of this disease. The CFTR Gene and Discovery-Based Science  In 1935, American physician Dorothy Andersen determined that cystic fibrosis is a genetic disorder. Persons with CF have inherited two faulty CFTR genes, one from each parent. (We now know this gene encodes a protein named the cystic fibrosis transmembrane regulator, abbreviated CFTR.) In the 1980s, researchers used discovery-based science to identify this gene. Their search for the CFTR gene did not require any preconceived hypothesis regarding the function of the gene. Rather, they used genetic strategies similar to those described in Chapter 21. Research groups headed by Lap-Chee Tsui, Francis Collins, and John Riordan identified the CFTR gene in 1989. The discovery of the CFTR gene made it possible to devise diagnostic testing methods to determine if a person carries a faulty version of that gene. In addition, the characterization of the CFTR gene provided important clues about its function. Researchers observed striking similarities between the CFTR gene and other genes that were already known to encode proteins that function in the transport of substances across membranes. Based on this observation, as well as other kinds of data, the scientists hypothesized that the function of the normal CFTR gene is to encode a transport protein. In this way, the identification of the CFTR gene led them to conduct experiments aimed at testing a hypothesis about its function.

Proper Cl – export occurs, and water balance is normal.

Cl – export is defective, affecting water balance and causing sticky mucus.

Cl –

Cl –

Cl Transporter encoded with normal CFTR gene

Defective transporter

Cl

Lung cell with normal CFTR gene

Lung cell with faulty CFTR gene

Figure 1.15  A hypothesis suggesting an explanation for the

defective function of a gene in patients with cystic fibrosis.  The normal CFTR gene, which does not carry a mutation, encodes a protein that transports chloride ions (Cl−) across the plasma membrane to the outside of the cell. In persons with CF, this protein is defective due to a mutation in the CFTR gene. Concept Check:   Explain how discovery-based science helped researchers to hypothesize that the CFTR gene encodes a transport protein. 

The CFTR Gene and Hypothesis Testing  Researchers interested in the CFTR gene also considered studies showing that patients with CF have an abnormal regulation of salt balance across their plasma membranes. They hypothesized that the normal CFTR gene encodes a protein that functions in the transport of chloride ions (Cl−) across the membranes of cells (Figure 1.15). This hypothesis led to experimentation that tested normal cells and cells from CF patients for their ability to transport Cl−. The CF cells were found to be defective in chloride transport. In 1990, scientists successfully transferred the normal CFTR gene into cells from CF patients in the laboratory. The introduction of the normal gene corrected the cells’ defect in chloride transport. Overall, the results showed that the CFTR gene encodes a protein that transports Cl− across the plasma membrane. A mutation in this gene causes it to encode a defective protein, leading to a salt imbalance that affects water levels outside the cell, which explains the thick and sticky mucus in CF patients. In this example, hypothesis testing provided a way to evaluate a hypothesis about how a disease is caused by a genetic change.

Biology Is a Social Discipline Finally, it is worthwhile to point out that biology is a social as well as a scientific discipline. Several laboratories often collaborate on scientific projects. After performing observations and experiments, biologists communicate their results in different ways. Most importantly, papers are submitted to scientific journals. Following submission, a paper usually undergoes a peer-review process in which other scientists, who are experts in the area, evaluate the paper and make comments regarding its quality. As a result of peer review, a paper is either accepted for publication or rejected, or the authors of the paper



AN INTRODUCTION TO BIOLOGY 17

Figure 1.16  One of the social aspects of science. ©Dita Alangkara/AP Images

Core Skill: Communication and Collaboration  At scientific meetings, researchers from various disciplines gather together to discuss new data and discoveries. Research that is conducted by professors, students, lab technicians, and industrial participants is sometimes hotly debated.

may be given suggestions for how to revise the work or conduct additional experiments to make it acceptable for publication. Another social aspect of research is that biologists often attend meetings where they report their most recent work to the scientific community (Figure 1.16). They comment on each other’s ideas and results, eventually putting together the information that builds into scientific theories over many years. As you develop your skills at scrutinizing experiments, it is helpful to discuss your ideas with other people, including fellow students and faculty members. Importantly, you do not need to “know all the answers” before you enter into a scientific discussion. Instead, a more realistic way to view science is as an ongoing and never-ending series of questions.

1.6 

Core Skills of Biology

Learning Outcomes:

1. CoreSKILL » Describe the core skills of biology as identified by “Vision and Change.” 2. CoreSKILL » Explain the process of science. 3. CoreSKILL » Describe what a model is in biology, and explain why models are useful. 4. CoreSKILL » List the types of problem-solving skills you will develop by completing BioTIPS.

In addition to the five core concepts of biology (see Section 1.2), the participants in “Vision and Change” also identified certain skills that students should develop so they can become successful in careers in biology. Educators need to focus on these skills, which are also referred to as core competencies: ∙ The ability to apply the process of science ∙ The ability to use quantitative reasoning

∙ The ability to use models and simulation ∙ The ability to tap into the interdisciplinary nature of science ∙ The ability to communicate and collaborate with professionals in other disciplines ∙ The ability to understand the relationship between science and society In this section, we will consider the features of this textbook that will help you to develop these skills. These features are summarized below: ∙ Each chapter has a Feature Investigation that allows you to apply the process of science. Likewise, the BioTIPS features are aimed at helping you refine and apply your problemsolving skills. ∙ Quantitative reasoning is also a key component of the Feature Investigations. It is involved in answering many of the questions at the end of Feature Investigations, as well as many end-ofchapter questions and BioTIPS questions. ∙ A new feature of the fifth edition, introduced later in this section, is the Modeling Challenges. After learning about a particular topic in biology, you will be asked to either interpret a given model or propose your own model based on a scenario or data. ∙ The interdisciplinary nature of science is highlighted in features titled “Connections” that follow some figure legends. ∙ Another new feature of the fifth edition is the addition of a core skill called “Science and Society” following some of the figure legends. The “Vision and Change” icon, ,  that highlights core concepts throughout the text, also highlights material that promotes the core skills.

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Core Skill: Process of Science

Feature Investigation  |  Observation and Experimentation Form the Core of Biology Biology is largely about the process of discovery. Therefore, a recurring theme of this textbook is how scientists design experiments, analyze data, and draw conclusions. Although each chapter contains many examples of data collection and experiments, a consistent element is a Feature Investigation—which presents an actual study by current or past researchers. Some of these involve discovery-based science, in which biologists collect and interpret data in an attempt to make discoveries that are not hypothesis driven. Most Feature Investigations, however, involve hypothesis testing in which a hypothesis is stated and the experiment and resulting data are presented. Figure 1.14, illustrating the experiment with maple trees, shows the general form of Feature Investigations. The Feature Investigations allow you to appreciate the connection between science and scientific theories. As you read a Feature

Model-Based Learning Will Enhance Your Understanding of Biological Concepts and Improve Your Critical-Thinking Skills What is a model? A scientific model, or simply a model, is a conceptual, mathematical, or physical depiction of a real-world phenomenon. A model is a simplification and abstraction of a researcher’s perception of reality. In biology, models are testable ideas that are usually derived from observations and experiments. Because of the vast amount of complexity and variation found in nature, all but the simplest models are imperfect depictions of living things, their working parts, and their interactions with the environment. The majority of figures in this textbook are models, based on the ideas of biologists and drawn by professional illustrators. Why are models useful? One reason is they promote communication. Models allow scientists to convey their ideas in a relatively simple way. For example, a model of the human heart depicts how the parts of the heart work together to pump blood (look ahead to Figure 48.6). Another useful aspect of a model is that it can be used as a working hypothesis that helps researchers visualize or explain biological phenomena. Such models form the basis for conducting further experiments. Models are evaluated by their consistency with experimental data, which enables researchers to accept, reject, or refine them. Likewise, models allow biologists to make meaningful predictions. Such predictions can be refuted or supported via experimentation. A model for gene regulation in Chapter 14 predicts that a repressor protein inhibits gene expression (look ahead to Figure 14.7). This prediction was verified by experimentation, as shown in Figure 14.9. Finally, models can lead to conceptual frameworks. For example, the concept of a species niche, which is described in Chapter 57, was derived from species competition models and has subsequently become one of the most important concepts in ecology. Models take on many different forms. Let’s consider some common categories of models that you will see.

Investigation, you may find yourself thinking about different approaches and alternative hypotheses. Different people can view the same data and arrive at very different conclusions. As you progress through the experiments in this textbook, we hope you will try to develop your own skills at formulating hypotheses, designing experiments, and interpreting data. Experimental Questions 1. Discuss the difference between discovery-based science and hypothesis testing. 2. What are the steps in the scientific method, also called hypothesis testing?  3. CoreSKILL » In an experiment, explain how a control group and an experimental group differ from each other. 

∙ Structural models. A structural model shows the physical structures of components that make up living organisms. Biochemists and biologists have proposed many different models that depict biological structures at the cellular and molecular level. Figure 3.13 is a collection of 20 models of the structures of amino acids that are found in proteins. ∙ Mechanistic models. A mechanistic model (also called a physiological model) describes the workings of the individual parts of a complex system, and the manner in which they interact. As an example, plant biologists have proposed two models, called symplastic and apoplastic transport, which describe two possible pathways by which minerals are taken into the root of a plant (look ahead to Figure 39.7). ∙ Mathematical models. A mathematical model is a description of a process or a system using mathematical concepts, symbols, and diagrams. Many mathematical models are presented as one or more equations. For example, ecologists use equations to describe two different modes of population growth, termed exponential and logistic growth. Such equations allow biologists to make predictions about population growth, which can be illustrated graphically (look ahead to Figure 56.10). ∙ Temporal models. A temporal model depicts a biological process as it occurs over a short or long period of time. In cell biology, some processes occur very quickly. For example, the absorption of light energy during photosynthesis occurs in less than a second (look ahead to Figure 8.11). In contrast, the evolution of new groups of species may occur on a timescale of millions of years (look ahead to Figure 26.4). ∙ Hierarchical models. In a hierarchical model, organisms, parts of organisms, or observations fall into nested levels. For example, the field of taxonomy organizes species into progressively smaller groups, such as kingdom, family, and genus (plural, genera). One or more genera are found within a family, and many different families are found within a kingdom (see Figure 1.11).



AN INTRODUCTION TO BIOLOGY 19

Some models incorporate two or more of these categories. Take a look at the model for DNA replication in Figure 11.17, which is a combination of a structural model, a mechanistic model, and a temporal model. Model-based learning is an educational approach in which students evaluate or generate models as a way to enhance their understanding of scientific concepts and improve their criticalthinking skills. In this textbook, you will be engaged in this strategy via figures that present a modeling challenge. Each of these figures shows a model that pertains to a particular topic in biology. After you study this model, your modeling skills will be challenged in one of two different ways. In some cases, you will be given a second model and asked to explain it or describe what types of predictions can be made based on it (Figure 1.17). In other cases, you will be given a scenario and asked to generate your own model that is consistent with the scenario (Figure 1.18). Even though explaining and

3ʹ Amino acid attachment site at the 3ʹ single-stranded region

Outer membrane Intermembrane space Inner membrane Mitochondrial matrix

Cristae

Cytosol

5ʹ

0.3 μm

Figure 1.18  A modeling challenge to make a prediction.  This

figure shows the structure of a mitochondrion. It emphasizes the membrane organization of the mitochondrion, which has outer and inner membranes. The invaginations (infoldings) of the inner membrane, which are called cristae, occur because of the large surface area of that membrane. The modeling challenge below involves proposing an altered model. ©Don W. Fawcett/Science Source

Stem-loop

Hydrogen bonds G

G C

Anticodon

Figure 1.17  A modeling challenge to explain a revised model.  This figure shows a model for the structure of a tRNA molecule, which is described in Chapter 12. The stem regions are regions where the RNA is double stranded as a result of complementary base pairing, in which A hydrogen-bonds to U, and G hydrogen-bonds with C. The modeling challenge below involves an alteration in this model. Core Skill: Modeling  In this modeling challenge, you are asked to explain how the model below differs from the one in Figure 1.17. Modeling Challenge: In a tRNA molecule, four of the bases were changed. One A was changed to a G, and three C’s were changed to U’s. A model of the secondary structure of this altered tRNA is shown to the right. Explain where the altered bases are located and how the alteration affects the structure of the tRNA.

Core Skill: Modeling  This modeling challenge asks you to propose a model for the structure of a mitochondrion in the presence of a drug that decreases the surface area of the inner membrane. Modeling Challenge: Let’s suppose a cell is exposed to a drug that decreases the surface area of the inner mitochondrial membrane, but has no effect on the outer mitochondrial membrane. Draw a model of the structure of the mitochondrion in the presence of this drug.

generating models can be a challenge, the educational benefits are worth it. Give the modeling challenges a try.

BioTIPS Will Help You Improve Your Problem-Solving Skills As you progress through this textbook, your learning will involve two general goals: ∙ You will gather foundational knowledge. In other words, you will be able to describe basic ideas and discoveries in biology. For example, you will be able to explain how photosynthesis works. ∙ You will develop skills that will allow you to apply that foundational knowledge in different ways. For example, you will learn how to use statistics to determine if a hypothesis is consistent with experimental data.

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The combination of foundational knowledge and skills will enable you not only to understand biology but also to apply your knowledge in different situations. To help you develop these skills, Chapters 2 through 60 contain solved problems called BioTIPS, which stands for Topic, Information, and Problem-Solving Strategy. These solved problems follow a consistent pattern.

BIO TIPS

THE QUESTION  All of the BioTIPS begin with a question. As an example, let’s consider the following question:

The following base sequence is found within a messenger RNA molecule:

AUG GGC CUU AGC This segment carries the information to make a region of a polypeptide with the amino acid sequence methionine-glycineleucine-serine. What would be the consequences if a mutation in the gene that encodes this mRNA changed the second cytosine (C) in the base sequence to an adenine (A)? T OPIC  What topic in biology does this question address? The topic is gene expression. More specifically, the question is about the relationship between a base sequence and the genetic code. I NFORMATION  What information do you know based on the question and your understanding of the topic? In the question, you are given the base sequence of a short segment of an mRNA and told that one of the bases has been changed. From your understanding of the topic, you may remember that a polypeptide sequence is determined by reading the mRNA (transcribed from a gene) in groups of three bases called codons. P ROBLEM-SOLVING  S TRATEGY  Compare and contrast. Predict the outcome. One strategy to begin to solve this problem is to compare the mRNA sequence before and after the mutation:

Original:  AUG GGC CUU AGC Mutant:  AUG GGC  AUU AGC

        ↑ ANSWER The mutation has altered the sequence of bases in the mRNA, changing the third codon from CUU to AUU (see the arrow). Because codons specify amino acids, this may change the third amino acid in the polypeptide to something else. Note: If you look ahead to Table 12.1, you will see that CUU specifies leucine, whereas AUU specifies isoleucine. Therefore, you can predict that the mutation will change the third amino acid from leucine to isoleucine.

Though many different problem-solving strategies exist, BioTIPS will focus on 11 strategies that will help you solve problems. You will see these strategies over and over again as you progress through this textbook: 1. Make a drawing. Biology problems are often difficult to solve in your head. Making a drawing may make a big difference in your ability to see the solution. 2. Compare and contrast. Making a direct comparison between two biological structures or processes may help you understand how they are similar and how they are different. 3. Relate structure and function. A recurring theme in biology is that structure determines function. This relationship holds true at many levels of biology, including the molecular, microscopic, and macroscopic levels. For some questions, you will need to understand how certain structural features are related to their biological functions. 4. Sort out the steps in a complicated process. At first, some questions may be difficult to understand because they involve mechanisms that occur in a series of several steps. Sometimes, if you sort out the steps, you will be able to identify the key step that you need to understand to solve the problem. 5. Propose a hypothesis. A hypothesis is an attempt to explain an observation or data. Hypotheses may be made in many forms including statements, models, equations, and diagrams. 6. Design an experiment. Experimental design lies at the heart of science. In many cases, an experiment begins with some type of starting material(s), such as strains of organisms or purified molecules, and then the starting materials are subjected to a series of steps. The Feature Investigations throughout the textbook will also help you refine the skill of designing experiments. 7. Predict the outcome. Biologists may want to predict the outcome of an experiment. 8. Interpret data. Experimentation involves the analysis of data. Such an analysis often involves the use of statistics to determine if the experimental and control data show significant differences. The interpretation of data allows scientists to propose models that describe what the data may mean. 9. Use statistics. A variety of different statistical methods are used to analyze data and make conclusions about what they mean. 10. Make a calculation. Biology is a quantitative science. Researchers have devised mathematical relationships that help them understand and predict biological phenomena. Becoming familiar with these mathematical relationships will help you to better understand biological concepts and to make predictions. 11. Search the literature. The goal here is to be able to read and explain a scientific article, and extract useful information. For most problems in this textbook, one or more of these strategies may help you arrive at the correct solution. BioTIPS will provide you with practice in applying these problem-solving strategies.



AN INTRODUCTION TO BIOLOGY 21

Summary of Key Concepts ∙∙ Biology is the study of life. Discoveries in biology help us understand how life exists, and they also have many practical applications, such as the development of drugs to treat human diseases (Figures 1.1, 1.2, Table 1.1.).

1.1  Levels of Biology ∙∙ Living organisms can be viewed at different levels of biological organization: atoms, molecules and macromolecules, cells, tissues, organs, organisms, populations, communities, ecosystems, and the biosphere (Figure 1.3).

1.2  Core Concepts of Biology ∙∙ “Vision and Change” has identified five core concepts in biology (Figure 1.4). These are evolution; structure and function; information flow, exchange, and storage; pathways and transformations of energy and matter; and systems.

1.3  Biological Evolution ∙∙ Changes in species often occur as a result of modification of preexisting structures (Figure 1.5). ∙∙ During vertical evolution, mutations in a lineage alter the characteristics of species from one generation to the next. Individuals with greater reproductive success are more likely to contribute to future generations, a process known as natural selection. Over the long run, this process alters species and may produce new species (Figure 1.6). ∙∙ Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring. Along with vertical descent with mutation, it is an important process in biological evolution, producing a web of life (Figures 1.7, 1.8). ∙∙ An analysis of genomes and proteomes helps us to understand how information at the molecular level relates to the characteristics of individuals and how they survive in their native environments (Figure 1.9).

1.4  Classification of Living Things ∙∙ Taxonomy is the grouping of species according to their evolutionary relatedness to other species. Going from broad to narrow groups, each species is placed into a domain, supergroup, kingdom, phylum, class, order, family, and genus (Figures 1.10, 1.11). ∙∙ The classification of species changes as biologists gather new information (Figure 1.12).

1.5  Biology as a Scientific Discipline ∙∙ Biological science is the observation, identification, experimental investigation, and theoretical explanation of natural phenomena. ∙∙ Biologists study life at different levels, ranging from ecosystems to the molecular components in cells (Figure 1.13). ∙∙ A hypothesis is a proposal to explain a natural phenomenon. A useful hypothesis makes a testable prediction. A biological theory is a broad explanation that is substantiated by a large body of evidence. ∙∙ Discovery-based science is an approach in which researchers conduct experiments and analyze data without a preconceived hypothesis.

∙∙ The scientific method, also called hypothesis testing, is a series of steps to formulate and test the validity of a hypothesis. The experimentation often involves a comparison between control and experimental groups (Figure 1.14). ∙∙ The study of cystic fibrosis provides an example in which both discovery-based science and hypothesis testing led to key insights regarding the nature of the disease (Figure 1.15). ∙∙ Biology is a social discipline in which scientists often work in teams. To be published, a scientific paper is usually subjected to a peerreview process in which other scientists evaluate the paper and make suggestions regarding its quality. Advances in science often occur when scientists gather and discuss their data (Figure 1.16).

1.6  Core Skills of Biology ∙∙ “Vision and Change” recognized the need to focus on the development of certain skills in students: the ability to apply the process of science; the ability to use quantitative reasoning; the ability to use models and simulation; the ability to tap into the interdisciplinary nature of science; the ability to communicate and collaborate with professionals in other disciplines; and the ability to understand the relationship between science and society. ∙∙ Each chapter in this textbook has a “Feature Investigation,” an actual study by current or past researchers that highlights the experimental approach and helps you appreciate how science has led to key discoveries in biology. ∙∙ Biologists use models to convey their ideas, evaluate experiments, and make predictions that apply to their research studies. Modeling challenges will help you to understand and propose models (Figure 1.17, Figure 1.18). ∙∙ BioTIPS are intended to develop your problem-solving skills.

Assess & Discuss Test Yourself 1. Which of the following is not a core concept of biology, as advocated by “Vision and Change”? a. Evolution b. Information flow, exchange, and storage c. Structure and function d. Taxonomy e. Pathways and transformation of energy and matter  2. Populations of organisms change over the course of many generations. Many of these changes are the result of greater reproductive success. This phenomenon is a. evolution. d. genetics. b. homeostasis. e. metabolism.  c. development. 3. A biologist is studying the living organisms in a valley in western Colorado. She is studying a. an ecosystem. d. a viable land mass. b. a community. e. a population.  c. the biosphere. 4. Which of the following is an example of horizontal gene transfer? a. the transmission of an eye color gene from father to daughter b. the transmission of a mutant gene causing cystic fibrosis from father to daughter

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c. the transmission of a gene conferring pathogenicity (the ability to cause disease) from one bacterial species to another d. the transmission of a gene conferring antibiotic resistance from a mother cell to its two daughter cells e. all of the above. 5. The scientific name for humans is Homo sapiens. The name Homo is the _____ to which humans are classified. a. kingdom d. genus b. phylum e. species c. order 6. The complete genetic makeup of an organism is called its a. genus. d. genotype. b. genome. e. phenotype. c. proteome. 7. After observing certain desert plants in their native environment, a researcher proposes that they drop their leaves to conserve water. This is an example of a. a theory. d. a hypothesis. b. a law. e. an experiment. c. a prediction. 8. In science, a theory should a. be viewed as knowledge. b. be supported by a substantial body of evidence. c. provide the ability to make many correct predictions. d. do all of the above. e. b and c only. 9. Conducting research without a preconceived hypothesis is called a. discovery-based science. b. the scientific method. c. hypothesis testing.

d. a control experiment. e. none of the above. 10. What is the purpose of using a control group in a scientific experiment? a. A control group allows the researcher to practice the experiment first before actually conducting it. b. A researcher can compare the results in the experimental group and control group to determine if a single variable is causing a particular outcome in the experimental group. c. A control group provides the framework for the entire experiment so the researcher can recall the procedures that should be conducted. d. A control group allows the researcher to conduct other experimental changes without disturbing the original experiment. e. all of the above.

Conceptual Questions 1. Of the five core concepts of biology described in Figure 1.4, which apply to individuals and which apply to populations?  2. Explain how it is possible for evolution to result in unity among different species yet also produce amazing diversity.  3.

Core Concept:  In your own words, describe the five core concepts of biology that are detailed at the beginning of this chapter in Figure 1.4.

Collaborative Questions 1. Discuss whether or not you think that theories in biology are true. Outside of biology, how do you decide if something is true? 2. In certain animals, such as alligators, sex is determined by temperature. When alligator eggs are exposed to low temperatures, most alligator embryos develop into females. Discuss how this phenomenon is related to genomes and proteomes.

UNIT I

CHEMISTRY

2

Living organisms are composed of chemicals, which are altered via chemical reactions. These reactions occur between atoms and molecules and may require, or in some cases release, energy. Chemical reactions and interactions between molecules play a role in virtually all aspects of a cell’s activities. In order to understand how living organisms function, grow, develop, behave, and interact with their environments, therefore, we first need to understand some basic principles of atomic and molecular structure and the forces that allow atoms and molecules to interact with each other. We begin this unit with an overview of inorganic chemistry—that is, the nature of atoms and molecules, with the exception of those that contain rings or chains of carbon. Such carbon-containing molecules form the basis of organic chemistry and are covered in Chapter 3.

3 The following Core Concepts and Core Skills will be emphasized in this unit: • Energy and matter: We will see how the chemical energy stored in the bonds of molecules, such as sugars and fats, can be released and used by living organisms to perform numerous functions that support life, including growth, digestion, and locomotion. • Structure and function: As described in Chapter 3, the threedimensional structure of molecules is critical in enabling them to carry out their function. • Information: Nucleic acids, the basis of inherited genetic material, are first introduced in Chapter 3. • Systems: You will learn in this unit how simple molecules are joined to create a more complex molecule with new biological properties. The newly created molecule has properties that are different from those of its component atoms. • Science and society: In Chapter 2, we will see how an understanding of chemistry has transformed the ability of physicians to diagnose disease in humans. One example of an application of chemistry to medicine is the PET scan.

(2): ©Dr. Parvinder Sethi; (3): ©Zoonar GmbH/Alamy Stock Photo

CHAPTER OUTLINE

The Chemical Basis of Life I: Atoms, Molecules, and Water

2

2.1 Atoms 2.2 Chemical Bonds and Molecules 2.3 Properties of Water 2.4 pH and Buffers Summary of Key Concepts Assess & Discuss

2.1  Atoms Learning Outcomes:

Crystals of sodium chloride (NaCl), a compound composed of two elements. ©Dr. Parvinder Sethi

B

iology—the study of life—is founded on the principles of chemistry and physics. All living organisms are a collection of atoms and molecules bound together and interacting with each other through the forces of nature. Throughout this textbook, we will see how chemistry can be applied to living organisms as we discuss the components of cells, the functions of proteins, the flow of nutrients in plants and animals, and the evolution of new genes. This chapter lays the groundwork for understanding these and other concepts. We will begin with an overview of the nature of atoms and molecules, focusing on the structure of the atom and how it was discovered. We next explore the various ways that atoms combine with other atoms to create molecules, looking at the different types of chemical bonds between atoms, how these bonds form, and how they determine the structures of molecules. We end with an examination of the water molecule and the properties that make it a crucial component of living organisms and their environment.

1. Describe the general structure of atoms. 2. CoreSKILL » Interpret the results of an experiment indicating that most of an atom is empty space. 3. Define orbital and electron shell. 4. Relate atomic structure to the periodic table of the elements. 5. CoreSKILL » Quantify atomic mass using units of daltons and moles. 6. Explain how a single element may exist in two or more forms, called isotopes, and how certain isotopes have importance in human medicine. 7. List the elements that make up most of the mass of all living organisms.

All life-forms are composed of matter, which is defined as anything that contains mass and occupies space. In living organisms, matter may exist in any of three states: solid, liquid, or gas. All matter is composed of atoms, which are the smallest functional units of matter that form all chemical substances and ultimately all organisms; they cannot be further broken down into other substances by ordinary chemical or physical means. Atoms, in turn, are composed of different types of smaller, subatomic particles. Chemists study the properties of atoms and molecules, which are two or more atoms bonded together. A major interest of the physicist, by contrast, is to uncover the properties of subatomic particles. Chemistry and physics merge in attempts to understand the mechanisms by which atoms and molecules interact. When atoms and molecules are studied in the context of a living organism, the science of biochemistry emerges. In this section, we will explore the physical properties of atoms so we can understand how atoms combine to form molecules of biological importance.

Atoms Are Composed of Subatomic Particles The chemicals within living organisms are composed of many different types of atoms. The simplest atom, hydrogen, is approximately



THE CHEMICAL BASIS OF LIFE I: ATOMS, MOLECULES, AND WATER 25

0.1 nanometer (nm) in diameter, roughly one-millionth the diameter of a human hair. Each specific type of atom—nitrogen, hydrogen, oxygen, and so on—is called an element (or chemical element), which is defined as a pure substance made up of only one kind of atom. Three subatomic particles—protons (p+), neutrons (n0), and electrons (e–)—are found within atoms (Figure 2.1). The protons and neutrons are confined to a very small volume at the center of an atom, the atomic nucleus, whereas the electrons are found in regions at various distances from the nucleus. In most atoms, the numbers of protons and electrons are identical, but the number of neutrons may vary. Each of the subatomic particles has a different electric charge. Protons have one unit of positive charge, electrons have one unit of negative charge, and neutrons are electrically neutral. Like charges repel each other, and opposite charges attract each other. The positive charges in the nucleus attract the negatively charged electrons. Because the protons are located in the atomic nucleus, the nucleus has a net positive charge equal to the number of protons it contains. The entire atom has no net electric charge, however, because the number of negatively charged electrons around the nucleus is equal to the number of positively charged protons in the nucleus.

Electrons Neutron –

–

+

+

+

Nucleus Proton

Hydrogen

Helium

1 proton 1 electron

2 protons 2 neutrons 2 electrons

–

Figure 2.1  Diagrams of two simple atoms.  These are models of the

two simplest atoms, hydrogen and helium. The nucleus consists of protons and neutrons, whereas electrons are found outside the nucleus. Note: In all figures of atoms, the sizes and distances are not to scale.

This basic concept of the structure of the atom was not established until a landmark experiment conducted by Ernest Rutherford during the years 1909–1911, as described next.

Core Skill: Process of Science

Feature Investigation  |  Rutherford Determined the Modern Model of the Atom Nobel laureate Ernest Rutherford was born in 1871 in New Zealand, but he did his greatest work at McGill University in Montreal, Canada, and later at the University of Manchester in England. At that time, scientists knew that atoms contained charged particles but had no idea how those particles were distributed. Neutrons had not yet been discovered, and many scientists, including Rutherford, hypothesized that the positive charge and the mass of an atom were evenly dispersed throughout the atom. In a now-classic experiment, Rutherford aimed a fine beam of positively charged α (alpha) particles at an extremely thin sheet of gold foil only 400 atoms thick (Figure 2.2). α particles consist of two

protons and two neutrons and are thus identical to the nuclei of helium atoms; you can think of them as helium atoms without their electrons (see Figure 2.1). Surrounding the gold foil were zinc sulfide screens that registered any α particles passing through or bouncing off the foil, much like film in a camera detects light. Rutherford hypothesized that if the positive charges of the gold atoms were uniformly distributed, many of the positively charged α particles would be slightly deflected, because one of the most important features of electric charge is that like charges repel each other. Due to their much smaller mass, he did not expect electrons in the gold atoms to have any effect on the ability of an α particle to move through the metal foil.

Figure 2.2  Rutherford’s gold foil experiment, demonstrating that most of the volume of an atom is empty space. HYPOTHESIS Atoms in gold foil are composed of diffuse, evenly distributed positive charges that should usually cause α particles to be slightly deflected as they pass through. KEY MATERIALS Thin sheet of gold foil, α particle emitter, zinc sulfide detection screen. Experimental level

1

Conceptual level

Emit beam of α particles.

+

+

α particle α particle emitter

2

Pass beam through gold foil.

Zinc sulfide detection screens

Gold foil

+

+

+

+

+

+

+

+

Gold atom

Gold foil

Positive charges of the gold atom

+

α particle emitter

26

2

CHAPTER 2

Pass beam through gold foil.

Zinc sulfide detection screens

Gold foil

+

+

+

+

+

Gold atom

Gold foil

Positive charges of the gold atom

α particle Undeflected α particles Slightly deflected α particle α particle that bounced back α particle that bounced back

3

4

α particle that was undeflected

Detect α particles on zinc sulfide screens after they pass through foil or bounce back. Record number of α particles detected on zinc sulfide screens and their locations.

α particle that was slightly deflected Detection of α particles

THE DATA

% of α particles detected on zinc sulfide screens

Location

98%

Undeflected

0), requiring the addition of free energy, it is termed endergonic. An endergonic reaction is not a spontaneous reaction. If ΔG for a chemical reaction is negative, the reaction favors the conversion of reactants to products, whereas a reaction with a positive ΔG favors the formation of reactants. Chemists have determined free-energy changes for a variety of chemical reactions, which allows them to predict their direction. As an example, let’s consider adenosine triphosphate (ATP), which is a molecule that is a common energy source for all cells. ATP is broken down to adenosine diphosphate (ADP) and inorganic phosphate (HPO42–, abbreviated Pi). Because water is used to remove a phosphate group, chemists refer to this reaction as the hydrolysis of ATP (Figure 6.3). For the conversion

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of 1 mole of ATP to 1 mole of ADP and Pi, ΔG equals –7.3 kcal/ mol. Because this is a negative value, the formation of the products is strongly favored. As discussed later, the energy liberated by the hydrolysis of ATP is used to drive a variety of cellular processes.

The energy to synthesize ATP comes from chemical reactions that are exergonic. Energy input (endergonic)

Synthesis

Chemical Reactions Eventually Reach a State of Equilibrium Even when a chemical reaction is associated with a negative freeenergy change, not all of the reactants are converted to products. The reaction reaches a state of chemical equilibrium in which the rate of formation of products equals the rate of formation of reactants. Let’s consider the generalized reaction aA + bB ⇌ cC + dD where A and B are the reactants, C and D are the products, and a, b, c, and d are the number of moles of reactants and products. The reaction reaches equilibrium, such that Keq =

[C]c[D]d [A]a[B]b

where Keq is the equilibrium constant. Each type of chemical reaction has a specific value for Keq. When Keq is greater than 1, the reaction favors the formation of products; when it is less than 1, the reaction favors the formation of reactants.

Cells Use ATP to Drive Endergonic Reactions Many biological processes require the addition of free energy; that is, they are endergonic and do not occur spontaneously. How do cells overcome this problem? One strategy is to couple exergonic reactions with endergonic reactions. If an exergonic reaction is coupled with an endergonic reaction, the endergonic reaction will proceed spontaneously if the net free-energy change for both processes combined is negative. For example, consider the following reactions: Glucose + Phosphate2− → Glucose-6-phosphate2− + H2O Δ G = + 3.3 kcal/mol ATP4−+ H2O → ADP2− +  Pi2−

Δ G = − 7.3 kcal/mol

Coupled reaction: Glucose + ATP4− → Glucose-6-phosphate2− + ADP2−  Δ G = − 4.0 kcal/mol The first reaction, in which phosphate is covalently attached to glucose, is endergonic, and by itself is not spontaneous. The second reaction, the hydrolysis of ATP, is exergonic. If the two reactions are coupled, however, the combined net free-energy change for both is negative (ΔG = –4.0 kcal/mol), and the coupled reaction is exergonic. In the coupled reaction, a phosphate is directly transferred from ATP to glucose, in a process called phosphorylation. This coupled reaction proceeds spontaneously because the net free-energy change is negative. Exergonic reactions, such as the breakdown of ATP, are commonly coupled to chemical reactions and other cellular processes that would otherwise be endergonic.

ADP +

Pi

Hydrolysis elease Energy release c) (exergonic)

ATP + H2O

ATP hydrolysis provides the energy to drive cellular processes that are endergonic.

Figure 6.4  The ATP cycle. Living cells continuously recycle ATP. The energy released from the breakdown of food molecules into smaller molecules is used to synthesize ATP from ADP and Pi. The hydrolysis of ATP to ADP and Pi is used to drive many different endergonic reactions and processes that occur in cells. Concept Check:   If a large amount of ADP was broken down in a cell, how would this affect the ATP cycle? 

In humans, a typical cell uses millions of ATP molecules per second to drive endergonic processes. At the same time, the breakdown of food molecules to form smaller molecules (an exergonic reaction) releases energy that allows cells to make more ATP from the phosphorylation of ADP (an endergonic reaction). The recycling of ATP from ADP and phosphate occurs at a remarkable pace. An average person hydrolyzes about 100 pounds of ATP per day, yet at any given time we do not have 100 pounds of ATP in our bodies. For this to happen, each molecule of ATP undergoes about 10,000 cycles of hydrolysis and regeneration during an ordinary day (Figure 6.4).

Core Concepts: Information, Energy and Matter Genomes Encode Many Proteins That Use ATP as a Source of Energy Over the past several decades, researchers have studied the functions of many proteins and discovered numerous examples in which a protein uses the hydrolysis of ATP to drive a chemical reaction or other type of cellular process (Table 6.2). By studying the structures of proteins that use ATP in this way, biochemists have discovered that particular amino acid sequences within proteins function as ATP-binding sites. This information has allowed researchers to predict whether a newly discovered protein uses ATP or not. When an entire genome sequence of a species has been determined, the genes that encode proteins can be analyzed to find out if the encoded proteins have ATP-binding sites in their amino acid sequences. Using this approach, researchers have been able to analyze proteomes—all of the proteins that a given cell



AN INTRODUCTION TO ENERGY, ENZYMES, AND METABOLISM 131

Table 6.2     Examples of Proteins That Use ATP for Energy

Type

Description

Metabolic enzymes

Many enzymes use ATP to catalyze endergonic reactions. For example, hexokinase uses ATP to attach phosphate to glucose, producing glucose6-phosphate.

Transporters

Ion pumps, such as Na+/K+-ATPase, use ATP to pump ions against a gradient (see Chapter 5).

Motor proteins

Motor proteins, such as myosin, use ATP to facilitate cellular movement, as in muscle contraction (see Chapter 45).

Chaperones

Chaperones are proteins that use ATP to aid in the folding and unfolding of cellular proteins (see Chapter 4).

DNA-modifying enzymes

Many proteins, such as helicases and topoisomerases, use ATP to modify the conformation of DNA (see Chapter 11).

Aminoacyl-tRNA These synthetases are enzymes that use ATP to synthetases attach amino acids to tRNAs (transfer RNAs; see Chapter 12). Protein kinases

Protein kinases are regulatory proteins that use ATP to attach a phosphate to a protein, thereby phosphorylating the protein and affecting its function (see Chapter 9).

or organism makes—and estimate the percentage of proteins that are able to bind ATP. This approach has been applied to the proteomes of bacteria, archaea, and eukaryotes. On average, over 20% of all proteins bind ATP. However, this number is likely an underestimate because all of the types of ATPbinding sites in proteins may not have been identified. In humans, whose genome has an estimated size of 22,000 different proteinencoding genes, a minimum of 4,400 of those genes encode proteins that use ATP. From these numbers, we can see the enormous importance of ATP as a source of energy for living cells.

6.2  Enzymes and Ribozymes Learning Outcomes: 1. Explain how enzymes increase the rates of chemical reactions by lowering the activation energy. 2. Describe how enzymes bind their substrates with high specificity and undergo induced fit. 3. CoreSKILL » Analyze the velocity of chemical reactions, and evaluate the effects of competitive and noncompetitive inhibitors. 4. Explain how additional factors, such as nonprotein molecules or ions, temperature, and pH, influence enzyme activity. 5. Identify the unique feature of ribozymes.

For most chemical reactions in cells to proceed at a rapid pace, a catalyst is needed. A catalyst is an agent that speeds up the rate of a chemical reaction without being permanently changed or consumed by it. In living cells, the most common catalysts are enzymes, which are proteins. The term was coined in 1876 by a German physiologist,

Wilhelm Kühne, who discovered trypsin, an enzyme in pancreatic juice that is needed for the digestion of food proteins. In this section, we will explore how enzymes increase the rates of chemical reactions. Interestingly, some biological catalysts are RNA molecules called ribozymes. We will examine a few examples in which RNA molecules carry out catalytic functions.

Enzymes Increase the Rates of Chemical Reactions If a chemical reaction has a negative free-energy change, the reaction will be spontaneous; it will tend to proceed in the direction of reactants to products. Although thermodynamics governs the direction of an energy transformation, it does not determine the rate of a chemical reaction. For example, the breakdown of the molecules in gasoline to smaller molecules is an exergonic reaction. Even so, we could place gasoline and oxygen in a container and nothing much would happen (provided the container wasn’t near a flame). If we came back several days later, we would expect to see the gasoline still sitting there. Perhaps if we came back in a few million years, the gasoline would have been broken down. On a timescale of months or a few years, however, the chemical reaction would proceed very slowly. In living cells, the rates of enzyme-catalyzed reactions typically occur millions of times faster than the corresponding uncatalyzed reactions. A dramatic example involves the enzyme catalase, which catalyzes the breakdown of hydrogen peroxide (H2O2) into water and oxygen. Catalase speeds up this reaction so that it occurs 1015-fold faster than the uncatalyzed reaction! Why are catalysts necessary to speed up a chemical reaction? Chemical reactions between molecules involve bond breaking and bond forming. When a covalent bond is broken or formed, this process initially involves the straining or stretching of one or more bonds in the starting molecule(s) and/or the positioning of two molecules so that they interact with each other properly. Enzymes help to facilitate these kinds of events. As an example, let's consider the reaction in which ATP is used to phosphorylate glucose: Glucose + ATP4– → Glucose-6-phosphate2– + ADP2– For a reaction to occur between glucose and ATP, the molecules must collide in the correct orientation and possess enough energy so the chemical bonds can be changed. As glucose and ATP get close together, the electrons in the outer shells of their atoms repel each other. To overcome this repulsion, an initial input of energy, called the activation energy, is required (Figure 6.5). Activation energy (EA) allows the molecules to get close enough to cause a rearrangement of bonds. With the input of activation energy, glucose and ATP can achieve a transition state in which the original bonds have stretched to their limit. Once the reactants have reached the transition state, the chemical reaction can readily proceed to the formation of products, which in this case are glucose-6-phosphate and ADP. The activation energy required to achieve the transition state is a barrier to the formation of products. This barrier is the reason why the rate of many chemical reactions is very slow. Enzymes lower the activation energy to a point where a small amount of available heat can push the reactants to the transition state.

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ATP

∙ Enzymes are proteins that bind relatively small reactants. When reactant molecules are bound to an enzyme, their bonds can be strained, thereby making it easier for them to achieve the transition state (see Figure 6.5).

Reactant molecules Glucose

Enzyme

An enzyme strains chemical bonds in the reactant molecules and/or brings them close together. Transition state Activation energy (EA) without enzyme Free energy (G)

Activation energy (EA) with enzyme Reactants

Change in free energy (ΔG) Products

Progress of an exergonic reaction

Figure 6.5  Activation energy of a chemical reaction.  This figure depicts an exergonic reaction. The activation energy (EA) is needed for molecules to achieve a transition state. One way that enzymes lower the activation energy is by straining chemical bonds in the reactants so less energy is required to attain the transition state. A second way is by binding two reactants so they are close to each other and in a favorable orientation. Concept Check:    How does lowering the activation energy affect the rate of a chemical reaction? How does it affect the direction? 

How do enzymes lower the activation energy barrier of chemical reactions? Let's consider two common ways that enzymes exert their effects.

∙ In addition, when a chemical reaction involves two or more reactants, the enzyme provides a site where the reactants are positioned very close to each other in an orientation that facilitates the formation of new covalent bonds. This favorable orientation also lowers the necessary activation energy for a chemical reaction.

Enzymes Recognize Their Substrates with High Specificity and Undergo Conformational Changes Thus far, we have considered how enzymes lower the activation energy of a chemical reaction, and thereby increase its rate. Let’s consider some other features of enzymes that enable them to serve as effective catalysts in chemical reactions. The active site is the location in an enzyme where the chemical reaction takes place. The substrates for an enzyme are the reactant molecules that bind to an enzyme at the active site and participate in the chemical reaction. For example, hexokinase is an enzyme whose substrates are glucose and ATP (Figure 6.6). The binding between enzyme and substrate produces an enzyme-substrate complex. A key feature of nearly all enzymes is their ability to bind their substrates with a high degree of specificity. For example, hexokinase recognizes glucose but does not recognize other similar sugars, such as fructose and galactose, very well. In 1894, a German chemist Emil Fischer proposed that the recognition of a substrate by an enzyme resembles the interaction between a lock and key: Only the correctly shaped key (the substrate) will fit into the keyhole (active site) of the lock (the enzyme). Further research

ADP

Glucose ATP

Active site

Glucose-6phosphate

Enzyme-substrate complex

Hexokinase

1

Substrates (ATP and glucose) bind to the enzyme (hexokinase).

2

Enzyme undergoes a conformational change that binds the substrates more tightly. This induced fit strains chemical bonds within the substrates and/or brings them closer together.

3

Substrates are converted to products.

4

Products (ADP and glucose-6-phosphate) are released. Enzyme is ready to be reused.

Figure 6.6  The steps of an enzyme-catalyzed reaction.  The example shown here involves the enzyme hexokinase, which binds glucose and ATP. The products are glucose-6-phosphate and ADP, which are released from the enzyme. Core Concept: Structure and Function  A key function of enzymes is their ability to bind their substrates with high specificity. This specificity is due to the structure of the enzyme’s active site.

AN INTRODUCTION TO ENERGY, ENZYMES, AND METABOLISM 133

revealed that the interaction between an enzyme and its substrates also involves movements or conformational changes in the enzyme itself. As shown in step 2 in Figure 6.6, these conformational changes cause the substrates to bind more tightly to the enzyme, a phenomenon called induced fit, which was proposed by American biochemist Daniel Koshland in 1958. Only after induced fit takes place does the enzyme catalyze the conversion of reactants to products. Induced fit is a key phenomenon that lowers the activation energy.

Vmax D C Velocity (product/second)



Vmax 2 B Tube

Enzyme Function Is Influenced by the Substrate Concentration and by Inhibitors

E + S ⇌ ES → E + P where E is the enzyme, S is the substrate, ES is the enzyme-substrate complex, and P is the product.

0

B

D

C

1 μg 1 μg 1 μg Amount of enzyme 60 sec 60 sec 60 sec Incubation time Moderate High Low Substrate concentration

A

1 μg 60 sec Very high

[Substrate]

KM

(a) Reaction velocity in the absence of inhibitors

Velocity (product/second)

Vmax Plus competitive in inhibitor Substrate Enzyme Inhibitor

0 KM

KM with inhibitor

[Substrate] b t t ] bstrate]

(b) Competitive inhibition

Vmax Velocity (product/second)

The degree of attraction between an enzyme and its substrate(s) is called the affinity of the enzyme for its substrate(s). Some enzymes have very high affinity for their substrates, which means they readily recognize them. Such enzymes bind their substrates even when the substrate concentration is relatively low. Other enzymes have lower affinity for their substrates; the enzymesubstrate complex is likely to form only when the substrate concentration is higher. Let’s consider how biologists analyze the relationship between substrate concentration and enzyme function. In the experiment of Figure 6.7a, tubes labeled A, B, C, and D each contained 1 µg of enzyme, but they varied in the amount of substrate that was added. This enzyme recognizes a single substrate and converts it to a product. The samples were incubated for 60 seconds, and then the amount of product in each tube was measured. The velocity, or rate, of the chemical reaction is expressed as the amount of product produced per second. As we see in Figure 6.7a, the velocity increases as the substrate concentration increases, but eventually reaches a plateau. Why does the plateau occur? At high substrate concentrations, nearly all of the active sites of the enzyme are occupied with substrate, so further increasing the substrate concentration has a negligible effect. At this point, the enzyme is saturated with substrate, and the velocity of the chemical reaction is near its maximal rate, called its Vmax. Figure 6.7a also helps us understand the relationship between substrate concentration and velocity. The KM is the substrate con­ centration at which the velocity is half its maximal value. The KM is also called the Michaelis constant in honor of German biochemist Leonor Michaelis, who carried out pioneering work with Canadian biochemist Maud Menten on the study of enzymes. The KM is a measure of the substrate concentration required for a chemical reaction to occur. An enzyme with a high KM requires a higher substrate concentration to achieve a particular reaction velocity compared to an enzyme with a lower KM. For an enzyme-catalyzed reaction, we can view the formation of product as occurring in two steps: (1) binding or release of substrate and (2) formation of product:

A

Vmax with inhibitor Plus noncompetitive inhibitor Enzyme Allosteric site

Substrate

Inhibitor 0 KM

[Substrate]

(c) Noncompetitive inhibition

Figure 6.7  The relationship between velocity and substrate concentration in an enzyme-catalyzed reaction, and the effects of inhibitors.  (a) In the absence of an inhibitor, the maximal velocity (Vmax) of an enzyme-catalyzed reaction is achieved when the substrate concentration is high enough to be saturating. The KM value for an enzyme is the substrate concentration at which the velocity of the reaction is half the maximal velocity. (b) A competitive inhibitor binds to the active site of an enzyme and raises the KM. (c) A noncompetitive inhibitor binds to an allosteric site outside the active site and lowers the Vmax. Concept Check:    Enzyme A has a KM of 0.1 mM, whereas enzyme B has a KM of 1.0 mM. The reactions the two enzymes catalyze both have the same Vmax. If the substrate concentration was 0.5 mM, which reaction—the one catalyzed by enzyme A or the one catalyzed by enzyme B—would have the higher velocity?

CHAPTER 6

If the second step—the rate of product formation—is much slower than the rate of substrate release, the KM is inversely related to the affinity between the enzyme and the substrate. For example, let’s consider an enzyme that breaks down ATP into ADP and Pi. If the rate of formation of ADP and Pi is much slower than the rate of ATP release, the KM and affinity show an inverse relationship. Enzymes with a high KM have a low affinity for their substrates— they bind them more weakly. By comparison, enzymes with a low KM have a high affinity for their substrates—they bind them more strongly. Now that we understand the relationship between substrate concentration and the velocity of an enzyme-catalyzed reaction, we can explore how inhibitors may affect enzyme function. These can be categorized as reversible inhibitors that bind noncovalently to an enzyme or irreversible inhibitors that usually bind covalently to an enzyme and permanently inactivate its function. Reversible Inhibitors  Cells often use reversible inhibitors to modulate enzyme function. Competitive inhibitors are molecules that bind noncovalently to the active site of an enzyme and inhibit the ability of the substrate to bind. Such inhibitors compete with the substrate in binding to the enzyme. Competitive inhibitors usually have a structure or a portion of their structure that mimics the structure of the enzyme’s substrate. As seen in Figure 6.7b, when competitive inhibitors are present, the apparent KM for the substrate increases—a higher concentration of substrate is needed to achieve the same rate of the chemical reaction. In this case, the effects of the competitive inhibitor can be overcome by increasing the concentration of the substrate. By comparison, Figure 6.7c illustrates the effects of a noncompetitive inhibitor. This type of inhibitor lowers the Vmax for the reaction without affecting the KM. A noncompetitive inhibitor binds noncovalently to an enzyme at a location outside the active site, called an allosteric site, and inhibits the enzyme’s function. Irreversible Inhibitors  Irreversible inhibitors usually bind covalently to an enzyme to inhibit its function. For example, some irreversible inhibitors bind covalently to an amino acid at the active site of an enzyme, thereby preventing the enzyme from catalyzing a chemical reaction. An example of an irreversible inhibitor is diisopropyl phosphorofluoridate (DIFP). DIFP is a type of nerve gas that was developed as a chemical weapon. This molecule covalently reacts with the enzyme acetylcholinesterase, which is important for the proper functioning of neurons. Irreversible inhibition is not a common way for cells to control enzyme function. Why do cells usually control enzymes via reversible inhibitors? The answer is that a reversible inhibitor allows an enzyme to be used again, when the inhibitor concentration becomes lower. Being able to reuse an enzyme is energy-efficient. In contrast, irreversible inhibitors permanently inactivate an enzyme, thereby preventing its further use.

Additional Factors Influence Enzyme Function Enzymes, which are proteins, sometimes require nonprotein molecules or ions to carry out their functions.

∙ Prosthetic groups are small molecules that are permanently attached to the surface of an enzyme and aid in enzyme function. ∙ Cofactors are usually inorganic ions, such as Fe3+ or Zn2+, that temporarily bind to the surface of an enzyme and promote a chemical reaction. ∙ Some enzymes use coenzymes, organic molecules that temporarily bind to an enzyme and participate in the chemical reaction that the enzyme catalyzes, but are left unchanged when the reaction is completed. The ability of enzymes to increase the rate of a chemical reaction is also affected by their environment. In particular, the temperature, pH, and ionic conditions play an important role in the proper functioning of enzymes. Most enzymes function maximally in a narrow range of temperature and pH. For example, many human enzymes work best at 37°C (98.6°F), which is normal body temperature. If the temperature is several degrees above or below this optimal temperature due to infection or environmental causes, the function of many enzymes is greatly inhibited ( Figure 6.8). Very high temperatures may denature a protein, causing it to unfold and lose its three-dimensional shape, thereby inhibiting its function. Enzyme function is also sensitive to pH. Certain enzymes in the stomach function best at the acidic pH found in this organ. For example, pepsin is a protease—an enzyme that digests proteins into peptides—that is released into the stomach. The optimal pH for pepsin function is around pH 2.0, which is extremely acidic. By comparison, many cytosolic enzymes function optimally at a more neutral pH, such as pH 7.2, which is the pH normally found in the cytosol of human cells. If the pH was significantly above or below this value, function would be decreased for cytosolic enzymes.

Optimal temperature for a typical human enzyme is 37oC. High Rate of a chemical reaction

134

At high temperatures, an enzyme may be denatured. 0

0

10

20

30 40 Temperature (oC)

50

60

Figure 6.8  Effects of temperature on a typical human

enzyme.  Most enzymes function optimally within a narrow range of temperature. Many human enzymes function best at 37°C, which is normal body temperature.



AN INTRODUCTION TO ENERGY, ENZYMES, AND METABOLISM 135

Core Skill: Process of Science

Feature Investigation  | 

The Discovery of Ribozymes by Sidney Altman Revealed That RNA Molecules May Also Function as Catalysts

Until the 1980s, scientists thought that all biological catalysts are proteins. An avenue of study that dramatically changed this view came from the analysis of ribonuclease P (RNase P), a catalyst involved in the processing of tRNA molecules—a type of molecule required for protein synthesis. tRNA molecules are synthesized as longer precursor molecules called ptRNAs, which have 5′ and 3′ ends. (The 5′ and 3′ directionality of RNA molecules is described in Chapter 12.) RNase P breaks a covalent bond at a specific site in a ptRNA, which releases a fragment at the 5′ end and makes the precursor molecule shorter (Figure 6.9). Sidney Altman and his colleagues became interested in the processing of tRNA molecules and turned their attention to RNase P in E. coli. During the course of their studies, they purified this enzyme and, to their surprise, discovered it has two subunits—one is an RNA molecule that contains 377 nucleotides, and the other is a small protein with a mass of 14 kDa. In the 1980s, the finding that a catalyst had an RNA subunit was very unexpected. Even so, a second property of RNase P would prove even more exciting. Altman and colleagues were able to purify RNase P and study its properties in vitro. Cecilia Guerrier-Takada in Altman’s laboratory determined that magnesium ion (Mg2+) has a stimulatory effect on RNase P function. In the experiment described in Figure 6.10, the effects of Mg2+ were studied in greater detail. The researchers analyzed the effects of low (10 mM MgCl2) and high (100 mM MgCl2) magnesium concentrations on the processing of a ptRNA. At low or high magnesium concentrations,

5ʹ fragment 3ʹ

5ʹ

5ʹ

RNase P

ptRNA tRNA

Figure 6.9  The function of RNase P.  A specific bond in a precursor tRNA (ptRNA) is cleaved by RNase P, which releases a small fragment at the 5′ end. This results in the formation of a mature tRNA. Core Skill: Connections  Look ahead to Figure 12.20. How do you think translation would be affected if RNase P did not function properly? 

Figure 6.10  The discovery that the RNA subunit of RNase P is a catalyst. HYPOTHESIS The catalytic function of RNase P is carried out by its RNA subunit or by its protein subunit. KEY MATERIALS Purified precursor tRNA (ptRNA) and purified RNA and protein subunits of RNase P from E. coli.

1

Into each of five tubes, add ptRNA.

Experimental level

Conceptual level

ptRNA

3ʹ 5ʹ

ptRNA

2

MgCl2

In tubes 1−3, add a low concentration of MgCl2; in tubes 4 and 5, add a high MgCl2 concentration.

Low MgCl2 (10 mM)

3

Into tubes 2 and 5, add the RNA

RNA subunit

5ʹ

+ 3ʹ

Site of RNase P cleavage

High MgCl2 (100 mM) RNA subunit plus protein

3ʹ

RNA subunit alone cuts here

3ʹ 5ʹ

136

3

4

Low MgCl2 (10 mM)

CHAPTER 6

Into tubes 2 and 5, add the RNA subunit of RNase P alone; into tube 3, add both the RNA subunit and the protein subunit of RNase P. Incubate to allow digestion to occur. Note: Tubes 1 and 4 are controls that have no added subunits of RNase P.

Carry out gel electrophoresis on each sample. In this technique, samples are loaded into a well on a gel. They move toward the bottom of the gel and are separated according to their masses: Molecules with higher masses are closer to the top of the gel. The gel is exposed to ethidium bromide, which stains RNA.

High MgCl2 (100 mM)

RNA subunit alone

3ʹ 5ʹ +

1

2

3

4

Higher mass

5ʹ fragment 5ʹ

Catalytic function will result in the digestion of ptRNA into tRNA and a smaller 5ʹ fragment.

5 ptRNA tRNA

Lower mass

5

RNA subunit alone cuts here 5ʹ

3ʹ

RNA subunit plus protein subunit

THE DATA

5ʹ fragment

6

CONCLUSION The RNA subunit alone catalyzes the breakage of a covalent bond in ptRNA at high MgCl2 concentrations. It is a ribozyme.

7

SOURCE Altman, S. 1990. Enzymatic cleavage of RNA by RNA. Bioscience Reports 10: 317–337.

ptRNA tRNA

5ʹ fragment (4-5): Altman, S. 1990. Enzymatic Cleavage of RNA by RNA. Bioscience Reports, 10:317–337, Fig. 7. ©The Nobel Foundation

ptRNAs were incubated without RNase P (as a control), with the RNA subunit alone, or with intact RNase P (RNA subunit and protein subunit). Following incubation, the researchers performed gel electrophoresis on the samples to determine if the ptRNAs had been cleaved into two pieces—the tRNA and a 5′ fragment. (Gel electrophoresis separates molecules on the basis of their masses.) Let’s now look at the data. As a control, ptRNAs were incubated with low (lane 1) or high (lane 4) concentrations of MgCl2 in the absence of RNase P. As expected, no processing to lower molecular mass tRNAs was observed. When the RNA subunit alone was incubated with ptRNA molecules in the presence of low MgCl2 (lane 2), no processing occurred, but it did occur if the protein subunit was also included (lane 3). The surprising result is shown in lane 5, in which the ptRNA was incubated with the RNA subunit alone in the presence of a high concentration of MgCl2. The RNA subunit by itself was sufficient to cleave the ptRNA to a smaller tRNA and a 5′ fragment! Presumably, the high MgCl2 concentration helps to keep the RNA subunit in a conformation that is catalytically active. Alternatively, the protein subunit plays a similar role in a living cell. Subsequent work confirmed these observations and showed that the RNA subunit of RNase P is a true catalyst—it accelerates the rate of a chemical reaction and is not permanently altered by it. Around the same time, Thomas Cech and colleagues determined that a different RNA molecule found in the protist Tetrahymena thermophila also has

catalytic activity. The term ribozyme is now used to describe an RNA molecule that catalyzes a chemical reaction. In 1989, Altman and Cech received the Nobel Prize in Chemistry for their discovery of ribozymes. Since the pioneering work of Altman and Cech, researchers have discovered that ribozymes play key catalytic roles in cells (Table 6.3).

Table 6.3     Types of Ribozymes General function

Biological examples

Processing of RNA molecules

1. RNase P: As described earlier, RNase P cleaves precursor tRNA molecules (ptRNAs) to form mature tRNAs. 2. Spliceosomal RNA: As described in Chapter 12, eukaryotic pre-mRNAs often have regions called introns. These introns are later removed by a spliceosome that is composed of RNA and protein subunits. The RNA within the spliceosome is believed to function as a ribozyme that removes the introns from pre-mRNA. 3. Certain introns found in mitochondrial, chloroplast, and bacterial RNAs are removed by a self-splicing mechanism.

Synthesis of polypeptides

A ribosome has an RNA component that catalyzes the formation of covalent bonds between adjacent amino acids during polypeptide synthesis.



AN INTRODUCTION TO ENERGY, ENZYMES, AND METABOLISM 137

They are primarily involved in the processing of RNA molecules from precursor to mature forms. In addition, a ribozyme in ribosomes catalyzes the formation of covalent bonds between adjacent amino acids during polypeptide synthesis. Experimental Questions 1. Briefly explain why it was necessary to purify the individual subunits of RNase P to show that it is a ribozyme. 

6.3  Overview of Metabolism Learning Outcomes: 1. Explain the concept of a metabolic pathway, and distinguish between catabolic and anabolic reactions. 2. Describe how catabolic reactions are used to generate building blocks to make larger molecules and to produce energy intermediates. 3. Define redox reaction. 4. Compare and contrast three ways that metabolic pathways are regulated.

In the previous sections, we examined the underlying factors that govern individual chemical reactions and explored the properties of enzymes and ribozymes. In living cells, chemical reactions are coordinated with each other and often occur in a series of steps called a metabolic pathway, with each step catalyzed by a specific enzyme (Figure 6.11). These pathways are categorized according to whether the reactions lead to the breakdown or synthesis of substances. Catabolic reactions result in the breakdown of larger molecules into smaller ones. Such reactions are often exergonic. By comparison, anabolic reactions involve the synthesis of larger molecules from smaller precursor molecules. These reactions usually are endergonic and, in living cells, must be coupled to an exergonic reaction. In this section, we will survey the general features of catabolic and anabolic reactions and explore the ways in which metabolic pathways are controlled.

Catabolic Reactions Recycle Organic Building Blocks and Produce Energy Intermediates Such as ATP Catabolic reactions result in the breakdown of larger molecules into smaller ones. Such catabolic reactions have two uses.

Enzyme 1 O OH

OH

OH

Initial substrate

Enzyme 2 O OH

OH

PO4

2–

Intermediate 1

2. CoreSKILL » Explain why the researchers conducted experiments in which they measured the formation of mature tRNAs without adding the protein subunit or without adding the RNA subunit.  3. CoreSKILL » Analyze the results of Altman and colleagues, and explain how they indicated that RNase P is a ribozyme. How does the concentration of Mg2+ affect the function of the RNA subunit in RNase P? 

Recycling of Organic Building Blocks  One reason to break down macromolecules is to recycle their organic molecules, which are used as building blocks to construct new molecules and macromolecules. For example, polypeptides, which make up proteins, are composed of a linear sequence of amino acids. When a protein is improperly folded or is no longer needed by a cell, the peptide bonds between the amino acids in the protein are broken by enzymes called proteases. This generates amino acids that can be used in the construction of new proteins. Proteases Protein → → → → → → → → → → Many individual amino acids We will consider the mechanisms of recycling in Section 6.4. Breakdown of Organic Molecules to Obtain Energy  A second reason to break down macromolecules into smaller organic molecules is to obtain energy that is used to drive endergonic processes in the cell. Covalent bonds store a large amount of energy. However, when cells break covalent bonds in organic molecules such as glucose, they do not directly use the energy released in this process. Instead, the released energy is stored in energy intermediates, molecules such as ATP, which are directly used to drive endergonic reactions in cells. As an example, let’s consider the breakdown of glucose into two molecules of pyruvate. As discussed in Chapter 7, the breakdown of glucose to pyruvate involves a catabolic pathway called glycolysis. Some of the energy released during the breakage of covalent bonds in glucose is harnessed to synthesize ATP. Glycolysis involves a series of steps in which covalent bonds are broken and rearranged. This process produces molecules that readily donate a phosphate group to ADP, thereby producing ATP. For example, phosphoenolpyruvate has a phosphate group attached to pyruvate. Due to the arrangement of bonds in phosphoenolpyruvate, this phosphate bond is unstable and easily broken. Therefore, the phosphate can be readily transferred from phosphoenolpyruvate to ADP:

Enzyme 3 O PO 2– 4

OH

PO42 –

Intermediate 2

PO42–

O PO 2– 4

PO

2–

4

Final product

Figure 6.11  A metabolic pathway.  In this metabolic pathway, a series of different enzymes catalyze the attachment of phosphate groups at various positions on a sugar molecule, beginning with a starting substrate and ending with a final product.

Unstable phosphate bond O–

O– C

O

CO~ P CH2

+ ADP

Phosphoenolpyruvate

C

O

Pyruvate kinase C

O

CH3 Pyruvate

+ ATP

138

CHAPTER 6

This is an exergonic reaction (ΔG = −7.5 kcal/mol) and therefore favors the formation of products. In this step of glycolysis, the breakdown of an organic molecule, namely phosphoenolpyruvate, results in the formation of pyruvate and the synthesis of an energy intermediate, a molecule of ATP, which can then be used by a cell to drive an endergonic reaction. This way of synthesizing ATP, termed substrate-level phosphorylation, occurs when an enzyme directly transfers a phosphate from an organic molecule to ADP, thereby making ATP. Another way to make ATP is via chemiosmosis. In this process, energy stored in an ion electrochemical gradient is used to make ATP from ADP and Pi. We will consider this other mechanism in Chapter 7.

Redox Reactions Involve the Transfer of Electrons During the breakdown of small organic molecules, oxidation—the removal of one or more electrons from an atom or molecule—may occur. This process is called oxidation because oxygen is frequently involved in chemical reactions that remove electrons from other atoms or molecules. By comparison, reduction is the addition of one

or more electrons to an atom or molecule. Reduction is so named because the addition of a negatively charged electron reduces the net charge of an atom or molecule. Electrons do not exist freely in solution. When an atom or molecule is oxidized, the electron that is removed must be transferred to another atom or molecule, which becomes reduced. This type of reaction is termed a redox reaction, which is short for a reductionoxidation reaction. An electron may be transferred from molecule A to molecule B as shown in the following generalized equation: Ae−  +  B  →  A  +  Be−           (oxidized) (reduced) As shown on the right side of this reaction, A has been oxidized (that is, had an electron removed), and B has been reduced (that is, had an electron added). In general, a substance that has been oxidized has less energy, whereas a substance that has been reduced has more energy. During the oxidation of organic molecules such as glucose, the electrons that are removed may be used to produce energy intermediates such as NADH (Figure 6.12). In this process, an organic molecule

The 2 electrons and H+ can be added to this ring, which now has 2 double bonds instead of 3. H

O C

Nicotinamide

O P

CH2 O–

O O

P O

H

H

H

NH2

N

H

H

OH

OH

H

O N

H O

O O

P

CH2 O–

O

N

CH2

C

NH2

N Two electrons are released during the oxidation of the nicotinamide ring.

H

OH

OH

O–

O

Oxidation

O

H

H

NH2 + 2e– + H+

N+

O

H

Reduction

N

Adenine

P O

H

Nicotinamide adenine dinucleotide (NAD+)

H

O–

O

H

H

OH

OH

H

NH2

N

CH2

N

H N

O

NADH (an electron carrier)

H

H

H

OH

OH

N

H

H

Figure 6.12  The reduction of NAD+ to produce NADH.  NAD+ is composed of two nucleotides, one with an adenine base and one with a

nicotinamide base. The oxidation of organic molecules releases electrons that bind to NAD+ (and along with a hydrogen ion) result in the formation of NADH. The two electrons and H+ are incorporated into the nicotinamide ring. Note: The actual net charges of NAD+ and NADH are −1 and −2, respectively. They are designated NAD+ and NADH to emphasize the net charge of the nicotinamide ring, which is involved in reduction-oxidation reactions. Core Skill: Modeling  The goal of this modeling challenge is to make a model for the NADH cycle in a format that is similar to Figure 6.4. Modeling Challenge: Earlier in this chapter, we considered the ATP cycle (refer back to Figure 6.4). As discussed in Chapter 7, NADH is used by mitochondria to make ATP. Therefore, it plays a key role in the ATP cycle. NADH has its own cycle, in which it is converted to NAD+ and then back to NADH again. Draw a model for the NADH cycle using a format similar to that shown in Figure 6.4. Your model should incorporate the red squiggly arrows that are labeled “Energy input (endergonic)” and “Energy release (exergonic).” In addition to using NADH, NAD+, H+, and 2e− in your model (instead of ATP, etc.), you will need to change the sentences in the top and bottom text boxes of Figure 6.4 and to change the words “Synthesis” and “Hydrolysis.”



AN INTRODUCTION TO ENERGY, ENZYMES, AND METABOLISM 139

is oxidized, and NAD+ (nicotinamide adenine dinucleotide)  is reduced to NADH. Cells use NADH in two common ways. First, as we will see in Chapter 7, the oxidation of NADH is a highly exergonic reaction that can be used to make ATP. Second, NADH can donate electrons to other organic molecules and thereby energize them. Such energized molecules can more readily form covalent bonds. Therefore, as described next, NADH is often needed in reactions that involve the synthesis of larger molecules through the formation of covalent bonds between smaller molecules.

Anabolic Reactions Require an Input of Energy to Make Larger Molecules Anabolic reactions are also called biosynthetic reactions, because they are necessary to make larger molecules and macromolecules. We will examine the synthesis of macromolecules in several chapters of this textbook. For example, RNA and protein biosynthesis are described in Chapter 12. Cells also need to synthesize small organic molecules, such as amino acids and fats, if they are not readily available from food sources. Such molecules are made by the formation of covalent linkages between precursor molecules. For example, glutamate (an amino acid) is made by covalently linking α-ketoglutarate (a product of sugar metabolism) and ammonium (NH4+).

COO–

COO–

CH2

CH2

+ + CH2 + NH4 + NADH + H

CH2

C

O

COO– α-Ketoglutarate

H3N+

C

+ NAD+ + H2O COO–

H Glutamate

An energy intermediate, a molecule of NADH, is needed to drive this reaction forward.

Metabolic Pathways Are Regulated in Three General Ways The regulation of metabolic pathways is important for a variety of reasons. Catabolic pathways are regulated so organic molecules are broken down only when they are no longer needed or when the cell requires energy. During anabolic reactions, regulation ensures that a cell synthesizes molecules only when they are needed. The regulation of catabolic and anabolic pathways occurs at the genetic, cellular, and biochemical levels. Gene Regulation  Enzymes are protein molecules that are encoded by genes. One way that cells control metabolic pathways is via gene regulation. For example, if a bacterial cell is not exposed to a particular sugar in its environment, it will turn off the genes that encode the enzymes that are needed to break down

that sugar. Then, if the sugar becomes available, the genes are switched back on. Chapter 14 examines the steps of gene regulation in detail. Cellular Regulation  Metabolism is also coordinated at the cellular level. Cells integrate signals from their environment and adjust their metabolic pathways to adapt to those signals. As discussed in Chapter 9, cell-signaling pathways often lead to the activation of protein kinases—enzymes that covalently attach a phosphate group to a target protein. For example, when people are frightened, they secrete a hormone called epinephrine into their bloodstream. This hormone binds to the surface of muscle cells and stimulates an intracellular pathway that leads to the phosphorylation of specific enzymes involved in carbohydrate metabolism. These activated enzymes promote the breakdown of carbohydrates, an event that supplies the frightened individual with more energy. Epinephrine is sometimes called the fight-or-flight hormone because the added energy prepares an individual to either stay and fight or run away quickly. After a person no longer feels frightened, hormone levels drop, and other enzymes called phosphatases remove the phosphate groups from enzymes, thereby restoring the original level of carbohydrate metabolism. Biochemical Regulation  A third and very prominent way that metabolic pathways are controlled is at the biochemical level. In this case, the noncovalent binding of a molecule to an enzyme directly regulates the enzyme's function. As discussed earlier, one form of biochemical regulation involves the binding of molecules called competitive or noncompetitive inhibitors (see Figure 6.7). An example of noncompetitive inhibition is a type of regulation called feedback inhibition, in which the product of a metabolic pathway inhibits an enzyme that acts early in the pathway, thus preventing the overaccumulation of the product (Figure 6.13). Many metabolic pathways use feedback inhibition as a form of biochemical regulation. In such cases, the inhibited enzyme has two binding sites. One site is the active site, where the reactants are converted to products. In addition, enzymes controlled by feedback inhibition also have an allosteric site, where a molecule can bind noncovalently and affect the enzyme's function. The binding of a molecule to an allosteric site causes a conformational change in the enzyme that inhibits its catalytic function. Allosteric sites are often found in the enzymes that catalyze the early steps in a metabolic pathway. Such allosteric sites typically bind molecules that are the products of the metabolic pathway. When the products bind to these sites, they inhibit the function of these enzymes, thereby preventing the formation of too much product. As described earlier, in Figure 6.7c, this phenomenon is also called noncompetitive inhibition.  Regulation of the Rate-Limiting Step  Cellular regulation and biochemical regulation are important ways to control chemical reactions in a cell. For a metabolic pathway composed of several enzymecatalyzed reactions, which enzyme should be controlled? In many cases, a metabolic pathway has a rate-limiting step, which is the slowest step in the pathway. If the rate-limiting step is inhibited or enhanced, such changes will have the greatest influence on the

140

CHAPTER 6

Initial substrate

Intermediate 1

Intermediate 2

Final product

Active site Enzyme 2

Enzyme 1 Allosteric site

Enzyme 3 Feedback Inhibition: If the concentration of the final product becomes high, it will bind to enzyme 1 and cause a conformational change that inhibits the enzyme’s ability to convert the initial substrate into intermediate 1.

Conformational change

Final product

Figure 6.13  Feedback inhibition.  In this process, the final product of a metabolic pathway inhibits an enzyme that functions early in the pathway, thereby preventing the overaccumulation of the product.

Core Skill: Connections  Look ahead to Figure 7.3, which describes a metabolic pathway called glycolysis. Feedback inhibition occurs during this process in that high levels of ATP inhibit phosphofructokinase, an enzyme that catalyzes the conversion of fructose-6-phosphate and ATP to fructose-1,6-bisphosphate and ADP. How is this beneficial to the cell? 

formation of the product of the metabolic pathway. Rather than affecting all of the enzymes in a metabolic pathway, cellular or biochemical regulation is often directed at the enzyme that catalyzes the rate-limiting step. This is an efficient and rapid way to control the amount of product of a pathway.

BIO TIPS

THE QUESTION  The enzyme called 3-phosphoglycerate dehydrogenase catalyzes the following chemical reaction:

3-phospho-D-glycerate + NAD+⇌ 3-phosphonooxypyruvate + NADH + H+ This reaction is the rate-limiting step in a metabolic pathway that synthesizes serine, which is an amino acid. Serine inhibits 3-phosphoglycerate dehydrogenase by binding to an allosteric site on the enzyme, thereby preventing the overaccumulation of serine in a cell. This is an example of feedback inhibition. Researchers have identified a mutant version of 3-phosphoglycerate dehydrogenase that does not exhibit feedback inhibition. Cells that make the mutant enzyme tend to overaccumulate serine. Make a drawing that depicts how the mutant enzyme is different from the normal one. Your drawing should include binding sites for 3-phospho-D-glycerate, NAD+, and serine. T OPIC  What topic in biology does this question address? The topic is enzymes and feedback inhibition. More specifically, the question is about a mutant version of 3-phosphoglycerate dehydrogenase that does not exhibit feedback inhibition. I NFORMATION What information do you know based on the question and your understanding of the topic? From the question, you know that 3-phosphoglycerate dehydrogenase catalyzes the rate-limiting step in a metabolic pathway that

produces serine. Serine causes feedback inhibition of the normal version of the enzyme but does not inhibit a mutant version. From your understanding of the topic, you may recall that feedback inhibition occurs via an allosteric site. P ROBLEM-SOLVING  S TRATEGY Compare and contrast. Make a drawing. To solve this problem, you could begin by comparing the properties of the normal and mutant enzyme. The mutant enzyme does not exhibit feedback inhibition. However, because cells harboring the mutant version of the enzyme overaccumulate serine, you know that the catalytic properties of the enzyme must be functioning normally. In other words, the active site is functional. When making the drawing, you need to remember that the enzyme has two sites: an active site and an allosteric site.

ANSWER The mutation, designated by an X in the enzyme on the right, is an alteration in the structure of the allosteric site that prevents serine from binding there.

NAD+

Active site 3-phospho-Dglycerate

Normal enzyme

Allosteric site for serine

NAD+

Active site 3-phospho-Dglycerate

Mutant enzyme

Serine is unable to bind



AN INTRODUCTION TO ENERGY, ENZYMES, AND METABOLISM 141

6.4  R  ecycling of Organic Molecules

Cap

Learning Outcomes:

1

1. Explain the relationship between the recycling of organic molecules and cellular efficiency. 2. Outline how the building blocks of proteins are recycled. 3. Describe how the components of cellular organelles are recycled via autophagy.

As mentioned earlier in this chapter, an important feature of metabolism is the recycling of organic molecules, such as amino acids, which are the building blocks of proteins. Except for DNA, which is stably maintained and inherited from cell to cell, other large molecules such as RNA, proteins, lipids, and polysaccharides typically exist for a relatively short period of time. Biologists often speak of the half-life of molecules, which is the time it takes for 50% of a specific type of molecule in a cell to be broken down and recycled. For example, mRNA molecules in bacterial cells have an average half-life of about 5 minutes, whereas mRNAs in eukaryotic cells tend to exist for longer periods of time, on the order of 30 minutes to 24 hours or even several days. Why is recycling important? To compete effectively in their native environments, all living organisms must efficiently use and recycle the organic molecules that are needed as building blocks to construct larger molecules and macromolecules. Otherwise, they would waste a great deal of energy making such building blocks from smaller molecules. For example, organisms conserve an enormous amount of energy by reusing the amino acids that are needed to construct proteins. In this section, we will explore how amino acids are recycled and consider a mechanism for recycling all of the materials found in an organelle.

Proteins in Eukaryotes and Archaea Are Broken Down in the Proteasome Cells continually degrade proteins that are faulty or no longer needed. To be degraded, proteins are recognized by proteases—enzymes that cleave the bonds between adjacent amino acids. The primary pathway for protein degradation in archaea and eukaryotic cells occurs via a protein complex called a proteasome. The core of the proteasome consists of four stacked rings, each composed of seven protein subunits (Figure 6.14a). The proteasomes of eukaryotic cells also contain caps at each end that control the entry of proteins into the proteasome. Figure 6.14b describes the steps of protein degradation via eukaryotic proteasomes. A string of small proteins called ubiquitins is covalently attached to the target protein. This event directs the target protein to a proteasome cap, which has binding sites for ubiquitins. The cap also has enzymes that unfold the protein and inject it into the internal cavity of the proteasome core. The ubiquitins are removed during entry and released to the cytosol for reuse. Inside the proteasome, proteases degrade the target protein into small peptides and amino acids. The process is completed when the peptides and

2 3 4 Core proteasome (4 rings)

Cap (a) Structure of the eukaryotic proteasome

Ubiquitin 1

String of ubiquitins is attached to a target protein.

Target protein

2

3

Protein with attached ubiquitins is directed to the proteasome.

Protein is unfolded by enzymes in the cap and injected into the core proteasome. Ubiquitins are released back into the cytosol.

4

5

Protein is degraded to small peptides and amino acids.

Small peptides and amino acids are recycled back to the cytosol.

(b) Steps of protein degradation in eukaryotic cells

Figure 6.14    Protein degradation via the proteasome. Concept Check    What are advantages of protein degradation? 

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Outer membrane

Autophagosome

Inner membrane Lysosome

Organelle

2

1

Membrane tubule begins to enclose an organelle.

Double membrane completely encloses an organelle to form an autophagosome.

3

Autophagosome fuses with a lysosome. Contents are degraded and recycled back to the cytosol.

Figure 6.15    Autophagy.

amino acids are recycled back into the cytosol. The amino acids are reused to make new proteins. Ubiquitin targeting has three functions. ∙ The enzymes that attach ubiquitins to the target protein recognize improperly folded proteins, allowing cells to identify and degrade nonfunctional proteins. ∙ Changes in cellular conditions may warrant the rapid breakdown of particular proteins. For example, cell division requires a series of stages called the cell cycle, which depends on the degradation of specific proteins. After these proteins perform their functions in the cycle, ubiquitin targeting directs them to the proteasome for degradation. ∙ The amino acids that are released from the proteosome are recycled to make new proteins, thus saving the cell energy.

Autophagy Recycles the Contents of Entire Organelles As described in Chapter 4, lysosomes contain many different types of acid hydrolases that break down proteins, carbohydrates, nucleic acids, and lipids. This enzymatic function enables lysosomes to break down complex materials. One function of lysosomes involves the digestion of substances that are taken up from outside the cell. This process, called endocytosis, is described in Chapter 5. In addition, lysosomes help digest intracellular materials. In a process known as autophagy (from the Greek, meaning eating one’s self), cellular material, such as a worn-out organelle, becomes enclosed in a double membrane (Figure 6.15). This double membrane is formed from a tubule that elongates and eventually wraps around the organelle to form an autophagosome. The autophagosome then fuses with one or more lysosomes, and the material inside the autophagosome is digested. The small molecules released from this digestion are recycled back into the cytosol.

Summary of Key Concepts 6.1  Energy and Chemical Reactions ∙∙ The fate of a chemical reaction is determined by its direction and rate. ∙∙ Energy, the ability to promote change or do work, exists in many forms. According to the first law of thermodynamics, energy cannot be created or destroyed, but it can be converted from one form to another. The second law of thermodynamics states that energy interconversions involve an increase in entropy (Figures 6.1, 6.2, Table 6.1). ∙∙ Free energy is the amount of available energy that can be used to promote change or do work. Spontaneous or exergonic reactions, which release free energy, have a negative free-energy change, whereas endergonic reactions have a positive free-energy change (Figure 6.3). ∙∙ Chemical reactions proceed until they reach a state of chemical equilibrium, where the rate of formation of products equals the rate of formation of reactants. ∙∙ Exergonic reactions, such as the hydrolysis of ATP, are commonly coupled to cellular processes that would otherwise be endergonic. Cells continuously synthesize ATP from ADP and Pi and then hydrolyze it to drive endergonic reactions (Figure 6.4). ∙∙ Estimates from genome analysis indicate that over 20% of all proteins bind ATP (Table 6.2).

6.2  Enzymes and Ribozymes ∙∙ Enzymes are proteins that speed up the rate of a chemical reaction by lowering the activation energy (EA) needed to achieve a transition state (Figure 6.5). ∙∙ Enzymes recognize reactant molecules, also called substrates, with high specificity. Conformational changes in an enzyme cause its



AN INTRODUCTION TO ENERGY, ENZYMES, AND METABOLISM 143

substrate to bind more tightly to it, a phenomenon called induced fit (Figure 6.6). ∙∙ Each enzyme-catalyzed reaction has a maximal velocity (Vmax). The KM value for an enzyme is the substrate concentration at which the velocity of the reaction is half of the maximal value. Competitive inhibitors raise the KM for the substrate, whereas noncompetitive inhibitors lower the Vmax (Figure 6.7). ∙∙ Enzyme function may be affected by a variety of other factors, including prosthetic groups, cofactors, coenzymes, temperature, and pH (Figure 6.8). ∙∙ Altman and colleagues discovered that the RNA subunit within RNase P is a ribozyme, an RNA molecule that catalyzes a chemical reaction. Other ribozymes play key roles in the cell (Figures 6.9, 6.10, Table 6.3).

6.3  Overview of Metabolism ∙∙ Metabolism is the sum of the chemical reactions in a living organism. Metabolic pathways consist of coordinated chemical reactions that occur in steps and are catalyzed by specific enzymes (Figure 6.11). ∙∙ Catabolic reactions involve the breakdown of larger molecules into smaller ones. These reactions recycle organic molecules that are used as building blocks to make new molecules. The organic molecules are also broken down to make energy intermediates such as ATP. ∙∙ Some chemical reactions are redox reactions, in which electrons are transferred from one molecule to another. These reactions can be used to make energy intermediates such as NADH (Figure 6.12). ∙∙ Anabolic reactions require an input of energy to synthesize larger molecules and macromolecules. ∙∙ Metabolic pathways are controlled by gene regulation, cellular regulation, and biochemical regulation. An example of biochemical regulation is feedback inhibition. The enzyme that catalyzes the rate-limiting step in a pathway is often the target of cellular or biochemical regulation (Figure 6.13).

6.4  Recycling of Organic Molecules ∙∙ Recycling of organic molecules saves a great deal of energy for living organisms. ∙∙ Proteins in the cells of eukaryotes and archaea are degraded by proteasomes (Figure 6.14). ∙∙ Lysosomes digest intracellular material through the process of autophagy (Figure 6.15).

Assess & Discuss Test Yourself 1. Reactions that release free energy are a. exergonic. b. spontaneous. c. endergonic. d. endothermic. e. both a and b. 2. Enzymes speed up reactions by a. providing chemical energy to fuel a reaction. b. lowering the activation energy necessary to initiate a reaction.

c. causing an endergonic reaction to become an exergonic reaction. d. substituting for one of the reactants necessary for a reaction. e. none of the above. 3. For the idealized reaction aA + bB ⇌ cC + dD, suppose that the equilibrium constant, Keq, is 0.01. If the starting concentrations for A, B, C, and D are 1 M each, what would you predict based on the value of Keq? a. The forward reaction is favored. b. The reverse reaction is favored. c. The forward reaction is fast. d. The reverse reaction is fast. e. both b and d. 4. Researchers analyzed a cell extract—a mixture of molecules isolated from a certain type of cell—and studied a chemical reaction in which a carbohydrate was broken down into smaller molecules. When they added a protease to the cell extract, they discovered that the protease greatly inhibited the rate of the reaction. Based on this observation, you could conclude that the reaction is a. exergonic. b. endergonic. c. catalyzed by an enzyme. d. catalyzed by a ribozyme. e. Both b and c are true of this reaction. 5. In biological systems, ATP functions by a. providing the energy to drive endergonic reactions. b. acting as an enzyme and lowering the activation energy of certain reactions. c. adjusting the pH of intracellular solutions to maintain optimal conditions for enzyme activity. d. regulating the speed at which endergonic reactions proceed. e. interacting with enzymes as a cofactor to stimulate chemical reactions. 6. In a chemical reaction, NADH is converted to NAD+ + H+. We say that NADH has been a. reduced. b. phosphorylated. c. oxidized. d. decarboxylated. e. methylated. 7. Scientists identify proteins that use ATP as an energy source by a. determining whether a protein functions in anabolic or catabolic reactions. b. determining if a protein has a known ATP-binding site. c. predicting the free energy necessary for a protein to function. d. determining if a protein has an ATP synthase subunit. e. all of the above. 8. For a particular chemical reaction, an inhibitor raises the KM but does not affect the Vmax. This inhibitor a. is a competitive inhibitor. b. is a noncompetitive inhibitor. c. binds to the active site of the enzyme. d. binds to an allosteric site of the enzyme. e. is a competitive inhibitor and binds to the active site of the enzyme. 9. Which of the following is (are) key benefits of catabolic reactions? a. recycling of organic building blocks b. breakdown of organic molecules to obtain energy c. synthesis of important polymers, such as polypeptides d. all of the above e. a and b only

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10. Autophagy provides a way for cells to a. degrade entire organelles and recycle their components. b. control the level of ATP. c. engulf bacterial cells. d. export unwanted organelles out of the cell. e. inhibit the first enzyme in a metabolic pathway.

Conceptual Questions 1. With regard to rate and direction, discuss the differences between endergonic and exergonic reactions.  2. Describe the mechanism and purpose of feedback inhibition in a metabolic pathway.    3.

Core Concept: Energy and Matter  A core concept of biology is that living organisms use energy. Explain why the recycling of amino acids and nucleotides is energy-efficient. 

Collaborative Questions 1. Living cells are highly ordered units, yet the entropy of the universe is increasing. Discuss how life can maintain its order in spite of the second law of thermodynamics. Are we defying this law? 2. What is the advantage of using ATP as a common energy source; that is, how is using just ATP better than using a bunch of different food molecules? For example, instead of just having Na+/K+-ATPase in a cell, why not have many different ion pumps, each driven by a different food molecule, like Na+/K+-glucosase (a pump that uses glucose), Na+/ K+-sucrase (a pump that uses sucrose), Na+/K+-fatty acidase (a pump that uses fatty acids), and so on?

CHAPTER OUTLINE 7.1 7.2 7.3 7.4 7.5 7.6 7.7

Overview of Cellular Respiration Glycolysis Breakdown of Pyruvate Citric Acid Cycle Overview of Oxidative Phosphorylation A Closer Look at ATP Synthase Connections Among Carbohydrate, Protein, and Fat Metabolism

7.8 Anaerobic Respiration and Fermentation Summary of Key Concepts Assess & Discuss

Cellular Respiration and Fermentation

7

C

armen became inspired while watching the 2008 ­Summer Olympics and set a personal goal to run a ­marathon—a distance of 42.2 kilometers, or 26.2 miles. Although she was active in volleyball and downhill skiing in high school, she had never attempted distance running. At first, running an entire mile was pure torture. She was out of breath, overheated, and unhappy, to say the least. However, she became committed to endurance training and within a few weeks discovered that running a mile was a “piece of cake.” Two years later, Carmen participated in her first marathon and finished with a time of 4 hours and 11 minutes—not bad for someone who had previously struggled to run a single mile! How had Carmen’s training allowed her to achieve this goal? Perhaps the biggest factor is that the training altered the metabolism in her leg muscles. For example, the network of small blood vessels supplying oxygen to her leg muscles became more extensive, providing more efficient delivery of oxygen and removal of wastes. Second, her muscle cells developed more mitochondria. Recall from Chapter 4 that the primary role of mitochondria is to make ATP, which cells use as a source of energy. With these changes, Carmen’s leg muscles were better able to break down organic molecules in her food and utilize them to make ATP. The cells in Carmen’s leg muscles had become more efficient at cellular respiration, which comprises the metabolic reactions that a cell uses to get energy from food molecules and release waste products. When we eat food, we use much of that food for energy. People often speak of “burning calories.” Although metabolism does generate some heat, the chemical reactions that take place in the cells of living organisms are uniquely different from those that occur, say, in a fire. When wood is burned, the reaction produces enormous amounts of heat in a short period of time— the reaction lacks control. In contrast, the metabolism that occurs in living cells is extremely controlled. The food molecules from which we harvest energy give up that energy in a very restrained manner rather than all at once, as in a fire. An underlying theme of metabolism is the remarkable control that cells possess when they coordinate chemical reactions. A key emphasis of this chapter is how cells use the energy stored within the chemical bonds of organic molecules.

Physical endurance. Conditioned athletes, like these marathon runners, metabolize organic molecules such as glucose very efficiently. ©Michael Dwyer/AP Images

We will begin by surveying a group of chemical reactions that accomplish the breakdown of the main carbohydrate cells use as an energy source, namely, the sugar glucose. As you will learn, cells carry out an intricate series of reactions so that glucose can be “burned” in a very controlled fashion when oxygen is available. We will then examine how cells use organic molecules in the absence of oxygen via processes known as anaerobic respiration and fermentation.

7.1 Overview of Cellular Respiration Learning Outcome: 1. List and briefly describe the four metabolic pathways that are needed to break down glucose to CO2 and H2O.

Cellular respiration is a process by which living cells obtain energy from organic molecules and release waste products. A primary aim of cellular respiration is to make adenosine triphosphate, or ATP.

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When oxygen (O2) is used, this process is termed aerobic respiration. During aerobic respiration, O2 is consumed, and carbon dioxide (CO2) is released via the oxidation of organic molecules. When we breathe, we inhale the oxygen needed for aerobic respiration and exhale CO2, a by-product of the process. For this reason, the term respiration has a second meaning, which is the act of breathing.

a tremendous amount of free energy is released (−685 kcal/mol). Some of the energy is lost as heat, but much of it is used to make three energy intermediates: ATP, NADH, and FADH2. This process involves four metabolic pathways: (1) glycolysis, (2) the breakdown of pyruvate, (3) the citric acid cycle, and (4) oxidative phosphorylation (Figure 7.1):

C6H12O6  +  6 O2  →  6 CO2  +  6 H2O

1. Glycolysis. In glycolysis, glucose (a compound with six carbon atoms) is broken down to two pyruvate molecules (with three carbons each), producing a net energy yield of two ATP molecules and two NADH molecules. The two ATP molecules are synthesized via substrate-level phosphorylation, which occurs when an enzyme directly transfers a phosphate from an organic molecule to ADP. In eukaryotes, glycolysis occurs in the cytosol.

      (Glucose)                   ΔG  =  −685 kcal/mol We will focus on the breakdown of glucose in a eukaryotic cell in the presence of oxygen. Certain covalent bonds within glucose store a large amount of chemical potential energy. When glucose is broken down via oxidation, ultimately to CO2 and water,

1

Glycolysis: Glucose C C C C C C

Outer mitochondrial membrane Cytosol

2 pyruvate 2 C C C 2 NADH

Mitochondrial matrix

Inner mitochondrial membrane

2 NADH 2 pyruvate

2

Breakdown of pyruvate: 2 pyruvate 2 C C C 2 CO2 + 2 acetyl

6 NADH 2 FADH2

3

Citric acid cycle: 2 acetyl

4

2 C C

2 C C 2 CO2

2 CO2

+2 ATP Via substrate-level phosphorylation

2 acetyl

4 CO2 2 CO2

Oxidative phosphorylation: The oxidation of NADH and FADH2 via the electron transport chain generates an H+ gradient that is used to make more ATP via the ATP synthase. O2 is consumed.

+2 ATP

+30–34 ATP

Via substrate-level phosphorylation

Via chemiosmosis

Figure 7.1  An overview of cellular respiration.  The 30–34 ATP molecules produced via chemiosmosis represent the maximum number possible. As described later in this chapter, mitochondria may use NADH, FADH2, and the H+ electrochemical gradient for purposes other than ATP synthesis. Core Concept: Energy and Matter  Molecules such as glucose store a large amount of energy. The breakdown of glucose is used to make energy intermediates, such as ATP molecules, which drive many types of cellular processes.



CELLULAR RESPIRATION AND FERMENTATION 147

2. Breakdown of pyruvate. The two pyruvate molecules enter the mitochondrial matrix, where each one is broken down to an acetyl group (with two carbons each) and one CO2 molecule. For each pyruvate broken down via oxidation, one NADH molecule is made by the reduction of NAD+. 3. Citric acid cycle. Each acetyl group is incorporated into an organic molecule, which is later oxidized to liberate two CO2 molecules. One ATP, three NADH, and one FADH2 are made in this process. Because there are two acetyl groups (one from each pyruvate), the total yield is four CO2, two ATP via substratelevel phosphorylation, six NADH, and two FADH2. This process occurs in the mitochondrial matrix. 4. Oxidative phosphorylation. The NADH and FADH2 made in the three previous stages contain high-energy electrons that can be readily transferred in a redox reaction to other molecules. Once removed from NADH or FADH2, these high-energy electrons release some energy, and through an electron transport chain, that energy is harnessed to produce an H+ electrochemical gradient. In chemiosmosis, energy stored in the H+ electrochemical gradient is used to synthesize ATP from ADP and Pi. The overall process of electron transport and ATP synthesis is called oxidative phosphorylation because NADH or FADH2 has been oxidized and ADP has become phosphorylated to make ATP. Approximately 30–34 ATP molecules can be made via oxidative phosphorylation.

7.2  Glycolysis Learning Outcomes: 1. Outline the three phases of glycolysis, and identify the net products. 2. Describe the series of enzymatic reactions that constitute glycolysis. 3. CoreSKILL » Explain the underlying basis for the use of positronemission tomography to detect cancer.

Thus far, we have examined the general features of the four metabolic pathways that are involved in the breakdown of glucose. We will now turn our attention to a more detailed understanding of these pathways for glucose metabolism, beginning with glycolysis.

Glycolysis Is a Metabolic Pathway That Breaks Down Glucose to Pyruvate Glycolysis (from the Greek glykos, meaning sweet, and lysis, meaning splitting) involves the breakdown of glucose, a simple sugar, into two molecules of a compound called pyruvate. This process can occur in the presence of oxygen, that is, under aerobic conditions, and it can also occur in the absence of oxygen. During the 1930s, the efforts of several German biochemists, including Gustav Embden, Otto Meyerhof, and Jacob Parnas, established that glycolysis involves 10 steps, each one catalyzed by a different enzyme. The elucidation of these steps was a major achievement in the field of biochemistry—the study of the chemistry of living organisms. Researchers have since discovered that glycolysis is the common pathway for glucose breakdown in bacteria, archaea, and eukaryotes. Remarkably, the steps of glycolysis are virtually identical in nearly all living species, suggesting that glycolysis arose very early in the evolution of life on our planet. The 10 steps of glycolysis can be grouped into three phases (Figure 7.2).

   In eukaryotes, oxidation phosphorylation occurs along the cristae, which are projections formed by the invagination of the inner mitochondrial membrane. The cristae greatly increase the surface area of the inner membrane and thereby increase the amount of ATP that can be made. In bacteria and archaea, oxidative phosphorylation occurs along the plasma membrane.

Energy investment phase

Cleavage phase

Energy liberation phase

C C C

C C C O–

H Step 4

C C C C C C

C C C C C C

CH2OH O H

H HO

H OH H

Step 1

Step 2

Step 3

H OH

P

OCH2 H

ATP

H

O

Glucose

OH

C

O

CHOH

C

O

CH2O P

CH3

C

O

Step 6

Pi

NADH

Step 7

ATP

Step 8

Step 9

Step 10

ATP

CH2O P HO

OH

ATP

OH

Step 5

H

Fructose-1,6bisphosphate

C C C

C C C

H

O– O

C

O

CHOH

C

O

CH2O P

CH3

C

Pi

Two molecules of glyceraldehyde3-phosphate

NADH

ATP

ATP

Two molecules of pyruvate

Figure 7.2  Overview of glycolysis. Core Skill: Connections  Look ahead to Table 45.1. With regard to oxygen needs, what advantage do glycolytic muscle fibers ­provide? 

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∙ The first phase (steps 1–3) involves an energy investment. Two ATP molecules are hydrolyzed, and the phosphates from those ATP molecules are attached to glucose, which is converted to fructose-1,6-bisphosphate. The energy investment phase raises the free energy of glucose, thereby allowing later reactions to be exergonic.

Regulation of Glycolysis  How do cells control glycolysis? The rate of glycolysis is regulated by the availability of substrates, such as glucose, and by feedback inhibition. A key control point involves the enzyme phosphofructokinase, which catalyzes the third step in glycolysis, the step believed to be the slowest, or rate-limiting, step. When a cell has a sufficient amount of ATP, feedback inhibition occurs. At high concentrations, ATP binds to an allosteric site in phosphofructokinase, causing a conformational change that renders the enzyme functionally inactive. This prevents the further breakdown of glucose and thereby inhibits the overproduction of ATP.

∙ The cleavage phase (steps 4–5) breaks this six-carbon molecule into two molecules of glyceraldehyde-3-phosphate. ∙ The energy liberation phase (steps 6–10) produces four ATP, two NADH, and two molecules of pyruvate. Because two molecules of ATP are used in the energy investment phase, the net yield is two molecules of ATP.

BIO TIPS

THE QUESTION  During the process of glycolysis, glucose is broken down into two pyruvate molecules. As shown in Figure 7.3, this metabolic pathway consists of 10 consecutive chemical reactions. Describe the three major phases of glycolysis.

Figure 7.3 describes the details of the 10 reactions of glycolysis. The net reaction of glycolysis is as follows:

C6H12O6  +  2 NAD+  +  2 ADP2−  +  2 Pi2−  →       Glucose

T OPIC  What topic in biology does this question address? The topic is glycolysis. More specifically, the question asks you to describe the three major phases of this process.

2 CH3(C=O)COO−  +  2 H+  +  2 NADH  +  2 ATP4−  +  2 H2O   Pyruvate

I NFORMATION  What information do you know based on the question and your understanding of the topic? In the question, you are reminded that glycolysis consists of 10 consecutive chemical reactions. From your understanding of the topic, you may remember that different types of chemical reactions are occurring. Glycolysis: Glucose

2 NADH 2 NADH

P OCH2

2 FADH2

6 NADH

C

2 pyruvate

Citric acid cycle

2 CO2

Isomerase e

HO

ADP P OCH2

O H

H H OH H

OH

Glucose

1

Hexokinase

HO

H OH H

H OH OH

2

CH2OH

O H

H

Phosphogluco– isomerase OH

Glucose-6-phosphate

Glucose is phosphorylated by ATP. Glucose-6phosphate is more easily trapped in the cell than glucose.

ATP

P OCH2 O H

H

H OH

+30–34 ATP

+2 ATP

ATP

Dihydroxyacetone phosphate

2 CO2

+2 ATP CH2OH

Oxidative phosphorylation

2 CO2

Breakdown of pyruvate

O

CH2OH

HO

The structure of glucose-6phosphate is rearranged to fructose6-phosphate.

P OCH2 H

Phosphofructo– kinase

Fructose-6-phosphate

3

Dihydroxyacetone phosphate is rearranged (isomerized) to form another molecule of glyceraldehyde3-phosphate.

H

ADP

OH

H

5

H OH

CH2O P

O HO

OH

O

Aldolase

CH2O P

H

Fructose -1,6-bisphosphate

Fructose-6phosphate is phosphorylated to make fructose-1,6bisphosphate.

C

CHOH

4

Glyceraldehyde-3phosphate (× 2 )

Fructose-1,6bisphosphate is cleaved into dihydroxyacetone phosphate and glyceraldehyde3-phosphate.

Figure 7.3  A detailed look at the steps of glycolysis.  The pathway begins with a six-carbon molecule (glucose) that is broken down into two molecules that contain three carbons each. The notation x2 in the figure indicates that two of these three-carbon molecules are produced from each glucose molecule. Concept Check:  Which organic molecules donate a phosphate group to ADP during substrate-level phosphorylation? 



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P ROBLEM-SOLVING  S  TRATEGY  Sort out the steps in a complicated process. To solve this problem, it may be helpful to examine the process in a step-by-step manner to identify the key events.

ANSWER  First phase: During steps 1–3 of glycolysis, ATP is used to phosphorylate two different sites in the glucose molecule. This stage is called the energy investment phase because ATP is used to fuel the process. The energy investment phase prepares the ­glucose molecule for the next two phases. Second phase: During steps 4 and 5, glucose is cleaved into two three-carbon molecules, and then one of those is isomerized to glyceraldehyde-3-phosphate. This phase is called the cleavage phase because a six-carbon molecule is split (cleaved) into two three-carbon molecules. Third phase: During steps 6–10, ATP and NADH are made, molecules that are energy intermediates. ATP is made by substratelevel phosphorylation, in which a phosphate is removed from 1,3-bisphosphoglycerate or phosphoenolpyruvate and directly transferred to ADP. NADH is made when glyceraldehyde-3-phosphate is oxidized. This last phase is called the energy liberation phase because energy that was stored in organic molecules was released (liberated) and used to make energy intermediates (ATP and NADH).

Core Concept: Information The Overexpression of Certain Genes Causes Cancer Cells to Exhibit High Levels of Glycolysis In 1931, the German physiologist Otto Warburg discovered that certain cancer cells preferentially use glycolysis for ATP production, in contrast to healthy cells, which mainly generate ATP from oxidative phosphorylation. This phenomenon, termed the Warburg effect, is very common among different types of tumors. The Warburg effect is the basis for the detection of cancer via a procedure called positron-emission tomography (PET, see F ­ igure 2.6). In this technique, patients are injected with a radioactive glucose analogue called [18F]-fluorodeoxyglucose (FDG). FDG is taken up by cells that use high amounts of glucose, such as cancer cells. The scanner detects regions of the body that accumulate high amounts of FDG, which are visualized as bright spots on the PET scan. Figure 7.4 shows a PET scan of a patient with lung cancer. The bright regions that the arrows point at are tumors that show abnormally high levels of glycolysis. The tumors show up so well because the genome found in cancer cells exhibits an increased expression of genes that encode enzymes involved with glycolysis. Research has shown that the enzymes of glycolysis are overexpressed in approximately 80% of all types of cancer, including

Unstable phosphate bond 2 NAD+

2 NADH + 2 H+

2 ADP

P ~ OC

2 ATP

O

6

CH2O

–

O O

C

CHOH P

Phosphoglycero– kinase

1,3-bisphosphoglycerate (× 2 )

Glyceraldehyde-3phosphate is oxidized to 1,3-bisphosphoglycerate. NADH is produced. In 1,3-bisphosphoglycerate, the phosphate group in the upper left is destabilized, meaning that the bond will break in a highly exergonic reaction.

O– C

CHOH Glyceraldehyde3-phosphate 2 Pi dehydrogenase

Unstable phosphate bond

7

CH2O

P

Phosphoglycero– mutase

8

CH2OH

9

–

2 ADP

2 ATP

O

CO ~ P

P Enolase

2-phosphoglycerate (× 2 )

The phosphate group in 3-phosphoglycerate is moved to a new location, creating 2-phosphoglycerate.

O C

O

HCO

3-phosphoglycerate (× 2 )

A phosphate is removed from 1,3bisphosphoglycerate to form 3-phosphoglycerate. The removed phosphate is transferred to ADP to make ATP via substrate-level phosphorylation.

2 H2O

CH2

Pyruvate kinase

Phosphoenolpyruvate (× 2 )

A water molecule is removed from 2-phosphoglycerate to form phosphoenolpyruvate. In phosphoenolpyruvate, the phosphate group is destabilized, meaning that the bond will break in a highly exergonic reaction.

10

O

–

C

O

C

O

CH3

Pyruvate (× 2 )

A phosphate is removed from phosphoenolpyruvate to form pyruvate. The removed phosphate is transferred to ADP to make ATP via substrate-level phosphorylation.

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oxidative phosphorylation, which requires oxygen. Based on these findings, some current research is aimed at discovering drugs that inhibit glycolysis in cancer cells as a way to prevent their growth. metastases

7.3  Breakdown of Pyruvate Learning Outcome: 1. Describe how pyruvate is broken down and acetyl CoA is made.

Figure 7.4  A PET scan of a patient with lung cancer.  The bright regions in the lungs are tumors (indicated by the arrows). The brain, which is not cancerous in this patient, appears bright because it performs high levels of glucose metabolism. Also, the kidneys and bladder appear bright because they filter and accumulate FDG. (Note: FDG is taken up by cells and converted to FDG-phosphate by hexokinase, the first enzyme in glycolysis. However, because FDG lacks an —OH group, it is not metabolized further. Therefore, FDG-phosphate accumulates in cells that carry out glycolysis.) ©Steven Needell/Science Source

In eukaryotes, glycolysis produces pyruvate in the cytosol, which is then transported into the mitochondria. Once in the mitochondrial matrix, pyruvate molecules are broken down (oxidized) by an enzyme complex called pyruvate dehydrogenase (Figure 7.5). A molecule of CO2 is removed from pyruvate, and the remaining acetyl group is attached to an organic molecule called coenzyme A (CoA) to produce acetyl CoA. (In chemical equations, CoA is depicted as CoA−SH to emphasize how the −SH group participates in the chemical reaction.) During this process, two high-energy electrons are removed from pyruvate and transferred to NAD+, together with H+, to produce a molecule of NADH. For each pyruvate, the net reaction is as follows: O

O

O

CoA

SH + NAD+

O CoA

S

CH3 + CO2 + NADH

C

Acetyl CoA

Core Skill: Connections  Look back at Figure 2.6. Why is FDG radiolabeled? 

O– Pyruvate is made in the cytosol by glycolysis. It travels through a channel in the outer membrane and an H+/pyruvate symporter in the inner membrane to reach the mitochondrial matrix.

C O C O

lung, skin, colon, liver, pancreatic, breast, ovarian, and prostate cancers. The three enzymes of glycolysis whose overexpression is most commonly associated with cancer are glyceraldehyde3-phosphate dehydrogenase, enolase, and pyruvate kinase (shown in Figure 7.3). In many cancers, all 10 glycolytic enzymes are overexpressed! How does the overexpression of glycolytic enzymes affect tumor growth? While the genetic changes associated with tumor growth are complex, researchers have speculated that an increase in glycolysis favors the growth as a result of changes in oxygen levels. As a tumor grows, the internal regions of the tumor tend to become hypoxic, or deficient in oxygen. The hypoxic state inside a tumor may contribute to the overexpression of glycolytic genes and lead to a higher level of glycolytic enzymes within the cancer cells. This favors glycolysis as a means of making ATP, because glycolysis does not require oxygen. Making ATP via glycolysis is an advantage to cancer cells, because such cells would have trouble making ATP via

CH3 + CoA

C C Pyruvate

–

Outer membrane channel

CH3

O–

H+/pyruvate symporter

C O H+

C O CH3

+ CoA SH

+

NAD+

Pyruvate dehydrogenase S CoA C O + CO2 + NADH CH3 Acetyl CoA

Pyruvate is oxidized via pyruvate dehydrogenase to an acetyl group and CO2. NADH is made. During this process, the acetyl group is transferred to coenzyme A (CoA) and is later removed and enters the citric acid cycle.

Figure 7.5  Breakdown of pyruvate and the attachment of an acetyl group to CoA.



CELLULAR RESPIRATION AND FERMENTATION 151

The acetyl group is attached to CoA via a covalent bond to a sulfur atom. The hydrolysis of this bond releases a large amount of free energy, making it possible for the acetyl group to be transferred to other organic molecules. As described next, the acetyl group is removed from CoA and enters the citric acid cycle.

breakdown of carbohydrates to carbon dioxide. This cycle is called the citric acid cycle, or the Krebs cycle, in honor of Krebs, who was awarded the Nobel Prize in Physiology or ­Medicine in 1953. An overview of the citric acid cycle is shown in Figure 7.6. In the first step of the cycle, the acetyl group (with two carbons) is removed from acetyl CoA and attached to oxaloacetate (with four carbons) to form citrate (with six carbons), also called citric acid. Then, in a series of several steps, two CO2 molecules are released. As this occurs, three molecules of NADH, one molecule of FADH2, and one molecule of guanosine triphosphate (GTP) are made. The GTP, which is made via substrate-level phosphorylation, is used to make ATP. After a total of eight steps, oxaloacetate is regenerated, so the cycle can begin again, provided acetyl CoA is available. Figure 7.7 shows a more detailed view of the citric acid cycle. For each acetyl group attached to CoA, the net reaction of the citric acid cycle is as follows:

7.4  Citric Acid Cycle Learning Outcomes: 1. Explain the concept of a metabolic cycle. 2. Describe how an acetyl group enters the citric acid cycle, and list the net products of the cycle.

The third stage of glucose metabolism introduces a new concept, that of a metabolic cycle. During a metabolic cycle, particular molecules enter the cycle while others leave. The process is cyclical because it involves a series of organic molecules that are regenerated with each turn of the cycle. The idea of a metabolic cycle was first proposed in the early 1930s by German biochemist Hans Krebs. While studying carbohydrate metabolism in England, he analyzed cell extracts from pigeon muscle and determined that citric acid and other organic molecules participated in a cycle that resulted in the

Glycolysis: Glucose

Regulation of the Citric Acid Cycle  How is the citric acid cycle controlled? The rate of the cycle is largely regulated by the availability of substrates, such as acetyl-CoA and NAD+, and by feedback

2 NADH 2 FADH2

Citric acid cycle

2 CO2

Oxidative phosphorylation

2 CO2

Breakdown of pyruvate +2 ATP

CoA—SH  +  2 CO2  +  3 NADH  +  FADH2  +  GTP4–  +  3 H+

2 NADH 6 NADH

2 pyruvate

Acetyl-CoA  +  2 H2O + 3 NAD+  +  FAD  +  GDP2–  +  Pi2–→

NADH

CO2

2 CO2

Citrate

+30–34 ATP

+2 ATP

One turn of the cycle produces 2 molecules of CO2, 3 NADH, 1 FADH2, and 1 ATP.

NADH

C C C C C C

C C C C C C

CO2

3

2

C C C C C 4

1

O H3C C S CoA Acetyl CoA

C C

C C C C

Citric acid cycle

C C C C

5

Oxaloacetate 8 C C C C

7

NADH

6 C C C C

GTP

C C C C FADH2

Figure 7.6  Overview of the citric acid cycle. Concept Check:  What are the main products of the citric acid cycle? 

ATP

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2 1

The cycle begins when the acetyl group from acetyl CoA is attached to oxaloacetate to form citrate.

3

In a 2-step reaction, citrate is rearranged to an isomer called isocitrate. COO

Isocitrate is oxidized to α-ketoglutarate. CO2 is released and NADH is formed. COO–

–

CH2

CH2

HO

–

COO

HO

NADH

–

Isocitrate C C C C C C

COO–

C

C

CH COO

CH2

CH2 COO

S

CoA

C

O

CH3

2b

Citrate C C C C C C 2a

CO2

COO–

–

COO

α-Ketoglutarate C C C C C

NAD+

CH2

CoA—SH

α-Ketoglutarate dehydrogenase

+

CH2

NADH NAD+

4

Isocitrate dehydrogenase

Aconitase

α-Ketoglutarate is oxidized as it combines with CoA to form succinyl CoA. Once again, CO2 is released and NADH is formed.

O

3

–

CoA—SH

+

CH2

COO–

HC

4

C

O

S

CoA

CO2

Succinyl-CoA C C C C 5

GDP + Pi

+ H2O Citrate synthetase

Acetyl CoA C C

Citric acid cycle

ATP Succinyl-CoA synthetase

GTP ADP

Malate dehydrogenase

1 Oxaloacetate C C C C COO– O

C

NADH

NAD+

COO HO

Malate is oxidized to oxaloacetate. NADH is made. The cycle can begin again.

Succinate C C C C

H2O

–

CH

FADH2

Fumarate C C C C COO

5

COO–

7

Fumarate combines with water to make malate.

CH2 COO–

HC

COO –

CH2

FAD

–

CH

CH2

CoA—SH

COO–

7

Malate C C C C

COO–

6

Fumarase 8

CH2

8

Succinate dehydrogenase

6

Succinate is oxidized to fumarate. FADH2 is made.

Succinyl CoA is broken down to CoA and succinate. This exergonic reaction drives the synthesis of GTP, which can transfer its phosphate to ADP, thereby forming ATP.

Figure 7.7  A detailed look at the steps of the citric acid cycle.  The blue boxes indicate the location of the acetyl group, which is oxidized at step 6. (It is oxidized again in step 8.) The green boxes indicate the locations where CO2 molecules are removed. Core Concept: Systems  A metabolic cycle, such as the citric acid cycle, can be viewed as a small system. This system oxidizes organic molecules and produces 3 NADH, 1 FADH2, 1 ATP, and 2 CO2.



CELLULAR RESPIRATION AND FERMENTATION 153

inhibition. The three steps in the cycle that are highly exergonic are those catalyzed by citrate synthase, isocitrate dehydrogenase, and α-ketoglutarate dehydrogenase (see Figure 7.7). Each of these steps is rate-limiting under certain circumstances, and the way that each enzyme is regulated varies among different species. Let’s consider an example. In mammals, NADH and ATP act as feedback inhibitors of isocitrate dehydrogenase, whereas NAD+ and ADP act as activators. In this way, the citric acid cycle is inhibited when NADH and ATP levels are high, but it is stimulated when NAD+ and ADP levels are high.

7.5  O  verview of Oxidative Phosphorylation Learning Outcomes: 1. Describe how the electron transport chain produces an H+ electrochemical gradient. 2. Explain how ATP synthase utilizes the H+ electrochemical gradient to synthesize ATP.

During the first three stages of glucose metabolism, the oxidation of glucose yields 6 molecules of CO2, 4 molecules of ATP, 10 molecules of NADH, and 2 molecules of FADH2. Let’s now consider how highenergy electrons are removed from NADH and FADH2 to produce more ATP. This process is called oxidative phosphorylation. As mentioned earlier, the term refers to the observation that electrons are removed from NADH and FADH2, that is, these molecules are oxidized, and ATP is made by the phosphorylation of ADP. In this section, we will examine how the oxidative process involves the electron transport chain, whereas the phosphorylation of ADP occurs via ATP synthase.

The Electron Transport Chain Establishes an Electrochemical Gradient The electron transport chain (ETC) consists of a group of protein complexes and small organic molecules embedded in the inner mitochondrial membrane. These components are referred to as an electron transport chain because electrons are passed from one component to the next in a series of redox reactions (Figure 7.8). Most members of the ETC are protein complexes (designated I–IV in the figure) that have prosthetic groups, which are small molecules permanently attached to the surface of proteins that aid in their function. For example, cytochrome oxidase contains two prosthetic groups, each with an iron atom. The iron in each prosthetic group can readily accept and release an electron. One member of the ETC, ubiquinone (Q), is not a protein. Rather, ubiquinone is a small organic molecule that can accept and release an electron. The red line in Figure 7.8 shows the path of electron flow. The electrons, which are originally found in NADH or FADH 2, are transferred to components of the ETC. The electron path is

a series of redox reactions in which electrons are transferred to components with increasingly higher electronegativity. At the end of the chain is oxygen, which is the most electronegative component and the final electron acceptor. The ETC is also called the respiratory chain because the oxygen we breathe is used in this process. NADH and FADH2 donate their electrons at different points in the ETC. Two high-energy electrons from NADH are first transferred one at a time to NADH dehydrogenase (complex I). They are then transferred to ubiquinone (Q), cytochrome b-c1 (complex III), cytochrome c, and cytochrome oxidase (complex IV). The final electron acceptor is O2. By comparison, FADH2 transfers electrons to succinate reductase (complex II), then to ubiquinone, and the rest of the chain. As shown in Figure 7.8, some of the energy that is released during the movement of electrons is used to pump H+ across the inner mitochondrial membrane into the intermembrane space. This active transport establishes a large H+ electrochemical gradient, in which the concentration of H+ is higher outside of the mitochondrial matrix than inside and an excess of positive charge exists outside the matrix. Chemicals that inhibit the flow of electrons along the ETC have lethal effects. For example, one component of the ETC, cytochrome oxidase (complex IV), is inhibited by cyanide. The deadly effects of cyanide ingestion occur because the ETC is shut down, preventing cells from making enough ATP for survival.

ATP Synthase Makes ATP via Chemiosmosis The second event of oxidative phosphorylation is the synthesis of ATP by an enzyme called ATP synthase. The H+ electrochemical gradient across the inner mitochondrial membrane is a source of potential energy. How is this energy used? The passive flow of H+ back into the matrix is an exergonic process. The lipid bilayer is relatively impermeable to H+. However, H+ can pass through the membraneembedded portion of ATP synthase. This enzyme harnesses some of the free energy that is released as the H+ ions flow through its membrane-embedded region to synthesize ATP from ADP and Pi (see bottom of Figure 7.8). This is an example of an energy conversion: Energy in the form of an H+ gradient is converted to chemical potential energy in ATP. The synthesis of ATP that occurs as a result of pushing H+ across a membrane is called chemiosmosis (from the Greek osmos, meaning to push). The theory behind it was proposed by Peter Mitchell, a British biochemist who was awarded the Nobel Prize in Chemistry in 1978. Regulation of Oxidative Phosphorylation  How is oxidative phosphorylation controlled? This process is regulated by a variety of factors, including the availability of ETC substrates, such as NADH and O2, and by the ATP/ADP ratio. When ATP levels are high, ATP binds to a subunit of cytochrome oxidase (complex IV), thereby inhibiting the ETC and oxidative phosphorylation. By comparison, when ADP levels are high, oxidative phosphorylation is

154

CHAPTER 7

KEY Matrix

1a NADH is oxidized to NAD+. High-

energy electrons are transferred to NADH dehydrogenase. Some of the energy is harnessed to pump H+ into the intermembrane space. Electrons are then transferred to ubiquinone.

1b FADH2 is oxidized to FAD. High-energy

NADH dehydrogenase

NADH NAD+

H+ movement e– movement

Intermembrane space

+

I

H+

H+

H+

H+

Succinate reductase

electrons are transferred to succinate reductase and then to ubiquinone.

Q

FADH2

Ubiquinone

Electron transport chain

H+

II

H+

H+

FAD + 2 H+ Cytochrome b-c1

2

3

From ubiquinone, electrons travel to cytochrome b-c1. Some of the energy is harnessed to pump H+ into the intermembrane space. Electrons are transferred to cytochrome c.

From cytochrome c, electrons are transferred to cytochrome oxidase. Some of the energy is harnessed to pump H+ into the intermembrane space. Electrons are transferred to oxygen, and water is produced.

III

H+ H+

Matrix c

2 H+ + 1/2 O2 IV

Cytochrome c

H+

H+

Cytochrome oxidase H+

H+

H2O H+ H+ H+

4

Steps 1–3 produce an H+ electrochemical gradient. As H+ flow down their electrochemical gradient into the matrix through ATP synthase, the energy within this gradient causes the synthesis of ATP from ADP and Pi.

H+ ADP + Pi

ATP

H+

ATP synthase

Inner mitochondrial membrane

Intermembrane space

Figure 7.8  Oxidative phosphorylation.  This process consists of two distinct events: the electron transport chain (ETC) and ATP synthesis. The

ETC oxidizes, or removes electrons from, NADH or FADH2 and pumps H+ across the inner mitochondrial membrane. In chemiosmosis, ATP synthase uses the energy in this H+ electrochemical gradient to phosphorylate ADP, thereby synthesizing ATP. In this figure, an oxygen atom is represented as 1/2 O2 to emphasize that the ETC reduces oxygen when it is in its molecular (O2) form. Concept Check:  Explain the meaning of the name cytochrome oxidase. 



CELLULAR RESPIRATION AND FERMENTATION 155

stimulated for two reasons: (1) ADP stimulates cytochrome oxidase, and (2) ADP is a substrate that is used (with Pi) to make ATP.

For each molecule of NADH that is oxidized and each molecule of ATP that is made, the two chemical reactions of oxidative phosphorylation can be represented as follows: NADH  +  H+  +  1⁄2 O2  →  NAD+  +  H2O ADP2–  +  Pi2–  →  ATP4–  +  H2O When we add up the maximal amount of ATP that can be made by oxidative phosphorylation, most researchers agree it is in the range of 30–34 ATP molecules for each glucose molecule that is broken down to CO2 and H2O. However, that maximal amount of ATP is rarely achieved, for two reasons. ∙ First, although 10 NADH and 2 FADH2 are available to make the H+ electrochemical gradient across the inner mitochondrial membrane, a cell uses some of these molecules for anabolic pathways. For example, NADH is used in the synthesis of organic molecules such as glycerol (a component of phospholipids). ∙ Second, the mitochondrion may use some of the energy in the H+ electrochemical gradient for other purposes. For example, the gradient is used for the uptake of pyruvate into the matrix via an H+/pyruvate symporter (see Figure 7.5). Therefore, the actual amount of ATP synthesized is usually a little less than the maximum of 30 to 34 molecules. Even so, when we compare the amount of ATP that is made by glycolysis (2), the citric acid cycle (2), and oxidative phosphorylation (30–34), we see that oxidative phosphorylation provides a cell with a much greater capacity to make ATP.

Free-Energy Changes Drive Oxidative Phosphorylation and Other Stages of Glucose Breakdown Thus far, we have considered (1) glycolysis, (2) the breakdown of pyruvate, (3) the citric acid cycle, and (4) oxidative phosphorylation. All four of these stages are ultimately driven by the oxidation of glucose, which is a highly exergonic process that releases free energy. However, the energy is not released in one big blast, as in an explosion, but rather in small step-wise increments. Releasing the energy in small increments allows cells to couple the breakdown of glucose with useful chemical processes. For example, as we saw earlier in this chapter, the breakdown of glucose to pyruvate is coupled to the synthesis of ATP. Figure 7.9 shows how free energy is released as electrons move along the electron transport chain. At particular points along the ETC, some of the energy is used to pump H+ across the inner mitochondrial membrane and establish an H+ electrochemical gradient. This gradient is then used to power ATP synthesis.

NAD+

Free energy per electron (kcal/mol)

NADH Oxidation Makes a Large Proportion of a Cell’s ATP

NADH

25

20

H+ NADH dehydrogenase H+

I

Q Ubiquinone

Cytochrome b-c1

III

15

c Cytochrome c

10

Cytochrome oxidase

H+

IV

5

0

2 H+ + 1/2 O2

H2O

Direction of electron flow

Figure 7.9  The relationship between free energy and electron

movement along the electron transport chain.  As electrons are transferred from one site to another along the electron transport chain, they release energy. Some of this energy is harnessed to pump H+ across the inner mitochondrial membrane. The total energy released by a single electron is approximately −25 kcal/mol.

7.6  A Closer Look at ATP Synthase Learning Outcomes: 1. CoreSKILL » Analyze the results of an experiment that verified that ATP synthase uses an H+ electrochemical gradient to make ATP. 2. Describe the structure of ATP synthase. 3. Explain how a series of three conformational changes enables ATP synthase to make ATP. 4. CoreSKILL » Analyze the results of an experiment that showed that ATP synthase is a rotary machine.

The structure and function of ATP synthase are particularly intriguing and have received much attention over the past few decades. In this section, we will consider experiments that were aimed at elucidating this enzyme’s function and explore, in greater depth, how it is able to synthesize ATP.

Experiments with Purified Proteins in Membrane Vesicles Verified Chemiosmosis To show experimentally that ATP synthase makes ATP using an H+ electrochemical gradient, researchers needed to purify the enzyme and study its function in vitro. In 1974, Efraim Racker and Walther Stoeckenius purified ATP synthase and another protein called bacteriorhodopsin, which is found in certain species of archaea. Previous research had shown that bacteriorhodopsin is a light-driven H+ pump. Racker and Stoeckenius took both purified proteins and experimentally inserted them into membrane vesicles, a process called reconstitution (Figure 7.10). ATP synthase was oriented so its ATP-synthesizing region was on the outside of the

156

1

CHAPTER 7

ATP synthase and bacteriorhodopsin were incorporated into membrane vesicles.

ATP synthase Vesicle

Bacteriorhodopsin (light-driven H+ pump)

2

ADP and Pi were added on the outside of the vesicles.

ADP Pi

The nonmembraneembedded portion consists of 1 ε, 1 γ, 1 δ, 3 α, and 3 β subunits. Movement of H+ between a c subunit and the a subunit causes the γ subunit to rotate. The rotation, in 120° increments, causes the β subunits to progress through a series of 3 conformational changes that lead to the synthesis of ATP from ADP and Pi.

ADP + Pi

δ α

3a

One sample was kept in the dark. No ATP was made.

H+

γ c

b

α

β

ε c

The membrane-embedded portion consists of a ring of 9–12 c subunits, 1 a subunit, and 2 b subunits. H+ move between the c and a subunits.

ATP

Matrix

c

Intermembrane space

a

H+

Figure 7.11  The subunit structure and function of ATP synthase.

3b One sample was exposed to light. ATP was made. Light rays

No H

+ gradient

H+ gradient

ATP

Figure 7.10  The Racker and Stoeckenius experiment.  In this

experiment, bacteriorhodopsin pumped H+ into vesicles, and the resulting H+ electrochemical gradient was sufficient to drive ATP synthesis via ATP synthase.

Concept Check:  Is the functioning of the electron transport chain always needed to make ATP via ATP synthase? 

vesicles. Bacteriorhodopsin was oriented so it would pump H+ into the vesicles. The researchers added ADP and Pi on the outside of the vesicles. In the dark, no ATP was made. However, when they shone light on the vesicles, a substantial amount of ATP was synthesized. Because bacteriorhodopsin was already known to be a light-driven H+ pump, these results convinced the researchers that ATP synthase uses an H+ electrochemical gradient as an energy source to make ATP.

ATP Synthase Is a Rotary Machine That Makes ATP as It Spins ATP synthase is a rotary machine ( Figure 7.11). It spins! The region embedded in the membrane is composed of three types of subunits called a, b, and c. Approximately 10–14 c subunits form a ring in the membrane. One a subunit is bound to this ring, and

two b subunits are attached to the a subunit and protrude from the membrane. The nonmembrane-embedded subunits are designated with Greek letters. One ε and one γ subunit bind to the ring of c subunits. The γ subunit forms a long stalk that pokes into the center of another ring of three α and three β subunits. Each β subunit contains a catalytic site where ATP is made. Finally, the δ subunit forms a connection between the ring of α and β subunits and the two b subunits. When hydrogen ions pass through a narrow channel at the contact site between a c subunit and the a subunit, a conformational change causes the γ subunit to turn clockwise (when viewed from the intermembrane space). Each time the γ subunit turns 120°, it changes its contacts with the three β subunits, which, in turn, causes the β subunits to change their conformations. How do these conformational changes promote ATP synthesis? The answer is that the conformational changes occur in a way that favors ATP synthesis and release. As shown in Figure 7.12, the conformational changes in the β subunits happen in the following order: ∙ Conformation 1: ADP and Pi bind with good affinity. ∙ Conformation 2: ADP and Pi bind very tightly, which strains chemical bonds so that ATP is made. ∙ Conformation 3: ATP binds very weakly and is released. Each time the γ subunit turns 120°, it causes a β subunit to change to the next conformation. After conformation 3, a 120° turn by the γ subunit returns a β subunit back to conformation 1, and the cycle of ATP synthesis can begin again. Because ATP synthase has three β subunits, each subunit is in a different conformation at any given time. American biochemist Paul Boyer proposed the concept of a rotary machine in the late 1970s. In his model, the three β subunits alternate between three conformations, as described previously. Boyer’s



CELLULAR RESPIRATION AND FERMENTATION 157

Conformation 2: ADP and Pi bind so tightly that ATP is made.

Conformation 1: ADP and Pi bind with good affinity.

Conformation 3: ATP binds very weakly and is released.

ATP β Subunit

ATP

ADP + Pi 1 2

γ

3

3

2

β Subunit Rotation of the γ subunit

3

γ

1

Rotation of the γ subunit

1

γ

2

Figure 7.12  Conformational

changes that result in ATP synthesis.  For simplicity, the α subunits are not shown. This drawing emphasizes the conformational changes in the β subunit shown at the top. The other two β subunits also make ATP. All three β subunits alternate between three conformational states due to their interactions with the γ subunit.

β Subunit Rotation of the γ subunit

Core Skill: Modeling  The goal of this modeling challenge is to predict how a mutation in the β subunit of ATP synthase would affect ATP synthesis.

original idea was met with great skepticism, because the concept that part of an enzyme could spin was very novel, to say the least. In 1994, British biochemist John Walker and his colleagues determined the three-dimensional structure of the nonmembrane-embedded portion of the ATP synthase. The structure revealed that each of the three β subunits had a different conformation—one with ADP bound, one with ATP bound, and one without any nucleotide bound. This result supported Boyer’s model. In 1997, Boyer and Walker shared the Nobel Prize in Chemistry for their work on ATP synthase. As described next in the Feature Investigation, other researchers subsequently visualized the rotation of the γ subunit.

Modeling Challenge: Let’s suppose a 3 researcher has identified a mutation in the γ β subunit that only affects conformation 3. A 1 2 model that depicts the shape of the mutant β subunit is shown to the right. Look very carefully at the shape of the mutant subunit in Mutant β subunit conformation 3 and compare it to the normal β subunit in that conformation, as shown in Figure 7.12. Predict how this mutant subunit would affect ATP synthesis.

Core Skill: Process of Science

Feature Investigation  | Yoshida and Kinosita Demonstrated That the γ Subunit of ATP Synthase Spins

In 1997, Japanese biochemist Masasuke Yoshida, biophysicist Kazuhiko Kinosita, and colleagues set out to experimentally visualize the rotary nature of ATP synthase (Figure 7.13). The membraneembedded region of ATP synthase can be separated from the rest of the protein by treating mitochondrial membranes with a high concentration of salt, releasing the portion of the protein containing one γ, three α, and three β subunits. The researchers adhered the γα3β3 complex to a glass slide so that the γ subunit was protruding upward. Because the γ subunit is too small to be seen with a light microscope, the rotation of this subunit cannot be visualized directly. To overcome this problem, the researchers attached a long, fluorescently labeled actin filament to the γ subunit via linker proteins. The fluorescently labeled actin filament is very long compared to the γ subunit and can be readily seen with a fluorescence microscope. Because the membrane-embedded portion of the protein was missing, you may be wondering how the researchers could get the γ subunit to rotate. The answer is that they added ATP. Although the normal function of ATP synthase is to make ATP, it can also hydrolyze ATP. In other words, ATP synthase can run backward. As shown in the data

in Figure 7.13, when the researchers added ATP, they observed that the fluorescently labeled actin filament rotated in a counterclockwise direction, which is opposite to the direction that the γ subunit rotates when ATP is synthesized. Actin filaments were observed to rotate for more than 100 revolutions in the presence of ATP. These results convinced the scientific community that ATP synthase is a rotary machine. Experimental Questions 1. CoreSKILL » The components of ATP synthase are too small to be visualized by light microscopy. For the experiment of Figure 7.13, how did the researchers observe the movement of ATP synthase?  2. CoreSKILL » In the experiment of Figure 7.13, what observation indicated to the researchers that ATP synthase is a rotary machine? What was the control of this experiment? What did it indicate?  3. CoreSKILL » Were the rotations seen by the researchers in the data of Figure 7.13 in the same direction as they are expected to occur in mitochondria during ATP synthesis? Why or why not? 

Figure 7.13  Yoshida and Kinosita provide evidence that ATP synthase is a rotary machine.  (5): From Noji, H., Yoshida, M. 2001. The Rotary Machine in the Cell, ATP Synthase. Journal of Biological Chemistry 276: 1665–1668. ©2001 The American Society for Biochemistry and Molecular Biology

HYPOTHESIS ATP synthase is a rotary machine. KEY MATERIALS Purified complex containing 1 γ, 3 α, and 3 β subunits. Experimental level

1

Adhere the purified γα3 β3 complex to a glass slide so the base of the γ subunit is protruding upward.

Conceptual level

Add purified complex.

γ α

β

γα3 β3 complex α

Slide

2

3

4

Add linker proteins and fluorescently labeled actin filaments. The linker protein recognizes sites on both the γ subunit and the actin filament.

Add linker proteins and fluorescent actin filaments.

Add ATP. As a control, do not add ATP.

γ α

Add ATP

Fluorescent actin filament

α

Control: No ATP

Observe under a fluorescence microscope. The method of fluorescence microscopy is described in Figure 4.6.

γ Fluorescence microscope

5

β

Linker proteins

α

β

α

+ ATP: counterclockwise rotation

THE DATA Results from step 4: ATP

Rotation

No ATP added

No rotation observed.

ATP added

Rotation was observed as shown below. This is a time-lapse view of the rotation in action.

Row 1

Row 2

6

CONCLUSION The γ subunit rotates counterclockwise when ATP is hydrolyzed. It would be expected to rotate clockwise when ATP is synthesized.

Row 2



CELLULAR RESPIRATION AND FERMENTATION 159

6

CONCLUSION The γ subunit rotates counterclockwise when ATP is hydrolyzed. It would be expected to rotate clockwise when ATP is synthesized.

7

SOURCE Noji, H., Yoshida, M. 2001. The rotary machine in the cell, ATP synthase. Journal of Biological Chemistry 276: 1665–1668.

7.7  C  onnections Among Carbohydrate, Protein, and Fat Metabolism Learning Outcome: 1. Explain how carbohydrate, protein, and fat metabolism are interconnected.

Proteins Amino acids

Carbohydrates

Fats

Sugars

Glycerol Fatty acids

Glycolysis: Glucose Glyceraldehyde3-phosphate Pyruvate

Acetyl CoA

Citric acid cycle

Oxidative phosphorylation

Figure 7.14  Integration of carbohydrate, protein, and fat

metabolism.  Breakdown products of proteins and fats are used as fuel for cellular respiration, entering the same pathways used to break down carbohydrates. ©Ernie Friedlander/Cole Group/Getty Images Concept Check:   What advantage does integrating protein, carbohydrate, and fat metabolism have for cells? 

When you eat a meal, it usually contains not only carbohydrates (including glucose), but also proteins and fats. These molecules are broken down by some of the same enzymes involved with glucose metabolism. The use of the same pathways for the breakdown of sugars, amino acids, and fats makes cellular metabolism more efficient because the same enzymes are used for the breakdown of different starting molecules. As shown in Figure 7.14, proteins and fats can enter glycolysis or the citric acid cycle at different points. ∙ Proteins are first acted on by enzymes, either in digestive juices or within cells, that cleave the bonds connecting individual amino acids. Because the 20 amino acids differ in their side chains, amino acids and their breakdown products can enter at different points in the pathway. Breakdown products of some amino acids can enter at later steps of glycolysis, or an acetyl group can be removed from certain amino acids and become attached to CoA and then enter the citric acid cycle (see Figure 7.14). Other amino acids are modified and enter the citric acid cycle. ∙ Fats are typically broken down to glycerol and fatty acids. Glycerol can be modified to glyceraldehyde-3-phosphate and enter glycolysis. Lipid tails can have two carbon acetyl units removed, which bind to CoA and enter the citric acid cycle.

7.8  A  naerobic Respiration and Fermentation Learning Outcomes: 1. Describe how certain microorganisms make ATP using a final electron acceptor in the electron transport chain that is not oxygen. 2. Explain how muscle and yeast cells use fermentation to synthesize ATP under anaerobic conditions.

Thus far, we have surveyed catabolic pathways that result in the complete breakdown of glucose in the presence of oxygen. Cells also commonly metabolize organic molecules in the absence of oxygen. The term anaerobic is used to describe an environment that lacks oxygen. Many bacteria and archaea and some fungi exist in anaerobic

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environments but still have to oxidize organic molecules to obtain sufficient amounts of energy. Examples include microbes living in your intestinal tract and those living deep in the soil. Similarly, when a person exercises strenuously, the rate of oxygen consumption by muscle cells may greatly exceed the rate of oxygen delivery—particularly at the start of the strenuous exercise. Under these conditions, muscle cells become anaerobic and must obtain sufficient energy in the absence of oxygen to maintain their level of activity. Two different strategies may be used by cells to metabolize organic molecules in the absence of oxygen. One mechanism is to use a substance other than O2 as the final electron acceptor of the electron transport chain, a process called anaerobic respiration. A second approach is to produce ATP via substrate-level phosphorylation only, without any net oxidation of organic molecules, a process called fermentation. In this section, we will consider examples of both strategies.

Some Microorganisms Carry Out Anaerobic Respiration At the end of the ETC, as shown earlier in Figure 7.8, cytochrome oxidase recognizes O2 and catalyzes its reduction to H2O. The final electron acceptor of the chain is O2. Many species of bacteria that live under anaerobic conditions have evolved enzymes that function similarly to cytochrome oxidase but recognize molecules other than O2 and use them as the final electron acceptor. For example, under anaerobic conditions Escherichia coli, a bacterial species found in your intestinal tract, produces an enzyme called nitrate reductase. This enzyme uses nitrate (NO3–) as the final electron acceptor of the electron transport chain. Figure 7.15 shows a simplified ETC in E. coli in which nitrate is the final electron acceptor. In E. coli and other bacterial species, the ETC is in the plasma membrane that surrounds the cytoplasm. Electrons travel from NADH to NADH dehydrogenase to ubiquinone to cytochrome b and then to nitrate reductase. At the end of the chain, NO3– is converted to nitrite (NO2–). This process generates an H+ electrochemical gradient in three ways. First, NADH dehydrogenase pumps H+ out of the cytoplasm. Second, ubiquinone picks up H+ in the cytoplasm and carries it to the other side of the membrane. Third, the reduction of nitrate to nitrite consumes H+ in the cytoplasm. The generation of an H+ electrochemical gradient via these three processes allows E. coli cells to make ATP via chemiosmosis under anaerobic conditions.

Fermentation Is the Breakdown of Organic Molecules Without Net Oxidation Many organisms, including animals and yeast, use only O2 as the final electron acceptor of their ETCs. When confronted with anaerobic conditions, these organisms must have a different way of producing sufficient ATP. One strategy is to make ATP via glycolysis, which can occur under either anaerobic or aerobic conditions. Under anaerobic conditions, cells do not use the citric acid cycle or the ETC, but make ATP only via glycolysis. A key issue is that glycolysis requires NAD+ and generates NADH. Under aerobic conditions, NADH is oxidized to NAD+ to make more ATP. However, this cannot occur under anaerobic

KEY NADH dehydrogenase NADH

H+ movement e– movement

H+ H+ Ubiquinone

NAD++ H+

H+ H+

Cytochrome b

Cytoplasm

H+ –

NO3 +

2 H+

H+

Nitrate reductase H+

NO2– + H2O H+ ADP + Pi

ATP synthase

H+

H+

ATP

Figure 7.15  An example of anaerobic respiration in E. coli.  When oxygen is absent, E. coli can use nitrate instead of oxygen as the final electron acceptor of the electron transport chain. This generates an H+ electrochemical gradient that is used to make ATP via chemiosmosis. Note: As shown in this figure, ubiquinone picks up H+ on one side of the membrane and deposits it on the other side. A similar event happens during aerobic respiration in mitochondria (see Figure 7.8), except that ubiquinone transfers H+ to cytochrome b-c1, which pumps it into the intermembrane space. conditions in yeast and animals, and, as a result, NADH builds up and NAD+ decreases. This is a potential problem for two reasons: ∙ First, at high concentrations, NADH haphazardly donates its electrons to other molecules and promotes the formation of free radicals, highly reactive chemicals that damage DNA and cellular proteins. For this reason, yeast and animal cells exposed to anaerobic conditions must have a way to remove the excess NADH generated from the breakdown of glucose. ∙ The second problem is the decrease in NAD+. Cells need to regenerate NAD+ to keep glycolysis running and make ATP via substrate-level phosphorylation. Fermentation in Muscle Cells  How do muscle cells cope with the buildup of NADH and accompanying decrease in NAD+? When a muscle cell is working strenuously and its environment becomes anaerobic, as in high-intensity exercise, the pyruvate from glycolysis is reduced to make lactate. (The uncharged, or protonated, form is called lactic acid.) The electrons to reduce pyruvate are derived from NADH, which is oxidized to NAD+ (Figure 7.16a). Therefore, this process decreases NADH and reduces its potentially harmful effects. It also increases the level of NAD+, thereby allowing glycolysis to continue. The lactate is secreted from muscle cells. Once sufficient oxygen is restored, the



CELLULAR RESPIRATION AND FERMENTATION 161

Glucose is oxidized to 2 pyruvate molecules. Two pyruvates are reduced to 2 lactate molecules.

2 ADP+ 2 Pi

2 ATP

Glucose is oxidized to 2 pyruvate molecules. Two acetaldehyde molecules are reduced to 2 ethanol molecules.

O–

2 ADP+ 2 Pi

2 ATP

C O

C O Glucose

C O

Glycolysis

Glucose

CH3

C O

Glycolysis

CH3 2 pyruvate

2 pyruvate 2 NAD+ + 2 H+

O–

2 NAD+ + 2 H+

2 NADH

C OH

H

CH3 2H 2 lactate (secreted from the cell) +

(a) Production of lactic acid

2 CO2

2 NADH

H

C O H

O–

H

C OH

C O

CH3 2H 2 ethanol (secreted from the cell) +

CH3 2 acetaldehyde

(b) Production of ethanol

Figure 7.16  Examples of fermentation.  In these examples, NADH is produced by the oxidation of an organic molecule, and then the NADH is

converted back to NAD+ when it donates electrons to a different organic molecule such as pyruvate (a) or acetaldehyde (b). a: ©Homer W Sykes/ Alamy Stock Photo; b: ©FreeProd/Alamy Stock Photo Core Skill: Science and Society  Fermentation by microorganisms is used in wine making, beer brewing, and bread making.

lactate produced during strenuous exercise can be taken up by cells, converted back to pyruvate, and used for energy, or this lactate may be used by the liver and other tissues to make glucose. Fermentation in Yeast Cells  Yeast cells cope with anaerobic conditions differently. During wine making, a yeast cell metabolizes sugar under anaerobic conditions. The pyruvate is broken down to CO2 and a two-carbon molecule called acetaldehyde. The acetaldehyde is then reduced by NADH to make ethanol, while NADH is oxidized to NAD+ (Figure 7.16b). Similar to lactate production in muscle cells, this process decreases NADH and increases NAD+, thereby preventing the harmful effects of NADH and allowing glycolysis to continue. The term fermentation is used to describe the breakdown of organic molecules to harness energy without any net oxidation (that is, without any removal of electrons). The pathways for breaking down glucose to lactate or ethanol are examples of fermentation. Although electrons are removed from an organic molecule such as glucose to make pyruvate and NADH, the electrons are donated back to an organic molecule in the production of lactate or ethanol. Therefore, there is no net removal of electrons from an organic molecule. Compared with oxidative phosphorylation, fermentation produces far less ATP, for two reasons. First, glucose is not oxidized completely to CO2 and H2O. Second, the NADH

made during glycolysis cannot be used to make more ATP. Overall, the complete breakdown of glucose in the presence of oxygen yields 34–38 ATP molecules. By comparison, the anaerobic breakdown of glucose to lactate or ethanol yields only 2 ATP molecules.

Summary of Key Concepts 7.1  Overview of Cellular Respiration ∙∙ Cells obtain energy via cellular respiration, which involves the breakdown of organic molecules and the export of waste products. ∙∙ The breakdown of glucose occurs in four stages: glycolysis, pyruvate breakdown, citric acid cycle, and oxidative phosphorylation (Figure 7.1).

7.2  Glycolysis ∙∙ During glycolysis, which occurs in the cytosol, glucose is split into two molecules of pyruvate, with a net yield of two ATP and two NADH. The ATP is made by substrate-level phosphorylation (Figures 7.2, 7.3). ∙∙ Cancer cells exhibit high levels of glycolysis, which enables the detection of tumors via a procedure called positron-emission tomography (PET) (Figure 7.4).

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7.3  Breakdown of Pyruvate ∙∙ Pyruvate is broken down to CO2 and an acetyl group that becomes attached to CoA. NADH is made during this process (Figure 7.5).

7.4  Citric Acid Cycle ∙∙ During the citric acid cycle, an acetyl group is removed from acetyl CoA and attached to oxaloacetate to make citrate. In a series of steps, two CO2 molecules, three NADH, one FADH2, and one ATP are made, after which the cycle begins again (Figures 7.6, 7.7).

7.5  Overview of Oxidative Phosphorylation ∙∙ Oxidative phosphorylation involves two events: (1) The electron transport chain (ETC) oxidizes NADH or FADH2 and generates an H+ electrochemical gradient, and (2) this gradient is used by ATP synthase to make ATP via chemiosmosis (Figures 7.8, 7.9).

7.6  A Closer Look at ATP Synthase ∙∙ Racker and Stoeckenius showed that ATP synthase uses an H+ gradient to make ATP by reconstituting ATP synthase with a lightdriven H+ pump (Figure 7.10). ∙∙ ATP synthase is a rotary machine. The rotation is triggered by the passage of H+ through a channel between a c subunit and the a subunit, which causes the γ subunit to spin, resulting in three conformational changes in the β subunits that promote ATP synthesis (Figures 7.11, 7.12). ∙∙ Yoshida and Kinosita demonstrated rotation of the γ subunit of ATP synthase by attaching a fluorescently labeled actin filament and observing its movement during the hydrolysis of ATP (Figure 7.13).

7.7  C  onnections Among Carbohydrate, Protein, and Fat Metabolism ∙∙ Proteins and fats can enter into glycolysis or the citric acid cycle at different points (Figure 7.14).

7.8  Anaerobic Respiration and Fermentation ∙∙ Anaerobic respiration occurs in the absence of oxygen. Certain microorganisms carry out anaerobic respiration by using as the final electron acceptor of the ETC a substance other than oxygen, such as nitrate (Figure 7.15). ∙∙ During fermentation, organic molecules are broken down without any net oxidation (that is, without any net removal of electrons). Examples include lactic acid production in muscle cells and ethanol production in yeast cells (Figure 7.16).

Assess & Discuss Test Yourself 1. Which of the following pathways occurs in the cytosol? a. glycolysis b. breakdown of pyruvate to an acetyl group c. citric acid cycle d. oxidative phosphorylation e. all of the above

2. The net products of glycolysis are a. 6 CO2, 4 ATP, and 2 NADH. b. 2 pyruvate, 2 ATP, and 2 NADH. c. 2 pyruvate, 4 ATP, and 2 NADH. d. 2 pyruvate, 2 GTP, and 2 CO2. e. 2 CO2, 2 ATP, and glucose. 3. During glycolysis, ATP is produced by a. oxidative phosphorylation. b. substrate-level phosphorylation. c. redox reactions. d. all of the above. e. both a and b. 4. Which organic molecule supplies a two-carbon group to start the citric acid cycle? a. ATP b. NADH c. acetyl CoA d. oxaloacetate e. both a and b 5. The ability to diagnose tumors using [18F]-fluorodeoxyglucose (FDG) is based on the phenomenon that most types of cancer cells exhibit higher levels of a. glycolysis. b. pyruvate breakdown. c. citric acid metabolism. d. oxidative phosphorylation. e. all of the above. 6. In the experiment of Racker and Stoeckenius, bacteriorhodopsin was oriented in such a way that it pumped H+ into a vesicle. Each vesicle actually contained many molecules of bacteriorhodopsin. How would the results of the experiment have been affected if 50% of the bacteriorhodopsin molecules pumped H+ into the vesicle and 50% pumped H+ out of the vesicles? a. The same amount of ATP would be made in the presence of light, and no ATP would be made in the dark. b. More ATP would be made in the presence of light, and no ATP would be made in the dark. c. No ATP would be made in the presence of light, and no ATP would be made in the dark. d. No ATP would be made in the presence of light, but some ATP would be made in the dark. e. Some ATP would be made in the presence of light, and some ATP would be made in the dark. 7. Certain drugs, which are called ionophores, cause the mitochondrial membrane to be highly permeable to H+. How would such drugs affect oxidative phosphorylation? a. Movement of electrons down the ETC would be inhibited. b. ATP synthesis would be inhibited. c. ATP synthesis would be unaffected. d. ATP synthesis would be stimulated. e. Both a and b would occur. 8. The source of energy that directly drives the synthesis of ATP during oxidative phosphorylation is the a. oxidation of NADH. b. oxidation of glucose. c. oxidation of pyruvate. d. H+ electrochemical gradient. e. reduction of O2.



CELLULAR RESPIRATION AND FERMENTATION 163

9. Compared with oxidative phosphorylation in mitochondria, anaerobic respiration in bacteria differs in that a. more ATP is made. b. ATP is made only via substrate-level phosphorylation. c. O2 is converted to H2O2 rather than H2O. d. something other than O2 acts as a final electron acceptor of the ETC. e. both b and d occur. 10. When conditions in a muscle become anaerobic during strenuous exercise, why is it necessary to convert pyruvate to lactate? a. to decrease NAD+ and increase NADH b. to decrease NADH and increase NAD+ c. to increase NADH and increase NAD+ d. to decrease NADH and decrease NAD+ e. to keep oxidative phosphorylation running

Conceptual Questions 1. The electron transport chain is so named because electrons are transported from one component to another. Describe the purpose of the ETC. 

2. What causes the rotation of the γ subunit of ATP synthase? How does this rotation promote ATP synthesis?  3.

Core Concept: Energy and Matter How is glucose breakdown regulated to avoid the overproduction of ATP and NADH? What would be some potentially harmful consequences if glucose metabolism was not regulated properly? 

Collaborative Questions 1. Discuss the advantages and disadvantages of aerobic respiration, anaerobic respiration, and fermentation. 2. Read more about PET scans in other sources. Which types of cancers are most easily detected by this procedure, and which types are not readily detected? Is the ability to detect cancer via a PET scan related to the level of oxygen within a tumor?

CHAPTER OUTLINE

Photosynthesis

8

8.1 8.2 8.3 8.4

Overview of Photosynthesis Reactions That Harness Light Energy Molecular Features of Photosystems Synthesizing Carbohydrates via the Calvin Cycle 8.5 Variations in Photosynthesis Summary of Key Concepts Assess & Discuss

photosynthesis for their nourishment, either directly or indirectly. Photosynthesis is also responsible for producing the oxygen that makes up a large portion of the Earth’s atmosphere. Therefore, all aerobic organisms rely on photosynthesis for cellular respiration. We begin this chapter with an overview of photosynthesis as it occurs in plants and algae. We will then explore the two stages of photosynthesis in more detail. In the first stage, called the light reactions, light energy is absorbed by chlorophyll and converted to chemical energy in the form of two energy intermediates: ATP and NADPH. During the second stage, known as the Calvin cycle, ATP and NADPH are used to drive the synthesis of carbohydrates. We will conclude with a consideration of the variations in photosynthesis that occur in plants existing in hot and dry conditions. A tropical rain forest in the Amazon. Plant life in tropical rain forests carries out a large amount of the world’s photosynthesis and supplies the atmosphere with a sizable fraction of its oxygen. ©Travelpix Ltd/Getty Images

T

ake a deep breath. Nearly all of the oxygen in every breath you take is made by Earth's abundant plants, algae, and cyanobacteria. More than 20% of the world’s oxygen is produced in the Amazon rain forest in South America alone (see the chapter opening photo). Biologists are alarmed about the rate at which such forests are being destroyed by human activities such as logging, mining, and oil extraction. Rain forests once covered 14% of the Earth’s land surface, but they now occupy less than 6%. At their current rate of destruction, rain forests may be nearly eliminated in less than 40 years. Such a development may lower the level of oxygen in the atmosphere and thereby have a harmful effect on living organisms on a global scale. In rain forests and across all of the Earth, the most visible color on land is green. The green color of plants is due to a pigment called chlorophyll. This pigment provides the starting point for the process of photosynthesis, in which the energy from light is captured and used to synthesize glucose and other organic molecules. Nearly all living organisms ultimately rely on

8.1  Overview of Photosynthesis Learning Outcomes: 1. Write the general equations that represent the process of photosynthesis. 2. Explain how photosynthesis powers the biosphere. 3. Describe the general structure of chloroplasts. 4. Compare and contrast the two phases of photosynthesis: the light reactions and the Calvin cycle.

In the mid-1600s, a Flemish physician, Jan Baptista Van Helmont, conducted an experiment in which he transplanted the shoot of a young willow tree into a bucket of soil and allowed it to grow for 5 years. After this time, the willow tree had added 164 pounds to its original weight, but the soil had lost only 2 ounces. Van Helmont correctly concluded that the willow tree did not get most of its nutrients from the soil. He also hypothesized that the mass of the tree came from the water he had added over the 5 years. This hypothesis was partially correct, but we now know that CO2 from the air is also a major contributor to the growth and mass of plants. In the 1770s, Jan Ingenhousz, a Dutch physician, immersed green plants under water and discovered that they released bubbles of oxygen. Ingenhousz determined that sunlight was necessary for oxygen production. During this same period, Jean Senebier, a Swiss botanist,



PHOTOSYNTHESIS 165

found that CO2 is required for plant growth. With this accumulating information, Julius von Mayer, a German physicist, proposed in 1845 that plants convert light energy from the Sun into chemical energy. For the next several decades, plant biologists studied photosynthesis in plants, algae, and species of bacteria that are capable of photosynthesis. They discovered that some photosynthetic bacteria use hydrogen sulfide (H2S) instead of water (H2O) for photosynthesis, and these organisms release sulfur instead of oxygen. In the 1930s, based on this information, Dutch-American microbiologist Cornelis van Niel proposed a general equation for photosynthesis that applies to plants, algae, and photosynthetic bacteria: CO2 + 2 H2A + Light energy → CH2O + A2 + H2O where A is oxygen (O) or sulfur (S) and CH2O is the general formula for a carbohydrate. This is a redox reaction in which CO2 is reduced and H2A is oxidized. In plants and algae, A is oxygen and A2 is a molecule of oxygen that is designated O2. Therefore, this equation becomes CO2 + 2 H2O + Light energy → CH2O + O2 + H2O When the carbohydrate produced is glucose (C6H12O6), we multiply each side of the equation by 6 to obtain: 6 CO2 + 12 H2O + Light energy → C6H12O6+ 6 O2 + 6 H2O ΔG = +685 kcal/mol In this redox reaction, CO2 is reduced during the formation of glucose, and H2O is oxidized during the formation of O2. Notice that the free-energy change required for the production of 1 mole of glucose from carbon dioxide and water is a whopping +685 kcal/mol! As we learned in Chapter 6, an endergonic reaction is driven forward by being coupled with an exergonic process that releases free energy. In this case, the energy from sunlight ultimately drives the synthesis of glucose. In this section, we will survey the general features of photosynthesis as it occurs in plants and algae. The sections that follow will examine the various steps in this process.

Photosynthesis Powers the Biosphere The term biosphere describes the regions on the surface of the Earth and in the atmosphere where living organisms exist. Organisms can be categorized as heterotrophs and autotrophs. Heterotrophs must consume food—organic molecules from their environment—to sustain life. Most species of bacteria and protists, as well as all species of fungi and animals, are heterotrophs. By comparison, autotrophs sustain themselves by producing organic molecules from inorganic sources such as CO2 and H2O. Photoautotrophs are autotrophs that use light as a source of energy to make organic molecules. These include plants, algae, and some bacterial species such as cyanobacteria. Life in the biosphere is largely driven by the photosynthetic power of plants, algae, and cyanobacteria. The existence of most species relies on a key energy cycle that involves the interplay between organic molecules (such as glucose) and inorganic molecules, namely, O2, CO2, and H2O (Figure 8.1). Photoautotrophs make a large proportion of the Earth’s organic molecules via photosynthesis, using light

Organic molecules + O2 (C6H12O6)

Photosynthesis

Energy cycle in the biosphere

Cellular respiration Energy intermediates

Light

CO2 + H2O

ATP

Figure 8.1  An important energy cycle between photosynthesis

and cellular respiration.  Photosynthesis is a process in which light, CO2, and H2O are used to produce O2 and organic molecules. The organic molecules are broken down to CO2 and H2O via cellular respiration to supply energy in the form of ATP; O2 is reduced to H2O. Core Skill: Modeling  The goal of this modeling challenge is to increase the complexity of the model shown in Figure 8.1 by adding organisms that carry out photosynthesis and those that carry out cellular respiration. Modeling Challenge: The figure shows a simplified model for an energy cycle in the biosphere. Increase the complexity of the model in the following ways: On the left side, add drawings of three different broad categories of organisms that carry out photosynthesis. On the right, add drawings of three or more categories that carry out cellular respiration.

energy, CO2, and H2O. During this process, they also produce O2. To supply their energy needs, both photoautotrophs and heterotrophs metabolize organic molecules via cellular respiration. As described in Chapter 7, cellular respiration generates CO2 and H2O and is used to make ATP. The CO2 is released into the atmosphere and can be reused by photoautotrophs to make more organic molecules such as glucose. In this way, an energy cycle between photosynthesis and cellular respiration sustains life on our planet.

In Plants and Algae, Photosynthesis Occurs in the Chloroplasts Chloroplasts are organelles found in plant and algal cells that carry out photosynthesis. These organelles contain large quantities of chlorophyll, which is a pigment that gives plants their green color. All green parts of a plant contain chloroplasts and can perform photosynthesis, although the majority of photosynthesis in most species of plants occurs in the leaves (Figure 8.2). The tissue in the internal part of the leaf, called the mesophyll, contains cells with chloroplasts. For photosynthesis to occur, the mesophyll cells must receive light, and also obtain water and carbon dioxide. The water is taken up by the roots of the plant and is transported to the leaves by small veins. Carbon dioxide gas enters the leaf, and oxygen exits, via pores called stomata (singular, stoma or stomate; from the Greek, meaning mouth).

Leaf cross section Epidermal cells Mesophyll Mesophyll cells O2

Epidermal cells O2 CO2 enters the leaf via stomata, and O2, a product of photosynthesis, exits via stomata.

CO2

Like a mitochondrion, a chloroplast contains an outer and an inner membrane, with an intermembrane space lying between the two. A third membrane, called the thylakoid membrane, contains pigment molecules, including chlorophyll. The thylakoid membrane forms many flattened, fluid-filled tubules called thylakoids, each of which encloses a single compartment known as the thylakoid lumen. Thylakoids stack on top of each other to form a structure called a granum (plural, grana). The stroma is the fluid-filled region of the chloroplast between the thylakoid membrane and the inner membrane (see Figure 8.2).

Photosynthesis Occurs in Two Stages: Light Reactions and the Calvin Cycle How does photosynthesis take place? As mentioned, the process of photosynthesis occurs in two stages called the light reactions and the Calvin cycle. The term photosynthesis is derived from the association between these two stages: Photo refers to the light reactions that capture the energy from sunlight needed for the synthesis of carbohydrates that occurs in the Calvin cycle. The light reactions take place at the thylakoid membrane, and the Calvin cycle occurs in the stroma (Figure 8.3). The light reactions involve an amazing series of energy conversions, starting with light energy and ending with chemical energy that is stored in the form of covalent bonds. The light reactions produce three chemical products: ATP, NADPH, and O 2. ATP and NADPH are energy intermediates that provide the needed

CO2

Stomata

Mesophyll cell

Chloroplast Intermembrane space Outer membrane

15.5 μm

Inner membrane

The light reactions at the thylakoid membrane produce ATP, NADPH, and O2.

Thylakoid

Chloroplast

Light

Thylakoid lumen

Thylakoid membrane H2O

Granum

The Calvin cycle in the stroma uses CO2, ATP, and NADPH to make carbohydrates.

O2

CO2

Stroma NADP+ ADP + Pi

Light reactions ATP

Stroma

Calvin cycle

NADPH

Cytosol 3.8 μm

Figure 8.2  Leaf organization.  Leaves are composed of layers of

cells. The epidermal cells are on the outer surface, both top and bottom, with mesophyll cells sandwiched in the middle. The mesophyll cells contain chloroplasts and are the primary sites of photosynthesis in most plants. (1): ©McGraw-Hill Education/Mark Dierker, photographer; (2):

©Biophoto Associates/SPL/Science Source; (3): ©Omikron/Science Source

Core Skill: Connections  Look ahead to Figure 39.17. How many guard cells make up a stoma (plural, stomata)? 

O2 Cytosol

Sugars

Figure 8.3  An overview of the two stages of photosynthesis:

light reactions and Calvin cycle.  The light reactions, through which ATP, NADPH, and O2 are made, occur at the thylakoid membrane. The Calvin cycle, in which enzymes use ATP and NADPH to incorporate CO2 into carbohydrates, occurs in the stroma. Concept Check:   Can the Calvin cycle occur in the dark?



PHOTOSYNTHESIS 167

energy and electrons to drive the Calvin cycle. Like NADH, NADPH (nicotinamide adenine dinucleotide phosphate) is an electron carrier that can accept two electrons. Its structure differs from NADH by the presence of an additional phosphate group. The structure of NADH is described in Chapter 6 (see Figure 6.12).

8.2 R  eactions That Harness Light Energy

Increasing energy of photons Increasing wavelength Wavelength = Distance between 2 peaks

0.001 nm 10 nm Gamma rays

X-rays UV

0.1 cm

0.1 m

1000 m

Infrared Microwaves Radio waves

Visible

Learning Outcomes: 1. Describe the general properties of light. 2. Explain how pigments absorb light energy, and list the types of pigments found in plants and green algae. 3. Outline the steps by which photosystems II and I capture light energy and produce O2, ATP, and NADPH. 4. Describe the process of cyclic photophosphorylation, which produces only ATP.

According to the first law of thermodynamics, discussed in Chapter 6, energy cannot be created or destroyed, but it can be transferred from one place to another and transformed from one form to another. During photosynthesis, energy in the form of light is transferred from the Sun, some 92 million miles away, to a pigment molecule in a photosynthetic organism such as a plant. What follows is an interesting series of energy transformations in which light energy is transformed into electrochemical energy and then into energy stored within chemical bonds. In this section, we will explore this series of transformations, collectively called the light reactions of photosynthesis. We begin by examining the properties of light and then consider the features of chloroplasts that allow them to capture light energy. The remainder of this section focuses on how the light reactions of photosynthesis generate three important products: ATP, NADPH, and O2.

Light Energy Is a Form of Electromagnetic Radiation Light is essential to support life on Earth. Light is a type of electromagnetic radiation, so named because it consists of energy in the form of electric and magnetic fields. Electromagnetic radiation travels as waves caused by the oscillation of the electric and magnetic fields. The wavelength is the distance between the peaks in a wave pattern. The electromagnetic spectrum encompasses all possible wavelengths of electromagnetic radiation, from relatively short wavelengths (gamma rays) to much longer wavelengths (radio waves) (Figure 8.4). Visible light is the range of wavelengths detected by the human eye, commonly between 380 and 740 nm. As discussed later, visible light provides the energy to drive photosynthesis. Physicists have also discovered that light has properties that are characteristic of particles. Albert Einstein formulated the photon theory of light, in which he proposed that light is composed of discrete particles called photons—massless particles traveling in a wavelike pattern and moving at the speed of light (about 300 million m/sec). Each photon contains a specific amount of energy. An important

380 nm 430 nm

500 nm 560 nm 600 nm 650 nm

740 nm

Wavelength

Figure 8.4  The electromagnetic spectrum.  The bottom portion of

this figure emphasizes visible light—the wavelengths of electromagnetic radiation visible to the human eye. Light in the visible portion of the electromagnetic spectrum drives photosynthesis. Concept Check:   Which has higher energy, gamma rays or radio waves?

difference between the various types of electromagnetic radiation, shown in Figure 8.4, is the amount of energy of the photons. Shorter wavelength radiation carries more energy per unit of time than longer wavelength radiation. For example, the photons of gamma rays carry more energy than those of radio waves. The Sun radiates the entire spectrum of electromagnetic radiation, but the atmosphere prevents much of this radiation from reaching the Earth’s surface. For example, the ozone layer forms a thin shield in the upper atmosphere, protecting life on Earth from much of the Sun’s ultraviolet (UV) radiation. Even so, a substantial amount of electromagnetic radiation does reach the Earth’s surface. The effect of light on living organisms is critically dependent on the energy of the photons that reach them. The photons in gamma rays, X-rays, and UV radiation have very high energy. When molecules in cells absorb such energy, the effects can be devastating. Such radiation can cause mutations in DNA and even lead to cancer. By comparison, the energy of photons in visible light is much less intense. Molecules can absorb this energy in a way that does not cause damage. Next, we will consider how molecules in living cells absorb the energy within visible light.

Pigments Absorb Light Energy When light strikes an object, one of three things happens. First, light may simply pass through the object. Second, the object may change the path of light toward a different direction. A third possibility is that the object may absorb the light. The term pigment is used to describe a molecule that can absorb light energy. When light strikes a pigment, some of the wavelengths of light energy are absorbed, while others are reflected. For example, leaves look green to us because they reflect light energy with wavelengths in the green region of the visible spectrum. Various pigments in the leaves absorb the energy of other wavelengths. At the extremes of color reflection are white and black. A white object reflects nearly all of

168

CHAPTER 8 High-energy electron (photoexcited)

Photon

Electron

–

–

+

+

Nucleus Ground state

Excited state

Figure 8.5  Absorption of light energy by an electron.  When a photon of light having the correct amount of energy strikes an electron, the electron is boosted from the ground (unexcited) state to a higher energy level (an excited state). When this occurs, the electron occupies an orbital that is farther away from the nucleus of the atom. At this farther distance, the electron is held less firmly and is considered unstable. Concept Check:   Describe the three events that can enable a photoexcited electron to become more stable.

the visible light energy falling on it, whereas a black object absorbs nearly all of the light energy. This is why it is coolest to wear white clothes on a sunny, hot day. What do we mean when we say that light energy is absorbed? Light energy in the visible spectrum can be absorbed by an atom when it boosts an electron to a higher energy level (Figure 8.5). The location in which an electron is found is called its orbital. Electrons in different orbitals possess different amounts of energy. For an electron to absorb light energy and be boosted to an orbital with a higher energy, it must overcome the difference in energy between the orbital it is in and the orbital to which it is going. For this to happen, an electron must absorb a photon that contains precisely that amount of energy. Different pigment molecules contain a variety of electrons that can be shifted to different energy levels. The wavelength of light that a pigment absorbs depends on the amount of energy needed to boost an electron to a higher orbital. After an electron absorbs energy, it is said to be in an excited state. Usually, this is an unstable condition. To become stable again, one of four things can happen.

Plants Contain Different Types of Photosynthetic Pigments In plants, different pigment molecules absorb the light energy used to drive photosynthesis. Two types of chlorophyll pigments, termed chlorophyll a and chlorophyll b, are found in green plants and green algae. Their structure was determined in the 1930s by German chemist Hans Fischer (Figure 8.6a). In the chloroplast, both chlorophylls a and b are bound to integral membrane proteins in the thylakoid membrane. The chlorophylls contain a porphyrin ring and a phytol tail. A magnesium ion (Mg2+) is bound to the porphyrin ring. An electron in the porphyrin ring is able to hop from one atom in the ring to another. Because this electron isn’t restricted to a single atom, it is called a delocalized electron. The delocalized electron can absorb light energy. The phytol tail in chlorophyll is a long hydrocarbon chain that is hydrophobic. Its function is to anchor the pigment to the surface of hydrophobic proteins within the thylakoid membrane of chloroplasts. Carotenoids are another type of pigment found in chloroplasts (Figure 8.6b). These pigments impart a color that ranges from yellow to orange to red. Carotenoids are often the major pigments in flowers and fruits. In leaves, the more abundant chlorophylls usually mask the colors of carotenoids. In temperate climates where the leaves change colors, the quantity of chlorophyll in the leaf declines during autumn. The carotenoids become readily visible and produce the yellows, oranges, and reds of autumn foliage.

H2C H3C

N

∙ An excited electron can transfer its extra energy to an electron in a nearby molecule, a process called resonance energy transfer. ∙ Rather than releasing energy or transferring it to another molecule, an excited electron can be removed from the molecule in which it is unstable and transferred to another molecule where it is stable. When this occurs, the energy in the electron is said to be captured, because the electron does not readily drop down to a lower energy level and release heat or light.

N

N

H3C

CH2 CH2 C

N

COCH3

CH3

CH2CH3

Mg

∙ To become stable, an excited electron may drop back down to a lower energy level and release heat. For example, on a sunny day, the sidewalk heats up because it absorbs light energy that is released as heat. ∙ Alternatively, an electron can become stable by releasing energy in the form of light. Certain organisms, such as jellyfish, possess molecules that make them glow. This glowing is due to the release of light when electrons drop down to lower energy levels, a phenomenon called fluorescence.

CHO in chlorophyll b CH3 in chlorophyll a

CH

CH3

Porphyrin ring

CH3 H3C

CH CH3

O

CH3

O O

H3C

O

H3C

CH2

H3C

CH3 CH3

Phytol tail

CH CH3 CH3

CH3

CH3

CH3

(a) Chlorophylls a and b

(b) β-Carotene (a carotenoid)

Figure 8.6  Structures of pigment molecules.  (a) The structure of

chlorophylls a and b. As indicated, chlorophylls a and b differ only at a single site, at which chlorophyll a has a —CH3 group and chlorophyll b has a —CHO group. (b) The structure of β-carotene, an example of a carotenoid. The green- and orange-shaded areas of the structures in parts (a) and (b) are regions where a delocalized electron can hop from one atom to another.



PHOTOSYNTHESIS 169

An absorption spectrum is a graph that plots a pigment’s light absorption as a function of the light's wavelength. Each of the photosynthetic pigments shown in Figure 8.7a absorbs light in different regions of the visible spectrum. The absorption spectra of chlorophylls a and b are slightly different, though both chlorophylls absorb light most strongly in the red and violet parts of the visible spectrum and absorb green light poorly. Green light is reflected, which is why leaves appear green during the growing season. Carotenoids absorb light in the blue and blue-green regions of the visible spectrum, reflecting yellow and red. Why do plants have different pigments? Having different pigments allows plants to absorb light at many different wavelengths. In this way, plants are more efficient at capturing the energy in sunlight. This phenomenon is highlighted in an action spectrum, which plots the rate of photosynthesis as a function of wavelength (Figure 8.7b). The highest rates of photosynthesis in green plants correlate with the wavelengths that are strongly absorbed by the chlorophylls and carotenoids. Photosynthesis is poor in the green region of the spectrum, because these pigments do not readily absorb this wavelength of light.

Relative absorption of light at the wavelengths shown on the x-axis

Chlorophyll a

350

Chlorophyll b β-Carotene

400 450 500 Violet Blue Green

550

600 650 Yellow Red

700

750

Photosystem I and NADPH Synthesis  A key role of photosystem I is to make NADPH (see Figure 8.8, steps 2 and 3). When light strikes the light-harvesting complex of photosystem I, this energy is also transferred to a reaction center, where a high-energy electron is removed from a pigment molecule, designated P700, and transferred to a primary electron acceptor. A protein called ferredoxin (Fd) can accept two high-energy electrons, one at a time, from the primary electron acceptor. Fd then transfers the two electrons to the enzyme NADP+ reductase. This enzyme transfers the two electrons to NADP+, which also accepts an H+ to produce NADPH. The formation of NADPH results in fewer H+ in the stroma. The combined action of photosystem II and photosystem I is termed linear electron flow because the electrons move linearly from PSII to PSI and ultimately reduce NADP+ to NADPH. A key difference between PSII and PSI lies in the source of the electrons received by their respective pigment molecules. An oxidized pigment in PSII called P680 receives an electron from water. By comparison, an oxidized pigment in PSI called P700 receives an electron from the protein Pc. Therefore, PSI does not need to split water to reduce this pigment and does not generate oxygen.

Relative rate of photosynthesis

8 7 6 5 4 3 2 1 450

500

550

600

650

700

Events within Photosystem II  As described in step 1a of Figure 8.8, light excites electrons in pigment molecules, such as chlorophylls, which are located in a region of PSII called a light-harvesting complex. Rather than releasing their energy in the form of heat, the excited electrons begin to follow a path shown by the red arrow. Initially, the excited electrons move sequentially from a pigment molecule called P680 in PSII to other electron carriers called pheophytin (Pp), QA, and QB. PSII also oxidizes water, which generates O2 and adds H+ into the thylakoid lumen (see step 1b of Figure 8.8). The electrons released from oxidized water molecules replenish the electrons that are removed from P680.

750

Wavelength (nm)

400

A key feature of photosynthesis is the ability of pigments to absorb light energy and transfer it to other molecules that can hold the energy in a stable fashion and ultimately produce energy-intermediate molecules that can do cellular work. Let’s now consider how chloroplasts capture light energy. The thylakoid membranes of the chloroplast contain two distinct complexes of proteins and pigment molecules called photosystem I (PSI) and photosystem II (PSII) (Figure 8.8). Photosystem I was discovered before photosystem II, but photosystem II is the initial step in photosynthesis. Working together, these two systems enable chloroplasts to capture light energy and synthesize ATP, NADPH, and O2.

Electron Transport Chain  Via QB, the electrons exit PSII and enter an electron transport chain (ETC)—a series of electron carriers—located in the thylakoid membrane (see Figure 8.8, step 1a). This ETC functions similarly to the one found in mitochondria. From QB, an electron goes to a cytochrome complex; then to plastocyanin (Pc), a small protein; and then to photosystem I. Along its journey from photosystem II to photosystem I, the electron releases some of its energy at particular steps and is transferred to the next component that has a higher electronegativity. The energy released is harnessed to pump H+ into the thylakoid lumen.

(a) Absorption spectra

0 350

Photosystems II and I Work Together to Produce ATP and NADPH via Linear Electron Flow

Wavelength (nm) (b) Action spectrum

Figure 8.7  Properties of pigment function: absorption and

action spectra.  (a) These absorption spectra show the absorption of light by chlorophyll a, chlorophyll b, and β-carotene. (b) An action spectrum of photosynthesis depicting the relative rate of photosynthesis in green plants at different wavelengths of light. Concept Check:   What is the advantage of having different pigment molecules? 

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CHAPTER 8 CO2

Light

NADP+ ADP+ Pi

H2O O2

Light r reactions

Chloroplast

pigment molecules in the lightharvesting complex of PSII. The excited electrons move down an electron transport chain to more electronegative atoms as shown by the red arrow. This produces an H+ electrochemical gradient.

Calvin cycle

ATP NADPH

Electrons from PSII eventually reach PSI, where a second input of light boosts them to a very high energy level. They follow the path shown by the red arrow.

Light

Thylakoid membrane

2

Light

2 H+ P680 Pp

e–

QA PSII

NADP+ reductase

Fd

PSI NADP+ + 2 H+

Pc

e– flow

Two high-energy electrons and one H+ are transferred to NADP+ to make NADPH. This removes some H+ from the stroma.

P700

Cytochrome complex

QB

QB

3

Lightharvesting complex

CH2O (sugar)

Stroma Lightharvesting complex

2

1a Light excites electrons within

NADPH + H+

H2O Thylakoid lumen

1/

2 O2 +

2 H+

2 H+

H+ electrochemical gradient (High H+ in thylakoid lumen) 1b

Electrons are removed from water and transferred to a pigment called P680. This process creates O2 and places additional H+ in the lumen.

4

ATP synthase

The production of O2, the pumping of H+ across the thylakoid membrane, and the synthesis of NADPH all contribute to the formation of an H+ electrochemical gradient. This gradient is used to make ATP via an ATP synthase in the thylakoid membrane.

H+ ATP

ADP + Pi

Figure 8.8  The synthesis of ATP, NADPH, and O2 by the concerted actions of photosystems II and I.  The movement of electrons from photosystem II to photosystem I to NADPH is called linear electron flow. Concept Check:   Are ATP, NADPH, and O2 produced in the stroma or in the thylakoid lumen?

ATP Synthesis  The synthesis of ATP in chloroplasts is achieved by a chemiosmotic mechanism called photophosphorylation, which is similar to the oxidative phosphorylation used to make ATP in mitochondria. In chloroplasts, ATP synthesis is driven by the flow of H+ from the thylakoid lumen into the stroma via ATP synthase (Figure 8.8, step 4). The light reactions produce an H+ electrochemical gradient in which more H+ is in the thylakoid lumen and less in the stroma. The gradient is generated in three ways: 1. The splitting of water places H+ in the thylakoid lumen. 2. The movement of high-energy electrons along the ETC from photo­ system II to photosystem I pumps H+ into the thylakoid lumen. 3. The formation of NADPH consumes H+ in the stroma. Products of Photosynthesis  In summary, the steps of the light reactions of photosynthesis produce three chemical products: O2, NADPH, and ATP: 1. O2 is produced in the thylakoid lumen by the oxidation of water by photosystem II. Two electrons are removed from water, producing 2 H+ and 1/2 O2. The two electrons are transferred to P680 molecules.

2. NADPH is produced in the stroma using high-energy electrons that are first boosted to a higher energy level in photosystem II and then are boosted a second time in photosystem I. Two high-energy electrons and one H+ are transferred to NADP+ to produce NADPH. 3. ATP is produced in the stroma via ATP synthase that uses an H+ electrochemical gradient.

Cyclic Electron Flow Produces Only ATP The mechanism of harvesting light energy described in Figure 8.8 is called linear electron flow because it is a linear process. This electron flow produces ATP and NADPH in roughly equal amounts. However, as we will see later, the Calvin cycle uses more ATP than NADPH. How can plant cells avoid making too much NADPH and not enough ATP? In 1959, Daniel Arnon discovered a pattern of electron flow that is cyclic and generates only ATP (Figure 8.9). Arnon termed the process cyclic photophosphorylation because (1) the path of electrons is cyclic, (2) light energizes the electrons, and (3) ATP is made via the phosphorylation of ADP. Due to the path of electrons, the mechanism is also called cyclic electron flow.



PHOTOSYNTHESIS 171

When light strikes photosystem I, electrons are excited and sent to ferredoxin (Fd). From Fd, the electrons are then transferred to QB, to the cytochrome complex, to plastocyanin (Pc), and back to photosystem I. This produces an H+ electrochemical gradient, which is used to make ATP via ATP synthase. Thylakoid membrane Stroma

Fd

Light

e– flow

2 H+ PSII

Cytochrome complex

QB

P700

Pc

Thylakoid lumen 2 H+

H+ electrochemical gradient (High H+ in thylakoid lumen)

PSI

ATP synthase

H+ ATP

ADP + Pi

Figure 8.9  Cyclic photophosphorylation.  In this process, electrons follow a cyclic path that is powered by photosystem I (PSI). This contributes to the formation of an H+ electrochemical gradient, which is then used by ATP synthase to make ATP. Concept Check:   Why does cyclic photophosphorylation provide an advantage to a plant over using only linear electron flow?

When light strikes photosystem I, high-energy electrons are sent to the primary electron acceptor and then to ferredoxin (Fd). The key difference in cyclic photophosphorylation is that the high-energy electrons are transferred from Fd to QB. From QB, the electrons then go to the cytochrome complex, then to plastocyanin (Pc), and back to photosystem I. As the electrons travel along this cyclic route, they release energy, and some of this energy is used to transport H+ into the thylakoid lumen. The resulting H+ gradient drives the synthesis of ATP via ATP synthase. Cyclic photophosphorylation is favored when the level of NADP+ is low and NADPH is high. Under these conditions, there is sufficient NADPH to run the Calvin cycle, which is described later. Alternatively, when NADP+ is high and NADPH is low, linear electron flow is favored, so more NADPH can be made. Cyclic photophosphorylation is also favored when ATP levels are low.

Core Concepts: Evolution, Structure and Function The Cytochrome Complexes of Mitochondria and Chloroplasts Contain Evolutionarily Related Proteins A recurring theme in cell biology is that evolution has resulted in groups of genes that encode proteins that play similar but

specialized roles in cells—an example of descent with modification. When two or more genes are similar because they are derived from the same ancestral gene, they are called homologous genes. As discussed in Chapter 22, homologous genes encode proteins that have similar amino acid sequences and often perform similar functions. A comparison of the electron transport chains of mitochondria and chloroplasts reveals homologous genes. In particular, let’s consider the cytochrome complex found in the thylakoid membrane of plants and algae, called cytochrome b6-f (Figure 8.10a), and the complex cytochrome b-c1, which is found in the ETC of mitochondria (Figure 8.10b; also refer back to Figure 7.8). Both of these cytochrome complexes are composed of several proteins. One of the proteins is called cytochrome b6 in cytochrome b6-f and cytochrome b in cytochrome b-c1. By analyzing the sequences of the genes that encode these proteins, researchers discovered that cytochrome b6 and cytochrome b are homologous proteins. These proteins carry out similar functions: Both of them accept electrons from a quinone (QB, or ubiquinone), and both donate an electron to another protein within their respective complexes (cytochrome f or cytochrome c1). Likewise, both proteins function as H+ pumps that capture some of the energy that is released from electrons to transport H+ across the membrane. In this way, evolution has produced a family of cytochrome b proteins that play similar but specialized roles.

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CHAPTER 8

Cytochrome b6-f

Stroma

Cytochrome b

H+

2 H+ QB

Pc

Thylakoid lumen

2 H+ H+

(a) Cytochrome b6-f in the chloroplast

Figure 8.10  Homologous proteins in the electron transport

Cytochrome b-c1

Matrix H+ Q

Intermembrane space

H+

Cytochrome c

(b) Cytochrome b-c1 in the mitochondrion

8.3 M  olecular Features of Photosystems Learning Outcomes: 1. Explain how PSII absorbs and captures light energy and how it produces O2. 2. Diagram the variation in the energy of an electron as it moves from PSII to PSI to NADP+.

The previous section provided an overview of how chloroplasts absorb light energy and produce ATP, NADPH, and O2. As you have learned, two photosystems—PSI and PSII—play critical roles in two aspects of photosynthesis. First, both PSI and PSII absorb light energy and capture that energy in the form of excited electrons. Second, PSII oxidizes water, thereby producing O2. In this section, we will take a closer look at how these events occur at the molecular level.

Photosystem II Captures Light Energy and Produces O2 PSI and PSII have two main components: a light-harvesting complex and a reaction center. Figure 8.11 shows how these components function in PSII. Absorption of Energy by the Light-Harvesting Complex and Its Transfer to P680 via Resonance Energy Transfer  In 1932, American biologist Robert Emerson and an undergraduate student,

chains of chloroplasts and mitochondria.  (a) Cytochrome b6-f is a complex of proteins involved in electron and H+ transport in chloroplasts, and (b) cytochrome b-c1 is a complex of proteins involved in electron and H+ transport in mitochondria. These complexes contain homologous proteins designated cytochrome b6 in chloroplasts and cytochrome b in mitochondria. The inset shows the three-dimensional structure of cytochrome b, which was determined by X-ray crystallography. It is an integral membrane protein with several transmembrane helices and two heme groups, which are prosthetic groups involved in electron transfer. The structure of cytochrome b6 has also been determined and found to be very similar. Concept Check:   Explain why the three-dimensional structures of cytochrome b and cytochrome b6 are very similar. 

William Arnold, originally discovered the light-harvesting complex in the thylakoid membrane. It is composed of several dozen pigment molecules that are anchored to transmembrane proteins. The role of the complex is to directly absorb photons of light. When a pigment molecule absorbs a photon, an electron is boosted to a higher energy level. As shown in Figure 8.11, the energy (not the electron itself) is transferred to adjacent pigment molecules by a process called resonance energy transfer. The energy may be transferred among multiple pigment molecules until it is eventually transferred to a special pigment molecule designated P680, which is located within the reaction center of PSII. The P680 pigment is so named because it can directly absorb light at a wavelength of 680 nm. However, P680 is more commonly excited by resonance energy transfer from a chlorophyll pigment in the light-harvesting complex. In either case, when an electron in P680 is excited, the molecule is designated P680*. The light-harvesting complex is also called the antenna complex because it acts like an antenna that absorbs energy from light and funnels that energy to P680 in the reaction center. Rapid Transfer of a High-Energy Electron from P680* to the Primary Electron Acceptor  A high-energy (photoexcited) electron in a pigment molecule is very unstable. It may abruptly release its energy by giving off heat or light. Unlike the pigments in the light-harvesting complex that undergo resonance energy transfer, P680* can actually release its high-energy electron and become P680+. P680* → P680+ + e–



PHOTOSYNTHESIS 173

Stroma

Photosystem II Thylakoid lumen

11

2

3

Primary electron acceptor

Light Light energy isis absorb Lig Light ight energy absorbed bed d absorbed by a by a Ligh Lightpigment molecule. molecule. pigment harv harvesting This boosts an This boosts an com complex electron in in the the electron pigment to to aa higher higher pigment energy level. level. energy Pig Pigment molecule (ch (chlorophyll)

Reaction center P680* (unstable)

Energy is transferred among pigment molecules via resonance energy transfer until it reaches P680, converting it to P680*.

The high-energy electron on P680* is transferred to the primary electron acceptor (pheophytin), where it is very stable. P680* becomes P680+.

P680

A low-energy electron from water is transferred to P680+ to convert it to P680. O2 is produced.

Transfer of a Low-Energy Electron from Water to P680+  Let’s now consider what happens to P680+, which has given up its highenergy electron. After P680+ is formed, the electron that has been removed must be replaced so that P680 can function again. Therefore, another role of the reaction center is to replace the electron that is removed when P680* becomes P680+. This missing electron of P680+ is replaced with a low-energy electron from water (see Figure 8.11). H2O → 2H+ + 1/2 O2 + 2e– 2 P680+ + 2e– → 2 P680 (from water)

Reduced primary electron acceptor (very stable)

P680+

The oxidation of water results in the formation of oxygen gas (O2), which is used by many organisms for cellular respiration. Photosystem II is the only known protein complex that can oxidize water, resulting in the release of O2 into the atmosphere.

e–

BIO TIPS

THE QUESTION  Describe the roles of the lightharvesting complex, P680, and the primary electron acceptor during the absorption of light energy by photosystem II (PSII). At which step is the light energy captured?

P680

4

The role of the reaction center is to quickly remove the high-energy electron from P680* and transfer it to another molecule, where the electron is stable. This molecule is called the primary electron acceptor (see Figure 8.11). The transfer of the electron from P680* to the primary electron acceptor is remarkably fast. It occurs in less than a few picoseconds! (One picosecond equals one-trillionth of a second, or 10–12 sec.) Because this occurs so quickly, the excited electron does not have much time to release its energy in the form of heat or light. When the primary electron acceptor (pheophytin) has received this high-energy electron, the light energy has been captured and can be used to perform cellular work. As discussed earlier, the work it performs is to synthesize the energy intermediates ATP and NADPH (look back at Figure 8.8).

e–

e– H2O 2 H+ + 1/2 O2

Figure 8.11  A closer look at how photosystem II harvests light energy and oxidizes water.  Note: Two electrons are released during the oxidation of water, but they are transferred one at a time to P680+.

Core Concept: Energy and Matter  The pigments in PSII absorb light energy that is captured in a stable form when an excited electron is transferred to the primary electron acceptor (pheophytin).

T OPIC  What topic in biology does this question address? The topic is the absorption of light by PSII. More specifically, the question asks you to describe the various roles played by the light-harvesting complex, P680, and the primary electron acceptor. I NFORMATION  What information do you know based on the question and your understanding of the topic? In the question, you are reminded that PSII has a light-harvesting complex, P680, and a primary electron acceptor. From your understanding of the topic, you may remember that light absorption begins at the lightharvesting complex, which funnels energy to P680. The energy transforms P680 to P680*, which then transfers a high-energy electron to the primary electron acceptor. P ROBLEM-SOLVING  S TRATEGY  Sort out the steps in a complicated process. Compare and contrast. To begin to solve this problem, it may be helpful to review the steps of the lightabsorption process shown in Figure 8.11. As you do so, compare and contrast the roles of the light-harvesting complex, P680, and the primary electron acceptor.

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CHAPTER 8

∙ In photosystem II, light boosts such an electron to a much higher energy level.

ANSWER Light-harvesting complex: The role of the light-harvesting complex is to absorb light. Because it is composed of many pigment molecules (chlorophylls and β-carotene), the light-harvesting complex is the most likely place for visible light to be absorbed. When a pigment molecule absorbs light, an electron is boosted to a higher energy level, and that energy is transferred via resonance energy transfer to P680.   P680: The role of P680 is to provide a link between the lightharvesting complex and the primary electron acceptor. Although P680 can directly absorb light, P680 is far more likely to gain energy from the light-harvesting complex, which converts it to P680*. The high-energy electron of P680* is then transferred to the primary electron acceptor.   Primary electron acceptor: The role of the primary electron acceptor is to capture the light energy. The high-energy electron of P680* is unstable. However, when it is transferred to the primary electron acceptor, the electron becomes stable, meaning that it will not drop down to a lower energy level.

∙ As the electron travels from photosystem II to photosystem I, some of the energy is released. ∙ The input of light in photosystem I boosts the electron to an even higher energy than it attained in photosystem II. ∙ The electron releases a little energy before it is eventually transferred to NADP+.

8.4 S  ynthesizing Carbohydrates via the Calvin Cycle Learning Outcomes: 1. Outline the three phases of the Calvin cycle. 2. CoreSKILL » Analyze the results of Calvin and Benson, and explain how they identified the components of the Calvin cycle.

Electrons Vary in Energy as They Move from Photosystem II to Photosystem I to NADP+

In the previous sections, we learned how the light reactions of photosynthesis produce ATP, NADPH, and O2. We will now turn our attention to the second phase of photosynthesis, the Calvin cycle, in which ATP and NADPH are used to make carbohydrates. The Calvin cycle consists of a series of steps that occur in a metabolic cycle. In plants and algae, it occurs in the stroma of chloroplasts. In photosynthetic bacteria, the Calvin cycle occurs in the cytoplasm of the cell. The Calvin cycle takes CO2 from the atmosphere and incorporates the carbon into organic molecules, namely, carbohydrates. As mentioned earlier, carbohydrates are critical for two reasons. First, they provide the precursors to make the organic molecules and

In 1960, Robin Hill and Fay Bendall proposed that the light reactions of photosynthesis involve two photoactivation events. According to their model, known as the Z scheme, an electron proceeds through a series of energy changes during photosynthesis (Figure 8.12). The Z refers to the zigzag shape of this energy curve. Based on our modern understanding of photosynthesis, we now know that these events involve increases and decreases in the energy of an electron as it moves linearly from photosystem II through photosystem I to NADP+. ∙ An electron on a nonexcited pigment molecule in photosystem II has the lowest energy.

Primary electron acceptor

Primary electron acceptor e–

Energy of electrons

e–

e–

Fd QA

Light

e–

e–

QB

e– Cytochrome complex

H2O P680

NADP+ reductase

H+

NADPH + H+

Pc P700

Light

NADP+ + 2 H+

2 e– 2 H+ + 1/2 O2

Photosystem II

Photosystem I

Figure 8.12  The Z scheme, showing the energy of an electron moving from photosystem II to NADP+.  The oxidation of water releases two

electrons that travel one at a time from photosystem II to NADP+. As seen here, the input of light boosts the energy of the electron twice. At the end of the pathway, two electrons are used to make NADPH. Concept Check:   During its journey from photosystem II to NADP+, at what point does an electron have the highest amount of energy?



PHOTOSYNTHESIS 175

incorporated into a carbohydrate such as glucose (C6H12O6), 18 ATP molecules are hydrolyzed and 12 NADPH molecules are oxidized:

macromolecules of nearly all living cells. The second key reason is the storage of energy. The Calvin cycle produces carbohydrates, which store energy. These carbohydrates are accumulated inside plant cells. When a plant is in the dark and not carrying out photosynthesis, the stored carbohydrates are used as a source of energy. Similarly, when an animal consumes a plant, it uses the carbohydrates as an energy source. In this section, we will examine the three phases of the Calvin cycle. We will also explore the experimental approach of Melvin Calvin and his colleagues that enabled them to elucidate the steps of this cycle.

6 CO2 + 12 H2O → C6H12O6 + 6 O2 + 6 H2O 18 ATP + 18 H2O → 18 ADP + 18 Pi 12 NADPH → 12 NADP+ + 12 H+ + 24 e– Although biologists commonly describe glucose as a product of photosynthesis, glucose is not directly made by the Calvin cycle. Instead, molecules of glyceraldehyde-3-phosphate, which are products of the Calvin cycle, are used as starting materials for the synthesis of glucose and other molecules, including sucrose. After glucose molecules are made, they may be linked together to form a polymer of glucose called starch, which is stored in the chloroplast for later use. Alternatively, the disaccharide sucrose may be made and transported out of the leaf to other parts of the plant. The Calvin cycle can be divided into three phases: carbon fixation, reduction and carbohydrate production, and regeneration of ribulose bisphosphate (RuBP) (Figure 8.13).

The Calvin Cycle Incorporates CO2 into a Carbohydrate The Calvin cycle, also called the Calvin-Benson cycle, was determined by chemists Melvin Calvin and Andrew Adam Benson and their colleagues in the 1940s and 1950s. This cycle requires a massive input of energy. For every 6 carbon dioxide molecules that are Light

Figure 8.13  The Calvin cycle.  This cycle has three phases:

Chloroplast

CO2

(1) carbon fixation, (2) reduction and carbohydrate production, and (3) regeneration of RuBP.

NADP+ ADP+ Pi

H2O O2

Concept Check:   Why is NADPH needed during this cycle? Calvin cycle

Light reactions ATP NADPH

O2

CH2O (sugar) Input 6 × CO2 CH2

C

OPO32–

1

Phase 1: Carbon fixation. CO2 is incorporated into an organic molecule via rubisco.

O C O–

C O

H C OH

H C OH

CH2 OPO32– (3PG)

H C OH 12 × 3-phosphoglycerate (3PG) C C C 6 × Ribulose bisphosphate (RuBP) C C C C C 12 × 1,3-bisphosphoglycerate 6 ADP C C C Calvin cycle Rubisco

CH2 OPO32– (RuBP)

6 ATP 3

Phase 3: Regeneration of RuBP. Two G3P are used to make glucose and other sugars; the remaining 10 G3P are needed to regenerate RuBP via several enzymes. ATP is required for RuBP regeneration.

12 ATP 12 ADP (1,3-BPG) 12 NADPH 12 NADP+ 12 Pi

10 × G3P C C C

12 × Glyceraldehyde3-phosphate (G3P) C C C 2 × G3P C C C 2 Glucose and other sugars

O

O C OPO32– H C OH CH2 OPO32– (1,3-BPG)

C H H C OH CH2 OPO32– (G3P)

Phase 2: Reduction and carbohydrate production. ATP is used as a source of energy, and NADPH donates high-energy electrons.

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Carbon Fixation (Phase 1)  During carbon fixation, CO2 is incorporated into RuBP, a five-carbon sugar. The term fixation means that the carbon has been removed from the atmosphere and incorporated into an organic molecule that is not a gas. More specifically, the product of this reaction in phase 1 is a six-carbon intermediate that immediately splits in half to form two molecules of 3-phosphoglycerate (3PG). The enzyme that catalyzes this step is named RuBP carboxylase/oxygenase, or rubisco. It is the most abundant protein in chloroplasts and perhaps the most abundant protein on Earth! This observation underscores the massive amount of carbon fixation that happens in the biosphere. Reduction and Carbohydrate Production (Phase 2)  In the second phase of the Calvin cycle, ATP is used to convert 3PG to 1,3-bisphosphoglycerate (1,3-BPG). Next, electrons from NADPH reduce 1,3-BPG to glyceraldehyde-3-phosphate (G3P). G3P is a carbohydrate with three carbon atoms. The key difference between 3PG and G3P is that 3PG has a C—O bond, whereas the analogous carbon in G3P has a C—H bond (see Figure 8.13). The C—H bond results when the G3P molecule is reduced by the addition of two electrons from NADPH. Compared with 3PG, the bonds in G3P store more energy and enable G3P to readily form larger organic molecules such as glucose. As shown in Figure 8.13, only some of the G3P molecules are used to make glucose or other carbohydrates. Phase 1 begins with 6 RuBP molecules and 6 CO2 molecules. Twelve G3P molecules are made at the end of phase 2, and only 2 of these G3P molecules are used in

carbohydrate production. As described next, the other 10 G3P molecules are needed to keep the Calvin cycle turning by regenerating RuBP. Regeneration of RuBP (Phase 3)  In the last phase of the Calvin cycle, a series of enzymatic steps converts the 10 G3P molecules into 6 RuBP molecules, using 6 molecules of ATP. After the RuBP molecules are regenerated, they serve as acceptors for CO2, thereby allowing the cycle to continue. As we have just seen, the Calvin cycle begins by using carbon from an inorganic source, that is, CO2, and ends with organic molecules that will be used by the plant to make other molecules. You may be wondering why CO2 molecules cannot be directly linked to form these larger molecules. The answer lies in the number of electrons that are around the carbon atoms. In CO2, the carbon atom is considered electron poor. Oxygen is a very electronegative atom that monopolizes the electrons it shares with other atoms. In a covalent bond between carbon and oxygen, the shared electrons are closer to the oxygen atom. By comparison, in an organic molecule, the carbon atom is electron-rich. During the Calvin cycle, ATP provides energy and NADPH donates high-energy electrons, so the carbon originally in CO2 has been reduced. The Calvin cycle combines less electronegative atoms with carbon atoms so that C—H and C—C bonds are formed. This allows the eventual synthesis of larger organic molecules, including glucose, amino acids, and so on. In addition, the covalent bonds within these molecules store large amounts of energy.

Core Skill: Process of Science

Feature Investigation  |  The Calvin Cycle Was Determined by Isotope-Labeling Methods The steps in the Calvin cycle involve the conversion of one type of molecule to another, eventually regenerating the starting material, RuBP. In the 1940s and 1950s, Calvin and his colleagues used 14C, a radioisotope of carbon, to label and trace molecules produced during the cycle (Figure 8.14). They injected 14C-labeled CO2 into cultures of the green alga Chlorella pyrenoidosa grown in an apparatus called a “lollipop” (because of its shape). The Chlorella cells were given different lengths of time to incorporate the 14C-labeled carbon, ranging from fractions of a second to many minutes. After this incubation period, the cells were abruptly placed into a solution of alcohol to inhibit enzymatic reactions and thereby stop the cycle. The researchers separated the newly made radiolabeled molecules by a variety of methods. The most commonly used method was two-dimensional paper chromatography. In this approach, a sample containing radiolabeled molecules was spotted onto a corner of the paper at a location called the origin. The edge of the paper was placed in a solvent, such as phenol-water. As the solvent rose through the paper, so did the radiolabeled molecules. The rate at which they rose depended on their structures, which determined how strongly they interacted with the paper. This step separated the mixture of molecules spotted onto the paper at the origin. The paper was then dried, turned 90°, and then the edge was placed in a different solvent, such as butanol-propionic acid-water.

Again, the solvent rose through the paper (in a second dimension), thereby separating molecules that may not have been adequately separated during the first separation step. After this second separation step, the paper was dried and exposed to X-ray film, a procedure called autoradiography. Radioactive emission from the 14C-labeled molecules caused dark spots to appear on the film. The pattern of spots changed depending on the length of time the cells were incubated with 14C-labeled CO2. When the incubation period was short, only molecules that were made in the first steps of the Calvin cycle were seen—3-phosphoglycerate (3PG) and 1,3-bisphosphoglycerate (1,3-BPG). Longer incubations revealed molecules synthesized in later steps—glyceraldehyde-3-phosphate (G3P) and ribulose bisphosphate (RuBP). A challenge for Calvin and his colleagues was to identify the chemical nature of each spot. They achieved this by a variety of chemical methods. For example, a spot could be cut out of the paper, the molecule within the paper could be washed out or eluted, and then the eluted molecule could be subjected to the same procedure that included a radiolabeled molecule whose structure was already known. If the unknown molecule and known molecule migrated to the same spot in the paper, this indicated they were likely to be the same molecule. During the late 1940s and 1950s, Calvin and his coworkers identified all of the 14C-labeled spots and the order in which they appeared. In this way, they determined the



PHOTOSYNTHESIS 177

Figure 8.14  The determination of the Calvin cycle using 14C-labeled CO2 and paper chromatography.  (6): Calvin, M. 1961. The path of carbon in photosynthesis, Nobel Lecture pp. 618–644, Fig. 4. ©The Nobel Foundation

GOAL The incorporation of CO2 into carbohydrate involves a biosynthetic pathway. The aim of this experiment was to identify the steps. KEY MATERIALS The green alga Chlorella pyrenoidosa and 14C-labeled CO2. Experimental level

1

Grow Chlorella in an apparatus called a “lollipop.” Add 14C-labeled CO2 and incubate for various lengths of time (from fractions of a second to many minutes). Stop the Calvin cycle by placing a sample of cells into a solution of alcohol.

Conceptual level 14CO

2

Addition of 14CO 2 Chlorella

Alcohol

Lollipop Lamp

2

Cycle stopped

Calvin cycle

Alcohol solution

Take a sample of the internal cell contents and spot on the corner of chromatography paper. This spot is called the origin.

1,3-BPG

Origin

3PG G3P RuBP

3

Place edge of paper in a solvent, such as phenol-water, and allow time for solvent to rise and separate the mixture of molecules that were spotted at the origin.

1,3-BPG G3P 3PG

Solvent

RuBP

4

Dry paper, turn 90°, and then place the edge in a different solvent such as butanol-propionic acid-water. Allow time for solvent to rise.

1,3-BPG G3P RuBP

3PG

5

Dry paper and place next to X-ray film. The developed film reveals dark spots where 14C-labeled molecules were located. This procedure is called autoradiography. X-ray film

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THE DATA*

G3P 3PG

Origin

Butanol-propionic acid-water

178

7

CONCLUSION The identification of the molecules in each spot elucidated the steps of the Calvin cycle.

8

SOURCE Calvin, M. 1961. The path of carbon in photosynthesis, Nobel Lecture, 618–644.

Phenol-water 30-second incubation *An autoradiograph from one of Calvin’s experiments.

series of reactions of what we now know as the Calvin cycle. For this work, Calvin was awarded the Nobel Prize in Chemistry in 1961. Experimental Questions 1. What was the purpose of the study conducted by Calvin and his colleagues? 

8.5 Variations in Photosynthesis Learning Outcomes: 1. Explain the concept of photorespiration. 2. Compare and contrast the strategies used by C4 and CAM plants to avoid photorespiration and conserve water.

Thus far, we have considered photosynthesis as a two-stage process in which the light reactions produce ATP, NADPH, and O2 and the Calvin cycle uses the ATP and NADPH for the synthesis of carbohydrates. This two-stage process is a universal feature of photosynthesis in all green plants, algae, and cyanobacteria. However, certain environmental conditions such as temperature, water availability, and light intensity alter the way in which the Calvin cycle operates. In this section, we begin by examining how hot and dry conditions may reduce the output of photosynthesis. We will then explore two adaptations that certain plant species have evolved that conserve water and help to maximize photosynthetic efficiency in such environments.

Photorespiration Decreases the Efficiency of Photosynthesis In the previous section, we learned that rubisco adds a CO 2 molecule to an organic molecule, RuBP, to produce two molecules of 3-phosphoglycerate (3PG): RuBP + CO2→ 2 3PG

2. CoreSKILL » In Calvin’s experiment shown in Figure 8.14, why did the researchers use 14C-labeled CO2? Why did they examine samples taken after several different time periods? How were the different molecules in the samples identified?  3. CoreSKILL » Interpret the results of Calvin’s study.

For most species of plants, the incorporation of CO2 into 3PG via RuBP is the only way for carbon fixation to occur. Because 3PG is a three-carbon molecule, these plants are called C3 plants. Examples of C3 plants include wheat and oak trees (Figure 8.15). About 90% of the plant species on Earth are C3 plants. Researchers have discovered that the active site of rubisco can also add O2 to RuBP, although its affinity for CO2 is more than 10-fold better than its affinity for O2. Even so, when CO2 levels are low and O2 levels are high, rubisco adds an O2 molecule to RuBP. This produces only one molecule of 3PG and a two-carbon molecule called phosphoglycolate. The phosphoglycolate is then dephosphorylated to glycolate, which is released from the chloroplast. In a series of several steps, the two-carbon glycolate molecule is eventually oxidized in peroxisomes and mitochondria to produce an organic molecule plus a molecule of CO2: RuBP + O2→ 3PG + Phosphoglycolate Phosphoglycolate → Glycolate →→ Organic molecule + CO2 This process, called photorespiration, uses O2 and liberates CO2. Photorespiration is considered wasteful because it releases CO 2, thereby limiting plant growth. Photorespiration is more likely to occur when plants are exposed to a hot and dry environment. To conserve water, the stomata of the leaves close, inhibiting the uptake of CO2 from the air and trapping the O2 that is produced by photosynthesis. When the level of CO2 is low and O2 is high, photorespiration is favored. If C3 plants are subjected to hot and dry environmental conditions, as much as 25–50% of their photosynthetic work is reversed by the process of photorespiration.



PHOTOSYNTHESIS 179

Figure 8.15  Examples of C3

plants.  The structures of (a) wheat and (b) oak leaves are similar to that shown in Figure 8.2. a: ©David Noton Photography/Alamy Stock Photo; b: ©McGraw-Hill Education/Vicki

(a) Wheat plants

(b) Oak leaves

Why do plants carry out photorespiration? The answer is not entirely clear. One possibility is that photorespiration may have a protective advantage. On hot and dry days when the stomata are closed, CO2 levels within the leaves fall, and O2 levels rise. Under these conditions, highly toxic oxygen-containing molecules such as free radicals may be produced that could damage the plant. Therefore, plant biologists have hypothesized that the role of photorespiration may be to protect the plant against the harmful effects of such toxic molecules by consuming O2 and releasing CO2.

C4 Plants Have Evolved a Mechanism to Minimize Photorespiration Certain species of plants have developed a way to minimize photorespiration. In the early 1960s, Hugo Kortschak discovered that the first product of carbon fixation in sugarcane is not 3GP but instead is a molecule with four carbon atoms. Species such as sugarcane are called C4 plants because of this four-carbon molecule. Later, Marshall Hatch and Roger Slack confirmed this result and identified the molecule as oxaloacetate. For this reason, the pathway is sometimes called the Hatch-Slack pathway. Some C4 plants have a unique leaf anatomy that allows them to avoid photorespiration (Figure 8.16). An interior layer in the leaves of many C4 plants has a two-cell organization composed of mesophyll cells and bundle-sheath cells. CO2 from the atmosphere enters the mesophyll cells via stomata. Once inside, the enzyme PEP carboxylase attaches CO2 to phosphoenolpyruvate (PEP), a three-carbon molecule, to produce oxaloacetate, a four-carbon molecule. PEP carboxylase does not recognize O2. Therefore, unlike rubisco, PEP carboxylase does not promote photorespiration when CO2 is low and O2 is high. Instead, PEP carboxylase continues to fix CO2. As shown in Figure 8.16, oxaloacetate is converted to the fourcarbon molecule malate, which is transported into the bundle-sheath cell. Malate is then broken down into pyruvate and CO2. The pyruvate returns to the mesophyll cell, where it is converted to PEP via ATP, and the cycle in the mesophyll cell can begin again. The CO2 enters the Calvin cycle in the chloroplasts of the bundle-sheath cells. Because the mesophyll cell supplies the bundle-sheath cell with a steady supply of CO2, the concentration of CO2 remains high in the

Copeland, photographer

bundle-sheath cell. Also, the mesophyll cells shield the bundle-sheath cells from high levels of O2. This strategy minimizes photorespiration, which requires low CO2 and high O2 levels to proceed. Which is better—being a C3 or a C4 plant? The answer is that it depends on the environment. In warm and dry climates, C4 plants have an advantage. During the day, they can keep their stomata partially closed to conserve water. Furthermore, they minimize photorespiration. Examples of C4 plants are sugarcane, crabgrass, and corn. In cooler climates, C3 plants have the edge because they use less energy to fix CO2. The process of carbon fixation that occurs in C4 plants uses ATP to regenerate PEP from pyruvate (see Figure 8.16), and C3 plants do not have to expend that ATP.

CAM Plants Are C4 Plants That Take Up CO2 at Night We have just learned that certain C4 plants prevent photorespiration by providing CO2 to the bundle-sheath cells, where the Calvin cycle occurs. This mechanism spatially separates the processes of carbon fixation and the Calvin cycle. Another strategy followed by other C4 plants, called CAM plants, separates these processes in time. CAM stands for crassulacean acid metabolism, because the process was first studied in members of the plant family Crassulaceae. Most CAM plants are water-storing succulents such as cacti, bromeliads (including pineapple), and sedums. To avoid water loss, CAM plants keep their stomata closed during the day and open them at night, when it is cooler and the relative humidity is higher. How, then, do CAM plants carry out photosynthesis? Figure 8.17 compares CAM plants with the other type of C4 plants we considered in Figure 8.16. Photosynthesis in CAM plants occurs entirely within mesophyll cells, but the synthesis of a C4 molecule and the Calvin cycle occur at different times. During the night when temperatures are cooler, the stomata of CAM plants open, thereby allowing the entry of CO2 into mesophyll cells. CO2 is joined with PEP to form the fourcarbon molecule oxaloacetate. This is then converted to malate, which accumulates during the night in the central vacuoles of the cells. In the morning, the stomata close to conserve moisture. The accumulated malate in the mesophyll cells leaves the vacuole and is broken down to release CO2, which then drives the Calvin cycle during the daytime.

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Mesophyll cells: Form a protective layer around bundle-sheath cells so they are not exposed to high O2.

PEP C C C Oxaloacetate C C C C

AMP + PPi

O2

Bundle-sheath cells: Site of the Calvin cycle.

Mesophyll cell—exposed to high O2 and low CO2 PEP carboxylase

CO2

High O2 and low CO2 diffuse around the mesophyll cells.

ATP

O2 O2 O2 CO2

O2

+ Pi

Malate C C C C

Pyruvate C C C Stomata

CO2 Calvin cycle

Vein

Bundle-sheath cell—accumulates CO2, not exposed to high O2 levels

Epidermal cells

Vein Sugar

Figure 8.16  Leaf structure and its relationship to the C4 cycle.  C4 plants have mesophyll cells, which initially take up CO2, and bundle-sheath cells, where much of the carbohydrate synthesis occurs. Compare this leaf structure with the structure of C3 leaves shown in Figure 8.2. Concept Check:   How does the cellular arrangement in C4 plants minimize photorespiration? 

CO2

CO2

Mesophyll cell 3C

Mesophyll cell

3C

C4 4 C cycle

C4 cycle

4C 3C

Calvin cycle

Vein

3C

CO2 Bundlesheath cell

Sugar C4 plants

CO2 is initially incorporated into a 4-carbon molecule.

CO2 Calvin cycle

4C Night 4C

Day

The 4-carbon molecule releases CO2, which is incorporated into the Calvin cycle. Vein

Sugar

CAM plants

Figure 8.17  A comparison of C4 and CAM plants.  The name C4 designates those plants in which the first organic product of carbon fixation is a four-carbon molecule. Using this definition, CAM plants are a type of C4 plant. CAM plants, however, do not separate the functions of making a four-carbon molecule and the Calvin cycle into different types of cells. Instead, they make a four-carbon molecule at night and break down that molecule during the day so the CO2 can be used in the Calvin cycle. (left): ©Wesley Hitt/Getty Images; (right): ©John Foxx/Getty Images Concept Check:   What are the advantages for C3, C4, and CAM plants? 



PHOTOSYNTHESIS 181

Summary of Key Concepts 8.1  Overview of Photosynthesis ∙∙ Photosynthesis is the process by which plants, algae, and photosynthetic bacteria capture light energy that is used to synthesize carbohydrates. ∙∙ During photosynthesis, carbon dioxide, water, and energy are used to make carbohydrates and oxygen. ∙∙ Heterotrophs must obtain organic molecules in their food, whereas autotrophs make organic molecules from inorganic sources. Photoautotrophs use the energy from light to make organic molecules. ∙∙ An energy cycle occurs in the biosphere in which photosynthesis uses light, CO2, and H2O to make organic molecules, and the organic molecules are broken back down to CO2 and H2O via cellular respiration to supply energy in the form of ATP (Figure 8.1). ∙∙ In plants and algae, photosynthesis occurs within chloroplasts, organelles with an outer membrane, inner membrane, and thylakoid membrane. The stroma is the fluid-filled region between the thylakoid membrane and inner membrane. In plants, the leaves are the major site of photosynthesis (Figure 8.2). ∙∙ The light reactions of photosynthesis capture light energy to make ATP, NADPH, and O2. These reactions occur at the thylakoid membrane. Carbohydrate synthesis via the Calvin cycle uses ATP and NADPH from the light reactions and happens in the stroma (Figure 8.3).

8.2  Reactions That Harness Light Energy ∙∙ Light is a form of electromagnetic radiation that travels in waves and is composed of photons with discrete amounts of energy (Figure 8.4). ∙∙ Electrons can absorb light energy and be boosted to a higher energy level—an excited state (Figure 8.5). ∙∙ Photosynthetic pigments include chlorophylls a and b and carotenoids. These pigments absorb light energy in the visible spectrum to drive photosynthesis (Figures 8.6, 8.7).

∙∙ The Z scheme proposes that an electron absorbs light energy twice, at both PSII and PSI, losing some of that energy as it flows along the ETC in the thylakoid membrane (Figure 8.12).

8.4  S  ynthesizing Carbohydrates via the Calvin Cycle ∙∙ The Calvin cycle is composed of three phases: carbon fixation, reduction and carbohydrate production, and regeneration of ribulose bisphosphate (RuBP). In this cycle, ATP is used as a source of energy, and NADPH is used as a source of high-energy electrons to incorporate CO2 into a carbohydrate (Figure 8.13). ∙∙ Calvin and Benson determined the steps in the Calvin cycle by isotope-labeling methods in which the products of the Calvin cycle were separated by paper chromatography (Figure 8.14).

8.5  Variations in Photosynthesis ∙∙ C3 plants incorporate CO2 into RuBP to make 3PG, a three-carbon molecule (Figure 8.15). ∙∙ Photorespiration occurs when the level of O2 is high and CO2 is low, which happens under hot and dry conditions. During this process, some O2 is used and CO2 is liberated. Photorespiration is inefficient because it reverses the incorporation of CO2 into an organic molecule. ∙∙ Some C4 plants avoid photorespiration by first incorporating CO2, via PEP carboxylase, into a four-carbon molecule, which is pumped from mesophyll cells into bundle-sheath cells. This maintains a high concentration of CO2 in the bundle-sheath cells, where the Calvin cycle occurs. The high CO2 concentration minimizes photorespiration (Figure 8.16). ∙∙ CAM plants, a type of C4 plant, prevent photorespiration by fixing CO2 into a four-carbon molecule at night and then running the Calvin cycle during the day with their stomata closed to reduce water loss (Figure 8.17).

Assess & Discuss Test Yourself

∙∙ During linear electron flow, electrons from photosystem II (PSII) follow a pathway along an electron transport chain (ETC) in the thylakoid membrane. This pathway generates an H+ gradient that is used to make ATP. In addition, light energy striking photosystem I (PSI) boosts electrons to a very high energy level that allows the synthesis of NADPH (Figure 8.8).

1. The water necessary for photosynthesis a. is split into H2 and O2. b. is directly involved in the synthesis of carbohydrates. c. provides the electrons to replace those lost in photosystem II. d. provides the H+ needed to synthesize G3P. e. does none of the above.

∙∙ During cyclic photophosphorylation, electrons are activated in PSI and flow through the ETC back to PSI. This cyclic electron flow produces an H+ gradient that is used to make ATP (Figure 8.9).

2. In PSII, P680 differs from the pigment molecules of the light-harvesting complex in that it a. is a carotenoid. b. absorbs light energy and transfers that energy to other molecules via resonance energy transfer. c. transfers an excited electron to the primary electron acceptor. d. transfer an excited electron to O2. e. acts like ATP synthase to produce ATP.

∙∙ Cytochrome b6 in chloroplasts and cytochrome b in mitochondria are homologous proteins involved in electron transport and H+ pumping (Figure 8.10).

8.3  Molecular Features of Photosystems ∙∙ In the light-harvesting complex of PSII, pigment molecules absorb light energy that is transferred to the reaction center via resonance energy transfer. A high-energy electron from P680* is transferred to a primary electron acceptor. An electron from water then replaces the electron lost by P680* (Figure 8.11).

3. The cyclic electron flow that occurs via photosystem I produces a. NADPH. b. oxygen. c. ATP. d. all of the above. e. a and c only.

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4. During linear electron flow, the high-energy electron from P680* a. eventually moves to NADP+. b. becomes incorporated in water molecules. c. is pumped into the thylakoid space to drive ATP production. d. provides the energy necessary to split water molecules. e. falls back to the low-energy state in photosystem II. 5. During the first phase of the Calvin cycle, carbon dioxide is incorporated into ribulose bisphosphate (RuBP) by a. oxaloacetate. b. rubisco. c. RuBP. d. quinone. e. G3P. 6. The NADPH produced during the light reactions is necessary for a. the carbon fixation phase, which incorporates carbon dioxide into an organic molecule during the Calvin cycle. b. the reduction phase, which produces carbohydrates in the Calvin cycle. c. the regeneration of RuBP of the Calvin cycle. d. all of the above. e. a and b only. 7. The majority of the G3P produced during the reduction and carbohydrate production phase is used in making a. glucose. b. ATP. c. RuBP to continue the cycle. d. rubisco. e. all of the above. 8. Photorespiration a. is the process in which plants use sunlight to make ATP. b. is an inefficient way that plants can produce organic molecules by using O2 and releasing CO2. c. is a process that plants use to convert light energy to NADPH. d. occurs in the thylakoid lumen. e. is the normal process of carbohydrate production in cool, moist environments.

9. Photorespiration is avoided by C4 plants because a. these plants separate the formation of a four-carbon molecule from the rest of the Calvin cycle in different cells. b. these plants carry out only anaerobic respiration. c. the enzyme PEP carboxylase functions to maintain high CO2 concentrations in the bundle-sheath cells. d. all of the above. e. a and c only. 10. Plants commonly found in hot and dry environments that carry out carbon fixation at night are a. oak trees. b. C3 plants. c. CAM plants. d. all of the above. e. a and b only.

Conceptual Questions 1. What are the two stages of photosynthesis? What are the key products of each stage?  2. What is the function of NADPH in the Calvin cycle?  3.

Core Concept: Energy and Matter  At the level of the biosphere, what is the role of photosynthesis in the utilization of energy by living organisms? 

Collaborative Questions 1. Discuss the advantages and disadvantages of being a heterotroph or a photoautotroph. 2. Biotechnologists are trying to genetically modify C3 plants to convert them to C4 or CAM plants. Why would this be useful? What genes might you introduce into C3 plants to convert them to C4 or CAM plants?

CHAPTER OUTLINE 9.1 General Features of Cell Communication 9.2 Cellular Receptors and Their Activation 9.3 Signal Transduction and the Cellular Response 9.4 Hormonal Signaling in Multicellular Organisms 9.5 Apoptosis: Programmed Cell Death Summary of Key Concepts Assess & Discuss

O

ver 2 billion cells will die in your body during the next hour. In an adult human body, approximately 50–70 billion cells die each day due to programmed cell death—the process in which a cell breaks apart into small fragments (see the chapter opening photo). In a year, your body produces and purposely destroys a mass of cells that is equal to its total weight! Though this may seem like a scary process, it’s actually keeping you healthy. Programmed cell death, also called apoptosis, ensures that your body maintains a proper number of cells. It also eliminates cells that are worn out or potentially harmful, such as cancer cells. Programmed cell death can occur via signals that intentionally cause particular cells to die, or it can result from a failure of proper cell communication. It may also happen when environmental agents cause damage to a cell. Programmed cell death is one example of a response that involves cell communication—the process by which cells can detect, interpret, and respond to signals in their environment. A signal is an agent that can influence the properties of cells. In this chapter, we will examine how cells detect environmental signals and also how they produce signals that enable them to communicate with other cells. Communication at the cellular level involves not only receiving and sending signals but also their interpretation. For this to occur, a signal must be recognized by a cellular protein called a receptor. When a signal and a receptor interact, the receptor changes shape, or conformation, thereby changing the way the receptor interacts with cellular factors. These interactions eventually lead to some type of response in the cell. We begin the chapter with the general features of cell communication, and then discuss the main ways in which cells receive, process, and respond to signals sent by other cells. As you will learn, cell communication involves an amazing diversity of signaling molecules and cellular proteins that are devoted to this process. We conclude by looking at the role of cell communication in apoptosis, in which a cell becomes programmed to die.

Cell Communication

9 Programmed cell death. The two cells shown here are breaking apart because signaling molecules initiated a pathway that programmed their death. ©David McCarthy/SPL/Science Source

9.1    General Features of Cell Communication Learning Outcomes: 1. Explain the two general reasons for cell signaling: responding to environmental changes and cell-to-cell communication. 2. Compare and contrast the five ways that cells communicate with each other based on the distance between them. 3. Outline the three-stage process of cell signaling.

All living cells, including those of bacteria, archaea, protists, fungi, plants, and animals, must engage in cell communication to survive. Cell communication, also known as cell signaling, involves both incoming and outgoing signals. For example, on a sunny day, cells can sense their exposure to ultraviolet (UV) light—a physical signal—and respond accordingly. In humans, UV light acts as an incoming signal to promote the synthesis of melanin, a protective

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pigment that helps to prevent the harmful effects of UV radiation. In addition, cells produce outgoing signals that influence the behavior of neighboring cells. Plant cells, for example, produce hormones that influence the pattern of cell elongation so the plant grows toward light. Cells of all living organisms both respond to incoming signals and produce outgoing signals. Cell communication is a two-way street. In this section, we begin by considering why cells need to respond to signals. We will then examine various forms of signaling that are based on the distance between the cells that communicate with each other. Finally, we will examine the main steps that occur when a cell is exposed to a signal and produces a response to it.

Yeast cell

Responding to Changes in the Environment  The first reason for cell communication is that cells need to respond to a changing environment. Changes in the environment are a persistent feature of life, and living cells are continually faced with alterations in temperature and availability of nutrients, water, and light. A cell may even be exposed to a toxic chemical in its environment. Being able to respond to change at the cellular level is called a cellular response. As an example, let’s consider the response of a yeast cell to glucose in its environment (Figure 9.1). Some of the glucose acts as a signaling molecule that binds to a receptor and causes a cellular response. In this case, the cell responds by increasing the number of glucose transporters needed to take glucose into the cell and also by increasing the number of metabolic enzymes required to utilize glucose once it is inside. The cellular response allows the cell to use glucose efficiently. Cell-to-Cell Communication  A second reason for cell communication is the need for cells to share information with each other—a

Glucose

Glucose transporter

Exposure to glucose Metabolic enzyme Due to glucose in the environment, the yeast cell on the right has undergone a cellular response by synthesizing more glucose transporters and enzymes that are needed to metabolize glucose.

Cells Detect and Respond to Signals from Their Environment and from Other Cells Before getting into the details of cell communication, let’s take a general look at why cell communication is necessary.

Glucose receptor

Figure 9.1  Response of a yeast cell to glucose.  When glucose is

absent from the extracellular environment, the cell is not well prepared to take up and metabolize this sugar. However, when glucose is present, some of that glucose binds to receptors in the membrane, which leads to changes in the amounts and properties of intracellular and membrane proteins so the cell can readily use glucose. Concept Check:  What is the signaling molecule in this example? 

type of cell communication called cell-to-cell communication. In one of the earliest experiments demonstrating cell-to-cell communication, Charles Darwin and his son Francis Darwin studied phototropism, the phenomenon in which plants grow toward light (Figure 9.2). The Darwins observed that the actual bending occurs in a zone below the growing shoot tip. They concluded that a signal must be transmitted from the growing tip to lower parts of the shoot. Later research revealed that the signal is a molecule called auxin, which is transmitted from cell to cell. A higher amount of auxin accumulates on the nonilluminated side of the shoot and promotes cell elongation on that side of the shoot only, thereby causing the shoot to bend toward the light source.

Cells in the growing shoot tip sense light and send a signal (auxin) to cells on the nonilluminated side of the shoot.

Growing shoot tip of plant

Phototropism

Cells located below the growing tip receive this signal and elongate, thereby causing a bend in the shoot. In this way, the tip grows toward the light.

Figure 9.2  Phototropism in plants.  This process involves cell-to-cell communication that leads to a shoot bending toward light just beneath its actively growing tip. (inset): ©Cordelia Molloy/SPL/Science Source

Core Skill: Connections  Look ahead to Figure 37.5. How does light affect the distribution of auxin produced by a plant’s growing shoot tip?



CELL COMMUNICATION 185

Signaling molecule

Gap junction

Membrane-bound signaling molecule

Target cell Target cell

Receptor (a) Direct intercellular signaling: Signals pass through a cell junction from the cytosol of one cell to adjacent cells.

(b) Contact-dependent signaling: Membrane-bound signals bind to receptors on adjacent cells.

(c) Autocrine signaling: Cells release signals that affect themselves and nearby target cells.

Hormone

Target cell

Bloodstream

Target cell

Endocrine cell

(d) Paracrine signaling: Cells release signals that affect nearby target cells.

(e) Endocrine signaling: Cells release signals that travel long distances to affect target cells.

Figure 9.3  Types of cell-to-cell communication based on the distance between cells. Concept Check:  Which type of signal, paracrine or endocrine, is likely to exist for a longer period of time? Explain why this longer existence is necessary. 

Cell-to-Cell Communication Can Occur Between Adjacent Cells and Between Cells That Are Long Distances Apart Organisms have a variety of different mechanisms to achieve cell-tocell communication. The mode of communication depends, in part, on the distance between the cells that need to communicate with each other. Let’s first examine the various ways in which signals are transferred between cells. Later in this chapter, we will learn how such signals elicit a cellular response. One way to categorize cell signaling is by the manner in which the signal is transmitted from one cell to another. Signals are relayed between cells in five common ways, all of which involve a cell that produces a signal and a target cell that receives the signal (Figure 9.3). Direct Intercellular Signaling  In a multicellular organism, cells adjacent to each other may have contacts, called cell junctions, that enable them to pass ions, signaling molecules, and other materials between the cytosol of one cell and the cytosol of the other (Figure 9.3a). For example, cardiac muscle cells, which cause your heart to beat, have intercellular connections called gap junctions that allow the passage of ions needed for the coordinated contraction of these cells. We will examine how gap junctions work in Chapter 10. Contact-Dependent Signaling  Not all signaling molecules diffuse from one cell to another. Some molecules are bound to the surface of

a cell and provide a signal to other cells that make contact with the surface of that cell (Figure 9.3b). In the case of contact-dependent signaling, one cell has a membrane-bound signaling molecule that is recognized by a receptor on the surface of another cell. This type of cell-to-cell communication occurs, for example, when portions of neurons (nerve cells) grow and make contact with other neurons. This is important for the formation of the proper connections between neurons. Autocrine Signaling  In autocrine signaling, a cell secretes signaling molecules that bind to receptors on its own cell surface and on the surfaces of neighboring cells of the same cell type, stimulating a response (Figure 9.3c). What is the purpose of autocrine signaling? It is often important for groups of cells to sense cell density. When cell density is high, the concentration of autocrine signals is also high. In some cases, such signals inhibit further cell growth, thereby limiting cell density. Paracrine Signaling  In paracrine signaling, a specific cell secretes a signaling molecule that does not affect that cell but instead influences the behavior of target cells in close proximity (Figure 9.3d). Paracrine signaling is typically of short duration. Usually, the signal is broken down too quickly to be carried to other parts of the body and affect distant cells. A specialized form of paracrine signaling occurs in the nervous systems of animals. Neurotransmitters—molecules made in neurons that transmit a signal to an adjacent cell—are released at the end of a neuron and traverse a narrow space called the synapse (see Chapter 42). The neurotransmitter then binds to a receptor in a target cell.

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3

Receptor activation: The binding of a signaling molecule causes a conformational change in a receptor that activates its function.

Signaling molecule

2 Activated receptor protein

Inactive receptor protein

Cellular response: The signal transduction pathway affects the functions and/or amounts of cellular proteins, thereby producing a cellular response.

Signal transduction: The activated receptor stimulates a series of proteins that forms a signal transduction pathway.

Signal transduction pathway

Intracellular targets

Cellular response

Enzyme

Altered metabolism or other cell functions

Structural proteins

Altered cell shape or movement

Transcription factor

Altered gene expression, which changes the types and the amounts of proteins that are made in the cell

Nucleus

Figure 9.4  The three stages of cell signaling: receptor activation, signal transduction, and a cellular response. Concept Check:  Explain why a signal transduction pathway is necessary for most signaling molecules to have an effect. 

Endocrine Signaling  In contrast to the previous mechanisms of cell-to-cell communication, endocrine signaling occurs over relatively long distances (Figure 9.3e). In both animals and plants, molecules involved in long-distance signaling are called hormones. They usually last longer than signaling molecules involved in autocrine and paracrine signaling. In mammals, endocrine signaling involves the secretion of hormones into the bloodstream, which may affect virtually all cells of the body, including those that are far from the cells that secrete the signaling molecules. In flowering plants, hormones move through the plant vascular system and also move through adjacent cells. Some hormones are even gases that diffuse into the air. Ethylene, a gas given off by plants, plays a variety of roles, such as accelerating the ripening of fruit.

Cells Usually Respond to Signals via a ThreeStage Process Up to this point, we have seen how signals influence the behavior of cells in close proximity or at long distances, interacting with receptors to elicit a cellular response. What events occur when a cell receives a signal? In most cases, the binding of a signaling molecule to a receptor causes the receptor to activate a signal transduction pathway, which then leads to a cellular response. Figure 9.4 diagrams the three common stages of cell signaling: receptor activation, signal transduction, and a cellular response. Stage 1: Receptor Activation  In the initial stage, a signaling molecule binds to a receptor of the target cell, causing a conformational change in the receptor that activates its function. In most cases, the activated receptor initiates a response by causing changes in a series of proteins that collectively forms a signal transduction pathway, as described next.

Stage 2: Signal Transduction  During signal transduction, the initial signal is converted—or transduced—to a different signal inside the cell. This process is carried out by a group of proteins that form a signal transduction pathway. These proteins undergo a series of changes that may result in the production of an intracellular signaling molecule. However, some receptors are intracellular and do not activate a signal transduction pathway. As discussed later, certain types of intracellular receptors directly cause a cellular response. Stage 3: Cellular Response  Cells respond to signals in several different ways. Figure 9.4 shows three common categories of proteins that are controlled by cell signaling: enzymes, structural proteins, and transcription factors. 1. Many signaling molecules exert their effects by altering the activity of one or more enzymes. For example, certain hormones provide a signal that the body needs energy. These hormones activate enzymes that are required for the breakdown of molecules such as carbohydrates. 2. Cells also respond to signals by altering the functions of structural proteins in the cell. For example, when animal cells move during embryonic development or when an amoeba moves toward food, signals play a role in the rearrangement of actin filaments, which are components of the cytoskeleton. The coordination of signaling and changes in the cytoskeleton enables a cell to move in the correct direction. 3. Signaling molecules may also affect the function of transcription factors—proteins that regulate the transcription of genes. Some transcription factors activate gene expression. For example, when cells are exposed to sex hormones, transcription factors activate genes that change the properties of cells, which can lead to changes in the sexual characteristics of entire organisms. As discussed in Section 51.3, estrogens and androgens are



CELL COMMUNICATION

responsible for the development of secondary sex characteristics in humans, including breast development in females and beard growth in males.

9.2         C  ellular Receptors and Their Activation Learning Outcomes: 1. CoreSKILL » Calculate the affinity, measured as a dissociation constant, that a receptor has for its signaling molecule, or ligand. 2. Explain how a signaling molecule activates a receptor. 3. Identify three general types of cell surface receptors. 4. Describe intracellular receptors, using estrogen receptors as an example.

In this section, we will take a closer look at receptors and their interactions with signaling molecules. We will compare receptors based on whether they are located on the cell surface or inside the cell. In this chapter, our focus will be on receptors that respond to chemical signaling molecules. Other receptors discussed in Units VI and VII respond to mechanical motion (mechanoreceptors), temperature changes (thermoreceptors), and light (photoreceptors).

Signaling Molecules Bind to Receptors The ability of cells to respond to a signal usually requires precise recognition between a signal and its receptor. In many cases, the signal is a molecule, such as a steroid or a protein, that binds to the receptor. A signaling molecule binds to a receptor in much the same way that a substrate binds to the active site of an enzyme, as described in Chapter 6. The signaling molecule, which is called a ligand, binds noncovalently to the receptor with a high degree of specificity. The binding occurs when the ligand and receptor happen to collide in the correct orientation with enough energy to form a ligand∙receptor complex.

Kd is called the dissociation constant between a ligand and its receptor. The Kd value is inversely related to the affinity between the ligand and receptor. A low Kd value indicates that a receptor has a high affinity for its ligand. Let’s look carefully at the left side of this equation and consider what it means. At a ligand concentration at which half of the receptors are bound to a ligand, the concentration of the ligand∙receptor complex equals the concentration of receptor that doesn’t have ligand bound. At this ligand concentration, [Receptor] and [Ligand∙Receptor complex] cancel out of the equation because they are equal. Therefore, at a ligand concentration at which half of the receptors have bound ligand: Kd = [Ligand] When the ligand concentration is above the Kd value, most of the receptors are likely to have ligand bound to them. In contrast, if the ligand concentration is substantially below the Kd value, most receptors will not be bound by their ligand. The Kd values for many different ligands and their receptors have been experimentally determined. How is this information useful? It allows researchers to predict when a signaling molecule is likely to cause a cellular response. If the concentration of a signaling molecule is far below the Kd value, a cellular response is not likely because relatively few receptors will form a complex with a signaling molecule.

Receptors Undergo Conformational Changes Unlike enzymes, which convert their substrates into products, receptors do not usually alter the structure of their ligands. Instead, the ligands alter the structure of their receptors, causing a conformational change (Figure 9.5). In this case, the binding of the ligand to its receptor changes the receptor in a way that activates its ability to initiate a cellular response. Because the binding of a ligand to its receptor is a reversible process, the ligand and receptor will dissociate. Once the ligand is released, the receptor is no longer activated.

              kon

Ligand (signaling molecule)

[Ligand] + [Receptor]   ⇌   [Ligand∙Receptor complex]

                koff Square brackets, [ ], indicate concentration. The value kon is the rate at which binding occurs. After a complex forms between the ligand and its receptor, the noncovalent interaction between ligand and receptor remains stable for a finite period of time. The term koff is the rate at which the ligand•receptor complex falls apart or dissociates. In general, the binding and dissociation of a ligand and its receptor occur relatively rapidly, and therefore an equilibrium is reached when the rate of formation of new ligand•receptor complexes equals the rate at which existing ligand∙receptor complexes dissociate: kon [Ligand][Receptor] = koff [Ligand•Receptor complex] Rearranging the equation gives   [Ligand][Receptor]     koff _______________________ = _____ = Kd [Ligand•Receptor complex]    kon

187

Inactive receptor

d Ligan ng i d bin

Activated receptor

Cytosol

The binding of a ligand to its receptor causes a conformational change in the receptor, resulting in receptor activation.

Figure 9.5  Receptor activation.  ore Skill: Connections  Look back at Figure 6.6. C How is the binding of a ligand to its receptor similar to the binding of a substrate to an enzyme? How are these processes different?

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Cells Contain a Variety of Cell Surface Receptors That Respond to Extracellular Signals Most signaling molecules are either small hydrophilic molecules or large molecules that do not readily pass through the plasma membrane of cells. Such extracellular signaling molecules bind to cell surface receptors— receptors found in the plasma membrane. A typical cell usually contains dozens or even hundreds of different cell surface receptors that enable the cell to respond to different kinds of extracellular signaling molecules. By analyzing the functions of cell surface receptors from many different organisms, researchers have determined that most fall into one of three categories: enzyme-linked receptors, G-protein-coupled receptors, and ligand-gated ion channels, which are described next. Enzyme-Linked Receptors  Receptors known as enzyme-linked receptors are found in all living species. Many human hormones bind to this type of receptor. For example, when insulin binds to an enzymelinked receptor in muscle cells, it enhances the ability of those cells to use glucose. Enzyme-linked receptors typically have two important domains: an extracellular domain, which binds to a signaling molecule, and an intracellular domain, which has a catalytic function (Figure 9.6a). When a signaling molecule binds to the extracellular domain, a conformational change is transmitted through the membraneembedded portion of the protein and affects the conformation of the intracellular catalytic domain. In most cases, this conformational change causes the intracellular catalytic domain to become functionally active.

Most types of enzyme-linked receptors function as protein kinases, enzymes that transfer a phosphate group from ATP to specific amino acids in a protein (Figure 9.6b). For example, tyrosine kinases attach phosphate to the amino acid tyrosine, whereas serine/threonine kinases attach phosphate to the amino acids serine and threonine. In the example shown in Figure 9.6b, the catalytic domain of the receptor remains inactive when no signaling molecule is present. However, when a signal binds to the extracellular domain, the catalytic domain is activated. Under these conditions, the receptor may phosphorylate itself, or it may phosphorylate intracellular proteins. The attachment of a negatively charged phosphate changes the structure of a protein and thereby alters its function. Later in this chapter, we will explore how this event leads to a cellular response, such as the activation of enzymes that affect cell function. G-Protein-Coupled Receptors  Receptors called G-protein-coupled receptors (GPCRs) are found in the cells of all eukaryotic species and are particularly common in animals. GPCRs typically contain seven transmembrane segments that wind back and forth through the plasma membrane. The receptors interact with intracellular proteins called G proteins, which are so named because of their ability to bind guanosine triphosphate (GTP) and guanosine diphosphate (GDP). GTP is similar in structure to ATP except it has guanine as a base instead of adenine. In the 1970s, the existence of G proteins was first proposed by Martin Rodbell and colleagues, who found that GTP is needed for certain hormone receptors to cause an intracellular response. Later,

Inactive receptor Signaling molecule

A signaling molecule binds and activates the catalytic domain of the receptor.

Signaling molecule Activated receptor

Extracellular signalbinding domain

Extracellular environment

Cytosol

(a) Structure of enzyme-linked receptors

Intracellular catalytic domain Intracellular catalytic domain becomes active when signaling molecule is bound.

Unphosphorylated protein

ATP

+

ADP

Phosphorylated protein (b) A receptor that functions as a protein kinase

The receptor then can catalyze the transfer of a phosphate group from ATP to an intracellular protein.

Figure 9.6  Enzyme-linked receptors. Core Skill: Modeling  The goal of this modeling challenge is to predict the possible locations where an amino acid substitution may prevent receptor activation. Modeling Challenge: Figure 9.6 is a general model that shows how the binding of a ligand to an enzyme-linked receptor results in receptor activation. Let’s suppose that researchers have identified a mutant version of this type of receptor in which the ligand can still bind to the receptor correctly, but the receptor is not activated. In other words, the binding of the ligand does not cause the receptor to phosphorylate intracellular proteins. The mutation changes just one amino acid in the receptor protein by substituting a glycine (found in the normal protein) to a glutamic acid. On the model shown in part (a) of the figure, put two X’s in places where you think the glutamic acid might be found in the mutant receptor, and place a Y where you think it would not be found. Briefly explain your chosen locations.



CELL COMMUNICATION

1

2

A signaling molecule binds to a GPCR, causing it to bind to a G protein.

Receptor protein (GPCR)

The G protein exchanges GDP for GTP. The G protein then dissociates from the receptor and separates into an active α subunit and a β/γ dimer. The activated subunits promote cellular responses. Signaling molecule

α GDP

189

β

+

GTP

γ GDP released

Inactive G protein

Activated G protein α subunit

Activated G protein β/γ dimer

Pi Cytosol

3

The signaling molecule eventually dissociates from the receptor, and the α subunit hydrolyzes GTP into GDP + Pi. The α subunit and the β/γ dimer reassociate.

Figure 9.7  The activation of G-protein-coupled receptors (GPCRs) and G proteins.  Note: All three receptors shown in this figure are the same receptor, but the one on the left is drawn with greater detail to emphasize that it has seven transmembrane segments. Concept Check:  What has to happen before the α and β/γ subunits of the G protein can reassociate with each other? 

Alfred Gilman and coworkers used genetic and biochemical techniques to identify and purify a G protein. In 1994, Rodbell and Gilman won the Nobel Prize in Physiology or Medicine for their pioneering work. Figure 9.7 shows how a GPCR and a G protein interact. At the cell surface, a signaling molecule binds to a GPCR, causing a conformational change that activates the receptor, enabling it to bind to a G protein. The G protein, which is a lipid-anchored protein, releases GDP and binds GTP instead. The binding of GTP changes the conformation of the G protein, causing it to dissociate into an α subunit and a β/γ dimer. Later in this chapter, we will examine how the α subunit interacts with other proteins in a signal transduction pathway to elicit a cellular response. The β/γ dimer also plays a role in signal transduction. For example, it can regulate the function of ion channels in the plasma membrane. When a signaling molecule and a GPCR dissociate, the GPCR is no longer activated, and the cellular response is reversed. For the G protein to return to the inactive state, the α subunit first hydrolyzes its bound GTP to GDP and Pi. After this occurs, the α and β/γ subunits reassociate with each other to form an inactive G protein. Ligand-Gated Ion Channels  As described in Chapter 5, ion channels are proteins that allow the diffusion of ions across cell membranes. Ligand-gated ion channels are a third type of cell surface receptor found in the plasma membranes of animal, plant, and fungal cells. When signaling molecules (ligands) bind to this type of receptor, the ion channel opens and allows the flow of ions through the membrane, changing the concentration of the ions in the cell (Figure 9.8). In animals, ligand-gated ion channels are important in the transmission of signals between neurons and muscle cells and between two

Signaling molecule Ions

Cytosol

The binding of two extracellular signaling molecules (ligands) opens the ion channel, permitting ions to pass through the membrane.

Figure 9.8  The function of a ligand-gated ion channel. neurons. In addition, ligand-gated ion channels in the plasma membrane allow the influx of Ca2+ into the cytosol. Changes in the cytosolic concentration of Ca2+ often play a role in signal transduction.

Cells Also Have Intracellular Receptors Activated by Signaling Molecules That Pass Through the Plasma Membrane Although most receptors for signaling molecules are located in the plasma membrane, some are found inside the cell. In these cases, an extracellular signaling molecule must diffuse through the plasma membrane to gain access to its receptor.

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2

Estrogen receptor subunits form a dimer, bind next to specific genes, and activate their transcription. The mRNAs are then translated into proteins that affect the structure and function of the cell.

Estrogen

Active Estrogen receptor mRNA Inactive estrogen receptor subunit

1

Estrogen diffuses across the plasma membrane, enters the nucleus, and binds to estrogen receptor subunits. The subunits undergo a conformational change.

Protein that affects cell structure and function

Chromosomal DNA Nucleus

Figure 9.9  Estrogen receptor in mammalian cells.  This is an example of an intracellular receptor. Core Concept: Structure and Function  The structure of the estrogen receptor, which is a dimer, has two important sites: the estrogen-binding site and the DNA-binding site. When estrogen binds to its receptor, a conformational change occurs that allows the DNA-binding site to function. The estrogen receptor then binds to the DNA and activates the transcription of specific genes.

In vertebrates, receptors for steroid hormones are intracellular. As discussed in Chapter 51, steroid hormones, such as estrogens and androgens, are secreted into the bloodstream from cells of endocrine glands. The behavior of estrogen is typical of many steroid hormones (Figure 9.9). Because estrogen is hydrophobic, it can diffuse through the plasma membrane of a target cell and bind to receptor subunits inside the cell. Some steroids bind to receptor subunits in the cytosol, which then travel into the nucleus. Other steroid hormones, such as estrogen, bind to receptor subunits already in the nucleus. After this binding occurs, the estrogen receptor subunit undergoes a conformational change that enables it to form a dimer with another subunit that also has estrogen bound. The dimer, which is the active estrogen receptor, then binds to the DNA and activates the transcription of specific genes. The estrogen receptor is an example of a transcription factor—a protein that regulates the transcription of genes. The expression of specific genes changes cell structure and function in a way that results in a cellular response.

9.3        Signal Transduction and the Cellular Response Learning Outcomes: 1. For signaling molecules that bind to receptor tyrosine kinases or G-protein-coupled receptors, describe the signal transduction pathways and how those pathways lead to a cellular response. 2. Relate the function of second messengers to signal transduction pathways.

3. List examples of second messengers, and explain how they exert their effects.

We now turn our attention to the intracellular events that enable a cell to respond to a signaling molecule that binds to a cell surface receptor: signal transduction and a cellular response. In most cases, the binding of a signaling molecule to its receptor stimulates a signal transduction pathway. We will begin by examining a pathway that is controlled by an enzyme-linked receptor, and then consider G-protein-coupled receptors.

Receptor Tyrosine Kinases Activate Signal Transduction Pathways Involving a Protein Kinase Cascade That Alters Gene Transcription Receptor tyrosine kinases are a category of enzyme-linked receptors that are found in all animals and also in choanoflagellates, which are the protists that are most closely related to animals (see Chapter 28). However, they are not found in bacteria, archaea, or other eukaryotic species. (Bacteria do have receptor histidine kinases, and all eukaryotes have receptor serine/threonine kinases.) The human genome contains about 60 different genes that encode receptor tyrosine kinases that recognize various types of signaling molecules such as hormones. Figure 9.10 shows a simplified signal transduction pathway for epidermal growth factor (EGF). A growth factor is a signaling molecule that promotes cell division. Multicellular organisms, such as plants and animals, produce a variety of different growth factors to coordinate cell division throughout the body. In vertebrate animals,



CELL COMMUNICATION 191

KEY 1

Signaling molecules

Receptor activation: Two EGF molecules bind to 2 EGF receptor subunits, causing them to dimerize and phosphorylate each other on tyrosines.

Receptor Relay proteins 5

P

EGF molecules Relay proteins

P

Grb

P

P

P

Protein kinases

Cellular response: Myc and Fos stimulate the transcription of specific genes. The mRNAs are translated into proteins that cause the cell to advance through the cell cycle and divide.

Phosphorylated tyrosines

Transcription factors Newly made proteins

Translation

P

EGF receptor subunits

mRNA

Newly made proteins involved with cell division

P

GDP

P

Myc

Sos Ras

Fos

Erk P

Ras GDP GTP

2

Relay between the receptor and protein kinase cascade: Grb binds to the phosphorylated receptor and then to Sos. Sos stimulates Ras to release GDP and bind GTP.

GTP

Raf

P P

P

Ras

Mek

Mek

Erk

Raf

Raf

Protein kinase cascade

3

Protein kinase cascade: Ras activates Raf, which starts a protein kinase cascade in which Raf phosphorylates Mek, and then Mek phosphorylates Erk.

4

Activation of transcription factors: Erk enters the nucleus and phosphorylates transcription factors, Myc and Fos.

Signal transduction (steps 2–4)

Figure 9.10  The epidermal growth factor (EGF) pathway that promotes cell division. Core Skill: Connections  Look ahead to Figures 15.11 and, in particular, 15.12. Certain mutations alter the structure of the Ras protein so it does not hydrolyze GTP. Such mutations cause cancer. Explain why.

EGF is secreted from endocrine cells, travels through the bloodstream, and binds to a receptor tyrosine kinase, which is located on target cells and called the EGF receptor. EGF is responsible for stimulating epidermal cells, such as skin cells, to divide. Following receptor activation, the three general parts of the signal transduction pathway are (1) relay proteins activate a protein kinase cascade; (2) the protein kinase cascade phosphorylates intracellular proteins such as transcription factors; and (3) the phosphorylated transcription factors stimulate gene transcription. Next, we will consider the details of this pathway. EGF Receptor Activation  For receptor activation to occur, two EGF receptor subunits each bind to a molecule of EGF. The binding of EGF causes the subunits to dimerize and phosphorylate each other on tyrosines within the receptors, which is why they are named receptor tyrosine kinases. Once the EGF receptor is activated, the signal transduction pathway starts.

Relay Proteins  The phosphorylated form of the EGF receptor is first recognized by a relay protein of the signal transduction pathway called Grb. This interaction changes the conformation of Grb, causing it to bind another relay protein in the signal transduction pathway termed Sos, causing it to undergo a conformational change. This activation of Sos causes a third relay protein called Ras to release GDP and bind GTP. The GTP form of Ras is the active form. Protein Kinase Cascade  The function of the relay proteins is to activate a protein kinase cascade. This cascade involves the sequential activation of three protein kinases. Activated Ras binds to Raf, the first protein kinase in the cascade. Raf then phosphorylates Mek, which becomes active and, in turn, phosphorylates Erk. Activation of Transcription Factors and the Cellular Response  The phosphorylated form of Erk enters the nucleus and

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phosphorylates transcription factors such as Myc and Fos. What is the cellular response? Once these transcription factors are phosphorylated, they stimulate the transcription of genes that encode proteins that promote cell division. After these proteins are made, the cell is stimulated to divide. Growth factors such as EGF cause a rapid increase in the expression of many genes in mammals, perhaps as many as 100. As discussed in Chapter 15, growth factor signaling pathways are often involved in cancer. Mutations that cause proteins in these pathways to become hyperactive result in cells that divide uncontrollably!

BIO TIPS

THE QUESTION  One of the genes that is activated by the EGF signaling pathway is a gene called HSF1, which encodes a protein that is thought to be important for regulating cell division. Let’s suppose that researchers have identified a drug that prevents EGF from activating the HSF1 gene. In the laboratory, this drug seems to prevent the growth of certain types of cancer cells. Propose a hypothesis for how this drug exerts its effect. In other words, which protein in the cell might drug X be binding to, and how does drug X affect that protein’s function? T OPIC  What topic in biology does this question address? The topic is cell communication. More specifically, the question asks you to propose a hypothesis explaining how a drug might interfere with the EGF pathway and prevent cancer. I NFORMATION  What information do you know based on the question and your understanding of the topic? From the question, you have learned that the EGF signaling pathway activates the HSF1 gene, which plays a role in regulating cell division. Drug X prevents EGF from turning on the HSF1 gene and inhibits the growth of certain kinds of cancer cells. From your understanding of the topic, you may remember that the EGF pathway involves a series of steps, beginning with the binding of EGF to its receptor. P ROBLEM-SOLVING  S   STRATEGY  Sort out the steps in a complicated process. Propose a hypothesis. One strategy to begin to solve this problem is to analyze the steps in the EGF pathway (see Figure 9.10) and identify the proteins involved. Any of these proteins could potentially be the target of drug X. Propose a hypothesis for how drug X could bind to one of these proteins and alter its function in a way that would prevent the expression of the HSF1 gene and thus prevent cancer cells from dividing.

ANSWER For drug X to exert its effect, it must be inhibiting one of the steps of the EGF pathway. Here are some possible hypotheses for how drug X works: 1. Drug X binds to the EGF receptor and inhibits the ability of EGF to bind to the receptor. 2. Drug X binds to the EGF receptor and inhibits its ability to phosphorylate itself. 3. Drug X binds to Grb and inhibits its ability to bind to the EGF receptor or to Sos.

4. Drug X binds to Sos and inhibits its ability to bind to Grb or to Ras. 5. Drug X binds to Ras and inhibits its ability to bind to Sos or Raf. 6. Drug X binds to Ras and inhibits its ability to release GDP or to bind GTP. 7.  Drug X binds to Raf, Mek, or Erk and inhibits the phosphorylation of its target protein. 8. Drug X binds to Myc or Fos and inhibits the ability to activate a gene.

Second Messengers Such as Cyclic AMP Are Key Components of Many Signal Transduction Pathways Let’s now turn to examples of signal transduction pathways and cellular responses that involve G-protein-coupled receptors (GPCRs). Extracellular signaling molecules that bind to cell surface receptors are sometimes referred to as first messengers. After first messengers bind to receptors such as GPCRs, many signal transduction pathways lead to the production of second messengers—small molecules or ions that relay signals inside the cell. The signals that result in second messenger production often act quickly, in a matter of seconds or minutes, but their duration is usually short. Therefore, such signaling typically occurs when a cell needs a quick and short cellular response. Production of cAMP  Mammalian and plant cells make several different types of G protein α subunits. One type of α subunit binds to adenylyl cyclase, an enzyme in the plasma membrane. This interaction stimulates adenylyl cyclase to synthesize cyclic adenosine monophosphate (cyclic AMP, or cAMP) from ATP (Figure 9.11). cAMP is an example of a second messenger. Signal Transduction Pathway Involving cAMP  Let’s explore a signal transduction pathway in which the GPCR recognizes the hormone epinephrine (also called adrenaline). This hormone is sometimes called the fight-or-flight hormone. Epinephrine is produced when an individual is confronted with a stressful situation and helps the individual deal with a perceived threat or danger. First, epinephrine binds to its receptor and activates a G protein (Figure 9.12). The α subunit then activates adenylyl cyclase, which catalyzes the production of cAMP from ATP. One effect of cAMP is to activate protein kinase A (PKA), which is composed of four subunits: two catalytic subunits that phosphorylate specific cellular proteins, and two regulatory subunits that inhibit the catalytic subunits when they are bound to each other. cAMP binds to the regulatory subunits of PKA. The binding of cAMP separates the regulatory and catalytic subunits, which allows each catalytic subunit to be active. Cellular Response via PKA  How does PKA activation lead to a cellular response? The catalytic subunit of PKA phosphorylates specific cellular proteins such as enzymes, structural proteins, and transcription factors. The phosphorylation of enzymes and structural proteins influences the structure and function of the cell. Likewise, the phosphorylation of transcription factors leads to the synthesis of new proteins that affect cell structure and function. As a specific example of a cellular response, Figure 9.13 shows how a skeletal muscle cell responds to elevated levels of epinephrine.



CELL COMMUNICATION 193 NH2 N

N

H N

CH2

O

O O

P O–

O O

P O–

O O

P

–

O

O–

OH

Adenylyl cyclase

N

N

H

N

Phosphodiesterase

H

N

O

CH2 O

O

O P

O–

P

HO

O–

O

O

H2O

OH

ATP

N

H

CH2

O

PPi (pyrophosphate)

N

N

H H

N

OH

NH2

NH2 N

OH

Cyclic AMP (cAMP)

OH

AMP

Figure 9.11  The synthesis and breakdown of cyclic AMP.  Cyclic AMP (cAMP) is a second messenger formed from ATP by adenylyl cyclase, an enzyme in the plasma membrane. cAMP is inactivated by the action of an enzyme called phosphodiesterase, which converts cAMP to AMP. When PKA becomes active, it phosphorylates two enzymes— phosphorylase kinase and glycogen synthase. Both of these enzymes are involved with the metabolism of glycogen, which is a polymer of glucose used to store energy.

∙ When PKA phosphorylates glycogen synthase, the function of this enzyme is inhibited rather than activated (see Figure 9.13). The function of glycogen synthase is to make glycogen. Therefore, the effect of cAMP is to prevent glycogen synthesis. Taken together, the effects of epinephrine in skeletal muscle cells are to stimulate glycogen breakdown and inhibit glycogen synthesis. This provides these cells with more glucose molecules, which they can use for the energy needed for muscle contraction. In this way, the individual is better prepared to fight or flee.

∙ When phosphorylase kinase is phosphorylated, it becomes activated. The function of phosphorylase kinase is to phosphorylate another enzyme in the cell called glycogen phosphorylase, which then becomes activated. This enzyme causes glycogen breakdown by phosphorylating glucose units at the ends of a glycogen polymer, which releases individual glucose-phosphate molecules from glycogen:

Reversal of the Cellular Response  As mentioned, signaling that involves second messengers is typically of short duration. When the signaling molecule is no longer produced and its concentration falls, a larger percentage of the receptors are not bound by their ligands. When a ligand dissociates from a GPCR, the GPCR becomes deactivated. Intracellularly, the α subunit hydrolyzes its GTP to GDP, and the α subunit and β/γ dimer reassociate to form an inactive G protein

         Glycogen          phosphorylase Glycogenn + Pi Glycogenn−1 + Glucose-phosphate where n is the number of glucose units in the glycogen polymer.

2 1

The binding of epinephrine activates a GPCR. This causes the G protein to bind GTP, thereby promoting the dissociation of the α subunit from the β/γ dimer.

Activated adenylyl cyclase

The binding of the α subunit to adenylyl cyclase promotes the synthesis of cAMP from ATP.

cAMP binds to the regulatory subunits of PKA, which releases the catalytic subunits of PKA.

3 cAMP GTP

P

Epinephrine (signaling molecule) Activated G-protein β/γ dimer Activated G-protein-coupled receptor (GPCR)

Activated G-protein α subunit

ATP

ATP Activated PKA Catalytic subunits

Regulatory subunits

4

ADP

Phosphorylated protein

The catalytic subunits of PKA use ATP to phosphorylate specific cellular proteins and thereby cause a cellular response.

Inactive PKA

Figure 9.12  A signal transduction pathway involving cAMP.  The pathway leading to the formation of cAMP and subsequent activation of protein kinase A (PKA), which is mediated by a G-protein-coupled receptor (GPCR). Concept Check:  In this figure, where does the signal transduction pathway begin and end, and what is the cellular response? 

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Figure 9.13  A cellular response of a

Epinephrine

Activated GPCR

Skeletal muscle cell

Activated adenylyl cyclase

GTP Activated G-protein α subunit

PKA (inactive)

PKA (active)

Phosphorylase kinase – P (active)

ATP

Concept Check:  Does phosphorylation activate or inhibit enzyme function? 

cAMP

ATP

Phosphorylase kinase (inactive)

skeletal muscle cell to epinephrine.

Glycogen synthase (active)

ATP

Glycogen synthase – P (inactive)

ATP

Glycogen phosphorylase (inactive)

Glycogen phosphorylase – P (active)

Glycogen breakdown is stimulated.

(refer back to step 3, Figure 9.7). The amount of cAMP decreases due to the action of an enzyme called phosphodiesterase, which converts cAMP to AMP: Phosphodiesterase

AMP

cAMP

As the cAMP level falls, the regulatory subunits of PKA release cAMP, and the regulatory and catalytic subunits reassociate, thereby inhibiting PKA. Finally, enzymes called protein phosphatases are responsible for removing phosphate groups from proteins, which reverses the effects of PKA: Phosphorylated protein P

Protein phosphatase

Pi

Glycogen synthesis is inhibited.

The Main Advantages of Second Messengers Are Signal Amplification and Speed In the 1950s, Earl Sutherland determined that many different hormones cause the formation of cAMP in a variety of cell types. This observation, for which he won the Nobel Prize in Physiology or Medicine in 1971, stimulated great interest in the study of signal transduction pathways. Since Sutherland’s discovery, the production of second messengers such as cAMP has been found to have two important advantages: signal amplification and speed. Signal Amplification  Amplification of the signal involves the synthesis of many cAMP molecules, which, in turn, activate many PKA proteins (Figure 9.14). Likewise, each PKA protein phosphorylates many target proteins in the cell to promote a cellular response. Speed   A second advantage of second messengers such as cAMP is speed. Because second messengers are relatively small and watersoluble, they can diffuse rapidly through the cytosol. For example, Brian Bacskai and colleagues studied the response of neurons to a signaling molecule called serotonin, which is a neurotransmitter that binds to a GPCR. In humans, low serotonin is believed to play a role in depression, anxiety, and other behavioral disorders. To monitor cAMP levels, neurons grown in a laboratory were injected with a fluorescent protein that



CELL COMMUNICATION 195

Signal/receptor

cAMP

Activated PKA

T

TT ==Target Targetprotein proteinphosphorylated phosphorylatedbybyPKA PKA Phosphate

Figure 9.14  Signal amplification.  An advantage of a signal transduction pathway is the amplification of a signal. In this case, a single signaling molecule leads to the phosphorylation of many, perhaps hundreds or thousands of, target proteins (designated T). Concept Check:  In the case of signaling pathways involving hormones, why is signal amplification an advantage? 

of responses. As you will learn, the type of cellular response that is caused by a given hormone depends on the type of cell. Each cell type responds to a particular hormone in its own unique way. The variation in a cellular response is determined by the types of proteins, such as receptors and signal transduction proteins, that each cell type makes, which is determined by the genes expressed in that type of cell.

Add serotonin HO

NH

NH2

+ 20 seconds

Figure 9.15  The rapid speed of cAMP production.  The schematic drawing on the left shows a neuron prior to its exposure to serotonin, a signaling molecule; the drawing on the right shows the same cell 20 seconds after exposure. Blue indicates a low level of cAMP, yellow is an intermediate level, and purple is a high level. changes its fluorescence when cAMP is made. As shown schematically in the drawing on the right in Figure 9.15, such cells made a substantial amount of cAMP within 20 seconds after the addition of serotonin.

9.4         Hormonal Signaling in Multicellular Organisms Learning Outcomes: 1. Explain how the cellular response to a particular hormone can vary among different cell types. 2. Describe how a cell’s response to a hormone depends on the genes it expresses.

Thus far, we have considered how signaling molecules bind to particular types of receptors, thereby activating a signal transduction pathway that leads to a cellular response. In this section, we will consider how hormones in multicellular organisms exert a variety

The Cellular Response to a Given Hormone Varies Among Different Cell Types As we have seen, signaling molecules usually exert their effects on cells via signal transduction pathways that control the functions and/ or synthesis of specific proteins. In multicellular organisms, one of the amazing effects of hormones is their ability to coordinate cellular activities. One example is epinephrine, which is secreted from endocrine cells. As mentioned earlier, epinephrine is also called the fightor-flight hormone because it quickly prepares the body for strenuous physical activity in response to a perceived danger. Epinephrine is also secreted into the bloodstream when a person is exercising. Epinephrine has different effects throughout the body (Table 9.1). We have already discussed how it promotes the breakdown of glycogen in

Table 9.1     Effects of Epinephrine in Humans Organ/Tissue

Effect

Eye

Dilates pupils

Salivary glands

Inhibits the production of saliva

Skeletal muscle

Stimulates cells to break down glycogen and release glucose

Skin

Constricts blood vessels; stimulates sweating

Lungs

Relaxes airways so more oxygen is taken in

Heart

Increases the rate of beating

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skeletal muscle cells (refer back to Figure 9.13). In the lungs, it relaxes the airways, allowing a person to take in more oxygen. In the heart, epinephrine stimulates heart muscle cells so the heart beats faster. Interestingly, one of the effects of caffeine can be explained by this mechanism. Caffeine inhibits phosphodiesterase, which is the enzyme that converts cAMP to AMP. Phosphodiesterase functions to remove cAMP once a signaling molecule, such as epinephrine, is no longer present. When phosphodiesterase is inhibited by caffeine, cAMP persists for a longer period of time and prolongs the effects of signaling molecules like epinephrine. Therefore, even low levels of epinephrine have a greater effect. This is one of the reasons why drinks containing caffeine, including coffee and many energy drinks, provide a feeling of vitality and energy.

Core Concept: Information A Cell’s Response to Hormones and Other Signaling Molecules Depends on the Genes It Expresses As Table 9.1 shows, the hormone epinephrine produces diverse responses throughout the body. How do we explain the observation that various cell types respond so differently to the same hormone? As a multicellular organism develops from a fertilized egg, the cells of the body become differentiated into particular types, such as heart and lung cells. The mechanisms that underlie this differentiation process are described in Chapter 20. Although different cell types, such as heart and lung cells, contain the same set of genes—the same genome—those genes are not expressed in the same pattern in all cells. Certain genes that are turned off in heart cells are turned on in lung cells, whereas some genes that are turned on in heart cells are turned off in lung cells. This phenomenon, which is called differential gene regulation, causes each cell type to have its own distinct proteome. The set of proteins made in any given cell type is critical to a cell’s ability to respond to signaling molecules. The following are examples of how differential gene regulation affects the cellular response: 1. A cell may or may not express a receptor for a particular signaling molecule. For example, not all cells of the human body express a receptor for epinephrine. Cells without such a receptor are not affected when epinephrine is released into the bloodstream. 2. Different cell types have different cell surface receptors that recognize the same signaling molecule. In humans, for example, a signaling molecule called acetylcholine has two different types of receptors. One acetylcholine receptor is a ligand-gated ion channel that is expressed in skeletal muscle cells. Another acetylcholine receptor is a G-proteincoupled receptor (GPCR) that is expressed in heart muscle cells. Because of this, acetylcholine activates different signal transduction pathways in skeletal and heart muscle cells. Therefore, these cells respond differently to acetylcholine. 3. Two (or more) receptors may work the same way in different cell types but have different affinities for the same signaling molecule. For example, two different GPCRs may recognize

the same hormone, but the receptor expressed in liver cells may have a higher affinity (that is, a lower Kd) for the hormone than does the receptor expressed in muscle cells. If this is the case, liver cells will respond to a lower hormone concentration than muscle cells do. 4. The expression of proteins involved in intracellular signal transduction pathways may vary in different cell types. For example, one cell type may express the proteins that are needed to activate PKA, but another cell type may not. 5. The expression of proteins that are controlled by signal transduction pathways may vary in different cell types. For example, the presence of epinephrine in skeletal muscle cells leads to the activation of glycogen phosphorylase, an enzyme involved in glycogen breakdown. However, this enzyme is not expressed in all cells of the body. Glycogen breakdown is only stimulated by epinephrine if glycogen phosphorylase is expressed in that cell.

9.5        Apoptosis: Programmed Cell Death Learning Outcomes: 1. Define and describe apoptosis. 2. CoreSKILL » Analyze the results of experiments indicating that certain hormones control apoptosis. 3. Outline the extrinsic pathway of apoptosis.

We will end our discussion of cell communication by considering one of the most dramatic responses that eukaryotic cells exhibit—apoptosis, or programmed cell death. During this process, a cell orchestrates its own destruction! The cell first shrinks and becomes rounder due to the internal destruction of its nucleus and cytoskeleton (Figure 9.16). The plasma membrane then forms irregular extensions that eventually become blebs—small cell fragments that break away from the cell as it destroys itself (also look back at the chapter opening photo). Cell biologists have discovered that apoptosis plays many important roles. ∙ During embryonic development in animals, it is needed to sculpt the tissues and organs. For example, the fingers on a human hand are initially webbed, but become separated during embryonic development when the cells between the fingers undergo apoptosis (see Figure 20.4). ∙ Apoptosis is also necessary in adult organisms to maintain the proper numbers of cells in tissues and organs. ∙ Programmed cell death also eliminates cells that have become worn out or infected by viruses, or have the potential to cause cancer. During the past few decades, clinical research has revealed that many human diseases are associated with irregularities in apoptosis. Table 9.2 describes a few examples. In this section, we will examine the pioneering work that led to the discovery of apoptosis and explore its molecular mechanism.



CELL COMMUNICATION 197

Bleb

Bleb

13 μm

1

Cell beginning apoptosis

2

Condensation of nucleus and cell shrinkage

3

Multiple extensions of the plasma membrane

4

Further blebbing

Figure 9.16  Stages of apoptosis. (1–4): ©Prof. Guy Whitley/Reproductive and Cardiovascular Disease Research Group at St. George’s University of London

Table 9.2     Relationship Between Certain Diseases and Abnormal Levels of Apoptosis Disease

Description/Examples

Diminished levels of apoptosis Cancer

Cancer cells proliferate in an uncontrolled manner. In some forms of cancer, a decrease in the normal rate of apoptosis contributes to the faster proliferation rate. Examples include particular types of prostate and ovarian cancers.

Elevated levels of apoptosis Viral diseases

Certain viral diseases are associated with elevated levels of apoptosis. For example, infection by human immunodeficiency virus (HIV) results in an increased rate of apoptosis of helper T cells.

Neurodegenerative diseases

Some neurodegenerative diseases occur because specific neurons undergo an unusually high rate of apoptosis. An example is Parkinson’s disease, which arises from a loss of dopaminergic neurons.

Core Skill: Process of Science

Feature Investigation  |  Kerr, Wyllie, and Currie Found That Hormones May Control Apoptosis  How was apoptosis discovered? One line of evidence involved the microscopic examination of tissues in mammals. In the 1960s, British pathologist John Kerr microscopically examined liver tissue that was deprived of oxygen. He observed that, within hours of oxygen deprivation, some cells underwent a process that involved cell shrinkage. Around this time, similar results had been noted by other researchers, such as Scottish pathologists Andrew Wyllie and Alastair Currie, who had studied cell death in the adrenal glands. In 1973, Kerr, Wyllie, and Currie joined forces to study this process further. Prior to that collaboration, other researchers had already established that certain hormones affect the growth of the adrenal glands, which sit atop the kidneys. Adrenocorticotropic hormone (ACTH) was known to increase the number of cells in the adrenal cortex, which is the outer layer of the adrenal glands. By contrast, the drug prednisolone was shown to suppress the synthesis of ACTH and cause a decrease in the number of cells in the cortex. In the experiment described in Figure 9.17, Kerr, Wyllie, and Currie wanted to understand how ACTH and prednisolone exert their effects. They subjected rats to four types of treatments. The control rats were injected with saline (salt water). Other rats were injected with prednisolone alone, prednisolone plus ACTH, or ACTH alone. After 2 days, samples of adrenal cortex were obtained from the rats and observed by light microscopy. Even in control samples,

the researchers occasionally observed cell death via apoptosis (see the micrograph in step 4). However, in prednisolone-treated rats, the cells in the adrenal cortex were found to undergo a dramatically higher rate of apoptosis. Multiple cells undergoing apoptosis were found in 9 out of every 10 samples observed under the light microscope. Such a high level of apoptosis was not observed in control samples or in samples obtained from rats treated with both prednisolone and ACTH or with ACTH alone. Therefore, ACTH appears to prevent apoptosis. The results of Kerr, Wyllie, and Currie are important for two reasons. First, their results indicated that tissues decrease their cell number via a mechanism that involves cell shrinkage and eventually blebbing. Second, they showed that cell death followed a program that, in this case, was induced by the presence of prednisolone (which decreases ACTH). They coined the term apoptosis to describe this process. As you may know, prednisone is an anti-inflammatory and immunosuppressive drug that is used to treat a wide variety of disorders, including asthma and rheumatoid arthritis. When taken into the body, it is converted to prednisolone by the liver. In recent years, prednisone has been used in conjunction with other therapies to treat certain forms of cancer, such as leukemia, which is cancer of white blood cells. Prednisone is thought to exert its effect by promoting apoptosis in the cancer cells.

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Figure 9.17  Discovery of apoptosis in the adrenal cortex by Kerr, Wyllie, and Currie. (4): ©Dr. Thomas Caceci, Virginia-Maryland Regional College of Veterinary Medicine

HYPOTHESIS Hormones may affect cell number in the adrenal gland by controlling the rate of apoptosis. KEY MATERIALS Laboratory rats, prednisolone, and ACTH. Conceptual level

Experimental level

1 Inject 5 rats with saline (control).

Inject 5 rats with prednisolone alone. Inject 5 rats with prednisolone + ACTH. Inject 5 rats with ACTH alone.

2

Previous studies indicated that prednisolone alone may promote apoptosis by lowering ACTH levels.

After 2 days, obtain samples of adrenal tissue from all 20 rats.

Adrenal gland Cell undergoing apoptosis

3

Observe the samples via light microscopy, described in Chapter 4.

4

THE DATA Micrograph o of adrenal tissu tissue showing occasional ce cells undergoing apoptosis (see arrows)

39.7 μm

Treatment

Number of animals

Glands with enhanced apoptosis*/ Total number of animals

Saline

5

0/10

Prednisolone

5

9/10

Prednisolone + ACTH

5

0/10

ACTH

5

0/10

*Samples from two adrenal glands were removed from each animal. Enhanced apoptosis means that cells undergoing apoptosis were observed in every sample under the light microscope.

5

CONCLUSION Prednisolone alone, alone which lowers ACTH ACT levels, causes some cells to undergo apoptosis. During this process, the cells shrink and form blebs as they kill themselves. Apoptosis is controlled by hormones.

6

SOURCE Wyllie, A. H., Kerr, J. F. R., Macaskill, I. A. M., and Currie, A. R. 1973. Adrenocortical cell deletion: the role of ACTH. Journal of Pathology 111: 85–94.



CELL COMMUNICATION 199

Experimental Questions 1. CoreSKILL » In the experiment of Figure 9.17, explain the effects on apoptosis in the control rats (injected with saline) versus those injected with prednisolone alone, predinisolone + ACTH, or ACTH alone. 

3. CoreSKILL » Of the four groups of rats—control, prednisolone alone, prednisolone + ACTH, and ACTH alone—which would you expect to have the lowest level of apoptosis? Explain. 

2. Prednisolone inhibits the production of ACTH in rats. Do you think it inhibited the ability of rats to make their own ACTH when they were injected with both prednisolone and ACTH? Explain. 

Signal Transduction Pathways Lead to Apoptosis Apoptosis involves the activation of cell-signaling pathways. One pathway, called the extrinsic pathway, begins with the activation of death receptors on the cell surface. When death receptors bind to extracellular signaling molecules, a pathway is stimulated that leads

1

A signaling molecule, which is a trimer, binds to 3 death receptors, causing them to aggregate and exposing the death domain.

2

to apoptosis. Figure 9.18 shows a simplified pathway for this process. In this example, the signaling molecule is a protein composed of three identical subunits—a trimeric protein. Such trimeric signaling molecules are typically produced by cells of the immune system that recognize abnormal cells and target them for destruction. For example, when a cell is infected with a virus, cells of the immune system may

Adaptor proteins and initiator procaspase bind to the death domain, forming a death-inducing signaling complex.

Figure 9.18  The extrinsic pathway

Deathinducing signaling complex

Signaling molecule

for apoptosis in mammals.  This simplified pathway leads to apoptosis when cells are exposed to an extracellular signal that causes cell death.

Death receptor Death domain

Initiator caspase (active)

4

Concept Check:  How do the roles of the initiator and the executioner caspases differ in the extrinsic pathway? 

Adaptor Initiator procaspase (inactive)

3

The initiator caspase cleaves the executioner procaspase, making it active.

The initiator procaspase is cleaved, and a smaller active initiator caspase is released.

Executioner caspase (active)

Executioner procaspase (inactive)

5

Actin filament Broken actin filament

The executioner caspase cleaves cellular proteins, such as actin filaments, thereby causing the cell to shrink and eventually form blebs.

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target the infected cell for apoptosis. The signaling molecule binds to three death receptors, which causes them to aggregate into a trimer. This results in a conformational change that exposes a domain on the death receptors called the death domain. Once the death domain is exposed, it binds to adaptors, which then bind to an initiator procaspase. The complex between the death receptors, adaptors, and initiator procaspase is called the death-inducing signaling complex (DISC). Once the initiator procaspase, which is inactive, is part of the death-inducing signaling complex, it is converted by proteolytic cleavage to an initiator caspase, which is active. An active caspase functions as a protease—an enzyme that digests other proteins. After it is activated, the initiator caspase is then released from the DISC. This caspase is called an initiator caspase because it initiates the activation of many other caspases in the cell. These other caspases are called executioner, or effector, caspases because they are directly responsible for digesting intracellular proteins and causing the cell to die. The executioner caspases digest a variety of intracellular proteins, including the proteins that constitute the cytoskeleton and nuclear lamina as well as proteins involved with DNA replication and repair. In this way, the executioner caspases cause the cellular changes shown in Figure 9.16. The caspases also activate an enzyme called DNase that chops the DNA in the cell into small fragments. This event may be particularly important for eliminating virally infected cells because it also destroys viral genomes that are composed of DNA. Alternatively, another pathway of apoptosis, called the intrinsic pathway or mitochondrial pathway, is stimulated by DNA damage that could cause cancer. Mitochondria release cytochrome c (a small mitochondrial protein) into the cytosol, where it forms a complex with other proteins called an apoptosome. The apoptosome then initiates the activation of caspases.

Summary of Key Concepts 9.1  General Features of Cell Communication

∙∙ G-protein-coupled receptors (GPCRs) interact with G proteins to initiate a cellular response (Figure 9.7). ∙∙ Ligand-gated ion channels are receptors that allow the flow of ions across the plasma membrane (Figure 9.8). ∙∙ Although most receptors involved in cell signaling are found on the cell surface, some receptors, such as the estrogen receptor, are intracellular receptors (Figure 9.9).

9.3  S  ignal Transduction and the Cellular Response ∙∙ Signaling pathways influence whether or not a cell divides. An example is the pathway that is stimulated by epidermal growth factor, which binds to a receptor tyrosine kinase (Figure 9.10). ∙∙ Second messengers, such as cAMP, play a key role in signal transduction pathways, such as those that occur via GPCRs. These pathways are reversible once the signal is degraded (Figures 9.11, 9.12). ∙∙ An example of a pathway that uses cAMP is found in skeletal muscle cells responding to elevated levels of epinephrine, the fightor-flight hormone. Epinephrine enhances the function of enzymes that increase glycogen breakdown and inhibits enzymes that cause glycogen synthesis (Figure 9.13). ∙∙ Second messengers amplify the signal and increase the speed of signaling pathways (Figures 9.14, 9.15).

9.4  H  ormonal Signaling in Multicellular Organisms ∙∙ Hormones such as epinephrine exert different effects throughout the body (Table 9.1). ∙∙ The way in which any particular cell type responds to a signaling molecule depends on the set of proteins it makes. The amounts of these proteins are controlled by differential gene regulation.

9.5  Apoptosis: Programmed Cell Death

∙∙ A signal is an agent that can influence the properties of cells. A signal binds to a receptor to elicit a cellular response. Cell signaling enables cells to sense and respond to environmental changes and to communicate with each other (Figures 9.1, 9.2).

∙∙ Apoptosis is the process of programmed cell death in which the nucleus and cytoskeleton break down and eventually the cell breaks apart into blebs. Irregularities in apoptosis are associated with some diseases (Figure 9.16, Table 9.2).

∙∙ Cell-to-cell communication varies in terms of the mechanism of signal transmission and the distance that a signal travels. Signals are relayed between cells in five common ways: direct intercellular, contact-dependent, autocrine, paracrine, and endocrine signaling (Figure 9.3).

∙∙ Microscopy studies of Kerr, Wyllie, and Currie, in which they studied the effects of ACTH on the adrenal cortex, were instrumental in the identification of apoptosis (Figure 9.17).

∙∙ Cell signaling is usually a three-stage process involving receptor activation, signal transduction, and a cellular response. A signal transduction pathway is a group of proteins that convert an initial signal to a different signal inside the cell (Figure 9.4).

9.2  Cellular Receptors and Their Activation ∙∙ A signaling molecule, also called a ligand, binds to a receptor with an affinity that is measured as the value of a dissociation constant, Kd. The binding of a ligand to a receptor is usually very specific and alters the conformation of the receptor (Figure 9.5). ∙∙ Enzyme-linked receptors have some type of catalytic function. Many of them are protein kinases that phosphorylate proteins (Figure 9.6).

∙∙ Apoptosis occurs via extrinsic or intrinsic pathways. The extrinsic pathway is stimulated when an extracellular signaling molecule binds to death receptors (Figure 9.18).

Assess & Discuss Test Yourself 1. An agent that allows a cell to respond to changes in its environment is termed a. a cell surface receptor. b. an intracellular receptor. c. a structural protein. d. a signal. e. apoptosis.



CELL COMMUNICATION 201

2. When a cell secretes a signaling molecule that binds to receptors on neighboring cells as well as the cell itself, this is called signaling. a. direct intercellular b. contact-dependent c. autocrine d. paracrine e. endocrine

8. All cells of a multicellular organism may not respond in the same way to a particular ligand (signaling molecule) that binds to a cell surface receptor. The difference in response may be due to a. the type of receptor for the ligand that the cell expresses. b. the affinity of the ligand for the receptor in a given cell type. c. the type of signal transduction pathways that the cell expresses. d. the type of target proteins that the cell expresses. e. all of the above.

3. Which of the following does not describe a typical cellular response to signaling molecules? a. activation of enzymes within the cell b. change in the function of structural proteins, which determine cell shape c. alteration of levels of certain proteins in the cell by changing the level of gene expression d. change in a gene sequence that encodes a particular protein e. all of the above are examples of cellular responses.

9. Apoptosis is the process of a. cell migration. b. cell signaling. c. signal transduction. d. signal amplification. e. programmed cell death.

4. A receptor has a Kd for its ligand of 50 nM. This receptor a. has a higher affinity for its ligand than does a receptor with a Kd of 100 nM. b. has a higher affinity for its ligand than does a receptor with a Kd of 10 nM. c. is mostly bound by its ligand when the ligand concentration is 100 nM. d. must be an intracellular receptor. e. both a and c are true of this ligand. 5.

binds to receptors inside cells.

a. Estrogen b. Epinephrine c. Epidermal growth factor d. all of the above bind to such receptors. e. none of the above binds to such receptors.

6. The relay protein Ras is part of the EGF pathway that promotes cell division (see Figure 9.10). The active form of Ras has GTP bound to it, whereas the inactive form has GDP. GTP is hydrolyzed to GDP and Pi to switch Ras from the active to the inactive form. Researchers have discovered that certain forms of cancer involve mutations in the gene that encodes the Ras protein. Which of the following types of mutations would you expect to promote cell division and thereby lead to cancer? a. a mutation that prevents the synthesis of Ras b. a mutation that causes Ras to bind GDP more tightly c. a mutation that prevents the GTP bound to Ras from being hydrolyzed d. a mutation that prevents Ras from binding to Raf e. both b and c 7. The benefit of second messengers in signal transduction pathways is a. an increase in the speed of a cellular response. b. duplication of the ligands in the system. c. amplification of the signal. d. all of the above. e. a and c only.

10. Which statement best describes the extrinsic pathway for apoptosis? a. Caspases recognize an environmental signal and expose their death domain. b. Death receptors recognize an environmental signal, which then leads to the activation of caspases. c. Initiator caspases digest the nuclear lamina and cytoskeleton. d. Executioner caspases are part of the death-inducing signaling complex (DISC). e. All of the above are true of the extrinsic pathway.

Conceptual Questions 1. What are the two general reasons that cell communication is essential?  2. What are the three stages of cell signaling? What stage does not occur when the estrogen receptor is activated?  3.

Core Concept: Systems Discuss how cell signaling helps organisms to interact with their environment. 

Collaborative Questions 1. Discuss and compare several different types of cell-to-cell communication. What are some advantages and disadvantages of each type? 2. How does differential gene regulation enable various cell types to respond differently to the same signaling molecule? Why is this useful to multicellular organisms?

CHAPTER OUTLINE

Multicellularity

10.1 Extracellular Matrix and Cell Walls 10.2 Cell Junctions 10.3 Tissues Summary of Key Concepts Assess & Discuss

10 The General Sherman in Sequoia National Park, a striking example of the size that multicellular organisms can reach. This tree is thought to be the largest organism (by mass) in the world. ©Altrendo Panoramic/Getty Images

W B

hat is the largest living organism on Earth? The size of an organism can be defined by its volume, mass, height, length, or the area it occupies. A giant fungus (Armillaria ostoyae), growing in the soil in Malheur National Forest in Oregon, spans 8.9 km2, or 2,200 acres, which makes it the largest known organism by area. Most of this organism lies below ground, so it is not visible from the surface. In the Mediterranean Sea, marine biologists discovered a giant aquatic plant (Posidonia oceanica) whose length is 8 km, or 4.3 miles, making it the world’s longest known organism. With regard to mass, the largest organism is probably a tree named the General Sherman, which is 83.8 m tall (275 feet), nearly the length of a football field (see the chapter opening photo). This giant sequoia tree (Sequoiadendron giganteum) is estimated to weigh nearly 2 million kg (over 2,000 tons)—equivalent to a herd of 400 elephants! An organism composed of more than one cell is said to be multicellular. The preceding examples illustrate the amazing sizes that certain multicellular organisms have attained.

As we will discuss in Chapter 26, multicellular organisms came into being approximately 1 billion years ago. Some species of protists are multicellular, as are most species of fungi. In this chapter, we will focus on plants and animals, which are always multicellular species. The main benefit of multicellularity arises from the division of labor between different types of cells in an organism. For example, the intestinal cells of animals and the root cells of plants have become specialized for nutrient uptake. Other types of cells in a multicellular organism perform different roles, such as reproduction. In animals, most of the cells of the body—somatic cells—are devoted to the growth, development, and survival of the organism, whereas specialized cells— gametes—function in sexual reproduction. Multicellular species usually have much larger genomes than unicellular species. The increase in genome size is associated with an increase in proteome size—multicellular organisms produce a larger array of proteins than do unicellular species. The additional proteins play a role in three general phenomena.

• First, in a multicellular organism, cell communication is vital • •

for the proper organization and functioning of cells. Many more proteins involved in cell communication are made in multicellular species. Second, both the arrangement of cells within the organism and the attachment of cells to each other require a greater variety of proteins in multicellular species than in unicellular species. Finally, additional proteins play a role in cell specialization because proteins that are needed for the structure and function of one cell type may not be needed in a different cell type, and vice versa. Likewise, additional proteins are needed to regulate the expression of genes so that all proteins are expressed in the proper cell types.

In this chapter, we will consider the cellular characteristics that are specific to multicellular organisms. We begin by exploring the material that is produced by animal and plant cells to form an extracellular matrix or cell wall, respectively. This material plays many important roles in the structure, organization,

and functioning of cells within multicellular organisms. We will then turn our attention to cell junctions, specialized structures that enable cells to make physical contact with one another. Cells within multicellular organisms form junctions that help the cells function in a cohesive and well-organized way. Finally, we

10.1

 xtracellular Matrix E and Cell Walls

will examine the organization and function of tissues, groups of cells that have a similar structure and function. In this chapter, we will survey the general features of tissues from a cellular perspective. Units VI and VII will explore the characteristics of particular plant and animal tissues in greater detail.

Some cells are attached to the ECM on one side. Some cells are embedded within the ECM.

Learning Outcomes: 1. Explain the functional roles of the extracellular matrix in animals. 2. Outline the major structural components of the ECM of animals. 3. Describe the structure and function of plant cell walls.

Polysaccharides attached to a protein (a proteoglycan)

ECM

Organisms are not composed solely of cells. A large portion of an animal or plant consists of a network of material that is secreted from cells and forms a complex meshwork outside of cells. In animals, this is called the extracellular matrix (ECM), whereas plant cells are surrounded by a cell wall. The ECM and cell walls are a major component of certain parts of animals and plants, respectively. For example, bones and cartilage in animals are composed largely of ECM, and the woody portions of plants are composed mostly of cell walls. Although the cells within wood eventually die, the cell walls they have produced provide a rigid structure that supports the plant for years or even centuries. In this section, we begin by examining the structure and functions of the ECM in animals, focusing on the major ECM components: proteins and polysaccharides. We will then explore the cell wall that surrounds plant cells.

Protein fiber

Protein fibers give strength and elasticity to the ECM.

Polysaccharides help the ECM resist compression.

10.7 µm

1.2 µm

Figure 10.1  The extracellular matrix (ECM) of animal cells.  The

The Extracellular Matrix in Animals Supports and Organizes Cells and Plays a Role in Cell Signaling Unlike the cells of bacteria, archaea, fungi, and plants, the cells of animals are not surrounded by a rigid cell wall that provides structure and support. However, animal cells secrete materials that form an ECM that provides support and helps to organize cells. Certain animal cells are completely embedded within an extensive ECM, whereas other cells may adhere to the ECM on only one side. Figure 10.1 illustrates the general features of the ECM and its relationship to cells. The major macromolecules of the ECM are proteins and polysaccharides. The most abundant proteins are those that form large fibers. The polysaccharides attract water and give the ECM a gel-like character. As we will see, the ECM found in animals performs many important functions, including strength, structural support, organization, and cell signaling. ∙ Strength. The ECM is the “tough stuff” of animals’ bodies. The strength of the ECM in the skin of mammals prevents tearing.

micrograph (SEM) at the bottom left shows collagen fibers, a type of protein fiber found in the ECM. The micrograph (TEM) at the bottom right shows a proteoglycan, which consists of polysaccharides attached to a protein. (left): ©Biophoto Associates/Science Source;

(right): Courtesy of Dr. Joseph Buckwalter/University of Iowa

Concept Check:   What are the four functions of the ECM in animals?

The ECM found in cartilage resists compression and provides protection to the joints. Similarly, the ECM protects the soft parts of the body, such as the internal organs. ∙ Structural support. The bones of many animals are composed primarily of ECM. Skeletons not only provide structural support but also facilitate movement via the functioning of attached muscles. ∙ Organization. The attachment of cells to the ECM plays a key role in the proper arrangement of cells throughout the body. In addition, the ECM binds many body parts together, such as tendons to bones.

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∙ Cell signaling. A less obvious role of the ECM is cell signaling. One way that cells in multicellular organisms sense their environment is via changes in the ECM. Let’s now consider the synthesis and structure of ECM components found in animals.

Adhesive and Structural Proteins Are Major Components of the ECM of Animals In the 1850s, German biologist Rudolf Virchow suggested that all extracellular materials are made and secreted by cells. Around the same time, biologists realized that gelatin and glue, which are produced by the boiling of animal tissues, contain a common fibrous substance. This substance was named collagen (from the Greek, meaning glue-producing). Since that time, experimental techniques in chemistry, microscopy, and biophysics have enabled scientists to probe the structure of the ECM. We now understand that the ECM contains a mixture of several different components, including proteins such as collagen, which form fibers. The proteins found in the ECM are grouped into adhesive proteins, such as fibronectin and laminin, and structural proteins, such as collagen and elastin (Table 10.1). How do adhesive proteins work? Fibronectin and laminin have multiple binding sites that bind to other components in the ECM, such as protein fibers and polysaccharides. These same proteins also have binding sites for receptors on the surfaces of cells. Therefore, adhesive proteins are so named because they make ECM components adhere to one another and to the cell surface. They provide organization to the ECM and facilitate the attachment of cells to the ECM. Structural proteins, such as collagen and elastin, form large fibers that give the ECM its strength and elasticity. A key function of collagen is to impart tensile strength, which is a measure of how much stretching force a material can bear without tearing apart. Collagen provides high tensile strength to many parts of an animal’s body. It is the main protein found in bones, cartilage, tendons, skin, and the lining of blood vessels and internal organs. In the bodies of mammals, more than 25% of the total protein mass consists of collagen, much more than any other protein. Approximately 75% of the protein in mammalian skin is composed of collagen. Leather is largely a pickled and tanned form of collagen.

Table 10.1

1

Procollagen polypeptides are synthesized into the ER lumen, where they assemble into a triple helix. Cytosol

Procollagen polypeptide (α chain)

ER lumen

Procollagen triple helix

Extension sequences

Collagen molecule 2

Procollagen is secreted from the cell, and the extension sequences are removed. The protein is now called collagen.

3

The removal of extension sequences allows collagen to assemble into fibrils.

4

Collagen fibrils assemble into larger collagen fibers.

Proteins in the ECM of Animals

General type

Example

Function

Adhesive

Fibronectin

Connects cells to the ECM and helps to organize components in the ECM.

Structural

As described in Chapter 4 (see Figure 4.32), proteins, such as collagen, that are secreted from eukaryotic cells are first directed from the cytosol to the endoplasmic reticulum (ER), then to the Golgi apparatus, and subsequently are secreted from the cell via vesicles that fuse with the plasma membrane. Figure 10.2 depicts the synthesis and assembly of collagen. Individual procollagen polypeptides (called α chains) are synthesized into the lumen of the ER. Three procollagen polypeptides then associate with each other to form a procollagen triple helix. The amino acid sequences at both ends of the polypeptides, termed extension sequences, promote the formation of procollagen and prevent the formation of a larger fiber. After procollagen is secreted from the cell, extracellular enzymes remove the extension sequences. Once this occurs, the protein, now called collagen, can form larger structures. Collagen proteins assemble in a staggered way to form relatively thin collagen fibrils, which then align and produce large collagen fibers. The many layers of these proteins give collagen fibers their great tensile strength.

Laminin

Connects cells to the ECM and helps to organize components in the ECM.

Collagen

Forms large fibers and interconnected fibrous networks in the ECM. Provides tensile strength.

Elastin

Forms elastic fibers in the ECM that can stretch and recoil.

Collagen fibril

Collagen fiber

Figure 10.2  Formation of collagen fibers.  Collagen is one type of structural protein found in the ECM of animal cells. Concept Check:   What prevents large collagen fibers from forming intracellularly?



MULTICELLULARITY 205 Elastic fiber In the absence of a stretching force, the elastin proteins are in a compact conformation.

Force

Single elastin protein

Force

Crosslink

When subjected to a stretching force, the elastin proteins elongate but remain attached to each other via crosslinks.

Figure 10.3  Structure and function of elastic fibers.  Elastic fibers are made of elastin, one type of structural protein found in the ECM surrounding animal cells. Concept Check:   Suppose you started with an unstretched elastic fiber and treated it with a chemical that breaks the crosslinks between adjacent elastin proteins. What would happen when the fiber was stretched?

In addition to tensile strength, elasticity is needed in regions of the body such as the lungs and blood vessels, which regularly expand and return to their original shape. In these places, the ECM contains elastic fibers composed primarily of the protein elastin (Figure 10.3). Elastin proteins form many covalent crosslinks to make a fiber with remarkable elastic properties. In the absence of a stretching force, each protein tends to adopt a compact conformation. When subjected to a stretching force, however, the compact proteins become more linear, with the covalent crosslinks holding the fiber together. When the stretching force stops, the proteins naturally return to their compact conformation. In this way, an elastic fiber behaves much like a rubber band, stretching under tension and snapping back when the tension is released.

BIO TIPS  THE QUESTION  Two structural proteins found in

the ECM of animals are collagen and elastin. How are the structures of these proteins related to their functions?

T OPIC  What topic in biology does this question address? The topic is structural proteins in the ECM. More specifically, the question asks you to relate the structures and functions of collagen and elastin. I NFORMATION  What information do you know based on the question and your understanding of the topic? In the question, you are reminded that collagen and elastin are structural proteins found in the ECM of animals. From your understanding of the topic, you may remember that collagen is composed of long, relatively thick fibers, and its role is to provide tensile strength. Elastin is a more compact protein that forms crosslinked elastic fibers, which provide elasticity. P ROBLEM-SOLVING  S TRATEGY  Relate structure and function. Take a closer look at the structures of these proteins, and consider how the structures determine the proteins’ functions.

ANSWER Collagen: A collagen fiber is composed of many smaller fibrils. Three procollagen polypeptides associate with each other to form a protein with a triple helix structure. These collagen proteins then assemble in a staggered way to form relatively thin collagen fibrils. The fibrils, in turn, align with each other and produce larger collagen fibers. The many layers of fibrils give collagen fibers their tensile strength. Elastin: Elastin has a very different structure from collagen. It is a fairly compact protein that forms elastic fibers with many covalent crosslinks between the proteins. In the absence of a stretching force, the elastin proteins remain in the compact conformation. However, when subjected to a stretching force, they become more linear. The covalent crosslinks keep the proteins within the elastic fiber from coming apart. When the stretching force ends, the proteins naturally return to their compact conformation.

Core Concepts: Evolution, Structure and Function Collagens Are a Family of Proteins That Give the ECM of Animals a Variety of Properties Researchers have determined that animals make many different types of collagen fibers. These are designated as type I, type II, and so on. At least 27 different types of collagens have been identified in humans. To make different types of collagens, the human genome, as well as the genomes of other animals, has many different genes that encode procollagen polypeptides. Some inherited human diseases are caused by mutations in genes that encode collagen proteins. For example, Ehlers-Danlos syndrome is caused by mutations in one of several different collagen genes. Characteristic symptoms are very stretchable skin and hyperflexible joints. Why are different collagens made? Each of the many different types of collagen polypeptides has a similar yet distinctive amino acid sequence that affects the structure of not only individual collagen proteins but also the resulting collagen fibers. For example, the amino acid sequence may cause the α chains within each collagen protein to bind to each other very tightly, thereby creating rigid proteins that form a relatively stiff fiber. Such collagen fibers are found in bone and cartilage. The amino acid sequence of the α chains also influences the interactions between the collagen proteins within a fiber. For example, the amino acid sequences of certain α chains promote a looser interaction that produces a more bendable or thinner fiber. More flexible collagen fibers support the lining of your lungs and intestines. In addition, domains within the collagen polypeptide affect the spatial arrangement of collagen proteins. The collagen shown in Figure 10.2 forms fibers in which collagen proteins align themselves in parallel arrays. However, not all collagen proteins form long fibers. For example, type IV collagen proteins interact with each other in a meshwork pattern. This meshwork acts as a filter around capillaries. Gene regulation controls which types of collagens are made throughout the body and in what amounts they are made. Of the

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Table 10.2 Type

Sites of synthesis*

Structure and function

I

Tendons, ligaments, bones, and skin

Forms a relatively rigid and thick fiber. Very abundant, provides most of the tensile strength to the ECM.

II

Cartilage, discs between vertebrae

Forms a fairly rigid and thick fiber but is more flexible than type I. Permits smooth movements of joints.

Arteries, skin, internal organs, and around muscles

Forms thin fibers, often arranged in a meshwork pattern. Allows for greater elasticity in tissues.

Skin, intestine, and kidneys; also found around capillaries

Does not form long fibers. Instead, the proteins are arranged in a meshwork pattern that provides organization and support to cell layers. Functions as a filter around capillaries.

III

IV

Repeating disaccharide unit

Examples of Collagen Types in Humans COO – O

OH

O

O

OH

HO

CH2OSO3 – O

COO – O

OH

HNCOCH3

O

OH

O

HO

CH2OSO3 – O

COO – O

HNCOCH3

OH

O

OH

(a) Structure of chondroitin sulfate, a glycosaminoglycan Glycosaminoglycans (GAGs) Core protein

*The sites of synthesis indicate where a large amount of the collagen type is made.

27 types of collagens identified in humans, Table 10.2 considers types I to IV, each of which varies as to where it is primarily synthesized and its structure and function. In skin cells, for example, the genes that encode the polypeptides that make up collagen types I, III, and IV are turned on, but the synthesis of type II collagen is minimal. The regulation of collagen synthesis has received a great deal of attention due to the phenomenon of wrinkling. As we age, the amount of collagen that is synthesized in our skin significantly decreases. The underlying network of collagen fibers, which provides scaffolding for the surface of our skin, loosens and unravels. This is one factor that causes the skin of older people to sink, sag, and form wrinkles. Various therapeutic and cosmetic agents have been developed to prevent or reverse the appearance of wrinkles, most with limited benefits. For example, many face and skin creams contain collagen as an ingredient. Another approach is collagen injections, in which small amounts of collagen (from cows) are injected into areas where the body’s collagen has weakened, filling the depressions to the level of the surrounding skin. Because collagen is naturally broken down in the skin, the injections are not permanent and last only about 3 to 6 months.

Animal Cells Also Secrete Polysaccharides into the ECM Polysaccharides are the second major component of the ECM of animals. As discussed in Chapter 3, polysaccharides are polymers of many simple sugars. Among vertebrates, the most abundant types of polysaccharides in the ECM are glycosaminoglycans (GAGs). These macromolecules are long, unbranched polysaccharides containing a repeating disaccharide unit (Figure 10.4a). GAGs are highly negatively charged molecules that tend to attract positively charged ions and water. The majority of GAGs in the ECM are linked to core proteins, forming proteoglycans (Figure 10.4b). Providing resistance to compression is the primary function of GAGs and proteoglycans. Once secreted from cells, these

(b) General structure of a proteoglycan

Figure 10.4  Structures of glycosaminoglycans and proteoglycans.  These macromolecules are found in the ECM, which is located outside of animal cells. (a) Glycosaminoglycans (GAGs) are composed of repeating disaccharide units. They range in length from several dozen to 25,000 disaccharide units. The GAG shown here is chondroitin sulfate, which is a component of cartilage. (b) Proteoglycans are composed of a long, linear core protein with many GAGs attached. Note that each GAG is typically 80 disaccharide units long but only a short chain of sugars is shown in this illustration. Concept Check:   What structural feature of GAGs gives the ECM a gel-like character?

macromolecules form a gel-like component in the ECM. How is this gel-like property important? Due to its high water content, the ECM is difficult to compress and thereby serves to protect cells. GAGs and proteoglycans are found abundantly in regions of the body that are subjected to harsh mechanical forces, such as the joints of the human body. Two examples of GAGs are chondroitin sulfate, which is a major component of cartilage, and hyaluronic acid, which is found in the skin, eyes, and joint fluid. Purified hyaluronic acid is also used to treat wrinkles and give skin fullness. Among many invertebrates, an important ECM component is chitin, a nitrogen-containing polysaccharide. Chitin forms the hard protective outer covering (called an exoskeleton) of insects, such as crickets and grasshoppers, and crustaceans, such as lobsters and shrimp. As these animals grow, they periodically shed this rigid outer layer and secrete a new, larger one—a process called molting (look ahead to Figure 33.13).

The Cell Wall of Plants Provides Strength and Resistance to Compression Let’s now turn our attention to the cell walls of plants. Plant cells are surrounded by a cell wall, a protective layer that forms outside of the plasma membrane. Like animal cells, the cells of plants are surrounded by material that provides tensile strength and resistance to compression. The cell walls of plants, however, are usually thicker, stronger, and more rigid than the ECM found in animals. Plant cell walls provide rigidity for mechanical support and also play a role in the maintenance of cell shape and the direction of cell growth.



MULTICELLULARITY 207

As described in Chapter 5, the cell wall also prevents expansion when water enters the cell, thereby preventing osmotic lysis. The main macromolecule of the plant cell wall is cellulose, a polysaccharide made of repeating molecules of glucose attached end to end. These glucose polymers associate with each other via hydrogen bonding to form microfibrils that provide great tensile strength (Figure 10.5). Cellulose was discovered in 1838 by French chemist Anselme Payen, who was the first scientist to attempt to separate wood into its component parts. After treating different types of wood with nitric acid, Payen obtained a fibrous substance that was also found in cotton and other plants. His chemical analysis revealed that the fibers were made of the carbohydrate glucose. Payen called this substance cellulose (from the Latin, meaning consisting of cells). Cellulose is probably the single most abundant organic molecule on Earth. Wood consists mostly of cellulose, and cotton and paper are almost pure cellulose.

OH

OH

OH

OH

OH

OH

OH

OH

OH

OH

OH

OH

OH

OH

OH

OH

OH

OH

OH

OH

Plant Cell Walls Consist of Primary and Secondary Walls The cell walls of plants are composed of a primary cell wall and a secondary cell wall (Figure 10.6). These walls are named based on the timing of their synthesis—the primary cell wall is made before the secondary cell wall. Primary Cell Wall  During cell division, the primary cell wall develops between two newly formed daughter cells. It is usually very flexible and allows the new cells to increase in size. The main constituent of the primary cell wall is cellulose. In addition to cellulose, other components found in the primary cell wall include hemicellulose, glycans, and pectins (see Figure 10.6).

Many polymers associate with each other to form a microfibril. 494.8 nm Microfibril

Figure 10.5  Structure of cellulose, the main macromolecule of the

plant cell wall.  Cellulose is made of repeating glucose units linked end to end that hydrogen-bond to each other to form microfibrils (SEM). ©SciMAT/Science Source Cellulose microfibrils

Crosslinking glycan

Plasma membrane

Pectin The primary cell wall is thin and flexible. It contains cellulose microfibrils in a meshwork pattern, along with other components shown on the far right.

The secondary cell wall is made in successive layers. Each layer contains strong cellulose microfibrils in parallel arrays. The direction of cellulose microfibrils in each layer is varied, as shown on the right.

Secondary cell wall Primary cell wall

Hemicellulose 50 nm

Figure 10.6  Structure of the cell wall of plant cells.  The primary cell wall is relatively thin and flexible. It contains cellulose (tan), hemicellulose (red), crosslinking glycans (blue), and pectin (green). The secondary cell wall, which is produced only by certain plant cells, is made after the primary cell wall and is synthesized in successive layers.

Core Skill: Modeling  The goal of this modeling challenge is to draw layers of a plant's secondary cell wall in colors that reflect the timing of their synthesis. Modeling Challenge: After making its primary cell wall, a particular type of plant cell makes its secondary cell wall in three successive layers. Draw a model that is similar to the model shown in the middle of Figure 10.6, but don’t show any components in the cytoplasm. The colors of your model should be as follows: primary cell wall, blue; first-made layer of the secondary cell wall, yellow; second-made layer of the secondary cell wall, green; and third-made layer of the secondary cell wall, black.

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Hemicellulose is another linear polysaccharide, with a structure similar to that of cellulose, but it contains sugars other than glucose in its structure and usually forms thinner microfibrils. Glycans, polysaccharides with branching structures, are also important in cell wall structure. The crosslinking glycans bind to cellulose and provide organization to the cellulose microfibrils. Pectins, which are highly negatively charged polysaccharides, attract water and have a gel-like character that provides the cell wall with the ability to resist compression. Secondary Cell Wall  The secondary cell wall is synthesized and deposited between the plasma membrane and the primary cell wall (see Figure 10.6) after a plant cell matures and has stopped increasing in size. It is made in layers by the successive deposition of cellulose microfibrils and other components. Whereas the primary wall structure is relatively similar in nearly all cell types and species, the structure of the secondary cell wall is more variable. Some plant cells have no secondary cell wall. For example, leaf cells that are involved in photosynthesis lack a secondary wall, allowing light to enter the cells more readily. The secondary cell wall often contains components in addition to those found in the primary cell wall. These include phenolic compounds called lignins, which are found in the woody parts of plants. Lignins are very hard and impart considerable strength to the secondary wall structure.

10.2 Cell Junctions Learning Outcomes: 1. Compare and contrast the structures and functions of anchoring junctions, tight junctions, and gap junctions found between animal cells. 2. CoreSKILL » Analyze the results of experiments that determined the size of gap junction channels. 3. Describe the structures and functions of the middle lamella and plasmodesmata that connect adjacent plant cells.

Thus far, we have learned that the cells of animals and plants produce an ECM or a cell wall that provides strength, support, and organization. In a multicellular organism, cells within the organism must be linked to each other. In animals and plants, this is accomplished by specialized structures called cell junctions (Table 10.3). Animal cells, which lack the structural support provided by the cell wall, have a more varied group of cell junctions than plant cells. In animals, three types of junctions are found between cells: anchoring junctions play a role in anchoring cells to each other or to the ECM; tight junctions seal cells together to prevent small molecules from leaking across a layer of cells; and gap junctions allow the passage of materials between adjacent cells. In plants, cellular organization is somewhat different because plant cells are surrounded by a rigid cell wall. Plant cells are connected to each other by a component called the middle lamella, which cements their cell walls together. They also have junctions termed plasmodesmata that allow the passage of materials between adjacent cells. In this section, we will examine these various types of junctions found between the cells of animals and plants.

Table 10.3 Type

Common Types of Cell Junctions Description

Animals Anchoring junctions

Cell junctions that hold adjacent cells together or attach cells to the ECM. Anchoring junctions are mechanically strong.

Tight junctions

Junctions between adjacent cells in a layer that prevent the leakage of material between cells.

Gap junctions

A cluster of channels that permit the direct exchange of ions and small molecules between the cytosols of adjacent cells.

Plants Middle lamella

A polysaccharide layer that cements together the cell walls of adjacent cells.

Plasmodesmata

Passageways between the cell walls of adjacent cells that can be opened or closed. When open, they permit the direct diffusion of ions and molecules between the cytosols of the adjacent cells.

Anchoring Junctions Link Animal Cells to Each Other and to the ECM Electron microscopy allows researchers to explore the types of junctions that occur between adjacent cells and between cells and the ECM. In the 1960s, Marilyn Farquhar, George Palade, and colleagues conducted several studies showing that various types of cell junctions connect cells to each other. Collectively called anchoring junctions, these junctions attach cells to each other and to the ECM. Anchoring junctions are common in parts of the body where the cells are tightly connected and form linings. An example is the layer of cells that line the small intestine. Anchoring junctions keep these intestinal cells tightly adhered to one another, thereby forming a strong barrier between the lumen of the intestine and the blood. A key component of anchoring junctions are integral membrane proteins called cell adhesion molecules (CAMs), which form the actual connections. Two types of CAMs are cadherins and integrins. Anchoring junctions are grouped into four main categories, according to their functional roles and their connections to cellular components. Figure 10.7 shows these junctions between cells of the mammalian small intestine. 1. Adherens junctions connect cells to each other via cadherins. In many cases, these junctions are organized into bands around cells. In the cytosol, adherens junctions bind to cytoskeletal filaments called actin filaments. 2. Desmosomes also connect cells to each other via cadherins. They are spotlike points of intercellular contact that rivet cells together. Desmosomes are connected to cytoskeletal filaments called intermediate filaments. 3. Hemidesmosomes connect cells to the extracellular matrix via integrins. Like desmosomes, they interact with intermediate filaments. 4. Focal adhesions also connect cells to the ECM via integrins. In the cytosol, focal adhesions bind to actin filaments.



MULTICELLULARITY 209

In adherens junctions, cadherins connect cells to each other and to actin filaments.

In desmosomes, cadherins connect cells to each other and to intermediate filaments. Band of actin filaments

Cadherins

Intermediate filaments

Linker proteins

ECM

Integrin

In hemidesmosomes, integrins connect the ECM to intermediate filaments.

Actin filament Blood vessel

In focal adhesions, integrins connect the ECM to actin filaments.

Figure 10.7  Types of anchoring junctions.  This figure shows the four types of anchoring junctions in three adjacent intestinal cells. The tops of these cells face the lumen of the intestine, whereas the bottoms are adjacent to the ECM and a blood vessel. Concept Check:   Which anchoring junctions are cell-to-cell junctions and which are cell-to-ECM junctions?

Cell Adhesion Molecules (CAMs) Form Links Between Cells and to the ECM Let’s now consider the molecular components of anchoring junctions. Cadherins  As shown in Figure 10.7, cadherins are CAMs that create cell-to-cell junctions. The extracellular domains of two cadherin proteins, each in adjacent cells, bind to each other to promote cell-to-cell adhesion (Figure 10.8a). This binding requires the presence of calcium ions (Ca2+), which change the conformation of the cadherin protein such that cadherins in adjacent cells bind to each other. (This calcium dependence gives cadherin its name—Ca2+-dependent adhering molecule.) On the interior of

the cell, linker proteins connect cadherins to actin or intermediate filaments of the cytoskeleton. This promotes a more stable interaction between two cells because their strong cytoskeletons are connected to each other. The genomes of vertebrates and invertebrates contain multiple cadherin genes, which encode slightly different cadherin proteins. The expression of cadherins in particular cell types allows cells to recognize each other. Dimer formation follows a homophilic, or like-to-like, binding mechanism. To understand the concept of homophilic binding, let’s consider an example. One type of cadherin is called E-cadherin, and another is N-cadherin. E-cadherin in one cell binds to E-cadherin in an adjacent cell to form a homodimer. However, E-cadherin in one cell does not bind to N-cadherin in an adjacent cell to form a heterodimer. Similarly, N-cadherin binds to N-cadherin but not to E-cadherin in an adjacent cell. Why is such homophilic binding important? By expressing only certain types of cadherins, each cell binds only to other cells that express the same cadherin types. This phenomenon plays a key role in the proper arrangement of cells throughout the body, particularly during embryonic development. Integrins  Another type of CAM is a group of proteins called integrins, which form connections between cells and the ECM. Integrins do not require Ca2+ to function. Each integrin protein is composed of two nonidentical subunits. In the example shown in Figure 10.8b, an integrin is bound to fibronectin, an adhesive protein in the ECM that binds to other ECM components such as collagen fibers. Like cadherins, integrins also bind to actin or intermediate filaments in the cytosol of the cell, via linker proteins, to promote a strong association between the cytoskeleton and the ECM. Thus, integrins have an extracellular domain for the binding of ECM components and an intracellular domain for the binding of cytosolic proteins. When CAMs were first discovered, researchers imagined that cadherins and integrins played only a mechanical role. In other words, their functions were described as holding cells together or to the ECM. More recently, however, experiments have shown that cadherins and integrins are important in cell communication. The formation or breaking of cell-to-cell and cell-to-ECM anchoring junctions affects signal transduction pathways within the cell. Similarly, intracellular signal transduction pathways affect cadherins and integrins in ways that alter intercellular junctions and the binding of cells to ECM components. Abnormalities in CAMs such as integrins are associated with the ability of cancer cells to metastasize, that is, to move to other parts of the body. CAMs are critical for keeping cells in their correct locations. When these adhesion molecules become defective due to cancer-causing mutations, cells lose their proper connections with the ECM and adjacent cells and may move to other parts of the body.

Tight Junctions Prevent the Leakage of Materials Across Animal Cell Layers In animals, tight junctions are a second type of junction, one that forms a tight seal between adjacent cells, thereby preventing material from leaking between the cells. As an example, let’s consider the

Cytosol Cadherin dimer

ECM

Actin Linker protein

Integrin

Ca2+ Actin

Plasma membranes of adjacent cells Linker protein

(a) Cadherins—link cells to each other

Collagen fiber

Plasma membrane

Fibronectin

ECM

(b) Integrins—link cells to the extracellular matrix

Figure 10.8  Types of cell adhesion molecules (CAMs).  Cadherins and integrins are CAMs that form connections in anchoring junctions. (a) A cadherin in one cell binds to a cadherin of an identical type in an adjacent cell. This binding requires Ca2+. In the cytosol, cadherins bind to actin or intermediate filaments of the cytoskeleton via linker proteins. (b) Integrins link cells to the ECM and form intracellular connections to actin or intermediate filaments. Each integrin protein is a heterodimer, composed of two nonidentical subunits. intestine. The cells that line the intestine form a sheet that is one cell thick. One side of each cell faces the intestinal lumen, and the other faces the ECM and a blood vessel (Figure 10.9). Tight junctions between these cells prevent the leakage of materials from the lumen of the intestine into the blood, and vice versa. Tight junctions are made by integral membrane proteins, called occludin and claudin, that form interlaced strands in the plasma membrane (see inset in Figure 10.9). These strands of proteins, located in adjacent cells, bind to each other, thereby forming a tight seal between cells. Tight junctions are not mechanically strong like anchoring junctions, because they do not have strong connections with the cytoskeleton. Therefore, adjacent cells that have tight junctions also have anchoring junctions to hold them in place. Tight junctions perform several important roles. Let’s consider a few examples. ∙ Tight junctions between intestinal cells prevent leakage of materials between the lumen of the intestine and the blood. ∙ Tight junctions help maintain the polarity of intestinal cells by preventing the lateral diffusion of integral membrane proteins between the apical side (which faces the lumen of the intestine) and the basolateral side (which faces a blood vessel). For example, proteins involved with receptor-mediated endocytosis are restricted to the apical side, and proteins involved with exocytosis are located at the basolateral side. Thus, intestinal cells are able to take up nutrients from the intestinal lumen and export them into the bloodstream, a phenomenon called transepithelial transport. ∙ Tight junctions prevent microbes from entering the body. In mammals, the skin on the exterior of the body and the lining of

Lumen of intestine

Tight junction

Extracellular space Strands of Blood occludin vessel and claudin

Plasma membranes of adjacent cells

Peeled-back leaflet

Figure 10.9  Tight junctions between adjacent intestinal cells.  In this example, tight junctions form a seal between cells of the intestinal lining. The inset shows the interconnected network of occludin and claudin that forms the tight junction. Core Skill: Connections  Look ahead to Figure 46.8. What problems might arise if tight junctions did not connect the cells that line your small intestine?



MULTICELLULARITY 211

the digestive tract are formed from interconnected cells that have tight junctions. Some pathogenic microorganisms, such as those that cause certain forms of diarrhea, are able to cause infection by disrupting tight junctions. The amazing ability of tight junctions to prevent the leakage of material across cell layers has been demonstrated by dye-injection studies. In 1972, Daniel Friend and Norton Gilula injected lanthanum into the bloodstream of a rat. Lanthanum is an electron-dense element that can be visualized using electron microscopy. A few minutes later, a sample of a cell layer in the digestive tract was removed and observed under an electron microscope. As seen in the micrograph in Figure 10.10, lanthanum diffused into the region between the cells that faces the blood, but it could not move past the tight junction to the side of the cell layer facing the lumen of the digestive tract.

Side of cell layer facing lumen of the digestive tract

Tight junction

Lanthanum (between two adjacent cells)

Side of cell layer facing the blood

Figure 10.10  An experiment demonstrating the function of a

Gap Junctions Between Animal Cells Provide Passageways for Intercellular Transport A third type of junction found between animal cells is called a gap junction, because a small gap occurs between the plasma membranes of cells connected by these junctions (Figure 10.11). Gap junctions are abundant in tissues and organs where the cells need to communicate with each other. For example, cardiac muscle cells, which cause your heart to beat, are interconnected by many gap junctions. Because gap junctions allow the passage of ions, electrical changes in one cardiac muscle cell are easily transmitted to an adjacent cell that is connected via gap junctions. These connections are needed for the coordinated contraction of cardiac muscle cells. In vertebrates, gap junctions are composed of an integral membrane protein called connexin. Invertebrates have a structurally similar protein called innexin. Six connexin proteins in one vertebrate cell form a channel called a connexon. A connexon in one cell aligns with a connexon in an adjacent cell to form an intercellular channel (see the middle drawing in Figure 10.11). The term gap junction refers to

tight junction.  When lanthanum was injected into the bloodstream of a rat, it diffused between the cells in the region up to a tight junction but could not diffuse past the junction to the other side of the cell layer. ©Dr. Daniel Friend Concept Check:   What results would you expect if a rat was fed lanthanum and then a sample of a cell layer in the digestive tract was observed under an electron microscope?

a cluster of many connexons that are close to each other in the plasma membrane and form many intercellular channels. Gap junction channels allow the passage of ions and small molecules, including amino acids, sugars, and signaling molecules such as Ca2+ and cAMP, between cells. In this way, gap junctions allow adjacent cells to share metabolites and directly signal each other. However, gap junction channels are too small to allow the passage of RNA, proteins, or polysaccharides. Therefore, cells that communicate via gap junctions still maintain their own distinctive sets of macromolecules.

Intercellular gap

Gap junction Gap junction

Small solute

2 connexons forming an intercellular channel

30 nm

Figure 10.11  Gap junctions between adjacent cells.  Gap junctions form intercellular channels that allow the passage of

small solutes with masses less than 1,000 Da. One connexon consists of six proteins called connexins. Two connexons align to form an intercellular channel. The micrograph shows a gap junction, which is composed of many connexons, between intestinal cells. (right): Courtesy Dr. Dan Goodenough/Harvard Medical School

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Core Skill: Process of Science

Feature Investigation  | Loewenstein and Colleagues Followed the Transfer of Fluorescent Dyes to Determine the Size of Gap-Junction Channels As just mentioned, gap junctions allow the passage of ions and small molecules, those with a mass up to about 1,000 Da. This property of gap junctions was determined in experiments involving the transfer of fluorescent dyes. In 1964, Werner Loewenstein and colleagues observed that a fluorescent dye could move from one cell to an adjacent cell, which prompted them to investigate this phenomenon further. In the experiment shown in Figure 10.12, Loewenstein and colleagues grew rat liver cells in the laboratory, where they formed a single layer. The adjacent cells formed gap junctions. Single cells were injected with various dyes composed of fluorescently labeled amino acids or peptide molecules with different masses, and then the cell layers were observed via fluorescence microscopy. As the data in Figure 10.12 show, dyes with a molecular mass up to 901 Da passed from cell to cell. Dyes with a larger mass, however, did not move

intercellularly. Loewenstein and other researchers subsequently investigated dye transfer in other cell types and species. Though some variation is found among different cell types and species, the researchers generally observed that molecules with a mass greater than 1,000 Da do not pass through gap junctions. Experimental Questions 1. What was the purpose of the study conducted by Loewenstein and colleagues?  2. CoreSKILL » Explain the experimental procedure used by Loewenstein and colleagues to determine the sizes of molecules that can pass through gap-junction channels.  3. CoreSKILL » What do the results of the experiment in Figure 10.12 indicate about the size of gap-junction channels? 

Figure 10.12  Use of fluorescent molecules by Loewenstein and colleagues to determine the size of gap-junction channels. HYPOTHESIS Gap-junction channels allow the passage of ions and molecules, but there is a limit to how large the molecules can be. KEY MATERIALS Rat liver cells grown in the laboratory, a collection of fluorescent dyes. Experimental level

1

Grow rat liver cells in a laboratory on solid growth medium until they become a single layer. At this point, adjacent cells have formed gap junctions.

Conceptual level

Tissue culture bottle

Gap junction

Rat liver cells

2

Inject 1 cell in the layer with fluorescently labeled amino acids or peptides. Note: Several dyes with different molecular masses were tested.

Rat liver cells

Gap junction channels

3

4

Incubate for various lengths of time (for example, 40–45 minutes). Observe cell layer under the fluorescence microscope to determine if the dye has moved to adjacent cells.

THE DATA

Note: In this case, the dye was transferred to adjacent cells.

Note: In this case, the dye was transferred to adjacent cells.

layer under the fluorescence microscope to determine if the dye has moved to adjacent cells.



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4

THE DATA Mass of dye (in daltons)

Transfer to adjacent cells*

376 464 536 559 665 688 817

++ ++ ++ ++ ++ + ++ ++ + ++ ++ ++ +

Mass of dye 851** 901 946 1004 1158 1678 1830

Transfer to adjacent cells* – +++ – – – – –

*The number of pluses indicates the relative speed of transfer. Four pluses denotes fast transfer, whereas one plus is slow transfer. A minus indicates that transfer between cells did not occur. **In some cases, molecules with less mass did not pass between cells compared with molecules with a higher mass. This may be due to differences in their structures (for example, charges) that influence whether or not they can easily penetrate the channel.

5

CONCLUSION Gap junctions allow the intercellular movement of molecules that have a mass of approximately 900 Da or less.

6

SOURCE Flagg-Newton, J., Simpson, Il, and Loewenstein, W. R. 1973. Permeability of the cell-to-cell membrane channels in mammalian cell junctions. Science 205: 404–407.

The Middle Lamella Cements Adjacent Plant Cell Walls Together In animals, cell-to-cell contact via anchoring junctions, tight junctions, and gap junctions involves interactions between membrane proteins in adjacent cells. In plants, cell junctions are biochemically different. Rather than using membrane proteins to form cell-to-cell connections, plant cells make an additional component called the middle lamella (plural, lamellae), which is found between most adjacent plant cells (Figure 10.13). When plant cells are dividing, the middle lamella is the first layer formed. The primary cell wall is then made. The middle lamella is rich in pectins, negatively charged polysaccharides that are also found in the primary cell wall (see Figure 10.6). Pectins attract water and thus produce a hydrated gel. Ca2+ and Mg2+ interact with the negative charges in the pectins and cement the cell walls of adjacent cells together. The process of fruit ripening illustrates the importance of pectins in holding plant cells together. An unripened fruit, such as a green tomato, is very firm because the rigid cell walls of adjacent cells are firmly attached to each other. During ripening, the cells secrete a group of enzymes called pectinases, which digest pectins in the middle lamella as well as those in the primary cell wall. As this process continues, the attachments between cells are broken, and the cell walls become less rigid. For this reason, a red ripe tomato is much less firm than an unripe tomato.

Plasmodesmata Are Channels Connecting the Cytoplasm of Adjacent Plant Cells In 1879, Eduard Tangl, a Russian botanist, observed intercellular connections in the seeds of the strychnine tree and hypothesized that the cytoplasm of adjacent cells is connected by ducts in the cell walls.

He was the first to propose that direct cell-to-cell communication integrates the functioning of plant cells. The ducts or intercellular channels that Tangl observed are now known as plasmodesmata (singular, plasmodesma).

The middle lamella is a layer made outside of the primary cell wall and is composed largely of negatively charged polysaccharides, such as pectins. Ca2+ and Mg2+ bind to these polysaccharides and fuse the cell walls of adjacent cells.

Primary cell wall

Middle lamella

1 μm

Plant cell walls

Figure 10.13  Plant cell-to-cell connections consist of middle lamellae. ©Purbasha Sarkar Concept Check:   How are middle lamellae similar to the anchoring junctions and desmosomes found between animal cells? How are they different?

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Plasmodesmata are functionally similar to gap junctions in animal cells because they are open pores that allow the passage of ions and molecules between the cytosols of adjacent plant cells. However, the structure of the plasmodesmata is quite different from that of gap junctions. As shown in Figure 10.14, the plasma membrane of one cell is continuous with the plasma membrane of the adjacent cell, which forms a pore that permits the diffusion of molecules from the cytosol of one cell to the cytosol of the other. In addition to a cytosolic connection, plasmodesmata also have a central tubule, called a desmotubule, connecting the smooth ER membranes of adjacent cells. Plant cells can alter the diameter of the channel formed by plasmodesmata. The channel can occur in the closed, open, and dilated states. In the open state, plasmodesmata allow the passage of ions and small molecules, such as sugars and cAMP. In this state, plasmodesmata

play a similar role to gap junctions between animal cells. Plasmodesmata tend to close when a large pressure difference occurs between adjacent cells. Why does this happen? One reason is related to cell damage. When a plant is wounded, damaged cells lose their turgor pressure. (Turgor pressure is described in Chapter 39, look ahead to Figure 39.4.) The closure of plasmodesmata between adjacent cells helps to prevent the loss of water and nutrients from the wound site. Unlike gap junctions between animal cells, plasmodesmata can dilate to also allow the passage of macromolecules and even viruses between adjacent plant cells. Though the mechanism of dilation is not well understood, the wider opening of plasmodesmata is important for the passage of proteins and mRNA during plant development. It also provides a key mechanism whereby viruses can move from cell to cell.

10.3 Tissues Learning Outcomes: 1. List the six basic cell processes that produce tissues and organs. 2. Outline the structures and functions of the four types of animal tissues: epithelial, connective, nervous, and muscle tissues. 3. Summarize the structures and functions of the three types of plant tissues: dermal, ground, and vascular tissues. Plasmodesmata

Plasma membrane

Cell walls of adjacent plant cells Smooth endoplasmic reticulum Desmotubule passing through a plasmodesma

Cytosol Cell 1

Middle lamella

Cytosol Cell 2

Figure 10.14  Structure of a plasmodesma.  Plasmodesmata are

cell junctions connecting the cytosols of adjacent plant cells, allowing water, ions, and molecules to pass from cell to cell. At these pores, the plasma membrane of one cell is continuous with the plasma membrane of an adjacent cell. In addition, the smooth ER from one cell is connected to that of the adjacent cell via a desmotubule. ©Biophoto Associates/Science Source Core Skill: Connections  Look ahead to Figure 39.8. How do plasmodesmata play a role in the movement of nutrients through a plant root?

A tissue is a part of an animal or plant consisting of a group of cells having a similar structure and function. In this section, we will view tissues from the perspective of cell biology. Animals and plants contain many different types of cells. Humans, for example, have over 200 different cell types, each with a specific structure and function. Even so, these cells can be grouped into a few general categories. For example, muscle cells found in your heart (cardiac muscle cells), in your biceps (skeletal muscle cells), and around your arteries (smooth muscle cells) look somewhat different under the microscope and have unique roles in the body. Yet due to structural and functional similarities, all three types are categorized as muscle tissue. In this section, we begin by surveying the basic processes that cells undergo to make tissues. Then, we will examine the main categories of animal and plant tissues.

Six Different Cellular Processes Produce Tissues and Organs A multicellular organism, such as a plant or animal, contains many cells. For example, an adult human has somewhere between 10 and 100 trillion cells in her or his body. Cells are organized into tissues, and tissues are organized into organs. An organ is a collection of two or more tissues that performs a specific function or set of functions. The heart is an organ found in the bodies of complex animals, and a leaf is an organ found in plants. We will examine the structures and functions of organs in Units VI and VII. How are tissues and organs formed? To form tissues and organs, cells undergo six different processes that influence their morphology, arrangement, and number: division, growth, differentiation, migration, apoptosis, and formation of connections. 1. Division. As discussed in Chapter 16, eukaryotic cells advance through a cell cycle that leads to cell division.



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2. Growth. Following cell division, cells take up nutrients and usually expand in volume. Cell division and growth are the primary mechanisms for increasing the size of tissues, organs, and organisms. 3. Differentiation. Due to gene regulation, cells differentiate into specialized types of cells. Cell differentiation is described in Chapter 20. 4. Migration. During embryonic development in animals, cells migrate to their appropriate positions within the body. Also, adults have cells that can move into regions that have become damaged. Cell migration does not occur during plant development. 5. Apoptosis. Programmed cell death, also known as apoptosis (discussed in Chapter 9), is necessary to produce certain morphological features of the body. For example, during development in mammals, the formation of individual fingers and toes requires the removal, by apoptosis, of the skin cells between them. 6. Formation of connections. In the first section of this chapter, we learned that cells produce an extracellular matrix or cell wall that provides strength and support. In animals, the ECM serves to organize cells within tissues and organs. In plants, the connections and structures of cell walls are largely responsible for the shapes of plant tissues. Different types of cell junctions in both animal and plant cells enable cells to maintain physical contact and communicate with one another.

Animals Are Composed of Epithelial, Connective, Nervous, and Muscle Tissues The body of an animal contains four general types of tissue— epithelial, connective, nervous, and muscle—that serve very different purposes (Figure 10.15).

Nervous: Brain Epithelial: Skin (top layer) Nerve

Intestinal lining

Muscle: Heart

Connective: Cartilage

Skeletal

Bone

Figure 10.15  Examples of the four general types of tissues— epithelial, connective, nervous, and muscle—found in animals. Concept Check:   Which of the four general types of tissues has the most extensive ECM?

Epithelial Tissue  Epithelial tissue is composed of cells that are joined together via tight junctions and form continuous sheets. (Epithelial cells are shown in Figure 10.9.) Epithelial tissue covers or forms the lining of all internal and external body surfaces. For example, epithelial tissue lines organs such as the lungs and digestive tract. In addition, epithelial tissue forms the outer layer of the skin, a protective surface that shields the body from the outside environment. Connective Tissue  Most connective tissue provides support to the body and/or helps to connect different tissues to each other. Connective tissue is rich in ECM. Examples of connective tissue include cartilage, tendons, bone, fat tissue, and the inner layers of the skin. Blood is also considered a form of connective tissue because it provides liquid connections to various regions of the body. Figure 10.16 shows a micrograph of cartilage, a connective tissue found in joints such as your knees. The cells that synthesize cartilage, known as chondrocytes, actually represent a small proportion of the total volume of cartilage. As shown in Figure 10.16, the chondrocytes are found in small cavities within the cartilage called lacunae (singular, lacuna). In some types of cartilage, the chondrocytes represent only 1–2% of the total volume of the tissue! Chondrocytes are the only cells found in cartilage. They are solely responsible for the synthesis of protein fibers, such as collagen, as well as the glycosaminoglycans and proteoglycans that are found in cartilage.

Lacuna with 2 chondrocytes ECM

213.7 μm

Figure 10.16  An example of connective tissue in animals that is rich in extracellular matrix.  This micrograph of cartilage shows chondrocytes in the ECM. The chondrocytes, which are responsible for making the components of cartilage, are found in cavities called lacunae. ©Victor P. Eroschenko Nervous Tissue  Nervous tissue receives, generates, and conducts electrical signals throughout the body. In vertebrates, these electrical signals are integrated by nervous tissue in the brain and transmitted down the spinal cord to the rest of the body.

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Chapter 42 considers the cellular basis of nerve signals, and Chapters 43  and 44  examine the organization of nervous systems in animals. Muscle Tissue  Muscle tissue generates a force that facilitates movement. Muscle contraction is needed for body movements, such as walking and running, and also plays a role in the movement of materials throughout the body. For example, contraction of heart muscle propels blood through your body, and smooth muscle contractions move food through the digestive system. The properties of muscle tissue in animals are examined in Chapter 45.

Plants Contain Dermal, Ground, and Vascular Tissues Plant biologists classify tissues as simple or complex. Simple tissues are composed of one or possibly two cell types. Complex tissues are composed of two or more cell types but lack an organization that would qualify them as organs. The bodies of most plants contain three general types of simple or complex tissues—dermal, ground, and vascular—each with a different structure suited to its functions (Figure 10.17).

Stem

Root

Dermal

Ground Tissue  Most of a plant’s body is made of ground tissue, which has a variety of functions, including photosynthesis, storage of carbohydrates, and support. Ground tissue is subdivided into three types of simple tissues: parenchyma, collenchyma, and sclerenchyma. Let’s look briefly at each of these types of ground tissue (also see Figure 36.7). 1. Parenchyma is very active metabolically. The mesophyll, the central part of the leaf that carries out the bulk of photosynthesis, is composed of parenchyma. Parenchyma also functions in the storage of carbohydrates. The cells of parenchyma usually lack a secondary cell wall. 2. Collenchyma provides structural support to the plant body, particularly to growing regions such as the periphery of the stems and leaves. Cells in collenchyma tend to have thick, secondary cell walls but do not contain much lignin. Therefore, they provide support but are also able to stretch. 3. Sclerenchyma also provides structural support to the plant body, particularly to those parts that are no longer growing, such as the dense, woody parts of stems. The secondary cell walls of sclerenchyma cells tend to have large amounts of lignin, which provides rigid support. In many cases, sclerenchyma cells are dead at maturity, but their cell walls continue to provide structural support during the life of the plant.

Leaf

KEY

Dermal Tissue  Dermal tissue is a complex tissue that forms a covering on various parts of the plant. The term epidermis refers to the newly made dermal tissue on the surfaces of leaves, stems, and roots. Plant epidermal cells have a thick primary cell wall and are tightly interlocked by their middle lamellae. As a consequence, these cells are held closely together, much like epithelial cell layers in animals. The epidermal cells of leaves usually secrete a waxy cuticle to prevent water loss. In addition, leaf epidermis often has hairs, or trichomes, which are specialized types of epidermal cells. Trichomes have diverse functions, including the secretion of oils and leaf protection. In leaves, epidermal cells called guard cells form pores known as stomata, which permit gas exchange. The function of the root epidermis is the absorption of water and nutrients. The root epidermis does not have a waxy cuticle because such a cuticle would inhibit water and nutrient absorption.

Ground

Vascular

Figure 10.17  Locations of the three general types of tissues— dermal, ground, and vascular—found in plants. Concept Check:   Which of these three types of plant tissues is found on the surfaces of leaves, stems, and roots?

Vascular Tissue  Some types of modern plants, such as mosses, are nonvascular plants that lack conducting vessels. These plants tend to be small and live in damp, shady places. Most plants living today, however, are vascular plants. In these species, which include ferns and seed plants, the vascular tissue is a complex tissue composed of cells that are interconnected and form conducting vessels for water and nutrients. As described in greater detail in Chapter 39, the two types of vascular tissue are called xylem and phloem. The xylem transports water and mineral ions from the root to the rest of the plant, and the phloem distributes the products of photosynthesis and a variety of other nutrients throughout the plant.



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Summary of Key Concepts 10.1  Extracellular Matrix and Cell Walls ∙∙ The extracellular matrix (ECM) is a network of material that forms a complex meshwork outside of animal cells; the cell wall is a similar component of plant cells. ∙∙ Proteins and polysaccharides are the major constituents of the ECM in animals. These materials are involved in strength, structural support, organization, and cell signaling (Figure 10.1). ∙∙ Adhesive proteins, such as fibronectin and laminin, help adhere cells to the ECM. Structural proteins include collagen, which forms fibers and fibrous networks that provide tensile strength, and elastin, which forms elastic fibers that stretch and recoil (Table 10.1, Figures 10.2, 10.3). ∙∙ Animals make many different types of collagen fibers, and gene regulation controls the locations in the body where they are made (Table 10.2). ∙∙ Glycosaminoglycans (GAGs) are polysaccharides of repeating disaccharide units that give a gel-like character to the ECM of animals. Proteoglycans consist of a long, linear core protein with many GAGs attached (Figure 10.4). ∙∙ Plant cells are surrounded by a cell wall composed largely of cellulose. The primary cell wall is made first and tends to be thin and flexible. The secondary cell wall is made after the primary cell wall and is often thick and rigid (Figures 10.5, 10.6).

10.2  Cell Junctions ∙∙ The three common types of cell junctions found in animals are anchoring, tight, and gap junctions (Table 10.3). ∙∙ Key components of anchoring junctions are cell adhesion molecules (CAMs), which bind cells to each other or to the ECM. The four types of anchoring junctions are adherens junctions, desmosomes, hemidesmosomes, and focal adhesions (Figure 10.7). ∙∙ Cadherins and integrins are two types of CAMs. Cadherins link cells to each other, whereas integrins link cells to the ECM. In the cytosol, CAMs bind to actin or intermediate filaments (Figure 10.8). ∙∙ Tight junctions between cells, composed of occludin and claudin, prevent the leakage of materials across a layer of cells (Figures 10.9, 10.10). ∙∙ Gap junctions consist of many channels called connexons, which permit the direct passage of ions and small molecules between adjacent cells (Figure 10.11). ∙∙ Loewenstein and colleagues showed that gap junctions permit the passage of substances with a molecular mass of less than about 1,000 Da (Figure 10.12). ∙∙ The cell walls of adjacent plant cells are cemented together via middle lamellae, which are rich in pectins—negatively charged polysaccharides (Figure 10.13). ∙∙ The plasma membranes and endoplasmic reticula of adjacent plant cells are connected via plasmodesmata that allow the passage of water, ions, and molecules between the cytosols of adjacent cells (Figure 10.14).

10.3  Tissues ∙∙ Cells are organized into tissues, and tissues are organized into organs. A tissue is a group of cells that have a similar structure and function, and an organ is composed of two or more tissues that carry out a particular function or set of functions.

∙∙ Six processes—cell division, cell growth, differentiation, migration, apoptosis, and formation of cell-to-cell connections—produce tissues and organs. ∙∙ The four general kinds of tissues found in animals are epithelial, connective, nervous, and muscle tissues (Figures 10.15, 10.16). ∙∙ The three general kinds of tissues found in plants are dermal, ground, and vascular tissues (Figure 10.17).

Assess & Discuss Test Yourself 1. The function of the extracellular matrix (ECM) in animals is a. to provide strength. b. to provide structural support. c. to organize cells and other body parts. d. cell signaling. e. all of the above. 2. The protein found in the ECM of animals that provides strength and resistance to tearing when stretched is a. elastin. b. cellulose. c. collagen. d. laminin. e. fibronectin. 3. The polysaccharide that forms the hard outer covering of many invertebrates is a. collagen. b. chitin. c. chondroitin sulfate. d. pectin. e. cellulose. 4. The extension sequence found in procollagen polypeptides a. causes procollagen to be synthesized into the ER lumen. b. causes procollagen to form a triple helix. c. prevents procollagen from forming large collagen fibers. d. causes procollagen to be secreted from the cell. e. both b and c. 5. The dilated state of plasmodesmata allows the passage of a. water. b. ions. c. small molecules. d. macromolecules and viruses. e. all of the above. 6. The gap junctions of animal cells differ from the plasmodesmata of plant cells in that a. gap junctions serve as communicating junctions and plasmodesmata serve as anchoring junctions. b. gap junctions prevent extracellular material from moving between adjacent cells but plasmodesmata do not. c. gap junctions allow for direct exchange of cellular material between cells but plasmodesmata cannot allow the same type of exchange. d. gap junctions are formed by specialized proteins that form channels through the membranes of adjacent cells and plasmodesmata are formed by connecting the plasma membranes of adjacent cells. e. all of the above are correct.

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7. Which of the following is (are) involved in the process of tissue and organ formation in multicellular organisms? a. cell division b. cell growth c. cell differentiation d. cell connections e. all of the above 8. The tissue type common to animals that functions in the conduction of electrical signals is a. epithelial. b. dermal. c. muscle. d. nervous. e. ground. 9. A type of tissue that is rich in ECM or has cells with a thick cell wall is a. dermal tissue in plants. b. ground tissue in plants. c. nervous tissue in animals. d. connective tissue in animals. e. both b and d. 10. Which of the following is not a correct statement comparing plant tissues and animal tissues? a. Nervous tissue of animals plays the same role as vascular tissue in plants. b. The dermal tissue of plants is similar to epithelial tissue of animals in that both provide a covering for the organism. c. The epithelial tissue of animals and the dermal tissue of plants have special characteristics that limit the movement of material between cell layers.

d. The ground tissue of plants and the connective tissue of animals provide structural support for the organism. e. The ground tissue of plants and the connective tissue of animals have large amounts of extracellular material (that is, thick cell walls in plants and lots of ECM in animals).

Conceptual Questions 1. What are key differences between the primary cell wall and the secondary cell wall of plant cells?  2. What are similarities and differences in the structures and functions of cadherins and integrins, proteins found in animal cells?  3.

Core Concept: Systems We can view the body of a multicellular organism, such as a plant or animal, as a system of interconnected cells. Discuss how cell junctions play a key role in forming this system. 

Collaborative Questions 1. Discuss the similarities and differences between the ECM of animals and the cell walls of plants. 2. Cell junctions in animals are important in preventing cancer cells from metastasizing—moving to other parts of the body. Certain drugs bind to CAMs and influence their structure and function. Some of these drugs may help to prevent the spread of cancer cells. What would you hypothesize to be the mechanism by which such drugs work? What might be some harmful side effects?

UNIT III

11

GENETICS Genetics is the branch of biology that deals with inheritance— the transmission of characteristics from parent to offspring. We begin this unit by examining the structure of the genetic material, namely DNA, at the molecular and cellular levels. We will explore the structure and replication of DNA and see how it is packaged into chromosomes (Chapter 11). We will then consider how segments of DNA are organized into units called genes, and how those genes are expressed at the molecular level to produce mRNA, proteins, and noncoding RNAs (Chapters 12 and 13). In Chapter 14, we will consider how the expression of genes is regulated. We will also examine how mutations alter the properties of genes and even lead to diseases such as cancer (Chapter 15). In Chapter 16, we turn our attention to the mechanisms by which genes are transmitted from parent to offspring, beginning with a discussion of how chromosomes are sorted and transmitted during cell division. Chapters 17 and 18 explore the relationships between the transmission of genes and the outcome of an offspring’s traits. We will look at genetic patterns called Mendelian inheritance and more complex patterns that could not have been predicted from Mendel’s work. The remaining chapters of this unit explore additional topics that are of interest to biologists. In Chapter 19, we will examine some of the unique genetic properties of bacteria and viruses. Chapter 20 considers the central role genes play in the development of animals and plants from a fertilized egg to an adult. We end this unit by exploring genetic technologies that are used by researchers, clinicians, and biotechnologists to unlock the mysteries of genes and provide tools and applications that benefit humans (Chapter 21).

The following Core Concepts and Core Skills will be emphasized in this unit: • Information: Throughout this unit, we will see how the genetic material carries the information to sustain life. • Structure and Function: In Chapters 11 through 15, we will examine how the structures of DNA, RNA, genes, and chromosomes underlie their functions. • Quantitative Reasoning: In Chapters 17 and 18, we will consider methods used to predict the outcome of genetic crosses. • Science and Society: In Chapter 21, we will examine genetic technologies that have many applications in our society. • Process of Science: Every chapter in this unit has a Feature Investigation that describes a pivotal experiment that provided insights into our understanding of genetics.

13

Ribosome

Polypeptide

mRNA

12 0.4 μm

15

14 17

16 18

20

19

21

(11): ©Pieter Van De VijverI/Science Photo Library/Corbis; (12): ©Elena Kiseleva/Science Source; (13): ©Mauro Giacca, Ana Eulalio, Miguel Mano; (14): ©Daniel Gage, University of Connecticut; (15): ©Yvette Cardozo/Workbook Stock/Getty Images; (16): ©Biophoto Associates/Science Source; (17): ©Radu Sigheti/Reuters; (18): ©Andia/Alamy Stock Photo; (19): ©CAMR/A. Barry Dowsett/Science Source; (20): ©Medical-on-Line/Alamy Stock Photo; (21): ©Fumihiro Sugiyama

1 mm

CHAPTER OUTLINE

Nucleic Acid Structure, DNA Replication, and Chromosome Structure

11

A molecular model for the structure of a DNA double helix. ©Pieter Van De VijverI/Science Photo Library/Corbis

O

n October 17, 2001, Mario K. was set free after serving 16 years in prison. He had been convicted of a sexual assault and murder that occurred in 1985. The charges were dropped because investigators discovered that another person, Edwin M., had actually committed the crime. How was Edwin M. identified as the real murderer? In 2001, he committed another crime, and his DNA was entered into a computer database. Edwin’s DNA matched the DNA that had been collected from the victim in 1985, and other evidence was then gathered indicating that Edwin M. was the true murderer. Like Mario K., over 200 other inmates have been exonerated when DNA tests have shown that a different person was responsible for the crime. Deoxyribonucleic acid, or DNA, is the genetic material that provides the blueprint to produce an individual’s traits. Each person’s DNA is distinct and unique. Even identical twins show minor differences in their DNA sequences. We begin our survey of genetics by examining DNA at the molecular level. Once we understand how DNA works at this level, it becomes easier to see how DNA functions to control the properties of cells and ultimately the

11.1 Biochemical Identification of the Genetic Material 11.2 Nucleic Acid Structure 11.3 Overview of DNA Replication 11.4 Molecular Mechanism of DNA Replication 11.5 Molecular Structure of Eukaryotic Chromosomes Summary of Key Concepts Assess & Discuss

characteristics of unicellular and multicellular organisms. The past several decades have seen exciting advances in techniques and approaches for investigating and even altering the genetic material. These advances have greatly expanded our understanding of molecular genetics, and the techniques are widely used in related disciplines, including biochemistry, cell biology, and microbiology. Likewise, genetic techniques have many important applications in biotechnology and are used in the field of criminal justice, especially in forensics, to provide evidence of guilt or innocence. To a large extent, our understanding of genetics comes from our knowledge of the molecular structure of DNA. In this chapter, we begin by considering some classic experiments that provided evidence that DNA is the genetic material. We will then survey the molecular features of DNA, which will allow us to appreciate how DNA can store information and be accurately copied. We will also consider the components of ribonucleic acid (RNA), which show striking similarities to those of DNA. Lastly, we will examine the molecular composition of chromosomes, where the DNA is found.

11.1  Biochemical Identification of the Genetic Material Learning Outcomes: 1. List the four key criteria that the genetic material must fulfill. 2. CoreSKILL » Analyze the results of experiments that identified DNA as the genetic material.

DNA carries the genetic instructions for the traits of living organisms. In the case of multicellular organisms such as plants and animals, the information stored in the genetic material enables a fertilized egg to develop into an embryo and eventually into an adult organism. In addition, the genetic material allows organisms to survive in their native environments. For example, an individual’s DNA provides the blueprint to produce enzymes that are needed to metabolize nutrients in food. To fulfill its role, the genetic material must meet the following key criteria: 1. Information. The genetic material must contain the information necessary to construct an entire organism.



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2. Replication. The genetic material must be accurately copied, a process known as replication. 3. Transmission. After it is replicated, the genetic material can be passed from parent to offspring. It also must be passed from cell to cell during the process of cell division. 4. Variation. Differences in the genetic material must account for the known variation within each species and among different species. How was the genetic material discovered? The quest to identify the genetic material began in the late 19th century, when a few scientists postulated that living organisms possess a blueprint that has a biochemical basis. In 1883, German biologist August Weismann and his Swiss colleague Karl Nägeli championed the idea that a chemical substance exists within living cells that is responsible for the transmission of traits from parents to offspring. During the next 30 years, experimentation along these lines centered on the behavior of chromosomes, the cellular structures that we now know contain the genetic material. The term chromosome is from the Greek words chromo and soma, meaning colored body, which refers to the observation of early microscopists that chromosomes are easily stained by colored dyes. By studying the transmission patterns of chromosomes from cell to cell and from parent to offspring, researchers were convinced that chromosomes carry the determinants that control the outcome of traits. Ironically, the study of chromosomes initially misled researchers regarding the biochemical identity of the genetic material. Chromosomes contain two classes of macromolecules: proteins and DNA. Scientists of that era viewed proteins as being more biochemically complex because they are made from 20 different amino acids. Furthermore, biochemists already knew that proteins perform an amazingly wide range of functions, and complexity seemed an important prerequisite for the blueprint of an organism. By comparison, DNA seemed less complex, because it contains only four types of repeating units, called nucleotides, which will be described later in this chapter. In addition, the functional role of DNA in the nucleus had not been extensively investigated prior to the 1920s. Therefore, from the 1920s to the 1940s, most scientists were expecting research studies to reveal that proteins are the genetic material. Contrary to this expectation, however, several different experiments revealed that DNA carries out this critical role. In this section, we will examine one early line of study that involved research in microbiology.

Griffith’s Bacterial Transformation Experiments Indicated the Existence of a Genetic Material In the late 1920s, an English microbiologist, Frederick Griffith, studied a type of bacterium known then as pneumococci and now classified as Streptococcus pneumoniae. Some strains of S. pneumoniae secrete a polysaccharide capsule, but other strains do not. When streaked on petri plates containing solid growth media, capsule-secreting strains have a smooth colony morphology. Those strains unable to secrete a capsule have a colony morphology that looks rough. In mammals, smooth strains of S. pneumoniae may cause pneumonia and other symptoms. In mice, such infections are usually fatal. As shown in Figure 11.1, Griffith injected live and/or heat-killed bacteria into mice and then observed whether or not the bacteria caused them to die. He investigated the effects of two strains of S. pneumoniae: type S for smooth and type R for rough.

1. When injected into a live mouse, the type S strain killed the mouse (Figure 11.1, step 1). The capsule made by type S strains prevents the mouse’s immune system from killing the bacterial cells. Following the death of the mouse, many type S bacteria were found in the mouse’s blood. 2. When type R bacteria were injected into a mouse, the mouse survived, and after several days, living bacteria were not found in the live mouse’s blood (Figure 11.1, step 2). 3. Griffith also heat-killed the type S bacteria and then injected them into a mouse. As expected, the mouse survived (Figure 11.1, step 3). 4. A surprising result occurred when Griffith mixed live type R bacteria with heat-killed type S bacteria and then injected them into a mouse—the mouse died (Figure 11.1, step 4). The blood from the dead mouse contained living type S bacteria! How did Griffith explain these results? He postulated that a substance from dead type S bacteria transformed the type R bacteria into Treatment

1

Result

Control: Injected living type S bacteria into mouse.

Conclusion Type S cells are virulent.

2 Control:

Type R cells are benign.

3 Control:

Heat-killed type S cells are benign.

Injected living type R bacteria into mouse.

Injected heatkilled type S bacteria into mouse.

4

Injected living type R and heat-killed type S bacteria into mouse.

Virulent type S strain in dead mouse’s blood

Living type R cells have been transformed into virulent type S cells by a substance from the heat-killed type S cells.

Figure 11.1  Griffith’s experiments showing that genetic material

can be transferred from one bacterium to another.  Note: To determine if a mouse’s blood contained live bacteria, a sample of blood was also applied to solid growth media. (This part of the procedure is not shown.) For steps 1 and 4, smooth bacterial colonies were observed. For step 2, no bacterial colonies were observed because the type R cells were killed by the immune system of the mouse.    ore Skill: Connections  Look ahead to Figure 19.17. C How does bacterial transformation play a role in the transfer of genes, such as antibiotic resistance genes, from one bacterial species to another?

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type S bacteria. Griffith called this process transformation, and he termed the unidentified material responsible for this phenomenon the “transformation principle.” Let’s consider what these observations mean with regard to the four criteria of the genetic material: information, replication, transmission, and variation. According to Griffith’s results, the transformed bacteria had acquired the information (criterion 1) to make a capsule from the heat-killed cells. For the transformed bacteria to proliferate and thereby kill the mouse, the substance conferring the ability to make a capsule must be replicated (criterion 2) and then transmitted

(criterion 3) from mother to daughter cells during cell division. Finally, Griffith already knew that variation (criterion 4) existed in the ability of his strains to produce a capsule (S strain) or not produce a capsule (R strain). Taken together, these observations are consistent with the idea that the formation of a capsule is governed by genetic material. In the experiment of Figure 11.1, step 4 indicated that some genetic material from the heat-killed type S bacteria had been transferred to the living type R bacteria and provided those bacteria with a new trait. At the time of his studies, however, Griffith could not determine the biochemical composition of the transforming substance.

Core Skill: Process of Science

Feature Investigation  | Avery, MacLeod, and McCarty Used Purification Methods to Reveal That DNA Is the Genetic Material

Exciting discoveries sometimes occur when researchers recognize that another scientist’s experimental approach may be modified and then used to dig deeper into a scientific question. In the 1940s, American physician Oswald Avery and American biologists Colin MacLeod and Maclyn McCarty were also interested in the process of bacterial transformation. During the course of their studies, they realized that Griffith’s observations could be used as part of an experimental strategy to biochemically identify the genetic material. They asked, “What substance is being transferred from the dead type S bacteria to the live type R bacteria?” To answer this question, Avery, MacLeod, and McCarty needed to purify the general categories of substances found in living cells. They used established biochemical procedures to purify classes of macromolecules, such as proteins, DNA, and RNA, from the type S streptococcal

strain. Initially, they discovered that only the purified DNA could convert type R bacteria into type S. To further verify that DNA is the genetic material, they performed the investigation outlined in Figure 11.2. They purified DNA from the type S bacteria and mixed it with type R bacteria. After allowing time for DNA uptake into the type R bacteria, they added an antibody that aggregated any nontransformed type R bacteria, which were then removed by centrifugation. The remaining bacteria were placed on solid growth media within petri plates and incubated overnight to allow the division and growth of cells to form visible bacterial colonies. As a control, no DNA extract was added, and no type S bacterial colonies were observed on the petri plates (see plate A in step 6). When the researchers mixed their S strain DNA extract with type R bacteria, some of the bacteria were converted to type S bacteria (see

Figure 11.2  The Avery, MacLeod, and McCarty experiments that identified DNA as Griffith’s transformation principle—the genetic

material.

HYPOTHESIS A purified macromolecule from type S bacteria, which functions as the genetic material, will be able to convert type R bacteria into type S. KEY MATERIALS Type R and type S strains of Streptococcus pneumoniae. Experimental level

1

Conceptual level DNA fragments in a purified DNA extract

Purify DNA from the type S strain. This involves breaking open cells and separating the DNA away from other components by centrifugation.

± DNase ± RNase ± Protease + Type R cells A

2

A

3

B

C

D

E

Mix the DNA extract with type R bacteria. Also, carry out the same steps but add the enzyme DNase, RNase, or protease to the DNA extract, which digests DNA, RNA, or proteins, respectively. As a control, don’t add any DNA extract to some type R cells.

Allow time for the DNA to be taken up

B

C

D

E

Control

+ DNA

+ DNA + DNase

+ DNA + RNase

A

B

C

D

+ DNA + Protease E

don’t add any DNA extract to some type R cells. A

B

3

E

Control + DNA + DNA + DNA + DNA + DNase + RNase + Protease NUCLEIC ACID STRUCTURE, DNA REPLICATION, AND CHROMOSOME STRUCTURE 223

B

C

D

E

Add an antibody, a protein made by the immune system of mammals, that specifically recognizes type R cells that haven’t been transformed. The binding of the antibody causes the type R cells to aggregate. B

B B B

Control Control Control

C

D

E

A

B

C

D

E

A A A

B B B

C C C

D D D

E E E

Add antibody

C

D

E

Type S cell in S the Type supernatant Type S cell cell in in the the supernatant supernatant Type R cells cells inType the R pellet Type R cells in in the the pellet pellet Centrifuge Centrifuge Centrifuge

pellet at the while typebottom S cellsof remain in the pelletthe at the the bottom of the tubes, tubes, while S remain supernatant. Pour the supernatant while the the type type S cells cells remain in in the the supernatant. Pour the onto solid growth within petri supernatant. Pourmedia the supernatant supernatant onto solid growth media within petri plates. Allow time for cellswithin to divide onto solid growth media petri Allow for toplates. form bacterial colonies. plates. Allow time time for cells cells to to divide divide to to form form bacterial bacterial colonies. colonies.

A A A

B

Antibody

the tubes to centrifugation. 5 Subject Subject the to The aggregated type R cells form a 5 Subject the tubes tubes to centrifugation. centrifugation. 5 pellet The type cells form at the bottom of R the tubes, The aggregated aggregated type R cells form a a

6 THE DATA 6 THE DATA DATA 6 THE

A Type S cell

A

7 7 7 8 8 8

D

Allow time for the DNA to be taken up by the type R cells, converting some of them to type S.

A

4

C

D D D

C C C DNA extract DNA DNA extract extract

DNA extract + DNase DNA DNA extract extract + + DNase DNase

Smooth bacterial colony Smooth composed of type colony S cells Smooth bacterial bacterial colony composed composed of of type type S S cells cells E E E

DNA extract + RNase DNA DNA extract extract + + RNase RNase

DNA extract + protease DNA DNA extract extract + + protease protease

CONCLUSION DNA is responsible for transforming type R cells into type S cells. CONCLUSION CONCLUSION DNA DNA is is responsible responsible for for transforming transforming type type R R cells cells into into type type S S cells. cells. SOURCE Avery, O.T., MacLeod, C.M., and McCarty, M. 1944. Studies on the Chemical Nature of the Substance Inducing Transformation of SOURCE Avery, C.M., M. Studies the Types. Journal of McCarty, Experimental Medicine 79:on 137–158. SOURCE Pneumococcal Avery, O.T., O.T., MacLeod, MacLeod, C.M., and and McCarty, M. 1944. 1944. Studies on the Chemical Chemical Nature Nature of of the the Substance Substance Inducing Inducing Transformation Transformation of of Pneumococcal Pneumococcal Types. Types. Journal Journal of of Experimental Experimental Medicine Medicine 79: 79: 137–158. 137–158.

plate B in step 6 of Figure 11.2). This result was consistent with the idea that DNA is the genetic material. Even so, a careful biochemist could argue that the DNA extract might not have been 100% pure. For this reason, the researchers realized that a small amount of contaminating material in the DNA extract could actually be the genetic material. The most likely contaminating substances in this case would be RNA or protein. To address this possibility, Avery, MacLeod, and McCarty treated the DNA extract with an enzyme that digests either DNA (called DNase), RNA (RNase), or protein (protease) (see step 2). When the DNA extracts were treated with RNase or protease, the type R bacteria were still converted into type S bacteria, indicating that contaminating RNA or protein in the extract was not acting as the genetic material (see step 6, plates D and E). Moreover, when

the extract was treated with DNase, it lost the ability to convert type R bacteria into type S bacteria (see plate C). Taken together, these results were consistent with the idea that DNA is the genetic material. Experimental Questions 1. CoreSKILL » Avery, MacLeod, and McCarty worked with two strains of Streptococcus pneumoniae to determine the biochemical identity of the genetic material. Explain the characteristics of the S. pneumoniae strains that made them particularly well suited for the researchers' experiment.  2. What is a DNA extract?  3. CoreSKILL » In the experiment of Avery, MacLeod, and McCarty, what was the purpose of using protease, RNase, and DNase if only the DNA extract caused transformation? 

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11.2      Nucleic Acid Structure

Nucleotides

Learning Outcomes: 1. Outline the structural features of DNA at five levels of complexity. 2. Describe the structures of nucleotides, a DNA strand, and the DNA double helix. 3. CoreSKILL » Discuss and interpret the work of Franklin; Chargaff; and Watson and Crick.

A core concept in biology is that structure determines function. When biologists want to understand the function of a material at the molecular and cellular level, they focus some of their efforts on determining its biochemical structure. In this regard, an understanding of DNA’s structure has proven to be particularly exciting because the structure makes it easier for us to understand how DNA can store information, how it is replicated and then transmitted from cell to cell, and how variation in its structure can occur. DNA and its molecular cousin, RNA, are known as nucleic acids, polymers consisting of nucleotides, which are responsible for the storage, expression, and transmission of genetic information. This term is derived from the discovery of DNA by Swiss physician Friedrich Miescher in 1869. He identified a novel phosphoruscontaining substance from the nuclei of white blood cells found in waste surgical bandages. He named this substance nuclein. As the structure of DNA and RNA became better understood, they were found to be acidic molecules, which means they release hydrogen ions (H+) in solution and have a net negative charge at neutral pH. Thus, the name nucleic acid was coined. DNA is a very large macromolecule composed of smaller building blocks. We can consider the structural features of DNA at different levels of complexity (Figure 11.3): 1. Nucleotides are the building blocks of DNA. 2. A strand of DNA is formed by the covalent linkage of nucleotides in a linear manner. 3. Two strands of DNA hydrogen-bond with each other to form a double helix. In a DNA double helix, two DNA strands are twisted together to form a structure that resembles a spiral staircase. 4. In living cells, DNA is associated with an array of different proteins to form chromosomes. The association of proteins with DNA organizes the long double helix into a compact structure. 5. A genome is the complete complement of an organism’s genetic material. For example, the genome of most bacteria is a single circular chromosome, whereas eukaryotic cells have DNA in their nucleus, mitochondria, and chloroplasts. The first three levels of complexity will be the focus of this section. Level 4 will be discussed in Section 11.5, and level 5 is examined in Chapter 21.

Nucleotides Contain a Phosphate, a Sugar, and a Base A nucleotide has three components: a phosphate group, a pentose (five-carbon) sugar, and a nitrogen-containing base (Figure 11.4). The nucleotides in DNA and RNA contain different sugars. Deoxyribose

Single strand

Double helix

DNA associates with proteins to form a chromosome.

Figure 11.3  Levels of DNA structure within a chromosome. is found in DNA, and ribose is found in RNA. Five different bases are found in nucleotides, although any given nucleotide contains only one base. The five bases are subdivided into two categories, the purines and the pyrimidines, due to differences in their structures (see Figure 11.4). The purine bases, adenine (A) and guanine (G), have a double-ring structure, whereas the pyrimidine bases, thymine (T), cytosine (C), and uracil (U), have a single-ring structure. Adenine, guanine, and cytosine are found in both DNA and RNA. Thymine is found only in DNA, whereas uracil is found only in RNA. A conventional numbering system describes the locations of carbon and nitrogen atoms in the sugars and bases (Figure 11.5). The prime symbol (′) is used to distinguish the numbering of carbons in the sugar. The atoms in the ring structures of the bases are not given the prime designation. The sugar carbons are designated 1′ (read as "one prime"), 2′, 3′, 4′, and 5′, with the carbon atoms numbered in a clockwise direction starting with the carbon atom to the right of the ring oxygen atom. The fifth carbon is outside the ring. A base is attached to the 1′ carbon atom, and a phosphate group is attached at the 5′ position. Compared with ribose (see Figure 11.4), deoxyribose lacks a single oxygen atom at the 2′ position; the prefix deoxy- (meaning without oxygen) refers to this missing atom.

A Strand Is a Linear Linkage of Nucleotides with Directionality The next level of nucleic acid structure is the formation of a strand of DNA or RNA in which nucleotides are covalently attached to each other



NUCLEIC ACID STRUCTURE, DNA REPLICATION, AND CHROMOSOME STRUCTURE 225 Purines (double ring)

O

P

NH2

Base

O–

O

N O

CH2

O–

Phosphate

H

H

N

H

OH

H

CH3

N

H

O

Pyrimidines (single ring)

H

N

H

O

O CH3

Deoxyribose N

C

NH2

C

C

N

C

N

H

C

N

NH2

H

H

H

C C

C

N

5ʹ

N C

O

O

P O–

O

H

O– CH2 5ʹ 4ʹ H H

Cytosine (C) O

O

P

NH2 N

O

CH2

O–

Phosphate

H

1ʹ H 2ʹ H H

NH2 N

N

H

H

OH

OH

H

H

N

H

H

N

Ribose

N

Phosphodiester linkage

NH2

N

N

H N

N

H

NH2

CH2 5ʹ 4ʹ H H

N 1ʹ H 2ʹ H H

P O–

H

H

N

O

CH2 5ʹ 4ʹ H H

O

Cytosine (C)

Figure 11.4  Nucleotides and their components.  For simplicity,

Single nucleotide

Concept Check:  Which pyrimidine(s) is (are) found in both DNA and RNA?  O 4 N

6 H

O– O

P

O

O–

Phosphate

CH2 O 5ʹ 4ʹ H H 3ʹ OH

1

N

Guanine (G) O N

N

H

P

O

O–

Phosphate

CH2 5ʹ 4ʹ H H 3ʹ OH

the carbon atoms in the ring structures are shown only for guanine and cytosine in part (a).

CH3 5

1ʹ H 2ʹ H H

O O

Cytosine (C) O

N

O

3ʹ

H

Guanine (G)

N

H

N H

NH2 H

O O

Adenine (A) H

N

O

3ʹ

Uracil (U)

O

O

O

H

Adenine (A)

(b) RNA nucleotide

O– H

H

N

H

O

O

P

N

H

O

Base

Thymine (T) O

N

O

3ʹ

H

Guanine (G)

O–

H

N

Thymine (T)

O

(a) DNA nucleotide

Bases

H

Adenine (A)

H

Backbone

N

H

H

H

N

N

N

H

NH2

O 1ʹ H 2ʹ H H

Sugar (deoxyribose)

3ʹ

H 3

Thymine

2 O

1ʹ H H 2ʹ H

Deoxyribose

Figure 11.5  Conventional numbering in a DNA nucleotide.  The

carbons in the sugar are given a prime designation, whereas those in the base are not. Concept Check:  What is the numbering designation of the carbon atom to which the phosphate is attached? 

in a linear fashion. Figure 11.6 depicts a short strand of DNA with four nucleotides. The linkage is a phosphoester bond (a covalent bond between phosphorus and oxygen) involving a sugar molecule in one nucleotide and a phosphate group in the next nucleotide. Another way of viewing this linkage is to notice that a phosphate group connects two sugar molecules. From this perspective, the linkage in DNA and RNA strands is called a phosphodiester linkage, which has two phosphoester bonds.

Figure 11.6  The structure of a DNA strand.  Nucleotides are

covalently bonded to each other in a linear manner. Notice the directionality of the strand and that it carries a particular sequence of bases. An RNA strand has a very similar structure, except the sugar is ribose rather than deoxyribose, and uracil is substituted for thymine. Core Concept: Information  The covalent linkage of a sequence of bases allows DNA to store information.

The phosphates and sugar molecules form the backbone of a DNA or RNA strand, and the bases project from the backbone. The backbone is negatively charged due to the negative charges of the phosphate groups. An important structural feature of a DNA strand is the orientation of the nucleotides. Each phosphate in a phosphodiester linkage is covalently bonded to the 5′ carbon in one nucleotide and to the 3′ carbon in the other. In a strand, all sugar molecules are oriented in the same direction. For example, in the strand shown in Figure 11.6, all of the 5′ carbons in every sugar molecule are above the 3′ carbons. A strand has a directionality based on the orientation of the sugar molecules within that strand. In Figure 11.6, the direction of the strand is said to be 5′ to

226

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3′ when going from top to bottom. The 5′ end of a DNA strand has a phosphate group, whereas the 3′ end has an —OH group. From the perspective of function, a key feature of DNA and RNA structure is that a strand contains a specific sequence of bases. In Figure 11.6, the sequence of bases is thymine–adenine–cytosine–guanine, or TACG. To indicate the directionality, the sequence of the strand is abbreviated 5′–TACG–3′. Because the nucleotides within a strand are attached to each other by stable covalent bonds, the sequence of bases in a DNA strand remains the same over time, except in rare cases when mutations occur. The sequence of bases in DNA and RNA is the critical feature that allows them to store and transmit information.

A Few Key Experiments Paved the Way to Solving the Structure of DNA What experimental approaches were used to analyze DNA structure? Let's consider some of the key experiments. X-ray Diffraction Pattern Produced by Franklin  X-ray diffraction was an important experimental tool that led to the discovery of the DNA double helix. When a substance is exposed to X-rays, the atoms in the substance cause the X-rays to be scattered (Figure 11.7). If the substance has a repeating structure, the pattern of scattering, known as the diffraction pattern, is related to the structural arrangement of the atoms causing the scattering. The diffraction pattern is analyzed using mathematical theory to provide information regarding the three-dimensional structure of the molecule. British biophysicist Rosalind Franklin, working in the 1950s in the same laboratory as Maurice Wilkins, was a gifted experimentalist who made marked advances in X-ray diffraction techniques involving DNA. The diffraction pattern of DNA fibers produced by Franklin suggested a helical structure with a diameter that is relatively uniform and too wide to be a single-stranded helix. In addition, the pattern provided

X-rays diffracted by DNA onto photographic plate Pattern represents the atomic array in wet fibers

Wet DNA fibers

X-ray beam

Figure 11.7  Franklin’s X-ray diffraction of DNA fibers.  The

exposure of DNA wet fibers to X-rays causes the X-rays to be scattered and the pattern of scattering is related to the position of the atoms in the DNA fibers. Core Skill: Process of Science  This method was instrumental in solving the structure of the DNA double helix.

Table 11.1    Base Composition of DNA from a Variety

of Organisms as Determined by Chargaff Percentages of bases (%)

Organism

Adenine

Thymine

Guanine

Cytosine

Escherichia coli (bacterium)

26.0

23.9

24.9

25.2

Streptococcus pneumoniae (bacterium)

29.8

31.6

20.5

18.0

Saccharomyces cerevisiae (yeast)

31.7

32.6

18.3

17.4

Turtle

28.7

27.9

22.0

21.3

Salmon

29.7

29.1

20.8

20.4

Chicken

28.0

28.4

22.0

21.6

Human

30.3

30.3

19.5

19.9

information regarding the number of nucleotides per turn and was consistent with a 2-nm (nanometer) spacing between the strands, which corresponds to a purine (A or G) bonding with a pyrimidine (T or C). Base Composition Determined by Chargaff  Another piece of evidence that proved to be critical for the determination of the double helix structure came from the studies of Austrian-born American biochemist Erwin Chargaff. In 1950, Chargaff analyzed the base composition of DNA that was isolated from many different species. His experiments consistently showed that the amount of adenine in each sample was similar to the amount of thymine, and the amount of cytosine was similar to the amount of guanine (Table 11.1). Model Building by Pauling  In the early 1950s, more information was known about the structure of proteins than that of nucleic acids. American biochemist Linus Pauling correctly proposed that some regions of proteins fold into a structure known as an α helix. To determine the structure of the α helix, Pauling built large models by linking together simple ball-and-stick units. In this way, he could see if atoms fit together properly in a complicated three-dimensional structure. This approach is still widely used today, except that now researchers construct threedimensional models using computers. Use of the ball-and-stick approach was instrumental in solving the structure of the DNA double helix.

Watson and Crick Deduced the Double Helix Structure of DNA Thus far, we have considered the experimental studies that led to the determination of the DNA double helix. American biologist James Watson and English biologist Francis Crick, working together at Cambridge University, assumed that nucleotides are linked together in a linear fashion and that the chemical linkage between two nucleotides is always the same. In collaboration with Wilkins, they then set out to build ball-and-stick models that incorporated all of the known experimental observations. Modeling of chemical structures involves trial and error. Watson and Crick initially considered several incorrect models. One model was a double helix in which the bases were on the outside of the helix. In another model, each base formed hydrogen bonds with the identical base in the



NUCLEIC ACID STRUCTURE, DNA REPLICATION, AND CHROMOSOME STRUCTURE 227

opposite strand (A to A, T to T, G to G, and C to C). However, modelbuilding revealed that purine-purine pairs were too wide and pyrimidinepyrimidine pairs were too narrow to fit the uniform diameter of DNA revealed from Franklin’s work. Eventually, they realized that the hydrogen bonding of adenine to thymine was structurally similar to that of guanine to cytosine. In both cases, a purine base (A or G) bonds with a pyrimidine base (T or C). With an interaction between A and T and between G and C, the ball-and-stick models showed that the two strands would form a double helix structure in which all atoms would fit together properly. Watson and Crick proposed the structure of DNA, which was published in the journal Nature in 1953. In 1962, Watson, Crick, and Wilkins were awarded the Nobel Prize in Physiology or Medicine.

Unfortunately, Rosalind Franklin had died before this time, and the Nobel Prize is awarded only to living recipients.

DNA Has a Repeating, Antiparallel Helical Structure Formed by the Complementary Base Pairing of Nucleotides The structure that Watson and Crick proposed is a double-stranded, helical structure with the sugar-phosphate backbone on the outside and the bases on the inside (Figure 11.8a). This structure is stabilized by hydrogen bonding between the bases in opposite strands to form base pairs. A distinguishing feature of base pairing is its specificity. An adenine (A) base in one strand forms two hydrogen bonds with a

5ʹ end Bases

3ʹ end

5ʹ end

3ʹ end HO

H H

Adenine N

H

Hydrogen bond

Sugar-phosphate backbone

O

P

O

CH2

O– H

H

H

P O

CH2 H

Complete turn of the helix 3.4 nm

H

H

H

H

N

P

CH2

O– H

3ʹ hydroxyl

N

H

OH

H

H

P

O

O

N H

H

Guanine H H

N

N

H

N

H

H H

H O

N

5ʹ end

3ʹ end 2 nm

(a) Double helix

P

O

O–

N O

H

H

Cytosine

Hydrogen bond

3ʹ end One nucleotide 0.34 nm

O–

CH2 O

H

N

H N

H

O–

CH2 O

O

N

O

H

O H

Cytosine O

O

H H

H

N

H

O O

N

H N

H

H

H

H

N

O

H

H

Guanine

O

O O–

H

Thymine

H

O

N

CH3

H

O

O

N H

O

N

O

H

O–

CH2 O P

H

N

5ʹ phosphate

O

N

N

H N

O

O–

H H

H

5ʹ end

(b) Base pairing Key Features • Two strands of DNA form a double helix. • The bases in opposite strands hydrogenbond according to the AT/GC rule. • The 2 strands are antiparallel. • There are ~10 nucleotides in each strand per complete turn of the helix.

Figure 11.8  Structure of the DNA double helix.  As seen in part (a), DNA is a helix composed of two antiparallel strands. Part (b) shows the AT/GC base pairing that holds the strands together via hydrogen bonds. Core Skill: Modeling  The goal of this modeling challenge is to predict the hydrogen-bonding relationship between O6-MeG and cytosine. Modeling Challenge: As discussed in Chapter 15, certain chemicals, such as nitrogen mustard and ethyl methanesulfonate, can modify the structures of DNA bases. For example, a methyl group (−CH3) can be attached to the oxygen atom on guanine, thereby creating 6-O-methylguanine (O6-MeG), as shown to the right. When O6-MeG is included in a DNA strand, it can form only two hydrogen bonds with cytosine instead of three. Draw a model for the base pairing between O6-MeG and cytosine.

H H

H

N

N 2

N

1

3

6

N

4

9

5

7

8

N

O CH3 6 O -MeG

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thymine (T) base in the opposite strand, or a guanine (G) base forms three hydrogen bonds with a cytosine (C) base (Figure 11.8b). This AT/GC rule is consistent with Chargaff’s observation that DNA contains approximately equal amounts of A and T, and equal amounts of G and C. According to the AT/GC rule, purines (A and G) always bond with pyrimidines (T and C) (recall that purines have a doublering structure, whereas pyrimidines have single rings). This keeps the width of the double helix relatively constant. One complete turn of the double helix is 3.4 nm in length and comprises about 10 base pairs. Due to the AT/GC rule, the base sequences of two DNA strands are complementary to each other. That is, you can predict the sequence in one DNA strand if you know the sequence in the opposite strand. For example, if one DNA strand has the sequence 5′–GCGGATTT–3′, the opposite strand must be 3′–CGCCTAAA–5′. With regard to their 5′ and 3′ directionality, the two strands of a DNA double helix are antiparallel. If you look at Figure 11.8, one strand runs in the 5′ to 3′ direction from top to bottom, whereas the other strand is oriented 3′ to 5′ from top to bottom. The DNA model in Figure 11.8a, which clearly shows the components of the DNA molecule, is called a ribbon model. However, other models are also used to visualize DNA. The model for the DNA double helix shown in Figure 11.9 is a space-filling model in which

Major groove

the atoms are depicted as spheres. Why is this model useful? This type of structural model emphasizes the surface of DNA. As you can see in this model, the sugar-phosphate backbone is on the outermost surface of the double helix; the backbone has the most direct contact with water in the surroundings. The atoms of the bases are more internally located within the double-stranded structure. The indentations where the atoms of the bases make contact with the surrounding water are termed grooves. Two grooves, called the major groove and the minor groove, spiral around the double helix. As discussed in later chapters, the major groove provides a location where a protein can bind to a particular sequence of bases and affect the expression of a gene (for example, look ahead to Figure 14.10).

11.3       Overview of DNA Replication Learning Outcomes: 1. CoreSKILL » Discuss and interpret the experiments of Meselson and Stahl. 2. Describe the double-stranded structure of DNA, and explain how the AT/GC rule underlies the ability of DNA to be replicated semiconservatively.

The structure of DNA immediately suggested to Watson and Crick a mechanism by which DNA can be copied. They proposed that during this process, known as DNA replication, the original DNA strands are used as templates for the synthesis of new DNA strands. In this section, we will look at an early experiment that helped to determine the mechanism of DNA replication and then examine the structural characteristics that enable a double helix to be faithfully copied.

Minor groove

Meselson and Stahl Investigated Three Proposed Mechanisms of DNA Replication Major groove

Minor groove

Figure 11.9  A space-filling model of the DNA double helix.  In the sugar-phosphate backbone, sugar molecules are shown in blue, and phosphate groups are yellow. The backbone is on the outermost surface of the double helix. The atoms of the bases, shown in green, are more internally located within the double-stranded structure. Notice the major and minor grooves that are formed by this arrangement. Core Concept: Structure and Function  The major groove provides a binding site for proteins that control the expression of genes.

Researchers in the late 1950s considered three different models for the mechanism of DNA replication (Figure 11.10). In all of these models, the two newly made strands are called the daughter strands, and the original strands are the parental strands. ∙ The first model is a semiconservative mechanism (Figure 11.10a). In this model, the double-stranded DNA is half conserved following the replication process; that is, the new doublestranded DNA contains one parental strand and one daughter strand. This model is consistent with the proposal of Watson and Crick. ∙ According to a second model, called a conservative mechanism, both parental strands of DNA remain together following DNA replication (Figure 11.10b). The original arrangement of parental strands is completely conserved, and the two newly made daughter strands are also together following replication. ∙ A third possibility, called a dispersive mechanism, proposed that segments of parental DNA and newly made daughter DNA are interspersed in both strands following the replication process (Figure 11.10c).



NUCLEIC ACID STRUCTURE, DNA REPLICATION, AND CHROMOSOME STRUCTURE 229 Original double helix

First round of replication

Second round of replication

1

Grow bacteria in 15N media.

2

Transfer to 14N media and continue growth for 1 million

Kingdom

Animalia

>1 million

Phylum

Chordata

~50,000

Class

Mammalia

5,513

Order

Carnivora

282

Family

Canidae

Genus

Canis

7

Species

lupus

1

34

Figure 25.2  A taxonomic classification of the gray wolf (Canis lupus). Core Concept: Evolution  A goal of taxonomy is to relate the diversity of species to their evolutionary relationships. Note: The numbers in this figure will change as new species are discovered and some species become extinct. Concept Check:   Which group is broader, a phylum or a family?



TAXONOMY AND SYSTEMATICS 519

is called Carnivora and has 282 species that are meat-eating animals with prominent canine teeth. The gray wolf is placed in the family Canidae, which is a relatively small family of 34 species, including different species of wolves, jackals, foxes, wild dogs, and the coyote and domestic dog. All species in the family Canidae are doglike animals. The smallest grouping that contains the gray wolf is the genus Canis, which has four species of jackals, the coyote, and two types of wolves. The species Canis lupus encompasses several subspecies, including the domestic dog (Canis lupus familiaris).

Binomial Nomenclature Is Used to Name Species As originally advocated by Linnaeus, binomial nomenclature is the standard format for naming species. The scientific name of every species has two names, its genus name and its unique specific epithet. For the gray wolf, the genus is Canis and the species epithet is lupus. The genus name is always capitalized, but the specific epithet is not. Both names are italicized. After the first mention, the genus name is abbreviated to a single letter. For example, we write that Canis lupus is the gray wolf, and in subsequent sentences, the species is referred to as C. lupus. When naming a new species, genus names are always nouns or treated as nouns, whereas species epithets may be either nouns or adjectives. The names often have a Latin or Greek origin and refer to characteristics of the species or to features of its habitat. For example, the genus name of the newly discovered African forest elephant, Loxodonta, is from the Greek loxo, meaning slanting, and odonta, meaning tooth. The species epithet cyclotis refers to the observation that the ears of this species are rounder than those of L. africana. The rules for naming animal species, such as Canis lupus and Loxodonta africana, were established by the International Commission on Zoological Nomenclature (ICZN). The ICZN provides and regulates a uniform system of nomenclature to ensure that every animal has a unique and universally accepted scientific name. Who is allowed to identify and name a new species? As long as ICZN rules are followed, new animal species can be named by anyone, not only scientists. The rules for naming plants are described in the International Code of Botanical Nomenclature (ICBN), and the naming of bacteria and archaea is overseen by the International Committee on Systematics of Prokaryotes (ICSP).

25.2             Phylogenetic Trees Learning Outcomes: 1. Define phylogeny, and explain how it is depicted in phylogenetic trees. 2. Explain the process of cladogenesis, the primary way that new species arise.  3. Describe how homology is used to construct phylogenetic trees.

Systematics is the study of biological diversity and evolutionary relationships. By studying the similarities and differences among species, biologists can construct a phylogeny, which is the evolutionary history of a species or group of species. To propose a phylogeny, biologists use the tools of systematics. For example, the classification of the gray wolf in Figure 25.2 is based on systematics. Therefore, one

use of systematics is to place species into taxa and to understand the evolutionary relationships among different taxa. In this section, we will consider the features of diagrams or trees that describe the evolutionary relationships among various species, both extant and extinct. As you will learn, such trees are usually based on morphological or genetic data.

A Phylogenetic Tree Depicts Evolutionary Relationships Among Species A phylogenetic tree is a diagram that describes the evolutionary relationships among various species, based on the information available to and gathered by systematists. Phylogenetic trees should be viewed as hypotheses that are proposed, tested, and later refined as additional data become available. Let’s look at what information a phylogenetic tree contains and the form in which it is presented. Figure 25.3 shows a hypothetical phylogenetic tree of the relationships among various flowering plant species, in which the species are labeled A through K. The vertical axis represents time, and the oldest species is at the bottom. New species can be formed by anagenesis, in which a single species evolves into a different species. However, the primary way that new species arise is by cladogenesis, in which a species diverges into two or more species. The branch points in a phylogenetic tree, also called nodes, indicate times when cladogenesis has occurred. For example, approximately 12 mya, species A diverged into species A and species B. Figure 25.3 also shows anagenesis in which species C evolved into species G. The tips of branches represent species that became extinct in the past, such as species B and E, or living species, such as F, I, G, J, H, and K, which are at the top of the tree. Species A and D are also extinct but gave rise to species that are still in existence. The branch points of a phylogenetic tree group species according to common ancestry. A clade consists of a common ancestral species and all of its descendant species. For example, the group highlighted in light green in Figure 25.3 is a clade derived from the common ancestral species labeled D. Likewise, the entire tree forms a clade, with species A as a common ancestor. Therefore, smaller and more recent clades are nested within larger clades that have older common ancestors.

Systematics Constructs Taxonomic Groups Based on Evolutionary Relationships A key goal of modern systematics is to create taxonomic groups that reflect evolutionary relationships. Systematics attempts to organize species into clades, so that each group includes an ancestral species and all of its descendants. A monophyletic group is a taxon that is a clade. Ideally, every taxon, whether it is a domain, supergroup, kingdom, phylum, class, order, family, or genus, should be a monophyletic group. What is the relationship between a phylogenetic tree and taxonomy? The relationship depends on how far back we go to identify a common ancestor. For broader taxa, such as a kingdom, the common ancestor existed a very long time ago, on the order of hundreds of millions or even billions of years ago. For smaller taxa, such as a family or genus, the common ancestor occurred much more recently, on the order of millions or tens of millions of years ago. This concept is shown in a schematic way in Figure 25.4. This small, hypothetical kingdom is a clade that contains 64 living species. (Actual kingdoms

520

CHAPTER 25 Species F, I, G, J, H, and K at the tips of branches in the present are extant species that still exist.

Present

F

I

Species B and E at the tips of branches in the past are extinct species.

G

Millions of years ago (mya)

Time

Anagenesis: Species C evolved into species G.

J

H

K

E

B

5 C

D

B

Clade: This group includes all of the species that were derived from the ancestor, species D.

10

Branch points or nodes indicate when a species diverged into 2 or more different species.

Cladogenesis: Species A diverged into species A and B.

A

Figure 25.3  How to read a phylogenetic tree.  This hypothetical tree shows the proposed relationships between various flowering plant

species. Species are placed into clades, groups of organisms containing an ancestral organism and all of its descendants. Note: Anagenesis is a possible way for a new species to arise, but as shown in this figure, cladogenesis is the primary mechanism. Concept Check:   Can two different species have more than one common ancestor? 

Present

Species (43) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 2021 222324252627 28293031 3233 34 353637 38394041 4243 44 454647 48495051 525354555657 58596061 626364

500 million

Family (species 41–44) Order (species 41–48) Class (species 33–48) Phylum (species 33–64)

1 billion

Millions of years ago (mya)

Time

Genus (species 43–44)

Kingdom (species 1–64)

Figure 25.4  Schematic relationship between a phylogenetic tree and taxonomy, when taxonomy is correctly based on evolutionary

relationships.  The shaded areas highlight the kingdom, phylum, class, order, family, and genus for species number 43. All of the taxa are clades. Broader taxa, such as phyla and classes, are derived from more ancient common ancestors. Smaller taxa, such as families and genera, are derived from more recent common ancestors. These smaller taxa are subsets of the broader taxa. Concept Check:   Which taxon would have a more recent common ancestor, a phylum or an order?



TAXONOMY AND SYSTEMATICS 521

H

I

J

D

K

L

E

M

N

F

B

O

H

G C

A

I

J

D

K

L

E

(a) Monophyletic group

N

F

B

A monophyletic group contains a common ancestor and all of its descendants.

M

O

H

G

I

D

C

A

J

K

L

E

M

F

B

O

G C

A

A paraphyletic group contains a common ancestor but not all of its descendants.

N

(b) Paraphyletic group

A polyphyletic group contains groups of species with different common ancestors. (c) Polyphyletic group

Figure 25.5  A comparison of monophyletic, paraphyletic, and polyphyletic taxonomic groups.

The Study of Systematics Is Usually Based on Morphological or Genetic Homology As discussed in Chapter 22, the term homology refers to a similarity that occurs due to descent from a common ancestor. Such features are said to be homologous. For example, the arm of a human, the wing of a bat, and the flipper of a whale are homologous structures (refer back to Figure 22.12). Similarly, genes found in different species are homologous if they have been derived from the same ancestral gene (refer back to Figure 22.13). In systematics, researchers identify homologous features that are shared by some species but not by others, which allows them to group

KEY

Reptiles (a) Reptiles as a paraphyletic taxon

Birds

Crocodiles

Lizards and snakes

Turtles

Birds

Crocodiles

Lizards and snakes

Orders Classes

Turtles

are obviously larger and exceedingly more complex.) The diagram emphasizes the taxa that contain the species designated number 43. The common ancestor that gave rise to this kingdom existed approximately 1 billion years ago. Over time, more recent species arose that subsequently became the common ancestors to the phylum, class, order, family, and genus that contain species number 43. How does research in systematics affect taxonomy? As researchers gather new information, they sometimes discover that some of the current taxonomic groups are not monophyletic. Figure 25.5 compares a monophyletic group with taxonomic groups that are not. A paraphyletic group contains a common ancestor and some, but not all, of its descendants (Figure 25.5b). In contrast, a polyphyletic group consists of members of several evolutionary lines and does not include the most recent common ancestor of the included lineages (Figure 25.5c). As scientists learn more about evolutionary relationships, taxonomic groups are reorganized to recognize only monophyletic groups. For example, traditional classification schemes once separated birds and reptiles into separate classes (Figure 25.6a). In this scheme, the reptile class (officially named Reptilia) contained orders that included turtles, lizards and snakes, and crocodiles, with birds constituting a different class. Research indicated that the reptile taxon was paraphyletic, because birds were excluded from the group. This group can be made monophyletic by including birds as a class within the reptile clade and elevating the other groups to a class status (Figure 25.6b).

Reptiles (b) Reptiles as a monophyletic taxon

Figure 25.6  An example of a taxon that is not monophyletic.  (a) The class of reptiles as a paraphyletic taxon. (b) The group can be made monophyletic if birds and the other orders are classified as classes within the reptile clade. species based on shared similarities. Researchers usually study homology by examining morphological features or genetic data. In addition, the data they gather are viewed in light of geographic data. Many organisms do not migrate extremely long distances. Species that are closely related evolutionarily are relatively likely to inhabit neighboring or overlapping geographic regions, though many exceptions are known to occur. Morphological Analysis  The first studies in systematics focused on morphological features of extinct and living species. Morphological traits continue to be widely used in systematic studies, particularly in those studies pertaining to extinct species and those involving groups that have not been extensively studied at the molecular level. To establish evolutionary relationships based on morphological homology, many traits have to be analyzed to identify similarities and differences.

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CHAPTER 25

the number of toes, and modifications in the jaw and teeth consistent with a dietary shift from tender leaves to more fibrous grasses. How do evolutionary biologists explain these changes in horses’ traits? The changes can be attributed to natural selection, which acted on existing variation and resulted in adaptations to changes in climate. Over North America, where much of horse evolution occurred, changes in climate caused large areas of dense forests to be replaced with grasslands. The increase in size and changes in foot structure enabled horses to escape predators more easily and travel greater distances in search of food. The changes seen in horses’ teeth are consistent with a shift from eating the tender leaves of bushes and trees to eating grasses and other more abrasive types of vegetation that require more chewing.

By studying morphological features of extinct species in the fossil record, paleontologists can propose phylogenetic trees that chart the evolutionary lineages of species, including those that still exist. In this approach, the trees are based on morphological features that change over the course of many generations. As an example, Figure 25.7 depicts a current hypothesis of the evolutionary changes that led to the development of the modern horse. This figure shows representative species from various genera. Many morphological features were used to propose this tree. Because hard parts of the body are more commonly preserved in the fossil record, this tree is largely based on the analysis of skeletal changes in foot structure, lengths and shapes of various leg bones, skull shape and size, and jaw and tooth morphology. Over an evolutionary timescale, the accumulation of many genetic changes has had a dramatic effect on species’ characteristics. In the genera depicted in this figure, a variety of morphological changes occurred, such as an increase in size, a reduction in

Molecular Systematics  The field of molecular systematics involves the analysis of genetic data, such as DNA sequences or amino acid sequences, to identify and study genetic homologies and propose

0 Hippidium and other genera

Equus

5

Nannippus Neohipparion Hipparion

Stylohipparion 10

Callippus

Millions of years ago (mya)

Time

Sinohippus

20

Pliohippus

Anchitherium

Megahippus Archaeohippus

Merychippus

Hypohippus

Parahippus Miohippus Mesohippus 40

An analysis of fossilized bones provided the phylogenetic tree described here.

Paleotherium Epihippus

Propalaeotherium Pachynolophus

55

Orohippus

Hyracotherium

Figure 25.7  Evolution of horse populations.  An analysis of morphological traits was used to produce this phylogenetic tree, which shows the

evolutionary history that gave rise to the modern horse. As shown next to some of the genera, three important morphological changes were larger size, fewer toes, and a shift toward teeth suited for grazing. Core Concept: Structure and Function  The changes in structural features during horse evolution are related to changes in functional needs. During the course of their evolution, horse populations shifted from feeding on leaves in forested regions to feeding on grasses in more open spaces.



TAXONOMY AND SYSTEMATICS 523

phylogenetic trees. In 1963, Austrian biologist Emile Zuckerkandl and American chemist Linus Pauling were the first to suggest that molecular data could be used to establish evolutionary relationships. How can a comparison of genetic sequences help to establish evolutionary relationships? As discussed later in this chapter, DNA sequences change over the course of many generations due to the accumulation of mutations. Therefore, when comparing homologous sequences in different species, DNA sequences from closely related species are more similar to each other than they are to sequences from distantly related species.

With regard to species D and E, having 2 eyes is a shared primitive character, whereas having 2 front flippers is a shared derived character.

D

E

F

G

25.3              Cladistics Learning Outcomes: 1. Distinguish between shared primitive characters and shared derived characters. 2. Outline the steps involved in using a cladistics approach to construct a phylogenetic tree, and explain how the principle of parsimony is used to choose among phylogenetic trees. 3. Describe how maximum likelihood is also used to discriminate among phylogenetic trees. 4. CoreSKILL » Explain how DNA can be analyzed to explore relationships among extant and extinct species.

Cladistics is the classification of species based on evolutionary relationships. A cladistic approach constructs phylogenetic trees by considering the possible pathways of evolutionary change that involve characteristics that are shared or not shared among various species. Such trees are known as cladograms. In this section, we will consider how biologists produce phylogenetic trees.

Species Differ with Regard to Primitive and Derived Characters A cladistic approach compares homologous features, also called characters, which may exist in two or more character states. For example, among different species, a front limb, which is a character, may exist in different character states such as a wing, an arm, or a flipper. The various character states are either shared or not shared by different species. To understand the cladistic approach, let’s take a look at a simplified phylogeny (Figure 25.8). We can place the species that currently exist into two groups: D and E, and F and G. The most recent common ancestor to D and E is B, whereas species C is the most recent common ancestor to F and G. With these ideas in mind, let’s focus on the front limbs (flippers versus legs) and eyes. A character that is shared by two or more different taxa and inherited from ancestors older than their last common ancestor is called a shared primitive character, or symplesiomorphy. Such characters are viewed as being older—ones that occurred earlier in evolution. With regard to species D, E, F, and G, having two eyes is a shared primitive character. It originated prior to species B and C. By comparison, a shared derived character, or synapomorphy, is a character that is shared by two or more species or taxa and originated in their most recent common ancestor. With regard to species D and E, having two front flippers is a shared derived character that originated in species B, their most recent common ancestor (see Figure 25.8). Compared with shared primitive characters, shared derived characters are more

C

B

2 eyes, 2 front legs

2 eyes, 2 front flippers

A

2 eyes, 2 front legs

Figure 25.8  A comparison of shared primitive characters and shared derived characters.

recent traits on an evolutionary timescale. For example, among mammals, only some species, such as whales and dolphins, have flippers. In this case, flippers were derived from the two front limbs of an ancestral species. The word derived indicates that evolution involves the modification of traits in pre-existing species. In other words, populations of organisms with new traits are derived from changes in pre-existing populations. The basis of the cladistic approach is to analyze many shared derived characters among groups of species to deduce the pathway that gave rise to those species. The terms primitive and derived do not indicate the complexity of a character. For example, the flippers of a dolphin do not appear more complex than the front limbs of ancestral species A (see Figure 25.8), which were limbs with individual toes. Derived characters can be similar in complexity, less complex, or more complex than primitive characters.

A Cladistic Approach Produces a Cladogram Based on Shared Derived Characters To illustrate how shared derived characters are used to propose a phylogenetic tree, Figure 25.9a compares several characters among five species of animals. The proposed cladogram in Figure 25.9b is consistent with the distribution of shared derived characters among these species. A branch point is where two species differ in a character. The oldest common ancestor, which is now extinct, had a notochord and was an ancestor to all five species. Vertebrae are a shared derived character of the lamprey, salmon, lizard, and rabbit, but not the lancelet, which is an invertebrate. By comparison, a hinged jaw is a shared derived character of the salmon, lizard, and rabbit, but not of the lamprey or lancelet.

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Lancelet Notochord Vertebrae Hinged jaw Tetrapod Mammary glands

Lamprey

Yes No No No No

Salmon

Lizard

Rabbit

Yes Yes No No No

Yes Yes Yes No No

Yes Yes Yes Yes No

Yes Yes Yes Yes Yes

Salmon

Lizard

(a) Characters among species Lancelet

Lamprey

Rabbit

Mammary glands

Tetrapod

Hinged jaw

Vertebrae Notochord (b) Cladogram based on morphological traits

Figure 25.9  Using shared primitive characters and shared

derived characters to propose a phylogenetic tree.  (a) A comparison of characters among these species. (b) This phylogenetic tree illustrates both shared primitive and shared derived characters in a cladogram of five animal species. Concept Check:   What shared derived character is common to the salmon, lizard, and rabbit, but not the lamprey? 

In a cladogram, an ingroup is the group whose evolutionary relationships we wish to understand. By comparison, an outgroup is a species or group of species that is assumed to have diverged before the species in the ingroup. An outgroup lacks one or more shared derived characters that are found in the ingroup. A designated outgroup can be closely related or more distantly related to the ingroup. In the tree shown in Figure 25.9, if the salmon, lizard, and rabbit are an ingroup, the lamprey is an outgroup. The lamprey has a notochord and vertebrae but lacks a character shared by the ingroup, namely, a hinged jaw. Thus, for the ingroup, the notochord and vertebrae are shared primitive characters, whereas the hinged jaw is a shared derived character not found in the outgroup. Likewise, the concept of shared derived characters can apply to molecular data, such as a gene sequence. Let’s consider an example

to illustrate this idea. Our example involves molecular data obtained from seven different hypothetical plant species called A–G. In these species, a homologous region of DNA was sequenced as shown here: 12345678910 A: GATAGTACCC B: GATAGTTCCC C: GATAGTTCCG D: GGTATTACCC E: GGTATAACCC F: GGTAGTACCA G: GGTAGTACCC The cladogram of Figure 25.10 is a hypothesis of how these DNA sequences arose. A mutation that changes the sequence of nucleotides is comparable to a modification of a character. For example, let’s designate species D as an outgroup and species A, B, C, F, and G as the ingroup. In this case, a G (guanine) at the fifth position is a shared derived character. The genetic sequence carrying this G is derived from an older primitive sequence. Now that you have an understanding of shared primitive and derived characters, let’s consider the steps a researcher would follow to propose a cladogram using a cladistic approach. 1. Choose the species whose evolutionary relationships are of interest. In a simple cladogram, such as those described in this chapter, individual species are compared with each other. In more complex cladograms, species may be grouped into larger taxa (for example, families) and compared with each other. If such grouping is done, the results are not reliable if the groups are not clades. 2. Choose characters for comparing the species selected in step 1. As mentioned, a character is a general feature of an organism and may come in different versions called character states. For example, a front limb is a character in mammals, which exists in different character states including wing, arm, and flipper. 3. Determine the polarity of character states. In other words, determine if a character state came first and is primitive or came later and is a derived character. This information may be available by examining the fossil record, for example, but is usually done by comparing the ingroup with the outgroup. For a character with two character states, an assumption is made that a character state shared by the outgroup and ingroup is primitive. A character state shared only by members of the ingroup is derived. 4. Analyze cladograms based on the following principles: ∙ All species (or higher taxa) are placed on tips in a phylogenetic tree, not at branch points. ∙ Each cladogram branch point should have a list of one or more shared derived characters that are common to all species above the branch point unless the character is later modified. ∙ All shared derived characters appear together only once in a cladogram unless they arose independently during evolution more than once. 5. Among many possible options, choose the cladogram that provides the simplest explanation for the data. A common approach is to use a computer program that generates many



TAXONOMY AND SYSTEMATICS 525

GGTATAACCC E

GGTATTACCC D

GGTAGTACCC G

GGTAGTACCA F

GATAGTACCC A

GATAGTTCCC B

GATAGTTCCG C C10 A7

C10

T5 A6

A

G2

G

T

A

G

T

GGTATAACCC 1 2 3 4 5 6 7 8 910 Proposed primitive sequence

Figure 25.10  The use of shared derived characters applied to molecular data.  This phylogenetic tree illustrates a cladogram involving

homologous gene sequences found in seven hypothetical plant species. Mutations that alter a primitive DNA sequence are shared among certain species but not others. Note: A, T, G, and C refer to nucleotide bases, and the numbers refer to the position of the base in the nucleotide sequences. For example, A6 refers to an adenine at the sixth position. Concept Check:   What nucleotide change is a shared derived character for species A, B, and C, but not for species G? 

possible cladograms. Analyzing the data and choosing among the possibilities are key aspects of this process. As described later, different theoretical approaches, such as the principle of parsimony, can be used to choose among possible phylogenies. 6. Provide a root to the phylogenetic tree by choosing a noncontroversial outgroup. In this textbook, most phylogenetic trees are rooted, which means that a single node at the bottom of the tree corresponds to a common ancestor for all of the species or groups of species in the tree. A method for rooting trees is the use of a noncontroversial outgroup. Such an outgroup typically shares morphological traits and/or DNA sequence similarities with the members of the ingroup, to allow a comparison between the ingroup and outgroup. Even so, the outgroup must be noncontroversial in that it has enough distinctive differences with the ingroup to be considered a clear outgroup. For example, if the ingroup was a group of mammalian species, an outgroup could be a reptile species.

The Principle of Parsimony Is Used to Choose from Among Possible Cladograms One approach for choosing among possible cladograms is to assume that the best hypothesis is the one that requires the fewest number of evolutionary changes. This concept, called the principle of parsimony, states that the preferred hypothesis is the one that is the simplest for all the characters and their states. For example, if two species possess a tail, we would initially assume that a tail arose once during evolution and that both species have descended from a common ancestor with a tail. Such a hypothesis is simpler, and more likely to be correct, than assuming that tails arose

twice during evolution and that the tails in the two species are not due to descent from a common ancestor.

Maximum Likelihood Is Also Used to Discriminate Among Possible Phylogenetic Trees In addition to the principle of parsimony, evolutionary biologists also apply other approaches to the evaluation of phylogenetic trees. These methods involve the use of an evolutionary model—a set of assumptions about how evolution is likely to happen. For example, mutations affecting the third base in a codon are often neutral because they don’t affect the amino acid sequence of the encoded protein and therefore don’t affect the fitness of an organism. As discussed in Chapter 23, such neutral mutations are more likely to become prevalent in a population than are mutations in the first or second base. Therefore, one possible assumption of an evolutionary model is that neutral mutations are more likely than nonneutral mutations. According to an approach called maximum likelihood, researchers may ask, “What is the probability that an evolutionary model and a proposed phylogenetic tree would give rise to observed molecular data?” To answer this question, they must devise rules about how DNA sequences change over time. For example, one rule may be that neutral mutations are more likely to occur than nonneutral mutations. A second rule might be that the rate of change of DNA sequences is relatively constant from one generation to the next in a particular lineage. With a set of probability rules, researchers can analyze different possible trees and predict the relative probabilities for each of them. The phylogenetic tree that gives the highest probability of producing the observed data is preferred to any trees that give lower probabilities.

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BIO TIPS  THE QUESTION  The principle of parsimony can be applied to the analysis of data on gene sequences. In this case, the most

likely hypothesis is the one requiring the fewest base changes. Let’s consider a hypothetical example involving molecular data from four taxa (A–D), where A is presumed to be the outgroup.

12345 A:  GTACA  (outgroup) B: GACAG C: GTCAA D: GACCG Given that B, C, and D comprise the ingroup, three possible phylogenetic trees that have the given base sequences are shown below. GTACA A

GACAG B

GTCAA C

GACCG D

GTACA

GTACA A

Tree 1

GACCG D

GACAG B

GTCAA C

GTACA A

Tree 2

GTACA

GTCAA C

GACAG B

GACCG D

GTACA

Tree 3

Based on the principle of parsimony, which of these trees is the most likely to be correct?

T OPIC  What topic in biology does this question address? The topic is phylogeny. More specifically, the question asks you to compare three phylogenetic trees and decide which one is most likely to be correct based on the principle of parsimony. I NFORMATION  What information do you know based on the question and your understanding of the topic? In the question, you have learned that the principle of parsimony can be applied to the analysis of molecular data. You are given four base sequences and three possible phylogenetic trees. From your understanding of the topic, you may remember that the principle of parsimony states that the preferred hypothesis is the one that is the simplest for all the characters and their states. P ROBLEM-SOLVING  S TRATEGY  Compare and contrast. Make a calculation. One strategy for solving this problem is to compare the base sequence of the outgroup with those of the ingroup and identify the base changes. Then you can calculate which of the three possible phylogenetic trees proposes the fewest number of changes. ANSWER The diagrams below show the base changes in the three trees. GTACA A

GACAG B T2 C4 A5

GTCAA C A C4 A G

A3

GACCG D A T2 A5

GTACA A A G

GACCG D T2 A5

GTCAA C A G C4

C

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Tree 2 requires 6 mutations.

Tree 1 requires 7 mutations. GTACA

GACAG B A T2 G A5

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C Tree 3 requires 5 mutations.

GTACA

Tree 1 requires seven mutations, tree 2 requires six, and tree 3 requires only five. Tree 3 requires the smallest number of mutations and is considered the most parsimonious, and therefore the most likely to be correct. (Note: In practice, researchers usually have multiple base sequences that are much longer than the ones shown here, so computer programs are used to find the most parsimonious tree.)



TAXONOMY AND SYSTEMATICS 527

Core Skill: Process of Science

Feature Investigation  | Cooper and Colleagues Compared DNA Sequences from Extinct Flightless Birds and Existing Species to Propose a New Phylogenetic Tree

DNA sequencing is primarily used for studying relationships among existing species. However, in some cases, DNA can be obtained from extinct organisms. Starting with small tissue samples (usually bone, dried muscle, or preserved skin) from extinct species, scientists have discovered that it is occasionally possible to obtain DNA sequence information. This approach is called ancient DNA analysis, or molecular paleontology. Since the mid-1980s, some researchers have become excited about the information derived from sequencing DNA of extinct

specimens. Debate has centered on how long DNA can remain intact after an organism has died. Over time, the structure of DNA is degraded by hydrolysis and the loss of purines. Nevertheless, under certain conditions (such as cold temperature and low oxygen), DNA samples may be stable for as long as 50,000–100,000 years. In recent years, this approach has been used to study evolutionary relationships between living and extinct species. As shown in Figure 25.11, Alan Cooper, Cécile Mourer-Chauviré, Geoffrey Chambers, Arndt von Haeseler, Allan Wilson, and Svante Pääbo

Figure 25.11  DNA analysis of phylogenetic relationships among living and extinct flightless birds by Cooper and colleagues. GOAL To gather molecular information to hypothesize about the evolutionary relationships among these species. KEY MATERIALS Tissue samples from 4 extinct species of moas were obtained from museum specimens. Tissue samples were also obtained from 3 species of kiwis, 1 emu, 1 cassowary, 1 ostrich, and 2 species of rheas. Experimental level

1

Conceptual level Tissue sample

Treat the cells so that the DNA is released.

Cells in tissue

Isolate and purify the DNA released from the tissue.

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Individually, mix the DNA samples with a pair of PCR primers that are complementary to the SSU rRNA gene.

Mitochondrial DNA Add PCR primers. Primers

DNA

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Mitochondrial DNA

Subject the samples to PCR, as described in Chapter 21, which makes many copies of the SSU rRNA gene. PCR technique Many copies of the SSU rRNA gene are made.

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Subject the amplified DNA fragments to DNA sequencing, as described in Chapter 21.

Sequence the amplified DNA.

The amplification of the SSU rRNA gene allows it to be subjected to DNA sequencing.

5 Align the DNA sequences to each other, using computer techniques.

Align sequences,

Align sequences to compare

4

The amplification of the SSU rRNA gene allows it to be subjected to DNA sequencing.

Sequence the amplified DNA.

Subject the amplified DNA fragments to DNA sequencing, as described in

528 Chapter CHAPTER 25 21.

5 Align the DNA sequences to each other, using computer techniques.

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Align sequences, using computer programs.

Align sequences to compare the degree of similarity.

THE DATA Moa 1 Kiwi 1 Emu Cassowary Ostrich Rhea 1

GC T T A G CCC T A AA T CC A G A T A C T T A C CC T A C A C AA G T A T CC G CCC G A G A A C T A C G A G C A C AAA C G C T T AAAA C T C T AA GG A C T T GG C GG T G CCCC A AA CCC A T G CT C GT T

Moa 1 Kiwi 1 Emu Cassowary Ostrich Rhea 1

CC T A G A G G A G CC T G T T C T A T A A T C G A T A A T CC AC G A T A C A CCC G A C C A T CC C T CG CCC G T – G C A G CC T A C A T A C C G CC G T C CC C A G CCC G CC T – – AA T G A A A G A AA A A C– A G C T T T T

Moa 1 Kiwi 1 Emu Cassowary Ostrich Rhea 1

G – AA C AA T AG C G A G C A C AA C A G CCC T CCCCC G C T AA C AA G A C A GG T C A AGG T A T A G C A T A T G A G A T G GAAGAAA T G GG C T A C A T T T T C T AA C A T A G AA C A CC A TA – A C T T C – A G – T T T A C– – T T – G T T A C– – T – G AG A T T A– – A G – C AG T T T A–– – TC

Moa 1 Kiwi 1 Emu Cassowary Ostrich Rhea 1

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A

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7

CONCLUSION This discovery-based investigation led to a hypothesis regarding the evolutionary relationships among these bird species, which is described in Figure 25.12.

8

SOURCE Cooper, A., et al. 1992. Independent origins of New Zealand moas and kiwis. Proceedings of the National Academy of Sciences 89: 8741–8744.

investigated the evolutionary relationships among some extant and extinct species of flightless birds. In this example of discovery-based science, the researchers gathered data with the goal of proposing a hypothesis about the evolutionary relationships among several bird species. The kiwis and moas are two groups of flightless birds that existed in New Zealand during the Pleistocene. Species of kiwis still exist, but the moas are now extinct. Eleven known species of moas formerly existed. In this study, the researchers investigated the phylogenetic relationships among four extinct species of moas, which were available as museum samples; three species of New Zealand kiwis; and living species of other flightless birds, including the emu and the

A A A A

cassowary (both found in Australia and/or New Guinea), the ostrich (found in Africa and formerly Asia), and two rheas (found in South America). Samples from the various species were subjected to polymerase chain reaction (PCR) to amplify a region of the gene that encodes SSU rRNA (an RNA found in the small subunits of mitochondrial ribosomes of all organisms, as discussed in Chapter 12). This provided enough DNA for sequencing. The data in Figure 25.11 illustrate a comparison of the sequences of a continuous region of the SSU rRNA gene from these species. The first line shows the DNA sequence for one of the four extinct moa species. Below it are the

TAXONOMY AND SYSTEMATICS 529

Kiwi 1

New Zealand

Moa 2

Moa 3

Moa 1

Kiwi 2

Kiwi 3

Australia and New Guinea

Emu

Ostrich

Rhea 1

Rhea 2

Africa

Moa 4

Experimental Questions

South America

Time

sequences of several of the other species that were analyzed. When the other sequences are identical to the first sequence, a dot is placed in the corresponding position. When the sequences are different, the changed nucleotide base (A, T, G, or C) is placed there. In a few regions, the genes are different lengths. In these cases, a dash is placed to indicate missing nucleotides. As you can see from the large number of dots, the gene sequences among these flightless birds are very similar, though some differences occur. If you look carefully at the data, you will notice that the sequence from the kiwi (a New Zealand species) is actually more similar to the sequence from the ostrich (an African species) than it is to that of the moa, which was once found in New Zealand. Likewise, the kiwi is more similar to the emu and cassowary (found in Australia and New Guinea) than to the moa. How were these results interpreted? The researchers concluded that the kiwis are more closely related to African and Australian flightless birds than they are to the moas. From these results, they concluded that New Zealand was colonized twice by ancestors of flightless birds. The researchers used a maximum likelihood analysis to propose a new phylogenetic tree that illustrates the revised relationships among these living and extinct species (Figure 25.12).

Cassowary



1. What is molecular paleontology? What was the purpose of the study conducted by Cooper and colleagues?  2. What birds were examined in the Cooper study, and what are their geographic distributions? Why were the different species selected for this study?  3. CoreSKILL » What results did Cooper and colleagues obtain by comparing these DNA sequences? How did the results of this study affect the proposed phylogeny of flightless birds? 

25.4             Molecular Clocks Learning Outcomes: 1. Explain how molecular clocks are used in the dating of evolutionary events. 2. CoreSKILL » Compare and contrast the use of different genes to produce phylogenetic trees.

As we have seen, researchers employ different methods to choose a phylogeny that describes the evolutionary relationships among various species. Researchers are interested not only in the most likely pathway of evolution (the branches of the trees), but also the timing of evolutionary change (the lengths of the branches). How can researchers determine when different species diverged from each other in the past? As shown earlier in Figure 25.7, the fossil record can sometimes help researchers apply a timescale to a phylogeny. Another way to infer the timing of past events is by analyzing genetic sequences. The neutral theory of evolution proposes that most genetic variation that exists in populations is due to the accumulation of neutral mutations—changes in genes and proteins that are not acted on by natural selection. The reasoning behind this concept is that

Figure 25.12  A revised phylogenetic tree of flightless

birds.  This tree is based on a comparison of DNA sequences from extinct and living flightless birds, as described in Figure 25.11. Concept Check:   With regard to geography, why are the results of Cooper and his colleagues surprising?

favorable mutations are likely to be very rare and detrimental mutations are likely to be eliminated from a population by natural selection. A large body of evidence supports the idea that much of the genetic variation observed in living species is due to the accumulation of neutral mutations. From an evolutionary point of view, if neutral mutations occur at a relatively constant rate, they can serve as a molecular clock to measure evolutionary time. In this section, we will consider the concept of a molecular clock and its application in phylogenetic trees.

The Timing of Evolutionary Change May Be Inferred from Molecular Clock Data Figure 25.13 illustrates the concept of a molecular clock. The graph’s vertical axis measures the number of base differences in a homologous gene between different pairs of species. The horizontal axis plots the amount of time that has elapsed since each pair of species shared a common ancestor.  As an example, let’s suppose a researcher compared a gene sequence that was 500 bp long. Between species A and species B, this sequence might differ at 10 places and be identical at 490 places. By comparison, the 500-bp sequence might differ at 20 places between species A and species C and be the same at 480 places. Such a result is consistent with

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This data point came from two species that had a distant common ancestor and show many base differences. Base differences in one DNA strand of a homologous gene between different pairs of species

This data point came from two species that had a recent common ancestor and show few base differences. 0

Evolutionary time since divergence of pairs of species (millions of years)

Figure 25.13  A molecular clock.  According to the concept of a

molecular clock, neutral mutations accumulate at a relatively constant rate over evolutionary time. In a comparison of the same homologous gene between pairs of different species, those species that diverged more recently tend to have fewer differences than do those whose common ancestor occurred in the distant past. Core Skill: Connections  Look back at Table 12.1, which shows the genetic code. Propose three changes to a codon sequence that you think would be neutral mutations.

the idea that species A and species B shared a more recent common ancestor than do species A and species C. The explanation for this phenomenon is that the gene sequences of various species accumulate independent mutations after they have diverged from each other. A longer period of time since their divergence allows for a greater accumulation of mutations, which makes their sequences of bases more different. Figure 25.13 suggests a linear relationship between the number of base changes and the time of divergence. For example, a linear relationship predicts that a pair of species with, say, 20 base differences in a given gene sequence would have a common ancestor that lived roughly twice as long ago as a pair showing 10 nucleotide differences. Although actual data sometimes show a relatively linear relationship over a defined time period, evolutionary biologists do not think that molecular clocks are perfectly linear over very long periods of time. Several factors can contribute to nonlinearity of molecular clocks. These include differences in the generation times of the species being analyzed and variation in the mutation rates of genes between different species. To obtain reliable data, researchers must calibrate their molecular clocks. How much time does it take to accumulate a certain percentage of base changes? To perform such a calibration, researchers must have information regarding the date when two species diverged from a common ancestor. Such information could come from the fossil record, for instance. The genetic differences between those species are then divided by the amount of time since their last common ancestor to calculate a rate of evolutionary change.

As an example of clock calibration, let’s consider primates. The fossil evidence suggests that humans and chimpanzees diverged from a common ancestor approximately 6 mya. The percentage of base differences between the mitochondrial DNA of humans and chimpanzees is 12%. From these data, the molecular clock for changes in the sequence of bases in mitochondrial DNA of primates is calibrated at roughly 2% base changes per million years. However, molecular dating based on the use of a single fossil as a calibration point can lead to significant inaccuracies in the molecular clock. When possible, researchers advocate using multiple fossils in the calibration process.

Different Genes Are Analyzed to Study Phylogeny and Evaluate the Timing of Evolutionary Change For evolutionary comparisons, the DNA sequences of many genes have been obtained from a wide range of sources. Many different genes have been studied to propose phylogenetic trees and evaluate the timing of past events. For example, the SSU rRNA gene used by Cooper and colleagues in their research on flightless birds (see Figure 25.11) is commonly used in evolutionary studies. As noted in Chapter 12, the gene for SSU rRNA is found in the genomes of all living organisms. Therefore, its function must have been established at an early stage in the evolution of life on this planet, and its sequence has changed fairly slowly. Furthermore, SSU rRNA is a rather large molecule, so it contains a large amount of sequence information. This gene has been sequenced for thousands of different species (see Figure 12.17). Slowly changing genes such as the gene that encodes SSU rRNA are useful for evaluating distant evolutionary relationships, such as comparing higher taxa. For example, SSU rRNA data can be used to place eukaryotic species into their proper phyla or orders. Other genes have changed more rapidly during evolution because of a greater tolerance of neutral mutations. For example, the mitochondrial genome and DNA sequences within introns can more easily incur neutral mutations (compared to the coding sequences of genes), and so their sequences change frequently during evolution. More rapidly changing DNA sequences have been used to study recent evolutionary relationships, particularly among eukaryotic species such as species of large animals that have long generation times and therefore tend to evolve more slowly. In these cases, slowly evolving genes may not be very useful for establishing evolutionary relationships because two closely related species may have identical or nearly identical DNA sequences for such genes. Figure 25.14 shows a simplified phylogeny of closely related species of primates. A molecular clock was used to give a timescale to this phylogenetic tree. The tree was proposed by comparing DNA sequence changes in the gene for cytochrome oxidase subunit II, one of several subunits of cytochrome oxidase, a protein in the mitochondrial inner membrane that is involved in cellular respiration. This gene tends to change fairly rapidly on an evolutionary timescale. The vertical scale of Figure 25.14 represents time, and the branch points labeled with letters represent common ancestors. Let’s take a look at three branch points (labeled A, D, and E) and relate them to the accumulation of neutral mutations. Ancestor A:  This ancestor diverged into two species that ultimately gave rise to siamangs and the other five species. Since this divergence,

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Pygmy chimpanzees (Bonobos) (Pan paniscus)

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Gorillas (Gorilla gorilla)

TAXONOMY AND SYSTEMATICS 531

Siamangs (Hylobates syndactylus)



E D

C

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A

Figure 25.14  The use of DNA sequence changes to study

primate evolution.  This phylogenetic tree, which shows relationships among closely related species of primates, is based on a comparison of mitochondrial gene sequences encoding the protein cytochrome oxidase subunit II. Core Skill: Modeling  The goal of this modeling challenge is to propose a phylogenetic tree based on molecular data. Modeling Challenge: Figure 22.13 compares a short amino acid sequence within the p53 protein among nine species. Propose an evolutionary tree that describes the evolutionary relationships of these species. You should also consider the data in the right column of Figure 22.13, which shows the percentages of amino acids in the whole p53 protein that are identical to the human sequence. The top of your tree should show the nine species with their names (as in Figure 25.14). Above the name of each species, put the number amino acid differences that occur within the short amino acid sequence for each species compared with that of humans.

there has been a long time (approximately 23 million years) for the siamang genome to accumulate a relatively high number of random neutral changes that would be different from the random changes that have occurred in the genomes of the other five species (see the yellow bar in Figure 25.14). Therefore, the gene in the siamangs is fairly different from the genes in the other five species. Ancestor D:  This ancestor diverged into two species that eventually gave rise to humans and chimpanzees. This divergence occurred a moderate time ago, approximately 6 mya, as illustrated by the red bar. The differences in gene sequences between humans and chimpanzees are relatively moderate. Ancestor E:  This ancestor diverged into two species of chimpanzees. Since the divergence of species E into two species, approximately 3 mya, the time for the molecular clock to “tick” (that is, accumulate random mutations) is relatively short, as depicted by the green bar in

Figure 25.14. Therefore, the two existing species of chimpanzees have fewer differences in their gene sequences compared to other primates.

25.5             Horizontal Gene Transfer Learning Outcome: 1. Explain how horizontal gene transfer affects evolution and the relationships among different taxa.

Thus far, we have considered various ways to construct phylogenetic trees, which describe the relationships between ancestors and their descendents. The type of evolution depicted in the phylogenetic trees in previous sections, which involves changes in groups of species due to descent from a common ancestor, is sometimes called vertical evolution. Since the time of Darwin, vertical evolution has been the traditional way biologists have viewed the evolutionary process. However, over the past

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CHAPTER 25 Archaea

Bacteria

Eukarya

Present Fungi

Animals

Plants

Time

Bacterium that gave rise to chloroplasts

Bacterium that gave rise to mitochondria

KEY

4 billion years ago

Vertical evolution Horizontal gene transfer

Common ancestral community of primitive cells

Figure 25.15  A web of life.  This phylogenetic tree shows not only the vertical evolution of life but also the contribution of horizontal gene transfer. In this scenario, horizontal gene transfer was prevalent during the early stages of evolution, when all organisms were unicellular, and continues to be a prominent factor in the speciation of bacteria and archaea. Note: This tree is schematic. Also, although the introduction of chloroplasts into the eukaryotic domain is shown as a single event, such events have occurred multiple times and by different mechanisms. Concept Check:   How does the phenomenon of horizontal gene transfer muddle the concept of monophyletic groups? 

couple of decades, researchers have come to realize that evolution is not so simple. In addition to vertical evolution, horizontal gene transfer has also played a significant role in the phylogeny of living species. As discussed in Chapters 1 and 22, horizontal gene transfer (also called lateral gene transfer) is used to describe any process in which an organism incorporates genetic material from another organism without being the offspring of that organism. As discussed next, this phenomenon has reshaped the way biologists view the evolution of species.

Core Concept: Evolution Due to Horizontal Gene Transfer, the “Tree of Life” Is Really a “Web of Life” Horizontal gene transfer has played a major role in the evolution of many species. As discussed in Chapter 19, bacteria can transfer genes via conjugation, transformation, and transduction. Bacterial gene transfer can occur between strains of the same species or, occasionally, between cells of different bacterial species. The transferred genes may encode proteins that provide a survival

advantage, such as resistance to antibiotics or the ability to metabolize an organic molecule in the environment. Horizontal gene transfer is also fairly common among certain unicellular eukaryotes. However, its relative frequency and importance in the evolution of multicellular eukaryotes remains difficult to evaluate. Scientists have debated the role of horizontal gene transfer in the earliest stages of evolution, prior to the divergence of the bacterial and archaeal domains. The traditional viewpoint was that the three domains of life—Bacteria, Archaea, and Eukarya—arose from a single type of prokaryotic (or pre-prokaryotic) cell called the universal ancestor. However, genomic research has suggested that horizontal gene transfer may have been particularly common during the early stages of evolution on Earth, when all species were unicellular. Horizontal gene transfer may have been so prevalent that the universal ancestor may have actually been an ancestral community of cell lineages that evolved as a whole. If that were the case, the tree of life cannot be traced back to a single ancestor. Figure 25.15 illustrates a schematic scenario for the evolution of life that includes the roles of both vertical evolution and horizontal gene transfer. This has been described as a “web of life”



TAXONOMY AND SYSTEMATICS 533

rather than a “tree of life.” In this scenario, instead of a universal ancestor, a community of primitive cells frequently transferred genetic material in a horizontal fashion. Horizontal gene transfer was also prevalent during the early evolution of bacteria and archaea, and when eukaryotes first emerged as unicellular species. In living bacterial and archaeal species, it remains a prominent way to foster evolutionary change. By comparison, the region of the diagram that contains most eukaryotic species has a more treelike structure. Researchers have speculated that multicellularity and sexual reproduction have presented barriers to horizontal gene transfer in most eukaryotes. For a gene to be transmitted to eukaryotic offspring, it would have to be transferred into a eukaryotic cell that is a gamete or a cell that gives rise to gametes. Horizontal gene transfer has become less common in eukaryotes, particularly among multicellular species, though it does occur occasionally.

Summary of Key Concepts 25.1  Taxonomy ∙∙ Taxonomy is the field of biology concerned with describing, naming, and classifying extant and extinct species. Systematics is the study of biological diversity and classification of evolutionary relationships among species, both extant and extinct. ∙∙ Taxonomy places all living organisms into progressively smaller hierarchical groups called taxa (singular, taxon). The broadest groups are the three domains, called Bacteria, Archaea, and Eukarya, followed by supergroups, kingdoms, phyla, classes, orders, families, genera, and species (Figures 25.1, 25.2, Table 25.1). ∙∙ Binomial nomenclature is the standard format for naming species that provides each species with a genus name and a species epithet.

25.2     Phylogenetic Trees ∙∙ The evolutionary history of a species or group of species is its phylogeny. A phylogenetic tree is a diagram that describes the phylogeny of particular species and should be viewed as a hypothesis (Figure 25.3). ∙∙ A key goal of systematics is to construct taxa and phylogenetic trees based on evolutionary relationships. Smaller taxa, such as families and genera, are derived from more recent common ancestors than are broader taxa such as kingdoms and phyla (Figure 25.4). ∙∙ Ideally, all taxa should be monophyletic groups, consisting of the most recent common ancestor and all of its descendants, though previously established taxa sometimes turn out to be paraphyletic or polyphyletic groups (Figures 25.5, 25.6). ∙∙ Both morphological and genetic data are used to propose phylogenetic trees. Molecular systematics, which involves the analysis of genetic sequences, has led to major revisions in taxonomy (Figure 25.7).

25.3     Cladistics ∙∙ In the cladistic approach to creating a phylogenetic tree, also called a cladogram, species are grouped together according to shared derived characters (Figure 25.8).

∙∙ An ingroup is the group whose evolutionary relationships are of interest, whereas an outgroup is a species or group of species that lacks one or more shared derived characters (synapomorphies). A comparison of an ingroup and outgroup is used to determine which character states are derived and which are primitive (Figures 25.9, 25.10). ∙∙ The cladistic approach produces many possible cladograms. The most likely phylogenetic tree is chosen by a variety of methods, including analysis of fossils, the application of the principle of parsimony, and the approach of maximum likelihood. ∙∙ Cooper and colleagues analyzed DNA sequences from extinct and living flightless birds and proposed a new phylogenetic tree showing that New Zealand was colonized twice by ancestors of flightless birds (Figures 25.11, 25.12).

25.4     Molecular Clocks ∙∙ The neutral theory of evolution proposes that most genetic variation is due to the accumulation of neutral mutations. Assuming that neutral mutations occur at a relatively constant rate, genetic data can serve as a molecular clock to measure the timing of evolutionary changes (Figure 25.13). ∙∙ Slowly changing genes are useful for analyzing distant evolutionary relationships, whereas rapidly changing genes are used to analyze more recent evolutionary relationships, particularly among eukaryotic species that have long generation times and evolve more slowly (Figure 25.14).

25.5     Horizontal Gene Transfer ∙∙ Horizontal gene transfer is the phenomenon in which an organism incorporates genetic material from another organism without being the offspring of that organism. Due to horizontal gene transfer, the tree of life may more accurately be described as a web of life (Figure 25.15).

Assess & Discuss Test Yourself 1. The study of biological diversity based on evolutionary relationships is a. paleontology. d. phylogeny. b. evolution. e. both a and b. c. systematics. 2. Which of the following is the correct order of the taxa used to classify organisms? a. kingdom, supergroup, domain, phylum, class, order, family, genus, species b. domain, supergroup, kingdom, class, phylum, order, family, genus, species c. domain, kingdom, supergroup, phylum, class, family, order, genus, species d. domain, supergroup, kingdom, phylum, class, order, family, genus, species e. supergroup, kingdom, domain, phylum, order, class, family, species, genus 3. Which type of taxon consists of organisms with the greatest similarity? a. kingdom d. family b. class e. genus c. order

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4. Which of the following characteristics is (are) not shared by bacteria, archaea, and eukaryotes? a. DNA is the genetic material. b. Messenger RNA encodes the information to produce proteins. c. All cells are surrounded by a plasma membrane. d. The cytoplasm is compartmentalized into organelles. e. Both a and d are not shared by bacteria, archaea, and eukaryotes. 5. Which of the following occur at branch points, or nodes, in a phylogenetic tree? a. anagenesis d. a and b b. cladogenesis e. b and c c. horizontal gene transfer 6. The evolutionary history of a species is its a. systematics. d. phylogeny. b. taxonomy. e. embryology. c. evolution. 7. A taxon composed of all species derived from a common ancestor is referred to as a. a phylum. b. a monophyletic group or clade. c. a genus. d. an outgroup. e. all of the above. 8. A goal of modern taxonomy is to a. classify all organisms based on morphological similarities. b. classify all organisms into monophyletic groups. c. classify all organisms based solely on genetic similarities. d. determine the evolutionary relationships only between similar species. e. None of the above is a goal of modern taxonomy.

9. The concept that the preferred hypothesis is the one that is the simplest is a. phylogeny. d. maximum likelihood. b. cladistics. e. both b and d. c. the principle of parsimony. 10. Research indicates that horizontal gene transfer is less prevalent in eukaryotes because of a. the presence of organelles. b. multicellularity. c. sexual reproduction. d. all of the above. e. b and c only.

Conceptual Questions 1. Explain how the names of species conform to binomial nomenclature. Give an example of a species’ name.  2. What is a molecular clock? How is it useful in the construction of phylogenetic trees?    3. 

Core Concept: Evolution What are some advantages and potential pitfalls of using changes in morphology to construct phylogenetic trees? 

Collaborative Questions 1. Discuss how taxonomy is useful. Make a list of some practical applications that are derived from taxonomy. 2. Discuss how systematics is used to propose a phylogenetic tree and the rationale behind using the principle of parsimony to evaluate such a tree.

CHAPTER OUTLINE 26.1 The Fossil Record 26.2 History of Life on Earth 26.3 Human Evolution Summary of Key Concepts Assess & Discuss

T

History of Life on Earth and Human Evolution

26

he amazing origin of the universe is difficult to comprehend. Astronomers think the universe began with a cosmic explosion called the Big Bang about 13.7  billion years ago (bya), after which the first clouds of the elements hydrogen and helium were formed. Over a long time period, gravitational forces collapsed these clouds to create stars that converted hydrogen and helium into heavier elements, including carbon, nitrogen, and oxygen, which are the atomic building blocks of life on Earth. These elements were returned to interstellar space by exploding stars called supernovas, which created clouds in which simple molecules such as water, carbon monoxide, and hydrocarbons formed. The clouds then collapsed to make a new generation of stars and solar systems. Our solar system began about 4.6 bya after one or more local supernova explosions. According to one widely accepted A fossil fish. This 50-million-year-old fossil of a unicorn fish (Naso rectifrons) is an example of the many different kinds of scenario, hundreds of planetesimals (small celestial bodies like organisms that have existed during the history of life on Earth. asteroids) occupied the region where Venus, Earth, and Mars ©George Bernard/SPL/Science Source are now found. The Earth, which is estimated to be 4.55 billion years old, grew from the aggregation of such planetesimals photo, have provided biologists with evidence of the history of over a period of 100–200 million years. For the first half billion life on Earth from its earliest beginnings to the present day. The years or so after its formation, the Earth was too hot to allow liqlast section focuses on one of the most interesting stories of uid water to accumulate on its surface. By 4 bya, the Earth had evolution, which is the lineage that gave rise to modern humans. cooled enough for the outer layers of the planet to solidify and for oceans to begin to form. The period between 4.0 and 3.5 bya marked the emergence of life on our planet. The first forms of life that we know about produced well-preserved microscopic fossils, such as those found in west625 μm ern Australia. These fossils, estimated to be about 3.5 billion years old, resemble modern cyanobacteria, (a) Fossil prokaryote (b) Modern cyanobacteria which are photosynthetic bacteria (Figure 26.1). This chapter emphasizes when particular forms Figure 26.1  Earliest fossils and living cyanobacteria.  (a) A fossilized of life arose. We will begin by considering how prokaryote about 3.5 billion years old that is thought to be an early cyanobacterium. researchers analyze and date fossils, which are the (b) A modern cyanobacterium, which has a similar morphology. Cyanobacterial remains of past life-forms. We will then consider how cells are connected to each other to form chains, as shown here. a: ©J. W. Schopf; fossils, such as the one shown in the chapter opening b: ©Michael Abbey/Science Source

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26.1 The Fossil Record Learning Outcomes: 1. Describe how fossils are formed. 2. CoreSKILL » Explain how radiometric dating is used to estimate the age of a fossil. 3. List several factors that affect the completeness of the fossil record.

We will begin this chapter by considering a process that has given us a window into the history of life over the past 3.5 billion years. Fossils are the preserved remains of past life on Earth. They can take many forms, including bones, shells, and leaves, and the impression of cells or other evidence, such as footprints or burrows. Scientists who study fossils are called paleontologists (from the Greek palaios, meaning ancient). Because our understanding of the history of life is derived primarily from the fossil record, it is important to appreciate how fossils are formed and dated and to understand why the fossil record cannot be viewed as complete.

Fossils Are Formed Within Sedimentary Rock How are fossils usually formed? Many of the rocks observed by paleontologists are sedimentary rocks that were formed from particles of older rocks broken apart by water or wind. These particles, in the form of gravel, sand, or mud, settle and bury living and dead organisms at the bottoms of rivers, lakes, and oceans. Over time, more particles pile up, and sediments at the bottom of the pile eventually become rock. Gravel particles form rock called conglomerate, sand becomes sandstone, and mud becomes shale. Most fossils are formed when organisms are buried quickly, and then during the process of sedimentary rock formation, their hard parts are gradually replaced over millions of years by minerals, producing a recognizable representation of the original organism (see, for example, the chapter opening photo). The relative ages of fossils can sometimes be revealed by their locations in sedimentary rock formations. Because sedimentary rocks are formed by small particles settling in layers, the layers are piled one on top of the other. In a sequence of layered rock, the lower layers are usually older than the upper layers. Paleontologists often study changes in life-forms over time by studying the fossils in layers from bottom to top (Figure 26.2). The more ancient lifeforms are found in the lower layers, and newer species are found in the upper layers. However, such an assumption can occasionally be misleading when geological processes such as folding have flipped the layers.

The Analysis of Radioisotopes Is Used to Date Fossils A common way to estimate the age of a fossil is by analyzing the decay of radioisotopes within the accompanying rock, a process called radiometric dating. As discussed in Chapter 2, many elements occur in multiple forms, called isotopes, that differ in

Figure 26.2  An example of layers of sedimentary rock that contain fossils.  ©Simon Fraser/SPL/Science Source

Concept Check:   Which rock layer in this photo is most likely to be the oldest? 

the number of neutrons their atoms contain. A radioisotope is an unstable isotope of an element that decays spontaneously, releasing radiation at a constant rate. The half-life is the length of time required for a radioisotope to decay to exactly one-half of its initial quantity. Each radioisotope has its own unique half-life (Figure 26.3a). Within a sample of rock, scientists can measure the amount of a given radioisotope as well as the amount of the decay product—the isotope that is produced when the original isotope decays. For dating geological materials, several types of isotope decay patterns are particularly useful: carbon to nitrogen, potassium to argon, rubidium to strontium, and uranium to lead (Figure 26.3b). To determine the age of a rock using radiometric dating, paleontologists need to have a way to set the clock—extrapolate back to a starting point at which a rock did not have any amount of the decay product. Except for fossils less than 50,000 years old, in which carbon-14 (14C) dating can be employed, fossil dating is not usually conducted on the fossil itself or on the sedimentary rock in which the fossil is found. Most commonly, igneous rock—rock formed through the cooling and solidification of lava—in the vicinity of the sedimentary rock is dated. Why is igneous rock chosen? One reason is that igneous rock derived from an ancient lava flow initially contains uranium-235 (235U) but no lead-207 (207Pb). The decay product of 235U is 207Pb. By comparing the relative proportions of 235U and 207Pb in a sample, the age of igneous rock can be accurately determined.



HISTORY OF LIFE ON EARTH AND HUMAN EVOLUTION 537

T OPIC What topic in biology does this question address? The topic is radiometric dating of fossils. More specifically, the question asks you to calculate an estimated age for a particular fossil.

100

Isotope (%)

75

50 Buildup of decay product Decay of radioisotope 25

0

0

1

3

2 Time (half-lives)

4

(a) Decay of a radioisotope

Radioisotope

Decay product

Half-life (years)

Useful dating range (years)

Carbon-14

Nitrogen-14

5,730

100–50,000

Potassium-40

Argon-40

1.3 billion

100,000–4.5 billion

Rubidium-87

Strontium-87

47 billion

10 million–4.5 billion

Uranium-235

Lead-207

710 million

10 million–4.5 billion

Uranium-238

Lead-206

4.5 billion

10 million–4.5 billion

(b) Radioisotopes that are useful for geological dating

Figure 26.3  Radiometric dating of fossils.  (a) A rock can be

dated by measuring the relative amounts of a radioisotope and its decay product within the rock. (b) These five radioisotopes are particularly useful for the dating of fossils. Concept Check:   If you suspected a fossil to be 50 million years old, which pair of radioisotope and decay product would you choose to analyze?

BIO TIPS

THE QUESTION  The process of decay for a radioisotope is represented by the following equation:

N = ​​N0​  ​​​​​e​​  –(0.693t/​T​  ​​)​​ 1/2

where N is the number of atoms of a radioisotope after a certain time, N0 is the number of atoms of the radioisotope that were originally present (prior to any decay), e is the natural logarithm, t is the time during which decay has occurred, and T1/2 is the half-life of the radioisotope. A paleontologist discovered a fossil of a previously unidentified reptile. A sample of nearby igneous rock contained 0.11 mg of uranium-235 (235U) and 0.035 mg of lead-207 (207Pb). Estimate the age of this fossil.

I NFORMATION What information do you know based on the question and your understanding of the topic? In the question, you are given an equation that describes the decay process for a radioisotope. You are also given the relative amounts of uranium-235 and lead-207 in an igneous rock that was near the fossil of interest. From your understanding of the topic, you may recall that very old fossils are often dated by analyzing nearby igneous rock because such rock initially contains only uranium-235. P ROBLEM-SOLVING   S TRATEGY Make a calculation. You first need to calculate the number of atoms of 235U and 207Pb in the sample of igneous rock. The atomic masses of 235U and 207Pb are approximately 235 g/mol and 207 g/mol, respectively. For 235U, the number of atoms in the sample, which is N, is 0.11 N = ____ ​​    ​​ × 6.022 × ​​10​​  23 ​​= 2.82 × ​​10​​  20​​ 235

For 207Pb, the number of atoms in the sample is 0.035 _____ ​​  207 ​​   × 6.022 × ​​10​​  23​​ = 1.02 × ​​10​​  20​​

It is assumed that all of the 207Pb is the decay product of 235U. Therefore, the original number of atoms of 235U, which is ​​N0​  ​​​, was ​​N​  0​​​ = (2.82 × ​​10​​  20​​) + (1.02 × ​​10​​  20​​) = 3.84 × ​​10​​  20​​ The half-life (​​T​  1/2​​​) for 235U is 710 million years (see Figure 26.3). ​  ​​​ into the given You substitute these values for N, N0, and ​​T1/2 equation and solve for t.

ANSWER The fossil is approximately 316 million years old.

Several Factors Affect the Completeness of the Fossil Record The fossil record should not be viewed as a complete and balanced representation of the species that existed in the past. Several factors affect the likelihood that extinct organisms have been preserved as fossils and will be identified by paleontologists (Table 26.1). First, certain organisms are more likely than others to become fossilized. Organisms with hard shells or bones tend to be over-represented in the fossil record. Factors such as anatomy, size, number, and the environment and time in which they lived also play important roles in determining the likelihood that organisms will be preserved in the fossil record. In addition, geological processes may favor the fossilization of certain types of organisms. Finally, unintentional biases arise that are related to the efforts of paleontologists. For example, scientific interests may favor searching for and analyzing certain species over others: Many paleontologists have been greatly interested in finding the remains of dinosaurs.

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CHAPTER 26

Table 26.1

Factors That Affect the Fossil Record

Factor

Description

Anatomy

Organisms with hard body parts, such as animals with a skeleton or thick shell, are more likely to be preserved than are organisms composed of soft tissues.

Size

The fossil remains of larger organisms are more likely to be found than those of smaller organisms.

Number

Species that existed in greater numbers or over a larger area are more likely to be preserved within the fossil record than those that existed in smaller numbers or in a smaller area.

Environment

Inland species are less likely to become fossilized than are those that lived in a marine environment or near the edge of water because sedimentary rock is more likely to be formed in or near water.

Time

Species that lived relatively recently or existed for a long time are more likely to be found as fossils than species that lived very long ago or for a relatively short time.

Geological processes

Due to the chemistry of fossilization, certain organisms are more likely to be preserved than are other organisms.

Paleontology

Certain types of fossils may be more interesting to paleontologists. In addition, a significant bias exists with regard to the locations where paleontologists search for fossils. For example, they tend to search in regions where other fossils have already been found.

Although the fossil record is incomplete, it has provided a wealth of information regarding the history of the types of life that existed on Earth. The rest of this chapter will survey the emergence of life-forms from 3.5 bya to the present.

26.2 History of Life on Earth Learning Outcomes: 1. List the types of environmental changes that have affected the history of life on Earth. 2. Describe the cell structure and energy utilization of the first living organisms that arose during the Archaean eon. 3. Explain how the origin of eukaryotic cells involved a union between bacterial and archaeal cells. 4. Describe the key features of multicellular organisms, which arose during the Proterozoic eon. 5. Outline the major events and changes in species diversity during the Paleozoic, Mesozoic, and Cenozoic eras.

In Chapter 4, we considered hypotheses concerning how the first cells came into existence. The first known fossils of single-celled organisms were preserved approximately 3.5 bya. In this section, we will begin with a brief description of the geological changes on Earth that

have affected the emergence of new forms of life and then examine some of the major changes in life that have occurred since it began.

Many Environmental Changes Have Occurred Since the Origin of the Earth The geological timescale is a timeline of Earth’s history and major events from its origin approximately 4.55 bya to the present (Figure 26.4). This timeline is subdivided into four eons—the Hadean, Archaean, Proterozoic, and Phanerozoic—and then further subdivided into eras. The first three eons are collectively known as the Precambrian because they preceded the Cambrian era, a geological era that saw a rapid increase in the diversity of life. The names of several eons and eras end in -zoic (meaning animal life), because these time intervals have been defined on the basis of animal life. We will examine these time periods later in this chapter. The changes that occurred in living organisms over the past 4 billion years are the result of two interactive processes. First, as discussed in the previous chapters, genetic changes in organisms can affect their characteristics. Such changes influence organisms’ abilities to survive and reproduce in their native environment. Second, the environment on Earth has undergone dramatic changes that have profoundly influenced the types of organisms that have existed during different periods of time. In some cases, an environmental change has allowed new types of organisms to flourish. Alternatively, environmental changes have resulted in extinction—the complete loss of a species or group of species. Major types of environmental changes are described next. Temperature  During the first 2.5 billion years of its existence, the surface of the Earth gradually cooled. However, during the last 2 billion years, the Earth has undergone major fluctuations in temperature, producing Ice Ages that alternate with warmer periods. Furthermore, the temperature on Earth is not uniform, which produces environments where the temperatures are quite different, such as tropical rain forests and the arctic tundra. Atmosphere  The chemical composition of the gases surrounding the Earth has changed substantially over the past 4 billion years. One notable change involves the amount of oxygen. Prior to 2.4 bya, relatively little oxygen gas was in the atmosphere, but at that time, levels of oxygen in the form of O2 began to rise significantly. The emergence of organisms that are capable of photosynthesis added oxygen to the atmosphere. Our current atmosphere contains about 21% O2. Increased levels of oxygen are thought to have a played a key role in various aspects of the history of life, including the following: ∙ The origin of many animal body plans coincided with a rise in atmospheric O2. ∙ The conquest of land by arthropods (about 410 mya) and a second conquest by arthropods and vertebrates (about 350 mya) occurred during periods in which O2 levels were high or increasing. ∙ Increases in animal body sizes are associated with higher O2 levels. Higher levels of O2 could have contributed to these events because higher O2 levels may enhance the ability of animals to carry out

PHANEROZOIC

206 248 290 354 417 443

Periods

65 144

Eras

Eons

0 1.8

Quaternary

Cretaceous

135 mya—Flowering plants first appear

Jurassic

160 mya—Birds first appear

Triassic

225−200 mya—Dinosaurs and mammals first appear

Tertiary

7 mya—Hominoids first appear

Permian PALEOZOIC

Millions of years ago (mya)

CENOZOIC

HISTORY OF LIFE ON EARTH AND HUMAN EVOLUTION 539

MESOZOIC



490

Carboniferous

300 mya—Reptiles first appear

Devonian

400 mya—Seed plants first appear; tetrapods and insects first appear

Silurian Ordovician Cambrian

543

440 mya—Large terrestrial colonization by plants and animals 520 mya—First vertebrates; first land plants 533–525 mya—Cambrian explosion results in diverse animal life

LATE

543 mya—Shelled animals first appear myya—Bilateral invertebrate animals first app 590 mya—Bilateral appear 632 mya—First animals appear

1.5 bya—Multicellular eukaryotic organisms first appear

LATE

1.8 bya—Eukaryotic cells first appear

MIDDLE

3,000

ARCHAEAN

2,500

PRECAMBRIAN

EARLY

1,600

MIDDLE

PROTEROZOIC

900

EARLY

3,400

3,800

3.5 bya—Fossils of primitive cyanobacteria

HADEAN

3.8–3.5 bya—Prokaryotic cells first appear

4,550

Figure 26.4  The geological timescale and an overview of the history of life on Earth.

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Landmasses  As the Earth cooled, landmasses formed that were surrounded by bodies of water. This produced two different environments: terrestrial and aquatic. Furthermore, over the course of billions of years, the major landmasses, known as the continents, shifted their positions, changed their shapes, and separated from each other. This phenomenon, called continental drift, is shown in Figure 26.5.

Volcanic Eruptions  The eruptions of volcanoes harm organisms in the vicinity of an eruption, sometimes causing extinctions. In addition, volcanic eruptions in the oceans lead to the formation of new islands. Massive eruptions may also spew so much debris into the atmosphere that they affect global temperatures and limit solar radiation, which restricts photosynthetic production.

Floods and Glaciations  Catastrophic floods have periodically had major effects on the organisms in the flooded regions. Glaciers have moved across continents and altered the composition of species on those landmasses. As an extreme example, in 1992, American geobiologist Joseph Kirschvink proposed the snowball Earth hypothesis, which suggests that the Earth was entirely covered by ice during parts of the period from 790 to 630 mya. This hypothesis was developed to explain various types of geological evidence including sedimentary deposits of glacial origin that are found at tropical latitudes. Although the existence of a completely frozen Earth remains controversial,

Meteorite Impacts  During its long history, the Earth has been struck by many meteorites. Large meteorites have significantly affected Earth’s environment.

0

CENOZOIC

Millions of years ago (mya)

Eras

massive glaciations over our planet have had an important effect on the history of life.

Eons

aerobic respiration. These events are discussed later in this chapter and in more detail in Unit V.

North Europe America Atlantic Ocean Africa

Asia

Indian Ocean

South America

Pacific Ocean Australia

Antarctica

Cenozoic period (modern Earth)

65

MESOZOIC

PHANEROZOIC

Laurasia Pacific Ocean

Tethys Ocean Go

nd wa

na

Mesozoic period

248

PALEOZOIC

Panthalassic Ocean

Pangaea

Tethys Ocean

Paleozoic period (Pangaea)

750

PROTEROZOIC

543 Panafrican Ocean

Rodinia

Panthalassic Ocean

Pre-Paleozoic period

Figure 26.5  Continental drift.  The relative locations of the continents on Earth have changed dramatically over time.

The effects of one or more of the changes described above have sometimes caused large numbers of species to go extinct at the same time. Such events are called mass extinctions. Five large mass extinctions occurred near the ends of the Ordovician, Devonian, Permian, Triassic, and Cretaceous periods. The boundaries between geological time periods are often based on the occurrences of mass extinctions. A recurring pattern seen in the history of life is the extinction of some species and the emergence of new ones. The rapid extinction of many modern species due to human activities is sometimes referred to as the sixth mass extinction. We will examine mass extinctions and the current biodiversity crisis in more detail in Chapter 60.

Prokaryotic Cells Arose During the Archaean Eon The Archaean (from the Greek, meaning ancient) was an eon when diverse microbial life flourished in the primordial oceans. As mentioned previously, the first known fossils of living cells were preserved in rocks that are about 3.5 billion years old (see Figure 26.1), though scientists postulate that cells arose many millions of years prior to this time. Based on the morphology of their fossilized remains, the first cells were prokaryotic. During the more than 1 billion years of the Archaean eon, all life-forms were prokaryotic. Because Earth’s atmosphere had very little free O2, the microorganisms of this eon almost certainly used only anaerobic (without oxygen) respiration. Organisms with prokaryotic cells are divided into two groups: bacteria and archaea. Bacteria are more prevalent on modern Earth, though many species of archaea have also been identified. Archaea are found in many different environments, with some occupying extreme environments such as hot springs. Bacteria and archaea share fundamental similarities, indicating that they are derived from a common ancestor. Even so, certain differences suggest that these two types of prokaryotes diverged from each other quite early in the history of life. In particular, bacteria and archaea show some interesting differences in metabolism, lipid composition, and genetic pathways (refer back to Table 25.1).

Biologists Are Undecided About Whether Heterotrophs or Autotrophs Came First An important factor that greatly influenced the emergence of new species is the availability of energy. As we learned in Unit II, all



HISTORY OF LIFE ON EARTH AND HUMAN EVOLUTION 541

organisms require energy to survive and reproduce. Organisms follow two different strategies to obtain energy. ∙ Some are heterotrophs, which means their energy is derived from the chemical bonds within the organic molecules they consume. Because the most common sources of organic molecules today are other organisms, heterotrophs typically consume other organisms or materials from other organisms. ∙ Alternatively, many organisms are autotrophs, which directly harness energy from either inorganic molecules or light. Among modern species, plants are an important example of autotrophs. Plants directly absorb light energy and use it (via photosynthesis) to synthesize organic molecules such as glucose. On modern Earth, heterotrophs ultimately rely on autotrophs for the production of food. Were the first forms of life heterotrophs or autotrophs? The answer is not resolved. Some biologists have speculated that autotrophs, such as those living near deep-sea vents, may have arisen first. These organisms would have used chemicals that were made near the vents as an energy source to make organic molecules. Alternatively, many scientists have hypothesized that the first living cells were heterotrophs. They reason that it would have been simpler for the first primitive cells to use the organic molecules in the prebiotic soup as a source of energy. If heterotrophs came first, why were cyanobacteria preserved in the earliest fossils, rather than heterotrophs? One possible reason is related to their manner of growth. Certain cyanobacteria promote the formation of a layered structure called a stromatolite (Figure 26.6). The aquatic environment where these cyanobacteria survive is rich in minerals such as calcium. The cyanobacteria grow in large mats that form layers. As they grow, they deplete the carbon dioxide (CO2) in the surrounding water. This causes calcium carbonate in the water to gradually precipitate over the bacterial cells, calcifying the older cells in the lower layers and also trapping grains of sediment. Newer cells produce

(a) Fossil stromatolite

a layer on top. Over time, many layers of calcified cells and sediment are formed, thereby producing a stromatolite. This process still occurs today in places such as Shark Bay in western Australia, which is renowned for the stromatolites along its beaches (Figure 26.6b). The emergence and proliferation of ancient cyanobacteria had two critical consequences. First, the autotrophic nature of these bacteria enabled them to produce organic molecules from CO2. This ability prevented the depletion of organic foodstuffs that would have been exhausted if only heterotrophs existed. Second, cyanobacteria produce O2 as a waste product of photosynthesis. During the Archaean and Proterozoic eons, the activity of cyanobacteria led to the gradual rise in atmospheric O2 noted earlier. The increase in O2 spelled doom for many anaerobic species, which became restricted to a few anoxic (without oxygen) environments, such as deep within the soil. However, O2 enabled the emergence of new bacterial and archaeal species that used aerobic (with oxygen) respiration (see Chapter 7). In addition, aerobic respiration is likely to have played a key role in the emergence and eventual explosion of eukaryotic life-forms, which typically have high energy demands. These eukaryotic life-forms are described next.

Core Concept: Evolution The Origin of Eukaryotic Cells Involved a Union Between Bacterial and Archaeal Cells Eukaryotic cells arose during the Proterozoic eon, which began 2.5 bya and ended 543 mya (see Figure 26.4). The manner in which the first eukaryotic cell originated is not entirely understood. In modern eukaryotic cells, genetic material is found in three distinct organelles. All eukaryotic cells contain DNA in the nucleus and mitochondria, and plant and algal cells also have DNA in their chloroplasts. To address the issue of the origin of

(b) Modern stromatolites

Figure 26.6  Fossil and modern stromatolites: evidence of autotrophic cyanobacteria.  Each stromatolite is a rocklike structure, typically

1 m in diameter. (a) Section of a fossilized stromatolite. The layers are mats of mineralized cyanobacteria, one layer on top of the other. The existence of fossil stromatolites provides evidence of early autotrophic organisms. (b) Modern stromatolites that have formed in western Australia.

a: ©Dirk Wiersma/SPL/Science Source; b: ©Horst Mahr/age fotostock

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eukaryotic species, scientists have examined the DNA sequences found in these three organelles. They have concluded that the nuclear, mitochondrial, and chloroplast genomes appear to be derived from once-separate cells that came together.

Ancient archaeon

Nuclear Genome Both bacteria and archaea contributed sub-

stantially to the nuclear genome of eukaryotic cells. Eukaryotic nuclear genes encoding proteins involved in metabolic pathways and lipid biosynthesis appear to be derived from ancient bacteria, whereas genes involved with transcription and translation appear to be derived from an archaeal ancestor. To explain the origin of the nuclear genome, several hypotheses have been proposed. The most widely accepted involves an association between ancient bacteria and archaea, which is hypothesized to have been endosymbiotic. In an endosymbiotic relationship, a smaller organism (the endosymbiont) lives inside a larger organism (the host). Researchers have suggested that an archaeal species evolved the ability to invaginate its plasma membrane, which could have two results (Figure 26.7). First, it could eventually lead to the formation of an extensive internal membrane system and enclosure of the genetic material in a nuclear envelope. Second, the ability to invaginate the plasma membrane provided a mechanism for taking up materials from the environment via endocytosis, which is described in Chapter 5. Along these lines, the closest modern relative to eukaryotes is thought to be a phylum of archaea called Lokiarchaeota, which carries many genes that are hypothesized to play a role in membrane remodeling. In the scenario described in Figure 26.7, an ancient archaeon engulfed a bacterium via endocytosis, maintaining the bacterium in its cytoplasm as an endosymbiont. Over time, some genes from the bacterium were transferred to the archaeal host cell, and the resulting genetic material eventually became the nuclear genome.

Mitochondrial and Chloroplast Genomes As discussed in Chapter 4, the analyses of genes from mitochondria, chloroplasts, and bacteria are consistent with the endosymbiosis theory, which proposes that mitochondria and chloroplasts originated from bacteria that took up residence within a primordial eukaryotic cell (refer back to Figure 4.31). Mitochondria found in eukaryotic cells are likely derived from a bacterial species that resembled modern α-proteobacteria, a diverse group of bacteria that carry out oxidative phosphorylation to make ATP. One possibility is that an endosymbiotic event involving an ancestor of this bacterial species produced the first eukaryotic cell and that the mitochondrion is a remnant of that event. Alternatively, endosymbiosis may have produced the first eukaryotic cell, and then a subsequent endosymbiosis resulted in mitochondria (see Figure 26.7). DNA-sequencing data indicate that chloroplasts were derived from a separate endosymbiotic relationship between a primitive eukaryotic cell and a cyanobacterium. As discussed in Chapter 28, plastids, such as chloroplasts, have arisen on several independent occasions via primary, secondary, and tertiary endosymbiosis (see Figure 28.13). Interestingly, an endosymbiotic relationship involving two different proteobacteria was reported in 2001. In mealybugs, bacteria

1

An archaeon species evolved the ability to invaginate its plasma membrane.

2

The invagination process led to the formation of a nuclear envelope.

3

Invagination

Nuclear envelope

The invagination process also allowed the archaeon to engulf a bacterium and establish an endosymbiosis.

Ancient bacterium

4

Many bacterial genes were transferred to the nucleus. This event may have resulted in mitochondria, or mitochondria may have arisen by a second endosymbiotic event.

5

A subsequent endosymbiotic event involving cyanobacteria resulted in chloroplasts. Mitochondrion

Ancient cyanobacterium Chloroplast Eukaryotic cells: Plants and algae

Eukaryotic cells: Animals, fungi, and some protists

Figure 26.7  Possible endosymbiotic relationships that gave rise to the first eukaryotic cells.

Core Skill: Connections  Look back at Figure 5.22. Explain how endocytosis played a role in endosymbiosis.



HISTORY OF LIFE ON EARTH AND HUMAN EVOLUTION 543

survive within the cytoplasm of large host cells of a specialized organ called a bacteriome. Recent analysis has shown that different species of bacteria inside the host cells share their own endosymbiotic relationship. In particular, γ-proteobacteria live endosymbiotically inside β-proteobacteria. Such an observation demonstrates that an endosymbiotic relationship can occur between two prokaryotic cells.

Multicellular Eukaryotes and the Earliest Animals Arose During the Proterozoic Eon The first multicellular eukaryotes are thought to have emerged about 1.5 bya, in the middle of the Proterozoic eon. The oldest fossil evidence for multicellular eukaryotes was an organism that resembled modern red algae; this fossil was dated at approximately 1.2 billion years old. Simple multicellular organisms are believed to have originated in one of two different ways. One possibility is that several individual cells found each other and aggregated to form a colony. Cellular slime molds, discussed in Chapter 28, are examples of modern organisms in which groups of single-celled organisms can come together to form a small multicellular organism. According to the fossil record, such organisms have remained very simple for hundreds of millions of years. Alternatively, another way that multicellularity can occur is when a single cell divides and the resulting cells stick together. This pattern occurs in many simple multicellular organisms, such as algae and fungi, as well as in species with more complex body plans, such as plants and animals. Biologists cannot be certain whether the first multicellular eukaryotes arose by an aggregation process or by cell division and adhesion. However, the development of complex, multicellular organisms now occurs by cell division and adhesion. An interesting example showing changes in the level of complexity from unicellular eukaryotes to more complex multicellular

organisms is found among evolutionarily related species of volvocine green algae. These algae exist as unicellular species, as small clumps of cells of the same cell type, or as larger groups of cells with two distinct cell types. Figure 26.8  compares four species of volvocine algae. Chlamydomonas reinhardtii is a unicellular alga (Figure 26.8a). It is called a biflagellate because each cell has two flagella. Gonium pectorale is a multicellular organism composed of 16 cells (Figure 26.8b). This simple multicellular organism is formed from a single cell by cell division and adhesion. All of the cells in this species are biflagellate. Other volvocine algae have evolved into larger and more complex organisms. Pleodorina californica has 64–128 cells (Figure 26.8c), and Volvox aureus has about 1,000–2,000 cells (Figure 26.8d). A feature of these more complex organisms is they have two cell types: somatic and reproductive cells. The somatic cells are biflagellate cells, but the reproductive cells are not. V. aureus has a higher percentage of somatic cells than P. californica. Overall, an analysis of these four species of algae illustrates three important principles found among complex multicellular species: 1. Multicellular organisms arise from a single cell that divides to produce daughter cells that adhere to one another. 2. The daughter cells can follow different fates, thereby producing multicellular organisms with different cell types. 3. As organisms get larger, a greater percentage of their cells tend to be somatic cells. The somatic cells carry out the activities required for the survival of the multicellular organism, whereas the reproductive cells are specialized for the sole purpose of producing offspring. Toward the end of the Proterozoic eon, multicellular animals emerged. The first animals were invertebrates—animals without a backbone. Most animals, except for organisms such as sponges and jellyfish, exhibit bilateral symmetry—a two-sided body plan with a right and left side that are mirror images. Because each side of the body has appendages such as legs, one advantage of bilateral symmetry is

Flagella

3 μm (a) Chlamydomonas reinhardtii, a unicellular alga

10 μm (b) Gonium pectorale, composed of 16 identical cells

30 μm (c) Pleodorina californica, composed of 64–128 cells, has 2 cell types, somatic and reproductive

100 μm (d) Volvox aureus, composed of about 1,000–2,000 cells, has 2 cell types, somatic and reproductive

Figure 26.8  Variation in the level of multicellularity among volvocine algae.  a: Courtesy of Dr. Barbara Surek, Culture Colection of Algae at the University of Cologne (CCAC); b: ©William Bourland; c–d: ©Dr. Cristian A. Solari, Department of Ecology and Evolutionary Biology, University of Arizona

Core Concept: Systems  The formation of different cell types is an emergent property of multicellularity

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that it facilitates locomotion. Bilateral animals also have anterior and posterior ends, with the mouth at the anterior end, as noted in Chapter 20. In southern China in 2004, Chinese paleontologist Jun-Yuan Chen, American paleobiologist David Bottjer, and their colleagues discovered a fossil, which they described as the earliest known ancestor of animals with bilateral symmetry. This minute creature, called Vernanimalcula guizhouena, has a shape like a flattened helmet and is barely visible to the naked eye (Figure 26.9). The fossil is approximately 580–600 million years old. However, the interpretation that Vernanimalcula guizhouena was the earliest ancestor of animals with bilateral symmetry remains controversial and is under active investigation.

Mouth

Anterior

Left

Right

Phanerozoic Eon: The Paleozoic Era Saw the Diversification of Invertebrates and the Colonization of Land by Plants and Animals The proliferation of multicellular eukaryotic life has been extensive during the Phanerozoic eon, which started 543 mya and extends to the present day. Phanerozoic means well-displayed life, referring to the abundance of fossils of plants and animals that have been identified from this eon. As shown in Figure 26.4, the Phanerozoic eon is subdivided into three eras: the Paleozoic, Mesozoic, and Cenozoic. Because they are relatively recent and we have many fossils from these eras, each of them is further subdivided into periods. We will consider each era with its associated conditions and prevalent forms of life separately. The term Paleozoic means ancient animal life. The Paleozoic era covers approximately 300 million years, from 543 to 248 mya, and is subdivided into six periods: Cambrian, Ordovician, Silurian, Devonian, Carboniferous, and Permian. Periods are usually named after regions where rocks and fossils of that age were first discovered. Cambrian Period (543–490 mya)  The climate in the Cambrian period was generally warm and wet, with no evidence of ice at the poles. During this time, the diversity of animal species increased

50 μm

Posterior

Figure 26.9  Fossil of an early invertebrate animal showing

bilateral symmetry.  This fossil of an early animal, Vernanimalcula guizhouena, dates from 580 to 600 mya. Courtesy of Prof. Junyuan Chen. Concept Check:   Name three other species that exhibit bilateral symmetry.

rapidly, an event called the Cambrian explosion. However, recent evidence suggests that many types of animal groups present during the Cambrian period actually arose prior to this period. Many fossils from the Cambrian period were found in the Canadian Rockies in a rock bed called the Burgess Shale, which was discovered by American paleontologist Charles Walcott in 1909. At this site, both soft- and hard-bodied (shelled) invertebrates were buried in an underwater mudslide and preserved in water that was so deep and oxygen-free that decomposition was minimal (Figure 26.10a). The excellent preservation of the softer tissues is what makes this deposit unique (Figure 26.10b).

0.7 cm (a) The Burgess Shale

(b) A fossilized arthropod, Marrella

Figure 26.10  The Cambrian explosion and the Burgess Shale.  (a) This photograph shows the original site in the Canadian Rockies

discovered by Charles Walcott. Since its discovery, this site has been made into a quarry for the collection of fossils. (b) A fossil of an extinct arthropod, Marrella, which was found at this site. a: ©L. Newman & A. Flowers/Science Source; b: ©O. Louis Mazzatenta/National Geographic/Getty Images



HISTORY OF LIFE ON EARTH AND HUMAN EVOLUTION 545

By the middle of the Cambrian period, all of the major types of invertebrates that exist today were present, plus many others that no longer exist. Over 100 major animal groups with significantly different body plans have been identified in the fossil record. Examples of groups that still exist include echinoderms (sea urchins and starfish), arthropods (insects, spiders, and crustaceans), mollusks (clams and snails), chordates (organisms with a dorsal nerve chord), and vertebrates (animals with backbones). Interestingly, although many new species of animals have arisen since this time, these later species have not shown a major reorganization of body plan, but instead exhibit variations on themes that were established during or prior to the Cambrian explosion. Three possible causes of the Cambrian explosion are the following. ∙ Because it occurred shortly after marine animals evolved shells, some scientists have speculated that the changes observed in animal species may have allowed them to exploit new environments.

2 cm (a) Trilobite

∙ Alternatively, others have suggested that the increase in diversity may be related to atmospheric oxygen levels. During this period, oxygen levels were increasing, and perhaps more complex body plans became possible only after the atmospheric oxygen surpassed a certain threshold. In addition, as atmospheric oxygen reached its present levels, an ozone (O3) layer was produced that screens out harmful ultraviolet radiation, thereby allowing complex life to live in shallow water and eventually on land. ∙ Another possible contributor to the Cambrian explosion was an “evolutionary arms race” between interacting species. The ability of predators to capture prey and the ability of prey to avoid predators may have been major factors that resulted in a diversification of animals into many different species. Ordovician Period (490–443 mya)  As in the Cambrian period, the climate of the early and middle parts of the Ordovician period was warm, and the atmosphere was moist. During this period, a diverse group of hard-shelled marine invertebrates, including trilobites and brachiopods, appeared in the fossil record (Figure 26.11). Marine communities consisted of invertebrates, algae, early jawless fishes (a type of early vertebrate), mollusks, and corals. Fossil evidence also suggests that early land plants and arthropods may have first invaded the land during this period. Toward the end of the Ordovician period, the climate changed rather dramatically. Large glaciers formed, which drained the relatively shallow oceans, causing the water levels to drop. This resulted in a mass extinction in which as much as 60% of the existing marine invertebrates became extinct. Silurian Period (443–417 mya)  In contrast to the dramatic climate changes observed during the Ordovician period, the climate during the Silurian period was relatively stable. The glaciers largely melted, which caused the ocean levels to rise. No new major types of invertebrate animals appeared during this period, but significant changes were observed among existing vertebrate and plant species. Many new types of fishes appeared in the fossil record. In addition, coral reefs made their first appearance during this period.

3 cm (b) Brachiopod

Figure 26.11  Shelled, invertebrate fossils of the Ordovician

period.  Trilobites existed for millions of years before becoming extinct about 250 mya. Many species of brachiopods exist today. a: ©Francois Gohier/Science Source; b: ©kavring/Shutterstock

The Silurian marked a major colonization of land by terrestrial plants and animals. For this to occur, certain species evolved adaptations that prevented them from drying out, such as an external cuticle. Ancestral relatives of spiders and centipedes became prevalent. The earliest fossils of vascular plants, which have tissues that are specialized for the transport of water, sugar, and salts throughout the plant body, were observed in this period. Devonian Period (417–354 mya)  In the Devonian period, generally dry conditions occurred across much of the northern landmasses. However, the southern landmasses were mostly covered by cool, temperate oceans. The Devonian saw a major increase in the number of terrestrial species. At first, the vegetation consisted primarily of small plants, only a meter tall or less. Later, ferns, horsetails, and seed plants, such as gymnosperms, also emerged. By the end of the Devonian, the first trees and forests were formed. A major expansion of terrestrial animals also occurred. Insects first appeared in the fossil record, and other invertebrates became plentiful. In addition, the first tetrapods—vertebrates with four legs—are believed to have arisen in the

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Devonian. Early tetrapods included amphibians, which lived on land but required water in which to lay their eggs. In the oceans, many types of invertebrates flourished, including brachiopods, echinoderms, and corals. This period is sometimes called the Age of Fishes, as many new types of fishes emerged. During a period of approximately 20 million years near the end of the Devonian period, a prolonged series of extinctions eliminated many marine species. The cause of this mass extinction is not well understood. Carboniferous Period (354–290 mya)  The term Carboniferous refers to the deposits of coal, a sedimentary rock primarily composed of carbon, that were formed during this period. The Carboniferous period had the ideal conditions for the subsequent formation of coal. It was a cooler period, and much of the land was covered by forest swamps. Coal was formed over many millions of years from compressed layers of rotting vegetation. Plants and animals further diversified during the Carboniferous period. Very large plants and trees became prevalent. For example, tree ferns such as Psaronius grew to a height of 15 m or more (Figure 26.12). The first flying insects emerged. Giant dragonflies with a wingspan of over 2 ft inhabited the forest swamps. Terrestrial vertebrates also became more diverse. Amphibians were very prevalent. One innovation that seemed particularly beneficial was the amniotic egg. In reptiles, the amniotic egg was covered with a leathery or hard shell, which prevented the desiccation of the embryo inside. This innovation was critical for the emergence of reptiles during this period. Permian Period (290–248 mya)  At the beginning of the Permian, continental drift had brought much of the Earth’s total land together into a supercontinent known as Pangaea (see Figure 26.5). The interior regions of Pangaea were dry, with great seasonal fluctuations.

The forests of fernlike plants were replaced with gymnosperms. Species resembling modern conifers first appeared in the fossil record. Amphibians were prevalent, but reptiles became the dominant vertebrate species. At the end of the Permian period, the largest known mass extinction in the history of life on Earth occurred; 90–95% of marine species and a large proportion of terrestrial species were eliminated. The cause of the Permian extinction is the subject of much research and controversy. One possibility is that glaciation destroyed the habitats of terrestrial species and lowered ocean levels, which would have caused greater competition among marine species. Another hypothesis is that enormous volcanic eruptions in Siberia produced large ash clouds that abruptly changed the climate on Earth.

Phanerozoic Eon: The Mesozoic Era Saw the Rise and Fall of the Dinosaurs The Permian extinction marks the division between the Paleozoic and Mesozoic eras. Mesozoic means middle animals. It was a time that saw great changes in animal and plant species. This era is sometimes called the Age of Dinosaurs, because those animals flourished during this time. The climate during the Mesozoic era was consistently hot, and terrestrial environments were relatively dry. Little if any ice was found at either pole. The Mesozoic is divided into three periods: the Triassic, Jurassic, and Cretaceous. Triassic Period (248–206 mya)  Reptiles were plentiful in this period, including new groups such as crocodiles and turtles. The first dinosaurs emerged during the middle of the Triassic. Dinosaurs were reptiles that shared certain anatomical features, including an erect posture. The first mammals also emerged, such as the small Megazostrodon (Figure 26.13). Gymnosperms were the dominant

Psaronius

Figure 26.12  A giant tree fern, Psaronius, from the

Carboniferous period.  This genus became extinct during the Permian. The illustration is a re-creation based on fossil evidence. The inset shows a fossilized section of the trunk, also known as petrified wood. ©Natural History Museum, London/SPL/Science Source

Figure 26.13  Megazostrodon, the first known mammal of the

Triassic period.  The illustration is a re-creation based on fossilized skeletons. The Megazostrodon was 10 to 12 cm long.

Core Skill: Connections  Look ahead to Table 35.1. What are the common characteristics of mammals?



HISTORY OF LIFE ON EARTH AND HUMAN EVOLUTION 547

tropical conditions were replaced by a colder, drier climate. During this time, mammals became the largest terrestrial animals, which is why the Cenozoic is sometimes called the Age of Mammals. However, the Cenozoic era also saw an amazing diversification of many types of organisms, including birds, fishes, insects, and flowering plants.

Figure 26.14  A fossil of an early birdlike animal, Archaeopteryx, which emerged in the Jurassic period. ©Jason Edwards/Getty Images

land plant. Volcanic eruptions near the end of the Triassic are thought to have caused global warming, resulting in mass extinctions that eliminated many marine and terrestrial species. Jurassic Period (206–144 mya)  Gymnosperms, such as conifers, continued to be the dominant vegetation in the Jurassic period. Mammals were not prevalent. Reptiles continued to be the dominant land vertebrate. Some dinosaurs attained enormous sizes, including the massive Brachiosaurus, which reached a length of 25 m (80 ft) and weighed up to 100 tons! Modern birds are descendants of a dinosaur lineage called theropod (meaning beast-footed) dinosaurs. Tyrannosaurus rex is one of the best known theropod dinosaurs. An early birdlike animal, Archaeopteryx (Figure 26.14), emerged in the Jurassic period. However, paleontologists are debating whether or not Archaeopteryx is a true ancestor of modern birds. Cretaceous Period (144–65 mya)  On land, dinosaurs continued to be the dominant animals in the Cretaceous period. The earliest flowering plants, called angiosperms, which form seeds within a protective chamber, emerged and began to diversify. The end of the Cretaceous witnessed another mass extinction, which brought an end to many previously successful groups of organisms. Except for the lineage that gave rise to birds, dinosaurs abruptly died out, as did many other species. As with the Permian extinction, the cause or causes of this mass extinction are still debated. One plausible hypothesis suggests that a large meteorite hit the region that is now the Yucatan Peninsula of Mexico, lifting massive amounts of debris into the air and thereby blocking the sunlight from reaching the Earth’s surface. Such a dense haze could have cooled the Earth’s surface by 11–15°C (20–30°F). Evidence also points to strong volcanic eruptions as a contributing factor for this mass extinction.

Phanerozoic Eon: Mammals and Flowering Plants Diversified During the Cenozoic Era The Cenozoic era spans the most recent 65 million years. It is divided into two periods: Tertiary and Quaternary. In many parts of the world,

Tertiary Period (65–1.8 mya)  On land, the mammals that survived from the Cretaceous began to diversify rapidly during the early part of the Tertiary period. Angiosperms became the dominant land plant, and insects became important for their pollination. Fishes also diversified, and sharks became abundant. Toward the end of the Tertiary period, about 7 mya, hominoids came into existence. Hominoids include humans, chimpanzees, gorillas, orangutans, and gibbons, plus all of their recent ancestors. The subset of hominoids called hominins includes modern humans, extinct human species (for example, of the Homo genus), and our immediate ancestors. In 2002, a fossil of the earliest known hominin, Sahelanthropus tchadensis, was discovered in Central Africa. This fossil was dated at between 6 and 7 million years old. Another early hominin genus, called Australopithecus, first emerged in Africa about 4 mya. Australopithecines walked upright and had a protruding jaw, prominent eyebrow ridges, and a small braincase. Quaternary Period (1.8 mya–present)  Periodic Ice Ages have been prevalent during the last 1.8 million years, covering much of Europe and North America. This period has witnessed the widespread extinction of many species of mammals, particularly larger ones. Certain species of hominins became increasingly more like living humans. Fossils of Homo habilis, or handy man, so called because stone tools were found with the fossil remains, have been dated to close to the beginning of the Quaternary period. Homo sapiens— modern humans—first appeared about 200,000 years ago. The evolution of hominins is discussed in more detail in the next section.

26.3 Human Evolution Learning Outcomes: 1. List the common characteristics of primates and describe their evolutionary relationships. 2. Explain how human species evolved from other primate species, and describe how they spread across the Earth. 3. Provide examples of how populations of Homo sapiens are still evolving. 4. Compare and contrast modern human variation at the phenotype and genotype levels.

Hardly a topic in biology has evoked more interest or public debate than human evolution. The question of “where did we come from” has been considered by people for thousands of years. In this section, we will tackle this question from an evolutionary perspective. We begin with an overview of primate evolution, in which we explore how humans are evolutionarily related to their closest nonhuman relatives. We then take a closer look at the evolutionary events that gave rise to modern humans. As you will see, many extinct species of humans have existed, including the Denisovans, which were

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discovered as recently as 2010! Finally, we will turn our attention to the genetic variation found among modern humans and consider whether our species is still evolving.

Haplorrhini

Strepsirrhini

Anthropoidea

∙ Large brain. Acute vision and other senses enhancing the ability to move quickly through the trees require the efficient processing of large amounts of information. As a result, primate brains are relatively large for their body sizes and are well developed. ∙ Complex social behavior and well-developed parental care. Compared to other mammals, primates have a tendency toward complex social behavior and relatively long parental care. Some of these characteristics are found in other animals. For example, binocular vision occurs in owls and some other birds, grasping hands are found in raccoons, and relatively large brains occur in marine mammals. Primates are defined by possessing the whole suite of these characteristics. The evolutionary relationships among primates are described in Figure 26.15. Taxonomists divide them into two broad groups: the strepsirrhini and the haplorrhini. The strepsirrhini are smaller species, such as bush babies, lemurs, and pottos. These are generally nocturnal and smaller-brained primates with eyes positioned a little more toward the side of their heads (Figure 26.16a). The strepsirrhini are named for their wet noses with no fur at the tip. The haplorrhini have dry noses and fully forward-facing eyes. This group consists of the tarsiers and the larger-brained and diurnal anthropoidea: monkeys and the hominoidea (gibbons, orangutans, gorillas, chimpanzees, and humans) (Figure 26.16b and c). A key feature of anthropoidea is an opposable thumb, which makes it easier to grasp and handle objects. What differentiates monkeys from hominoids? Most monkeys have tails, but hominoids do not. In addition, hominoids

Subfamily Homininae

Tribe Hominini

Humans

Chimpanzees

Tribe Gorillini

Tribe Panini

Gorillas

Orangutans

Gibbons

Family Hominidae

∙ Grasping hands. All primates have grasping hands, a characteristic that enables them to hold onto branches. Monkeys, gibbons, orangutans, gorillas, chimpanzees, and humans also possess an opposable thumb, a thumb that can be placed opposite the fingers of the same hand, which gives them a precision grip and enables the manipulation of small objects. All of these primates except humans also have an opposable big toe.

Subfamily Ponginae

∙ At least some digits with flat nails instead of claws. This feature is believed to aid in the manipulation of objects.

Family Hylobatidae

∙ Binocular vision. Primates have forward-facing eyes that are positioned close together on a flattened face. Jumping from branch to branch requires accurate judgment of distances. This is facilitated by binocular vision in which the field of vision for both eyes overlaps, producing a single image.

Monkeys

Primates are primarily tree-dwelling species that evolved from a group of small, arboreal, insect-eating mammals about 85 mya, before dinosaurs went extinct. Primates have several defining characteristics, mostly relating to their tree-dwelling nature:

Tarsiers

Primates Evolved from a Tree-Dwelling Species and Exhibit a Distinctive Set of Characteristics

Bush babies, lemurs, pottos

Hominoidea

No tails Opposable thumbs Binocular vision, flat nails, grasping hands

Figure 26.15  Evolutionary tree of the primates.

have more mobile shoulder joints, broader rib cages, and a shorter spine. These features aid in brachiation, a swinging movement in trees. Hominoids also possess relatively long limbs and short legs and, with the exception of gibbons, are much larger than monkeys. The 20 species of hominoids are split into two groups: the lesser apes (family Hylobatidae), consisting of gibbons; and the greater apes (family Hominidae), consisting of orangutans, gorillas, chimpanzees, and humans ( Figure 26.17). The lesser apes are strictly arboreal, whereas the greater apes often descend to the ground to feed. Although humans are closely related to chimpanzees and gorillas, they did not evolve directly from them. Rather, all hominoid species shared a common ancestor. Recent molecular studies show that gorillas, chimpanzees, and humans are more closely related to one another than they are to gibbons and orangutans, so scientists have split the family Hominidae into groups, including the subfamily Ponginae (orangutans) and the subfamily Homininae (gorillas, chimpanzees, and humans and their ancestors) (see Figure 26.15). In turn, the Homininae are split into three tribes: the Gorillini (gorillas), the Panini (chimpanzees), and the Hominini (humans and their ancestors).



HISTORY OF LIFE ON EARTH AND HUMAN EVOLUTION 549

(a) Strepsirrhini (lesser bush baby)

(b) Anthropoidea (capuchin monkey)

(c) Hominoidea (white-handed gibbon)

Figure 26.16  Primate classification.  The primates are divided into two groups: (a) the strepsirrhini (smaller, nocturnal species such as this

bush baby), and the haplorrhini (larger, diurnal species). Haplorrhini comprise (b) the monkeys and tarsiers, such as this capuchin monkey (Cebus capucinus), and (c) the hominoids, species such as this white-handed gibbon (Hylobates lar). a: ©David Haring/DUPC/Getty Images; b: ©Brand X Pictures/ PunchStock/Getty Images; c: ©Katerina Novakova/catherinka/123RF

Concept Check:   What are the defining features of primates?

(a) Gorilla (Gorilla gorilla)

(b) Chimpanzee (Pan troglodytes)

(c) Human (Homo sapiens)

Figure 26.17  Members of the family Hominidae.  (a) Gorillas, the largest of the living primates, are ground-dwelling herbivores that inhabit the forests of Africa. (b) Chimpanzees are smaller, omnivorous primates that also live in Africa. The chimpanzees are close living relatives of modern humans. (c) Humans are members of the family Hominidae. The orangutan is also a member of this group. a: Source: Richard Ruggiero/USFWS; b: ©imageBROKER/Alamy Stock Photo; c: ©Tetra Images/Getty Images

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Core Concept: Evolution Comparing the Genomes of Humans and Chimpanzees A male chimp called Clint, which lived at a primate research center in Atlanta provided the DNA used to sequence the chimp genome. In 2005, the Chimpanzee Sequencing and Analysis Consortium published an initial sequence of the chimpanzee genome. The draft sequence followed the 2003 publication of the human genome (see Chapter 21) and allowed scientists to make detailed comparisons between the two species. These comparisons revealed that the sequences of base pairs of the two genomes differ by only 1.23%, which is 10 times less than the difference between the mouse and rat genomes. Comparisons of human and chimpanzee proteomes also showed that 29% of all proteins are identical, with most others differing by one or two amino acid substitutions. Many of the genetic differences between chimps and humans result from chromosome inversions and duplications. Over 1,500 inversions occur between the chimp and human genomes. Although many inversions are in the noncoding regions of the genome, the DNA in these regions may regulate the expression of the genes in the coding regions. Duplications and deletions are also common. For example, humans have lost a gene called caspase-12, which in other primates may protect against Alzheimer's disease. Some interesting genetic differences were apparent between chimps and humans even before their entire genomes were sequenced. In 2002, Swedish molecular geneticist Svante Päab̈ o discovered differences between humans and chimps in a gene called FOXP2, which plays a role in speech development. Proteins encoded by this gene differ in just two amino acids of a 715-aminoacid sequence. Researchers propose that the mutations in this gene have been crucial for the development of human speech. In 2006, a team led by American geneticist David Reich discovered that the human X chromosome diverged from the chimpanzee X chromosome about 1.2 million years more recently than the other chromosomes. This indicated to the researchers that the human and chimp lineages split apart, then began interbreeding before diverging again. If so, the interbreeding explains why many fossils appear to exhibit traits of both humans and chimps: Those primates may actually have been human-chimpanzee hybrids.

Bipedalism Is a Distinguishing Feature of Humans About 7 mya in Africa, a lineage that led to modern humans diverged from other primate lineages. The evolution of humans should not be viewed as a neat, stepwise progression from one species to another. Rather, human evolution, like the evolution of all species, can be visualized more like a tree, with one or two hominin species—members of the Hominini tribe—likely coexisting at the same point in time, with some eventually going extinct and some giving rise to other species (Figure 26.18).

The key characteristic differentiating hominins from other apes is that hominins walk on two feet; that is, they are bipedal. At about the time when hominins diverged from other ape lineages, the Earth’s climate had cooled, and the forests of Africa gave way to grassy savannas. Bipedal locomotion and an upright stance may have been advantageous in allowing hominins to peer over the tall grasses of the savanna to see predators or prey. Bipedalism is correlated with important anatomical changes in hominins. First, the opening of the skull where the spinal cord enters shifted forward, causing the spine to be more directly underneath the head. Second, the hominin pelvis became broader to support the additional weight. And third, the lower limbs, used for walking, became relatively larger than those in other apes. These are the types of anatomical changes paleontologists look for in the fossil record to determine whether fossil remains are hominins. The earliest known hominin, Sahelanthropus tchadensis, was discovered in Central Africa in 2002. Fossils of this species are dated at 7 million years old. The evolutionary relationship between S. tchadensis and later hominin species is unclear. Another early group of hominins included several species of the genus Australopithecus, which first emerged in Africa about 4 mya. As shown in Figure 26.18, Australopithecus afarensis is generally regarded as the direct ancestor of most hominin species, but it could be a close relative of an unknown species that was the direct ancestor. From there, the evolution of different human species is still debated. It is generally agreed that two genera evolved from Australopithecus: the more robust Paranthropus and the genus Homo. The early stages of the evolution of Homo species, and their differentiation from at least two possible Australopithecus species, have not yet been determined with great certainty. However, the later divergence of various Homo species is better understood.

Australopithecus and Paranthropus Are Early Human Genera Let’s consider some of the general features of the two early human genera, Australopithecus and Paranthropus. In 1924, the first fossil was found in South Africa for a member of the genus Australopithecus (from the Latin austral, meaning southern, and the Greek pithecus, meaning ape). Since then, hundreds of fossils of this group have been unearthed all over southern and eastern Africa, the areas where fossil deposits are best exposed to paleontologists. This group was widespread, with at least six species. In 1974, American paleontologist Donald Johanson discovered the skeleton of a female A. afarensis in the Afar region of Ethiopia and dubbed her Lucy. (The Beatles’ song “Lucy in the Sky with Diamonds” was playing in the camp the night when Johanson was sorting the unearthed bones.) Over 40% of the skeleton had been preserved, enough to provide a good idea of the physical appearance of australopithecines. Compared with modern humans, they were relatively small, about 1–1.5 m in height and approximately 18 kg in weight (Figure 26.19). Females were much smaller than males, a characteristic known as sexual dimorphism. Examination of the bones revealed that A. afarensis walked on two legs. They had a facial structure and a brain size (about 500 cubic centimeters [cm3]) similar to those of a chimp.



HISTORY OF LIFE ON EARTH AND HUMAN EVOLUTION 551

Time 5.0

Millions of years ago (mya) 3.0 2.0

4.0

1.0

0 Denisovan

H. heidelbergensis Paranthropus boisei

Enlarged jaw

Paranthropus robustus

Australopithecus afarensis (“Lucy”) Australopithecus ancestor Bipedalism

Slender body

Homo sapiens

H. ergaster A. africanus

A. garhi

H. neanderthalensis

Stocky body

Homo habilis

H. erectus

Large brains, stone tools

Figure 26.18  A possible scenario for human evolution.  In this human family tree (based on the work of Donald Johanson and others), several hominin species lived during the same time period as others, but only one lineage gave rise to modern humans (Homo sapiens).

In the 1930s, the remains of bigger-boned hominins were found. Two of these larger species, now considered to be a separate genus, Paranthropus, weighed about 40 kg and lived during the same time period as australopithecines and early Homo species. Paranthropus were vegetarians with enormous jaws used for grinding tough roots

and tubers. Both Paranthropus species died out rather suddenly about 1.5–2.0 mya. Although Australopithecus africanus was thought to have evolved slightly later than A. afarensis, its bones had been found much earlier than those of A. afarensis. In the 1920s, Australian anthropologist Raymond Dart described A. africanus from infant bones discovered in a cave in Taung, South Africa. The well-preserved skull was small but was well rounded, unlike the skulls of chimpanzees and gorillas. Also, the positioning of the head on the vertebral column indicated bipedalism. These observations suggested to Dart that he had found a transitional form between apes and humans. However, it would take another 20 years and the discovery of more fossils to convince the scientific world to support Dart’s view. In 1996, remains of another species, Australopithecus garhi, were also found in the Afar region. The discoverers were surprised to find that the teeth had similarities with Paranthropus boisei. Garhi means surprise in the local Afar language. The proposal that both A. garhi and A. africanus are ancestors of modern humans has been the subject of much debate. They have been viewed as either deadend cousins or the ancestors of the first members of the genus Homo.

The Genus Homo Includes Modern Humans and Their Most Recent Relatives Seven different species in the Homo genus are shown in Figure 26.18. Let’s consider how they are evolutionarily related to each other.

Figure 26.19  A modern woman compared to an

australopithecine.  Compared with modern humans, australopithecines, as illustrated by this reconstruction based on the famous fossil called Lucy, were much smaller and lighter.

Homo habilis  In the 1960s, British paleontologist Louis Leakey found hominin fossils estimated to be about 2 million years old in Olduvai Gorge, Tanzania. Two particularly interesting observations

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Homo ergaster  Although the evidence is not entirely clear, H. habilis probably gave rise to one of the most important species of Homo: Homo ergaster. This hominin species arose in Africa about 2 million years ago; it had a human-looking face and skull, with downward-facing nostrils. H. ergaster was also a tool user, and the tools, such as hand axes, were larger and more sophisticated than those associated with H. habilis. H. ergaster evolved in a period of global cooling and drying that reduced tropical forests even more and promoted savanna conditions. Hairlessness and the regulation of body temperature through sweating may also have evolved at this time as adaptations to the sunny environment. A leaner body shape was evident. We know this from so-called Turkana boy, a fossil teenage boy found in Kenya in 1984. Though only 13 years old, scientists predict he would have been about 185 cm (6 ft 1 in.) when adult, much the same height as the Masai tribesman that inhabit the area today. A dark skin probably protected H. ergaster from the Sun’s rays. The pelvis had narrowed, promoting efficiencies in walking upright, and the size of the brain and hence the skull increased, which may have produced more difficulty in childbirth. Mothers had to push increasingly largebrained infants through a narrowed pelvis. Researchers think that as a result, the human gestation period was shortened. Earlier birth leads to prolonged care of human infants compared with that in other apes. Prolonged child care required well-nourished mothers, who would have benefited from the support of their male partner and other members of a social group. Some anthropologists have suggested this was the beginning of the family. H. ergaster is thought to have given rise to many species, including Homo erectus, Homo heidelbergensis, Homo neanderthalensis, and Homo sapiens. A possible timeline and geographic locations for these species are shown in Figure 26.20. H. ergaster probably was the first type of human to leave Africa, as similar bones have been found in the Eurasian country of Georgia. This species is believed to be a direct ancestor of modern humans, with Homo heidelbergensis viewed as an intermediary step. Living at the same time as

Denisovans 0 0.2

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about these fossils stand out. First, reconstruction of the skull showed a brain size of about 680 cm3, larger than that of Australopithecus. Second, the fossils were found with a wealth of stone tools. As a result, Leakey assigned the fossils to a new species, Homo habilis, from the Latin, meaning handy man. The discovery of several more Homo fossils followed, but there have been no extensive finds, as there were for australopithecines. This relative scarcity of fossils makes it difficult to determine which Australopithecus lineage gave rise to the Homo lineage (see Figure 26.17), and paleontologists remain divided on this point. Homo habilis lived alongside Paranthropus in East Africa but had much smaller jaws and teeth, indicating that it probably ate large quantities of meat. The smaller jaw provided more space in the skull for brain development. Homo habilis probably scavenged most of its meat from the kills of large predators. A meatier diet is easier to digest and is rich in nutrients and calories. The human brain uses a lot of energy, 20% of the body’s total energy production. The meateating habit thus helped propel the evolution of increasing brain size in humans. Cut marks on animal bones of the period reveal that early humans used stone tools to smash open bones and extract the proteinrich bone marrow.

Age (millions of years ago)

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Figure 26.20  One view of the temporal and geographic evolution of hominid populations.  Though not shown in this figure, the range of the Denisovans and Homo neanderthalensis also extended into Asia. H. heidelbergensis was another descendent of H. ergaster, H. erectus, though some researchers consider H. ergaster and H. erectus as the same species. We will treat them as separate species here. Homo erectus  Homo erectus was a large hominin, as large as a modern human but with heavier bones and a smaller brain capacity of between 750 and 1,225 cm3 (modern human brain size is about 1,350 cm3). Fossil evidence shows that H. erectus was a social species that used tools, hunted animals, and cooked over fires. The meat-eating habit may have sparked the migration of H. erectus. Carnivores tend to have larger ranges than similar-sized herbivores, because the food sources of carnivores (prey) are usually scarcer per unit area. H. erectus spread out of Africa soon after the species appeared, over a million years ago, and fossils have been found as far away as China and Indonesia. The first fossil was found by Dutch physician Eugene Dubois in 1891 on the Indonesian island of Java. Stone tools are rarely found in these Asian sites, suggesting H. erectus based their technology on other materials, such as bamboo, which was abundant at that time. Bamboo is strong yet lightweight and could have been used to make spears. These humans may even have used rafts to take to the seas. H. erectus went extinct about 100,000 years ago, for reasons that are unclear but may be related to the spread of H. sapiens into its range. Homo heidelbergensis  Homo heidelbergensis was similar in body form to modern humans. Large caches of this species’ bones were found in Spain, at the bottom of a 14-m (45-ft) shaft known as La Sima de Los Huesos (the pit of bones). Similar remains were also found at Boxgrove in England. Shinbones recovered from Boxgrove suggest that males had heights around 180 cm (6 ft) and weighed 88 kg (196 pounds). Skulls were large, with brain volumes from 1,100 to



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1,400 cm3, similar to those of modern humans. Animal bones from these sites showed cut marks from stone blades beneath tooth marks from carnivores. This indicated that humans were killing large prey before scavengers arrived. Horses, giant deer, and rhinoceroses were common prey, and successfully hunting them would have required much skill and cooperation. H. heidelbergensis gave rise to three species, Homo neanderthalensis, the Denisovans, and Homo sapiens. However, some scientists view these as three subspecies. In the discussion that follows, we will consider them to be three different species. Homo neanderthalensis  Homo neanderthalensis was named for the Neander Valley of Germany, where the first fossils of this species were found. In the Pleistocene epoch, glaciers were locked in a cycle of advance and retreat, and the European landscape was often covered with snow. Over the course of many generations, the more slender body form of H. heidelbergensis evolved into a shorter, stockier build that was better equipped to conserve heat; we now call this type of human Neanderthal. Neanderthals also possessed a more massive skull and larger brain size than modern humans, about 1,450 cm3, perhaps associated with their bulk. Males were about 168 cm (5 ft 6 in.)

tall and would have been very strong by modern standards. They had a large face with a prominent bridge over the eyebrows, a large nose, and no chin (Figure 26.21a). They lived predominantly in Europe, with a range extending to the Middle East and Asia (Figure 26.21b). Their stocky and muscular physique was well suited to the rigors of cold climates and hunting prey. Paleontologists have found a high rate of head and neck injuries in Neanderthal bones, similar to that seen in present-day rodeo riders. This suggests that close encounters with large prey often resulted in blows that knocked the hunters off their feet. The hyoid bone, which holds the larynx (voice box) in place, was well developed, suggesting speech was used. The Neanderthals went extinct about 40,000 to 30,000 years ago. Denisovans  In 2010, scientists sequenced DNA from a fossilized pinky finger of a young female found in Denisova Cave in Siberia, Russia, and found it to be genetically distinct from the DNA of H. neanderthalensis and H. sapiens. Because it is such a recent discovery, its species name is yet to be agreed upon. The common name given to this type of human is a Denisovan. Using carbon radioisotope dating, the fossil was estimated to be about 400,000 years old. Thus far, the remains of 4 Denisovans have been discovered.

(a) An adult male Neanderthal

Figure 26.21  Neanderthals.  (a) Artist’s rendition of a Neanderthal human. Neanderthals were shorter and stockier than modern humans, with larger elbow and ankle joints, shorter forearms, and a larger, broader rib cage. (b) The range of Neanderthals was confined to Europe and western Asia, with a northerly limit that corresponds to about 50° north, the southern limit of glaciation. Total population size may only have been 70,000 at its peak.

(b) Geographic range of Neanderthals

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Scientists now hypothesize that Denisovans were a sister group to the Neanderthals, diverging from the Neanderthals about 400,000 years ago. It is difficult to reconstruct the physical traits of Denisovans, because only a finger bone, a toe bone, and a few molar teeth have been discovered thus far. Even so, the finger bone was unusually broad and robust, suggesting the Denisovans were similar in build to the Neanderthals. Like the Neanderthals, the Denisovans are thought to have gone extinct about 40,000 to 30,000 years ago. Homo sapiens  Homo sapiens (from the Latin, meaning wise man) is our own species. H. sapiens is a slender, lighter-weight species with a slightly smaller brain capacity than that of the Neanderthals. Researchers hypothesize a variety of reasons why H. sapiens thrived while the Neanderthals disappeared; it may have been due to a more efficient body type with lower energy needs, increased longevity, and/or differences in social structure and cultural adaptations.

Evidence Suggests That Homo sapiens Arose in Africa and Then Migrated to Other Parts of the World Two models have been proposed to explain where the species of modern humans, Homo sapiens, arose. The first model, the out-of-Africa hypothesis, suggests that H. sapiens evolved in Africa from H. heidelbergensis. Some members of H. sapiens later migrated to other parts of the world, and gradually replaced species such as H. erectus and H. neanderthalensis. An alternative hypothesis, called the multiregional hypothesis, which is not widely accepted, suggests that human groups have evolved from H. ergaster populations in a number of different parts of the world. According to this hypothesis, gene flow between neighboring populations prevented the formation of several different H. sapiens species. In 1987, American evolutionary biologists Rebecca Cann, Allan Wilson, and colleagues analyzed the sequences of mitochondrial DNA (mtDNA) that was collected from many different people from around the world. By comparing these sequences to each other, they concluded that H. sapiens arose in Africa about 200,000 years ago. These results and those of subsequent studies support the outof Africa hypothesis. According to this hypothesis, H. ergaster arose in Africa and spread to Asia and Europe. Later, H. erectus diverged from H. ergaster in Africa and spread into Asia, and H. neanderthalensis diverged from H. heidelbergensis in Europe. Both of these species and the Denisovans became extinct as H. sapiens migrated across the world. Some researchers have suggested that the extinction of these other human species may have occurred because they were outcompeted by H. sapiens. However, further research is needed to confirm or refute that idea. The analysis of DNA sequences from modern humans across the world can also be used to construct a map that describes the migration of humans out of Africa. Figure 26.22 shows a simplified version of such a map. However, the time periods should be considered as approximate. As researchers gather more data from people in various regions of the world, this map undergoes frequent revision. Modern humans spread first into the Middle East and Asia, then later into Europe and Australia, finally crossing the Bering Strait to the Americas.

Much remains to be resolved in our understanding of human evolution, and new data provide paleontologists with information to revise their hypotheses. For example, in 2004, the remains of a small human were discovered on the Indonesian island of Flores and were given the name Homo florensiensis, nicknamed hobbits by the media. Many species—for example, deer and elephants—develop into small forms in insular situations, so hobbit-sized humans seemed plausible. Since then, many researchers have suggested these people were modern humans who were suffering from a genetic disorder. Even modern humans on Flores are pygmies. Pathological dwarfism would have made these people even smaller. Only tools associated with H. sapiens have been found at the area where the bones occur, suggesting these individuals were indeed dwarf forms of modern humans. A 2014 study showed that the small brain size of one of the H. floresiensis fossils was in the range predicted for an individual with Down syndrome, and it was suggested that this is evidence that H. florensiensis is an invalid species.

Human Evolution Has Involved Interbreeding Among Closely Related Species Because the remains of Neanderthals and Denisovans are less than 50,000 years old, researchers have been able to extract DNA from their fossils and compare their DNA sequences to each other and to those of  H. sapiens. Detailed comparisons of Neanderthal, Denisovan, and modern human genomes have revealed interbreeding among the three species as H. sapiens spread into Europe and Asia. The genomes of modern humans of African descent contain little or no DNA that is derived from Neanderthals or Denisovans. However, 1% to 4% of the DNA from a person of European descent is derived from Neanderthals, and 4% to 6% of the DNA from a person of Southeast Asia descent is derived from Denisovans. These results indicate that H. sapiens ancestors interbred with Neanderthals and Denisovans while spreading across Europe and Asia. Interestingly, some people of African descent carry very small amounts of Neanderthal DNA. How is this possible? By analyzing the DNA sequences of certain African people, researchers speculate that some H. sapiens from Europe may have migrated back to Africa about 3,000 years ago and interbred with a few isolated African populations of H. sapiens. When analyzing the human genome on a population level, at least 20% of the Neanderthal genome is found in the genome of modern humans of European descent. No one individual has all 20%; rather, any given person of European descent has about 1% to 4%. Researchers have speculated that certain Neanderthal genes may have provided a survival advantage, and that may explain why they have been retained in particular human populations. For example, a group of related proteins called keratins form filaments that play a role in the formation of human skin, hair, and nails. Such filaments may differ among populations that have evolved in a warm climate versus a cold one. Some alleles of keratin genes encode keratins that provide better insulation, a trait that is advantageous in cold climates. In people of European descent, genes that encode keratins are often of Neanderthal origin. This observation is consistent with the idea that some Neanderthal alleles may have helped European H. sapiens adapt to colder European environments.



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30°N

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Figure 26.22  A simplified model for the origin and spread of Homo sapiens throughout the world.  This map, based on differences of mtDNA throughout current members of the world’s population, suggests Homo sapiens originated in East Africa. About 100,000 years ago, the species spread into the Middle East and from there to Europe, Asia, Australia, and the Americas. Core Skill: Modeling  The goal of this modeling challenge is to revise the model shown in Figure 26.22 to account for recent data indicating that some modern Africans have a small amount of Neanderthal DNA. Modeling Challenge: As discussed in this section, between 1% and 4% of the DNA of modern humans of European descent is derived from that of Neanderthals. Though most modern humans of African descent do not carry Neanderthal DNA, recent evidence has shown that some of them carry a very small amount. Assuming that the presence of this Neanderthal DNA is not due to recent interbreeding between modern humans of European and African descent, revise the model shown in Figure 26.22 to account for the observation.

On the downside, scientists also speculate that Neanderthals carried an allele of a gene involved with fatty acid uptake that helped them store fat better than H. sapiens. Such a gene was an advantage for a Neanderthal lifestyle in which hunter-gatherers gorged on prey and then went for days without eating. However, in modern humans, fat storage can put them at risk for developing various diseases, such as type 2 diabetes mellitus. In certain human populations, particularly native Americans and those of Latin American descent, this Neanderthal allele is fairly common. Some people are heterozygous, carrying one allele that is derived from the Neanderthal genome and one from the H. sapiens genome. Such individuals are 20% more likely to develop type 2 diabetes compared to people who are homozygous for the H. sapiens allele. Furthermore, people who are homozygous for the Neanderthal allele are 40% more likely to develop diabetes.

Are Human Populations Still Evolving? As discussed in Chapter 23, natural selection is the process by which individuals with greater reproductive success are more likely to pass

their genes to future generations. Natural selection results in evolution. (Other processes, such as genetic drift, can also promote evolutionary change.) One factor that often plays a role in natural selection is the environment. Various types of environmental factors such as temperature, predators, and food sources can affect reproductive success and thereby cause a population to evolve in a particular direction. For example, a prolonged decrease in temperature may favor the survival of mammals with thicker fur, a trait that will increase in frequency over the course of many generations. Modern humans have great control over their environment. They live in dwellings where they can control the temperature, they can largely avoid predators, and they usually don’t rely entirely on locally grown food for their survival. For such reasons, the impact of the natural environment on the evolution of human populations may have lessened compared to its impact on humans that lived long ago. Even so, human evolution via natural selection is still occurring. For example, we continue to evolve genetic resistance to infectious diseases. The bubonic plague of the 14th century killed about one-third of the Asian and European populations, yet many people survived and passed on alleles that confer greater resistance to this deadly disease.

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As another example, eye color in certain human populations has also changed in recent times. Over 10,000 years ago, all or nearly all humans had brown eyes. About 10,000 years ago, someone who lived near the Baltic Sea inherited a mutation that resulted in blue eyes in the homozygous state. In 2008, researchers discovered that this mutation decreases the expression of the Oca2 gene, which encodes a protein that is needed for the production of melanin pigment in the iris and other parts of the body. The frequency of this allele increased, especially in northern Europe (Figure 26.24), and by about 3,000 years ago, blue eyes had spread across Europe. Why did the frequency of blue eyes increase in such a rapid fashion in human populations? The dramatic rise in blue eye color suggests that natural selection was playing a role, but researchers have yet to come up with a definitive answer regarding its selective advantage. One possible explanation has to do with vitamin D deficiency. Vitamin D is an important human vitamin that the body can produce only if there is skin exposure to the UV rays in sunlight. People living in northern latitudes are exposed to much less sunlight compared to those living nearer the equator, putting them at greater risk for vitamin D deficiency. A decrease in melanin synthesis not only affects eye color (brown to blue) but also results in lighter skin, which more easily absorbs UV rays. Therefore, one hypothesis for the spread of blue eyes (and lighter skin) through the human population is that it may have enabled humans to avoid the harmful health effects of vitamin D deficiency, which includes weakness and bone abnormalities. In this scenario, natural selection acted on skin color, and the eye color phenotype increased due to its association with a lighter skin color.

Similarly, alleles that confer resistance to malaria are becoming more common in certain African populations. A classic example of recent human evolution is the ability to digest lactose, a sugar found in milk. In most human populations, the ability to readily digest lactose is lost after the age when babies are weaned from their mother’s milk. After weaning, lactose becomes indigestible to most people and they suffer bloating, abdominal cramps, flatulence, diarrhea, nausea, or vomiting if they eat or drink dairy products. However, the ability to consume dairy products may have provided a survival advantage as people began to domesticate cows, sheep, and goats. In human populations where such domestication took place, the ability to digest lactose, called lactose tolerance, is expected to increase in frequency due to natural selection if it provides people with greater reproductive success. Recent studies suggest that mutations that confer lactose tolerance arose several thousand years ago in a few different places. The frequency of this mutation increased dramatically over the past few thousand years in populations where dairy products are commonly consumed. The genetic mutation for digesting lactose after weaning is now carried by most northern Europeans. Lactose intolerance is less common in this geographical region (Figure 26.23). For this population, the trait is linked to a single mutation that affects the expression of the lactase gene, which encodes an enzyme that is needed to digest lactose. The mutation prevents the gene from being turned off after weaning. Lactose tolerance has also been found in other populations, such as Africa and the Middle East, but these mutations occurred independently of the one that is usually found in lactose-tolerant people of European descent.

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Figure 26.23  The frequency of lactose intolerance in human populations.  This map emphasizes lactose intolerance, which is the inability to digest lactose after weaning. In contrast, most northern Europeans can digest the sugar lactose found in dairy products; they are lactose tolerant.



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Baltic Sea

80% or more (a) Blue eye color

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Figure 26.24  Blue eye color and its spread throughout Europe.  (a) In humans, blue eye color is due to a lack of melanin in the iris. This mutation probably appeared only about 10,000 years ago. (b) Many people in western and northern Europe have blue eyes due to the spread of this single mutation that originated in someone living near the Baltic Sea. Note: The indicated percentages include blue eye color and other light eye colors, such as green. a: ©harpazo_hope/Getty Images

Modern Humans Show Relatively Little Genetic Variation Yet Exhibit a Significant Amount of Phenotypic Variation Looks can be deceiving. If you take a plane ride around the world and make stops in Japan, Nigeria, Norway, Brazil, and Australia, you might get the impression that the human species is genetically diverse (Figure 26.25). The physical differences among humans in many parts of the globe are striking. To assess the level of genetic variation, the 1000 Genomes Project was launched in January 2008; it is an international research effort to establish the level of human genetic

(a) Japan

(b) Nigeria

(c) Norway

variation. By 2015, this project had sequenced the genomes of over 2,500 people from around the world and compared those sequences to each other. The results indicate that, genetically speaking, humans are very, very similar to each other. Our level of genetic variation is lower than most species of mammals whose genomes have been sequenced, and it is even lower than the variation within certain fruit fly species. This may seem surprising; if you compared two fruit flies of the same species to each other, they would probably look very similar! Most human genetic variation is in the form of single nucleotide polymorphisms (SNPs), which are places where two humans’ genomes differ at a single base pair (see Chapter 23). DNA

(d) Brazil

(e) Australia

Figure 26.25  Examples of human phenotypic variation in different parts of the world.  The women seen here are from (a) Japan, (b) Nigeria, (c) Norway, (d) Brazil, and (e) Australia. They are genetically very similar even though they look somewhat different. a: ©William Perugini/123RF; b: ©Filipe Frazao/Shutterstock; c: ©Andrea Magugliani/Alamy Stock Photo; d: ©Daniel Ernst/Alamy Stock Photo; e: ©David Freund/Getty Images

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sequencing allows researchers to identify sites where two people’s genomes differ. The data have revealed that greater than 99.9% of those differing sites are due to SNPs. If you compared your DNA with that of any unrelated person, you would probably find about 4.5 million SNP sites where your SNP was different from his or hers. This might sound like a lot, but consider that your genome is 3 billion base pairs long. If 4.5 million SNP differences occur between two people, this amounts to a genome difference of only 0.15%. This difference is much less than 1%! Furthermore, this very low value of genetic variation is not greatly affected by the pairs of people who are analyzed. Let’s suppose you compared the SNPs between two people of Japanese descent and compared the SNPs between a person of Japanese descent and a person of northern European descent. Both comparisons would show a low level of SNP variation, around 0.15%. The value for the first pair of people (Japanese and Japanese) would probably be a little lower (say, 0.14%), and that for the other pair (Japanese and northern European) might be a little higher (say, 0.16%), but both pairs would be remarkably similar. Genetic variation in human populations is very low and most of it occurs within all populations. Relatively little additional genetic variation is observed when comparing individuals from populations that are geographically separated. Why is the genetic diversity of our species low? Various factors are involved. First, Homo sapiens has not been around that long. Even though 200,000 years might seem like a long time, humans have a long generation time, and evolution occurs over the course of generations. Second, until recently, human populations have been relatively small. About 10,000 years ago, the human population size is estimated to have been about 5 million. Small populations tend to be less genetically diverse than larger ones. Although the human population has grown enormously over the past few centuries, this expansion is very recent on an evolutionary timescale. How do we explain the disparity between a low level of genetic variation and a seemingly higher level of phenotypic diversity? The answer is not entirely understood, but it may be related to the traits that influence our perception of diversity. Some of the traits that are most visually obvious, such as eye and skin color, may be dramatically influenced by natural selection even though they involve changes in a relatively small number of genes. For example, we have already considered how blue eye color and light skin color spread rapidly throughout Europe, and this phenotypic change involved a mutation in a single gene. This observation underscores how our visual perception of diversity may be biased by traits not rooted in major genetic differences.

Summary of Key Concepts ∙∙ Life began on Earth between 4.0 and 3.5 bya (Figure 26.1).

26.1        The Fossil Record ∙∙ Fossils, which are preserved remnants of past life-forms, are formed in sedimentary rock (Figure 26.2). ∙∙ Radiometric dating is one way of estimating the age of a fossil. Fossils provide an extensive record of the history of life on Earth, though the record is incomplete (Figure 26.3, Table 26.1).

26.2  History of Life on Earth ∙∙ The geological timescale, which is divided into four eons and many eras and periods, charts the major events that occurred during the history of life on Earth (Figure 26.4). ∙∙ Both the emergence of new species and mass extinctions are correlated with changes in temperature, amount of O2 in the atmosphere, landmass locations, floods and glaciation, volcanic eruptions, and meteorite impacts (Figure 26.5). ∙∙ During the Archaean eon, bacteria and archaea arose. The proliferation of cyanobacteria led to a gradual rise in O2 levels (Figure 26.6). ∙∙ Eukaryotic cells arose during the Proterozoic eon. This origin involved a union between bacterial and archaeal cells that is hypothesized to have been endosymbiotic. The origins of mitochondria and chloroplasts were also the result of endosymbiosis (Figure 26.7). ∙∙ Multicellular eukaryotes arose about 1.5 bya during the Proterozoic eon. Multicellularity now occurs via cell division and the adherence of the resulting cells to each other. A multicellular organism can have multiple cell types (Figure 26.8). ∙∙ The first animal showing bilateral symmetry emerged toward the end of the Proterozoic eon (Figure 26.9). ∙∙ The Phanerozoic eon is subdivided into the Paleozoic, Mesozoic, and Cenozoic eras. During the Paleozoic era, invertebrates greatly diversified, particularly during the Cambrian explosion, and the land became colonized by plants and animals. Terrestrial vertebrates, including tetrapods, became more diverse (Figures 26.10– 26.12). ∙∙ Dinosaurs were prevalent during the Mesozoic era, particularly during the Jurassic period. Mammals and birds also emerged (Figures 26.13, 26.14). ∙∙ During the Cenozoic era, mammals diversified, and flowering plants became the dominant plant species. The first hominoids emerged approximately 7 mya. Homo sapiens, our species, first appeared about 200,000 years ago.

26.3  Human Evolution ∙∙ Many defining characteristics of primates relate to their treedwelling nature; these include grasping hands, large brain, nails instead of claws, and binocular vision (Figures 26.15–26.17). ∙∙ About 7 mya in Africa, a lineage that led to humans began to separate from other primate lineages. A key characteristic of hominins (extinct and modern humans) is bipedalism. Human evolution can be visualized like a tree, with a few hominin species coexisting at the same point in time, some eventually going extinct, and some giving rise to other species (Figures 26.18–26.21). ∙∙ Data from the sequencing of human mitochondrial DNA suggest that H. sapiens originated in East Africa. From there, H. sapiens spread to Asia and then to all other parts of the globe (Figure 26.22). ∙∙ Human evolution has involved interbreeding between closely related species, such as H. sapiens and the Neanderthals and the Denisovans. ∙∙ Evidence that human populations are still evolving includes traits such as lactose tolerance and blue eye color (Figures 26.23, 26.24). ∙∙ Modern humans show relatively little genetic variation yet exhibit a significant amount of phenotypic variation (Figure 26.25).



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Assess & Discuss Test Yourself 1. The movement of landmasses that has changed their positions, shapes, and association with other landmasses is called a. glaciation. b. Pangaea. c. continental drift. d. biogeography. e. geological scale. 2. Paleontologists estimate the dates of fossils using a. the layer of rock in which the fossils are found. b. analysis of radioisotopes found in nearby igneous rock. c. the complexity of the body plan of the organism. d. all of the above. e. a and b only. 3. The fossil record does not give us a complete picture of the history of life on Earth because a. not all past organisms have become fossilized. b. only organisms with hard skeletons can become fossilized. c. fossils of very small organisms have not been found. d. fossils of early organisms are located too deep in the crust of the Earth to be found. e. All of the above are true. 4. The endosymbiosis hypothesis explaining the evolution of eukaryotic cells is supported by a. DNA-sequencing analysis comparing bacterial genomes, mitochondrial genomes, and eukaryotic nuclear genomes. b. naturally occurring examples of endosymbiotic relationships between bacterial cells and eukaryotic cells. c. the presence of DNA in mitochondria and chloroplasts. d. all of the above. e. a and b only. 5. Which of the following evolutionary innovations was advantageous for survival in a terrestrial environment?  a. the amniotic egg in animals b. the seed in plants c. the shell in marine invertebrates d. all of the above e. both a and b  6. Which of the following explanations of multicellularity in eukaryotes is seen in the development of complex, multicellular organisms today? a. endosymbiosis b. aggregation of cells to form a colony c. division of cells followed by cell adhesion of the resulting cells d. multiple cell types aggregating to form a complex organism e. None of the above phenomena are evident today. 7. The earliest fossils of vascular plants were formed during the _________ period. a. Ordovician b. Silurian c. Devonian d. Triassic e. Jurassic

8. The first mammal arose during the _______ period. a. Triassic b. Jurassic c. Cretaceous d. Tertiary e. Quaternary 9. The appearance of the first hominoids dates to the __________ period. a. Triassic b. Jurassic c. Cretaceous d. Tertiary e. Quaternary 10. Which of the following statements regarding modern humans, H. sapiens, is false?  a. Some modern humans have a small amount of DNA that is derived from Neanderthals. b. Some modern humans have a small amount of DNA that is derived from Denisovans. c. H. sapiens probably arose in Africa. d. Modern humans are very genetically diverse compared to most other species. e. Modern humans are still evolving. 

Conceptual Questions 1. How are the ages of fossils determined? In your answer, you should discuss which types of rocks are analyzed and explain the concepts of radiometric dating and half-life.   2. How was the phenomenon of endosymbiosis important in the evolution of the first eukaryotic cells?   3.

Core Concept: Evolution  Describe two examples in which changes in the global climate affected the evolution of species.

Collaborative Questions 1. Discuss the factors that have contributed to the dramatic changes in lifeforms since the origin of life on Earth about 3.5 to 4 billion years ago. 2. Discuss how the human body has changed since the human lineage diverged from other primates about 7 million years ago.

UNIT V

DIVERSITY Biological diversity, also called biodiversity, encompasses the variety of living things that exist now, as well as all the life-forms that lived in the past. Knowing about species that lived in the past and how they are related to modern microorganisms, plants, and animals aids our comprehension of evolution, which is the source of biological diversity. Knowing about the many different kinds of modern organisms also helps us understand how life-forms are structured in ways that allow them to function differently in nature (as discussed in Units VI and VII) and how species interact with each other and with their environments (described in Unit VIII). This unit begins with bacteria and archaea, the oldest, simplest, and most numerous of Earth’s life-forms, whose prominent ecological roles are described in Chapter 27. In Chapter 28, we survey the surprisingly diverse protists, which affect humans and other organisms in many important ways. The mysteries of the fungi, essential to the brewing and baking industries as well as to ecological stability, are revealed in Chapter 29. These first three chapters of the unit provide background essential to understanding microbiomes, systems of microbes that occur on and around us, explained in Chapter 30. Next, Chapter 31 explores the evolutionary origin of the first plants, a process that explains the features and functions of the seed plants that are vital sources of human food, fiber, and medicine, as described in Chapter 32. An overview of the diversity and evolutionary history of the animals in Chapter 33 provides the basis for exploring the simplest animals, the invertebrates, in Chapter 34. More complex vertebrate animals, including humans and their closest relatives, are the focus of Chapter 35.

27 28 29 30

31 32

The following Core Concepts and Core Skills will be emphasized in this unit: • Structure and Function: Many of Earth’s present and past species have bodies consisting of only one or a few cells, whereas other species display more complex bodies composed of many cells. • Evolution: This unit provides many examples of the concept that all Earth species are related by an evolutionary history. • Connections: Chapter 31  explains how ancient plants dramatically changed the composition of Earth’s atmosphere, and how their modern descendants continue to influence today’s atmosphere and climate. • Process of Science: Every chapter has a Feature Investigation that illustrates how we understand ways in which diversity is important. • Modeling: Every chapter has a Modeling Challenge to refine this important skill. 

34 33

35 (27): ©Dr. Jeremy Burgess/SPL/Science Source; (28): ©Photographs by H. Cantor-Lund reproduced with permission of the copyright holder Freshwater Biological Association and J. W. G. Lund; (29): ©Brian Lightfoot/ naturepl.com; (30): ©Eye of Science/Science Source; (31): ©Craig Tuttle/ Corbis/Getty Images; (32): ©Gallo Images/Corbis/Getty Images; (33): ©John Visser/Photoshot; (34): ©Georgie Holland/agefotostock; (35): ©Gary Meszaros/Science Source

CHAPTER OUTLINE 27.1 Diversity and Evolution 27.2 Structure and Movement 27.3 Reproduction 27.4 Nutrition and Metabolism 27.5 Ecological Roles and Biotechnology Applications Summary of Key Concepts Assess & Discuss

O

ne late-summer afternoon, a veterinarian was about to close the clinic at the end of a busy day when an emergency case, a very sick dog, arrived. The dog had collapsed after taking a lakeside walk with its owner. Responding to the vet’s questions, the owner reported that the thirsty dog had consumed lake water thick with blue-green material. The vet deduced that the bluegreen substance represented a large population of toxin-producing bacteria and that drinking the lake water had poisoned the dog—a conclusion that aided treatment. Bacteria and archaea are examples of microorganisms, organisms so small they can usually be seen only with the use of a microscope. However, in phosphorus-rich bodies of water, some species of photosynthetic bacteria known as cyanobacteria grow rapidly into large, visible populations—known as blooms—that color the water blue-green or cyan (see the chapter opening photo). The individual cells release small amounts of toxins that help to keep small aquatic animals from eating them, but when blooms occur, toxins can rise to levels that poison humans, pets, livestock, and wildlife. Consequently, public health authorities often warn people that they should not swim in waters with visible blue-green blooms and should not allow pets and livestock to drink such water. People can prevent the formation of harmful cyanobacterial blooms by reducing the flow of phosphorus-rich fertilizers, manure, and sewage into bodies of water. Despite the harmful effects of some species, cyanobacteria provide important benefits to humans and other organisms, such as producing atmospheric oxygen. Many cyanobacteria also have the ability to convert abundant but inert atmospheric nitrogen gas into ammonia, which algae and plants can use to synthesize amino acids and proteins. This process enriches nutrient-poor soils, particularly in wet paddy fields where rice is grown in many regions of the world, thereby helping to provide food for billions of people. In this chapter, we will survey the diversity, structure, reproduction, metabolism, and ecology of archaea and bacteria. We

Archaea and Bacteria

27 Cyanobacterial bloom. A visible growth of cyanobacteria, called a bloom, gives a blue-green coloration to this lake. ©Dr. Jeremy Burgess/ SPL/Science Source

Core Skill: Science and Society  Cyanobacterial blooms affect society by poisoning humans and organisms that people value. However, cyanobacteria can also have a positive impact by generating nitrogen-containing molecules that serve as fertilizer in soil and water.

will see how bacteria and archaea were important to the evolution of eukaryotic cells and other events in Earth’s ancient history. The importance of some bacterial phyla to everyday human life illustrates the concept that relatively few bacterial species are harmful, and many benefit us. We will also learn how horizontal gene transfer increases the diversity of microbial genomes and how this process affects human societies. Our survey will reveal additional surprising ways in which these microorganisms affect the lives of humans and the world we inhabit.

CHAPTER 27

27.1 Diversity and Evolution Learning Outcomes:

1. CoreSKILL » Make a drawing that shows the evolutionary relationship among the domains Archaea, Bacteria, and Eukarya. 2. Explain how many species of archaea are able to grow in extreme habitats. 3. Discuss the medical, environmental, and evolutionary importance of cyanobacteria and proteobacteria. 4. List common mechanisms of horizontal gene transfer.

Life on Earth is classified into three domains. Members of the domain Eukarya—animals, plants, fungi, and protists—have cells with a eukaryotic structure. In contrast, Archaea (often referred to as simply archaea) and Bacteria (often referred to as simply bacteria) are

domains of microorganisms whose cells have a prokaryotic structure. Archaeal and bacterial cells lack nuclei with porous envelopes and other cellular features typical of eukaryotes (see Chapter 4). Although archaea and bacteria are sometimes collectively termed prokaryotes, such an aggregation is not a monophyletic group, but rather a paraphyletic group—one that does not include all of the descendants of a single common ancestor. That’s because domain Archaea is more closely related to domain Eukarya than either is to domain Bacteria (Figure 27.1). Even so, archaea and bacteria display some common features in addition to a prokaryotic cell structure. Archaea and bacteria include the smallest known cells and are the most abundant organisms on Earth. About half of Earth’s total biomass consists of an estimated 1030 individual bacteria or archaea. Just a pinch of garden soil can contain 2 billion prokaryotic cells, and about a million occur in 1 mL of seawater. Archaea and bacteria

Lokiarchaeota

Eukarya

Korarchaeota

Thaumarchaeota

Euryarchaeota

Proteobacteria

Planctomycetes

Chlamydiae

Archaea

Bacteroidetes

Spirochaetes

Cyanobacteria

Actinobacteria

Firmicutes

Chloroflexi

Deinococcus-Thermus

Bacteria

Crenarchaeota

562

Mitochondria

Plastids

KEY Phyla Examples of horizontal gene transfer

Figure 27.1  Evolutionary relationships among selected phyla of Bacteria and Archaea to each other and to Eukarya.  Bacteria and Archaea

are the two domains featuring prokaryotic cells. Eukarya is the domain consisting of organisms whose cells are eukaryotic. Archaea, particularly the phylum Lokiarchaeota and close relatives, is more closely related to Eukarya than is Bacteria. Each domain has diversified into multiple phyla (not all are shown here, for simplicity). Many cases of horizontal gene transfer among phyla and domains are known. Some of these are depicted with blue bars and include the acquisition of mitochondria and chloroplasts by eukaryotes.



ARCHAEA AND BACTERIA 563

live in nearly every conceivable habitat, including extremely hot or salty waters that support no other life, and they are also Earth’s most ancient organisms, having originated more than 3 bya. Their long evolutionary history and varied habitats have resulted in extraordinary metabolic diversity. Today, the many millions of species of archaea and bacteria collectively display more diverse metabolic processes than occur in any other group of organisms. Many of these metabolic processes are important on a global scale, influencing Earth’s climate, atmosphere, soils, and water quality, as well as human health and technology. Most archaea and many bacteria have CRISPR-Cas systems that combat invading viruses and have proven useful in genetic engineering technology (see Chapter 21). In the past, microbiologists studied diversity by isolating archaea and bacteria from nature and growing cultures in the laboratory to observe variation in cell structure and metabolism. Today, biologists also use molecular techniques to assess diversity of archaea and bacteria and infer metabolic functions. Such molecular studies reveal that archaea and bacteria are vastly more diverse than was previously realized. In this section, we will first survey the major kingdoms and phyla of the domains Archaea and Bacteria and then explore how horizontal gene transfer—the transfer of genes between different species—has influenced their evolution.

Domain Archaea Was Ancestral to Domain Eukarya Organisms classified in the domain Archaea, referred to as archaea, share a number of features with those classified in Eukarya,

Peptidoglycan cell wall

suggesting common ancestry. For example, histone proteins are typically associated with the DNA of both archaea and eukaryotes, but they are absent from most bacteria. Archaea and eukaryotes share more than 30 ribosomal proteins that are not present in bacteria, and archaeal RNA polymerases are closely related to their eukaryotic counterparts. However, archaea possess distinctive membrane phospholipids, which are formed with ether bonds; in contrast, ester bonds characterize the membrane phospholipids of bacteria and eukaryotes (Figure 27.2). Ether-bonded membranes are resistant to damage by heat and other extreme conditions, which helps explain why many archaea are able to grow in extremely harsh environments. Also, archaea have isoprene chains instead of fatty-acid chains in their membranes. Another key difference is the biochemical composition of the cell wall. In most bacteria, the cell wall is composed of carbohydrates that are cross-linked by peptides, forming a substance called peptidoglycan, whereas the cell wall of archaea is usually a surface layer of proteins. Some bacterial species also have an outer envelope (membrane) composed of lipids and polysaccharides. Though many archaea occur in soils and surface ocean waters in moderate conditions, diverse archaea occupy habitats with very high salt content, acidity, methane levels, or temperatures that would kill most bacteria and eukaryotes. Organisms that occur primarily in extreme habitats are known as extremophiles. One example is the methane producer Methanopyrus, which grows best at deep-sea thermal vent sites where the temperature is 98°C. At this temperature, the proteins of most organisms would denature, but those of Methanopyrus are resistant to such damage. Methanopyrus is so adapted to its extremely hot environment that it cannot grow when the temperature is less than 84°C. Such archaea are known as hyperthermophiles.

Cell membrane

Plasma membrane Outer envelope 1 μm

(a) Bacterial cell O D-Glycerol C O CH2 C O C H O O Unbranched fatty acids O P O– H2C O– Ester bond

(c) Ester-bonded phospholipid

Protein cell wall

10.8 μm

(b) Archaeal cell Ether bond C C Branched isoprene chains

(d) Ether-bonded phospholipid

O– H2C

O C H O CH2

O P O– O L-Glycerol

Figure 27.2  Bacteria and Archaea.  (a) Bacteria and (b) archaea both have prokaryotic cell structure, but (c) bacterial membrane lipids are formed with ester linkages, whereas (d) archaeal membrane lipids feature ether linkages, which are more stable under extreme environmental conditions. As shown in the transmission electron microscopic (TEM) images in (a) and (b), most bacteria feature a cell wall made of a material known as peptidoglycan and are often enclosed by an outer envelope, whereas archaea lack these features. Most archaea have outer coverings made of protein. a: ©Linda Graham; b: ©Eye of Science/Science Source

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Some archaea prefer habitats having both high temperatures and extremely low pH. For example, the archaeal genus Sulfolobus was discovered in samples taken from sulfur hot springs having a pH of 3 or lower. Archaea help biologists better understand the origin of life, the origin of eukaryotes, how life on Earth has evolved in extreme environments, and what kinds of extraterrestrial life might exist. The domain Archaea includes several phyla, including Lokiarchaeota, Korarchaeota, Thaumarchaeota, Crenarchaeota, and Euryarchaeota (see Figure 27.1). Lokiarchaeota and close relatives named for Norse deities are collectively known as the Asgard superphylum and are particularly closely related to eukaryotes (Eukarya). Members of Korarchaeota are primarily known from hot springs. Thaumarchaeota species are widespread in terrestrial and aquatic environments, and include archaea that oxidize ammonia, making them important  in global nitrogen cycling. Crenarchaeota includes organisms that live in extremely hot or cold habitats and also some that are widespread in aquatic and terrestrial habitats. Early-diverging Euryarchaeota includes some hyperthermophiles, diverse methane producers, and extreme halophiles—species able to grow in higher than usual salt concentrations.

Domain Bacteria Includes Cyanobacteria, Proteobacteria, and Many Other Phyla Domain Bacteria is considerably more diverse than Archaea. Molecular studies suggest the existence of 50 or more bacterial phyla, though many are poorly characterized. Though some members of domain

Table 27.1

Bacteria live in extreme environments, most favor moderate conditions. Many bacteria form symbiotic associations with eukaryotes and are thus of concern in medicine and agriculture.  The characteristics of 10 prominent bacterial phyla are briefly summarized in Table 27.1. Bacterial phyla mentioned later in this chapter because of their medical, ecological, or evolutionary significance include Firmicutes, Bacteroidetes, Chlamydiae, Planctomycetes, Spirochaetes, Actinobacteria, Chloroflexi, and Deinococcus-Thermus. Because Cyanobacteria and Proteobacteria are particularly diverse and relevant to eukaryotic cell evolution, global ecology, and human affairs, we will consider them in greater detail next. Cyanobacteria  The phylum Cyanobacteria contains photosynthetic bacteria that are abundant in fresh waters, oceans, and wetlands and on the surfaces of arid soils. Cyanobacteria are named for the typical blue-green (cyan) coloration of their cells. Blue-green pigmentation results from the presence of photosynthetic pigments called phycobilins that help chlorophyll absorb light energy. Cyanobacteria are the only bacteria known to generate oxygen as a product of photosynthesis. Ancient cyanobacteria produced Earth’s first oxygen-rich atmosphere, which allowed the eventual rise of eukaryotes. The chloroplasts of eukaryotic algae and plants were derived from cyanobacteria. Cyanobacteria display the greatest diversity in body type found among bacterial phyla (Figure 27.3). Some occur as single cells called unicells (Figure 27.3a); others form colonies of cells held

Representative Bacterial Phyla

Phyla

Characteristics

Firmicutes

Diverse Gram-positive bacteria, some of which produce endospores. The disease-causing Clostridium difficile is an example.

Bacteroidetes

Includes representatives with diverse metabolic processes; some are common in the human intestinal tract, and others are primarily aquatic.

Chlamydiae

Notably tiny, obligate intracellular parasites. Some cause eye disease in newborns or sexually transmitted diseases.

Planctomycetes

Reproduce by budding rather than binary fission; cell walls lack peptidoglycan; cytoplasm may contain nucleus-like bodies, and endocytosis may occur.

Spirochaetes

Motile bacteria having distinctive corkscrew shapes, with flagella held close to the body. They include the pathogens Treponema pallidum, the agent of syphilis, and Borrelia burgdorferi, which causes Lyme disease.

Actinobacteria

Gram-positive bacteria producing branched filaments; many form spores. Mycobacterium tuberculosis, the agent of tuberculosis in humans, is an example. Actinobacteria are notable antibiotic producers; over 500 different antibiotics are known from this group. Some fix nitrogen in association with plants.

Chloroflexi

Known as the green nonsulfur bacteria; conduct photosynthesis without releasing oxygen (anoxygenic photosynthesis).

Deinococcus-Thermus

Extremophiles. The genus Deinococcus is known for high resistance to ionizing radiation, and the genus Thermus inhabits hot springs. Thermus aquaticus has been used in commercial production of Taq polymerase, an enzyme used in polymerase chain reaction (PCR), an important procedure in molecular biology laboratories.

Cyanobacteria

Includes the oxygen-producing photosynthetic bacteria (some are also capable of anoxygenic photosynthesis). Photosynthetic pigments include chlorophyll a and phycobilins, which often give cells a blue-green pigmentation. Occur as unicells, colonies, unbranched filaments, and branched filaments. Many of the filamentous species produce specialized cells: dormant akinetes and heterocytes in which nitrogen fixation occurs. In waters having excess nutrients, cyanobacteria produce blooms and may release toxins harmful to the health of humans and wild and domesticated animals.

Proteobacteria

A very large group of Gram-negative bacteria, collectively having high metabolic diversity. Includes many species important in medicine, agriculture, and industry such as Agrobacterium tumifaciens, Escherichia coli, and Haemophilus influenzae. Myxococcus xanthus is a Gram-negative bacterium that is able to glide across surfaces, forming swarms of thousands of cells. This behavior aids feeding by concentrating digestive enzymes secreted by the bacteria. When food is scarce, the swarms form tiny tree-shaped structures from which tough spores disperse. By this means, cells move to new, food-rich places.



ARCHAEA AND BACTERIA 565

250 μm

0.1 mm (b) Colony of cells

(a) Unicells

Figure 27.4  Agrobacterium tumifaciens infection.  This 50 μm

700 μm (c) Unbranched filaments

proteobacterium causes cancer-like tumors to grow on plants (see the arrows). ©Linda Graham

(d) Branched filaments

Figure 27.3  Major body types found in the phylum

Cyanobacteria.  (a) The genus Chroococcus occurs as unicells. (b) The genus Merismopedia forms a flat colony of cells held together by mucilage. (c) The genus Oscillatoria forms an unbranched filament. (d) The genus Stigonema forms a branched filament having a mucilage sheath; sunscreen compounds that protect the cells from damage by ultraviolet (UV) radiation cause the brown color of the sheath. a: ©Linda Graham; b: ©Michael Abbey/Science Source; c: ©Sinclair Stammers/SPL/Science Source; d: ©Lee W. Wilcox

together by a thick gluey substance called mucilage (Figure 27.3b), and many cyanobacteria form filaments in which cells are attached end-to-end (Figure 27.3c) or filaments that branch (Figure 27.3d). Some of the filamentous cyanobacteria display hallmarks of multicellularity: cellular attachment, specialized cells, intercellular chemical communication, and programmed cell death. Proteobacteria  Though Proteobacteria share molecular and cellwall features, this phylum displays amazing diversity of form and metabolism. Genera of this phylum are classified into five major subgroups: alpha (α), beta (β), gamma (γ), delta (δ), and epsilon (ε). As we saw in Chapter 26 (refer back to  Figure 26.7), the ancestry of mitochondria can be traced to the α-proteobacteria, which also include several genera noted for mutually beneficial relationships with animals and plants. For example, Rhizobium and related genera of α-proteobacteria form nutritionally beneficial associations with the roots of legume plants such as beans and peas and are thus agriculturally important. Another α-proteobacterium, Agrobacterium

tumifaciens, causes destructive cancer-like tumors called galls to develop on susceptible plants, including grapes and ornamental crops (Figure 27.4). A. tumifaciens induces gall formation by injecting DNA into plant cells. This property has allowed researchers to use the bacterium in the production of transgenic plants, which are plants that carry genes from another species. The genus Nitrosomonas, soil inhabitants important in the global nitrogen cycle, represents the β-proteobacteria. Neisseria gonorrhoeae, the agent of the sexually transmitted disease gonorrhea, is one of the γ-proteobacteria. Vibrio cholerae, another γ-proteobacterium, causes cholera epidemics when drinking water becomes contaminated with animal waste during floods and other natural disasters. The γ-proteobacteria Salmonella enterica and Escherichia coli strain O157:H7 also cause human disease, so food and water are widely tested for their presence. The δ-proteobacteria include the colonyforming myxobacteria and predatory bdellovibrios, which drill through the cell walls of other bacteria in order to consume them. Helicobacter pylori, which causes stomach ulcers, belongs to the ε-proteobacteria.

Horizontal Gene Transfer Influences the Diversity and Evolution of Archaea and Bacteria As we have seen, Bacteria and Archaea are domains of life displaying an amazing level of diversity. One reason for this diversity is horizontal gene transfer, the process in which an organism receives genetic material from another organism without being the offspring of that organism. Horizontal gene transfer is common among archaea and bacteria, occurring most frequently between species that are

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closely related or that live in close proximity. Evolutionary change due to horizontal gene transfer contrasts with vertical evolution, in which gene transfer occurs from parent to progeny. During vertical evolution, genetic changes occur in a series of ancestors that form a lineage; species evolve from pre-existing species by the accumulation of mutations.  Horizontal gene transfer can result in large genetic changes that confer new metabolic capacities. For example, at least 17% of the genes present in the common human gut inhabitant E. coli were horizontally transferred from other bacteria. Studies of nearly 200 genomes have revealed that about 80% of prokaryotic genes have been involved in horizontal transfer at some point in their history. Genes also move among the bacterial, archaeal, and eukaryotic domains. For example, salt-tolerant (halophytic) archaea originated after an ancient horizontal transfer of more than a thousand genes from bacteria. Horizontal gene transfer can occur between different bacterial species via transduction, transformation, and conjugation, as discussed in Chapter 19. In addition, horizontal gene transfer occurs by means of endosymbiosis, the process in which one species— the endosymbiont—lives in the body or cells of another species— the host. For example, certain γ-proteobacteria occupy the cells of β-proteobacterial hosts, which themselves live within insect cells. Such close proximity increases the odds that gene exchange will occur between distantly related species. During the process by which the mitochondria of eukaryotic cells originated from α-proteobacteria and plastids originated from cyanobacteria (see Chapter 26), so many bacterial genes were transferred to host nuclei that modern mitochondria and chloroplasts cannot reproduce outside the host cell.

a high level of variation in cell structure and shape, surface and cellwall features, and movement.

Prokaryotic Cells Display a Surprising Degree of Complexity Although bacteria, like archaea, have a much simpler cellular organization than do eukaryotes, many prokaryotic cells display cellular structural adaptations that increase their complexity. Features of this complexity illustrate the core concept that structure determines function, partly explain why prokaryotic organisms have such high metabolic diversity, and help us understand how the first eukaryotes arose. Cyanobacteria and other photosynthetic bacteria, for example, are able to use light energy to produce organic compounds because their cells contain large numbers of thylakoids, flattened tubular membranes that grow inward from the plasma membrane (Figure 27.5). The extensive membrane surface of the thylakoids bears large amounts of chlorophyll and other components that are needed for photosynthesis. Thylakoids are also abundant in plant chloroplasts, which descended from cyanobacterial ancestors. Thylakoids enable photosynthetic bacteria and chloroplasts to take maximum advantage of light energy in their environments. Aquatic photosynthetic bacteria also commonly contain many gas vesicles. These protein-walled structures increase cell buoyancy and thus help the organisms float within well-illuminated surface waters (see Figure 27.5).

Thylakoids provide a greater surface area for chlorophyll and other molecules involved in photosynthesis.

27.2 Structure and Movement Learning Outcomes:

Thylakoids

1. Discuss the structural adaptations that have increased the complexity of prokaryotic cells. 2. Explain how mucilage influences the behavior of bacterial cells. 3. CoreSKILL » Make a drawing that shows the structural differences between Gram-positive and Gram-negative bacterial cells, and predict how these features might influence disease treatments. 4. List the different means by which prokaryotic cells can move.

Bulbnose unicorn fish (Naso tonganus) living in Australian coastal ocean waters contain cigar-shaped bacterial symbionts (Epulopiscium) whose cells are more than 600 µm long, larger than most eukaryotic cells (whose largest dimension is between 10 and 100 µm). Spherical cells of the bacterial species Thiomargarita namibiensis, which lives in African coastal regions, likewise reach record-setting sizes, some being 800 µm in diameter and large enough to be seen without a microscope. However, most bacteria (and archaea) are much smaller: a few micrometers in diameter. Small cell size limits the amount of materials that can be stored within each cell but allows much faster cell division. When nutrients are sufficient, many bacteria can divide many times within a single day. This explains how bacteria can spoil food rapidly and why bacterial infections can spread quickly within the human body. Despite their generally small size, bacteria display

Gas vesicles (cross sections)

Gas vesicles (long sections) 0.6 μm

The gas vesicles buoy this photosynthetic organism to the lighted water surface, where it often forms conspicuous scums.

Figure 27.5  Photosynthetic thylakoid membranes and

numerous gas vesicles in a cell of an aquatic cyanobacterium. 

©Norma Lang

Core Concept: Structure and Function  Thylakoids, which contain chlorophyll and other components that are needed for photosynthesis, are the locations of the light-harvesting reactions. Gas vesicles allow photosynthetic cells to float in well-lit surface waters.



ARCHAEA AND BACTERIA 567

Flagellum

Row of magnetosomes, each containing a magnetite particle 0.4 μm

Figure 27.6  Magnetosomes found in Magnetospirillum magnetotacticum. An internal row of iron-rich magnetite crystals, each enclosed by a membrane derived from the plasma membrane, functions like a compass needle, allowing this bacterium to detect the Earth’s magnetic field. This feature allows M. magnetotacticum to orient itself in space and thereby locate its preferred habitat, lowoxygen subsurface waters. These and other bacterial cells use flagella to move to more favorable locations. ©Dr. Richard P. Blakemore, University of New Hampshire

Core Skill: Connections  Look ahead to Section 44.4, which describes electromagnetic sensing by animals. What animals are like M. magnetotacticum in being able to sense and respond to magnetic fields? 

In other bacteria, plasma membrane ingrowth has generated additional intriguing adaptations—magnetosomes and nucleus-like bodies—that are sometimes described as bacterial organelles. Magnetosomes are tiny crystals of an iron mineral known as magnetite, each surrounded by a membrane. These structures occur in the bacterium Magnetospirillum and related genera (Figure 27.6). In each of these bacteria, about 15 to 20 magnetosomes occur in a row, together acting as a compass needle that responds to the Earth’s magnetic field. Magnetosomes help the bacteria to orient themselves in space and

1 μm (a) Sphere-shaped cocci (Lactococcus lactis)

11.4 μm (b) Rod-shaped bacilli (Lactobacillus plantarum)

thereby locate the submerged, low-oxygen habitats they prefer. Magnetosome development begins with invagination of the plasma membrane to form a row of spherical vesicles. If Magnetospirillum cells are grown in media having low iron levels, the vesicles remain empty. But if iron is available, a magnetite crystal forms within each vesicle. Fibrils of an actin-like protein keep the magnetosomes aligned in a row. (Recall from Chapter 4 that actin is a major cytoskeletal protein of eukaryotes.) Mutant bacteria lacking a functional form of this protein produce magnetosomes, but they do not remain aligned in a row. Instead, magnetosomes scatter around mutant cells, disrupting their ability to detect a magnetic field. Plasma membrane invaginations produce nucleus-like bodies in Gemmata obscuriglobus and other members of the bacterial phylum Planctomycetes. In G. obscuriglobus, an envelope composed of a double membrane encloses all cellular DNA and some ribosomes. Although this bacterial envelope lacks the nuclear pores characteristic of the eukaryotic nuclear envelope, it likely plays a similar adaptive role in isolating DNA from other cellular influences. G. obscuriglobus and related bacterial species are also known to accomplish endocytosis by means of membrane coat proteins similar to those present in eukaryotic cells. The cellular diversity and surprising complexity of bacterial cell structure help us to understand not only how bacteria function in nature, but also how important features of eukaryotic cells first evolved.

Prokaryotic Cells Vary in Shape Although prokaryotic cells occur in multiple forms, they have five common shapes (Figure 27.7): spheres (cocci), elongate rods (bacilli), comma-shaped cells (vibrios), and spiral-shaped cells that are either flexible (spirochaetes) or rigid (spirilli; see Figure 27.6). Cytoskeletal proteins similar to those present in eukaryotic cells control these cell shapes. For example, helical strands of an actinlike protein are responsible for the rod shape of bacilli; if this protein is not produced, bacilli become spherical in shape. Cellular shape

2.5 μm (c) Comma-shaped vibrios (Vibrio cholerae)

7.5 μm (d) Spiral-shaped spirochaetes (Leptospira sp.)

Figure 27.7  Major types of prokaryotic cell shapes. These images are scanning electron micrographs. a: ©SciMAT/Science Source; b, d: ©Dennis Kunkel Microscopy, Inc./Phototake; c: ©Media for Medical/UIG/Getty Images

Core Concept: Systems  In the case of unicellular bacteria and archaea, a single cell constitutes an entire organism.

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is an important component of bacterial function in nature. Cocci tend to have a greater surface area/volume ratio, which facilitates exchange of materials with the environment, but bacilli can often store more nutrients.

Slimy Mucilage Often Coats Cellular Surfaces Many bacteria exude a coat of slimy mucilage, sometimes called a glycocalyx, capsule, or extracellular polymeric substance (EPS). Mucilage, which varies in consistency and thickness, is composed of hydrated polysaccharides and proteins, as well as lipids and nucleic acids. A capsule helps some disease-causing bacteria evade the defense system of their host. You may recall that Frederick Griffith discovered the transfer of genetic material while experimenting with capsule-producing pathogenic strains and capsule-less nonpathogenic strains of the bacterium Streptococcus pneumoniae (refer back to Figure 11.1). The immune system cells of mice are able to destroy this bacterium only if it lacks a capsule. Mucilage plays many additional roles: holding cells together closely enough for chemical communication and DNA exchange to occur, helping aquatic species to float in water, binding mineral nutrients, and repelling attack. Pigmented slime sheaths (see Figure 27.3d) coat some bacterial filaments, helping to prevent UV damage.  Biofilms are aggregations of microorganisms that secrete adhesive mucilage, thereby gluing themselves to surfaces. Formation of a biofilm helps microbes remain in favorable locations for growth; otherwise body or environmental fluids would wash them away. A mechanism known as quorum sensing fosters biofilm formation. During quorum sensing, individual microbes secrete small molecules having the potential to influence the behavior of nearby microbes. If enough individuals are present (a quorum), the concentration of signaling molecules builds to a level that causes collective behavior. In the case of biofilms, populations of microbes respond to chemical signals by moving to a common location and producing mucilage. Biofilms are environmentally and medically important. From a human standpoint, biofilms have both beneficial and harmful consequences. In aquatic and terrestrial environments, biofilms help to stabilize and enrich sand and soil surfaces, and help form mineral deposits. Biofilms that form on the surfaces of animal tissues, however, can be harmful. Dental plaque is an example of a harmful biofilm (Figure 27.8); if allowed to remain, the bacterial community secretes acids that can damage tooth enamel. Biofilms may also develop in industrial pipelines, where the attached microbes can contribute to corrosion by secreting enzymes that chemically degrade metal surfaces.

Prokaryotic Cells Vary in Cell-Wall Structure Whether coated with mucilage or not, most prokaryotic cells possess a rigid cell wall outside the plasma membrane. Cell walls maintain cell shape and help protect against attack by viruses or predatory bacteria. Cell walls also help microbes avoid lysing in hypotonic conditions, when the solute concentration is higher inside the cell than outside. The structure and composition of bacterial cell walls are medically important. Although some archaea lack cell walls, most possess a wall composed of protein. In contrast, the polymer known as peptidoglycan,

2.3 μm

Figure 27.8  A biofilm composed of a community of microorganisms glued by mucilage to a surface.  This SEM shows a view of the top surface of dental plaque, consisting of several types of bacteria—falsely colored purple, green, and blue—attached by mucilage to a tooth surface lying beneath. ©Science Photo Library/Alamy Stock Photo

Core Skill: Modeling  The goal of this modeling challenge is to make a model for the development of a biofilm of dental plaque. Such models are proving useful in finding new ways to reduce or prevent oral disease. Modeling Challenge: Using the SEM of dental plaque shown in Figure 27.8, which illustrates the relative positions and abundances of three types of bacteria, draw a flow diagram showing several sequential stages that hypothetically model the process by which this biofilm might have developed. Your model should indicate which bacteria are most likely to have attached first (purple, green, or blue) and which most recently.

lacking in archaea, is an important component of most bacterial cell walls. Peptidoglycan is composed of carbohydrates that are crosslinked by peptides. Bacterial cell walls occur in two major forms that differ in thickness of the peptidoglycan layer, staining properties, and response to antibiotics. Bacteria having these chemically different walls are called Gram-positive or Gram-negative bacteria, after the staining process used to distinguish them (Figure 27.9). The stain is named for its inventor, Danish scientist Hans Christian Gram. Gram-positive bacteria classified in the phyla Firmicutes and Actinobacteria have walls with a relatively thick peptidoglycan layer (Figure 27.10a). By contrast, the Gram-negative cell walls of Cyanobacteria, Proteobacteria, and other species have a thinner peptidoglycan layer and are enclosed by a thin, outer envelope whose outer leaflet is rich in lipopolysaccharides, which are lipids that have polysaccharides covalently attached to them (Figure 27.10b; see also Figure 27.2a). This outer envelope of Gram-negative bacteria contains a phospholipid bilayer that surrounds the outside of the cell wall, whereas the plasma membrane is found inside the cell wall. 



ARCHAEA AND BACTERIA 569

Acidic polysaccharides

Thick peptidoglycan layer 21 μm

21 μm

Plasma membrane (a) Gram-positive bacteria

(b) Gram-negative bacteria

Figure 27.9  Gram-positive and Gram-negative bacteria. 

(a) Streptococcus pneumoniae, a member of the phylum Firmicutes, stains positive (purple) with the Gram stain. (b) Escherichia coli, a member of the Proteobacteria, stains negative (pink) when the Gram stain procedure is applied. a: ©CNRI/Science Source; b: ©Lee W. Wilcox

Peptidoglycan and lipopolysaccharides can affect disease symptoms, the composition of vaccines, and bacterial responses to antibiotics. For example, part of the peptidoglycan covering of the Gram-negative bacterial species Bordetella pertussis is responsible for the extensive tissue damage to the respiratory tract associated with whooping cough, and whooping cough vaccines are improved by including antibodies that reduce the ability of the lipopolysaccharide layer to attach to host cells. The lipopolysaccharide-rich outer envelope of Gram-negative bacteria helps them to resist the entry of some antibiotics. However, this outer envelope also impedes the secretion of proteins from bacterial cells into the environment, a process that normally allows cells to communicate with each other, as in quorum sensing. Gram-negative bacteria have adapted to the presence of an outer envelope by evolving several types of protein systems that function in secretion. In Section 27.5, we will see how some of these secretion systems have been modified in ways that allow disease-causing bacteria to attack eukaryotic cells. Distinguishing Gram-positive from Gram-negative bacteria is an important factor in choosing the best antibiotics for treating infectious diseases. For example, Gram-positive bacteria are typically more susceptible than Gram-negative bacteria to penicillin and related antibiotics because these antibiotics interfere with synthesis of peptidoglycan, which Gram-positive bacteria require in larger amounts. For this reason, penicillin and related antibiotics such as methicillin are widely used to treat infections caused by Gram-positive bacteria. However, it is of societal concern that some strains of bacteria have become resistant to some antibiotics, an example being methicillinresistant Staphylococcus aureus, or MRSA.

Bacteria and Archaea Display Diverse Types of Movements Many bacteria and archaea have structures at the cell surface or within the cell that enable them to change position in their environment, an ability known as motility. Diverse motility adaptations allow microbes to respond to chemical signals emitted from other

(a) Gram-positive: thick peptidoglycan layer, no outer envelope

Lipopolysacchariderich outer envelope

Thin peptidoglycan layer

Plasma membrane

(b) Gram-negative: thinner peptidoglycan layer, with outer envelope

Figure 27.10  Cell-wall structures of Gram-positive and Gramnegative bacteria.  (a) The structure of the cell wall of Gram-positive bacteria. (b) The structure of the cell wall and lipopolysaccharide-rich envelope typical of Gram-negative bacteria.

cells during quorum sensing and mating, and to move to favorable conditions within gradients of light, gases, or nutrients. For example, we have already learned that gas vesicles help cyanobacteria float into well-illuminated waters close to the surface, where photosynthesis can occur (see Figure 27.5). In addition, prokaryotic cells may move by twitching, gliding, or swimming by means of flagella. Bacterial flagella (singular, flagellum) differ from eukaryotic flagella in several ways. Although bacterial flagella are largely built of about 30 types of proteins, they lack a plasma membrane covering, an internal cytoskeleton of microtubules made of the protein

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Flagellum

Filament

The motor rotates the hook, which links the internal motor to the external filament, composed of a protein known as flagellin. Hook Motor 1.6 μm Outer envelope

H+

(a) Bacteria with a single short flagellum

H+ channel proteins

3.9 μm

(b) Bacterium with multiple lon

Plasma membrane

Peptidoglycan (cell wall)

A set of protein rings anchors the flagellum in the plasma membrane and cell wall. As protons (H+) flow into the cell through channel proteins within the motor, these proteins change conformation, thereby turning the rings.

Figure 27.11  Diagram of a bacterial flagellum, showing a filament, hook, and motor. Concept Check:   Does the filament move more like the arms of a human swimmer or the shaft of a boat propeller?

1.6 μm

(a) Bacteria with a single short flagellum

tubulin, and the motor protein dynein—all features that characterize eukaryotic flagella (look back to Chapter 4). Unlike eukaryotic flagella, bacterial flagella do not repeatedly bend and straighten. Instead, bacterial flagella spin, propelled by molecular machines composed of a filament, hook, and motor that work together somewhat like a boat’s outboard motor and propeller (Figure 27.11). Lying outside the cell, the long, stiff, curved filament acts as a propeller. The hook links the filament with the motor that contains a set of protein rings at the cell surface. Hydrogen ions (protons), which have been pumped out of the cytoplasm, usually via an electron transport chain, diffuse back into the cell through channel proteins within the motor. This proton flow powers the turning of the hook and filament at rates of hundreds of revolutions per second. Archaeal flagella also rotate but are much thinner than bacterial flagella, are composed of different proteins, and are powered differently (by the hydrolysis of ATP). Prokaryotic species differ in the number and location of flagella, which may occur singly or in tufts at one pole or may emerge from around the cell (Figure 27.12). Differences in flagellar number and location cause microorganisms to exhibit different modes or rates of swimming. Some bacterial species are known to swim at rates of more than 150 μm per second! By contrast, spirochaetes tend to move slowly. Their flagella are located outside the peptidoglycan cell wall but within the confines of an outer membrane that holds them close to the cell. Rotation of these flagella causes spirochaetes to display characteristic bending, flexing, and twirling

3.9 μm (b) Bacterium with multiple long flagella

Figure 27.12  Differences in the number and location of flagella.  Depending on the species, microbial cells can produce one or more flagella at the poles or numerous flagella around the periphery. (a) Vibrio parahaemoliticus, a bacterium that causes seafood poisoning, has a single short flagellum. (b) Salmonella enterica, another bacterium that causes food poisoning, has many flagella distributed around the cell periphery. a: ©Dennis Kunkel Microscopy, Inc./ Phototake; b: ©Dr. Linda Stannard, UCT/SPL/Science Source

Core Skill: Connections  Look ahead to Figure 29.8b. Like the bacteria shown here, what heterotrophic eukaryote moves to its food source in the human gut by means of flagella?

motions. This allows spirochaetes to move within the thick bodily fluids of their hosts. Some prokaryotic species twitch or glide across surfaces, using threadlike cell surface structures known as pili (singular, pilus) (Figure 27.13a). Myxococcus xanthus cells, for example, move by alternately extending and retracting pili from one pole or the other. This process allows directional movement toward food materials. If nutrients are low, cells of these bacteria glide together to form tiny treelike colonies, which are part of a reproductive process Figure 27.13b. These and other motility adaptations help bacteria and archaea survive in their environments.



ARCHAEA AND BACTERIA 571

Pili

0.5 µm (a)

(b)

Figure 27.13  Pili that extend from prokaryotic cell surfaces may allow motility and sometimes foster the formation of complex colonies. a: Courtesy Dr. Esther Bullitt; b: ©Yoav Levy/Medical Images.com

Prokaryotic Cells Generally Divide by Binary Fission

27.3 Reproduction Learning Outcomes: 1. Explain how populations of prokaryotic organisms increase in number. 2. CoreSKILL » Describe how bacteria can be counted in medical and environmental samples. 3. Give examples of how some bacteria survive under stressful conditions.

Bacteria and archaea do not engage in the process of sexual reproduction used by eukaryotes, involving specialized gametes, gamete fusion, and meiosis. However, they can exchange some genes by conjugation, transformation, and transduction (described in Chapter 19). Bacteria and archaea usually reproduce asexually, generally by means of a type of cell division known as binary fission, but sometimes by forming small cells, known as buds, from one end. Both types of bacterial cell division increase the number of cells in populations. In addition, some bacteria produce tough cells that can withstand deleterious conditions for long periods in a dormant condition.

The cells of most bacteria and archaea divide by splitting in two, a process known as binary fission (Figure 27.14a; refer back to Figure 19.13). When sufficient nutrients are available, an entire population of identical cells can be produced from a single parental cell by repeated binary fission. This growth process allows microbes to become very numerous in water, food, or animal tissues, potentially causing harm. Binary fission is the basis of a widely used method for detecting and counting bacteria in food, water samples, or patients’ body fluids. Microbiologists who study the spread of disease need to quantify bacterial cells in samples taken from the environment. Medical technicians often need to count bacteria in body fluid samples to assess the likelihood of infection. However, because bacterial cells are small and often unpigmented, they are difficult to count directly. One way that microbiologists count bacteria is to place a measured volume of sample into laboratory dishes filled with a semisolid nutrient medium. Bacteria in the sample undergo repeated binary fission to form colonies of cells visible to the unaided eye (Figure 27.14b). Because each colony represents a single cell that was present in the original sample,

39 μm

1.4 μm (a) Bacterium undergoing binary fission

(b) Colonies developed from single cells

(c) Bacteria stained with fluorescent DNA-binding dye

Figure 27.14  Binary fission and counting microbes.  (a) Division of a bacterial cell as viewed by scanning electron microscopy. (b) When samples are spread onto the surfaces of laboratory dishes containing nutrients, single cells of bacteria or archaea may divide repeatedly to form visible colonies, which can be easily counted. The number of colonies is an estimate of the number of culturable cells in the original sample. (c) If a fluorescence microscope is available, cells can be counted directly by applying a fluorescent stain that binds to their DNA. Each cell glows brightly when illuminated with UV light. a: ©David Scharf/Science Source; b: ©Linda Graham; c: ©Lee W. Wilcox

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the number of colonies in the dish reflects the number of living bacteria in the original sample. Another way to detect and count prokaryotic cells is to treat samples with a stain that binds to bacterial DNA, causing cells to glow brightly when illuminated with UV light. The glowing cells can be viewed and counted by the use of a fluorescence microscope (Figure 27.14c). The fluorescence method must be used when the microbes of interest cannot be cultivated in the laboratory. For many bacteria and archaea, the conditions needed to foster population growth in the laboratory are not known.

Some Bacteria Survive Harsh Conditions as Akinetes or Endospores Some bacteria produce thick-walled cells that are able to survive unfavorable conditions in a dormant state. These specialized cells develop when bacteria have experienced stressful conditions, such as low nutrients or unfavorable temperatures. Such dormant cells may be able to germinate into metabolically active cells when conditions improve again. For example, aquatic filamentous cyanobacteria often produce akinetes, thick-walled, food-filled cells, when winter approaches (Figure 27.15a). Akinetes are able to survive winter at the bottoms of lakes, and they produce new filaments in spring when they are carried by water currents to the brightly lit surface. Persistence of such akinetes explains how harmful cyanobacterial blooms can develop year after year in overly fertile lakes. Heterocyte

Akinete

Endospore

Endospores (Figure 27.15b) are produced inside bacterial cells by the enclosure of DNA and other materials within a tough coat, and then are released when the enclosing cell dies and breaks down. Endospores can remain alive, though in a dormant state, for long periods, then reactivate when conditions are suitable. The ability to produce endospores allows some Gram-positive bacteria in the phylum Firmicutes to cause serious diseases. For example, Bacillus anthracis causes the disease anthrax and is thus a potential agent in bioterrorism and germ warfare. Most cases of human anthrax result when endospores of B. anthracis enter breaks in the skin, causing skin infections that are relatively easily cured by antibiotic treatment. But sometimes the endospores are inhaled or consumed in undercooked, contaminated meat, potentially causing more serious illness or death. Clostridium botulinum can contaminate improperly canned food that has not been heated to temperatures high enough to destroy its tough endospores. When the endospores germinate and bacterial cells grow in the food, they produce a deadly toxin, as well as NH3 and CO2 gases, which cause can lids to bulge. If humans consume the food, the toxin causes botulism, a severe type of food poisoning that can lead to respiratory and muscular paralysis. The botulism toxin is marketed commercially as Botox, which is injected into the skin, where it paralyzes facial muscles, thereby reducing the appearance of wrinkles. The toxin has also been used as a migraine treatment. Clostridium tetani produces a nerve toxin that causes lockjaw, also known as tetanus, when bacterial cells or endospores from soil enter wounds. The ability of the genera Bacillus and Clostridium to produce resistant endospores helps explain their widespread presence in nature and their effect on humans.

27.4 Nutrition and Metabolism Learning Outcomes: 1. List the major mechanisms of nutrition displayed by prokaryotic species. 2. CoreSKILL » Compare and contrast the effects of oxygen on the metabolism of different types of prokaryotic species; then predict the outcome when a gas gangrene patient is treated with oxygen. 3. Outline the process of biological nitrogen fixation, and explain why it is important and how oxygen interferes with this process.

13 μm (a) Cyanobacterial akinete

0.3 μm (b) Clostridium difficile

Figure 27.15  Specialized cells capable of dormancy. 

(a) Akinetes are thick-walled, food-filled cells produced by some cyanobacteria. Akinetes are able to resist stressful conditions and generate new populations when conditions improve. As discussed later, the heterocyte is a specialized cell in which nitrogen fixation occurs. (b) An endospore with a resistant wall develops within the cytoplasm of the pathogen Clostridium difficile. a: ©Lee W. Wilcox; b: ©Dr. Kari Lounatmaa/Science Source

Concept Check:   How do endospores affect the ability of some bacteria to cause disease?

All living cells require energy and a source of carbon to build their organic molecules. Bacteria and archaea use a wide variety of strategies to obtain energy and carbon for growth (Table 27.2). These microbes can be classified according to their energy source, carbon source, response to oxygen, and presence of specialized metabolic processes.

Mechanisms of Nutrition and Responses to Oxygen Cyanobacteria and some other prokaryotic species are autotrophs (from the Greek, meaning self-feeders), organisms that are able to produce all or most of their own organic molecules from inorganic sources. Autotrophs fall into two categories: photoautotrophs and chemoautotrophs. Photoautotrophs, including cyanobacteria, use light as a source of energy for the synthesis of organic molecules from CO2 and H2O or H2S. Chemoautotrophs use energy obtained by chemical modifications of inorganic compounds to synthesize organic compounds. Such chemical modifications include



ARCHAEA AND BACTERIA 573

Table 27.2 Type

Major Types of Archaea and Bacteria Based on Energy and Carbon Source Energy source

Carbon source

Example

Photoautotroph

Light

CO2

Cyanobacteria

Chemoautotroph

Inorganic compounds

CO2

Sulfolobus (Archaea)

Photoheterotroph

Light

Organic compounds

Chloroflexi (Bacteria)

Chemoheterotroph

Organic compounds

Organic compounds

Many

Autotroph

Heterotroph

nitrification (the conversion of ammonia to nitrate) and the oxidation of sulfur, iron, or hydrogen. For example, archaea of the genus Sulfolobus can oxidize certain sulfur-containing minerals. Heterotrophs (from the Greek, meaning other feeders) are organisms that require at least one organic compound, and often more, from their environment. Some microorganisms, including bacteria in the phylum Chloroflexi, are photoheterotrophs, meaning that they are able to use light energy to generate ATP, but they must take in organic compounds from their environment as a source of carbon. Chemoheterotrophs must obtain organic molecules both for energy and as a carbon source. Prokaryotic species differ in their need for and responses to oxygen. Like most eukaryotes (including humans), many prokaryotes are obligate aerobes, meaning that they require O2 to survive. In contrast to obligate aerobes, obligate anaerobes, such as the Firmicutes genus Clostridium, are poisoned by O2. People suffering from gas gangrene (caused by Clostridium perfringens and related species) are usually treated by placement in a chamber having a high oxygen content (called a hyperbaric chamber), which kills the organisms and deactivates the toxins. Aerotolerant anaerobes do not use O2, but they are not poisoned by it either. These organisms obtain their energy by fermentation or anaerobic respiration, which are described in Chapter 7 (look back at Section 7.8). Anaerobic metabolic processes include denitrification (the conversion of nitrate into N2 gas) and the reduction of manganese, iron, and sulfate, which are all important in the Earth’s cycling of minerals. Facultative anaerobes can use O2 via aerobic respiration, obtain energy via anaerobic fermentation, or use inorganic chemical reactions to obtain energy—shifting between modes depending on environmental conditions. One fascinating example of a facultative anaerobe is the species Thiomargarita namibiensis, a large proteobacterium mentioned earlier in this chapter. This chemoheterotroph obtains its energy in two ways: by oxidizing sulfide with oxygen when oxygen is available or, when oxygen is low or unavailable, by oxidizing sulfide with nitrate. In either case, the cells convert sulfide to elemental sulfur, which is stored within the cells in large globules.

Some Prokaryotic Species Play Important Roles as Nitrogen Fixers Many cyanobacteria and some other prokaryotic organisms carry out a specialized metabolic process called biological nitrogen fixation. The removal of nitrogen from the gaseous phase is called fixation, and microbes that perform this process are known as nitrogen fixers.

Nitrogen fixation is an important component of the cycling of nitrogen on a global basis. During nitrogen fixation, the enzyme nitrogenase converts inert atmospheric nitrogen gas (N2) into ammonia (NH3). Plants and algae can use ammonia (though not N2) to produce proteins and other essential nitrogen-containing molecules. As a result, many plants have developed close relationships with nitrogen fixers, which provide ammonia fertilizer to their plant partners. In addition to the aquatic photosynthetic cyanobacteria mentioned in the chapter opening, many types of heterotrophic soil bacteria also fix nitrogen. Examples include protobacteria of the genus Rhizobium, which live within the roots of legume plants (see Chapter 38). Nitrogenase is inhibited by O2, so most nitrogen fixers conduct nitrogen fixation only in low-oxygen conditions. Many cyanobacteria generate low-oxygen conditions in specialized cells known as heterocytes, allowing nitrogen fixation to occur in these cells (see Figure 27.15a). Heterocytes display adaptations that reduce nitrogenase exposure to oxygen. These include thick walls that reduce inward O2 diffusion, increased occurrence of cellular reactions that consume oxygen, and down-regulation of the oxygen-producing components of photosynthesis. The latter adaptation, involving reduction in chlorophyll synthesis, explains why heterocytes are paler in color than neighboring photosynthetic cells.

27.5 E  cological Roles and Biotechnology Applications Learning Outcomes: 1. Discuss the roles of bacteria and archaea in the carbon cycle. 2. List examples of bacteria-eukaryote symbiosis and of pathogenic microbes. 3. List ways in which bacteria contribute to industrial and biotechnology applications.

Bacteria and archaea play many key ecological roles. In addition to their roles in nitrogen fixation and other aspects of the global nitrogen cycle, bacteria and archaea produce or break down organic carbon, important in the global carbon cycle. Bacteria function as beneficial symbionts in plants and animals and as disease agents. In this section, we will focus on these ecological roles and also provide examples of ways that humans use the metabolic capabilities of bacteria in industry and biotechnology.

Bacteria and Archaea Play Important Roles in Earth’s Carbon Cycle The Earth’s carbon cycle is the sum of all the chemical changes that occur among compounds that contain carbon. (Look ahead to Chapter 59 for a detailed discussion of the carbon cycle.) One way that bacteria and archaea influence Earth’s carbon cycle is by producing and consuming methane. Methane (CH4)—the major component of natural gas—is a greenhouse gas more powerful than CO2; CH4 increases global warming over 20 times more per molecule than does CO2. Therefore, atmospheric CH4 has the potential to alter the Earth’s climate, and in recent years the level of CH4 has been increasing in Earth’s atmosphere as the result of human activities. Several groups of anaerobic archaea known as methanogens convert CO2, methyl groups, or acetate to CH4 and release CH4 from their cells into the atmosphere. Methanogens live in swampy wetlands, in deepsea habitats, or in the digestive systems of animals, including cattle

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and humans. Marsh gas produced in wetlands is largely composed of CH4, and large quantities of CH4 produced long ago are trapped in deep-sea and subsurface Arctic deposits. Certain bacteria known as methanotrophs consume CH4, thereby reducing its concentration in the atmosphere. In the absence of methanotrophs, Earth’s atmosphere would be much richer in the greenhouse gas CH4, which would substantially increase global temperatures. Bacteria and archaea are also important in producing and degrading complex organic compounds. For example, cyanobacteria

and other autotrophic bacteria are important producers. Such bacteria, together with algae and plants, remove CO2 from the atmosphere and, via photosynthesis, synthesize the organic compounds that are used by themselves and other organisms for food. Decomposers, also known as saprobes, include heterotrophic microorganisms (as well as fungi and animals). These organisms break down dead organisms and organic matter, releasing minerals for uptake by living things. Astonishingly, many bacteria are able to break down antibiotics for use as a source of organic carbon, as discussed next.

Core Skill: Process of Science

Feature Investigation  | Dantas and Colleagues Found That Many Bacteria Can Break Down and Consume Antibiotics as a Sole Carbon Source

Many microorganisms naturally secrete antibiotics, which are organic compounds that inhibit the growth of other microorganisms. Antibiotics are evolutionary adaptations that allow bacteria and other microbes to avoid attack or reduce competition for resources. People have taken advantage of high antibiotic production by certain bacteria, particularly species of the phylum Actinomycetes, to make antibiotics commercially. Such antibiotics are used to treat bacterial infections in humans and domesticated species.

Due to the widespread production of antibiotics by bacteria, these organic compounds are commonly found in natural habitats. Many species of chemoheterotrophic bacteria have evolved the ability to metabolize antibiotics and use them as a source of carbon. In 2008, Gautam Dantas, George Church, and their colleagues reported this finding after experimentally testing their hypothesis that soil bacteria might be able to metabolize antibiotics (Figure 27.16). The investigators first cultivated bacteria from 11 different soils in the laboratory, finding a diverse

Figure 27.16  Diverse bacteria isolated from different soils are able to grow on many types of antibiotics. HYPOTHESIS The soil bacterial community contains species that can take up and metabolize antibiotics. KEY MATERIALS Eleven diverse soil samples; 18 types of antibiotics. Experimental level

1

Inoculate soil samples onto growth media in culture dishes.

2

Isolate bacterial species that grow from single cells to visible colonies by repeated binary fission.

3

Grow isolates into large populations for testing on antibiotics.

4 Inoculate each bacterial isolate

Conceptual level

Plastic petri plates

Transfer loop –a device used to move microbial cells

Different species have distinctive colony characteristics (color, shape, size).

Bacterial cells undergo repeated binary fission to quickly form colonies large enough to see with the unaided eye.

Test the ability of each

unaided eye.



ARCHAEA AND BACTERIA 575

Test the ability of each isolate to grow on a range of antibiotics.

4 Inoculate each bacterial isolate

onto replicate dishes containing a different antibiotic as the only food source. Penicillin G (or one of 17 other antibiotics)

5

Allow time for bacterial population growth; compare growth among dishes.

6

THE DATA

Strong growth of forest soil bacterial isolate F1 on penicillin G food

Poor growth of urban soil bacterial isolate U3 on dicloxacillin food

Compare isolate ability to grow on different antibiotics.

Examples of growth differences Soils

Most soils tested contained bacterial species that were able to use antibiotics of many types for food and thus were resistant to those antibiotics.

Sole carbon source

F1 F2 F3 P1 P2 P3 P4 P5 U1 U2U3

D-Cycloserine Amikacin Gentamicin Kanamycin Sisomicin Chloramphenicol Thiamphenicol Carbenicillin Dicloxacillin Penicillin G Vancomycin Ciprofloxacin Levofloxacin Nalidixic acid Mafenide Sulfamethizole Sulfisoxazole Trimethoprim

Growth No growth

7

CONCLUSION Natural soils contain bacteria that are able to utilize antibiotics produced naturally by other species as food. Soil bacteria are a previously unrecognized source of antibiotic resistance genes that can be transferred to other species.

8

SOURCE Dantas, G., Sommer, M. O. A., Oluwasegun, R. D., and Church, G. M. 1998. Bacteria subsisting on antibiotics. Science 320: 100–103.

collection of different species. Almost 90% of the cultured bacteria were Gram-negative Proteobacteria, some closely related to human pathogens, while 7% of the cultures were Gram-positive Actinomycetes.  These researchers then tested the ability of the bacteria cultured from different soils (isolates) to use various antibiotics as a sole carbon source for growth. The 18 antibiotics tested included penicillin and related compounds, as well as the widely prescribed ciprofloxacin (Cipro). Every antibiotic tested supported the growth of bacteria from soil. Importantly, each antibiotic-eating isolate was resistant to several antibiotics at concentrations used in the medical treatment of infections. In today’s society, the widespread use of antibiotics in medicine and agriculture is of concern because it is thought to foster increases in antibiotic resistance (refer back to Section 19.5). The experiment by

Dantas and associates revealed that natural evolutionary processes— the widespread development by diverse soil bacteria of metabolic processes to utilize many types of antibiotics as food—represent a previously unrecognized source of antibiotic resistance. The study also indicated that natural bacteria are a potential source of antibioticresistance genes that could be transferred to disease-causing bacteria Experimental Questions 1. What features of soil bacteria attracted the attention of the researchers?  2. CoreSKILL » What processes did the researchers use to test their hypothesis that soil bacteria might use antibiotics as a food source? 

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BIO TIPS

THE QUESTION  The experiment conducted by Dantas and colleagues (Fig. 27.16) revealed that soil bacteria are able to metabolize many antibiotic compounds commonly used in medicine to treat infections. Bacteria that consume antibiotics are resistant to such compounds. Describe how a bacterial population that is not able to consume an antibiotic and is not resistant to that antibiotic evolves into one that is. Why is this evolutionary process important to society? T OPIC  What topic in biology does this question address? The topic is the evolution of certain species of soil bacteria that are able to consume natural antibiotics as a food source and are also resistant to them. The question also relates to a societal problem, the increasing resistance of disease-causing bacteria to antibiotics used in medicine.

ANSWER Mutations arise that confer the ability to metabolize antibiotics and/or provide resistance to the same antibiotics. For example, a mutation could alter the structure of a metabolic enzyme, enabling that enzyme to recognize and break down the antibiotic. Bacteria carrying such a mutation may also be resistant to being killed by the same antibiotic because it would not accumulate in their cytoplasm. Over the course of many generations, such bacteria may increase in number due to natural selection. These populations of bacteria can quickly become resistant to antibiotics at levels that are used in medical treatments. The larger such populations are, the greater the chances they will cause infections for which antibiotic treatment may not work as expected.

Many Bacteria Live in Symbiotic Associations

I NFORMATION  What information do you know based on the question and your understanding of the topic? This section of the chapter summarizes the major ways in which bacteria acquire organic carbon and energy. Information provided in Figure 27.16 indicates that some soil bacteria can utilize carbon from antibiotics for growth and are also resistant to those same antibiotics. From your knowledge of evolution (see Chapter 22), you may remember that mutation and natural selection can alter the characteristics of species from one generation to the next.

Many bacterial species live in close associations with one or more other species, a phenomenon called  symbiosis (from the Greek, meaning life together with). If symbiosis is beneficial to both partners, the interaction is known as mutualism. Many mutualistic bacteria live in associations of two or a few species that supply each other with essential nutrients. Alternatively, in other symbiotic relationships, some bacterial species may cause harm or even death to another species.

P ROBLEM-SOLVING    S  TRATEGY  Make a drawing. Begin

Mutualistic Partnerships Between Bacteria and Eukaryotes  Bacteria are involved in many mutually beneficial symbioses in which they provide aquatic or terrestrial eukaryotes with minerals or vitamins or other valuable services. Bioluminescent bacteria, bacteria that have the ability to produce and emit light (Figure 27.17), often form symbiotic relationships with squid and other marine animals. In deep-sea thermal vent communities, bacteria live within the tissues of tubeworms and mussels, supplying these animals with carbon compounds used as food. One terrestrial example of mutualism is a complex association involving four partners: ants, fungi that the ants cultivate for food, parasitic fungi that attack the food fungi, and Actinobacteria that produce antibiotics. The antibiotics control the growth of the parasitic fungi, preventing them from destroying the ants’ fungal food supply. The ants rear the useful bacteria in cavities on their body surfaces; glands near these cavities supply the bacteria with nutrients.

with a population of bacteria that are not able to consume the antibiotic and are not resistant to it. Next, show that a few bacteria have acquired one or more mutations, allowing them to consume the antibiotic without succumbing to it. These bacteria can be designated with a different color. Use your knowledge of natural selection to predict changes in the numbers of colored bacteria in subsequent panels over time.

Starting bacterial population

1

Mutation conferring the ability to metabolize an antibiotic Blue color indicates a mutation

2

Natural selection over several generations

Pathogenic Microbes  Microorganisms that cause disease in one or more types of host organism are known as pathogens. Cholera, leprosy, tetanus, pneumonia, whooping cough, diphtheria, Lyme disease, scarlet fever, rheumatic fever, typhoid fever, bacterial dysentery, and tooth decay are among the many examples of human diseases caused by bacterial pathogens. Bacteria also cause many plant diseases of importance in agriculture, including blights, soft rots, and wilts. How do microbiologists determine which bacteria cause these diseases? The pioneering research of the Nobel Prize–winning German physician Robert Koch provided the answer. In the mid- to late 1800s, Koch established a series of four steps to determine whether a particular organism causes a specific disease.  1. The presence of the suspected pathogen must correlate with occurrence of symptoms. 



ARCHAEA AND BACTERIA 577

deadly disease of growing concern in some parts of the world). More than 20 million people are infected by means of injectisomes every year. Several plant pathogenic bacteria also infect cells by means of injectisomes. Some other Gram-negative bacterial pathogens synthesize a type IV secretion system, which functions as channel to deliver toxins or DNA into cells. Examples of such bacteria that cause human disease include Helicobacter pylori, Legionella pneumophila, and Bordetella pertussis. The plant pathogen Agrobacterium tumifaciens uses a type IV secretion system to

Outer envelope

Plasma membrane Pathogenic bacterium

Flagellum-like injectisome

Figure 27.17  Bioluminescent bacteria.  These blue-green

colonies of Vibrio fischeri bacteria are growing on nutritive media in a culture plate. The colonies produce so much light that additional light was not needed to make this photo. ©Peter Durben. Animal cell

2. The pathogen must be isolated from an infected host and grown in pure culture if possible.  3. Cells from the pure culture should cause disease when inoculated into a healthy host.  4. The same pathogen should be isolatable from the second infected host.  Using these steps, known as Koch’s postulates, Koch discovered the bacterial causes of anthrax, cholera, and tuberculosis. Subsequent investigators have used Koch’s postulates to establish the identities of bacterial species that cause other infectious diseases.  How Pathogenic Bacteria Attack Cells  An important aspect of symbiosis is the way in which bacteria interact with other species, such as human hosts. Understanding how disease-causing bacteria attack host cells aids in developing strategies for disease prevention and treatment. Many pathogenic bacteria attack cells by binding to the surface and injecting substances that help them utilize cellular components. During their evolution, some Gramnegative pathogenic bacteria developed needle-like systems, made of components also found in flagella, that inject proteins into animal or plant cells as part of the infection process. Such structures are known as injectisomes ( Figure 27.18a ). Examples of bacteria whose injectisomes allow them to attack human cells are Yersinia pestis (the agent of bubonic plague), Salmonella enterica (which causes the food poisoning called salmonellosis), and Burkholderia pseudomallei (the cause of melioidosis, a

Nucleus

Infection proteins

(a) Injectisome Plasma membrane

Outer envelope

Pilus-like transporter

Plant cell wall

Agrobacterium tumifaciens

T DNA Plant cell

Nucleus

(b) Type IV secretion system

Figure 27.18  Attack systems of pathogenic bacteria.  (a) The injectisome functions like a syringe to inject proteins into host cells, in this case an animal cell, thereby initiating the disease process. (b) A type IV secretion system forms a channel through which DNA can be transmitted from a pathogenic bacterium to a host cell, in this case from the bacterium Agrobacterium tumifaciens into a plant cell. Some of the components in this system are related to those found in pili, which are described in Chapter 19.

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transfer DNA (T DNA) into plant cells ( Figure 27.18b ). The T DNA encodes an enzyme that affects normal plant growth, with the result that cancer-like tumors called galls develop (see Figure 27.4). 

Core Concept: Evolution The Evolution of Bacterial Pathogens Genomic and proteomic studies have illuminated the evolution of bacterial pathogens, providing insights that are useful in devising new ways to control infectious diseases. Such studies reveal that some pathogens have evolved small, compact genomes encoding specialized metabolic functions, whereas others have acquired large genomes that provide diverse metabolic capabilities. Horizontal gene transfer plays a major role in increasing disease severity. Mycoplasma pneumoniae, which causes pneumonia in humans, has one of the smallest genomes known to occur among self-replicating organisms. The tiny cells, only 0.3 μm in diameter, possess fewer than 700 protein-coding genes and make only 178 types of protein complexes. The bacterium is a model organism for investigating the minimal cellular machinery required for life. As one way of gaining

insight into what forms a minimal proteome, the locations of five types of protein complexes have been mapped in these bacteria by means of specialized microscopic techniques ( Figure 27.19 ). By contrast, Pseudomonas aeruginosa—which causes respiratory disease in humans and other animals, and also infects plants—has a larger genome containing about 5,000 proteinencoding genes. Diverse strains share a common genome core but also have strain-specific genes acquired by horizontal transfer, which confer a wide variety of metabolic abilities. This genomic variation allows P. aeruginosa to survive in a wide range of environments. As an example of the species’ wide metabolic capability, a strain of P. aeruginosa obtained from an infected human also possessed the genes and proteins necessary to degrade tough defensive resins produced by trees and use them as a food source! Escherichia coli strain O157:H7, which causes deadly outbreaks of food-borne illness and is the leading cause of acute kidney failure in children, evolved from harmless strains by the step-wise gain via horizontal transfer of toxin genes. These genomic features enable this strain to use its flagellar tips to attach to host intestinal epithelium and then attack cells with an injectisome. Bacterial toxin produced in the intestine enters the host circulation system and reaches the kidneys, where the toxin inhibits protein synthesis, resulting in severe tissue damage.

Ribosome

Pyruvate dehydrogenase

Protein-folding complex

Cell tip proteins

RNA polymerase

Figure 27.19  Locations of five protein complexes in the tiny pathogen Mycoplasma pneumoniae.  The cell tip is rich in proteins (colored

green) that help these bacteria attach to host epithelial cells. Other mapped protein complexes are pyruvate dehydrogenase (involved in energy metabolism), ribosomes, RNA polymerase, and a protein-folding complex (colored red).



ARCHAEA AND BACTERIA 579

Some Bacteria Are Useful in Industrial and Other Applications Several industries have harnessed the metabolic capabilities of microbes obtained from nature. The food industry uses bacteria to produce chemical changes in food—for example, to make dairy products, including cheese and yogurt, from milk. Cheese makers add pure cultures of certain bacteria to milk. The bacteria consume milk sugar (lactose) and produce lactic acid, which aids in curdling the milk. The chemical industry produces materials such as enzymes, vinegar, amino acids, vitamins, insulin, vaccines, antibiotics, and other useful pharmaceuticals by growing particular bacteria in giant vats. For example, the hot springs bacterial species Thermus aquaticus is a source of a form of DNA polymerase widely used in biology laboratories to amplify DNA in polymerase chain reaction (PCR). Industrially grown bacteria produce the antibiotics streptomycin, tetracycline, kanamycin, gentamycin, bacitracin, polymyxin-B, and neomycin. The field of synthetic biology utilizes bacteria as chemical factories by genetically modifying bacterial genomes so that the bacteria produce particular useful compounds, such as pharmaceuticals and renewable biofuels. For example, biologists have modified the genome of the bacterium Caldicellulosiruptor bescii so it can transform switchgrass into ethanol. The ability of some microorganisms to break down organic compounds or precipitate metals makes them very useful in treating wastewater, industrial discharges, and harmful substances such as explosives, pesticides, and oil spills. This process, known as bioremediation, is used to reduce levels of harmful materials in the environment. Agriculture employs several species of Bacillus, particularly B. thuringiensis (Bt), which produce toxins that kill the insects that ingest them but are harmless to many noninsect species. Tent caterpillars, potato beetles, gypsy moths, mosquitoes, and black flies are among the pests that can be controlled by the Bt toxin. For this reason, toxin-encoding genes from B. thuringiensis have been cloned and introduced into some crop plants, such as corn and cotton, to reduce conventional pesticide use and increase crop yields.

Summary of Key Concepts 27.1  Diversity and Evolution ∙∙ The three domains of life are Bacteria, Archaea, and Eukarya (whose members are referred to as bacteria, archaea, and eukaryotes). Domain Archaea is more closely related to domain Eukarya than either is to domain Bacteria (Figure 27.1). ∙∙ Many representatives of the domain Archaea occur in extremely hot, salty, or acidic habitats. Ether-linked membrane phospholipids are among the features of archaea that enable their survival in extreme habitats (Figure 27.2). ∙∙ The domain Bacteria includes 50 or more phyla, including Cyanobacteria and Proteobacteria, which are particularly diverse and of great evolutionary and ecological importance (Table 27.1, Figures 27.3, 27.4). ∙∙ Widespread horizontal gene transfer has occurred among bacteria and archaea. Horizontal gene transfer by means of transduction, transformation, or conjugation allows microorganisms to evolve rapidly.

27.2  Structure and Movement ∙∙ Bacteria and archaea have prokaryotic cells that are smaller and simpler than eukaryotic cells. Structural adaptations that increased the complexity of some types of prokaryotic cells include thylakoids, magnetosomes, and nucleus-like bodies (Figures 27.5, 27.6). ∙∙ Common prokaryotic cell shapes are spherical cocci, rod-shaped bacilli, comma-shaped vibrios, and coiled spirochaetes and spirilli. Some cyanobacteria display features of multicellular organisms (Figure 27.7). ∙∙ Many microbes secrete a coating of slimy mucilage, which plays a role in disease resistance and in the development of biofilms. Biofilm development is influenced by quorum sensing, a mechanism in which group activity is coordinated by chemical communication (Figure 27.8). ∙∙ Most bacterial cell walls contain peptidoglycan, which is composed of carbohydrates cross-linked by peptides. Gram-positive bacterial cells have thick peptidoglycan walls, whereas Gram-negative cells have less peptidoglycan in their walls and are enclosed by an outer lipopolysaccharide envelope (Figures 27.9, 27.10). ∙∙ Motility enables microbes to change positions within their environment, which aids in locating favorable conditions for growth. Some bacteria have gas vesicles, which enable them to float, whereas others swim by means of flagella or twitch or glide by the action of pili (Figures 27.11, 27.12, 27.13).

27.3  Reproduction ∙∙ Populations of most bacteria and archaea enlarge by binary fission, a simple type of cell division that provides a means by which culturable microbes can be counted (Figure 27.14). ∙∙ Some bacteria are able to survive harsh conditions as dormant akinetes or endospores (Figure 27.15).

27.4  Nutrition and Metabolism ∙∙ Bacteria and archaea can be grouped according to mechanism of nutrition, response to oxygen, or presence of distinctive metabolic features. Major nutritional types are photoautotrophs, chemoautotrophs, photoheterotrophs, and chemoheterotrophs (Table 27.2). ∙∙ Obligate aerobes require oxygen, whereas obligate anaerobes are poisoned by oxygen. Aerotolerant anaerobes do not use oxygen but are not poisoned by it. Both obligate and aerotolerant anaerobes obtain their energy by anaerobic respiration. Facultative aerobes are able to live with or without oxygen by using different processes for obtaining energy. ∙∙ Nitrogen fixation is a distinctive metabolic process displayed only by certain microorganisms, and is a key component of the global nitrogen cycle.

27.5  E  cological Roles and Biotechnology Applications ∙∙ Bacteria and archaea play key roles in Earth’s carbon cycle as producers, decomposers, beneficial symbionts, or pathogens. Methane-producing methanogens and methane-consuming methanotrophs influence the Earth’s climate because methane is a powerful greenhouse gas.

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∙∙ Some bacteria are able to consume antibiotics, a process linked to the evolution of antibiotic resistance (Figure 27.16). ∙∙ Bacteria may occur in symbiotic associations with other organisms. (Figure 27.17).  ∙∙ Pathogenic bacteria obtain organic compounds from living host cells. Bacteria attack eukaryotic cells by means of injectisomes or type IV secretion systems (Figures 27.18). ∙∙ During their evolution, some pathogenic bacteria have reduced their genomes and proteomes, whereas others have acquired large genomes conferring diverse metabolic capacities; horizontal gene transfer is a major process by which disease severity increases (Figure 27.19). ∙∙ Many bacteria and archaea are useful in industrial and other applications; others are used to make food products or antibiotics or to clean up polluted environments.

Assess & Discuss Test Yourself 1. Which of the following features is common to prokaryotic cells? a. a nucleus, featuring a nuclear envelope with pores b. mitochondria c. plasma membranes d. mitotic spindle e. none of the above 2. The bacterial phylum whose members typically produce oxygen gas as a product of photosynthesis is a. Proteobacteria. d. all of the above. b. Cyanobacteria. e. none of the above. c. the Gram-positive bacteria. 3. Gram-staining is a procedure that microbiologists use to a. determine if a bacterial strain is a pathogen. b. determine if a sample of bacteria sample can break down oil. c. infer the structure of the cell wall of bacteria and their response to antibiotics. d. count bacteria in medical or environmental samples. e. do all of the above. 4. Place the following steps in the correct order, according to Koch’s postulates:   I. Determine if pure cultures of bacteria cause disease symptoms when introduced to a healthy host.   II. Determine if disease symptoms correlate with presence of a suspected pathogen. III. Isolate the suspected pathogen and grow it in pure culture, free of other possible pathogens.  IV. Attempt to isolate pathogen from second-infected hosts. a. II, III, IV, I d. II, III, I, IV b. II, IV, III, I e. I, II, III, IV c. III, II, I, IV 5. What ecological role do cyanobacteria play? a. producers d. parasites b. consumers e. none of the above c. decomposers

6. Bacterial structures that pathogenic bacteria use in attacking host cells include a. injectisomes and IV secretion systems. b. magnetosomes. c. gas vesicles. d. thylakoids. e. none of the above. 7. The structures that enable some Gram-positive bacteria to remain dormant for extremely long periods of time are known as a. akinetes. d. lipopolysaccharide envelopes. b. endospores. e. pili. c. biofilms. 8. By means of what process do populations of bacteria or archaea increase their size? a. mitosis d. transduction b. meiosis e. none of the above c. conjugation 9. By what means do bacterial cells acquire new DNA? a. by conjugation, the mating of two cells of the same bacterial species b. by transduction, the injection of viral DNA into bacterial cells c. by transformation, the uptake of DNA from the environment d. by all of the above e. by none of the above 10. How do various types of bacteria move? a. by the use of flagella, composed of a filament, hook, and motor b. by means of pili, which help cells twitch or glide along a surface c. by using gas vesicles to regulate buoyancy in water bodies d. All of the above are used by bacteria for movement. e. None of the above are used by bacteria for movement.

Conceptual Questions 1. Explain why many bacterial populations grow more rapidly than do populations of eukaryotes and how such population growth influences the rate of food spoilage or infection.  2. What processes contribute to antibiotic resistance?  3.

Core Concept: Systems  As we have seen in this chapter, living organisms interact with their environment. What organisms are responsible for the blue-green blooms that often occur in warm weather on lake surfaces? Think carefully; the answer is not just “cyanobacteria,” as you might first guess. 

Collaborative Questions 1. How would you go about cataloging the phyla of bacteria and archaea that occur in a particular place? 2. How would you go about developing a bacterial product that could be used for remediation of a site contaminated with materials that are harmful to humans?

CHAPTER OUTLINE 28.1 An Introduction to Protists 28.2 Evolution and Relationships 28.3 Nutritional and Defensive Adaptations 28.4 Reproductive Adaptations Summary of Key Concepts Assess & Discuss

Protists

28

P

rotists are eukaryotes that live in moist habitats and are mostly microscopic in size. Despite their small size, protists have a greater influence on global ecology and human affairs than most people realize. For example, the photosynthetic protists known as algae generate at least half of the oxygen in the Earth’s atmosphere and produce organic compounds that feed marine and freshwater animals. The oil that fuels our cars and industries is derived from pressurecooked algae that accumulated on the ocean floor over millions of years. Today, algae are being engineered into systems for cleaning pollutants from water or air and for producing renewable biofuels. Protists also include some parasites that cause serious human illnesses. For example, in 1993, the waterborne protist Cryptosporidium parvum sickened 400,000 people in Milwaukee, Wisconsin, costing $96 million in medical expenses and lost work time. Because this protist is exceptionally tolerant of the disinfectant chlorine, it is currently the major cause of diarrhea illness associated with aquatic recreational facilities such as swimming pools and waterparks. Species of the related genus Plasmodium, which is carried by mosquitoes in many warm regions of the world, cause the disease malaria. Every year, nearly 500 million people become ill with malaria, and more than 2 million die of this disease. As we will see, sequencing the genomes of these and other protist species has suggested new ways of battling such deadly pathogens. In this chapter, we will survey protist diversity, including structural, nutritional, and ecological variations. We begin by exploring ways of informally labeling protists according to ecological role, habitat, and motility. We will then focus on the defining features, classification, and evolutionary importance of the major protist phyla. Next, the nutritional and defensive adaptations of protists are discussed, and we conclude by looking at the reproductive adaptations that allow protists to exploit and thrive in a variety of environments.

Protists such as these green algal cells and their plant descendants produce much of the Earth’s oxygen. Each of the cells in this population is surrounded by a coating of protective mucilage. ©Photographs by H. Cantor-Lund reproduced with permission of the copyright holder Freshwater Biological Association and J. W. G. Lund.

   28.1      A  n Introduction to Protists Learning Outcomes: 1. List three features that define protists. 2. Label protists informally by ecological role, habitat, and type of motility.

The term protist comes from the Greek word protos, meaning first, reflecting the observation that protists were Earth’s first eukaryotes. Protists are eukaryotes that are not classified in the plant, animal, or fungal kingdoms. Protists display two additional common characteristics: They are most abundant in moist habitats, and most of them are microscopic in size. Protists play diverse ecological roles, live in diverse habitats, and display diverse types of motility.

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Protists Play Diverse Ecological Roles Protists occur in three major ecological types: algae, protozoa, and fungus-like protists. The term algae (singular, alga; from the Latin, meaning seaweeds) applies to protists that are generally photoautotrophic, meaning that most can produce organic compounds from inorganic sources by means of photosynthesis. In addition to organic compounds that can be used as food by heterotrophs—organisms that obtain their food from other organisms—photosynthetic algae produce oxygen, which is also needed by most heterotrophs. Thanks to their photosynthetic abilities, algae are increasingly important sources of renewable biofuels. Despite the general feature of photosynthesis, algae do not form a monophyletic group descended from a single common ancestor. The term protozoa (from the Greek, meaning first life) is commonly used to describe diverse heterotrophic protists that feed by absorbing small organic molecules or by ingesting prey. For example, the protozoa known as ciliates consume smaller cells such as the single-celled photosynthetic algae known as diatoms (Figure 28.1). Like algae, protozoa do not form a monophyletic group. Several types of heterotrophic fungus-like protists have bodies, nutritional mechanisms, or reproductive mechanisms similar to those of the true fungi. For example, fungus-like protists often have threadlike, filamentous bodies and absorb nutrients from their environment, as do the true fungi (see Chapter 29). However, fungus-like

Algae (diatoms)

7 μm

Figure 28.2  A fungus-like protist, Phytophthora infestans.  This organism causes the disease of potato plants known as late blight, or potato-blight. The image is an SEM of the protist growing on a host leaf. ©Andrew Syred/Science Source

protists are not actually related to fungi; their similar features represent cases of convergent evolution, in which species from different lineages have independently evolved similar characteristics (see Chapter 22). Water molds, some of which cause diseases of fish, and Phytophthora infestans, which causes diseases of many crops and wild plants, are examples of fungus-like protists (Figure 28.2). Various types of slime molds, some of which can be observed on decaying wood in forests, are also fungus-like, though not closely related to water molds and Phytophthora. These examples illustrate that the terms algae, protozoa, and fungus-like protists, although very useful in describing ecological roles, lack taxonomic or evolutionary meaning.

Protists Live in Diverse Habitats Protozoan (ciliate) 21 μm

Figure 28.1  A heterotrophic protozoan feeding on

photosynthetic algae.  The ciliate shown here has consumed several oil-rich, golden-pigmented, silica-walled algal cells known as diatoms. Diatom cells that have avoided capture glide nearby. ©Photographs by H. Cantor-Lund reproduced with permission of the copyright holder Freshwater Biological Association and J. W. G. Lund.

Core Concept: Energy and Matter  The diatoms were ingested by the process of phagocytosis, and their organic components are digested by the ciliate as food.

Although protists occupy nearly every type of moist habitat, they are particularly common and diverse in oceans, lakes, wetlands, and rivers. Even extreme aquatic environments such as Antarctic ice and acidic hot springs serve as habitats for some protists. In such places, protists may swim or float in open water or live attached to surfaces such as rocks or beach sand. These different habitats influence protists’ structure and size. Protists that swim or float in fresh or salt water are members of an informal aggregate of organisms known as plankton, which also includes bacteria, viruses, and small animals. The photosynthetic protists in plankton are called phytoplankton (plantlike plankton). Planktonic protists are necessarily quite small in size; otherwise they would readily sink to the bottom. Staying afloat is a particularly important characteristic of phytoplankton, which need light for photosynthesis. For this reason, planktonic protists occur primarily as single cells, colonies of cells held together with mucilage, or short filaments of cells linked end to end (Figure 28.3a–c).



PROTISTS 583 Planktonic protists

Attached protists One cell

10 μm (a) Single-celled Chlamydomonas with flagella

32 μm

0.2 mm (b) The colonial genus Monactinus

(c) The filamentous genus Desmidium

25 μm (d) The branched filamentous genus Cladophora

15 mm (e) The seaweed genus Acetabularia

Figure 28.3  The diversity of algal body types reflects their habitats.  (a) The single-celled flagellate genus Chlamydomonas occurs in the

phytoplankton of lakes. (b) The colonial genus Monactinus is composed of several cells arranged in a lacy star shape, which helps to keep this alga afloat in water and avoid being consumed by aquatic animals. (c) The filamentous genus Desmidium occurs as a twisted row of cells. (d) The branched filamentous genus Cladophora grows attached to nearshore surfaces and is large enough to see with the unaided eye. (e) The relatively large seaweed genus Acetabularia lives on rocks and coral rubble in shallow tropical oceans. The body of Acetabularia is a single very large cell.

a: ©Brian P. Piasecki; b: ©Roland Birke/Phototake; c–e: ©Linda Graham

Many protists live within periphyton—communities of microorganisms attached by mucilage to underwater surfaces such as rocks, sand, and plants. Because sinking is not a problem for attached protists, these often produce multicellular bodies, such as branched filaments (Figure 28.3d). Photosynthetic protists large enough to see with the unaided eye are known as macroalgae, or seaweeds. Although the bodies of some macroalgae are very large single cells (Figure 28.3e), most macroalgae are multicellular, often producing large and complex bodies. Macroalgae usually grow attached to underwater surfaces such as rocks, sand, docks, ship hulls, or offshore oil platforms. Seaweeds require sunlight and carbon dioxide for photosynthesis and growth, so most of them grow along coastal shorelines, fairly near the water’s surface. Macroalgae serve as refuges for aquatic animals, generate large amounts of organic carbon that enters aquatic food chains, and play additional important ecological roles. Humans harvest some macroalgae for use as food or crop fertilizers or as sources of industrial chemicals to make diverse commercial products.

of one or only a few cells and are small—usually from 2 to 20 µm long—because flagellar motion is not powerful enough to keep larger bodies from sinking. Some flagellate protists are sedentary, living attached to underwater surfaces. These protists use flagella to collect bacteria and other small particles for food. Macroalgae and other immobile protists often produce small, flagellate reproductive cells that allow these protists to mate and disperse to new habitats. An alternative type of protist motility relies on cilia, tiny hairlike extensions on the outsides of cells. Cilia are structurally similar to eukaryotic flagella but are shorter and more abundant (Figure 28.4). Protists that move by means of cilia are ciliates. Having many cilia allows ciliates to achieve larger sizes than flagellates yet still remain buoyant in water. A third type of motility is amoeboid movement. This kind of motion involves extending cytoplasm into lobes, known as pseudopodia (from the Greek, meaning false feet). Once these pseudopodia move toward a food source or other stimulus, the rest of the cytoplasm flows after them, thereby changing the shape of the entire

Protists Display Diverse Types of Motility Microscopic protists have evolved diverse ways to propel themselves in moist environments. Swimming by means of flagella or cilia, amoeboid movement, and gliding are major types of protist movements. Many types of photosynthetic and heterotrophic protists are able to swim because they produce one or a few eukaryotic flagella—cellular extensions whose movement is based on interactions between microtubules and the motor protein dynein (refer back to Figure 4.17). Eukaryotic flagella rapidly bend and straighten, thereby pulling or pushing cells through the water. Protists that use flagella to move in water are commonly known as flagellates (Figure 28.3a). Flagellates are typically composed

Cilia

Figure 28.4  SEM image

142.9 μm

of a member of the ciliate genus Paramecium, showing numerous cilia on the cell surface. ©Dennis Kunkel

Microscopy, Inc./Phototake

584

CHAPTER 28 DOMAIN BACTERIA DOMAIN ARCHAEA Eukaryotic supergroups

250 μm

Opisthokonta

Amoebozoa

Rhizaria

Stramenopila

Alveolata

Land plants and relatives

Excavata

Pseudopod

Figure 28.5  SEM image of a member of the amoebozoan

genus Pelomyxa, showing pseudopodia. ©Steve Gschmeissner/Science

Source

Core Skill: Connections  Look ahead to Figure 34.3. What kind of mobile, amoeba-shaped cells carry materials within the bodies of the early-diverging animals known as sponges? 

organism as it creeps along. Protist cells that move by pseudopodia are described as amoebae (Figure 28.5). Finally, many diatoms, the malarial parasite genus Plasmodium, and some other protists glide along surfaces in a snail-like fashion by secreting protein or carbohydrate slime. With the exception of ciliates, the mode of motility does not correspond with the phylogenetic classification of protists, our next topic.

28.2        Evolution and Relationships Learning Outcomes: 1. Describe a distinctive structural characteristic for each of the seven eukaryotic supergroups. 2. List at least one species of each eukaryotic supergroup that is important to human life. 3. CoreSKILL » Draw a diagram showing how the process of endosymbiosis has affected eukaryotic diversity, and predict how this process could continue to affect biodiversity in the future.

At one time, protists were classified into a single kingdom. However, modern phylogenetic analyses based on comparisons of DNA sequences and cellular features reveal that protists do not form a monophyletic group. The relationships of some protists are uncertain or disputed, and new protist species are continually being discovered. As a result, concepts of protist evolution and relationships have been changing as new information becomes available. Even so, molecular and cellular data reveal that many protist phyla can be classified within several eukaryotic supergroups that each display distinctive features (Figure 28.6). All of the eukaryotic supergroups include phyla of protists; some, in fact, contain only protist phyla. The supergroup Opisthokonta includes the multicellular animal and fungal kingdoms and related protists, whereas

Figure 28.6  A phylogenetic tree showing the major eukaryotic

supergroups.  Each of the eukaryotic supergroups shown here includes some protist phyla, and most supergroups consist only of protists. Additional eukaryotic lineages exist but are not shown in this streamlined diagram. Core Concept: Evolution  All species (past and present) are related by an evolutionary history.

another supergroup includes the multicellular plant kingdom and the protists most closely related to it. The study of such protists helps to reveal how multicellularity originated in animals, fungi, and plants. In this section, we survey the eukaryotic supergroups, focusing on the defining features and evolutionary importance of the major protist phyla. We will also examine ways in which protists are important ecologically or in human affairs.

Cells of Many Protists Classified in Excavata have a Feeding Groove The protist supergroup known as the Excavata originated very early among eukaryotes, so this supergroup is important in understanding the early evolution of eukaryotes. Many of the Excavata feed by ingesting small particles of food in their aquatic habitats. Once food particles are collected within the feeding groove, they are then taken into cells by a type of endocytosis known as phagocytosis (from the Greek, meaning cellular eating; Figure 28.7). During phagocytosis, a vesicle of plasma membrane surrounds each food particle and pinches off within the cytoplasm. Enzymes within these food vesicles break the food particles down into small molecules that, upon their release into the cytosol, can be used for energy. Phagocytosis is also the basis for an important evolutionary process known as endosymbiosis, a symbiotic association in which a

PROTISTS

Bacterial prey

Flagellum

Feeding groove

Flagellum (a) A Excavata protist with feeding groove

1

Prey is enveloped by the plasma membrane at the feeding groove.

2

The membrane pinches off a food vesicle within the cytoplasm.

3

585

Other vesicles deliver digestive enzymes to food vesicles; prey is digested for food.

Feeding Bacterial prey groove surface Bacterial prey are consumed by the process of phagocytosis.

Bacterial cell breaking apart

Digestive enzymes

(b) The process of phagocytosis

Figure 28.7  Feeding groove and phagocytosis displayed by many species of supergroup Excavata.  (a) Diagram of Jakoba libera, showing flagella emerging from the feeding groove. (b) Diagram of phagocytosis, the process by which food particles are consumed in a feeding groove. Concept Check:   What happens to food particles after they enter a feeding groove?

smaller species known as the endosymbiont lives within the body of a larger species known as the host. Phagocytosis provides a way for protist cells that function as hosts to take in prokaryotic or eukaryotic cells that function as endosymbionts. Such endosymbiotic cells confer valuable traits and are not digested. Endosymbiosis has played a particularly important role in protist evolution. For example, early in protist history, endosymbiotic bacterial cells gave rise to mitochondria, the organelles that are the major site of ATP synthesis in most eukaryotic cells (look back at Figure 4.31). Consequently, most protists possess mitochondria, though these may be highly modified in some species. Three protist groups classified within Excavata are described next. Euglenoids  The members of Excavata known as euglenoids possess unique, interlocking, ribbon-like protein strips just beneath their plasma membranes (Figure 28.8a). These strips make the surfaces of some euglenoids so flexible that they can crawl through mud. Many euglenoids are colorless and heterotrophic, but Euglena and some other genera possess green plastids and are photosynthetic. Plastids are organelles in plant and algal cells that are distinguished by their synthetic abilities and that were acquired via endosymbiosis. Many euglenoids possess a light-sensing system that includes a conspicuous red structure known as an eyespot, or stigma, and light-detecting molecules located in a swollen region at the base of a flagellum. These structures enable green euglenoids to detect light environments that are optimal for photosynthesis. Most euglenoids produce conspicuous carbohydrate-storage particles that are held in the cytoplasm. Kinetoplastids  The heterotrophic protists informally known as kinetoplastids (formally Kinetoplastea) are named for a large mass of DNA known as a kinetoplast that occurs in their single large mitochondrion (Figure 28.8b). These protists lack plastids, but they do possess an unusual modified peroxisome in which glycolysis takes place, known as a glycosome. (Recall that in most eukaryotes, glycolysis occurs in the cytosol.) Some kinetoplastids, including Leishmania (see Figure 28.8b), which causes an ulcerative skin disease and can result in organ damage,

Eyespot Carbohydratestorage particle Green plastids Protein strips near surface

50 μm (a) Euglena

Nucleus

Red blood cell

Trypanosoma brucei

Kinetoplast 5 μm (b) Leishmania

8 μm (c) Trypanosoma

Figure 28.8  Representative euglenoids and kinetoplastids. 

(a) Euglena has ribbon-like protein strips near its surface, internal green plastids, white carbohydrate-storage particles, and a red eyespot. (b) Fluorescence light micrograph of Leishmania showing the kinetoplast DNA mass typical of kinetoplastid mitochondria. (c) In this artificially colorized SEM, an undulating kinetoplastid (Trypanosoma) appears near disc-shaped red blood cells. a: ©Gerd Guenther/SPL/Science Source; b: ©Ross Waller, University of Cambridge, UK; c: ©Eye of Science/Science Source

586

CHAPTER 28

and Trypanosoma brucei, the causative agent of sleeping sickness, are serious pathogens of humans and other animals (Figure 28.8c). Structural analyses of proteins specific to glycosomes have enabled the development of new ways to selectively kill Trypanosoma by interfering with these proteins. Metamonads  Metamonads (formally Metamonada) are heterotrophic flagellates; some are parasitic species that attack the cells of animal hosts and absorb food molecules released from them. For example, Trichomonas vaginalis causes a sexually transmitted infection of the human genitourinary tract. In this location, T. vaginalis  uses phagocytosis to consume bacteria and host epithelial and red blood cells, as well as carbohydrates and proteins released from damaged host cells. More than 170 million cases of infection by T. vagnalis are estimated to occur each year around the globe, and such an infection can predispose humans to other diseases. T. vaginalis has an undulating membrane and flagella that allow it to move over mucus-coated skin (Figure 28.9a). Giardia intestinalis (previously known as G. lamblia), another parasitic protist, contains two active nuclei and produces eight flagella (Figure 28.9b). G. intestinalis causes giardiasis, an intestinal

Undulating membrane

Undulating membrane with associated flagella 2 μm (a) Trichomonas vaginalis

Flagella

(b) Giardia intestinalis

Figure 28.9  Parasitic members of the supergroup Excavata. 

(a) Trichomonas vaginalis. (b) Giardia intestinalis. These specialized heterotrophic flagellates use flagella to disperse across the surfaces of moist host tissues; the flagellates then absorb nutrients from living cells. These images were made with a scanning electron microscope (SEM) that employs electrons rather than visible light, with the result that cellular structures do not appear in color. a: ©David M. Phillips/Science

Source; b: Source: CDC/Dr. Stan Erlandsen, Dr. Dennis Feely

Concept Check:   How do these two parasitic protists differ in how they are transmitted from one human host to another? 

infection that can result from drinking untreated water or from unsanitary conditions in day-care centers. Nearly 300 million human infections occur every year, and the disease also harms young farm animals, dogs, cats, and wild animals. In the animal body, flagellate cells cause disease and also produce infectious stages known as cysts that are transmitted in feces and can survive several weeks outside a host. When an animal ingests as few as 10 of these cysts, within 15 minutes stomach acids induce the flagellate stage to develop and adhere to cells of the small intestine. T. vaginalis and G. intestinalis were once thought to lack mitochondria, but they are now known to possess simple structures that are highly modified mitochondria.

Core Concept: Evolution Genome Sequences Reveal the Different Evolutionary Pathways of Trichomonas vaginalis and Giardia intestinalis In 2007, genome sequences were reported for T. vaginalis and G. intestinalis.  A comparison of their genomes reveals similarities and differences in the evolution of their parasitic lifestyles. One common feature is that horizontal gene transfer from bacterial or archaeal donors has powerfully affected both genomes. About 100 G. intestinalis genes are likely to have been acquired via horizontal gene transfer. In T. vaginalis, more than 150 cases of likely horizontal gene transfer were identified, with most transferred genes encoding metabolic enzymes such as those involved in carbohydrate or protein metabolism. Another similarity between T. vaginalis and G. intestinalis revealed by comparative genomics is the apparent absence of the cytoskeletal protein myosin, which is present in most eukaryotic cells. Despite these similarities, the genome sequences of T. vaginalis and G. lamblia reveal some dramatic differences. The G. intestinalis genome is quite compact, with only 11.7 megabase pairs (Mb), and the organism has relatively simple metabolic pathways and machinery for DNA replication, transcription, and RNA processing. In contrast, the T. vaginalis genome is a surprisingly large 160 Mb in size. T. vaginalis has a core set of about 60,000 protein-encoding genes, one of the greatest coding capacities known among eukaryotes. The additional genes provide an expanded capacity for biochemical degradation. Because most trichomonads inhabit animal intestines, the genomic data suggest that the large genome size of T. vaginalis is related to its ecological transition to a new habitat, the urogenital tract.

Land Plants and Related Algae Share Similar Genetic Features The supergroup that includes land plants also encompasses several protist phyla (Figure 28.10). The land plants, also known as the kingdom Plantae (described more fully in Chapters 31 and 32), evolved from green algal ancestors. Together, plants and some closely related



PROTISTS 587

Supergroup: Land plants and relatives

Kingdom Plantae

Streptophyte algae

Streptophyte algae

Streptophyte algae

Streptophyte algae

Chlorophyta

Rhodophyta a

Land plants and related green algae L

(a) Calliarthron

(b) Chondrus crispus

Figure 28.11  Representative red algae (Rhodophyta).  (a) The Multicellularity

genus Calliarthron has cell walls that are impregnated with calcium carbonate. This stony, white material makes the red alga appear pink. (b) Chondrus crispus is an edible red seaweed. a: ©Lee W. Wilcox; b:

©Andrew J. Martinez/Science Source

KEY Primary plastids Critical innovation

Figure 28.10  A phylogenetic tree of the supergroup that

includes land plants and their close protist relatives.  Note that plant multicellularity first arose in closely related streptophyte algae. Many chlorophyte and red algae are macroalgae in which multicellularity arose independently.

green algae form the clade Streptophyta, informally known as streptophytes, whereas most green algae are classified in the phylum Chlorophyta. The red algae, classified in the phylum Rhodophyta, are also regarded as close relatives of green algae and land plants. Green Algae  Diverse structural types of green algae (see Figure 28.3) occur in fresh water, the ocean, and on land or ice surfaces. Most of the green algae are photosynthetic, and their cells contain the same types of plastids and photosynthetic pigments that are present in land plants. Some green algae are responsible for harmful algal growths, but others are useful as food for aquatic animals, as model organisms, and as sources of renewable oil supplies. Many green algae possess flagella or the ability to produce them during the development of reproductive cells. Green algae are increasingly important in medicine because they produce channel rhodopsins, light-activated ion channels. Green algae use these channel proteins to detect and respond to light, and researchers are studying the proteins in an attempt to understand and possibly treat blindness in animals. Red Algae  Most species of the protists known as red algae are multicellular marine macroalgae (Figure 28.11). The red appearance of these algae is caused by the presence of distinctive photosynthetic pigments that are absent from green algae and land plants. Red algae characteristically lack flagella—a feature that has strongly influenced the evolution of this group, resulting in unusually complex life cycles (illustrated in Figure 28.26b). These life cycles are important to humans because red algae are cultivated in ocean waters for the production of billions of dollars worth of food or industrial and scientific materials yearly. For

example, the sushi wrappers called nori are composed of the sheetlike red algal genus Porphyra, which is grown in ocean farms. Carrageenan, agar, and agarose are complex polysaccharides that are extracted from red algae and are essential to the food industry and in biology laboratories for cultivating microorganisms and working with DNA. Primary Plastids and Primary Endosymbiosis  The plastids of red algae resemble those of green algae and land plants (and differ from those of most other algae) in having an enclosing envelope composed of two membranes (Figure 28.12). Such plastids, known as primary plastids, are thought to have originated via a process known as primary endosymbiosis (Figure 28.13). During primary endosymbiosis, heterotrophic host cells captured cyanobacterial cells via phagocytosis but did not digest them. These endosymbiotic cyanobacteria provided host cells with photosynthetic capability and other useful biochemical pathways and eventually evolved into primary plastids (Figure 28.13a). Endosymbiotic acquisitions of plastids and mitochondria resulted in massive horizontal gene transfer from the endosymbiont to the host nucleus. As a result of such gene transfer, many of the proteins needed by plastids and mitochondria are synthesized in the host cytosol and then targeted to these organelles. All cells of plants, green algae, and red algae contain one or more plastids, and most of these Envelope of 2 membranes

Thylakoids

Figure 28.12  A primary plastid, showing an envelope composed

of two membranes.  The plastid shown here is red, but primary plastids can also be green or blue-green in color. ©Joe Scott, Department of Biology, College of William and Mary, Williamsburg, VA 23187

588

CHAPTER 28

Cyanobacterium

Food vesicle

A protist without a plastid ingests a cyanobacterium.

Primary plastid

Feeding groove

Endosymbiotic cyanobacterium evolves into a primary plastid having an envelope of 2 membranes.

(a) Primary endosymbiosis

A protist without a plastid ingests a red or green alga.

Green alga

Secondary plastid

A plastid of eukaryotic alga is retained as a secondary plastid having more than 2 envelope membranes.

Red alga (b) Secondary endosymbiosis

A dinoflagellate ingests a eukaryotic protist having a secondary plastid.

Tertiary plastid Extended feeding structure

The endosymbiont’s plastid is retained by the host as a tertiary plastid having multiple membranes.

(c) Tertiary endosymbiosis

Figure 28.13  Primary, secondary, and tertiary endosymbiosis.  (a) Primary endosymbiosis involves the acquisition of a cyanobacterial

endosymbiont by a host cell without a plastid. During the evolution of a primary plastid, the bacterial cell wall is lost, and most endosymbiont genes are transferred to the host nucleus. (b) Secondary endosymbiosis involves the acquisition by a host cell of a eukaryotic endosymbiont that contains one or more primary plastids. During the evolution of a secondary plastid, most components of the endosymbiont cell are lost, but a plastid is often retained within an envelope of endoplasmic reticulum. (c) Tertiary endosymbiosis involves the acquisition by a host cell of a eukaryotic endosymbiont that possesses secondary plastids.

organisms are photosynthetic. However, some species (or some of the cells within the multicellular bodies of photosynthetic species) are heterotrophic because photosynthetic pigments are not produced in the plastids. In these cases, plastids play other essential metabolic roles, such as producing amino acids and fatty acids. Secondary Plastids and Secondary Endosymbiosis  In contrast to the primary plastids of plants and green and red algae, the plastids of most other photosynthetic protists are derived from a photosynthetic eukaryote. Such plastids are known as secondary plastids because they originated by the process of secondary endosymbiosis (see Figure 28.13b). Secondary endosymbiosis occurs when a eukaryotic host cell ingests and retains another type of eukaryotic cell that already has one or more primary plastids, such as a red or green alga. Such eukaryotic endosymbionts are often enclosed by the endoplasmic reticulum (ER), explaining why secondary plastids typically have envelopes of more than two membranes. Although most of the

endosymbiont’s cellular components are digested over time, its plastids are retained, providing the host cell with photosynthetic capacity and other biochemical capabilities. Cryptomonads (Figure 28.14a) and haptophytes are algal phyla that include single-celled flagellates whose plastids originated by secondary endosymbiosis involving the incorporation of plastids derived from a red alga. Occurring in marine and fresh waters, cryptomonads are excellent sources of the fatty-acid-rich food essential to aquatic animals. Haptophytes are primarily unicellular marine photosynthesizers; some have flagella and others do not. Some haptophytes are known as the coccolithophorids because they produce a covering of intricate white calcium carbonate discs known as coccoliths (Figure 28.14b). Coccolithophorids often form massive ocean growths that are visible from space and play important roles in Earth’s climate by reflecting sunlight. In some places, coccoliths produced by huge populations of ancient coccolithophorids accumulated on the ocean floor, together with the calcium carbonate remains of other protists, for millions



PROTISTS 589

Foraminifera

Chlorarachniophyta

Phaeophyceae

Bacillariophyceae

Oomycota

Dinozoa

Apicomplexa

Ciliophora

Alveolata

Radiolaria

Rhizaria

Stramenopila

Flagellum

59.5 μm (a) A cryptomonad

Coccoliths

Flagellar hairs

Alveoli

Filose pseudopodia

KEY 1.0 μm

(b) A haptophyte coccolithophorid

Algae Protozoa Fungus-like protists Critical innovations

Figure 28.15  A phylogenetic tree illustrating the close

relationship among the supergroups Alveolata, Stramenopila, and Rhizaria.  Some stramenopiles, such as giant kelps, are multicellular.

(c) Fossil deposit containing coccolithophorids

Figure 28.14  Representative cryptomonads and haptophytes.  (a) A cryptomonad flagellate. (b) A type of haptophyte known as a coccolithophorid, covered with disc-shaped coccoliths made of calcium carbonate. (c) Fossil carbonate remains of haptophyte algae and protozoan protists known as foraminifera that were deposited over millions of years formed the white cliffs of Dover in England. a: ©Dennis Kunkel Microscopy, Inc./Phototake; b: ©Steve Gschmeissner/Science Source; c: ©Stockbyte/Getty Images

of years. These deposits were later raised above sea level, forming massive limestone formations or chalk cliffs such as those visible at Dover, on the southern coast of England (Figure 28.14c).

Membrane Sacs Lie at the Cell Periphery of Alveolata The three supergroups Alveolata, Stramenopila, and Rhizaria seem to be closely related, based on recent phylogenetic studies (Figure 28.15). These photosynthetic protists have plastids acquired by secondary endosymbiosis or, in some cases, by tertiary endosymbiosis.

Turning first to Alveolata, we see that it includes three important phyla: (1) the Ciliophora, or ciliates; (2) the Apicomplexa, a medically important group of parasites; and (3) the Dinozoa, known as dinoflagellates. Apicomplexans include the malarial agent Plasmodium (see Section 28.4), the related protist Cryptosporidium parvum, whose effects were noted in the chapter opening, and other serious pathogens of humans and other animals. Dinoflagellates are recognized both for their mutualistic relationship with reef-building corals (look ahead to Figure 54.26b) and for the harmful blooms (red tides) that some species produce (see Section 28.3). The supergroup Alveolata is named for saclike membranous vesicles known as alveoli that are present at the cell periphery in all of these phyla (Figure 28.16a). The alveoli of some dinoflagellates seem empty, so the cell surface appears smooth. By contrast, the alveoli of many dinoflagellates contain plates of cellulose, which form an armor-like enclosure (Figure 28.16b). These plates are often modified in ways that provide an adaptive advantage, such as protection from predators or increased ability to float. About half of dinoflagellate species are heterotrophic, and half possess photosynthetic plastids of diverse types that originated by secondary or even tertiary endosymbiosis; therefore, these are known as secondary or tertiary plastids. Tertiary plastids were obtained by tertiary endosymbiosis—the acquisition by hosts of plastids from cells that possessed secondary plastids (see Figure 28.13c). Species having tertiary plastids have received genes by horizontal transfer from diverse genomes.

590

CHAPTER 28 Alveoli

Plastid

Alveoli

Extrusome

Nucleus

Figure 28.16  Dinoflagellates of the supergroup

0.5 μm (a) Cross section through characteristic alveoli

40 μm (b) A dinoflagellate with alveoli containing cellulose that here appears blue

Flagellar Hairs Distinguish Stramenopila The supergroup Stramenopila (referred to as the stramenopiles) encompasses a wide range of algae, protozoa, and fungus-like protists that usually produce flagellate cells at some point in their lives (see Figure 28.15). Stramenopila (from the Greek stramen, meaning straw, and pila, meaning hair) is named for distinctive strawlike hairs that occur on the surfaces of flagella of these protists (Figure 28.17).

Flagellar hairs

Food storage

Figure 28.17  A flagellate stramenopile cell, showing characteristic flagellar hairs. Concept Check:   How do the flagellar hairs aid stramenophile cell motion? 

Wong and Alvin Kwok

These flagellar hairs function something like oars to greatly increase swimming efficiency. Stramenopiles are also known as heterokonts (from the Greek, meaning different flagella), because the two flagella often present on swimming cells have slightly different structures. Heterotrophic stramenopiles include the fungus-like protist Phytophthora infestans, which causes the serious potato disease known as late blight. P. infestans is responsible for an estimated $7 billion in crop losses every year. Photosynthetic stramenopiles include diatoms (Bacillariophyceae), whose glasslike silicate cell walls are elaborately ornamented with pores, lines, and other intricate features (Figure 28.18a). Vast accumulations of the translucent walls of ancient diatoms, known as diatomite or diatomaceous earth, are mined for use in reflective paint and other industrial products. Recent genome sequencing projects have focused on the processes by which diatoms produce their detailed silicate structures; understanding

5 μm

Plastids Nucleus

Alveolata and their characteristic alveoli.  (a) Sacshaped membranous vesicles known as alveoli lie beneath the plasma membrane of a dinoflagellate, along with defensive projectiles, called extrusomes, that are ready for discharge. (b) Fluorescence microscopy reveals that alveoli of the dinoflagellate Alexandrium catenella contain cellulose plates, which glow blue when treated with a cellulosebinding dye. The nucleus appears green because DNA has bound a fluorescent dye, and chlorophyll self-fluoresces red. a: ©Lee W. Wilcox; b: Courtesy Joseph

(a) Diatom

(b) Kelp forest

Figure 28.18  Stramenopiles include diatoms and giant

kelps.  (a) SEM of the silicate cell wall of the common diatom Cyclotella meneghiniana, showing elaborate ornamentation of the structure. The many pores in the colorless silicate wall lighten the cell, helping to keep it afloat in the water. (b) Forests of giant kelps occur along many ocean shores, providing habitat for diverse organisms. a: ©Linda Graham; b: ©Jeff Rotman/Science Source Concept Check:   In what ways are kelp forests economically important? 



PROTISTS 591

Kingdom Fungi

Choanomonada

Kingdom Animalia

Supergroup: Opisthokonta

Nuclearia

of these processes may prove useful in industrial microfabrication applications. Diverse, photosynthetic brown algae (Phaeophyceae) are sources of industrial products such as the polysaccharide emulsifiers known as alginates. Brown algae acquired the ability to produce alginates by means of horizontal transfer of genes from bacteria. The brown algae known as giant kelps are ecologically important because they form extensive forests in cold and temperate coastal oceans (Figure 28.18b). Kelp forests are essential nurseries for fish and shellfish. The reproductive processes of diatoms and kelps are described in Section 28.4.

Multicellularity

Multicellularity

Spiky Cytoplasmic Extensions Are Present on the Cells of Many Protists Classified in Rhizaria Several groups of flagellates and amoebae that have thin, hairlike extensions of their cytoplasm—known as filose pseudopodia—are classified into the supergroup Rhizaria (from the Greek rhiza, meaning root) (see Figure 28.15). Rhizaria includes the phylum Chlorarachniophyta, whose spider-shaped cells possess secondary plastids obtained from endosymbiotic green algae. Other examples of Rhizaria are the Radiolaria (Figure 28.19a) and Foraminifera (Figure 28.19b)—two phyla of ocean plankton that produce exquisite mineral shells. Fossil shells of foraminiferans are widely used to infer past climatic conditions, because ratios of stable oxygen isotopes contained in the shells can be analyzed to reconstruct past water temperatures.

Amoebozoa Includes Many Types of Amoebae with Pseudopodia The supergroup Amoebozoa includes many types of amoebae that move by extension of pseudopodia (see Figure 28.5). Several types of protists known as slime molds are classified in this supergroup. One example, Dictyostelium discoideum, is widely used as a model organism for understanding movement, communication among cells, and development. In response to starvation, large numbers of Dictyostelium amoebae aggregate into a multicellular slug that Filose pseudopodium

Filose pseudopodium

0.5 mm (a) Radiolarian

(b) Foraminiferan

Figure 28.19  Representatives of supergroup Rhizaria.  (a) A

radiolarian, Acanthoplegma spp., showing long filose pseudopodia. (b) A foraminiferan, showing calcium carbonate shell with long filose pseudopodia extending from pores in the shell. a: ©Claude Nuridsany &

Marie Perennou/SPL/Science Source; b: ©O. Roger Anderson, Columbia University, Lamont-Doherty Earth Observatory

KEY Critical innovations

Figure 28.20  A phylogenetic tree of the supergroup

Opisthokonta.  This supergroup includes protist phyla as well as the kingdoms Fungi and Animalia. Multicellularity arose independently in these kingdoms.

produces a cellulose-stalked structure containing many single-celled, asexual spores. In favorable conditions, these spores produce new amoebae, which feed on bacteria. A recent study revealed that some Dictyostelium clones carry favored bacterial food through these reproductive stages, showing a simple “farming” behavior.

A Single Flagellum Occurs on Swimming Cells of Opisthokonta The supergroup Opisthokonta includes the animal and fungal kingdoms and related protists (Figure 28.20). This supergroup is named for the presence of a single posterior flagellum on swimming cells. Nuclearia is a protist genus that feeds by phagocytosis and seems particularly closely related to the kingdom Fungi (Figure 28.21a). The more than 125 species of protists known as choanoflagellates (formally Choanomonada) are single-celled or colonial protists featuring a distinctive collar surrounding the single flagellum (Figure 28.21b). The collar is made of cytoplasmic extensions that filter bacterial food from water currents generated by flagellar motion. Choanoflagellates are believed to represent the closest living relatives of animals. Evolutionary biologists interested in the origin of animals study choanoflagellates for molecular clues to this important event in our evolutionary history. Genomic studies have revealed genes that encode cell adhesion and extracellular matrix proteins. Such proteins help choanoflagellates attach to surfaces and were also essential to the evolution of multicellularity in animals. The choanoflagellate genome also encodes the p53 protein, a regulatory transcription factor that plays essential roles in the animal cell cycle, cancer, and reproduction (refer back to Figure 15.15). The preceding survey of protist diversity, summarized in Table 28.1, illustrates the enormous evolutionary and ecological importance of protists. Next, we consider the diverse ways in which protists have become adapted to their environments.

592

CHAPTER 28

Flagellum Collar of cellular extensions

10 µm

50 µm

(a)

(b)

Figure 28.21  Protist members of supergroup Opisthokonta.  (a) The amoeba Nuclearia represents protists most closely related to the

kingdom Fungi. Some of the cytoplasmic particles are food materials that were ingested by phagocytosis. (b) Several choanoflagellate cells are shown on the surface of a green alga. Each cell has a distinctive collar of cellular extensions around the single flagellum, which is used to obtain food particles for ingestion by phagocytosis. a: ©Stephen Fairclough, King Lab, University of California at Berkeley; b: ©Lee W. Wilcox Concept Check:   What features of the ancient choanoflagellate ancestors of animals were important in the evolution of multicellularity, and what function do such features serve in modern choanoflagellates? 

Table 28.1      Eukaryotic Supergroups and Examples of Constituent Kingdoms, Phyla, Classes, or Species Supergroup

KINGDOMS, Phyla, classes, or species

Distinguishing features

Excavata

Metamonada (metamonads)   Giardia intestinalis   Trichomonas vaginalis

Excavata are unicellular flagellates that are often characterized by a feeding groove. Metamonads have modified mitochondria.

Kinetoplastea (kinetoplastids)   Trypanosoma brucei Euglenida (euglenoids)

Kinetoplastid mitochondria are characterized by a large mass of DNA, the kinetoplast.

Land Plants and Relatives

Rhodophyta (red algae) Chlorophyta (green algae) KINGDOM PLANTAE and close green algal relatives

Land plants, green algae, and red algae have primary plastids derived from cyanobacteria; such plastids have two envelope membranes.

Alveolata

Ciliophora (ciliates) Apicomplexa (apicomplexans)   Plasmodium falciparum   Cryptosporidium parvum Dinozoa (dinoflagellates)   Alexandrium catenella

Peripheral membrane sacs (alveoli); some ciliates harbor endosymbiotic algal cells or organelles; apicomplexans may possess nonphotosynthetic secondary plastids; some dinoflagellates have secondary plastids derived from red algae, some have secondary plastids derived from green algae, and some have tertiary plastids derived from diatoms, haptophytes, or cryptomonads.

Stramenopila

Bacillariophyceae (diatoms) Phaeophyceae (brown algae) Phytophthora infestans (fungus-like)

Strawlike flagellar hairs; secondary plastids (when present) derived from red algae; accessory pigment fucoxanthin is common in autotrophic forms.

Rhizaria

Chlorarachniophyta Radiolaria Foraminifera

Thin, cytoplasmic projections; secondary plastids (when present) derived from endosymbiotic green algae

Amoebozoa

Entamoeba histolytica Dictyostelia (a slime mold phylum) Dictyostelium discoideum

Amoeboid movement by pseudopodia

Opisthokonta

Nuclearia spp. KINGDOM FUNGI Choanomonada (choanoflagellates) KINGDOM ANIMALIA

Swimming cells possess a single posterior flagellum.

Some euglenoids have secondary plastids derived from endosymbiotic green algae.



PROTISTS 593

28.3                 N  utritional and Defensive Adaptations Learning Outcomes: 1. List four mechanisms of protist nutrition. 2. CoreSKILL » Predict how photosynthetic protists might respond to a persistent period of darkness. 3. Give examples of major types of protist defensive adaptations.

Protists play diverse and important ecological roles in all kinds of moist habitats. In this section, we will survey nutritional and defensive adaptations that occur widely among protists, that is, in more than one supergroup. Such adaptations help to explain protists’ ecological roles.

Protists Display Four Basic Mechanisms of Nutrition Protists obtain nutrients by four basic mechanisms: phagotrophy, osmotrophy, photoautotrophy, and mixotrophy. Heterotrophic protists that feed by ingesting particles, or phagocytosis, are known as phagotrophs (see Figure 28.7). Protists that rely on osmotrophy—the uptake of small organic molecules across the cell membrane followed by their metabolism—are osmotrophs. Protists that feed on nonliving organic material function as decomposers, essential in breaking down wastes and releasing minerals for use by other organisms. Protists that feed on the living cells of other organisms are parasites that may cause disease in other organisms. Trichomonas vaginalis, Giardia intestinalis, and Phytophthora infestans are examples of pathogenic protists. Humans view such protists as pests when they harm us or our agricultural animals and crops, but pathogenic protists also play important roles in nature by controlling the population growth of other organisms. Photosynthetic protists (algae) are photoautotrophs, organisms that can make their own organic nutrients from inorganic sources by using light energy. Because water absorbs much of the red component of sunlight, algae have evolved photosynthetic systems that compensate by capturing more of the blue-green light available underwater. For example, red algae produce the red pigment phycoerythrin, which absorbs blue-green light and transfers energy to chlorophyll a (see Figure 28.11). Likewise, blue-green light-absorbing fucoxanthin generates the golden and brown colors of other algae (see Figures 28.1, 28.18b). Carotene (the source of vitamin A) and lutein play similar light-absorbing roles in green algae and were inherited by their land plant descendants, today playing important roles in animal nutrition. Sunlight energy is captured in the bonds of polysaccharide and lipid molecules that function in food storage, explaining why algae of diverse types are good sources of food for aquatic animals and of renewable energy materials. Mixotrophs are able to use photoautotrophy and phagotrophy or osmotrophy to obtain organic nutrients. The genus Dinobryon (Figure 28.22), consisting of photosynthetic stramenopiles that live in the phytoplankton of freshwater lakes, is a mixotrophic genus. These protists may switch back and forth between photoautotrophy and heterotrophy, depending on conditions in their environment. If sufficient light, carbon dioxide, and other minerals are available, Dinobryon cells produce their own organic food. If a shortage of

Figure 28.22  A mixotrophic

protist.  The genus Dinobryon consists of colonial flagellates that occur in the phytoplankton of freshwater lakes. The photosynthetic cells have golden photosynthetic plastids and also capture and consume bacterial cells. ©Lee W. Wilcox

any of these resources limits photosynthesis or if organic food is especially abundant, Dinobryon cells can function as heterotrophs, consuming enormous numbers of bacteria. Mixotrophs thus have remarkable nutritional flexibility, explaining why many lineages of photosynthetic eukaryotes seem to have mixotrophic capability.

Protists Defend Themselves in Diverse Ways Protists use a wide variety of defensive adaptations to ward off attack. Major types of defenses are sharp projectiles that can be explosively shot from cells, light flashes, toxic compounds, and cell coverings. Evolutionarily diverse protist cells contain structures known as extrusomes (extruded bodies) that are ejected when cells are disturbed, forming spear-like defenses (see Figure 28.16a). Some species of ocean dinoflagellates emit flashes of blue light when disturbed, explaining why ocean waters teeming with these protists display bioluminescence. The light flashes may deter herbivores by startling them, but when ingested, the dinoflagellates make the herbivores also glow, revealing them to hungry fishes. Light flashes benefit dinoflagellates by helping to reduce populations of herbivores that consume the algae. Various protist species produce toxins, compounds that inhibit animal physiology and may function to deter small herbivores. Dinoflagellates are probably the most important protist toxin producers; they synthesize several types of toxins that affect humans and other animals. Why does this happen? Under natural conditions, small populations of dinoflagellates produce low amounts of toxin that do not harm large organisms. Dinoflagellate toxins become dangerous to humans when people contaminate natural waters with excess mineral nutrients such as nitrogen and phosphorus from untreated sewage, industrial discharges, or fertilizer that washes off agricultural fields. The excess nutrients fuel the development of harmful algal blooms, which then produce sufficient toxin to affect birds, aquatic mammals, fishes, and humans. Toxins can become concentrated in organisms. Humans who ingest shellfish that have accumulated dinoflagellate toxins can suffer poisoning. The cell coverings produced by many protists also provide protection. Slimy mucilage (see the chapter opening photo) or spiny cell walls (see Figure 28.3b) provide protection from attack by herbivores or pathogens. Protective cell coverings made of polysaccharide polymers such as cellulose or minerals such as silica help to prevent osmotic damage and may enhance flotation in water. As we have seen, diatoms enclose themselves in glasslike silicate cell walls, haptophytes are covered with calcium carbonate scales, and the cells of brown and green algae secrete tough, cardboard-like cellulose walls. Cellulose-rich cell walls are also features of plant cells, but algal cellulose can be particularly resistant to chemical and microbial degradation, as described next. 

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Core Skill: Process of Science

Feature Investigation  | Cook and Colleagues Demonstrated That Cellulose Helps Green Algae Avoid Chemical Degradation

The periphytic, branched green alga Cladophora (see Figure 28.3d) is common along marine and freshwater shorelines around the world, where it provides essential habitat for dense populations of diverse microorganisms on its extensive surfaces. Amazingly tough cellulose cell walls allow this alga to harbor extensive microbial diversity without readily decomposing. Acting in this host role, Cladophora provides such an important ecological service that it has been called an

ecological engineer, which is a species that strongly affects its habitat. Cladophora is known to be resistant to microbial decay, leading to the buildup of organic carbon in aquatic environments, but the basis of this resistance was unknown until recently. In 2013, American cell biologist Martha Cook and associates performed an experiment to examine the effects of extreme chemical treatment on the cell structure of Cladophora (Figure 28.23).

Figure 28.23  Cook and colleagues showed that the green alga Cladophora produces tough cellulose walls that survive exposure to strong acids and high temperatures, suggesting the potential to leave fossil remains. (left): ©Martha Cook; (middle): ©Linda Graham; (right): ©Nicholas Butterfield GOAL To determine the degree and chemical basis of the resistance to degradation of Cladophora and compare the results to ancient fossils of related algae. KEY MATERIALS Samples of Cladophora collected from natural waters; concentrated acids

Experimental level

1

Conceptual level Holes in lid to release vapor

Treat the algae with a standard mixture of acids, heated to boiling for 30 minutes, then centrifuge to sediment the algal remains and remove acid.

Acid mixture

High-temperature acid treatment, known as acetolysis, would be expected to break down the cellulose microfibrils in land plants and other types of algae.

Plastic tube Pipette tip

Green algae

Acid to be removed

Organic algal remains

2

Examine algal remains by means of scanning electron microscopy to determine their structure.

Structure of the algal remains suggests that the biochemical composition includes fibrils made of celluose. Dimensions of microfibrils indicate the degree of chemical resistance: Microfibrils of greater width are known to have greater resistance to degradation.

3

Examine algal remains using a light microscope equipped with crossed polarizers. Compare microscopic appearance of the remains to that of 750-million-year-old fossils.

Crossed polarizers reveal birefringence, a sparkling white appearance typical of highly crystalline cellulose.



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5

Compare modern Cladophora to ancient algal fossils.

Compare the results of steps 3 and 4 to ancient fossils of related algae.

4

Cladophora and the ancient algal fossils look similar. Biochemical materials that survive high-temperature acid treatment are also likely to have survived microbial degradation long enough to have formed organic fossils.

THE DATA

100 μm

5 μm SEM of Cladophora after acetolysis. Microfibrils of cellulose are 100 nanometers in diameter, thicker than those in land plant cell walls, which are only 3.5 nm thick.

Light microscope view of acetolyzed Cladophora using crossed-polarizers. The sparkling white appearance is typical of highly crystalline cellulose.

50 μm A 750-million-year-old fossil, Proterocladus, shows similar dimensions and distinctive branching pattern to modern Cladophora, even when the latter has been treated by acetolysis.

6

CONCLUSION Tough cell-wall cellulose resists chemical degradation, allowing Cladophora-like algae to form as fossils and explaining modern ecological persistence in aquatic ecosystems.

7

SOURCE Graham, L. E., Cook, M. E., et al. 2013. Resistance of filamentous chlorophycean, ulvophycean, and xanthophycean algae to acetolysis: Testing Proterozoic and Paleozoic microfossil attributions. International Journal of Plant Sciences 174: 947–957.

In the first step of the experiment, the investigators treated the algae with concentrated acids at a boiling temperature to mimic harsh chemical and microbial degradation processes. The second and third steps used two different microscopy methods to examine the algal remains and to determine their chemical makeup. In a final step, the investigators compared the algal remains to fossils of related algae from deposits about 750 million years old. As seen in the data, they found that the remains of modern Cladophora after acid treatment contained cellulose microfibrils that are thicker than those found in plants. The researchers inferred that the microbial resistance of modern Cladophora is derived from the relatively thick cellulose microfibrils present in its cell walls. In addition, the remains of Cladophora

BIO TIPS

THE QUESTION  The experiment by Cook and colleagues revealed that the relatively thick cellulose microfibrils found in the cell walls of Cladophora resist chemical degradation. How much thicker are these algal cellulose microfibrils than the cellulose microfibrils in less-resistant plant cell walls? T OPIC  What topic in biology does this question address? The topic is protist defensive structures. More specifically, the question is about the biochemical makeup of the cellulose-rich cell walls of a common green alga.

closely resembled the ancient fossils of related algae. These results are consistent with the idea that a cell wall that can withstand acetolysis may also have resisted microbial degradation long enough to allow the formation of fossils. Experimental Questions 1. Why did the investigators collect the alga Cladophora from its natural habitat?  2. Why is boiling in concentrated acid a reasonable way to investigate the presence of biological materials that may resist decay long enough to form fossils? 

I NFORMATION  What information do you know based on the question and your understanding of the topic? From Chapter 10, you may remember that plant cells are typically enclosed by a cell wall that is rich in cellulose, a biochemical material that provides strength and compression resistance. You learned that the strength of cellulose derives from extensive hydrogen bonding between adjacent chains. In this chapter, you learned that protist cells are enclosed by a variety of protective materials, including cellulose that differs in structure (for example, forms microfibrils that are thicker) and is consequently

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more resistant to degradation than is cellulose present in land plant cell walls. You also learned that the aquatic green alga Cladophora is known to host dense populations of hundreds of microbial species on its surfaces, suggesting that it has adapted to resist microbial attack. P ROBLEM-SOLVING  S TRATEGY  Interpret data. Compare and contrast. Make a calculation. The data in Figure 28.23 include an SEM image of Cladophora cell-wall cellulose microfibrils, with a scale bar enabling an estimation of their width. The data also provide information as to the width of land plant cellulose microfibrils. To calculate their relative widths, compare the two types of microfibrils.

ANSWER The microfibrils of cellulose in Cladophora cell walls are 100 nm in diameter, whereas those of land plants are 3.5 nm wide. If you divide 100 nm by 3.5 nm, the Cladophora microfibrils are about 29 times thicker than those of land plants.  Note: This greater thickness reduces susceptibility to microbes, which start enzymatic attacks on cellulose at the microfibril surface. Thinner microfibrils have more exposed surface area where microbial attack can start. More extensive hydrogen bonding in the highly crystalline algal cellulose renders it less susceptible to chemical attack.

28.4                 R  eproductive Adaptations Learning Outcomes: 1. Briefly describe asexual reproduction of protists and three types of sexual life cycles observed in some protists. 2. CoreSKILL » Predict the number of chromosome sets (n or 2n) of an organism, given information about the type of cell that undergoes meiosis. 3. Give examples of how protist life cycles are important to humans.

Diverse reproductive adaptations allow protists to thrive in an amazing variety of environments, including the bodies of hosts in the cases of parasitic protists. These adaptations include specialized asexual reproductive cells, tough-walled dormant cells that allow protists to survive periods of environmental stress, and several types of sexual life cycles.

Protist Populations Increase by Means of Asexual Reproduction All protists are able to reproduce asexually by mitotic cell divisions of parental cells to produce progeny. When resources are plentiful, repeated mitotic divisions of single-celled protists generate large protist populations. Multicellular protists often generate specialized asexual cells that help disperse the organisms in their environment. Many protists produce unicellular cysts as the result of asexual (and in some cases, sexual) reproduction (Figure 28.24). Cysts often have thick, protective walls and can remain dormant through periods of unfavorable climate or low food availability. Dinoflagellates commonly produce cysts that can be transported in the water of a ship’s

Cysts

Active cell

Figure 28.24  Protistan cysts.  The round cells are dormant,

tough-walled cysts of the dinoflagellate Peridinium limbatum. The pointed cell is an actively growing cell of the same species. As cysts develop, the outer cellulose plates present on actively growing cells are cast off. ©Linda Graham Concept Check:   How are cysts involved in the spread of harmful algae and disease-causing parasitic protists? 

ballast from one port to another, a problem that has caused harmful dinoflagellate blooms to appear in harbors around the world. Ship captains can help to prevent such ecological disasters by heating ballast water before it is discharged from ships. Many disease-causing protists spread from one host to another via cysts. As noted in the chapter opener, the alveolate pathogen Cryptosporidium parvum infects humans via waterborne cysts. The amoebozoan Entamoeba histolytica infects people who consume food or water that is contaminated with its cysts. Once inside the human digestive system, E. histolytica attacks intestinal cells, causing amoebic dysentery.

Sexual Reproduction Provides Multiple Benefits to Protists Eukaryotic sexual reproduction, featuring gametes, zygotes, and meiosis, first arose among protists. Sexual reproduction has not been observed in some protist phyla but is common in others. Sexual reproduction is generally adaptive because it produces diverse genotypes, thereby increasing the potential for faster evolutionary responses to environmental change. Many protists reap additional ecological benefits from sexual reproduction. Protists illustrate three major types of sexual life cycles that were introduced in Chapter 16: haploid dominant, alternation of generations, and diploid dominant. Ciliates and protistan parasites that exist in different life cycle stages in different host species display variations of these basic types.  Haploid-Dominant Life Cycles  Most unicellular protists that reproduce sexually display a haploid-dominant life cycle, meaning that most stages in the life cycle are haploid (Figure 28.25). In this type of life cycle, haploid cells may develop into gametes. Some protists produce nonmotile eggs and smaller flagellate sperm. However, many other protists have gametes that look similar to each other



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2 1

Young cells

Populations of haploid (n) cells grow by repeated mitotic division.

Low nitrogen or other environmental change stimulates cells to develop into gametes. Gametes of different mating types (+ and –) are released. (–) gametes

Mitosis (+)

(–)

Mature cell 3 5

The zygote divides by meiosis, yielding 4 haploid cells.

(+) gametes 4

Mating occurs between gametes of opposite types.

A diploid (2n) dormant zygote forms and develops a tough wall. Fertilization

KEY Meiosis

Haploid Diploid

Figure 28.25  Haploid-dominant life cycle, illustrated by the unicellular flagellate genus Chlamydomonas.  In Chlamydomonas, most cells are haploid; only the zygote is diploid. structurally but have distinctive biochemical features and hence are known as + and – mating types, as shown in Figure 28.25. Gametes fuse (mate) to produce thick-walled diploid zygotes, the only diploid stage in this type of life cycle. Such zygotes often have tough cell walls and can survive stressful conditions, much like cysts. When conditions permit, the zygote divides by meiosis to produce haploid cells that increase in number via mitotic cell divisions. Alternation of Generations  Many multicellular green and brown seaweeds display a life cycle involving alternation of haploid and diploid generations (Figure 28.26). Giant kelps and some other protists having this kind of life cycle produce two types of multicellular organisms: a haploid gametophyte generation that produces gametes and a diploid sporophyte generation that produces spores by the process of meiosis (Figure 28.26a). Each of the two types of multicellular organisms can adapt to distinct habitats or seasonal conditions, allowing these protists to occupy more types of environments and for longer periods. Many red seaweeds display a life cycle that involves the alternation of three distinct multicellular generations (Figure 28.26b). This unique type of sexual life cycle has evolved as compensation for the lack of flagella on red algal sperm. Because these sperm are unable to swim to eggs, fertilization occurs only when sperm carried by ocean currents happen to drift close to eggs. As a consequence, fertilization can be rare. Many red algae therefore amplify the products of a rare fertilization by copying the zygote genome into millions of spores produced by two successive sporophyte generations. Small

diploid sporophytes that are nourished by the parental gametophyte produce diploid spores that may each grow into a larger sporophyte. This larger sporophyte produces many haploid spores. Diverse economically valuable red algae possess this type of life cycle, an understanding of which is critical to growing seaweed crops. Diploid-Dominant Life Cycles  Diatoms, which commonly occur as single cells that provide nutritious food for aquatic animals, represent protists known to display a diploid-dominant life cycle (Figure 28.27). In diploid-dominant life cycles, all cells except the gametes are diploid, and the gametes are produced by meiosis. Sexual reproduction in diatoms not only increases their genetic variability, but also has another major benefit related to cell size. In many diatoms, one daughter cell arising from asexual reproduction, which involves mitosis, is smaller than the other, and it is also smaller than the parent cell (Figure 28.27a). This happens because diatom cell walls are composed of two overlapping halves, much like two-part round laboratory dishes having lids that overlap the bottoms. After each mitotic division, each daughter cell receives one-half of the parent cell wall. The daughter cell that inherits a larger, overlapping parental “lid” then produces a new “bottom” that fits inside. This daughter cell will be the same size as its parent. However, the daughter cell that inherits the parental “bottom” uses this as its lid and produces a new, even smaller “bottom.” This cell will be smaller than its sibling or parent. Consequently, after many such mitotic divisions, the mean cell size of diatom populations declines over time. If diatom cells become too small, they cannot survive.

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KEY

1

Meiosis

When mature, the diploid (2n) seaweed produces haploid (n) spores by meiosis.

Mitosis

Zygotes grow into diploid sporophytes by mitosis.

Egg-producing gametophyte (n)

2b

Egg (n)

Another type of haploid (n) spore swims away and eventually settles, growing into a small egg-producing gametophyte.

Sperm (n)

Mitosis Mature sporophyte (2n)

One type of haploid (n) spore swims away and eventually attaches to a surface and grows into a small sperm-producing gametophyte.

Sperm (n)

Egg (n) Zygote (2n)

4

Sperm-producing gametophyte (n) Mitosis 2a

Spores (n)

Haploid Diploid

Fertilization

3

Eggs secrete chemicals that attract sperm, and fertilization occurs.

(a) Laminaria life cycle—alternation of 2 generations

Sperm (n) 3

Male gametophyte (n)

2

Female gametophytes produce eggs that remain on the gametophyte. Male gametophytes produce sperm that are dispersed.

Egg (n)

Fertilization Nourishing female gametophyte tissue (n)

Female gametophyte (n)

Mitosis

Haploid spores (n)

2n zygote nucleus

Small sporophyte (2n)

Diploid spores (2n) Large sporophyte (2n)

1

Some cells of the large diploid (2n) red algal sporophyte undergo meiosis, producing haploid (n) spores that grow by mitosis into haploid gametophytes.

Sperm, lacking flagella, drift to egg cells, and fertilization produces a zygote.

4 Mitosis

Meiosis 5

Diploid spores attach to a surface and grow into a large sporophyte.

The diploid (2n) zygote uses food from the female gametophyte to undergo many mitotic divisions, producing a small sporophyte that releases many diploid spores, which are dispersed.

(b) Polysiphonia life cycle—alternation of 3 generations

Figure 28.26  Alternation of generations.  (a) Life cycle with two alternating generations, illustrated by the brown seaweed Laminaria. (b) Life cycle involving three alternating generations, illustrated by the common red seaweed Polysiphonia. Sexual reproduction allows diatom species to attain maximal cell size. Diatom cells mate within a blanket of mucilage, with each partner undergoing meiotic divisions to produce gametes. The large, spherical diatom zygotes that result from fertilization (Figure 28.27b) later undergo a series of mitotic divisions to produce new diatom cells having the maximal size for the species. Maintaining size

consistent with survival is important because diatoms provide a large proportion of the organic food at the base of marine and freshwater food chains. Ciliate Reproduction  Ciliate protists reproduce asexually by mitosis and formation of cysts (Figure 28.28a). In addition, ciliates can reproduce



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After many cell divisions, some progeny cells are very small.

Figure 28.27  Diploid-dominant life cycle, as illustrated by

diatoms.  (a) Asexual reproduction in diatoms involves repeated mitotic division of cells having a two-piece cell wall—a top “lid” covering a “bottom.” Because a new bottom cell-wall is always synthesized at the end of each mitotic division, asexual reproduction may eventually cause a decline in the mean cell size of a diatom population. (b) Small cell size may trigger sexual reproduction, which regenerates maximal cell size.

(a) Asexual reproduction in diatoms

3 2

Blanketed by mucilage, each cell produces 1 or more haploid gametes by meiosis. The gametes may look alike or take the form of sperm and eggs.

Haploid (n) gametes

The gametes fuse to form a diploid zygote that is larger and rounder than a typical diatom cell.

Meiosis Fertilization

Diploid (2n) zygote

Mucilage

KEY Haploid Diploid

Mitosis

Lipid food storage Plastids

1

When diatom cells reach a critical small size or are stimulated by environmental factors, they may begin the process of sexual reproduction.

4

The 2n zygote undergoes mitotic divisions to produce diploid cells that have the typical shape and maximum size for that species.

(b) Sexual reproduction in diatoms

sexually by a process known as conjugation. Ciliates are unusual in having two types of nuclei: one or more smaller micronuclei and a single large macronucleus. Macronuclei, which contain many copies of the genome, serve as the source of information for cell function. Both macronuclei and micronuclei divide during asexual mitosis. The diploid micronuclei do not undergo gene expression during growth; instead, their role is to transmit the genome to the next generation during sexual reproduction via conjugation. Different species of ciliates vary as to the details of conjugation; the process for Paramecium caudatum is shown in Figure 28.28b.

Parasitic Protists May Use Alternate Hosts for Different Life Stages Many parasitic protists are notable for using more than one host organism, with different life stages occurring in each host. The

malarial parasite genus Plasmodium is a prominent example. Several species of Plasmodium infect humans, some infect humans and/or other primates, and others infect rodents or birds. The malarial parasite's alternate host is the mosquito in the genus Anopheles. About 40% of humans live in tropical regions of the world where malaria occurs, and as noted earlier, millions of infections and human deaths result each year. Malaria is particularly deadly for young children. Insecticides can be used to control mosquito populations, mosquito nets help to reduce infection, and antimalarial drugs can be used to treat infections. However, malarial parasites can develop drug resistance, and experts are concerned that human cases may double in the next 20 years. When an infected mosquito bites a human, Plasmodium enters the bloodstream in an asexual life stage known as a sporozoite (Figure 28.29). Upon reaching a victim’s liver, sporozoites enter

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Mitotic division Cilia Macronucleus Micronucleus

Cyst Unfavorable conditions

Swimming ciliate

(a) Asexual reproduction by mitosis and cysts

1

2

Two compatible cells conjugate— line up side by side and partially fuse together.

In each cell, the micronucleus undergoes meiosis, producing 4 haploid products, but 3 disintegrate.

3

In each cell, the remaining haploid micronucleus undergoes mitosis.

KEY Haploid Diploid

Haploid (n) micronuclei Micronucleus Macronucleus

Meiosis 7

The cell with 8 nuclei undergoes 2 rounds of cytokinesis to produce 4 mature cells that have 1 micronucleus and 1 macronucleus.

Diploid (2n) nuclei

Mitosis 6

Mitosis

The diploid nucleus undergoes 3 rounds of mitosis, producing 4 macronuclei and 4 micronuclei. Note: The diagram shows only 1 of the 2 cells from step 5.

4

5

The paired cells separate. In each cell, the genetically different micronuclei fuse to form a diploid nucleus.

The 2 cells exchange a haploid micronucleus, and each cell’s macronucleus disintegrates.

(b) Sexual reproduction by conjugation

Figure 28.28  Ciliate reproduction.  (a) The asexual reproductive process in ciliates. (b) The sexual reproductive process, known as conjugation, of the ciliate Paramecium caudatum.



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6

5

In mosquitoes, gametocytes produce gametes that fuse to form a diploid zygote. In the gut, zygotes divide by meiosis to produce haploid sporozoites, which move to the salivary glands of the mosquito.

Gametes

Some merozoites produce sexual structures called gametocytes, which can be taken up by a biting mosquito.

Fertilization

Zygote (2n) Mitosis

Meiosis

Gametocytes (n)

Insid

e mo

Insid

squi

e hu

to

man

Sporozoites (n) in salivary glands 1

4

Merozoites continue to infect more red blood cells, causing cycles of chills and fever in the infected person.

Red blood cell

Liver cell producing merozoites

Plasmodium sporozoites enter human blood by a mosquito bite.

Sporozoite

Merozoites (n)

Mitosis KEY Haploid Diploid

3

2

Sporozoites enter liver cells, where the merozoite stage of Plasmodium forms.

Merozoites are released from liver cells, enter red blood cells, and reproduce, causing red blood cells to burst.

Figure 28.29  Diagram of the life cycle of Plasmodium falciparum, a species that causes malaria in humans.  This life cycle requires two

alternate hosts, humans and Anopheles mosquitoes. Parasite life stages known as sporozoites are transmitted by a mosquito bite, then infect the liver. The parasite life stages known as merozoites are produced in the liver, and infect red blood cells. Concept Check:   In which of the hosts does sexual mating of P. falciparum gametes occur? 

Core Skill: Modeling  The goal of this modeling challenge is to make a simplified model of the one shown in Figure 28.29, to determine if the latter represents a life cycle that is diploid dominant, haploid dominant, or an alternation of generations. Modeling Challenge: Chapter 16 describes the three basic types of eukaryotic sexual life cycles (refer back to Figure 16.14). These cycles are modeled by circular diagrams that show life phases connected by the processes of fertilization, meiosis, and mitotic cell divisions. Animals display a diploid-dominant life cycle; fungi have a haploid-dominant life cycle, and the life cycle of plants involves an alternation of a haploid gametophyte with a diploid sporophyte. This chapter reveals that all of these basic life cycle types occur among protists. Use the detailed sexual life cycle shown in Figure 28.29 to identify the life cycle type (diploid dominant, haploid dominant, or alternation of generations) that is characteristic of Plasmodium. To make this decision, draw a very simple circular model representing the cycling of Plasmodium between haploid and diploid life phases and the occurrence of fertilization, meiosis and mitotic cell divisions. Then compare your simple model to the three models shown in Figure 16.14.

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liver cells, where they divide to form an asexual life stage known as merozoites. Hundreds of merozoites are produced within liver cells (see the inset in  Figure 28.29), which then release into the bloodstream packages of merozoites enclosed by a host-derived cell membrane. This membrane protects the merozoites from destruction by host immune cells, which would otherwise engulf the merozoites by phagocytosis and then destroy them. In the bloodstream, the protective host membranes disintegrate, releasing merozoites. The merozoites have protein complexes at their front ends, or apices, that allow them to invade human red blood cells. (The presence of these apical complexes gives rise to the phylum name Apicomplexa.) Within red blood cells, merozoites release more than 200 proteins, which enable the parasites to commandeer these cells, causing many changes. For example, infected red blood cells form surface knobs that function like molecular Velcro, attaching cells to capillary linings. This process allows infected red blood cells to avoid being transported to the spleen, where they would be destroyed. The attachment of infected red blood cells to capillary linings disrupts circulation in the brain and kidney, a process that can cause death of the animal host. While living within red blood cells, merozoites form rings, which often can be visualized by staining and the use of a microscope, allowing diagnosis. The merozoites consume the hemoglobin in red blood cells, which gives them fuel to reproduce asexually. Large numbers of new merozoites synchronously break out of red blood cells at intervals of 48 or 72 hours. These merozoite reproduction cycles correspond to cycles of chills and fever that an infected person experiences. Some merozoites produce sexual structures—gametocytes—which, along with blood, are transmitted to a female mosquito as it bites an infected person. Within the mosquito’s body, the gametocytes produce gametes and fertilization occurs, yielding a zygote, the only diploid cell in Plasmodium’s life cycle. Within the mosquito gut, the zygote undergoes meiosis, generating structures filled with many sporozoites, the stage that can be transmitted to a new human host. Sporozoites move to the mosquito’s salivary glands, where they remain until they are injected into a human host when the mosquito feeds. In recent years, genomic information has added to our knowledge of these life stages, thereby helping medical scientists develop new ways to prevent or treat malaria. For example, about 10% of the nuclear-encoded proteins of P. falciparum are likely imported into a non-photosynthetic plastid known as an apicoplast, where they are needed for fatty-acid metabolism and other processes. Plasmodium and some other apicomplexan protists possess plastids because they are descended from algal ancestors that had photosynthetic plastids. Because plastids are not present in mammalian cells, enzymes in metabolic pathways in the apicoplast are possible targets for development of drugs that will kill the parasite without harming the host. Mammals also lack calcium-dependent protein kinases (CDPKs), enzymes that are essential to the release of parasite merozoites from red blood cells and also needed for the parasite’s sexual development, offering another potential drug target.

Summary of Key Concepts 28.1  An Introduction to Protists ∙∙ Protists are eukaryotes that are not classified in the plant, animal, or fungal kingdoms; are abundant in moist habitats; and are mostly microscopic in size. ∙∙ Protists are often informally labeled according to their ecological roles: Algae are mostly photosynthetic protists; protozoa are heterotrophic protists that are often mobile; and fungus-like protists resemble true fungi in some ways (Figures 28.1, 28.2). ∙∙ Protists are particularly diverse in aquatic habitats, occurring as small floating or swimming phytoplankton, attached members of a periphyton, and more complex macroalgae (seaweeds) (Figure 28.3). ∙∙ Microscopic protists propel themselves by means of flagella (flagellates), cilia (ciliates), or pseudopodia (amoebae) or by gliding across surfaces (Figures 28.4, 28.5).

28.2     Evolution and Relationships ∙∙ Modern phylogenetic analysis has revealed that protists do not form a monophyletic group; instead, many are classified into one of seven major eukaryotic supergroups (Figure 28.6). ∙∙ The supergroup Excavata consists of flagellate protists whose cells often have a feeding groove. Excavata include the kinetoplastids and euglenoids, some of which are photosynthetic (Figures 28.7, 28.8, 28.9). ∙∙ Land plants are related to green algae and red algae (having primary plastids). Cryptomonads and haptophytes display secondary plastids (Figures 28.10, 28.11, 28.12, 28.13, 28.14). ∙∙ The supergroup Alveolata includes the ciliates, apicomplexans, and dinoflagellates, all of whose cells feature saclike membrane vesicles called alveoli. Many dinoflagellates display secondary plastids, and some feature tertiary plastids (Figures 28.15, 28.16). ∙∙ The supergroup Stramenopila includes protists whose flagella have strawlike hairs that aid in swimming. Stramenopiles include diatoms, giant kelps, and other groups of algae, as well as some fungus-like protists (Figures 28.17, 28.18). ∙∙ The supergroup Rhizaria consists of flagellates and amoebae with thin hairlike extensions of cytoplasm called filose pseudopodia. Three prominent phyla are Chlorarachniophyta, with secondary green plastids; silicateshelled Radiolaria; and Foraminifera, with calcium carbonate shells (Figure 28.19). ∙∙ The supergroup Amoebozoa is composed of many types of amoebae and includes slime molds such as Dictyostelium discoideum. ∙∙ The supergroup Opisthokonta includes organisms that are swimming cells having a single posterior flagellum. Opisthokonta includes the fungal and animal kingdoms and related protists (Figures 28.20, 28.21, Table 28.1).



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28.3     Nutritional and Defensive Adaptations ∙∙ Protists display four mechanisms of nutrition: phagotrophs feed by ingesting particles; osmotrophs absorb small organic molecules; photoautotrophs make their own organic food by using light energy; and mixotrophs use both photoautotrophy and heterotrophy to obtain nutrients (Figure 28.22). ∙∙ Protists possess defensive adaptations such as sharp projectiles, light flashes, toxic compounds, and protective cell coverings. The green alga Cladophora is a protist that has cellulose-rich cell walls so tough that they help to explain ancient fossils, and it also plays an important modern ecological role (Figure 28.23).

28.4     Reproductive Adaptations ∙∙ Protist populations grow by means of asexual reproduction involving mitosis, and many persist through unfavorable conditions by producing tough-walled cysts (Figure 28.24). ∙∙ Sexual reproduction is also observed among protists. In the haploid-dominant life cycle, haploid cells develop into gametes, which fuse to produce diploid zygotes. These zygotes often have tough cell walls that enable them to survive unfavorable conditions (Figure 28.25). ∙∙ In protists displaying a life cycle called alternation of generations, a haploid generation produces gametes and a diploid generation produces spores. Each generation can adapt to different environments or conditions, allowing protists to occupy multiple habitats (Figure 28.26). ∙∙ In the diploid-dominant life cycle, all cells except gametes are diploid. Sexual reproduction in diatoms, which have this type of life cycle, increases genetic variability and allows the protists to maintain an adequate cell size (Figure 28.27). ∙∙ Ciliate protists display both asexual reproduction and sexual reproduction by conjugation (Figure 28.28). ∙∙ Parasitic protists may have life cycles involving alternate hosts for different life stages. One example is Plasmodium, which causes malaria in humans and infects some other animals; certain mosquitoes are the alternate hosts (Figure 28.29).

Assess & Discuss Test Yourself 1. If you were studying the evolution of animal-specific cell-to-cell signaling systems, from which of the following would you choose representative species to observe? a. Rhodophyta b. Excavata c. Choanomonada d. Radiolaria e. Chlorophyta

2. If you were studying the origin of land plant traits, which of the following groups would you study? a. green algae b. radiolarians c. choanoflagellates d. diatoms e. ciliates 3. Which informal ecological group of protists includes photoautotrophs? a. protozoa b. algae c. fungus-like protists d. ciliates e. All of the above groups include photoautotrophs. 4. How would you recognize a primary plastid? It would a. have one envelope membrane. b. have two envelope membranes. c. have more than two envelope membranes. d. lack pigments. e. be golden brown in color. 5. What organisms have tertiary plastids? a. certain stramenopiles b. certain euglenoids c. certain cryptomonads d. certain opisthokonts e. certain dinoflagellates 6. What is surprising about mixotrophs? a. They have no plastids, but they occur in mixed communities with autotrophs. b. They have mixed heterotrophic and autotrophic mechanisms of nutrition. c. Their cells contain a mixture of red and green plastids. d. Their cells contain a mixture of haploid and diploid nuclei. e. They consume a mixed diet of algae. 7. What advantages do diatoms obtain from sexual reproduction? a. increased genetic variability b. increased ability of populations to respond to environmental change c. evolutionary potential d. regeneration of maximal cell size for the species e. all of the above 8. What are extrusomes? a. hairs on flagella b. membrane sacs beneath the cell surface c. tough-walled asexual cells d. spearlike defensive structures shot from cells under attack e. special types of survival cysts 9. How do pigments, such as phycoerythrin in red algae and fucoxanthin in brown algae, benefit these autotrophic protists? a. The pigments provide camouflage, so herbivores cannot see the algae. b. The pigments absorb blue-green underwater light and transfer the energy to chlorophyll a for use in photosynthesis. c. The pigments attract aquatic animals that carry gametes between seaweeds. d. The pigments absorb UV light that would harm the photosynthetic apparatus. e. All of the above are correct.

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10. What are the alternate hosts of the malarial parasite Plasmodium falciparum? a. humans and ticks b. ticks and mosquitoes c. humans and Anopheles mosquitoes d. humans and all types of mosquitoes e. sporophytes and gametophytes

Conceptual Questions 1. Explain why protists are classified into multiple supergroups, rather than as a single kingdom or phylum.  2. Why have molecular biologists sequenced the genomes of several parasitic protists?    3. 

Core Concept: Science and Society  Why are the cysts of protists important to epidemiologists, the biologists who study the spread of disease? 

Collaborative Questions 1. Imagine you are studying an insect species and you discover that the insects are dying of a disease that results in the production of cysts of the type that protists often generate. Thinking that the cysts might have been produced by a parasitic protist that could be used as an insect control agent, how would you go about identifying the disease-causing organism? 2. Imagine you are part of a marine biology team seeking to catalogue the organisms inhabiting a threatened coral reef. The team has found two new types of macroalgae (seaweeds), each of which occurs during a particular time of the year when the water temperature is at a certain point. You suspect that the two macroalgae might be different generations of the same species that have differing optimal temperature conditions. How would you go about testing your hypothesis?

CHAPTER OUTLINE 29.1 Evolution and Distinctive Features of Fungi 29.2 Overview of Asexual and Sexual Reproduction in Fungi 29.3 Diversity of Fungi 29.4 Fungal Ecology and Biotechnology Summary of Key Concepts Assess & Discuss

Fungi

29

Y

ou might think that the largest organism in the world is a whale or perhaps a giant redwood tree. Amazingly, giant fungi would also be good candidates. For example, an individual of the fungus species Armillaria ostoyae weighs hundreds of tons, is more than 2,000 years old, and spreads across 2,200 acres of Oregon forest soil! Scientists discovered the extent of this enormous fungus when they found identical DNA sequences in soil samples taken over this wide area. Other examples of such huge fungi have been found, and mycologists—scientists who study fungi—suspect that they may be fairly common, existing underfoot yet largely unseen. Regardless of their size, fungi typically occur within soil or other materials, becoming conspicuous only when the reproductive portions such as mushrooms extend above the surface. Even though fungi can be inconspicuous, they play essential roles in the Earth’s environment; are associated in diverse ways with other organisms, including humans; and have many applications in biotechnology. In this chapter, we will explore the distinctive features of fungal structure, growth, nutrition, reproduction, and diversity. In the process, we will see how fungi are connected to decomposition, forest growth, food production and food toxins, sick building syndrome, and other phenomena of great importance to humans.

29.1  E  volution and Distinctive Features of Fungi Learning Outcomes:

1. CoreSKILL » Use information about groups of fungi to draw a diagram showing their evolutionary relationships. 2. Outline the distinctive features of fungi, including how they obtain food. 3. Discuss how fungal feeding is related to fungal growth.

The eukaryotes known as fungi are so distinct from other organisms that they are placed in their own kingdom, the kingdom Fungi (Figure 29.1). Together with certain closely related protists, the kingdom Fungi and the kingdom Animalia form a eukaryotic supergroup known as Opisthokonta (refer back to

The aboveground reproductive parts of the fungus Armillaria ostoyae. Because of the large extent of its underground components, a member of this species may be the largest organism in the world. ©Brian Lightfoot/naturepl.com

Figure 28.6). The kingdom Fungi, also known as the true fungi, diverged from Animalia more than a billion years ago, during the Middle Proterozoic Era. Several types of slime molds, diseasecausing oomycetes, and other fungus-like protists—though often studied with fungi—are not classified as true fungi (see Chapter 28). The true fungi form a monophyletic group of an estimated 1.5 million species. Even greater diversity of this group is suggested by molecular evidence indicating the existence of many species that have not yet been cultivated or named. The earliest fungi probably originated in aquatic habitats, where they diverged from opisthokont protists closely related to the modern genus Nuclearia— an amoeba that feeds by ingesting algal and bacterial cells. Feeding on particles such as cells is a process known as phagocytosis (see Figure 28.7).  The earliest-diverging phylum of modern fungi, known as Cryptomycota, are unicellular and mostly occur in soil and water. Later-diverging fungi regularly produce a cell wall containing chitin, a tough polysaccharide polymer that contains nitrogen. Such a cell wall enables most fungi to resist the high osmotic pressure

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Supergroup Opisthokonta

Basidiomycota

Ascomycota

Mucoromycota

Blastocladiomycota and Zoopagomycota

Chytridiomycota

Cryptomycota

Nuclearia (protist)

Choanoflagellates (protists)

Metazoa (animal kingdom)

Kingdom Fungi

Septate hyphae, dikaryotic hyphae, fruiting bodies Beneficial associations with photosynthetic organisms and loss of flagella

Rigid chitin cell wall, osmotrophic nutrition

Figure 29.1  Evolutionary relationships of the

KEY Critical innovations Single flagellum

that results when they feed by absorbing small organic molecules, a process known as osmotrophy. The evolution of a rigid cell wall accompanied a key evolutionary transition in fungal nutrition from phagocytosis to osmotrophy (see Figure 29.1). Early-diverging phyla Cryptomycota, Blastocladiomycota, and Chytridiomycota, commonly live in aquatic habitats or moist soils, where they often reproduce by means of cells that swim using flagella. By contrast, later-diverging fungal phyla commonly occupy drier terrestrial environments and do not produce flagellate cells. Loss of flagella is regarded as an adaptation to life on land. Mucoromycota, Ascomycota (also known as ascomycetes, or sac fungi), and Basidiomycota (also known as  basidiomycetes, or club fungi) are notable for displaying symbiotic associations with land organisms, particularly plants. Because fungi are closely related to the animal kingdom, fungi and animals display some common features. For example, both are heterotrophic, meaning that they cannot produce their own food but must obtain it from the environment. Fungi use an amazing array of organic compounds as food, which is termed their substrate. The substrate can be soil, a rotting log, a piece of bread, a living tissue, or a wide array of other materials. Fungi are

fungi.  The kingdom Fungi arose from a protist ancestor similar to the modern genus Nuclearia. Several early-diverging phyla of fungi that commonly occupy moist environments are Cryptomycota, Chytridiomycota, and Blastocladiomycota. Laterdiverging fungal phyla that mostly live on land include Mucoromycota, Ascomycota, and Basidiomycota.

also like animals in using  absorptive nutrition. Both fungi and the cells of animal digestive systems secrete enzymes that break down complex organic materials and absorb the resulting small organic food molecules. In addition, both fungi and animals store surplus food as the carbohydrate glycogen in their cells. Despite these nutritional commonalities, fungal body structure, growth, and reproduction are distinct from those of animals and differ among fungal lineages. Because structure, growth, and reproductive differences are key to understanding fungal diversity, we will focus on these features before exploring fungal diversity in more detail in Section 29.3.

Fungi Have a Unique Body Form Most fungi have a distinctive body known as a mycelium (plural, mycelia), which is composed of individual microscopic, branched filaments known as hyphae (singular, hypha) (Figure 29.2). Even relatively large fungal structures such as fruiting bodies that function in reproduction are composed of hyphae. Hyphae and mycelia evolved even before fungi made the transition from aquatic to terrestrial habitats.



FUNGI 607

Fruiting body above the substrate Mated hyphae Spores

Mycelium within substrate (such as soil)

Region where hyphae mate, forming a fruiting body

Unmated mycelium

Different unmated mycelium

Figure 29.2  Fungal morphology.   The greater part of a typical fungus consists of microscopic food-gathering hyphae that grow and branch

from a central point to form a diffuse mycelium within a food substrate, such as soil. After a mating process occurs, mated hyphae may aggregate and grow out of the substrate, forming relatively large fruiting bodies that produce and disperse spores.

The hyphae of early-diverging fungi are not partitioned into smaller cells. Rather, these hyphae are aseptate and multinucleate (Figure 29.3a), a condition that results when nuclei repeatedly divide without intervening cytokinesis. Such aseptate hyphae are described as being coenocytic. By contrast, the hyphae of later-diverging fungi are subdivided into many small cells by cross walls known as septa (singular, septum) (Figure 29.3b). In such fungi, known as septate fungi, each round of nuclear division is followed by the formation of a septum that is perforated by a small pore. Septate hyphae appeared prior to the divergence of ascomycetes and basidiomycetes (see Figure 29.1). Whether septate or aseptate, a fungal mycelium may be very extensive, as in the case of Armillaria ostoyae (see the chapter opening photo), but is often inconspicuous because the component hyphae are so tiny and spread out within the substrate. The diffuse form of the fungal mycelium makes sense because most hyphae function to absorb organic food from the substrate. By spreading out, hyphae can absorb food from a large volume of substrate. The absorbed food is used for mycelial growth and for reproduction. Mushrooms are examples of fungal reproductive structures called fruiting bodies (see Figure 29.2). Fruiting bodies are composed of densely packed hyphae that have undergone a sexual mating process during which unmated hyphae of genetically different, but compatible, mycelia are attracted to each other and fuse. The resulting mated hyphae differ genetically and biochemically from unmated hyphae.

Researchers suspect that mating hyphae secrete signaling substances that cause many of them to cluster together and grow out of the substrate and into the air, where reproductive cells can be more easily dispersed. Amazingly diverse in form, color, and odor, mature fruiting bodies are specialized to produce and release reproductive cells known as spores. Produced by the process of meiosis and protected by tough cell walls, fungal spores are carried by wind or animals. When fungal spores settle in places where conditions are favorable for growth, they produce new mycelia. When the new mycelia undergo sexual reproduction, they produce new fruiting bodies.

Fungi Have Distinctive Growth Processes If you have ever watched bread or fruit become increasingly moldy over the course of several days, you have observed fungal growth. When a food source is plentiful, fungal mycelia can grow rapidly, adding as much as a kilometer of new hyphae per day. The mycelia grow at their edges as the fungal hyphae extend their tips through the undigested substrate. The narrow dimensions and extensive branching of hyphae provide a very high surface area for absorption of organic molecules, water, and minerals. Hyphal Tip Growth  Cytoplasmic streaming and osmosis are important cellular processes in hyphal growth. Osmosis (see Chapter 5) is the diffusion of water through a membrane, from a solution with a lower solute concentration into a solution with a higher solute

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CHAPTER 29 Nuclei

(a) Aseptate hypha

concentration. Water enters fungal hyphae by means of osmosis because their cytoplasm is rich in sugars, ions, and other solutes. Water entry swells the hyphal tip, producing the force necessary for tip extension. Masses of tiny vesicles carrying enzymes and cellwall materials made in the Golgi apparatus collect in the hyphal tip (Figure 29.4). The vesicles then fuse with the plasma membrane. Some vesicles release enzymes that digest materials in the environment, yielding small organic molecules that are absorbed as food. Other vesicles deliver cell-wall materials to the hyphal tip, allowing it to extend.

Cell wall

Cell wall

Pores

(b) Septate hypha Septa

Nuclei

Variations in Mycelium Growth Form  Fungal hyphae grow rapidly through a substrate from areas where the food has become depleted to food-rich areas. In nature, mycelia may take an irregular shape, depending on the distribution of the food substrate. A fungal mycelium may extend into food-rich areas for great distances, as noted at the beginning of the chapter. In liquid laboratory media,

Figure 29.3  Types of fungal hyphae. Core Concept: structure and Function  This figure compares the multinucleate hypha of an aseptate fungus in part (a) with a hypha of a septate fungus whose cells have a single nucleus in part (b).

1

Vesicle carrying digestive enzymes

Vesicle carrying cell-wall components

Vesicles fuse with plasma membrane, releasing digestive enzymes and cellwall components.

Secreted digestive enzymes

2 Golgi apparatus

Chitin-rich cell wall

5

Digestive enzymes break down extracellular organic polymers into small organic molecules. Small organic molecules

Plasma membrane 3 Site of new cell-wall deposition

Hypha growth

As a result, cells enlarge, and the hyphal tip extends. New cell-wall materials are added to cell wall.

Organic polymers

4

Water

The resulting organic molecules are taken into the hypha via membrane transport proteins.

Higher solute concentration in hypha causes water uptake via osmosis.

Mechanism of hyphal tip growth wth

Figure 29.4  Hyphal tip growth and absorptive nutrition.  Diagram of a hyphal tip, with two types of vesicles, showing the steps of hyphal

tip growth.

Concept Check:   What do you think would happen to fungal hyphae that begin to grow into a substrate with a higher solute concentration? How might your answer be related to food preservation techniques such as drying or salting?



FUNGI 609

(a) Mycelium growing in liquid medium

(b) Mycelium growing on flat, solid medium

Figure 29.5  Fungal shape shifting.   (a) When a mycelium, such

as that of this Rhizoctonia solani, is surrounded by food substrate in a liquid medium, it will grow into a spherical form. (b) When the food supply is limited to two dimensions, as shown by Neotestudina rosatii in a laboratory dish, the mycelium will form a disc. Likewise, distribution of the food substrate determines the mycelium shape in nature. a: ©Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London ON; b: Source: CDC

fungi will grow as a spherical mycelium that resembles a cotton ball floating in water (Figure 29.5a). When grown on the surface of solid media in flat laboratory dishes, the mycelium assumes a more twodimensional form (Figure 29.5b).

29.2      O  verview of Asexual and Sexual Reproduction in Fungi Learning Outcomes: 1. Give examples of fungal asexual reproduction. 2. Identify some of the distinctive sexual reproductive processes in fungi. 3. Explain why humans may safely consume some fungal fruiting bodies, whereas other fungal fruiting bodies are toxic to humans.

Many fungi reproduce either asexually or sexually by means of microscopic spores, each of which can grow into a new mature organism. Asexual reproduction is a natural cloning process; it produces genetically identical organisms. Production of asexual spores allows fungi that are well adapted to a particular environment to disperse to similar, favorable places. By comparison, sexual reproduction generates new allele combinations that may allow fungi to colonize new types of habitats.

Many fungi produce asexual spores known as conidia (from the Greek konis, meaning dust) at the tips of their hyphae (Figure 29.6). When they land on a favorable substrate, conidia germinate into a new mycelium that produces many more conidia. The green molds that form on citrus fruits are familiar examples of conidial fungi. A single fungus can produce as many as 40 million conidia per hour over a period of 2 days. Because they can spread so rapidly, asexual fungi are responsible for costly fungal food spoilage, allergies, and diseases. Medically important fungi that reproduce primarily by asexual means include the athlete’s foot fungus (Epidermophyton floccosum) and the infectious yeast Candida albicans. Yeasts are unicellular fungi of various lineages. Asexual reproduction in some yeasts occurs by budding (Figure 29.7).

Fungi Have Distinctive Sexual Reproductive Processes As is typical for eukaryotes, the fungal sexual reproductive cycle involves the union of gametes, the formation of zygotes, and the process of meiosis. In contrast to plants, whose life cycle is an alternation of haploid and diploid generations, and diploid-dominant animals, the fungal life cycle is typically haploid-dominant (look back at Figure 16.14). However, some early-diverging fungi are notable for a life cycle involving alternation of two generations, a haploid gametophyte and a diploid sporophyte. Some other aspects of fungal sexual reproduction are unique, including the function of hyphal branches as gametes and the development of fruiting bodies. Fungal Gametes and Mating  Early-diverging fungi that live in the water produce flagellate sperm that swim to nonmotile eggs, like the gametes of animals and many protists and some plants. By contrast, the gametes of terrestrial fungi are cells of hyphal branches rather than distinguishable male and female gametes. Fungal mycelia occur in multiple mating types that differ biochemically. The compatibility of these mating types is controlled by particular genes. During fungal sexual reproduction, hyphal branches of different, but compatible mycelia are attracted to each other by secreted peptides, and when hyphae have grown sufficiently close, they fuse. This distinctive mating process represents an adaptation to terrestrial life.

Figure 29.6  Asexual

reproductive cells of fungi.  SEM of the asexual spores (conidia) of Aspergillus versicolor, which causes skin infections in burn victims and lung infections in AIDS patients. Each of these small cells is able to detach and grow into an individual that is genetically identical to the parent fungus and so is able to grow in similar conditions. ©Dennis Kunkel Microscopy,

Fungi Reproduce Asexually by Dispersing Specialized Cells Asexual reproduction is particularly important to fungi, allowing them to spread rapidly. To reproduce asexually, fungi do not need to find compatible mates or expend resources on fruiting-body formation and meiosis. More than 17,000 fungal species reproduce primarily or exclusively by asexual means. DNA-sequencing studies have revealed that many types of modern fungi that reproduce only asexually have evolved from ancestors that used both sexual and asexual reproduction.

69 μm

Inc./Phototake

Concept Check:   How might you try to protect a burn patient from infection by a conidial fungus?

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Spores in a sticky matrix Daughter cell (bud)

Mother cell

(a) Fruiting bodies adapted for dispersal of spores by wind

Figure 29.7  The budding yeast Saccharomyces cerevisiae.  In

budding, a small daughter cell is formed on the surface of a larger mother cell, eventually pinching off and forming a new cell. ©Medical-

on-Line/Alamy Stock Photo

Core Skill: Connections  Look back at Table 14.1, which shows the genome characteristics of some model organisms. How does the genome of S. cerevisiae compare with genomes of other model organisms?

Fruiting Bodies  Under appropriate environmental conditions, such as a seasonal change, a mated mycelium may produce a fleshy fruiting body, such as a mushroom. Fungal fruiting bodies typically emerge from the substrate and produce haploid spores (see Figure 29.2). Each spore acquires a tough chitin-rich wall that protects it from drying out and other stresses. Wind, rain, or animals disperse the mature spores, which grow into haploid mycelia. If a haploid mycelium encounters hyphae of an appropriate mating type, hyphal branches will fuse and start the sexual cycle over again. Mycelium growth requires organic molecules, minerals, and water provided by the substrate, but in most cases, spores are more easily dispersed if released outside of the substrate. The structures of fruiting bodies vary in ways that reflect different adaptations that foster spore dispersal by wind, rain, or animals. For example, mature puffballs have delicate surfaces, and even a slight pressure on one causes the spores to puff out into wind currents (Figure 29.8a). Birds’ nest fungi form characteristic egg-shaped spore clusters. Raindrops splash on these clusters and disperse the spores. The fruiting bodies of stinkhorn fungi smell and look like rotting meat (Figure 29.8b), which attracts carrion flies. The flies land on the fungi to investigate the potential meal and then fly away, in the process dispersing spores that stick to their bodies. The fruiting bodies of fungal truffles are unusual in being produced underground. Truffles have evolved a spore dispersal process that depends on animals that eat fungi. Mature truffles emit an odor that attracts wild pigs and dogs, which break up the fruiting structures while digging for them, thereby dispersing the spores (look ahead to Figure 29.19). Collectors use trained leashed pigs or dogs to locate valuable truffles from forests for the market. Many fungal fruiting bodies such as truffles and morels are edible, and several species of edible fungi are cultivated for human consumption (Figure 29.9). However, many other fungi produce toxic substances that may deter animals from consuming them (Figure 29.10). For example, several fungi that attack stored grains,

(b) Fruiting body adapted for dispersal of spores by insects

Figure 29.8  Fruiting body adaptations that foster spore dispersal.  (a) When disturbed by wind gusts or animal movements, spores puff from fruiting bodies of the puffball fungus (Lycoperdon perlatum). (b) The fruiting bodies of stinkhorn fungi, such as this Phallus impudicus, smell and look like dung or rotting meat. This attracts carrion flies, which come into contact with the sticky fungal spores, thereby dispersing them. a: ©Bob Gibbons/ardea.com; b: ©RF Company/Alamy Stock Photo.

fruits, and spices produce aflatoxins that cause liver cancer and are a major health concern worldwide. When people consume the forest mushroom Amanita virosa, known as the “destroying angel,” they ingest a powerful toxin that may cause liver failure so severe that death may ensue unless a liver transplant is performed. Each year, many people in North America are poisoned when they consume similarly toxic mushrooms gathered in the wild. There is no reliable way for amateurs to distinguish poisonous from nontoxic fungi; it is essential to receive instruction from an expert before foraging for mushrooms in the woods. Therefore, many authorities recommend that it is better to search for mushrooms in the grocery store than in the wild. Several types of fungal fruiting structures produce hallucinogenic or psychoactive substances. As in the case of fungal toxins, fungal hallucinogens may have evolved as herbivore deterrents, but humans have

Figure 29.9  Several types of edible fungi available in supermarkets. ©Rob Casey/Alamy Stock Photo



FUNGI 611

Figure 29.10  Toxic fruiting body of Amanita muscaria.  Common in conifer forests, A. muscaria is both toxic and hallucinogenic. Ancient people used this fungus to induce spiritual visions and to reduce fear during raids. This fungus produces a toxin, amanitin, which specifically inhibits RNA polymerase II in eukaryotes. ©MyLoupe/UIG CALC/

Ergot

Universal Images Group/Getty Images

Core Skill: Connections  Look back at Figure 14.14, which illustrates the cellular role of RNA polymerase II in eu­karyotes. What effect would the toxin amanitin have on human cells?

inadvertently experienced their effects. For example, Claviceps purpurea, which causes a disease of rye crops and other grasses known as ergot, produces a psychogenic compound related to LSD (lysergic acid diethylamide) (Figure 29.11). Some experts speculate that cases of hysteria, convulsions, infertility, and a burning sensation of the skin that occurred in Europe during the Middle Ages and that were attributed to witchcraft resulted from ergot-contaminated rye used in foods. Another example of a hallucinogenic fungus is the “magic mushroom” (Psilocybe), which is used in traditional rituals in some cultures. Like ergot, the magic mushroom produces a compound similar to LSD. Consuming hallucinogenic fungi is risky because the amount used to achieve psychoactive effects is dangerously close to a poisonous dose.

29.3     Diversity of Fungi Learning Outcome:

Figure 29.11  Ergot of rye.  The fungus Claviceps purpurea infects rye and other grasses, producing hard masses of mycelia known as ergots in place of some of the grains (fruits). ©imageBROKER/Superstock Core Skill: Science and Society  Ergots such as the one illustrated produce alkaloids related to LSD and thus cause psychotic delusions in humans. LSD also harms pets that may accidentally consume it and farm animals that eat infected grains, causing lameness among other symptoms.

begin with a brief description of the early-diverging fungi and then focus on the largely terrestrial fungal lineages listed in Table 29.1: Mucoromycota, Ascomycota, and Basidiomycota. We will survey the habitats and characteristics of these groups of fungi and examine their distinctive ecological, structural, growth, and reproductive features.

1. Outline the distinguishing features of the fungal phyla Mucoromycota, Ascomycota, and Basidiomycota.

Cryptomycota, Chytridiomycota, and Blastocladiomycota Occur in Moist Habitats

As noted earlier, the kingdom Fungi is a monophyletic group that arose from a protist ancestor, diversifying first in aquatic habitats, then later in terrestrial environments (see Figure 29.1). In this section, we will

Single or few-celled Cryptomycota, Chytridiomycota, and Blastocladiomycota primarily live in moist locales, where they may reproduce using flagellate cells. Some classification schemes of

Table 29.1

Distinguishing Features of Later-Diverging Fungal Phyla

Phylum

Habitat

Ecological role

Reproduction

Examples cited in this chapter

Mucoromycota

Terrestrial

Form mutually beneficial associations with plants

Distinctive multinucleate asexual spores or sexual zygospores

The genus Glomus, the genus Rhizopus

Ascomycota

Mostly terrestrial

Decomposers; pathogens; many form lichens; some are plant symbionts

Asexual conidia; nonflagellate sexual spores (ascospores) in sacs (asci) on fruiting bodies (ascocarps)

Aleuria aurantia, Venturia inaequalis, Saccharomyces cerevisiae, Tuber melanosporum

Basidiomycota

Terrestrial

Decomposers; many are plant symbionts; less commonly form lichens

Several types of asexual spores; nonflagellate sexual spores (basidiospores) on club-shaped basidia on fruiting bodies (basidiocarps)

Coprinus disseminatus, Rhizoctonia solani, Armillaria mellea, Puccinia graminis, Ustilago maydis, Phanerochaete chrysosporium, Laccaria bicolor, Amanita muscaria, Phallus impudicus, Lycoperdon perlatum

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Cryptomycota include intracellular parasites known as microsporidia, which can be associated with animal disease. One example is Nosema ceranae, a single-celled organism that parasitizes honeybees, reproducing within host cells and then spreading to new cells and hosts by means of tough spore stages (Figure 29.12). However, recent evidence indicates that microsporidia may be protists rather than fungi. Members of Chytridiomycota are informally known as chytrids. Some chytrids occur as single, spherical cells that may produce hyphae (Figure 29.13). Most chytrids are decomposers, but some are parasites of algal protists or cause diseases of plants or animals. For example, the chytrid Batrachochytrium dendrobatidis has been associated with declining frog populations in Australia and the Americas (see the chapter opening photo in Chapter 54). 

Algal cell wall Hyphae

Chytrid 20 μm

Figure 29.13  Chytrids growing on a freshwater algal protist.  The colorless chytrids produce hyphae that penetrate the cellulose cell walls of the alveolate protist Ceratium hirundinella, absorbing organic materials. Chytrids use these materials as food and produce spherical flagellate spores that swim away to attack other algal cells. ©Photographs by H. Canter-Lund reproduced with permission of the

Mature spores Younger fungal cells

copyright holder Freshwater Biological Association and J.W.G.Lund.

Mucoromycota Produce Distinctive Sexual or Asexual Spores Maturing fungal spore

10 μm

Figure 29.12  The microsporidian Nosema ceranae, linked with honeybee decline.  In this bee cell, the microsporidian occurs as relatively large round or oblong structures that are each surrounded by a membrane. This membrane separates microsporidian cells from the surrounding bee cell cytoplasm. A narrow white space can be observed between each microsporidian cell and surrounding membrane. The more lightly stained microsporidian cells showing cytoplasmic structure are relatively young products of cell division. As the microsporidian cells mature into spores, they become increasingly more dense and darkly stained. ©Dr. Raquel Martín Martinez and collaborators Core Skill: Modeling  The goal of this modeling challenge is to make a diagram that models how a disease-causing microsporidian multiplies and develops inside an infected host cell. Modeling Challenge: Figure 29.12 is a transmission electron microscopic image showing a honey bee gut cell that has been infected with the microsporidian parasite N. ceranae, sometimes classified within the phylum Cryptomycota. Microsporidians are named for their ability to use host resources to divide by mitosis and then form tough microscopic spores that can be transmitted to other cells and hosts. Use the image and information in the caption to draw a diagram that shows how the parasite reproduces and develops into spores.

Mucoromycota includes the black bread mold  Rhizopus stolonifer, which produces sexual spores in dark-pigmented enclosures known as sporangia (singular, sporangium) (Figure 29.14a). A sporangium is a structure that produces spores. The formation of large numbers of these dark sporangia is what makes moldy bread appear black. These asexual sporangia may each release up to 100,000  spores into the air! The great abundance of such spores means that mold can grow on bread rather easily unless the baker adds retardant chemicals. Rhizopus can also reproduce sexually, forming distinctive zygospores (Figures 29.14b, 29.15). In black bread molds, zygospore production begins with the development of gametangia (from the Greek, meaning gamete-bearers). In these molds, gametangia are hyphal branches whose cytoplasm is isolated from the rest of the mycelium by cross walls. These gametangia enclose gametes that are basically a mass of cytoplasm containing several haploid nuclei.  When food supplies run low and if compatible mating strains are present, the gametangia of compatible mating types fuse, as do the gametes’ cytoplasms. The resulting cell becomes a sporangium that contains many haploid nuclei. Eventually these haploid nuclei fuse in pairs, producing many diploid nuclei (zygote nuclei). For this reason, a zygomycete sporangium produced by sexual reproduction is called a zygosporangium. A single darkpigmented, thick-walled, multinucleate zygospore matures within each zygosporangium.  The zygospore is capable of surviving stressful conditions, but when the environment is suitable, the diploid nuclei within the zygospore may undergo meiosis and germinate, dispersing many haploid spores. If the haploid spores land in a suitable place, they germinate to form aseptate hyphae that contain many haploid nuclei produced by mitosis. Most zygospore-producing fungi live



FUNGI 613 Asexual sporangia 1

Hyphae produce sporangia that contain asexual spores.

3

5 μm

Aseptate hyphae

Bread loaf Spores

The hyphae use bread as food to produce more hyphae and new sporangia.

2

Sporangia open, and spores disperse in air. If spores land in a suitable place such as bread, they germinate into hyphae.

(a) Asexual reproduction

2

If hyphae of compatible mating strains are present, gametangia fuse.

3

KEY

The resulting cell develops into a multinucleate heterokaryotic zygosporangium.

Haploid Diploid Heterokaryotic Fertilization

1

Gametangium

When food supplies run low, hyphae produce multinucleate gametangia.

4

Cross wall Aseptate hypha Spore 6

Hypha

Meiosis

Mitosis

Spores of diverse genetic types are released and dispersed in air. If they land on a suitable site, they germinate, each producing an aseptate hypha.

5

Zygosporangial nuclei fuse in pairs to produce many diploid nuclei and a dark, thick-walled zygospore develops within the sporangium.

When the environment is suitable, meiosis occurs within the zygospore, producing many haploid spores.

(b) Sexual reproduction

Figure 29.14  The asexual and sexual life cycles of the black bread mold Rhizopus stolonifer. (top right): ©Lee W. Wilcox Figure 29.15  Zygospores in zygosporangia.  These fungal

structures arise from sexual reproduction. They have been stained with a green dye. ©Ed Reschke/Getty Images

Zygospore within zygosporangium

Parental hyphae

on decaying materials in soil, but some are parasites of plants or animals. Some Mucoromycota, in common with some Ascomycota and Basidiomycota, are notable for forming mutually beneficial partnerships with land plants, often associated with plant roots. Root-fungal partnerships, known as mycorrhizae (from the Greek, meaning fungus roots), are discussed in more detail in Chapter 30. Some mycorrhizal fungi classified in Mucoromycota reproduce only asexually by means of distinctive large, tough-walled spores that each contain many nuclei (Figure 29.16).

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CHAPTER 29

Hypha

Spore

70 μm

Figure 29.16  The genus Glomus, an example of Mucoromycota. 

The hyphae of these fungi form symbioses with many types of plants, helping the plants acquire water and nutrients. These fungi produce distinctive large, tough-walled spores by asexual processes.

©Yolande Dalpé, Agriculture and Agri-Food Canada

Ascomycota Produce Sexual Spores in Saclike Asci Both the Ascomycota and the Basidiomycota (ascomycetes and basidiomycetes) are composed of hyphae subdivided into cells by septa. In ascomycetes, these septa display simpler pores than do the septa of basidiomycetes (Figure 29.17). Such pores allow cytoplasmic structures and materials to pass through the hyphae. Sexual reproduction in ascomycetes and basidiomycetes is distinctive, because it produces a dikaryotic mycelium, one whose cells

contain two nuclei of differing genetic types (Figure 29.18). In most sexual organisms, gametes undergo fusion of their cytoplasms— a process known as plasmogamy—and then the nuclei fuse in a process known as karyogamy. However, in ascomycetes and basidiomycetes, after plasmogamy the haploid gamete nuclei generally remain separate for a time, rather than immediately undergoing karyogamy. During this time period, the gamete nuclei both divide at each cell division, producing a mycelium whose cells each possess both parental nuclei. Although the nuclei of dikaryotic mycelia remain haploid, alternative forms of many alleles occur in the separate nuclei. Thus, dikaryotic mycelia are functionally diploid. Eventually, dikaryotic mycelia produce fruiting bodies, the next stage of reproduction. The name ascomycetes derives from unique sporangia known as asci (singular, ascus) from the Greek asco, meaning bags or sacs). During sexual reproduction, asci produce spores known as ascospores (see Figure 29.18b). The asci are produced on fruiting bodies known as ascocarps. Although many ascomycetes have lost the ability to reproduce sexually, their hyphal septa with simple pores (see Figure 29.17a) and their DNA sequences can be used to identify them as members of this phylum. Ascomycetes occur in terrestrial and aquatic environments, and they include many decomposers as well as pathogens. Important ascomycete plant pathogens include powdery mildews, chestnut blight (Cryphonectria parasitica), Dutch elm disease (the genus Ophiostoma), and apple scab (Venturia inaequalis). Cup fungi (see the photo of an ascocarp in Figure 29.18b) are common examples of ascomycetes. Many yeasts are also ascomycetes. Edible truffles (Figure 29.19) and morels are the fruiting bodies of ascomycetes whose mycelia form partnerships with plant roots, described in Section 29.4. Ascomycetes are the most common fungal components of lichens (look ahead to Section 30.3).

Pore Septum Septum

(a) Simple pore—ascomycetes

Endoplasmic reticulum (ER) (b) Complex pore—basidiomycetes

Figure 29.17  Septal pores of ascomycetes and basidiomycetes.  (a) The septa of ascomycetes have simple pores at the centers. (b) More complex pores distinguish the septa of most types of basidiomycetes. a: Courtesy of William Whittingham, and Linda Graham; b: ©Charles Mims



FUNGI 615

Figure 29.18  The asexual and sexual life cycles of ascomycete fungi.  During sexual reproduction, mating generates dikaryotic hyphae that may form a fruiting body. Nuclei in the dikaryotic surface cells of the fruiting body fuse to form zygotes that undergo meiosis to produce haploid spores. b (middle inset): ©Ed Reschke/Getty Images

Hyphae produce asexual conidia. Conidia grow into new hyphae that are genetically identical to parents.

(a) Asexual reproduction

3 2

1

Compatible hyphae mate by plasmogamy of hyphal branches, combining nuclei of 2 genetic types.

The mated cell produces a dikaryotic mycelium by mitotic division of both types of nuclei.

Diploid nucleus Ascus

Ascocarp Hyphal branches

Fertilization 7

Ascospores grow by mitosis into hyphae having 1 haploid nucleus per cell.

4 Dikaryotic mycelium

8 ascospores

6

Haploid Diploid

The 2 nuclei fuse to form a diploid zygote nucleus in the process known as karyogamy.

Dispersing spores

Mitosis

KEY

The dikaryotic mycelium produces a fruiting body known as an ascocarp. At the surface of the ascocarp, hyphae produce sac-shaped asci, each containing 2 haploid nuclei of distinct genotype.

When ascospores are mature, they are explosively released from asci into the air.

4 haploid nuclei

Meiosis

5 Fruiting body

The diploid nucleus undergoes meiosis, then each of the 4 haploid daughter nuclei divide again by mitosis. The cytoplasm around each nucleus secretes a spore wall, resulting in 8 ascospores.

Dikaryotic (b) Sexual reproduction of the ascomycete Aleuria aurantia

Basidiomycota Produce Diverse Fruiting Bodies DNA-sequencing comparisons indicate that the Basidiomycota (or basidiomycetes) and the ascomycetes are the most recently diverged groups of fungi. The mated dikaryotic mycelia of basidiomycetes can live for hundreds of years and produce many fruiting bodies. The name given to the basidiomycetes derives from basidia, the club-shaped cells of fruiting bodies that produce sexual spores known as basidiospores (Figure 29.20). Basidia are typically located on the undersides of fruiting bodies, which are generally known as basidiocarps. Though some basidiomycetes have lost the property of sexual reproduction, they can be identified as members of this phylum by unique hyphal structures known

as clamp connections that help distribute nuclei during cell division (see Figure 29.20). Basidiomycetes can also be identified by their distinctive septa having complex pores (see Figure 29.17b) and by DNA sequencing. Basidiomycetes reproduce asexually by various types of spores. An estimated 30,000 modern basidiomycete species are known. Basidiomycetes are very important as decomposers and in symbiotic associations with plants, producing diverse basidiocarps commonly known as mushrooms, puffballs, stinkhorns, shelf fungi, rusts, and smuts (Figure 29.21). Basidiocarps are also shown in Figures 29.8, 29.9, and 29.10. The fairy rings of mushrooms that sometimes occur in open, grassy areas are ring- or arc-shaped arrays of basidiomycete fruiting bodies.

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CHAPTER 29

(a) Corn smut

(b) Shelf fungi

Figure 29.21  Fruiting bodies of basidiomycetes.  (a) Corn smut Figure 29.19  The black truffle Tuber melanosporum, an ascomycete fungus. ©Nacivet/Getty Images

(Ustilago maydis) produces dikaryotic mycelial masses within the kernels (fruits) of infected corn plants. These mycelia produce many dark spores in which karyogamy and meiosis occur. Masses of these dark spores cause an infected kernel to enlarge and results in the smutty appearance. When the spores germinate, they produce basidiospores that can infect other corn plants. (b) Shelf fungi, such as this sulfur shelf fungus (Laetiporus sulphureus), are the fruiting bodies of basidiomycete fungi that have infected trees. a: ©Scott

Camazine/Alamy Stock Photo; b: ©Mark Turner/Botanica/Getty Imagess

KEY

3

Haploid Diploid Dikaryotic

1

Compatible hyphae mate by plasmogamy of hyphal branches, combining nuclei of 2 genetic types.

8

2

The dikaryotic cell divides by mitosis to produce a dikaryotic mycelium, which can be very long-lived.

Hyphal branches known as clamp connections bridge recently divided cells, ensuring that one of each nuclear type is regularly distributed to each daughter cell. Clamp connection forms Mitosis and cell growth in tip cell New septum forms Hyphal branch Nuclear carries 1 distribution nucleus complete

Basidiospores grow into mycelia, the cells of which each possess 1 haploid nucleus.

Basidium with haploid nuclei

4

Under appropriate conditions, dikaryotic mycelium may form a fruiting body, or basidiocarp. Gill of mushroom

Diploid nucleus

Basidiospore Basidiospores

Basidium

7

Basidia undergo meiosis to produce 4 haploid nuclei, which are incorporated into basidiospores that are dispersed.

6

Nuclei in basidia fuse to form diploid nuclei.

5

Dikaryotic basidia occur at the surfaces of gills (or pores of some mushrooms).

Figure 29.20  The sexual life cycle of the basidiomycete fungus Coprinus disseminatus. (left): ©Biophoto Associates/Science Source; (right): ©Dr. Jeremy Burgess/Science Source



FUNGI 617

Pathogenic Fungi Cause Plant and Animal Diseases

29.4       F  ungal Ecology and Biotechnology Learning Outcomes: 1. List several ecological roles of fungi. 2. Give examples of fungal diseases of plants and animals, including humans. 3. List several uses of fungi in biochemistry, biological studies, and industrial processes.

Fungi play diverse important ecological roles in addition to previously mentioned beneficial associations with plant roots (mycorrhizae), which are discussed in detail in the next chapter. These additional roles, which include decomposition, predation, disease agent, and protection, allow fungi to be useful in technological applications. 

Many Fungi Play Ecological Roles as Decomposers and Some Fungi Are Predators Decomposer fungi are essential components of the Earth’s ecosystems. Together with bacteria, they decompose dead organisms and wastes, preventing the buildup of organic debris in ecosystems. For example, only certain bacteria and fungi can break down cellulose and lignin, the main components of wood. Decomposer fungi and bacteria are Earth’s recycling engineers. They release CO2 into the air and other minerals into the soil and water, making these essential nutrients available to plants and algae. More than 200 species of predatory soil fungi use special adhesive or noose-like hyphae to trap tiny soil animals, such as nematodes, and absorb nutrients from their bodies (Figure 29.22). Such fungi help to control populations of nematodes, some of which attack plant roots. Other fungi obtain nutrients by attacking insects, and certain of these species have been used as biological control agents to kill black field crickets, red-legged earth mites, and other pests.

One of the most important ways in which fungi affect humans is by causing diseases of crop plants and animals. Five thousand fungal species are known to be plant pathogens that cause serious crop diseases. Plant pathogenic fungi typically produce specialized balloonshaped cells known as haustoria, whose increased cell membrane surface area aids in the absorption of organic food from plant cells (Figure 29.23). Pathogenic fungi use the absorbed organic compounds to grow, attack more plant cells, and produce reproductive spores capable of infecting more plants. Wheat rust is an example of a common crop disease caused by fungi (Figure 29.24). Rusts are named for the reddish spores that emerge from the surfaces of infected plants. Many types of plants can be attacked by rust fungi, but rusts are of particular concern when new strains attack crops. To control the spread of fungal diseases, agricultural experts work to identify effective fungicidal chemicals and develop resistant crop varieties. Agricultural customs inspectors closely monitor the entry of plants, soil, foods, and other materials that might harbor pathogenic fungi. Some fungi cause disease in animals. For example, the ascomycete Geomyces destructans is associated with white nose syndrome in bats, which has killed more than 1 million hibernating bats in the U.S. Athlete’s foot and ringworm are common human skin diseases caused by several types of fungi that are known as dermatophytes because they colonize the human epidermis. The ascomycete  Pneumocystis jiroveci and the basidiomycete Cryptococcus neoformans are fungal pathogens that infect individuals with weakened immune systems, such those with AIDS, sometimes causing death.  Dimorphic fungi (from the Greek, meaning two forms) live as spore-producing hyphae in the soil but transform into pathogenic yeasts when mammals inhale their wind-dispersed spores

Nematode

Hyphal loop 93.2 μm

Figure 29.22  A predatory fungus.  The fungus Arthrobotrys

anchonia traps nematode worms in hyphal loops that suddenly swell in response to the animal’s presence. Fungal hyphae then grow into the worm’s body and digest it. ©Science Source

2 μm

Figure 29.23  Fungal haustoria.  Fungi that parasitize plants often produce specialized balloon-shaped cells called haustoria that absorb organic food from plant cells, as shown in this electron micrograph. ©Dr. Eric Kemen and Dr. Kurt W. Mendgen

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CHAPTER 29 Wheat leaf tissue Puccinia graminis spores

0.1 mm

Figure 29.24  Wheat rust.  The plant pathogenic fungus

Puccinia graminis grows within the tissues of wheat plants, using plant nutrients to produce rusty streaks of red spores that erupt at the stem and leaf surfaces where they can be dispersed. Red spore production is but one stage of a complex life cycle involving several types of spores. Rusts infect many other crops in addition to wheat, causing immense economic damage. (left): ©Nigel Cattlin/Science Source; (right): ©Herve Conge/ISM/ Phototake

(Figure 29.25). Dimorphic fungi include the ascomycetes Blastomyces dermatitidis, which causes the disease blastomycosis; Coccidioides immitis, the cause of coccidiomycosis; and Histoplasma capsulatum, the agent responsible for histoplasmosis. These fungal diseases affect the lungs and may spread to other parts of the body, causing severe illness. The host's body temperature triggers the change from the hyphal form, which produces spores, to a yeast form. In an infected mammal, these pathogenic yeasts reproduce

10 μm Soil-dwelling hyphal phase

Figure 29.25  Dimorphic fungi.  The soil-dwelling hyphal stage

reproduces by airborne spores. When a mammal inhales the spores, body heat causes the budding yeast phase to develop and attack host tissues. Courtesy Bruce Klein. Reprinted with permission

by forming buds that more effectively stick to lung cells, spread within lung tissue, and move to other organs.

Some Fungi Play Protective Roles Although some fungi cause disease, some have recently been discovered to have protective roles. For example, fungi known as endophytes commonly live within plant tissues, providing protection against pathogens and physical stresses such as heat. Some endophytic associations also involve viruses.

Core Skill: Process of Science

Feature Investigation  | Márquez and Associates Discovered That a Three-Partner Symbiosis Allows Plants to Cope with Heat Stress

The endophytic fungus Curvularia protuberata commonly lives within aboveground tissues of the grass Dichanthelium lanuginosum. It can grow on very hot soils in areas of Yellowstone National Park. When the soil reaches 38°C, D. lanuginosum plants and C. protuberata fungi both die—unless they live together in a symbiosis. In the symbiotic association, the partners can survive temperatures near 65°C! In 2007, a team of investigators led by Luis Maˊrquez investigated the role of a virus in the symbiotic relationship between D. lanuginosum plants and C. protuberata fungi. Prior to the study described in Figure 29.26, these researchers discovered that C. protuberata may carry a virus, which they named Curvularia thermal tolerance virus (CthTV) to indicate its host and phenotype. In the laboratory, the investigators also noticed that some of their fungal cultures contained very little virus. They were able to use drying and freeze-thaw cycles

to cure such cultures of the virus. This procedure allowed them to experimentally determine the relative abilities of virus-infected and virus-free C. protuberata fungus to tolerate high temperatures and to confer this property to plant partners.  As shown in step 1 of Figure 29.26, the researchers began with containers of D. lanuginosum plants. One set of containers had neither the fungus nor the virus, another set had the virus-infected fungus, and a third set had the virus-free fungus. The plants in the three sets of containers were exposed to heat stress for 2 weeks, and then categorized as dead, dying, or healthy. As seen in the data, the researchers found that plants having virus-infected fungal endophytes tolerated high temperatures much better than plants that lacked fungal endophytes or possessed only virus-free fungal endophytes. In other experiments, the researchers determined that virus-infected fungi (but not virus-free fungi) could also protect a distantly related crop plant (tomato) from



FUNGI 619

Figure 29.26  Márquez and associates discovered that a three-partner symbiosis allows plants to cope with heat stress. GOAL To determine if a virus is essential to the protective role of endophytic fungi to host plants under heat stress. KEY MATERIALS Curvularia thermal tolerance virus (CthTV), cultures of the endophytic fungus Curvularia protuberata infected with CthTV, C. protuberata cultures free of CthTV, and Dichanthelium lanuginosum plants. Experimental level

1

Conceptual level

Plant 25 replicate containers with D. lanuginosum lacking fungal symbionts (a) or having C. protuberata endophytes that either did (b) or did not (c) have virus.

Compare the effects of virus on the ability of the fungus to confer heat stress protection.

(a) No fungus, no virus

(b) Fungus and virus

(c) Fungus, no virus

2

Expose plants to heat stress treatment (up to 65°C) for 2 weeks in a greenhouse.

Keep environmental conditions constant to reduce experimental error.

3

Count the number of plants that were green (alive), yellow (dying), or brown (dead).

Assess plant survival in the presence or absence of fungus and/or virus.

(a)

THE DATA

(c)

5

CONCLUSION A virus enhances the protective role of endophytic fungi in this grass species. The next step will be to try to determine just how the virus changes the fungus so that the fungus is able to protect the plant from heat stress.

6

SOURCE Marquez, L. M., et al. 2007. A virus in a fungus in a plant: three-way symbiosis required for thermal tolerance. Science 315: 513–515.

KEY

Number of plants

4

(b)

Brown, dead Yellow, dying Green, healthy

(a) (b) No fungus, Fungus no virus and virus

(c) Fungus, no virus

heat stress. These results add to accumulating evidence that multipartner symbioses are more common than previously realized and suggest that endophytic fungi may have useful agricultural applications. Experimental Questions 1. Would you expect plants that grow on unusually hot soils to have endophytic fungi or not? 

2. CoreSKILL » How did Maˊrquez and associates demonstrate that a virus was important in the heat tolerance due to the symbiosis between Dichanthelium lanuginosum and Curvularia protuberata?  3. How might the results of the work by Maˊrquez and associates be usefully applied in agriculture? 

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BIO TIPS

THE QUESTION  The data presented in step 4 of Figure 29.26 provide additional information about the relative effects of an endophytic fungus and a virus on heat tolerance in a species of plant. Compare the three bars in the graph and explain what these data mean. T OPIC  What topic in biology does this question address? The topic is related to species diversity involved in protective interactions. More specifically, the question addresses the relative effects of fungal endophytes and viruses on plant heat tolerance. I NFORMATION  What information do you know based on the question and your understanding of the topic? Step 4 in Figure 29.26 presents experimental data in the form of a bar graph that shows the relative numbers of plants in each of three groups that were dead, dying, and healthy at the end of the heat stress experiment. The three groups of plants differed as to whether an endophytic fungus and/or a virus was present in their containers. You have learned in this chapter what endophytic fungi are and how they can affect plants. P ROBLEM-SOLVING  S TRATEGY  Compare and contrast. Interpret data. Compare and contrast the bars in the graph, looking for differences in the responses of plants in each group.

The brewing and winemaking industries find yeasts essential, and the baking industry depends on the yeast Saccharomyces cerevisiae (see Figure 29.7) for bread production.  S. cerevisiae is also widely used as a model organism for fundamental biological studies. Yeasts are useful in the laboratory because they have short life cycles, they are easy and safe for lab workers to maintain, and their genomes show striking similarities to those of humans. About 31% of yeast proteins have human homologs, and nearly 50% of human genes that have been implicated in heritable diseases have homologs in yeasts.

Summary of Key Concepts 29.1  E  volution and Distinctive Features of Fungi ∙∙ Fungi form a monophyletic group of heterotrophs that, together with the animal kingdom and certain protists, form the supergroup Opisthokonta (Figure 29.1). ∙∙ Fungal cells typically possess cell walls rich in the polysaccharide chitin. Fungal bodies, known as mycelia, are composed of microscopic branched filaments known as hyphae. Early-diverging fungi have aseptate hyphae that are not subdivided into cells. The hyphae of later-diverging fungi are subdivided into cells by cross walls known as septa (Figures 29.2, 29.3). ∙∙ Fungal hyphae feed and grow at their tips (Figure 29.4).

ANSWER  First, compare the bars labeled (a) and (b). From this comparison, the presence of the virus-infected fungus is seen to confer heat resistance to the plant. However, from this comparison alone, you could infer that either the fungus or the virus or the combination of the two provided plants with protection from heat, but you could not discriminate among these possibilities. A comparison of the bars labeled (b) and (c) reveals that the fungus by itself does not confer thermal protection. Therefore, it is the virus-infected fungus that provides the plant with thermal protection.  Interestingly, a careful comparison of  the bars labeled (a) and (c) reveals that the proportion of dead plants to dying plants in the (c) group (fungus present but no virus) is higher than in the (a) group (no fungus or virus). These results suggest that the fungus by itself might actually make the plant more sensitive to heat.

Fungi Have Many Applications in Biotechnology In addition to the potential use of fungal endophytes to protect agricultural plants suggested by the experiments conducted by Márquez and associates, fungi have diverse additional technology applications. Enzymes extracted from fungi are widely used to break down tough plant materials for renewable bioenergy applications. A variety of industrial processes employ fungi to convert inexpensive organic compounds into valuable materials such as the citric acid used in the softdrink industry, glycerol, antibiotics such as penicillin, and cyclosporine, a drug widely used to prevent rejection of organ transplants. In the food industry, fungi are used to produce the distinctive flavors of blue cheese and other cheeses. Other fungi secrete enzymes that are used in the manufacture of protein-rich tempeh and other food products from soybeans. 

∙∙ Mycelial shape depends on the distribution of nutrients in the environment, which determines the direction in which cell division and hyphal growth will occur (Figure 29.5).

29.2  O  verview of Asexual and Sexual Reproduction in Fungi ∙∙ Fungi spread rapidly by means of spores produced by asexual or sexual reproduction. ∙∙ Asexual reproduction does not involve mating or meiosis, and it occurs by means of asexual spores called conidia or by budding (Figures 29.6, 29.7). ∙∙ Fungi display a haploid-dominant sexual life cycle. During sexual reproduction of terrestrial fungi, hyphal branches (gametes) fuse with those of a different mycelium of compatible mating type. Mated hyphae form fruiting bodies in which haploid spores are produced by meiosis. Dispersed spores germinate to produce haploid fungal mycelia. ∙∙ Fungi produce diverse types of fruiting bodies that foster spore dispersal by wind, water, or animals. Although many fungal fruiting bodies are edible, many others produce defensive toxins or hallucinogens (Figures 29.8, 29.9, 29.10, 29.11).

29.3  Diversity of Fungi ∙∙ The fungi include several early-diverging lineages and the laterdiverging phyla Mucoromycota, Ascomycota (ascomycetes), and Basidiomycota (basidiomycetes) (Table 29.1). ∙∙ Cryptomycota, Chytridiomycota, and Blastocladiomycota are among the simplest and earliest-diverging fungi. They commonly occur in aquatic habitats and moist soil, where they produce flagellate reproductive cells. Some are parasites of protists, animals, or plants (Figures 29.12, 29.13).



FUNGI 621

∙∙ Mucoromycota includes fungi that reproduce asexually or sexually by distinctive spores (Figures 29.14, 29.15, 29.16). ∙∙ Ascomycetes produce sexual ascospores in saclike asci located at the surfaces of fruiting bodies known as ascocarps. The septa of hyphae have simple pores (Figures 29.17, 29.18, 29.19). ∙∙ Basidiomycetes produce sexual basidiospores on club-shaped basidia located on the surfaces of fruiting bodies known as basidiocarps. Such fruiting bodies take a wide variety of forms, including mushrooms, puffballs, stinkhorns, shelf fungi, rusts, and smuts. The hyphae display complex septal pores and clamp connections. Mating commonly generates a long-lived dikaryotic mycelium that can produce many fruiting bodies (Figures 29.20, 29.21).

29.4  Fungal Ecology and Biotechnology ∙∙ Fungi play important roles in nature as decomposers, predators, and pathogens and in beneficial associations with other organisms. Pathogenic fungi cause plant and animal diseases (Figures 29.22, 29.23, 29.24, 29.25). ∙∙ Endophytic fungi live within the tissues of plants, providing protective services (Figure 29.26). ∙∙ Fungi are useful in the chemical, food-processing, waste-treatment, and renewable biofuel industries. The yeast Saccharomyces cerevisiae is a model organism and also important to the brewing and baking industries.

Assess & Discuss Test Yourself 1. Fungal cells differ from animal cells in that fungal cells a. lack ribosomes, though these are present in animal cells. b. lack mitochondria, though these occur in animal cells. c. have chitin-rich cell walls, whereas animal cells lack cell walls. d. lack cell walls, whereas animal cells possess cell walls. e. None of the above is true. 2. Conidia are a. cells produced by some fungi as the result of sexual reproduction. b. fungal asexual reproductive cells produced by the process of mitosis. c. structures that occur in septal pores. d. the unspecialized gametes of fungi. e. none of the above. 3. What are mycelia? a. the bodies of fungi, composed of hyphae b. fungi that attack plant roots, causing disease c. fungal hyphae that are massed together into stringlike structures d. fungi that produce harmful toxins e. protists that are closely related to fungi 4. Where could you find diploid nuclei in an ascomycete or basidiomycete fungus? a. in spores b. in cells at the surfaces of fruiting bodies c. in conidia d. in zygospores e. in all of the above

5. Which fungi are examples of hallucinogen producers? a. Claviceps and Psilocybe b. Epidermophyton and Candida c. Pneumocystis jiroveci and Histoplasma capsulatum d. Saccharomyces cerevisiae and Phanerochaete chrysosporium e. Cryphoenectria parasitica and Ventura inaequalis 6. What role do fungal endophytes play in nature? a. They are decomposers. b. They are human pathogens that cause skin diseases. c. They are plant pathogens that cause serious crop diseases. d. They live within the tissues of plants, helping to protect them from herbivores, pathogens, and heat stress. e. All of the above are correct. 7. What determines whether a mycelium is flat or spherical? a. sunlight b. the nature of the substrate c. the amount of carbon dioxide in the air d. the amount of phosphorus available e. all of the above 8. Among fungi, nutrition is a. photosynthetic. b. mixotrophic. c. absorptive. d. all of the above. e. none of the above. 9. How can ascomycetes be distinguished from basidiomycetes? a. Ascomycete hyphae have simple pores in their septa, whereas basidiomycete hyphae display complex septal pores. b. Ascomycetes produce sexual spores in sacs, whereas basidiomycetes produce sexual spores on the surfaces of club-shaped structures. c. Ascomycetes lack clamp connections, whereas basidiomycetes display clamp connections. d. Ascomycetes fruiting bodies include cup structures and morels, whereas basidiomycete fruiting bodies take different forms that include shelf fungi on tree trunks. e. All of the above are correct. 10. Which of the following groups of organisms is most closely related to the kingdom Fungi? a. the animal kingdom b. the green algae c. the land plants d. the bacteria e. the archaea

 Conceptual Questions 1. List three ways in which fungi are like animals and two ways in which fungi resemble plants.  2. Explain why some fungi produce toxic or hallucinogenic compounds.  3. 

 ore Concept: Systems  Describe three ways in which fungi C affect their environments. 

Collaborative Questions 1. Thinking about the natural habitats closest to you, where can you find fungi, and what roles do these fungi play? 2. Imagine that you are helping to restore the natural grassland vegetation in a region that has recently been used to grow crops. In what ways might you consider using fungi to aid in this restoration?

CHAPTER OUTLINE

Microbiomes: Microbial Systems On and Around Us

30

In this SEM image of a human fecal sample, the different colors indicate a diversity of bacteria present in the gut microbiome.

30.1

Microbiomes: Diversity of Microbes and Functions 30.2 Microbiomes of Physical Systems 30.3 Host-Associated Microbiomes 30.4 Engineering Animal and Plant Microbiomes Summary of Key Concepts Assess & Discuss

that are associated with a particular environment, such as the human body. Microbiologists are learning that oceans, ice, fresh waters, soils, and the bodies of organisms other than humans have distinctive microbiomes that influence nature and human life. Because microbes are generally small, microbiomes are often inconspicuous. New molecular approaches described in this chapter have enabled biologists to study microbiome compositions and functions. Using these new methods, medical scientists are identifying new ways in which people can improve their health. Agricultural scientists are discovering new strategies for engineering crop microbiomes to promote plant health. Exploring the microbiomes of other organisms and environments has revealed previously unrecognized global ecological effects. In this chapter, we will learn why the study of microbiomes has become an important and fast-growing area of modern biology.

©Eye of Science/Science Source

I

deally, all of the world’s children would have enough good food to start healthy lives. Unfortunately, malnutrition has left nearly 180 million children around the world stunted in their growth. Public health experts have tried to use dietary supplements to restore normal growth, a strategy that does not always work. New research on microbes living in the bodies of the stunted children has revealed why. These children retain an infantile set of gut microbes, in contrast to children whose more mature collection of gut microbes (illustrated by the chapter opening image) stimulates growth hormones. This understanding may help people to devise new ways to improve the health of millions of children. Chapters 27–29 introduced the diverse groups of microorganisms—archaea, bacteria, protists, and fungi—that influence our health and environments in many ways. This chapter builds on that foundation by describing how these diverse microbes occur together in microbiomes, assemblages of microbes

   30.1  Microbiomes: Diversity of Microbes and Functions Learning Outcomes: 1. Define microbiome. 2. List some reasons why microbiomes are considered to be complex systems. 3. Discuss how biologists use ribosomal RNA gene sequences and whole metagenomic sequencing to catalog the diverse types of microbes in a microbiome. 4. Explain how biologists identify microbiome functions.

As noted in the chapter opener, a microbiome is a particular assem­ blage of microbes (including their genes) that is associated with a particular environment. Microorganisms commonly present in microbiomes include archaea, bacteria, viruses, protists, and fungi (see Chapters 27–29), and sometimes microscopic animals. Visual­ izing such microbes requires the use of microscopes, such as scan­ ning or transmission electron microscopes. 



MICROBIOMES: MICROBIAL SYSTEMS ON AND AROUND US 623

Microbiomes can be associated with physical biomes such as water, ice, or soil, or with living hosts, such as animals, plants, fungi, and algae. Bacteria dominate the microbiomes of humans and other animals, though certain protists and fungi may also be pres­ ent (Figure 30.1). Microbes are found in many different places in the human body. The microbiomes of plants commonly harbor many types of fungi, and algal microbiomes often include many species of bacteria and protists (Figure 30.2). For example, the surface of Cladophora is covered with a biofilm of diverse bacteria (Figure 30.2b). A biofilm is a group of microbes that use mucilage to stick to each other and to surfaces.

Skin

Mouth

Stomach

Microbiomes Are Complex Biological Systems Microbiomes are complex systems, in part, because they contain many different microbial species that interact with each other in complicated ways. Microbiome studies often reveal new types of microbes that have not been studied in the lab and, so, have not even been formally named. These diverse life forms carry out many types of metabolism that influence their environments and other members of the same microbiome, but such ecological interactions are not fully understood. Microbes communicate with each other by means of chemical or elec­ trical signals that biologists are just beginning to explore. Particular microbes seem to serve as network hubs, receiving information from the environment and transmitting information to the broader microbial community. In these ways, microbiomes resemble culturally diverse human groups whose social networks and responses to outside influ­ ences are complex. Identifying what species occur together, how microbes affect each other and their environments, and the effects of environmental change are major goals of microbiome research. Determining the species compositions, functions, and re­ ­ sponses of microbiomes are challenging because microbes are so small and difficult to distinguish. For example, different bacterial species often have similar body structure, such as single cells only

Urogenital Intestines

Figure 30.1  The human microbiome includes diverse bacteria, but also some protists and fungi.

a few micrometers in diameter (see Figure 30.2b). Likewise, the bodies of millions of fungal species are composed of thin hyphae that often look alike, even with the use of a microscope (see Chapter 29).

50 μm (a)

40 μm μm (b)

Figure 30.2  An algal microbiome that includes diverse bacterial and protist species.  (a) The green alga Cladophora provides living

space, organic food, and oxygen to hundreds of species of bacteria, protists, fungi, and microscopic animals, visible as clouds of white, golden, and brown particles on the algal surface. (b) This SEM reveals that the algal surface is covered with a biofilm of structurally diverse bacteria. These bacteria have important ecological functions. a: ©Lee W. Wilcox; b: ©Linda Graham

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For these reasons, biologists commonly use genetic techniques to distinguish and identify microbial species within a given microbi­ ome. Such methods involve the identification of genes present in a complex microbiome, which may also allow biologists to infer their functions if similar genes have been studied previously. In addition to cataloging the types of microbes and genes present in a microbi­ ome, biologists examine proteins and metabolites to gain insight into function.

Evaluating the Taxonomic Complexity of Microbiomes by Amplicon Analysis All of Earth’s living things, including microbes, produce proteins by means of ribosomes, which contain ribosomal RNA (rRNA). Ribosomal RNA is so important to living things that rRNA struc­ ture tends to be conserved among different species, which means that its structure does not undergo major changes over the course of evolution. When rRNAs of closely related species are compared, the sequence of bases is usually very similar or highly conserved, whereas distantly related species show more differences in their sequences (refer back to Figure 12.17). For this reason, the level of difference in the sequences of rRNAs can be used to evaluate evo­ lutionary relationships. In microbiome studies, sequences of genes that encode rRNAs are commonly used to identify and classify microbes, even if the microbiome includes thousands of microbial species. Other types of genes may also be amplified for evaluating microbiome complexity. Biologists usually begin a microbiome study by obtaining a sample from a living organism or a physical environment and then extracting the DNA (Figure 30.3). As seen in step 3a, polymerase chain reaction (PCR) can be used to copy a particular region of an rDNA gene. This process yields many copies of that region from many different species that are in the sample. These copied rDNA regions are known as amplicons. Amplifying the DNA is generally required to generate sufficient DNA for sequencing (described in Chapter 21). The amplicons are then subjected to DNA sequencing, which yields the base sequence of each gene that was amplified in the origi­ nal sample. Biologists use computers to compare the DNA sequences of each amplicon to reference sequences in databases. These ref­ erence sequences come from microbes, the names and metabolic functions of which are already known. This relatively inexpensive way to examine the microbial diversity in a microbiome is called amplicon analysis. In amplicon analysis, researchers often use PCR primers that amplify a region of genes that encode 16S, 23S, 18S, and/or 28S rRNA (refer back to Table 12.3). 16S rRNA and 23S rRNA occur in the small and large ribosomal subunits of bacteria and archaea; 18S rRNA and 28S rRNA occur in the corresponding ribosomal subunits of eukaryotes. As an example,  Figure 30.4 shows the evolutionary relationships for members of a particular microbiome that plays a role in mineral formation. This phylogenetic tree was constructed by comparing the genes encoding 16S rRNA. As you can see, the micro­ biome composition is complex, containing representatives of many bacterial phyla and one archaeal phylum.

Core Skill: Quantitative Reasoning

BIO TIPS

THE QUESTION  Which prokaryotic phylum dominates the microbiome shown in Figure 30.4? Note: In this figure, the sizes of circles indicate the relative abundances of sequences, which are related to organism abundances. For reference, Figure 27.1 and Table 27.1 list prokaryotic phyla that occur in Figure 30.4.  T OPIC What topic in biology does this question address?  The topic is microbiomes. More specifically, the question focuses on the composition of a particular microbiome and identification of the prokaryotic phylum that is the most prevalent. I NFORMATION What information do you know based on the question and your understanding of the topic? In the question, you are referred to Figure 30.4, which is a phylogenetic tree that provides information about the prokaryotic genera, families, orders, classes, and phyla present in one microbiome. You are also reminded that Figure 27.1 and Table 27.1 list prokaryotic phyla that occur in Figure 30.4.  P ROBLEM-SOLVING   S TRATEGY Make a calculation. Interpret data. The common bacterial phyla Bacteroidetes, Verrucomicrobia, Chloroflexi, Cyanobacteria, Firmicutes, Planctomycetes, Proteobacteria, and Spirochaetes and the archaeal phylum Euryarchaeota, listed in Figure 27.1 and Table 27.1, are represented in this microbiome. Count the number of representatives of each phylum, giving greater weight to larger circles. Use these calculations to make a pie chart that groups bacteria and archaea into different phyla.

ANSWER  Of the nearly 60 taxa listed along the right edge of the phylogentic tree, more than half are classified in the phylum Proteobacteria, and the two most abundant genera inferred from sequence abundances (Rhodoferax and Rheinheimera) belong to this phylum. Your pie chart should show the phylum Proteobacteria making up its largest sector, indicating that this prokaryotic phylum dominates this particular microbiome.

Evaluating Taxonomic and Functional Complexity of Microbiomes by Whole Metagenomic Sequencing An alternative method for characterizing microbiome diversity is to obtain base sequences of all the DNA present in a sample, a process known as whole metagenomic sequencing (WMS) (see Figure 30.3, step 3b). A metagenome is defined as the genomes of all the organ­ isms present in a sample. WMS is carried out using an approach known as shotgun DNA sequencing, in which DNA fragments from a genome are randomly sequenced (refer back to Figure 21.11). This approach does not have to focus on the sequencing of one particular gene, such as the gene encoding 16S rRNA. Instead, many fragments of DNA are randomly sequenced, and then biologists use computers to identify places where the ends of DNA fragments have the same DNA



MICROBIOMES: MICROBIAL SYSTEMS ON AND AROUND US 625

1

Obtain a sample to analyze.

Sample from physical environment

Sample from living organism

2

Extract the DNA from the sample. This yields a collection of many DNA fragments from many different microbial species.

DNA fragments

3

3a Amplicon Analysis: Use primers that recognize a region of an rDNA gene and make many copies of that region using polymerase chain reaction (PCR). Subject the amplified segments of the rDNA gene to DNA sequencing. GG

C AC

TCT GCAG AG TG AC C

CT

CG

GCAGACT

G AG GC

Amplicon

TACGG T

T CCGGTG

T

T AC AG AC

CT

C AG GC

G CA G A GT

CCTG ACG

TCGG TCA

Sequences of rDNA genes that were in the sample.

4

3b Whole metagenome sequencing: Subject all of the DNA in the sample to shotgun DNA sequencing. GTAGCA GTAG CATC CGGT GTGG TGAG

G

C ACCTGA TCGGTC

GCAG TCTAC CGG

CTTC GGTC T G G C A T T C A TGGTG CCGGTG GCAGACTTCGGTCACCTGAT

GTC

CG GACTT CTGCA ACCGG

TACG GTTG CAG CC

ACTGACGGCA GGCTGTAGCA

TGC AGA A

Sequences of all of the DNA fragments that were in the sample.

Compare the DNA sequences obtained in step 3 to DNA sequences in a database. The database sequences are already known to come from particular microbial species. This allows researchers to match the sequences obtained in step 3 to known sequences. For example, if a DNA sequence obtained in step 3a matches an rDNA sequence from the bacterium E. coli, this result indicates that E. coli was in the microbiome of that sample.

Figure 30.3  Characterization of microbiome taxonomic complexity via amplicon analysis or whole metagenome sequencing. (right) ©Goodshoot/Alamy Stock Photo

Core Concept: Information  The information contained in DNA sequences can be used to gain information about taxonomic and functional diversity in microbiomes.

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Bacteroidia

Marinilabiliaceae

Bacteroidales

Porphyromonadaceae Cryomorphaceae

Flavobacteria

Bacteroidetes/Chlorobi group Bacteroidetes

Flavobacteriales

Flavobacteriaceae Chitinophagaceae

Sphingobacteria Sphingobacteriales

Saprospiraceae Sphingobacteriaceae

Chlamydiae/ Verrucomicrobia group

Opitutae

Verrucomicrobia

Verrucomicrobiae

Opitutales

Opitutaceae

Puniceicoccales

Puniceicoccaceae

Verrucomicrobiales

Verrucomicrobiaceae Chloroflexi

Alkaliflexus Paludibacter Fluviicola Cellulophaga Flavobacterium Niabella Haliscomenobacter Pedobacter Opitutus Pelagicoccus Prosthecobacter Chloroflexi Cyanobacteria

Clostridiaceae Clostridia

Clostridiales

Clostridiales incertae sedis

Clostridiales Family XII. Incertae Sedis

Firmicutes

Planctomycetes

Erysipelotrichia

Erysipelotrichales

Fusobacteria

Fusobacteria

Fusobacteriales

Planctomycetia

Planctomycetales

Planctomycetaceae Hyphomicrobiaceae

Rhizobiales

Rhizobiaceae Rhizobium/Agrobacterium group Rhodobacterales Rhodobacteraceae

Alphaproteobacteria

Acetobacteraceae

Rhodospirillales Root

Geosporobacter Fusibacter Lachnospiraceae

Unclassified Clostridiales

Cellular organisms

Alkaliphilus

Rhodospirillaceae

Bacteria

Erythrobacteraceae Sphingomonadales

Sphingomonadaceae

Ruminococcaceae Proteocatella Erysipelotrichaceae Fusobacteriaceae Planctomyces Devosia Rhizobium Ahrensia Oceanicola Rhodobacter Roseomonas Azospirillum Porphyrobacter Blastomonas Sandaracinobacter Acidovorax

Comamonadaceae Burkholderiales

Betaproteobacteria

Proteobacteria

Rhodocyclales

Rhodocyclaceae

Bdellovibrionales Bacteriovoracaceae Deltaproteobacteria

Desulfovibrionales

Desulfomicrobiaceae Myxococcales

Epsilonproteobacteria Campylobacterales Campylobacteraceae Aeromonadales

Aeromonadaceae

Alteromonadales

Shewanellaceae

Chromatiales

Chromatiaceae Moraxellaceae

Gammaproteobacteria

Pseudomonadales

Pseudomonadaceae Unclassified Gammaproteobacteria

Xanthomonadales Xanthomonadaceae

Spirochaetes

Hydrogenophaga Rhodoferax

Unclassified Burkholderiales Burkholderiales Genera incertae sedis

Delta/epsilon subdivisions

Giesbergeria

Spirochaetia

Spirochaetales

Leptospiraceae Spirochaetaceae Archaea

Simplicispira Ideonella Methylibium Propionivibrio Bacteriovorax Peredibacter Desulfomicrobium Sorangiineae Arcobacter Sulfurospirillum Aeromonas Shewanella Rheinheimera Perlucidibaca Cellvibrio Pseudomonas Alkalimonas Aquimonas Dyella Silanimonas Leptospira Spirochaeta Euryarchaeota

Figure 30.4  Example of the use of gene sequences encoding 16S rRNA to detect bacteria and archaea present in the microbiome of a photosynthetic organism and to produce a phylogenetic tree.  This phylogenetic tree shows how genera are clustered into phyla and intermediate taxonomic groups. The sizes of circles indicate relative sequence abundances, which are approximately related to organism abundances. Graham, L. E., Knack, J. J., Piotrowski, M. J., Wilcox, L. W., Cook, M. E., Wellman, C. H., Taylor, W., Lewis, L. A., and Arancibia-Avila, P. 2014. Lacustrine Nostoc (Nostocales) and associated microbiome generate a new type of modern clotted microbialite. Journal of Phycology 50: 280–291. doi: 10.1111/jpy.12152. This work is licensed under a Creative Commons Attribution 3.0 License.

sequences (Figure 30.5). These overlapping regions allow research­ ers to align the DNA fragments into longer sequences known as con­ tiguous sequences, or contigs. What is the advantage of constructing contigs? One advantage is that longer contigs provide greater amounts of information needed for more detailed classification.

If metagenomic sequences are relatively long, or if a microbiome contains relatively few microbes, it may be possible to use computer methods to assemble contigs into whole microbial genomes. A num­ ber of microbial species were discovered in this way and even today are known only from their genomic sequence. Some experts consider



MICROBIOMES: MICROBIAL SYSTEMS ON AND AROUND US 627

with oxygen-producing algae and plants. For example, peat mosses that dominate vast wetland areas, known as TTACGGTACCAGTTACAAATTCCAGACCTAGTACC peatlands, play an important role in global carbon cycling AATGCCATGGTCAATGTTTAAGGTCTGGATCATGG by hosting methane-oxidizing bacteria. Peat moss leaves GACCTAGTACCGGACTTATTCGATCCCCAATTTTGCAT CTGGATCATGGCCTGAATAAGCTAGGGGTTAAAACGTA display both oxygen-producing green photosynthetic cells and larger non-green cells that have undergone pro­ Figure 30.5  A comparison of two DNA fragments that contain an overlapping grammed cell death and whose cell walls are perforated region.  A contig consists of a series of DNA fragments that contain overlapping by large pores. Methane-oxidizing bacteria, many other regions. types of bacteria, and diverse protists enter through the pores (Figure 30.6), and many of these microbes use that one goal of WMS should be to assemble entire genome sequences mucilage to attach to inner cell wall surfaces (Figure 30.7). Peat moss of microbes, a process known as genome-centric metagenomics. microbiomes commonly contain MMO marker genes, indicating that a If sufficient DNA has been analyzed, WMS and computer meth­ microbiome function is to oxidize methane. ods can be used to identify both prokaryotic and eukaryotic species in Overlapping region

a microbiome at the same time. By contrast, amplicon analyses typi­ cally focus on the amplification of a particular gene from a selected group of species. For this reason, many experts consider that the term microbiome should be limited to microbial communities characterized by WMS. The term microbiota is commonly used to describe collec­ tions of microbial life cataloged by amplicon analysis.

Microbiome Functions Can Be Inferred by Identifying Protein-Encoding Genes In the analysis of microbiomes by WMS, another goal is to find and classify protein-encoding genes, providing a deeper view of micro­ bial function. To gain more information about microbiome function, biologists may look for particular protein-coding genes that indicate specialized microbial functions. For example, biologists have used metagenomic sequencing of DNA from natural microbiomes to find bacterial and archaeal genes that encode many previously undis­ covered proteins involved in CRISPR-Cas systems. These proteins, which serve as microbial immune systems, have become important tools in modern genetics (see Chapter 21). Three additional examples of important microbiome functions that are inferred from proteincoding genes are described next.

Metabolites  Some microbes produce very specific compounds that are not produced by most species of microbes. These compounds are called metabolites, because they are the products of metabolic path­ ways. Examples include vitamins, toxins, and antibiotics. In many cases, previous research has identified the enzymes that are needed to produce a particular metabolite. When analysis by WMS identifies the genes that encode these enzymes, this result indicates that one function of the microbiome is to produce that metabolite. Microbi­ omes are potential sources of new antibiotic compounds and other metabolites of industrial importance.

The Analysis of mRNAs, Proteins, and Metabolites Provides Additional Information About Microbiome Function Catalogs of microbial species and genes obtained by amplicon analysis or WMS don’t reveal which genes were actually being transcribed and which transcripts were being translated at the time a sample was collected. Large data collections known as metatranscriptomes, metaproteomes, and meta-metabolomes can help provide the missing information.

Nitrogen Fixation  One important microbial function is nitrogen fixation, the process in which atmospheric nitrogen gas is reduced to form ammonia, which is useful as fertilizer. Only certain pro­ karyotic species have the natural ability to accomplish nitrogen fixa­ tion (see Chapter 27). Plants and other photosynthetic organisms commonly require ammonia or another source of fixed nitrogen to make amino acids, chlorophyll, and other essential molecules. Con­ sequently, algal and plant microbiomes often include nitrogen-fixing prokaryotes. To obtain evidence for microbial species that are able to fix nitrogen, plant scientists may identify gene sequences known to encode enzymes essential for nitrogen fixation. One such gene is nifH, an indicator of nitrogen fixation. Such genes are known as marker genes, because they “mark” the occurrence of a particular function—in this case, nitrogen fixation. Methane Oxidation  Additional marker genes encode subunits of the enzyme methane monooxygenase (MMO). This enzyme uses oxygen gas to oxidize the greenhouse gas methane, which plays an important role in global carbon cycles and climate warming. Lakes and wetlands are sources of methane, so it is not surprising that methane-oxidizing bacteria are commonly found in these places, often in association

Figure 30.6  Peat moss leaf harboring microbes within specialized cells having wall pores.  Peat moss leaves feature narrow living cells having green chloroplasts and larger, non-green, water-filled cells having cell wall pores. Diverse prokaryotic and eukaryotic microbes enter through the pores and live within the larger cells. ©Lee W. Wilcox

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Having discussed microbiomes as complex systems and exam­ ined the methods that biologists use to study microbiome composi­ tion and function, we have a foundation for surveying the diversity of Earth’s microbiomes. We have seen that some microbiomes are found within physical systems such as oceans, ice, fresh waters, and soils, and others are associated with living organisms known as hosts. In this section, we focus on microbiomes within physical systems and the societal concerns related to them.

Mucilage

Microbes

200 nm

Figure 30.7  TEM showing a biofilm of microbes attached by mucilage to the inner cell wall surfaces of peat moss leaf cells. ©Linda Graham

Metatranscriptome  To learn which mRNAs were present in a microbiome at the time of sampling, biologists analyze transcriptomes. A transcriptome is a collection of all the mRNA sequences produced by a single organism under defined conditions. A metatranscriptome is a collection of all the mRNA sequences present in an environmental sample, that is, all of the mRNAs produced by all of the organisms sampled from a particular place at a particular time. Metaproteome  Biologists sometimes use the number of mRNA sequences of a particular type to infer abundance or activity level of a translated protein. However, mRNA abundance is influenced by the extent to which microbes were actively growing when they were collected, the lifetime of a particular transcript, and how often that transcript is translated. A proteome analysis can provide more direct information about what proteins are present in a particular microbi­ ome. A proteome analysis, accomplished by chromatographic and spectroscopy methods, reveals which proteins are present in a par­ ticular sample. A metaproteome is all the proteins produced by all the members of a microbiome. Meta-metabolome  Because proteins, even if present, might not be functionally active, researchers may analyze the products of metabolism. Metabolomes are collections of information about the types and abundances of molecules, such as sugars and fatty acids, produced by metabolism in a single organism. A meta-metabolome provides similar information for an entire microbiome.

30.2 M  icrobiomes of Physical Systems Learning Outcomes: 1. List some types of microbiomes that are found within physical systems. 2. Explain how microbiome analyses can help monitor environments for microbial activities that affect human health.

Microbiomes Are Abundant in the World’s Oceans and in Its Ice Although you might imagine that animals such as fish and whales dominate Earth’s oceans, in fact, microbes are far more numerous. Oceans occupy 71% of Earth’s surface and have a volume of 1.37 bil­ lion cubic kilometers. The concentration of microbes in ocean water is typically 104–106 microbial cells per mL. Therefore, the number of microbes in 1 liter of seawater reaches into the billions. That’s a lot of microbes! Collectively, ocean microbes represent an immense amount of genetic and functional diversity that influences the entire planet. For example, photosynthetic cyanobacteria and algae produce about half of the organic carbon and oxygen formed on Earth each year. Other ocean microbes play essential roles in degrading organic molecules and recycling dissolved minerals, a process essential to ocean pro­ ductivity. The cyanobacterial genus Synechococcus and its phages, together with stramenopile, alveolate, and rhizarian protists (see Chapters 27–28), are key to the movement of organic molecules into deep-ocean waters. Retention of carbon in the deep oceans for long periods affects global climate and is the mechanism by which exten­ sive oil and methane (fossil-fuel) deposits form in undersea locations. Biologists have recently used gene-sequencing techniques (described in Section 30.1) to catalog viruses, prokaryotic species, and small eukaryotes from 68 ocean locations worldwide. By also monitoring the physical features of these places, they have discovered that water temperature is a major factor influencing the compositions of ocean microbiomes, raising questions about the impact of global climate change. Earth’s icy environments—collectively known as the cryosphere—likewise contain a surprisingly large number of microbes, an estimated 1025–1028 cells. The sampling of microbes from sea ice and glaciers is challenging, so adventurous biologists use ice-breaking ships, helicopters, planes, tractors, drilling rigs, and remotely operated vehicles to access polar oceans, sea ice sheets, snowfields, and glaciers (Figure 30.8a). Biologists are intrigued by the possibility that Earth’s cold microbiomes might be similar to life on bodies such as Mars, Jupiter’s moon Europa, and Saturn’s moon Enceladus. Microbiome studies of cold habitats have revealed surpris­ ingly diverse types of microbiota that colorize otherwise white environments. Beneath floating sheets of sea ice live conspicuous growths of brown diatoms that dangle into the cold ocean. These photosynthetic algae supply organic molecules and oxygen to heterotrophic bacteria; ciliate, flagellate, and foraminiferan protists (see Chapter 28); and small animals. Algal cells on the surfaces of glaciers can be so abundant that they color the ice green, red,



MICROBIOMES: MICROBIAL SYSTEMS ON AND AROUND US 629

yellow, purple, or gray, in this way influencing the amount of light energy that glaciers reflect into space (Figure 30.8b). Blood Falls in Antarctica gets its dramatic red color from dissolved iron released from subsurface minerals by iron-metabolizing bacteria living in the cold darkness (Figure 30.8c).

Microbiomes Affect the Quality of Fresh Water and Soil

(a) Researchers sampling the cryosphere.  Darker areas of ice indicate growth of algae and other microbes.

Freshwater and soil microbiomes are also important to many human concerns, including drinking water safety and agricul­ tural production. Marker genes are commonly analyzed to detect infectious or toxic organisms in the water used for drinking and recreation. Experts are particularly concerned about the effects of global warming on freshwater and soil cyanobacteria, because these organisms grow more abundantly in warmer temperatures, particularly where humans have polluted environments with excess minerals. Some abundant cyanobacteria produce persistent and potent toxins that harm people and wildlife. For example, the cyanobac­ terial genus Microcystis (Figure 30.9) produces more than 100 different chemical forms of the toxin microcystin, which binds to and inhibits eukaryotic phosphatases, cellular enzymes that remove

Heterotrophic bacteria (b) A glacier colored by algae in ice microbiomes

50 μm

(c) Blood Falls in Antarctica colored red by iron released by bacteria in ice microbiomes

Figure 30.8  Microbiomes within and on ice.  (a) Researchers obtaining samples growing on and within ice for microbiome analysis. (b) The color of the ice seen here is due to the presence of algae. (c) Blood Falls in Antarctica. The red color is from iron that is released by bacteria, which are part of a microbiome within the ice. a: Courtesy of Cody S. Sheik; b: ©Jason Edwards/National Geographic Creative; c: Source: Peter Rejcek, NSF

Figure 30.9  The colony-forming cyanobacterial genus Microcystis.  This cyanobacterial colony has cells that look dark because they contain many light-refracting gas vesicles that aid in flotation. In addition to being an important microbial component of a physical (freshwater) microbiome, Microcystis hosts other microbes, such as smaller colorless heterotrophic bacteria. Microcystis and associated bacteria produce toxins harmful to human health. ©Lee W. Wilcox Core Skill: Science and Society  Microbiome characterization is important in evaluating the safety of water used by humans for drinking and recreation.

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phosphate from proteins and organic compounds. The inability to remove phosphate interferes with many cellular processes, includ­ ing cell signaling (see Chapter 9). By this mechanism, microcystin can cause severe liver damage and hemorrhage in mammals, and chronic exposure to microcystin is associated with high rates of human liver cancer. Humans and other animals become exposed to microcystin when large numbers of cyanobacteria exist in water used for drinking or swimming, a situation that is a growing pub­ lic health concern. Amplicon analyses of rRNA sequences are increasingly used to monitor aquatic microbiomes for cyanobac­ terial species likely to produce toxins. Because the genes encod­ ing all enzymes required for the biosynthesis of microcystin and other cyanobacterial toxins are known, metagenomic data can be analyzed for the presence of these genes to assess the potential for toxin production. Soil microbiomes, which include cyanobacteria and other types of microbes, are key to our ability to grow crops, because various soil microbes can foster or harm plant health (see Chapters 27 and 29). A single gram of soil contains as many as 50,000 bacterial species and fungi, many of which affect plants in some way. Soil microbiomes are important for understanding how terrestrial plants acquire microbi­ omes, described in Section 30.3.

30.3 Host-Associated Microbiomes Learning Outcomes: 1. Define the terms holobiont and hologenome. 2. Describe a few examples in which animal and plant hosts acquire microbiomes, and how microbiomes change during evolution. 3. Make a list of the benefits that are derived from the associations between microbiomes and their hosts. 4. CoreSKILL » Analyze the data that host microbiomes play a role in human health.

Many people have heard news media stories about the human micro­ biome, which includes thousands of different microbial species that live in various locations within and on the surface of the human body (see Figure 30.1). Consequently, humans are said to be microbiome hosts. The human body serves as an environment for many microbes, some of which provide us with nutritional or protective benefits. Our microbes, in turn, receive benefits from us, such as organic molecules that serve as microbial food. As noted in previous sections, the bodies of other animals, plants, fungi, protists, and even some prokaryotes support complex microbiomes. In this section, we will learn how hosts acquire microbiomes, how microbiomes evolve, and how the functions of microbiomes are important for their fungal, plant, and animal hosts.

Hosts Acquire Microbiomes in Different Ways The combination of a host organism and its microbiome is known as a holobiont. The host and microbiome genomes together are called the hologenome. Microbiomes contribute many more genes to the

hologenome than their hosts do. For example, the human genome contains about 22,000 protein-encoding genes, whereas the human microbiome is estimated to have millions of such genes! Having a functionally useful microbiome aids the survival of the young and thereby increases fitness. Different types of hosts acquire microbi­ omes in various ways. ∙∙ Certain insects coat the casings of their eggs with bacteria; when the young hatch, they become inoculated with beneficial microbes. ∙∙ Newborn bees get their microbiomes from sibling worker bees. ∙∙ Termites use specific behaviors to transfer among themselves microbes they need to break down plant materials into food. ∙∙ Mammals, including humans, transmit important microbes as the young transit the birth canal. ∙∙ Human intestinal bacteria, which often prefer low-oxygen environments, can be transmitted from one person to another as tough-walled spores that tolerate air exposure.  ∙∙ Plant seedlings acquire their microbiomes from the surrounding soil and air and use inherited mechanisms, such as the secretion of particular organic compounds, to attract beneficial microbes. These examples indicate that both host genetics and the environ­ ment play a role in microbiome establishment. The idea that genet­ ics plays a role in microbiome composition is further supported by evidence that compares the microbiomes among different hosts. For example, closely related tropical plants have microbi­ omes more similar to each other than to the microbiomes of more distantly related plant species. Likewise, strong similarities are observed between the gut microbiomes of African apes (chimpan­ zees, bonobos, and gorillas) and their close relative, humans, as described next.

Microbiomes Change During the Evolution of Their Hosts Researchers are interested in the relationship between the evolution of hosts and the changes in the microbiomes that the hosts support. In the case of humans, evolutionary studies indicate that some bac­ teria typical of the modern human gut microbiome descended from microbial ancestors that diversified in human and African ape hosts over millions of years. Changes in gut microbiomes may be related to changes in their hosts’ diet. After humans diverged from Afri­ can apes, the ape diet remained plant-rich, whereas the human diet became increasingly animal-rich. These dietary differences affected the environment of gut microbiomes (Figure 30.10), which were exposed to different types of nutrients.  Compared to the gut microbes of African apes, some humanassociated gut microbes have flourished under an animal-rich diet, whereas others were reduced. For example, humans have more gut microbes from the phylum Bacteroidetes, such as the genus Bacteroides, a feature  associated with diets rich in animal fats and proteins. By contrast to apes, humans have lower numbers of the archaeon genus Methanobrevibacter, which degrades complex plant



MICROBIOMES: MICROBIAL SYSTEMS ON AND AROUND US 631

Increased

Bacteroides, Bifidobacterium, Clostridium

Decreased

Methanobrevibacter, Fibrobacter, Sporobacter Human, Homo sapiens Increased

Fibrobacter, Sporobacter Chimpanzee, Pan troglodytes

Decreased

Bifidobacterium, Clostridium

Bonobo, Pan paniscus

Gorilla, Gorilla gorilla

Figure 30.10  Changes in gut microbiomes during the evolution of African apes and humans.  The changes seen in humans, chimpanzees, and bonobos are relative to the gut microbiome of gorillas, which diverged earlier. Source: Moeller, A. H. et al. 2014. Rapid changes in the gut microbiome during human evolution. Proceedings of the National Academy of Sciences of the United States of America 111: 16431–16435.

Core Concept: Evolution  Comparing the microbiomes of evolutionarily related hosts illustrates the concept that host organisms and associated microbiota evolve together over long time periods.

polysaccharides to methane. Humans also have lower numbers of Fibrobacter, a bacterial genus common in ape microbiomes, where it helps to break down the plant foods that apes consume. In cap­ tivity, primates whose diets are decreased in plant content tend to lose some native gut microbes and gain microbes more common to human guts. Overall, these observations indicate that microbiome composition is influenced by host environment, genetics, and evo­ lutionary history.

Lichens Are Partnerships Between a Fungal Host and Many Microbial Species We now turn our attention to microbiomes that are associated with fungi. Lichens are complex mutualistic associations between particular fungi and many other microbes, including photosyn­ thetic green algae or cyanobacteria. Researchers estimate that 20% of known fungal species occur in approximately 18,500 kinds of lichen. The association between fungi and other microbes results in a distinctive body form that attaches to surfaces in different ways: ∙∙ Crustose lichens are flat and adhere tightly to an underlying surface (Figure 30.11a).

∙∙ Foliose lichens are flattened and leaflike (Figure 30.11b). ∙∙ Fruticose lichens grow upright (Figure 30.11c) or hang down from tree branches. In the past, lichens were regarded as relatively simple associa­ tions between one fungal species and a single green algal or cya­ nobacterial species (or sometimes both). According to this simple model, the fungus obtained essential organic carbon and fixed nitro­ gen from the algal or cyanobacterial partner. The photosynthetic partner received inorganic nutrients and water from the spongy fun­ gal body, and benefited from fungal compounds that protect against intense sunlight and predation by other organisms. However, WMS studies have recently revealed that lichens are complex microbiomes that include hundreds of bacterial species and multiple types of algae and fungal species, in addition to the most abundant fungus, which is considered the host. This new concept of a lichen as a fungal host with a complex microbiome offers new insight into lichen diversity and function in nature.  In a lichen, the diverse microbiota occur in distinct locations. The photosynthetic green algae or cyanobacteria typically occupy a distinct layer close to the lichen’s surface, hyphae of the host fungus make up most of the body (Figure 30.11d), and other microbes pri­ marily occur on the surface (Figure 30.12). Lichen body structure

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(a) Crustose lichen

(b) Foliose lichen 5.00 μm

Figure 30.12  SEM view of a lichen microbiome.  The lichen Peltigera ponojensis harbors cyanobacteria in an internal layer as well as a diverse surface community of bacteria and protists. ©Linda Graham

(c) Fruticose lichen

(d) Microscopic view of a cross section of a lichen

Figure 30.11  Lichen structure.  (a) An orange-colored crustose

lichen grows tightly pressed to the substrate. (b) The flattened, leafshaped genus Umbilicaria is a common foliose lichen. (c) The highly branched genus Cladonia is a common fruticose lichen. (d) A handmade thin slice of Umbilicaria viewed with a light microscope reveals that the photosynthetic algae occur in a thin upper layer. Fungal hyphae make up the rest of the lichen. a: ©Perry

Mastrovito/Corbis/Getty Images; b, d: ©Lee W. Wilcox; c: ©Ed Reschke/Getty Images

Core Skill: Modeling  The goal of this modeling challenge is to propose a model that describes the location of algae within a fruticose lichen. Modeling Challenge: Parts (a) through (c) of Figure 30.11 illustrate three major structural types of lichens: crustose, foliose, and fruticose. Figure 30.11d shows a representative light microscope view of a thin slice of a foliose lichen, which reveals that the green algal cells are located near the upper surface of the flat lichen body. In this location, the photosynthetic cells of the algae are best able to absorb sunlight. Use this information to sketch a structural model of the likely distribution of algal cells in the body of a fruticose lichen. Your model should be a circular cross section through one of the branchlike segments of the lichen. Label the fungal and algal layers.

differs dramatically from that of the main fungal species grown sepa­ rately, indicating that microbiome components influence lichen form. Most lichens occur in terrestrial environments, but some are found in aquatic locales. They often grow on rocks, buildings, tombstones, tree bark, soil, or other surfaces that easily become dry. When water

is not available, the lichens lie dormant until moisture returns. Thus, lichens may spend much of their time in an inactive state, and for this reason, they often grow very slowly. However, because they can persist for long periods, lichens can be very old; some individuals are esti­ mated to be more than 4,500 years old. Lichens grow in some of the most extreme, forbidding sites on Earth—deserts, mountaintops, and the Arctic and Antarctic—places where most plants cannot survive.  Lichens provide important ecological services. They are a food source for reindeer and other animals. Though unpalatable, lichens are not toxic to humans and some have served as survival foods in times of shortages. Soil building is another important lichen function. Lichen acids help to break up the surfaces of rocks, beginning the process of soil development. Lichens that include nitrogen-fixing cya­ nobacteria are known to increase environmental fertility. One study showed that such lichens released 20% of the nitrogen they fixed into the environment, where it is available for uptake by plants. Recent studies of lichen microbiomes have revealed that bacterial compo­ nents play previously unknown roles in degrading complex organic materials, and that lichens serve as habitat for diverse protists.

Plant Microbiomes Are Associated with Leaves, Stems, and Roots WMS studies have been conducted on the microbiomes of modern bryophytes, which are nonvascular plants such as peat mosses (see Figures 30.6 and 30.7). The results revealed that bryophytes serve as hosts to diverse microbiomes, including microorganisms that provide important services such as nitrogen fixation. Because bryophytes are early-diverging land plants (see Chapter 31), this discovery of bryo­ phyte microbiomes suggests that plants have hosted beneficial micro­ biomes throughout their evolutionary history.  Compared to bryophytes, vascular plants have a more complex body, which includes aboveground leaves and stems and subterra­ nean roots. As described next, microbiomes are found on and within leaves, stems, and roots.



MICROBIOMES: MICROBIAL SYSTEMS ON AND AROUND US 633

Aboveground Plant Microbiomes  Leaf surfaces commonly host as many as 107 bacterial cells per square centimeter, and microbes also occur within leaf and stem tissues. Globally, leaf microbe num­ bers are estimated at 1026. Leaves of tropical forest trees may host more than 400 types of bacteria, and those of temperate forest trees likewise support diverse microbes whose diversity correlates with photosynthetic production.  Subterranean Root Microbiomes  Legumes and some other plants are known to form partnerships with soil bacteria that provide fixed nitrogen, greatly aiding plant growth, a process described more fully in Chapter 38. Plants foster specific partnerships with particular nitrogen-fixing bacteria by secreting peptides that cause the death of less valuable bacteria. Certain fungi are also important components of most plant root microbiomes. Plants acquire beneficial bacterial and fungal partners from the diverse assortment of microbes in the soil close to plant root surfaces, a region called the rhizosphere. Associations between the hyphae of certain fungi and the roots of most seed plants are known as mycorrhizae (from the Greek, meaning fungus roots). Similar associations also occur between fungi and bryo­ phytes, which lack roots, suggesting that fungi have aided plant suc­ cess on land from the beginning. Modern fungus-root associations are very important in nature and agriculture; more than 80% of terrestrial plants form mycorrhizae. Plants that have mycorrhizal partners receive an increased supply of water and mineral nutrients, primarily phosphate, copper, and zinc. They do so because an extensive fungal mycelium is able to absorb minerals from a much larger volume of soil than can roots alone (Figure 30.13). Added together, the branches of a fungal myce­ lium in 1 m3 of soil can reach 20,000 km in total length. Experiments have shown that mycorrhizae greatly enhance the growth of the plants they are associated with compared with plants lacking fungal partners. In return, plants provide fungi with organic food molecules, sometimes contributing as much as 20% of their photosynthetic products. The two most common types of mycorrhizae are endomycorrhizae, which occur within root tissue, and ectomycorrhizae, which coat roots. Endomycorrhizae (from the Greek endo, meaning inside) are partner­ ships between plants and fungi in which the fungal hyphae penetrate the spaces between root cell walls and plasma membranes and grow along the outer surface of the plasma membrane. In such spaces, endo­ mycorrhizal fungi often form highly branched, bushy arbuscules (from the word arbor, referring to the tree-like shape of these structures). As the arbuscules develop, the root plasma membrane also expands. Con­ sequently, the arbuscules and the root plasma membranes surrounding them have a very high surface area that facilitates rapid and efficient exchange of materials: Minerals flow from fungal hyphae to root cells, while organic food molecules move from root cells to hyphae. These fungus-root associations are known as arbuscular mycorrhizae, abbreviated AM (Figure 30.14). Fungi are associated in this way with apple and peach trees, coffee shrubs, and many herbaceous plants, including legumes, grasses, tomatoes, and strawberries. Ectomycorrhizae (from the Greek ecto, meaning outside) are partnerships between temperate forest trees and soil fungi, particu­ larly basidiomycetes. The fungi that engage in such associations are known as ectomycorrhizal fungi (Figure 30.15a). The hyphae of ectomycorrhizal fungi coat tree-root surfaces (Figure 30.15b) and grow into the spaces between root cells but do not penetrate the cell

Seedling root

Mycorrhizal hyphae

Figure 30.13  Tree seedling with mycorrhizal fungi.  Hyphae of a mycorrhizal fungus extend farther into the soil than do the seedling’s roots, helping the plant to obtain water and mineral nutrients. ©Dr. D. P. Donelley and Prof. J. R. Leake, University of Sheffield, Department of Animal & Plant Sciences

Core Skill: Connections  Figure 30.13 illustrates the close connection between microbial science, soil science, and forestry science, which studies trees.

membrane; they occupy the spaces between the cell walls of adjacent cells (Figure 30.15c). Some species of oak, beech, pine, and spruce trees will not grow unless their ectomycorrhizal partners are also present. Mycorrhizae are thus essential to the success of commercial nursery tree production and reforestation projects.

Animal Microbiomes Serve Many Useful Functions Animal microbiomes are commonly dominated by bacteria, but may also include viruses, archaea, fungi, protists, and microscopic animals. These species affect animal health and may play important environ­ mental roles or have medical applications. Termites, for example, are globally important in recycling plant biomass, a function enhanced by the hundreds of gut bacterial species these insects harbor. Tuni­ cates, an early-diverging lineage of chordates (see Chapter 35), occur worldwide as colonies of animals that filter microbial food from sea­ water. The guts of tunicates contain complex microbiomes, including beneficial cyanobacteria that synthesize sterols useful to the hosts and other bacteria that produce defensive molecules. Microbiomes are likewise important to mammals, such as the brown bear, Ursus arctos. Brown bears are notable for their seasonal lifestyle, which involves fat accumulation in summer

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Hyphae

Arbuscules Cell wall Plasma membrane 49 μm

Root cells

(a) Micrograph of arbuscular mycorrhizae

(b) Hyphae growing between cell walls and plasma membranes

Figure 30.14  Endomycorrhizae.  (a) Light micrograph showing black-stained endomycorrhizal fungi within the roots of the forest herb Asarum canadensis. The fungal hyphae penetrate plant root cell walls, then branch into the space between root cell walls and plasma membranes. (b) Diagram showing the position of highly branched arbuscules. Hyphal branches or arbuscules are found on the surface of the plasma membrane, which becomes highly invaginated. The result is that both hyphae and plant membranes have very large surface areas. a: ©Mark Brundrett

Core Concept: Structure and Function  The highly branched structure of intracellular portions of endomycorrhizal fungi is key to the ability of the fungus to take up sufficient organic nutrients and efficiently deliver minerals to the host plant.

and reliance on that fat during hibernation in winter.  Amplicon analysis of rRNAs (see Figure 30.3) reveals that the microbiomes in bear guts differ in winter versus summer. Winter microbiomes are less diverse and include higher numbers of bacteria from the phylum Bacteroidetes, which are associated with the breakdown of lipids and proteins. Bacteria linked to diets rich in plant fiber are also lower in winter than in summer, when plants are part of a bear's diet. The most intensively studied animal microbiome is that of humans, the subject of several large scientific projects involving many biologists. The Human Microbiome Project, for example, char­ acterized the microbes of 18 body sites on 300 healthy U.S. adults,

finding that humans have distinctive microbiomes in the gut, vagina, urogenital tract, mouth, nose, skin, and teeth. This and other stud­ ies have shown that human bodies host 100 trillion microbes that make up 1–3% of our body weight! The microbiomes associated with humans affect our health in many ways. ∙∙ The microbiomes of teeth form biofilms, known as plaque, that are detrimental to dental health. ∙∙ Up to 240 bacterial genera can be associated with human skin alone, performing beneficial functions. Some species within skin microbiomes break down dead skin, and others help to prevent infections or transform skin oil into natural moisturizer.

Ectomycorrhizal hyphae

Ectomycorrhizal hyphae coating a root tip (a) Ectomycorrhizal fruiting body

(b) SEM of ectomycorrhizal hyphae

Root cells 200 µm .m (c) Hyphae invading intercellular spaces

Figure 30.15  Ectomycorrhizae.  (a) The fruiting structure of the common forest fungus Laccaria bicolor. This is an ectomycorrhizal fungus that

is associated with tree roots. (b) SEM showing ectomycorrhizal fungal hyphae of L. bicolor covering the surfaces of young Pinus resinosa root tips. (c) Diagram showing that the hyphae of ectomycorrhizal fungi do not penetrate root cell walls but grow within intercellular spaces. By doing this, fungal hyphae are able to obtain organic food molecules produced by plant photosynthesis. a: ©Jacques Landry, Mycoquebec.org; b: Courtesy of Larry Peterson

and Hugues Massicotte

Concept Check:   What benefits do plants obtain from the association with fungi? 



MICROBIOMES: MICROBIAL SYSTEMS ON AND AROUND US 635

∙∙ Microbes of the digestive system, particularly the gut, are very important in early life. Bifidobacterium longum subspecies infantis, for example, is the most prevalent microbe in the gut of healthy infants. This bacterium has genes encoding proteins that bind, import, and metabolize milk polysaccharides into short fatty acids such as acetate. Some of these fatty acids serve

as food for the infant's colon cells, aid the immune system, and reduce gut pH, which deters some disease microbes. The best foods for B. longum are polysaccharides that are abundant in human milk but rare or absent in that of other animals. Breastfeeding thereby fosters the growth of these beneficial microbes.

Core Skill: Process of Science

Feature Investigation  | Blanton, Gordon, and Associates Found That Gut Microbiomes Affect the Growth of Malnourished Children

In a study published in 2016, Laura Blanton, Jeffrey Gordon, and colleagues described the effects of differences in gut micro­ biomes on the growth of malnourished children. These research­ ers began their work by analyzing DNA sequences that encode 16S rDNA to determine how microbiome bacteria change dur­

ing the first 32 months of life in malnourished children from the same locale (Figure 30.16). Some of these malnourished children appeared healthy based on their growth, but others were stunted in their growth and were underweight. The results revealed that the healthy children had microbiomes that changed over time, so that

Figure 30.16  Impact of the gut microbiome on growth. HYPOTHESIS Microbiomes from children who were stunted in their growth due to malnourishment will impair the growth of mice. KEY MATERIALS Fecal samples from healthy and stunted children, germ-free mice which are mice that have been raised in an aseptic environment and do not have any microbes in or on their bodies.

1

Obtain fecal samples from many healthy and stunted children of the same locale from birth to 32 months of age.

2

Perform an amplicon analysis on the fecal samples from birth to 32 months old.

3

Using a tube, introduce fecal samples from healthy and stunted children into the gut of 5-week-old germ-free mice.

4

Give the mice a diet that corresponds

Experimental level

See Figure 24.3.

Conceptual level

This method reveals which prokaryote species are in the gut microbiome and how they change over the course of 32 months.

Gut microbiome from children

The two different types of

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4

Give the mice a diet that corresponds to a diet that the children eat.

5

Monitor the weight of the mice over a 5-week period.

Received fecal material from a healthy donor

Received fecal material from a stunted donor

Weight gain is a measure of how the gut microbiomes affect growth.

THE DATA From step 2: Healthy children:

Stunted children:

From step 6: From birth to 32 months

From birth to 32 months

Microbiomes changed over 32 months

Microbiomes stayed similar over 32 months

Mice that received fecal transplant from healthy children

130 % Initial weight

6

The two different types of gut microbiomes may affect the ability of the mice to gain weight.

Mice that received fecal transplant from stunted children

120 110 100 90

0

10 20 30 Days after the fecal transplant was established in the mouse

7

CONCLUSION The gut microbiomes from stunted donors impaired the growth of mice.

8

SOURCE Blanton, Laura B., et al. 2016. Gut Bacteria That Prevent Growth Impairments Transmitted by Microbiota from Malnourished Children. Science 351: 830–837.

older children had a different, more mature microbiome than did infants. By contrast, children who were stunted in growth retained an immature type of microbiome (see the left side of the data in Figure 30.16). In a next phase of their work (see step 3 of Figure 30.16), these biologists transplanted the microbiomes of healthy or stunted chil­ dren into separate sets of microbe-free (“germ-free”) mice, so that the effects on growth could be monitored in ways that would have been difficult to accomplish with children. After this fecal transplan­ tation, the mice were fed germ-free food of the same type eaten by the children. This experiment revealed that mice having microbiomes transplanted from the stunted children gained less weight than mice that received microbiomes transplanted from healthy children, even

though the mice consumed the same amount of food (see the right side of data in  Figure 30.16). Though not shown in Figure 30.16, these researchers also used magnetic resonance imaging technology to determine lean and fat body mass, as well as micro-CT (computer­ ized tomography) to evaluate the femur bone structure of the mice. The results of these imaging studies also showed that the gut micro­ biome played an important role in proper growth, but the basis of the effect remained unclear. In further work that is not shown in Figure 30.16, the researchers took a closer look at the composition of the transferred microbiomes to identify potential microbes that were responsible for better growth. By performing an amplicon analysis, they determined that the micro­ biomes of mice that had received fecal samples from healthy donors



MICROBIOMES: MICROBIAL SYSTEMS ON AND AROUND US 637

tended to be dominated by a few bacterial species—Ruminococcus gnavus, Clostridium symbiosum, and a few others. To determine if any of these species were responsible for greater growth, research­ ers grew cultures of these bacterial species in the laboratory and then introduced them into mice that had received fecal samples from stunted children. The result was that the stunted mice grew larger! The researchers then characterized the gut microbiomes from these mice and determined that they were dominated by Ruminococcus gnavus and Clostridium symbiosum. Metabolomic studies revealed that these two bacterial species had the effect of decreasing amino acid oxidation and increasing amino acid incorporation into proteins

that contributed to increases in body mass. In this way, the microbes were inferred to help malnourished children better use amino acids for growth. Together, these experiments revealed a causal relation­ ship between microbiome composition and mouse growth, rather than merely a correlation.

30.4 E  ngineering Animal and Plant Microbiomes

industrialized countries have undergone shifts in their microbiomes that are implicated in gastrointestinal disorders, obesity, and autoim­ mune disease. For example, compared to people in isolated popula­ tions, people in industrialized countries consume less dietary fiber, composed of complex plant carbohydrates. Studies of mice show that the chronic lack of dietary fiber reduces gut microbiome diversity. Researchers use such information to assemble synthetic micro­­biomes by mixing cultures of beneficial microbial species. The effects on host health are determined by implanting these synthetic microbiomes into germ-free hosts, also known as axenic or gnotobi­ otic hosts, such as mice, rats, or guinea pigs. The microbe combina­ tions associated with the most positive effects on host health may be considered for use as treatments in humans.

Learning Outcomes: 1. Explain why engineering animal and plant microbiomes may be useful. 2. Describe how biologists produce synthetic microbiomes. 3. Describe how artificial selection can be used to identify the most beneficial microbiomes for plants and animals.

Because microbiomes affect the health of animals and plants, researchers are investigating the potential of altering microbiomes to benefit humans, domesticated animals, and crop plants. Manipulating the composition of a microbiome to improve host characteristics is known as microbiome engineering. Much animal microbiome engi­ neering research is done on mice or other laboratory animals, but the results may eventually be applied to humans.

Microbiomes Can be Manipulated As we saw in Figure 30.16, the gut microbiome can have an impor­ tant impact on health. For this reason, fecal transplants are performed to introduce the entire gut microbiome of a healthy animal host into the gut of an unhealthy host. However, because thousands of micro­ bial species and many complex interactions may be involved, the biological basis for success or failure of this treatment can be dif­ ficult to determine. Alternatively, biologists perform experiments to determine more precisely which particular microbiome members are consistently associated with host health. As shown by the studies of Blanton, Gordon, and colleagues, described in the previous section, comparing the microbiomes of healthy hosts with those of unhealthy hosts helps to reveal the key beneficial species. Additional information about healthy human microbiomes is gained by studying humans in nonindustrial societies. For example, the microbiomes of isolated Amerindians (indigenous peoples of the Americas), who have had no previous contact with Westerners, have the highest known diversity of gut and skin bacteria and microbiome functions. Compared to humans living in industrialized societies, isolated Amerindians have lower diversity of bacterial species from the phylum Bacteroidetes and higher diversity of other important microbiome species. Such differences indicate that humans living in

Experimental Questions 1. Why did the investigators feed experimental mice germ-free food?  2. CoreSKILL » Explain how the microbiomes from healthy or stunted children affected the growth of mice. 

Probiotic Treatments Add Beneficial Microbes A probiotic treatment involves the introduction of one or more microbial strains into the microbiome of a host organism. For exam­ ple, the bacterial genus Lactobacillus (phylum Firmicutes) has been used as a probiotic to treat vaginal conditions in humans. Probiotic treatments may also help in the fight against AIDS, a disease caused by HIV (see Chapter 19). Studies of female AIDS patients revealed that decreases in vaginal Lactobacillus can be accompanied by increases in other bacteria that are normally rare. Some of these bac­ teria cause inflammation that enhances susceptibility to HIV infec­ tion, and others break down HIV drugs administered in vaginal gels. These results help to explain why anti-HIV drugs sometimes work less well in females than in males, and suggest that manipulating the vaginal microbiome may help in the fight against AIDS. Recent studies in mice have shown that newborns lacking par­ ticular gut bacteria from the phylum Firmicutes are more susceptible to disease bacteria than newborns who have these Firmicutes species. Experimental addition of certain Firmicutes bacteria to the micro­ biota of newborn mice originally lacking them protected the animals from infection. Human newborns have less gut microbial diversity and are more susceptible to bacterial infections than adults whose gut microbiota include Firmicutes bacteria. These results suggest that probiotic treatments may offer the potential to increase protection from gut pathogens in early life.  Plants can also benefit from probiotic treatments. For exam­ ple, strawberry plants that grew in a particular soil for many years

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without being attacked by harmful fungi were found to benefit from the presence in the soil of a fungus that produces an antifun­ gal antibiotic. This observation suggests that the inoculation of soil with this fungus or the antibiotic could be beneficial to strawberry growers.

Artificial Selection Can Be Used to Engineer Microbiomes Yet another microbiome engineering approach relies on artificial selection, which is a human-controlled form of natural selection (see Chapter 23). In this process, biologists engineer bacterial communi­ ties by artificial selection of favorable microbiomes. As an example, the process of engineering plant microbiomes by artificial selection begins by planting seedlings bearing different microbiomes into sterilized soil. At the end of a period of growth, plants are assessed for an agriculturally important trait, such as height or time of flow­ ering. Those soils that resulted in plants showing the highest levels of the desirable trait are presumed to contain microbes that make up the most beneficial microbiomes. The soil microbiomes associated with plants having favorable phenotypes are selected to incorporate into soils for the next generation of plants. In this way, scientists

can use easily observed plant characteristics to select the most ben­ eficial microbiomes (Figure 30.17). Amplicon analysis or WMS is then used to determine the composition of the winning microbiome. Similar artificial selection strategies have been used to engineer the microbiomes of animals, such as bees (Figure 30.18). Like those of humans, bee gut microbiomes are dominated by bacteria that pre­ fer low oxygen environments. Bee gut bacteria are well-adapted to consume sugars, which are abundant in flower nectar, a component of bees’ diet. Phylogenetic analyses have revealed that, like the micro­ biomes of primates, bee microbiota have been co-evolving with their hosts over millions of years.  To begin the artificial selection process, bees having different gut microbiomes can be evaluated for health by examining particu­ lar phenotypic traits. Newborn bees lacking microbiomes can then be exposed to the microbiomes of the bees judged to have the best health. By repeating this process, the healthiest microbiomes can be inferred from indicators of bee health. Bees are important to human society because they aid plant reproduction in natural and agricultural systems and produce honey and wax. Bees around the world suffer from microbial infections (see Chapter 29), so micro­ biome engineering might be a valuable way to help improve bee survival.

Initial seedlings with different microbiomes planted in sterile soil

Repeat steps 1–4

1

Seedlings are allowed to grow.

2

Plants are measured for desirable traits (i.e., height).

3

Tallest plants are selected.

4

Microbiomes from soils with the largest plants are used to inoculate new sterile soil with seeds.

Figure 30.17  Artificial selection as a tool to engineer plant microbiomes. Source: Mueller, U. G., and Sachs, J. L. 2015. Engineering Microbiomes to Improve Plant and Animal Health. Trends in Microbiology 23: 606–617.



MICROBIOMES: MICROBIAL SYSTEMS ON AND AROUND US 639

Inital bee-microbiome associations before selection 1

Maturation of bees and gut-microbiomes

2

Bee phenotyping, e.g., testing bee health

3

Select microbiomes of healthy bees to transmit to new bees.

Repeat steps 1–4. Newly born bees without gut microbiomes

4

Inoculate new bees with microbiomes chosen in 3.

Figure 30.18  Artificial selection as a tool to engineer animal microbiomes.  Bee microbiomes provide an example of this method. Source: Mueller, U. G., and Sachs, J. L. 2015. Engineering Microbiomes to Improve Plant and Animal Health. Trends in Microbiology 23: 606–617.

Summary of Key Concepts 30.1  M  icrobiomes: Diversity of Microbes and Functions ∙∙ Microbiomes are complex biological systems that are difficult to characterize using a microscope alone (Figures 30.1, 30.2). ∙∙ The members of microbiomes are usually identified using genetic techniques such as amplicon analysis or whole metagenomic sequencing (WMS) (Figures 30.3–30.5). ∙∙ The analysis of protein-encoding genes can reveal important functions of microbiomes (Figure 30.6, Figure 30.7). ∙∙ Additional information regarding microbiome function can be obtained by characterizing the metatranscriptome, metaproteome, and meta-metabolome, which are all the types of mRNAs, proteins, and metabolic products, respectively, that are present in a microbiome.

30.2  Microbiomes of Physical Systems ∙∙ Seawater is a physical system containing varied microbiomes, which include important photosynthetic microbes such as cyanobacteria and algae. ∙∙ Biologists explore the microbiomes found within ice. These microbiomes can affect the color of ice and its ability to absorb light (Figure 30.8). ∙∙ Microbiomes are found in freshwater habitats and may produce human health concerns, such as toxins produced by Microcystis bacteria (Figure 30.9). ∙∙ The soil is another physical system containing microbiomes, which are known to have a great impact on the growth of crops.

30.3  Host-Associated Microbiomes ∙∙ The combination of a host organism and its microbiome is known as a holobiont. The host and microbiome genomes together form the hologenome.

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∙∙ Hosts acquire microbiomes in different ways, and these microbiomes may change as species diverge from each other during evolution (Figure 30.10). ∙∙ A variety of species, including fungi, plants, and animals, act as hosts for microbes, forming microbiomes. These associations result in an astonishing array of benefits for both the hosts and their microbial partners (Figures 30.11–30.15). ∙∙ Blanton, Gordon, and associates found that gut microbiomes affect the growth of children, and this effect was confirmed by studies in mice (Figure 30.16).

30.4  E  ngineering Animal and Plant Microbiomes ∙∙ Researchers are exploring a variety of approaches for engineering microbiomes, including the transplantation of gut microbiomes, the use of probiotics, and artificial selection (Figures 30.17, 30.18).

Assess & Discuss Test Yourself 1. A microbiome is a. an interaction between two different species of microorganisms. b. an environment that is microscopic. c. a particular assemblage of microbes (including their genes) that occurs in a defined environment. d. the entire genetic makeup of a particular microorganism. e. both a and d.  2. An example of a microbiome function is  a. nitrogen fixation. b. methane oxidation. c. the production of particular metabolites. d. All of the above are microbiome functions. e. Only b and c are microbiome functions.  3. In what order should the four DNA fragments below be placed to form a contig? DNA regions with the same sequence are shown in the same color (red, green, or blue). 

Fragment 1: Fragment 2: Fragment 3: Fragment 4: a. 1, 2, 3, 4 b. 2, 3, 4, 1 c. 1, 3, 2, 4

6. Which of the following categories of organisms can function as a host for a microbiome? a. cyanobacteria d. plants and animals b. algae e. all of the above c. fungi 7. In which of the following ways can an animal acquire a microbiome?  a. Certain insects coat the casings of their eggs with bacteria. b. Newborn bees get microbes from sibling worker bees. c. Mammals, including humans, transmit important microbes as the young transit the birth canal. d. Termites use specific behaviors to transfer among themselves microbes they need to break down plant materials into food. e. All of the above are ways that animals can acquire microbiomes.  8. What is a biofilm?  a. a microbiome within the gut of an animal b. a group of microbes that secrete mucilage and stick together c. a microbiome that forms an opaque film on ice d. a group of microbes that perform a metabolic function the host cannot perform e. a microbiome that floats on the surface of seawater  9. The goal of microbiome engineering is to  a. eliminate an unwanted microbiome from the host. b. manipulate the composition of a microbiome to cause its selfdestruction. c. manipulate the composition of a microbiome to benefit the host. d. identify all of the microbial species within a microbiome. e. alter the genome of the host so that it can support a different microbiome.  10. Which of the following is not an approach for microbiome engineering?  a. transplantation of gut microbiomes b. probiotics c. artificial selection d. All of the above are approaches for microbiome engineering. e. Only a and c are not approaches for microbiome engineering. 

Conceptual Questions 1. Describe two examples of microbiomes that are found within a physical system. Explain how such microbiomes can affect Earth’s environment on a global scale.  2. Pick one host-associated microbiome. Describe how the host benefits from the microbiome and how the microbes within the microbiome benefit from their association with the host. 

d. 3, 2, 1, 4 e. b or d

4. Which of the following is a microbiome of a physical system? a. a microbiome on the surface of a leaf b. a microbiome in the human gut c. a microbiome in a soil sample d. a microbiome in a sample of human saliva e. all of the above  5. The combination of a host organism and its microbiome is known as  a. a microbiome. b. a holobiont. c. a metagenome. d. a metabolome. e. both a and c.

3.

Core Concept: Systems  Give one example of how a microbiome of a plant can influence the plant’s ability to interact with the environment. 

Collaborative Questions 1. Microbiomes occur in places that you may have not imagined. Starting with the term microbiome or microbiota, search the literature using a search engine such as Pubmed, Google Scholar, or BioOne, and identify microbiomes that you never knew existed. Discuss your findings with fellow students. 2. This chapter described how the microbiomes of African apes and humans have changed since their evolutionary divergence. Pick your own example of a small group of closely related species and hypothesize how the microbiomes of these species may have changed since they diverged from each other. Explain your reasoning.

CHAPTER OUTLINE 31.1 31.2 31.3 31.4 31.5

Ancestry and Diversity of Modern Plants How Land Plants Have Changed the Earth Evolution of Reproductive Features in Land Plants Evolutionary Importance of the Plant Embryo The Origin and Evolutionary Importance of Leaves and Seeds 31.6 A Summary of Plant Features Summary of Key Concepts Assess & Discuss

Plants and the Conquest of Land

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hen thinking about plants, people envision lush green lawns, shady street trees, garden flowers, or leafy fields of valuable crops. On a broader scale, they might imagine lush rain forests (like that shown in the chapter opening photo), vast grassy plains, or tough desert vegetation. Shopping in the produce section of the local grocery store may remind us that plant photosynthesis is the basic source of our food. Just breathing crisp fresh air might bring to mind the role of plants as oxygen producers—the ultimate air fresheners. Do you start your day with a “wake-up” cup of coffee, tea, or hot chocolate? Then you may appreciate the plants that produce these and many other materials we use in daily life: medicines, cotton, linen, wood, bamboo, cork, and paper. In addition to their importance to humans and modern ecosystems, plants have played dramatic roles in the Earth’s past. Throughout their evolutionary history, they have influenced Earth’s atmospheric chemistry, climate, and soils. Plants have also affected the evolution of many other groups of organisms, including humans. In this chapter, we will survey the diversity of modern plant phyla and their distinctive features. This chapter also explains how early plants adapted to land and how plants have continued to adapt to changing terrestrial environments. During this process, we will gain insight into descent with modification and the core concept that all life is related by an evolutionary history.

31.1         A ncestry and Diversity of Modern Plants Learning Outcomes: 1. List key derived features that land plants share with their closest algal relatives. 2. Name several characteristics unique to land plants. 3. Compare and contrast the features of vascular and nonvascular plants. 4. CoreSKILL » Explain how cuticles, stomata, and internal conduction systems work together in vascular plants to maintain stable water content.

A temperate rain forest containing diverse plant phyla in Olympic National Park in Washington state. ©Craig Tuttle/Corbis/ Getty Images

Several hundred thousand modern species are formally classified into the kingdom Plantae, referred to informally as the plants or land plants (Figure 31.1). Plants are multicellular eukaryotic organisms that primarily live on land and are composed of cells that are surrounded by a cell wall that contains cellulose. Plant cells also contain plastids, such as chloroplasts. Most species of plants carry out photosynthesis, which is described in Chapter 8. Molecular and other evidence indicates that the plant kingdom evolved from green algal ancestors whose modern representatives primarily occupy freshwater habitats. Modern plants and their closest green algal relatives are together known as streptophytes. Figure 31.1 shows the evolutionary relationships among green algae and modern land plants. Compared to the algal counterparts, plants display traits that foster survival in terrestrial conditions, which are drier, sunnier, hotter, colder, and less physically supportive than aquatic habitats.  In this section, we will examine the modern algae that are most closely related to plants and survey the diverse phyla of living land plants. These comparisons reveal how plants gradually acquired diverse structural, biochemical, and reproductive adaptations that fostered survival on land.

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Streptophytes Land plants (kingdom Plantae) (embryophytes) Vascular plants (tracheophytes) Seed plants (spermatophytes)

Ordovician

Millions of years ago (mya)

PALEOZOIC

Silurian

Angiosperms

Conifers and gnetales

Ginkgo

Cycads Euphylls (megaphylls)

290

Devonian

Gymnosperms

Flowers, fruits, endosperm in seeds

Permian Carboniferous

Pteridophytes

Seedless vascular plants

Lycophytes

Hornworts

Liverworts

Complex streptophyte algae

248

Simple streptophyte algae

MESOZOIC

65

Chlorophyte green algae

CENOZOIC

0

Mosses

Bryophytes (nonvascular plants)

Green algae

Ovules, pollen, seeds, euphylls, wood

354 417

Lignin in walls of water-conducting cells; cutin common on epidermis; stomata common on plant surfaces; dominant sporophyte generation; true roots, stems, leaves

443

490 Cambrian 543

PROTEROZOIC

Sporic life cycle, embryo, sporopollenin-walled spores, tissue-producing apical meristem, gametangia, sporangia Plasmodesmata, plant-specific features of cell division, sexual reproduction

Cellulose-rich cell wall

2500

Chlorophyll a and b, starch produced in plastids Common protist ancestor

KEY Critical innovations

Figure 31.1  Evolutionary relationships among green algae and modern plant phyla.  The blue bars in the arrow on the left side show maximal evolutionary divergence times indicated by molecular clock and some fossil evidence, suggesting when clades may first have arisen. This is a simplified diagram; fewer branches of streptophyte algae are shown here than actually exist. (inset 1): ©Roland Birke/Phototake; (inset 2): ©the CAUP image database, http://botany.natur.cuni.cz/algo/database; (inset 3–6): ©Lee W. Wilcox; (inset 7): ©Ed Reschke/Getty Images; (inset 8): ©Patrick Johns/Corbis/VCG/Getty Images; (inset 9): ©Philippe Psaila/Science Source; (inset 10): ©Fancy Photography/Veer/Getty Images; (inset 11): ©imageBROKER/Alamy Stock Photo; (inset 12): ©Gallo Images/Corbis/Getty Images

Core Concept: Evolution  Land plants evolved from green algae and gradually acquired diverse structural, biochemical, and reproductive adaptations, allowing them to better survive in terrestrial habitats.



PLANTS AND THE CONQUEST OF LAND 643

Modern Green Algae Are Closely Related to the Ancestors of Land Plants Molecular, biochemical, and structural data indicate that the kingdom Plantae originated from a photosynthetic protist ancestor that, if present today, would be classified among the streptophyte algae (Figure 31.2 ). The streptophyte algae are related to other green algae, but have more features in common with land plants. The more complex, later-diverging streptophyte algae display several critical innovations—derived features shared with land plants that fostered plant success on land. Examples of these shared features are a distinctive type of cytokinesis,

1 cm

30 μm

(a) Complex streptophyte algae: Chara zeylanica (left) and Coleochaete pulvinata (right)

intercellular connections known as plasmodesmata (see Chapter 10), and sexual reproduction (see Figure 31.1). For this reason, complex streptophyte algae are good sources of information about the ancestors of land plants.

Distinctive Features of the Land Plants Land plants can be distinguished from their close algae relatives by several features that represent early adaptations to the land habitat. For example, the bodies of all land plants are primarily composed of three-dimensional tissues, defined as close associations of cells of the same type. Tissues provide land plants with an increased ability to avoid water loss at their surfaces. Water loss is decreased in land plants because bodies composed of tissues have lower surface area/volume ratios than do branched filaments or simpler algal bodies. Land plant tissues arise from one or more actively dividing cells that occur at growing tips. Such localized regions of cell division are known as apical meristems. The tissue-producing apical meristems of land plants produce relatively thick, robust bodies able to withstand drought and mechanical stress and produce tissues and organs with specialized functions. The land plants also have distinctive reproductive features.  ∙ Land plants feature a life cycle involving alternation of generations. Alternation of generations means that two types of multicellular bodies alternate in time (refer back to Figure 16.14c). The diploid (2n) sporophyte generation produces spores by meiosis, and the haploid (n) gametophyte generation produces gametes by mitosis. By contrast, streptophyte algae feature a haploid-dominant life cycle (refer back to Figure 16.14b).  ∙ During land plant sexual reproduction, a diploid zygote divides by mitosis to form a multicellular sporophyte embryo. A key feature is that the sporophyte embryo is nourished by maternal tissues. Although maternal cells of streptophyte algae may nourish zygotes, the algal zygotes do not develop into multicellular embryos. ∙ A mature land plant sporophyte undergoes meiosis to produce tough-walled non-flagellate reproductive cells known as spores that survive dispersal through dry air. Streptophyte algae differ in that spores produced by meiosis are adapted for dispersal in water; they possess flagella and lack protective walls. 

2 μm

10 μm

(b) Simple streptophyte algae: Chlorokybus atmophyticus (left) and Mesostigma viridae (right)

Figure 31.2  Streptophyte green algal relatives of the land

plants.  Streptophyte green algae occur (a) as more complex branched filaments or (b) as small colonies (left side) or single cells (right side). Streptophyte algae share cellular, biochemical, and molecular features with land plants. a (left, right): ©Lee W. Wilcox; b (left): ©the CAUP image database, http://botany.natur.cuni.cz/algo/database; b (right): ©Lee W. Wilcox

We will take a closer look at the reproductive features of land plants in Sections 31.3–31.5, and also in Chapter 32. How can we know about past events such as the origin and diversification of land plants? Some information comes from comparing molecular and other features of modern plants. For example, the genome sequence of the moss Physcomitrella patens, first reported in 2007, reveals the presence of genes that aid heat and drought tolerance, which are especially useful in the terrestrial habitat. Plant fossils, the preserved remains of plants that lived in earlier times, provide further information (Figure 31.3). The distinctive plant organic materials sporopollenin, cutin, and lignin (discussed later in this chapter) do not readily decay and thereby foster plant

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flowering plants dominate the modern world. A survey of these modern plant phyla reveals how land plants became increasingly better adapted to life on land.

Liverworts, Mosses, and Hornworts Are the Simplest Land Plants

Figure 31.3  Fossil moss leaf fragment  Fluorescence microscopy indicates the presence of decay-resistant lignin-like cell-wall materials that have fostered structural preservation over hundreds of millions of years of burial. The distinctive pattern of these cell-wall remains suggests a relationship to modern peat mosses, which are common worldwide and have important ecological roles, as discussed in Section 31.2. ©Linda Graham

Liverworts, mosses, and hornworts are Earth’s simplest land plants (Figures 31.4, 31.5, and 31.6), and each group is monophyletic. There are about 6,500 species of modern liverworts, 12,000 or more species of mosses, and about 100 species of hornworts. Collectively, liverworts, mosses, and hornworts are known informally as the bryophytes (from the Greek bryon, meaning moss, and phyton, meaning plant). This collective term reflects common structural, reproductive, and ecological features of liverworts, mosses, and hornworts. For example, the bryophytes are relatively small in stature and are most common and diverse in moist habitats because they lack traits allowing them to grow tall or reproduce in dry places. As described in Section 31.3, bryophytes display reproductive features that evolved early in the history of land plants, including a life cycle involving alternation of generations, multicellular embryos, and tough-walled spores.

fossilization. The study of fossils and the molecular, structural, and functional features of modern plants has revealed an amazing story—how plants gradually acquired adaptations, allowing them to conquer the land.

Modern Land Plants Can Be Classified into Nine Phyla Fossils reveal that a number of plant phyla that once lived are now extinct. In this textbook, nine phyla of living land plants are described (also see Figure 31.1): 

(a) The common liverwort, Marchantia polymorpha

∙ liverworts, formally known as Hepatophyta

Asexual gemmae

∙ mosses, formally Bryophyta ∙ hornworts, Anthocerophyta ∙ lycophytes, Lycopodiophyta ∙ pteridophytes, Pteridophyta ∙ cycads, Cycadophyta ∙ ginkgos, Ginkgophyta ∙ conifers, Coniferophyta ∙ flowering plants, also known as angiosperms, Anthophyta Although the order in which early land plant phyla diverged is not completely clear, fossil and molecular evidence indicates that relatively small and simple bryophytes—represented by modern liverworts, mosses, and hornworts—arose before the first vascular plants (see Figure 31.1). Vascular plants are distinguished by internal water and nutrient-conducting (vascular) tissues that also provide structural support, allowing these plants to become larger and more complex than are bryophytes. Among the modern vascular plants, lycophytes diverged earliest, pteridophytes arose next, and then seed plants. The

Upper surface of liverwort (b) Close-up of liverwort structures

(c) A species of leafy liverwort

Figure 31.4  Liverworts.  (a) The common liverwort, Marchantia

polymorpha, has a flat green body that produces raised, umbrellashaped structures bearing sexually produced sporophytes on the undersides. Mature sporophytes generate spores, then release them into the air. (b) A close-up of M. polymorpha showing surface cups that contain multicellular, Frisbee-shaped asexual structures known as gemmae, which are dispersed by wind and grow into new liverworts. (c) A species of liverwort that has leaflike structures and so is known as a leafy liverwort. a: ©Dr. Jeremy Burgess/SPL/Science Source;

b–c: ©Lee W. Wilcox



PLANTS AND THE CONQUEST OF LAND 645

Lycophytes and Pteridophytes Are Vascular Plants That Do Not Produce Seeds Teeth

Sporangium

Sporophyte

Gametophyte

Figure 31.5  Mosses.  The common moss genus Mnium has a leafy green gametophyte (multicellular body that generates gametes) and an unbranched, dependent sporophyte that bears a spore-producing sporangium at its tip. Inset: This SEM shows the tip of a moss sporangium. The sporangia often have teeth separated by spaces, so spores are sprinkled into the wind and dispersed over time, rather than being released all at once. (top): ©Eye of Science/Science Source;

(bottom): ©Lee W. Wilcox

As mentioned, vascular plants produce internal water and nutrientconducting (vascular) tissues that also provide structural support. Fossils and molecular comparisons indicate that the first vascular plants appeared later than the earliest bryophytes and that several early vascular plant lineages existed in the past but have become extinct. Molecular data indicate that the lycophytes are the oldest phylum of living vascular plants and that pteridophytes are the next oldest (see Figure 31.1). Hundreds of millions of years ago, lycophytes were more diverse than at present and included tall trees that contributed importantly to coal deposits. Now, only about 1,000 relatively small species exist (Figure 31.7). Pteridophytes have diversified more recently, and there are about 12,000 species of modern pteridophytes, including horsetails, whisk ferns, and other ferns (Figure 31.8). Because the lycophytes and pteridophytes diverged prior to the origin of seeds, they are informally known as seedless vascular plants. Together, lycophytes, pteridophytes, and seed-producing plants are known as the tracheophytes. The latter term takes its name from tracheids, a type of specialized cell that conducts water and minerals and provides structural support. Tracheids and other cells involved in the conduction of materials within plants form vascular tissues that are described more fully in Chapters 36 and 39. Vascular tissues occur in stems, roots, and leaves, which are the organs of the vascular plant body. Stems, Roots, and Leaves  Stems  of vascular plants are branching structures that contain vascular tissue and produce leaves and sporangia. Stems contain the specialized conducting tissues known as phloem and xylem, the latter of which contains tracheids. As described in Chapters 36 and 39, such conducting tissues enable vascular plants to move organic compounds, water, and minerals throughout the plant body. The xylem also provides structural support,

Concept Check:   Why might it be advantageous for a moss sporangium to release spores gradually?  Sporangia Spore dispersal tip

Sporophyte

Gametophyte

Figure 31.6  Hornworts.  Gametophytes of hornworts grow close

to the ground, whereas sporophytes generally grow up into the air. Mature hornwort sporophytes open at the top, dispersing spores into the wind. ©Lee W. Wilcox

Stem

Small leaves

Figure 31.7  An example of a lycophyte (Lycopodium obscurum).  The sporophyte stems bear many tiny leaves. The sporeproducing sporangia generally occur in club-shaped clusters. For this reason, lycophytes are often referred to as club mosses or spike mosses, though they are not true mosses. The gametophytes of lycophytes are small structures that often occur underground. ©Lee W. Wilcox

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Branches Sporangia

Stem

Figure 31.8  Pteridophyte diversity. 

(a) The leafless, rootless green stems of the whisk fern (Psilotum nudum) branch by forking and bear many clusters of yellow sporangia that disperse spores via wind. The gametophyte of this plant is a tiny pale (a) A whisk fern structure that lives underground in a symbiotic partnership with fungi. (b) The Sporangia on giant horsetail (Equisetum telmateia) a modified leaf displays branches in whorls around the green stems. The leaves of horsetail plants are tiny, light brown structures that encircle branches at intervals. Horsetail plants produce spores in cone-shaped structures, and the wind-dispersed spores grow into small green gametophytes. (c) The earlydiverging fern Botrychium lunaria, showing a green photosynthetic leaf with leaflets and a modified leaf that bears many round sporangia. (d) A later-diverging fern showing leaves having leaflets, and young leaves that are in the process of unrolling from the bases to the tips. The stem of this fern grows parallel to the ground and thus is not shown. Most ferns produce spores in sporangia on the undersides of leaves.

Forked stem

(b) The giant horsetail

Leaf with many leaflets Young leaf unrolling

Photosynthetic leaf with leaflets

a: ©Lee W. Wilcox; b: ©José Julián Rico Cerdá/Alamy Stock Photo; c: ©Patrick Johns/Corbis/VCG/Getty Images; d: ©Lee W. Wilcox

(c) An early-diverging fern

allowing vascular plants to grow taller than nonvascular plants. This support function relies on the presence of a compression- and decayresistant waterproof material known as lignin, which occurs in the cell walls of tracheids and some other types of plant cells. Most vascular plants also produce roots, which are organs specialized for uptake of water and minerals from the soil, and leaves, flattened plant organs that emerge from stems and generally have a photosynthetic function. Lycophyte roots and leaves differ from those of pteridophytes and seed plants. For example, lycophyte roots fork at their tips, whereas roots of pteridophytes branch from the inside like the roots of seed plants (look ahead to Figure 36.24). Lycophyte leaves are relatively small and possess only one unbranched vein, whereas pteridophyte

(d) A later-diverging fern

leaves are larger and have branched veins, as do those of seed plants (compare Figures 31.7 and 31.8d).  Adaptations That Foster Stable Internal Water Content  The stems, roots, and leaves of lycophytes and pteridophytes illustrate adaptations acquired by early vascular plants that help to maintain stable internal water content, also known as moisture homeostasis. In relatively dry habitats, lycophytes, pteridophytes, and other vascular plants are able to grow to larger sizes and remain metabolically active for longer periods than bryophytes. In addition to vascular tissue, two other adaptations that aid in moisture retention are a waxy cuticle and stomata. 



PLANTS AND THE CONQUEST OF LAND 647

∙ A protective waxy cuticle is present on most surfaces of vascular plant sporophytes (Figure 31.9a). The plant cuticle contains a polyester polymer known as cutin, which helps to prevent attack by pathogens, as well as wax, which helps to prevent desiccation (drying out). ∙ The surface tissue of vascular plant stems and leaves contains many stomata (singular, stoma or stomate)—specialized surface cells associated with pores that are able to open and close (Figure 31.9b). Stomata first arose in bryophytes, whose mature

Tracheids

Stomatal pore

Cuticle 120 μm (a) Stem showing tracheophyte adaptations

sporophytes must dry in order to discharge spores; stomatal pores may aid this drying process. By contrast, stomata occurring on the leaf and stem surfaces of vascular plants take in the carbon dioxide needed for photosynthesis and release oxygen to the air, while conserving plant water content. When the environment is moist, the pores open, allowing gas exchange to occur. When the environment is very dry, the pores close, thereby reducing water loss.

Gymnosperms and Angiosperms Are the Modern Seed Plants Collectively, the modern and extinct phyla of seed-producing plants are known as spermatophytes (the prefix sperm-, from the Greek, means seed) (see Figure 31.1). We will examine them more fully in Chapter 32. The modern seed plant phyla commonly known as cycads, ginkgos, conifers, and gnetophytes are collectively referred to as gymnosperms (Figure 31.10 shows an example). Gymnosperms reproduce using both spores and seeds, as do the flowering plants, the angiosperms (Figure 31.11). For this reason, gymnosperms and angiosperms are known informally as the seed plants. Seeds are complex structures having specialized tissues that protectively enclose embryos and contain stores of carbohydrate, lipid, and protein. Embryos use such food stores to grow and develop into seedlings. The ability to produce seeds helps to free plants from reproductive limitations experienced by the seedless plants, explaining why seed plants are dominant today. Though gymnosperms produce seeds, they lack several features unique to the flowering plants. The term gymnosperm comes from the Greek, meaning naked seeds, reflecting the observation that gymnosperm seeds are not enclosed within fruits. Despite their lack of flowers, fruits, and seed endosperm, the modern gymnosperms are diverse and abundant in many places (see Chapter 32).

Stomata

Location of pore when open 50 μm (b) Close-up of stomata

Figure 31.9  Tracheophyte adaptations for transporting and

conserving water.  (a) A cross section through a stem of the leafless pteridophyte Psilotum nudum. When viewed with fluorescence microscopy and illuminated with violet light, an internal core of xylem tracheids glows yellow, as does the surface cuticle. Stomatal pores can be seen at indentations of the cuticle. (b) SEM view of tracheophyte surface pores associated with specialized cells— together known as stomata—allow for gas exchange between plant and atmosphere. a: ©Linda Graham; b: ©Martha Cook Core Concept: Structure and Function  The structures illustrated in this figure help to explain how vascular land plants maintain moisture homeostasis.

Figure 31.10  An example of a gymnosperm, the pine (Pinus). 

Gymnosperms produce and disperse seeds from cones, but do not produce flowers or fruits. ©Stephen P. Parker/Science Source

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data indicate that the transition from bryophyte to lycophyte was less genetically complex than was the transition from lycophyte to angiosperm. Another interesting finding involves terpenes, which are secondary metabolites that plants produce as chemical defenses against pathogens and herbivores. Both seedless and seed plants carry genes encoding proteins that are required to synthesize terpenes. However, genomic analysis revealed that seedless plants rely on genes also present in microbes, but seed plants use different terpene-synthesis genes. The diversification of new types of terpene-synthesis genes is an example of an increase in genetic complexity that accompanied the rise of seed plants.

Figure 31.11  An example of an angiosperm, the bleeding heart plant (genus Dicentra).  The pink structures are flowers, which are a distinguishing feature of angiosperms. Flowers often develop into seed-containing fruits, another unique feature of angiosperm plants. ©imageBROKER/Alamy Stock Photo

The angiosperms are seed plants distinguished by the presence of flowers, fruits, and a specialized seed tissue known as endosperm. A flower is a short stem bearing reproductive organs that are specialized in ways that enhance seed production (see Figure 31.11). Fruits are structures that develop from flowers, enclose seeds, and foster seed dispersal in the environment. The term angiosperm comes from the Greek, meaning enclosed seeds, reflecting the observation that the flowering plants produce seeds within fruits. Endosperm is a nutritive seed tissue that increases the efficiency with which food is stored and used in the seeds of flowering plants (explained further in Section 31.5).

Core Concepts: Evolution, Information Comparison of Plant Genomes Reveals Genetic Changes That Occurred During Plant Evolution The first complete genome sequence for a seedless vascular plant was reported for the lycophyte Selaginella moellendorffii in 2011. This advance allowed plant evolutionary biologists to compare the new sequence with previously sequenced plant genomes, with the goal of identifying genes associated with major evolutionary transitions in plants. Such genome comparisons revealed that 6,820 gene families, representing a basic set of embryophyte genes, are present in all land plants. The majority of gene families that are involved in flowering plant development were also observed in the lycophyte Selaginella and the bryophyte Physcomitrella, a moss. A comparison of the genomes of Selaginella and Physcomitrella indicated that more than 500 genes were gained and nearly 90 genes were lost during the transition from nonvascular plants (bryophytes) to vascular plants (lycophytes). By contrast, 1,350 more genes were gained in the evolution of traits specific to angiosperms. These

31.2           How Land Plants Have Changed the Earth Learning Outcome: 1. Describe examples of how plants have altered the Earth's physical environment and also affected other life on Earth.

A billion years ago, Earth’s terrestrial surface was comparatively devoid of life. Green or brown crusts of cyanobacteria most likely grew in moist places, but there would have been very little soil, no plants, and no animal life. The origin of the first land plants was key to development of the first substantial soils, the rise to modern levels of atmospheric oxygen, the evolution of modern plant communities, and the colonization of land by animals. In this section, we will explore how plants have transformed Earth’s physical environment, especially the atmosphere, and how the rise of seed plants has greatly impacted the evolution of animals.

Plants Have Transformed the Earth’s Physical Environment As discussed in Chapter 8, the process of photosynthesis uses carbon dioxide (CO2) from the atmosphere to produce carbon-containing organic molecules. A by-product of photosynthesis is oxygen (O2). Throughout their evolutionary history, plants have influenced Earth’s climate by reducing the concentration of atmospheric CO2  and increasing the concentration of O2, and they continue to do so. Ecologists are concerned that the negative impact of humans on plant communities may also affect CO2 and O2 levels.  Ecological Effects of Ancient and Modern Bryophytes  Several types of decay-resistant materials evolved in early seedless plants, such as sporopollenin, cutin, and lignin (discussed in Section 31.1). When the plants died, some of these organic molecules were not completely degraded, but instead were buried in sediments that eventually transformed into rock. Such fossil carbon can accumulate and remain buried for very long time periods with the consequence of lowering the level of atmospheric CO2. As discussed in Chapter 59, CO2 is a greenhouse gas that causes global temperatures to rise. Therefore, the accumulation of fossil carbon is expected to lower global temperatures.



PLANTS AND THE CONQUEST OF LAND 649

Modern bryophytes also play important roles by storing CO2 as decay-resistant organic compounds, suggesting that ancient relatives likewise played this role (see Figure 31.3). Plants of the modern peat moss genus Sphagnum, for example, contain so much decay-resistant body mass that in many places, dead moss accumulated over long time periods has formed deep peat deposits. By storing very large amounts of organic carbon for a long time, diverse species of Sphagnum moss help to keep Earth’s climate steady. Under cooler than normal conditions, the mosses grow more slowly and thus absorb less CO2, allowing atmospheric CO2 to rise a bit, warming the climate a little. As the climate warms, the mosses grow faster and take up more CO2, storing it in peat deposits. Such a reduction in atmospheric CO2 returns the climate to slightly cooler conditions. Peat mosses also harbor bacteria that consume methane, another powerful greenhouse gas. In these ways, ancient and modern mosses have helped to moderate the world’s climate. Experts are concerned that large regions currently dominated by these helpful mosses may be harmed by land use changes, peat harvesting for commercial use, and climate change. Atmospheric O2 has been an important factor affecting the evolution of species on Earth. Eukaryotic species tend to have high demands for O2 because they use it to obtain energy via cellular respiration. Photosynthetic bacteria were the earliest organisms to produce O2, and later in evolution, algae also contributed to atmospheric O2. Even so, recent modeling studies have provided strong evidence that by 420–400 mya (early Devonian period) the activities of early seedless plants had raised oxygen levels in Earth's atmosphere to modern levels. These higher levels may have been key to the evolution of large, mobile, animals, which have a particularly high demand for oxygen.  Ecological Effects of Ancient Vascular Plants  Fossils tell us that extensive forests dominated by tree-sized lycophytes, pteridophytes,

and early seed plants occurred in widespread swampy regions during the warm, moist Carboniferous period (354–290 mya) (Figure 31.12). As dead plants fell into the water, low oxygen levels there inhibited microbes that would have caused the plant matter to decay. The dead plants were then buried in sediments that later formed coal. Much of today’s coal is derived from the abundant remains of ancient plants, explaining why the Carboniferous period is commonly known as the Coal Age. During that period, plants converted huge amounts of atmospheric CO2 into decay-resistant organic materials. Long-term burial of these materials, compressed into coal, together with chemical interactions between soil and the roots of vascular plants, dramatically changed Earth’s atmosphere and climate. The removal of large amounts of the greenhouse gas CO2 from the atmosphere by plants had a cooling effect on the climate, which also became drier because cold air holds less moisture than warm air. Mathematical models of ancient atmospheric chemistry, supported by measurements of natural carbon isotopes, led American paleoclimatologist Robert A. Berner to propose that the Carboniferous proliferation of vascular plants was correlated with a dramatic decrease in atmospheric CO2, which reached the lowest known levels about 290 mya (Figure 31.13). During this period of very low CO2, atmospheric O2 levels rose to the highest known levels, because less O2 was being used to convert organic carbon into CO2. High atmospheric O2 content may explain the occurrence during the Carboniferous period of giant dragonflies and other huge insects.  The great decline in CO2 level ultimately caused cool, dry conditions to prevail in the late Carboniferous and early Permian periods. As a result of this relatively abrupt global climate change, many of the tall seedless lycophytes and pteridophytes that had dominated earlier Carboniferous forests became extinct, as did the giant dragonflies.

Giant dragonfly

Giant horsetail (pteridophyte)

Giant lycophyte

Figure 31.12  Reconstruction of a Carboniferous period (Coal Age) forest.  This ancient forest was dominated by tree-sized lycophytes and pteridophytes, which later contributed to the formation of large coal deposits. ©Lee W. Wilcox

Concept Check:   Why did giant dragonflies exist during the Carboniferous period, but not now? 

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CHAPTER 31 Moss

Lycophyte

Fossil remains suggest that nonvascular land plants may have contributed to the early stages of CO2 decline.

The proliferation of vascular plants correlates with the most precipitous decrease in CO2.

mammals and flowering plants existed in the Mesozoic. Gymnosperms and early angiosperms were probably sources of food for early mammals as well as for herbivorous dinosaurs. For example, fossils of an aquatic angiosperm named Cobbania corrugata have been found with bones of the dinosaur Ornithomimus in Dinosaur Park, Alberta, Canada. This dinosaur may have fed on the plant when alive (Figure 31.14). One fateful day about 65 mya, disaster struck from the sky, causing a dramatic change in the types of plants and animals that dominated terrestrial ecosystems. That day, at least one large meteorite crashed into the Earth near the present-day Yucatán Peninsula in Mexico. This collision is known as the CretaceousPaleogene event (also sometimes referred to as the K/T event). The impact, together with substantial volcanic activity that also occurred at this time, is thought to have produced huge amounts of ash, smoke, and haze that dimmed the Sun’s light long enough to kill many of the world’s plants. Many types of plants, including Cobbania, became extinct, though others survived and their descendants persist to the present time. With a severely reduced food supply, most dinosaurs were also doomed, the exceptions being their descendants, the birds. The demise of the dinosaurs left room for birds and mammals to adapt to many kinds of terrestrial habitats formerly inhabited by dinosaurs. After the Cretaceous-Paleogene event, ferns dominated long enough to leave huge numbers of fossil spores, and then surviving groups of flowering plants began to diversify into the space opened up by the extinction of earlier plants. The rise of angiosperms fostered the diversification of beetles (see Chapter 34) and other insects that associate with

Conifer

The rise and diversification of seed plants occurred after the lowest known CO2 level.

Relative atmospheric CO2 level

25

20

15

10

5

0 600

500

400

300

200

100

0

modern plants.

Time (mya) Mathematical model Statistical uncertainty Estimates of atmospheric carbon dioxide obtained by measuring carbon isotopes in carbonate rocks of varying ages Carboniferous period (354−290 mya)

Figure 31.13  Changes in Earth’s atmospheric carbon dioxide

levels over geological time.  Geological evidence indicates that carbon dioxide levels in Earth’s atmosphere were once higher than they are now, but that the rise of land plants caused atmospheric CO2 to reach the lowest known level about 300 mya. (left): ©Linda Graham; (middle): ©Darlyne A. Murawski/Getty Images; (right): ©David R. Frazier/The Image Works

Cooler, drier conditions favored extensive diversification of the first seed plants, the gymnosperms. Compared with seedless plants, seed plants were better at reproducing in cooler, drier habitats (as we will see in Section 31.5). As a result, seed plants came to dominate Earth’s terrestrial communities, as they still do.

Plant Evolution Has Greatly Impacted the Survival and Evolution of Animals Diverse phyla of gymnosperms dominated Earth’s vegetation through the Mesozoic era (248–65 mya), which is sometimes called the Age of Dinosaurs. In addition, fossils provide evidence that early

Figure 31.14  Early angiosperms as sources of food for large

herbivorous dinosaurs of the Mesozoic era.  In this artist’s habitat reconstruction from fossils, the extinct angiosperm Cobbania corrugata is shown growing in wetlands that were also inhabited by large dinosaurs such as Ornithomimus, whose head is illustrated here. ©Marjorie C. Leggitt



PLANTS AND THE CONQUEST OF LAND 651

Multicellular haploid (n) gametophyte

Learning Outcomes:

A Comparison of Algal and Bryophyte Reproduction Highlights an Early Plant Adaptation to Life on Land: Alternation of Generations Because bryophytes diverged early in the evolutionary history of land plants (see Figure 31.1), they serve as models of the earliest terrestrial plants. A comparison of the life cycle of aquatic streptophyte algae with that of bryophytes reveals the adaptive value on land of bryophyte reproductive features. Streptophyte algae display a haploid-dominant life cycle in which the only diploid cell is the zygote, whose meiotic division produces relatively few spores (Figure 31.15a). By contrast, land plant zygotes do not undergo meiosis. Instead, they undergo mitosis to form a multicellular sporophyte in which many cells can undergo meiosis and thereby produce a large number of spores (Figure 31.15b). Producing more spores not only aids dispersal but also increases the genetic diversity of progeny. This life cycle difference allows bryophytes and other land plants to increase the number of spores generated per sexual cycle, an important advantage in terrestrial habitats.  Like related algae (see Figure 31.15a) and modern seedless plants, early land plants likely produced flagellate sperm that needed liquid water to swim to eggs to accomplish fertilization (see Figure 31.15b). On dry land, the number of successful fertilizations and resulting zygotes can be limited by lack of sufficient water. By producing multicellular sporophytes to greatly increase the number of spores resulting from each fertilization, land plants have overcome this problem. Genomic comparisons indicate that transcription factors encoded by KNOX genes were key to the origin of plant sporophytes. These transcription factors suppress gametophyte development, thereby allowing multicellular sporophytes to develop from zygotes.

Bryophyte Reproduction Illustrates Other Terrestrial Adaptations In addition to alternation of generations, other key features aided in terrestrial reproduction (Figure 31.16). As shown in step 3, the gametophytes of bryophytes and many other land plants produce

Fertilization

Single-celled diploid (2n) zygote

Egg

1. Compare and contrast a haploid-dominant life cycle and alternation of generations. 2. List critical innovations in bryophytes that result in reproductive features different from those of streptophyte algae. 3. Discuss additional reproductive changes that occurred during the evolution of vascular plants.

In Section 31.1, we considered the diversity of land plants and some critical innovations associated with life in a terrestrial environment. In this section, we will take a closer look at the evolution of reproductive adaptations. We will compare and contrast such adaptions among green algae, bryophytes, and seedless vascular plants. In Chapter 32, we will examine some additional reproductive adaptions that have arisen in the seed plants—gymnosperms and angiosperms. 

Sperm

Spores

Meiosis

Mitosis Disadvantage: only a few haploid spores produced per zygote (a) Haploid-dominant life cycle of streptophyte algae

KEY Haploid Diploid

Sperm Multicellular haploid (n) gametophyte

Evolutionary change

31.3           Evolution of Reproductive Features in Land Plants

Delay in meiosis: repeated mitotic divisions

Fertilization

Single-celled diploid (2n) zygote

Mitosis

Egg Spores Mitosis

Advantage: many haploid spores produced per zygote

Meiosis

New: multicellular diploid (2n) sporophyte

(b) Alternation of generation of early plants

Figure 31.15  Evolutionary transition from  (a) the life cycle of

primarily aquatic streptophyte algae to (b) the derived life cycle of primarily terrestrial bryophytes.

gametes in structures known as gametangia (from the Greek, meaning gamete containers). Certain cells of gametangia develop into gametes, and other cells form an outer protective jacket of tissue. This jacket protects the delicate gametes from drying out and from microbial attack while they develop. Flask-shaped gametangia that each enclose a single egg cell are known as archegonia (singular, archegonium). Spherical or elongate gametangia that each produce many sperm are known as antheridia (singular, antheridium). When bryophyte sperm are mature and moist conditions exist, antheridia open and release sperm into films of water. Under the influence of sex-attractant molecules secreted from archegonia, the sperm swim toward the eggs, twisting their way

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CHAPTER 31

6

Embryo develops into a mature sporophyte, which remains attached to the female gametophyte. Embryo (2n)

5

Mitosis

Delicate diploid zygote is protected and nourished by female gametophyte tissues while it grows into an embryo.

Archegonium (n)

Fertilization

4

Nutritional tissue (n)

Zygote (2n)

If water is present, flagellate sperm are released and swim toward the egg. Fertilization occurs.

2n p

hase

n ph

ase

Egg (n)

e cy

of lif

Meiosis

cle

e cy

cle

Protective jacket tissue

1 Spores (n) Sporangium (2n)

Female gametangium (n) (archegonium)

Protective jacket tissue

Meiosis within a sporophyte sporangium produces thousands of haploid spores. Sporangium pops open, releasing spores into the wind.

Female gametophyte 2

Male gametangium (n) (antheridium) Mitosis Gametophytes grow and mature, producing protective gametangia at their tips.

Mature haploid (n) gametophyte

of lif

Many sperm (n)

3

Diploid (2n) sporophyte

Female gametophyte (n)

Haploid spores grow into young gametophytes. Bryophytes may have separate male and female gametophytes.

Young hyte gametophyte KEY

Male M gametophyte g (n)

Male gametophyte

Haploid (gametophyte development) Diploid (sporophyte development) Male gametophyte cells (n) Female gametophyte cells (n) Sporophyte cells (2n)

Figure 31.16  The life cycle of the early-diverging moss genus Sphagnum.  The life cycle of this bryophyte illustrates reproductive adaptations that likely helped early plants reproduce on land. Among modern bryophytes, Sphagnum is the single most abundant and ecologically important genus. (top right inset): ©Larry West/Science Source; (bottom right inset, bottom left inset): ©Linda Graham

down the tubular neck of the archegonium. The sperm then fertilize egg cells to form diploid zygotes, which grow into embryos (see steps 4 and 5, Figure 31.16). A key reproductive advantage of the plant life cycle is that embryos remain enclosed by gametophyte tissues that provide protection and food. This critical innovation, known as matrotrophy (from the Latin, meaning mother, and the Greek, meaning food) gives zygotes a good start while they grow into embryos. Because all groups of land plants possess matrotrophic embryos, they are known as embryophytes (see Figure 31.1). Plant reproductive advantages also involve the formation of spores. To produce haploid spores, meiosis occurs in cells that are

within enclosures known as sporangia (from the Greek, meaning spore containers) (see step 1, Figure 31.16). The cells of such enclosures are surrounded by tough cell walls that protect developing spores from harmful UV radiation and microbial attack. Bryophyte sporangia open in specialized ways that foster dispersal of mature spores into the air, allowing spore transport by wind (see Figures 31.5–31.8). Another important adaptation involves the spores themselves. The cell walls of mature plant spores contain a tough material, known as sporopollenin, that helps to prevent cellular damage during transport in air. If spores reach habitats favorable for growth, their cell walls crack open, and new gametophytes develop by mitotic divisions. 



PLANTS AND THE CONQUEST OF LAND 653

The Evolution of Vascular Plants Coincided with an Increase in the Relative Size of the Mature Sporophyte and Its Independence As we have seen, bryophytes illustrate a number of valuable reproductive features that appeared early in plant evolution and were inherited by vascular plant descendants: alternation of generations, gametangia, embryos, matrotrophy, sporangia, and sporopollenin-enclosed spores. In bryophytes, the gametophyte is relatively large and the mature sporophyte is usually small and depends on the gametophyte for its nutrition. The evolution of vascular plants involved a shift in the relative sizes of gametophytes and sporophytes (Figure 31.17). The gametophyte generation has become smaller in later-diverging phyla, whereas the sporophyte generation has become larger and more complex. Although sporophyte embryos of vascular plants are dependent upon supportive gametophytes, these embryos eventually become independent, free-living organisms. Vascular-plant sporophytes can branch, continue to grow, and produce sporangia on lateral branches, often for many years (see  Figure 31.17b,c). These features allow vascular plants to produce more progeny than bryophytes, whose sporophytes remain small, never become independent of parental gametophytes, are unable to branch, and have short lifetimes (see Figure 31.17a). In vascular plants the diploid sporophyte generation is the dominant generation, meaning that it is larger, more complex, and longer-lived than the gametophyte. The evolutionary shift toward sporophyte dominance explains why vascular plants are more prevalent in most modern terrestrial habitats.  Life Cycle of Lycophytes and Pteridophytes  The seedless vascular plants, which include lycophytes and pteridophytes, exhibit a life cycle in which the sporophyte is the larger, more conspicuous

Bryophytes

organism whereas the gametophyte is smaller. Figure 31.18 describes the life cycle of a fern, which is a pteridophyte. The organism that we associate with the name fern is the sporophyte. Stem branching allows adult plants to produce many leaves, and roots supply stems with large amounts of soil water and minerals. Lycophytes and pteridophytes use such resources to produce large numbers of sporangia. You might have seen clusters of sporangia as dark brown dots or lines on the undersides of fern leaves. As seen in steps 2 and 3 of Figure 31.18, the sporangia produce many spores that are released and dispersed by the wind. When a spore lands in a favorable location, it will grow by mitotic divisions to form a gametophyte. Both lycophyte and pteridophyte gametophytes are small, delicate, and easily harmed by exposure to heat and drought. This explains why the gametophytes of lycophytes and pteridophytes are restricted to moist places, often existing underground, and why they have short lifetimes. The gametophyte of most ferns is thumbnail-sized. It doesn’t have roots, stems or leaves, but it does have rhizoids that anchor it to the soil.  The gametophyte produces eggs in female gametangia (archegonia) and sperm in male gametangia (antheridia). Lycophyte and pteridophyte sperm are flagellate, a feature inherited from algal and bryophyte ancestors. When released from antheridia into water films, sperm must swim to eggs in archegonia (Figure 31.18, step 6). For this reason, lycophyte and pteridophyte reproduction is inhibited by dry conditions, as is also the case for bryophytes. However, when fertilization occurs, lycophytes and pteridophytes can produce many spores, because the spore-producing sporophyte generation grows to a much larger size than do bryophyte sporophytes. After fertilization, lycophyte and pteridophyte embryos, like those of all land plants, are initially nourished by maternal gametophytes. As they mature, vascular plant sporophytes eventually become independent by producing leaves and roots able to harvest resources needed for photosynthesis (Figure 31.18, step 8). 

Ferns

Seed plants

Sporophyte (2n) Male gametophyte (n)

Sporophyte (2n)

Sporophyte (2n)

Female gametophyte (n)

Gametophyte (n)

Gametophyte (n)

Magnified (a)

(b)

Magnified (c)

Figure 31.17  Relative sizes of the sporophyte and gametophyte generations of bryophytes, ferns, and seed plants. Concept Check:   What is the advantage to ferns and seed plants of having larger sporophytes relative to those of bryophytes?

1

Sporophyte

The diploid sporophyte is the dominant generation in the life of ferns and other vascular plants.

1 2

Sporangia are multicellular structures that develop on the undersides of the mature fern sporophyte leaves. Sporangia occur in clusters known as sori (singular, sorus).

Sporangium

2

Meiosis

3

The embryo matures into a sporophyte. After developing a root and leaf, fern sporophytes become independent of their gametophyte parent, which eventually rots away.

8

Meiosis occurs in cells within sporangia to produce haploid spores, which are dispersed by the wind. 3

Spores

Spore (n) S

Sori

Protective sporopollenin wall

8

Mitosis

4 Young sporophyte (2n)

Gametophyte te

Gametophyte (n)

4

Young roots

Rhizoids

Mitosis Diploid zygote (2n)

KEY

Blue-stained gametophyte

Haploid Diploid Fertilization

7

Under favorable conditions, spores undergo mitosis to produce gametophytes. These are often thumbnail-sized and heart-shaped, anchored by cells known as rhizoids.

Sperm (n)

5

Female gametangium (archegonium)

7 Egg cell

The resulting diploid zygote is retained on the gametophyte, undergoes mitosis, and grows into a multicellular embryo that receives essential nutrients from the gametophyte.

6

Egg (n)

6

When water is present, the male gametangia release the flagellate sperm, which swim to the female gametangia and fertilize the eggs. 5

Mature gametophytes produce eggs in female gametangia and sperm in male gametangia.

Male gametangia (antheridia)

Figure 31.18  The life cycle of a typical fern.  The fern life cycle is often used to illustrate plant alternation of generations because both sporophyte and gametophyte are large enough for people to see with the unaided eye. (foreground inset): ©Carolina Biological Supply Company/Phototake; (inset 1): ©Ernst Kucklich/Getty

Images; (inset 2–3): ©Linda Graham; (inset 4–8): ©Lee W. Wilcox



PLANTS AND THE CONQUEST OF LAND 655

31.4          Evolutionary Importance of the Plant Embryo Learning Outcomes: 1. Describe how a plant embryo benefits from the maternal gametophyte. 2. CoreSKILL » Analyze the results of Browning and Gunning, and explain the role of placental transfer tissues in the movement of nutrients from mother plant to embryo.

The embryo was one of the first critical innovations acquired by land plants (see Figure 31.1). Recall that plant embryos are young sporophytes that develop from zygotes and are enclosed by maternal tissues that provide nutrients and protection. The presence of an embryo is critical to plant reproduction in terrestrial environments. Drought, heat, UV light, and microbial attack could kill delicate plant egg cells, zygotes, and embryos if these were not protected and nourished by enclosing maternal tissues. The first embryo-producing plants diversified into hundreds of thousands of modern species, as well as many species that have become extinct. A closer look at embryos reveals why their origin and evolution are so important.

tissues often occur in haploid gametophyte tissues that lie closest to embryos and in the diploid tissues of young embryos themselves. Such transfer tissues contain cells that are specialized in ways that promote the movement of solutes from gametophyte to embryo. For example, the cells of placental transport tissues display complex arrays of finger-like cell-wall ingrowths (Figure 31.19). Because the plant plasma membrane lines the plant cell wall, the ingrowths vastly increase the surface area of the plasma membrane. This increase allows for more abundant membrane transport proteins, which move solutes into and out of cells. With more transport proteins present, materials can move at a faster rate from one cell to another. (Similar finger-like structures in animal intestines and placenta likewise foster nutrient flow by increasing cellular surface area.) Dissolved sugars, amino acids, and minerals first move from maternal plant cells into the intercellular space between maternal tissues and the embryo. Then, transport proteins in the membranes of nearby embryo cells efficiently import the nutrients into the embryo. As described next in the Feature Investigation, the role of placental transfer tissue was revealed in experiments involving the use of radiolabeled carbon dioxide (CO2). Parental gametophyte cell

Plant Embryos Grow Protected Within the Maternal Plant Body A plant embryo has several characteristic features, some of which were previously described. First, plant embryos are multicellular and diploid. Plant embryos develop by repeated mitotic divisions from a single-celled zygote (see Figure 31.15b). In addition, plant eggs are fertilized while still enclosed by the maternal plant body, and embryos begin their development within the protective confines of maternal tissues (see Figure 31.16). Plant biologists say that plants retain their zygotes and embryos. Third, plant embryo development depends on organic and mineral materials supplied by the mother plant, in the process known as matrotrophy. Nutritive tissues composed of specialized placental transfer tissues aid in the transfer of nutrients from mother to embryo. A closer look at placental transfer tissues will reveal their valuable role. Placental transfer tissues function similarly to the placenta present in most mammals, which fosters nutrient movement from the mother’s bloodstream to the developing fetus. Plant placental transfer

Embryonic sporophyte cell

Cell-wall ingrowths

3 μm

Figure 31.19  Placental transfer tissue from a plant in the liverwort genus Monoclea.  Similar structures occur at the gametophyte-sporophyte junction in all other land plant phyla. Courtesy Prof. Roberto Ligrone. Fig. 6 in Ligrone et al., Protoplasma (1982), 154: 414–425

Core Skill: Process of Science

Feature Investigation  | Browning and Gunning Demonstrated That Placental Transfer Tissues Facilitate the Movement of Organic Molecules from Gametophytes to Sporophytes

In the 1970s, plant cell biologists Adrian Browning and Brian Gunning explored the function of placental transfer tissues. Using a simple moss as their experimental organism, they investigated the rate at which radiolabeled carbon moves through placental transfer tissues from green gametophytes into young sporophytes. Recall that embryos are very young,

few-celled sporophytes and that in mosses and other bryophytes, all stages of sporophyte development are nutritionally dependent on gametophyte tissues. Browning and Gunning investigated nutrient flow into young sporophytes because these slightly older and larger developmental stages were easier to manipulate in the laboratory than were tiny embryos.

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In a first step, the investigators grew many gametophytes of the moss Funaria hygrometrica in a greenhouse until young sporophytes developed as the result of sexual reproduction (Figure 31.20). In a second step, they placed black glass tubing over young sporophytes as a shade to prevent photosynthesis, enclosed the whole plants—gametophytes and their attached sporophytes—within transparent jars, and supplied the plants with radiolabeled 14CO2 for 15 minutes, an experimental procedure known as a pulse. Because the moss gametophytes were not shaded, their photosynthetic cells were able to incorporate some of the carbon from 14CO2 into organic compounds, such as sugars and amino acids, thereby making these compounds radiolabeled. Shading prevented the young sporophytes, which possess some photosynthetic tissue, from using the 14CO2 to produce organic compounds. In a third step, the researchers added an excess amount of nonradioactive CO2 to prevent the gametophytes from taking up more  14CO2, an experimental procedure known as a chase. This process stopped the radiolabeling of photosynthetic products because the vast majority of CO2 taken up was now unlabeled. (Experiments such

as this one are known as pulse-chase experiments.) In a final step, Browning and Gunning plucked young sporophytes of different sizes (ages) from the gametophytes and measured the amount of 14C present in the separated gametophyte and sporophyte tissues at various times following the chase. CO2 is rapidly incorporated into organic molecules via photosynthesis (refer back to Figure 8.13). Therefore, the researchers assumed that any transfer of radiolabeled carbon between gametophytes and sporophytes would be radiolabeled carbon within organic molecules. From their data, Browning and Gunning were able to calculate the relative amount of organic carbon that had moved from the moss gametophytes to their sporophytes. At the beginning of the chase, a group of gametophytes contained 228 units of radiolabeled carbon (see data set I in Figure 31.20). Eight hours after the chase, 51 units had been transferred to the young sporophytes. In other words, about 22% of the organic carbon produced by gametophyte photosynthesis was transferred to the young sporophytes during an 8-hour chase period. In addition, by comparing the amount of radioactive carbon accumulated by sporophytes of differing sizes, they

Figure 31.20  Browning and Gunning demonstrated that placental transfer tissues increase plant reproductive success. HYPOTHESES 1. Placental transfer tissues allow organic nutrients to flow from plant gametophytes to sporophytes faster than such nutrients move through plant tissues lacking transfer cells. 2. The rate of organic nutrient transfer into larger sporophytes is faster than into smaller sporophytes. KEY MATERIALS Moss Funaria hygrometrica, 14CO2 (radiolabeled carbon dioxide) Experimental level

1

Conceptual level

Grow moss gametophytes until young sporophytes develop from embryos, and measure sporophyte size.

Young sporophytes receive organic nutrients in the same way as embryos but are easier to handle.

2 Shade young sporophytes from light with

blackened glass tubing, and enclose whole plant in clear glass jar. Expose plants to 14CO for 15 minutes. This is called a pulse. 2

Sporophyte Dark tubing Gametophyte

14CO 2

Light 14CO

2

Photosynthesis, which requires light, will convert 14CO2 into 14 C-sugar in gametophytes but not sporophytes. 14 CO2 Labeled sugar

3

4

5

Expose plants to a large amount of nonradioactive CO2. This is called a chase. Incubate up to 8 hours.

Pluck young sporophytes of differing sizes from gametophytes. Assay 14C in both sporophytes and gametophytes using a scintillation counter. This was done immediately following the chase, and at 2 or 8 hours after the chase.

THE DATA I

Addition of excess nonlabeled CO2 is known as a chase because it chases away the ability of the cells to make any more radioactive sugars.

Nonradiolabeled CO2

Light Nonradiolabeled CO2

14CO no longer 2 taken up by plant.

Determine how much organic carbon flowed into sporophytes during each chase time. Scintillation counter

6

THE DATA II

4



5

Pluck young sporophytes of differing sizes from gametophytes. Assay 14C in both sporophytes and gametophytes using a scintillation counter. This was done immediately following the chase, and at 2 or 8 hours after the chase.

Determine how much organic carbon flowed into sporophytes during each chase time. Scintillation counter

PLANTS AND THE CONQUEST OF LAND 657

6

THE DATA I Organic carbon transfer from gametophyte to sporophyte:

THE DATA II Sporophyte size effect:

Mean 14C content of 5 gametophytes at 0 chase time

Mean 14C lost from gametophytes after 8-hour chase

Mean 14C gained by sporophytes after 8-hour chase

Sporophyte size

228 units

145 units

51 units

5–7 mm

8.47 ± 4.29 units

11–13 mm

9.93 ± 3.94 units

23–25 mm

Mean 14C content of 8 sporophytes after 2-hour chase

24.97 ± 5.30 units

7

CONCLUSION Organic carbon moves from photosynthetic gametophytes into developing sporophytes, facilitated by placental transfer tissues. Larger sporophytes absorb more organic carbon than smaller ones.

8

SOURCES Browning, A.J., and Gunning, B.E.S. 1979. Structure and function of transfer cells in the sporophyte haustorium of Funaria hygrometrica. III. Translocation of assimilate into the attached sporophyte and along the sets of attached and excised sporophytes. Journal of Experimental Botany 30: 1265–1273.

also learned that larger sporophytes absorbed 14C about three times faster than smaller ones (see data set II in Figure 31.20). Browning and Gunning also calculated the rate of nutrient transfer from gametophyte to sporophyte and compared this rate with the rate (determined in other studies) at which organic carbon moves between several other plant tissues that lack specialized transfer cells. They discovered that organic carbon moved from moss gametophytes to young sporophytes nine times faster than organic carbon moves between these other plant tissues. These investigators inferred that the increased rate of nutrient movement could be attributed to placental transfer cell structure, namely, that cell-wall ingrowths enhance plasma membrane surface area.  Taken together, these data are consistent with the hypothesis that placental transfer tissues increase plant reproductive success

Core Skill: Quantitative Reasoning

BIO TIPS

THE QUESTION  The experiment by Browning and Gunning revealed that placental transfer tissues are important for the movement of organic nutrients from moss gametophytes to young sporophytes. Organic nutrients are produced in photosynthetic tissues and transferred to nonphotosynthetic tissues. But diffusion from one generation to the next occurs too slowly, which explains why placental tissues evolved in plants (and placental mammals). According to the data of Browning and Gunning, how much more organic carbon do the largest sporophytes take up compared to the smallest ones? Based on the reproductive role of the sporophyte, propose a hypothesis that could explain this difference. T OPIC  What topic in biology does this question address?  The topic is the function of plant placental transfer tissues in moving organic carbon into embryonic sporophytes. More specifically, the question concerns the transfer of organic carbon into moss sporophytes of different sizes, which represent stages of developmental maturity.

by providing embryos and growing sporophytes with more nutrients than they would otherwise receive. Supplied with the greater amounts of nutrients, sporophytes are able to grow larger than they otherwise would, and eventually they produce more progeny spores. Experimental Questions 1. What were the goals of the Browning and Gunning investigation?  2. CoreSKILL » How did Browning and Gunning prevent photosynthesis from occurring in moss sporophytes during the experiment (shown in Figure 31.20), and why did they do this?  3. CoreSKILL » How did the measurements Browning and Gunning made after adding an excess amount of unlabeled CO2 lead them to their conclusions?

I NFORMATION  What information do you know based on the question and your understanding of the topic?  In the question, you are reminded of the experiment by Browning and Gunning that revealed the importance of placental transfer tissues in supplying nutrients to young sporophytes and referred to their data. From your understanding of cell biology, you may recall that all cells require organic compounds for energy and to synthesize larger macromolecules. Photosynthetic cells are able to generate organic compounds from inorganic compounds in the presence of light. Thus, photosynthetic tissues are a potential source of organic compounds for plant tissues whose primary function is not photosynthesis, such as sporangia, which carry out spore production. P ROBLEM-SOLVING   S  TRATEGY  Make a calculation. Propose a hypothesis.  Data set II in Figure 31.20 shows the amounts of 14 C taken up by moss sporophytes of differing sizes. From these data, calculate the relative difference between the smallest and largest sporophytes. Consider the reproductive role of the moss sporophyte, and propose one or more reasons why the transfer of nutrients would be higher in the larger sporophytes.

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ANSWER  If you compare the data for the smallest sporophytes (8.47 units) and the largest ones (24.97 units), you see that the largest have a mean content of radiolabeled carbon that is about three times that of the smallest. From this difference, you might infer that the rate of nutrient metabolism becomes three times higher as the sporophyte reaches maturity and produces spores that are ready for dispersal. One hypothesis to explain this difference is that the larger sporophytes are using nutrients at a faster rate because they are producing the tough spore coating containing sporopollenin, which would be an additional metabolic demand.

31.5      The Origin and Evolutionary Importance of Leaves and Seeds Learning Outcomes: 1. Describe how the leaves of ferns and seed plants likely evolved from branched-stem systems. 2. Discuss how seeds develop from fertilized ovules. 3. Name several advantages that seeds provide.

Like embryos, leaves and seeds are critical innovations that increased plant fitness and fostered diversification. Unlike the plant embryo, which likely originated just once at the birth of the plant kingdom, leaves and seeds may have independently evolved several times during plant evolutionary history. Comparative studies of diverse types of leaves and seeds in fossil and living plants suggest how these critical innovations originated.

The Large Leaves of Ferns Evolved from Branched-Stem Systems Leaves are the solar panels of the plant world. Their flat structure provides a large surface area that effectively captures sunlight for photosynthesis. Among the vascular plants, lycophytes produce the simplest and most ancient type of leaves. Modern lycophytes have tiny leaves, known as lycophylls (also known as microphylls), which typically have only a single unbranched vein (Figure 31.21a). Some experts think that these small leaves may have evolved from sporangia. By contrast to lycophytes, ferns and seed plants have leaves with extensively branched veins. Such leaves are known as euphylls (from the Greek, meaning true leaves) (Figure 31.21b). The branched veins of euphylls are able to supply relatively large areas of photosynthetic tissue with water and minerals. For this reason, euphylls are typically much larger than lycophylls, explaining why euphylls are also known as megaphylls. Euphylls provide considerable photosynthetic advantage to ferns and seed plants, because they provide more surface area for solar energy absorption than do small leaves. The evolution of relatively large leaves allowed plants to more effectively accomplish photosynthesis, enabling them to grow larger and produce more progeny.

The study of fern fossils indicates that euphylls likely arose from leafless, cylindrical, branched-stem systems by a series of steps (Figure 31.21c). First, one branch assumed the role of the main axis, while the other was reduced in size and became flattened in one plane, and then the spaces between the branches of this flattened system became filled with photosynthetic tissue. Such a process explains why euphylls have branched vascular systems; individual veins apparently originated from the separate branches of an ancestral branched stem. Plant evolutionary biologists suspect that euphylls arose several times by means of similar, parallel processes, and that leaves of ferns and seed plants are not homologous structures.

Seeds Develop from the Interaction of Ovules and Pollen The seed plants dominate modern ecosystems, suggesting that seeds offer reproductive advantages. Seed plants are also the plants with the greatest importance to humans, as described in Chapter 32. For these reasons, plant biologists are interested in understanding why seeds are so advantageous and how they evolved. To consider these questions, we must first take a closer look at seed structure and development. As mentioned earlier, plants produce spores by meiosis within sporangia, and seed plants are no exception. However, seed plants produce two distinct types of spores in two types of sporangia, a trait known as heterospory, meaning different spores. Microsporangia produce small microspores that give rise to male gametophytes, which develop into pollen grains. Megasporangia produce larger megaspores that give rise to female gametophytes, which develop and produce eggs while enclosed by protective megaspore walls. The enclosed female gametophytes are not photosynthetic, so they need help in feeding the embryos that develop from fertilized eggs. Female gametophytes get this help by remaining attached to the previous sporophyte generation, which provides gametophytes with the nutrients needed for embryo development. Plants produce seeds by reproductive structures known as ovules and pollen, which are unique to seed plants. An ovule is a sporangium that typically contains only a single spore that develops into a very small egg-producing gametophyte; the entire structure is enclosed by leaflike structures known as integuments (Figure 31.22a). You can think of an ovule as being like a nesting doll with four increasingly smaller dolls inside. The smallest doll corresponds to an egg cell; intermediate-sized doll represents the gametophyte, spore wall, and megasporangium; and the largest doll represents the integuments. Fertilization converts such layered ovules into seeds. In seed plants, the sperm needed for fertilization are supplied by pollen, tiny male gametophytes enclosed by protective sporopollenin-containing microspore walls. Embryos and seeds develop as the result of fertilization, which cannot occur until after pollination, the process by which pollen comes into contact with ovules. Pollination typically occurs by means of wind or animal transport (see Chapter 32). Fertilization occurs in seed plants when a male gametophyte extends a slender pollen tube that carries two sperm toward an egg. The pollen tube enters through an opening in the integument called the micropyle and releases the



PLANTS AND THE CONQUEST OF LAND 659

Single unbranched leaf vein

Branched vascular system

(b) Euphyll (large leaf)

(a) Lycophyll (small leaf)

1

Fern ancestors initially had a branched-stem system.

2

One branch began to dominate the stem system.

3

The branch system flattened into a single plane.

4

Photosynthetic tissue filled in the spaces between the branches of a system.

Euphyll

(c) Euphyll evolution process in pteridophytes

Figure 31.21  Lycophylls and euphylls.  (a) Most lycophylls possess only a single unbranched leaf vein with limited conduction capacity, explaining why lycophylls are generally quite small. (b) Euphylls possess branched vascular systems with greater conduction capacity, explaining why many euphylls are relatively large. (c) Fossil evidence suggests how pteridophyte euphylls might have evolved from ancestors with branchedstem systems. Core Skill: Modeling  The goal of this modeling challenge is to propose a visual model that compares the density of leaf veins between ferns and another plant group. Modeling Challenge: Figure 31.21 provides a model of the process by which fern leaves having branched vascular systems (euphylls) are hypothesized to have evolved from ancestors with branching stems. Imagine that the leaves of some other plant group evolved similarly, but from stem systems that were twice as highly branched. In other words, when flattened, the stem system ancestral to this other plant group had twice as many branches per unit area. Assuming that the branch density of ancestors is directly related to vein density of leaves in descendant plants, draw a pair of models that compare the leaves of ferns and this other plant group, emphasizing the vein density in each type of leaf. How does the venation differ in the two leaf models?

sperm. The fertilized egg becomes an embryo, and the ovule’s integument develops into a protective, often hard and tough seed coat (Figure 31.22b and c). Gymnosperm seeds contain female gametophyte tissue that has accumulated large amounts of proteins, lipids, and carbohydrates prior to fertilization. These nutrients feed both embryo development and seed germination. Angiosperm seeds also contain this useful food supply, but most angiosperm ovules do not store food materials before fertilization. Instead, angiosperm seeds generally store food only after fertilization occurs, ensuring that the food is not wasted if an embryo does not form. How is this accomplished? The answer is a process known as double fertilization. This process produces

both a zygote and a food storage tissue known as endosperm, a feature unique to angiosperms. One of the two sperm delivered by each pollen tube fuses with the egg, producing a diploid zygote, as you might expect. The other sperm fuses with different gametophyte nuclei to form an unusual cell that has more than the diploid number of chromosomes; this cell continues to divide and generates the endosperm food tissue. Endosperm will be discussed in more detail in Chapter 40. Seeds allow plant embryos access to food supplied by the previous sporophyte generation, an option not available to seedless plants. The layered structure of ovules explains why seeds are also layered, with a protective seed coat enclosing the embryo and

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Stored food:

Micropyle

Pollen tube with 2 sperm cells

•

Female gametophyte of gymnosperm seeds

•

Endosperm of angiosperm seeds

Integument

Embryonic leaves Young embryo Seed coat

Egg Development

Development

Spore wall

Megasporangium

Embryonic root

Mature embryo Multicellular female gametophyte

(a) Mature ovule just prior to fertilization

(b) Developing seed

(c) Light micrograph of mature angiosperm seed, sectioned and stained

Figure 31.22  Structure of an ovule developing into a seed. c: ©Lee W. Wilcox Concept Check:   Can you hypothesize why the mature angiosperm seed does not show obvious endosperm tissue? 

stored food. As described next, these seed features improve the chances of embryo and seedling survival, thereby increasing seed plant fitness.

Seeds Confer Important Reproductive Advantages Seeds provide plants with numerous reproductive advantages.  ∙ First, many seeds are able to remain dormant in the soil for long periods, until conditions become favorable for germination and seedling growth. Furthermore, seed coats are often adapted in ways that improve dispersal in diverse habitats. For example, many plants produce winged seeds that are effectively dispersed by wind. Other plants produce seeds with fleshy coverings that attract animals, which consume the seeds, digest the fleshy covering, and eliminate the bare seeds at some distance from the originating plants. ∙ Another advantage of seeds is that they can store considerable amounts of food, which supports embryo growth and helps plant seedlings grow large enough to compete for light, water, and minerals. This is especially important for seeds that must germinate in shady forests.  ∙ Finally, the sperm of most seed plants can reach eggs without having to swim through water, because pollen tubes deliver sperm directly to ovules. Consequently, seed plant fertilization is not typically limited by lack of water, in contrast to fertilization of seedless plants. Consequently, seed plants are better able to reproduce in arid and seasonally dry habitats.  For these reasons, seeds are considered to be a key adaptation to reproduction in a land habitat.

Ovule and Seed Evolution Illustrates Descent with Modification As we have seen, seed plants reproduce using both spores and seeds, but seed plants have not replaced spores with seeds. Seed plants still produce spores. Ovules and seeds have evolved from spore-producing structures by descent with modification. Recall that this evolutionary principle involves changes in pre-existing structures and processes. Fossils provide some clues about ovule and seed evolution, and other information can be obtained by comparing reproduction in living lycophytes and pteridophytes. Most modern lycophytes and pteridophytes release one type of spore that develops into one type of gametophyte. Such plants are considered to be homosporous, and their gametophytes live independently and produce both male and female gametangia (see Figure 31.18). However, some lycophytes and pteridophytes produce and release two distinct kinds of spores: relatively small microspores and larger megaspores, which grow into male and female gametophytes, respectively. As mentioned previously, production of two kinds of spores is called heterospory. As shown in steps 2a and 2b of Figure 31.23, an early step in the evolution of seed plants may have been a switch from homospory to heterospory. What are advantages of heterospory? One advantage is that it mandates cross-fertilization. The eggs and sperm that fuse are derived from different gametophytes, which are likely to be genetically different. Cross-fertilization increases the potential for genetic variation. As described in Chapter 23, such variation may enhance the survival and reproduction of individuals with favorable phenotypes and result in evolution from one



PLANTS AND THE CONQUEST OF LAND 661

1

Sporangium containing spores that are similar in size

2a Microsporangium

2b Megasporangium

containing many small microspores

containing fewer, larger megaspores

3

Early evolution of heterospory

Reduction to 1 megaspore per megasporangium

4

Enclosure of megasporangium within integuments to form ovule; when fertilized, ovule develops into a seed

Megaspore

+

Microsporangium

Ovule

Megasporangium

Integuments

Evolution of megasporangium that led to an ovule

Figure 31.23  Hypothetical stages in the evolution of seeds.  The parallel evolution of heterospory and endosporic gametophytes in some lycophytes and pteridophytes as well as in the seed plants suggests that these features were acquired early in the evolution of seeds. Lateroccurring events in the evolution of seeds included reduction of the number of megaspores to one per megasporangium and enclosure of the megasporangium by protective integuments. Core Skill: Connections  Look ahead to Figure 35.14, which illustrates the amniotic egg produced by many terrestrial animals. How is the plant seed like the amniotic egg? 

generation to the next. A second advantage is that the gametophytes produced by heterosporous plants grow within the confines of microspore and megaspore walls and therefore are known as endosporic gametophytes. Endosporic gametophytes receive protection from environmental damage from the surrounding spore walls. Plant evolutionary biologists infer that heterospory and endosporic gametophytes were features of seed plant ancestors and constitute early steps toward seed evolution. Whereas seedless plants produce multiple spores per sporangium, another key step in seed evolution may have been the production of only one megaspore per sporangium (see step 3 in  Figure 31.23). Having a single megaspore allowed plants to channel more nutrients into each megaspore, thereby enabling megaspores to store more food. Following fertilization, this increased food confers an advantage by providing greater nutritive support to developing sporophytes. A final step in seed evolution might have been the retention of megasporangia on parental sporophytes by the development of integuments (see step 4 in Figure 31.23). As mentioned earlier, this adaptation would allow food materials to flow from mature photosynthetic sporophytes to their dependent gametophytes and young embryos. Integuments also help ovules to receive pollen. Fossils provide information about when and how the process of ovule and seed evolution first occurred. Fossil reproductive structures of an extinct Devonian plant named Runcaria heinzelinii may represent a precursor to an ovule or seed (see Figure 31.24). These fossil structures had a lacy integument that did not completely

Lacy integument

Leaves

Megasporangium

1 mm

Figure 31.24  Reconstruction of reproductive parts of the fossil

Runcaria heinzelinii, a plant with a probable precursor to an ovule or seed. Concept Check:   Based on your knowledge of integument function in modern seed plants, can you hypothesize a function for the lacy integument of R. heinzelinii?

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enclose the megasporangium. Very early fossil seeds such as those of  Elkinsia polymorpha and Archaeosperma arnoldii were present by 365 mya. 

31.6           A Summary of Plant Features Learning Outcome: 1. Compare and contrast the distinguishing features of green algae and modern plant phyla.

The evolutionary journey involving the transition from aquatic streptophyte algae to bryophytes, to seedless plants, and finally to seed plants reveals adaptations to a terrestrial environment, as well as ways in which plants themselves have shaped Earth’s ecosystems. Throughout this chapter, we have considered many critical innovations that led to the development of modern plant phyla. Table 31.1 provides a list of the distinguishing features of land plants and their algal relatives.

Table 31.1

Distinguishing Features of Modern Streptophyte Algae and Land Plants

STREPTOPHYTES Streptophyte algae: Primarily aquatic habitat; haploid-dominant life cycle; sporangia absent; sporophytes absent EMBRYOPHYTES: Primarily terrestrial habitat; life cycle consisting of alternation of two multicellular generations (diploid sporophyte and haploid gametophyte); multicellular embryos nutritionally dependent on maternal gametophyte for at least some time during development; spore-producing sporangia; gamete-producing gametangia; spores with sporopollenin-containing walls Nonvascular plants (bryophytes) (liverworts, mosses, hornworts): Dominant gametophyte generation; supportive, lignin-containing vascular tissue absent; true roots, stems, and leaves absent; sporophytes unbranched and unable to grow independently of gametophytes VASCULAR PLANTS (TRACHEOPHYTES) (lycophytes, pteridophytes, spermatophytes):  Dominant sporophyte generation; lignified water-conducting tissue (xylem); specialized organic food-conducting tissue (phloem); sporophytes branched and eventually becoming independent of gametophytes LYCOPHYTES: Leaves generally small with a single, unbranched vein (lycophylls); sporangia borne on sides of stems; seeds absent PTERIDOPHYTES: Leaves relatively large with extensively branched vein system (euphylls or megaphylls); sporangia borne on leaves; seeds absent SEED PLANTS (SPERMATOPHYTES): Seeds present; leaves are euphylls that evolved independently from those of pteridophytes GYMNOSPERMS (cycads, ginkgos, conifers): Flowers and fruits absent; seed food stored before fertilization in female gametophyte; endosperm absent ANGIOSPERMS (flowering plants): Flowers and fruit present; seed food stored after fertilization in endosperm tissue Key: Phyla; LARGER MONOPHYLETIC CLADES (FORMAL SYNONYMS). All other classification terms are not clades.

Summary of Key Concepts 31.1  Ancestry and Diversity of Modern Plants ∙∙ Plants are multicellular eukaryotic organisms composed of cells having plastids; they display many adaptations to life on land. The modern plant kingdom consists of several hundred thousand species classified into nine phyla, informally called the liverworts, mosses, hornworts, lycophytes, pteridophytes, cycads, ginkgos, conifers, and angiosperms (Figure 31.1). ∙∙ The land plants evolved from ancestors that were probably similar to modern complex streptophyte algae (Figure 31.2). ∙∙ Paleobiologists and plant evolutionary biologists infer the history of land plants by analyzing the molecular features of modern plants and by comparing the structural features of fossil and modern plants (Figure 31.3). ∙∙ The nonvascular plants include the liverworts, mosses, and hornworts, phyla that are collectively known as the bryophytes (Figures 31.4, 31.5, 31.6). ∙∙ Lycophytes, pteridophytes, and other vascular plants generally possess stems, roots, and leaves having conductive vascular tissues composed of phloem and xylem, in addition to cuticle, and stomata. These features promote stable body water content (Figures 31.7, 31.8, 31.9). ∙∙ Cycads, ginkgos, conifers, and gnetophytes are collectively known as gymnosperms. Gymnosperms produce seeds, but not flowers and fruits. Angiosperms, the flowering plants, produce seeds, flowers, fruits, and seed endosperm (Figures 31.10, 31.11).

31.2  How Land Plants Have Changed the Earth ∙∙ Ancient seedless plants and later-emerging vascular plants transformed Earth’s ecology by altering atmospheric chemistry and climate (Figures 31.12, 31.13, 31.14). ∙∙ The Cretaceous-Paleogene event, a probable meteorite collision with Earth that occurred 65 mya, helped cause the extinction of previously dominant dinosaurs and many types of gymnosperms, leaving space into which angiosperms, insects, birds, and mammals diversified.

31.3    E  volution of Reproductive Features in Land Plants ∙∙ Bryophytes illustrate early-evolved features of land plants, which include a life cycle featuring alternation of generations, involving embryos that develop within protective, nourishing gametophyte tissues (Figure 31.15). ∙∙ Bryophytes differ from other plants in having a dominant gametophyte generation and a dependent, nonbranching, short-lived sporophyte generation (Figure 31.16). ∙∙ The evolution of vascular plants involved a shift in the relative sizes of gametophytes and sporophytes, with the sporophyte becoming the dominant generation (Figure 31.17). ∙∙ The fern life cycle includes the dominant sporophyte characteristic of vascular plants (Figure 31.18).

31.4    E  volutionary Importance of the Plant Embryo ∙∙ The origin of the plant embryo was a critical innovation that fostered diversification of the land plants. Like placental mammal



PLANTS AND THE CONQUEST OF LAND 663

mothers, plant female gametophytes provide embryos with nutrients through specialized placental tissues (Figure 31.19). ∙∙ In a classic experiment, Browning and Gunning demonstrated that placental transfer tissues were responsible for an enhanced rate of nutrient flow from plant gametophytes to embryos (Figure 31.20).

31.5     T  he Origin and Evolutionary Importance of Leaves and Seeds ∙∙ Leaves are specialized photosynthetic organs that evolved more than once during plant evolutionary history. The lycophylls of lycophytes are relatively small leaves having a single unbranched vein. The larger leaves of ferns and seed plants, known as euphylls, have extensively branched vascular systems. Fossils indicate that fern euphylls evolved from branched-stem systems (Figure 31.21). ∙∙ Seeds develop from ovules, integument-enclosed sporangia that typically contain only a single spore that develops into an eggproducing gametophyte. Pollen produces thin cellular tubes that deliver sperm to eggs produced by female gametophytes. Following pollination and fertilization, ovules develop into seeds. Mature seeds contain stored food and an embryonic sporophyte that develops from the zygote (Figure 31.22). ∙∙ Seeds confer many reproductive advantages, including dormancy through unfavorable conditions, greater protection for embryos from mechanical and pathogen damage, seed coat modifications that enhance seed dispersal, and reduction of plant dependence on water for fertilization (Figures 31.23, 31.24).

31.6      A Summary of Plant Features ∙∙ The distinctive traits of modern streptophyte algae and the different phyla of land plants indicate the occurrence of descent with modification (Table 31.1).

Assess & Discuss Test Yourself 1. The simplest and most ancient phylum of modern land plants is probably a. the pteridophytes. b. the cycads. c. the liverworts, mosses, or hornworts. d. the angiosperms. e. none of the above. 2. An important feature of land plants that originated during the diversification of streptophyte algae is a. the sporophyte. b. spores, which are dispersed in air and coated with sporopollenin. c. tracheids. d. plasmodesmata. e. fruits. 3. A seedless plant phylum that is included in the informal group known as bryophytes is a. liverworts. b. hornworts. c. mosses. d. All of the above phyla are included in the bryophytes. e. None of the above is included in the bryophytes.

4. Plants possess a life cycle that involves alternation of two multicellular generations: the gametophyte and a. the lycophyte. d. the lignophyte. b. the bryophyte. e. the sporophyte. c. the pteridophyte. 5. The seed plants are also known as a. bryophytes. b. spermatophytes. c. pteridophytes. d. lycophytes. e. none of the above. 6. A waxy cuticle is an adaptation that a. helps to prevent water loss from tracheophyte stem and leaf surfaces. b. helps to prevent water loss from streptophyte algae. c. helps to prevent water loss from spores. d. aids in water transport within the bodies of vascular plants. e. does all of the above. 7. Plant photosynthesis transformed a very large amount of atmospheric carbon dioxide into decay-resistant organic compounds, thereby contributing to a dramatic decrease in atmospheric carbon dioxide levels during the geological period known as the a. Cambrian. d. Permian. b. Ordovician. e. Pleistocene. c. Carboniferous. 8. Which of these plant phyla is likely to have the largest leaves? a. liverworts b. hornworts c. mosses d. lycophytes e. pteridophytes 9. Fern euphylls, also known as megaphylls, probably evolved from a. the leaves of mosses. b. lycophylls. c. branched-stem systems. d. modified roots. e. none of the above. 10. A seed develops from a. a spore. b. a fertilized ovule. c. a microsporangium covered by integuments. d. endosperm. e. none of the above.

Conceptual Questions 1. List several common traits that lead evolutionary biologists to infer that land plants evolved from ancestors related to modern streptophyte algae.  2. Why have bryophytes such as mosses been able to diversify into so many species even though they have relatively small, dependent sporophytes?    3. 

Core Concept: Structure and Function  Explain how several structural features help vascular plants maintain stable internal water content. 

Collaborative Questions 1. Discuss at least one difference in the environmental conditions experienced by early land plants and ancestral streptophyte algae. 2. Identify and describe as many plant adaptations to land as you can.

CHAPTER OUTLINE

The Evolution and Diversity of Modern Gymnosperms and Angiosperms

32

32.1 Overview of Seed Plant Diversity 32.2 The Evolution and Diversity of Modern Gymnosperms 32.3 The Evolution and Diversity of Modern Angiosperms 32.4 The Role of Coevolution in Angiosperm Diversification 32.5 Human Influences on Angiosperm Diversification Summary of Key Concepts Assess & Discuss

animals, and they also aid plant growth and reproduction. Though all plants produce secondary metabolites, these natural products are exceptionally diverse in gymnosperms and angiosperms. In this chapter, we will explore the many important roles that the hundreds of thousands of modern seed plants play in the lives of humans and modern ecosystems. This chapter builds on the introduction to seeds and seed plants provided in Chapter 31. We begin by focusing on the diversity of modern lineages of gymnosperms and angiosperms. Coevolutionary interactions among angiosperms and animals are presented as major factors influencing the diversification of these groups. This chapter concludes by considering human influences on seed plant evolution and the importance of seed plants in modern agriculture.

   32.1  Overview of Seed Plant Diversity The Madagascar periwinkle (Catharanthus roseus), one of the many seed plants on which humans depend. ©Gallo Images/Corbis/ Getty Images

T

he seed plants—gymnosperms and angiosperms—are particularly important in our everyday lives because they are the sources of many products, including wood, paper, beverages, food, cosmetics, and medicines. Leukemia, for example, is effectively treated with vincristine, a drug extracted from the beautiful flowering plant known as the Madagascar periwinkle (Catharanthus roseus), pictured in the chapter opening photo. Vinblastine—another extract from C. roseus—is used to treat lymphatic cancers. Taxol, a compound used in the treatment of breast and ovarian cancers, was first discovered in extracts of the bark of the Pacific yew tree, a gymnosperm called  Taxus brevifolia. Vincristine, vinblastine, taxol, and many other plant-derived medicines are examples of plant secondary metabolites, which are distinct from the products of primary metabolism (carbohydrates, lipids, proteins, and nucleic acids). Secondary metabolites play essential roles in protecting plants from disease-causing organisms and plant-eating

Learning Outcomes: 1. Describe the evolutionary relationships among seedless vascular plants and seed plants. 2. List the critical innovations that occurred during the evolution of seed plants.

The seed plants—gymnosperms and angiosperms—evolved from the seedless vascular plants, which were described in Chapter 31. Fossils indicate that gymnosperms originated from now extinct seedless plants known as progymnosperms, some of which were woody, representing the first trees. Gymnosperms then diversified into multiple lineages, some of which became extinct. However, a few gymnosperm phyla, including the conifers, have persisted to the modern day. Angiosperms arose from an unknown gymnosperm lineage, thereby inheriting the capacity to produce wood and other seed plant features.  Figure 32.1 shows our current understanding of the evolutionary relationships among seedless vascular plants and modern seed plants, which include three modern phyla of gymnosperms and the flowering plants (angiosperms).  Table 32.1 provides a summary of the critical innovations of all modern seed plants, conifers, and angiosperms.



THE EVOLUTION AND DIVERSITY OF MODERN GYMNOSPERMS AND ANGIOSPERMS 665

Seed plants (spermatophytes) Seedless vascular plants

Gymnosperms

KEY Critical innovations

Angiosperms

Conifers

& Gnetales

Ginkgo

Cycads

Pteridophytes

Lycophytes

Whole-genome duplication

Flowers; fruits; seed endosperm; vessels common Wood; ovules; seeds; pollen; euphylls

Euphylls

Figure 32.1  A phylogenetic tree for Supportive vascular tissue; dominant branched sporophyte generation

Table 32.1

Critical Innovations of Some Seed Plant Groups

modern seedless vascular plants and seed plants.

32.2     T  he Evolution and Diversity of Modern Gymnosperms

Plant group

Innovation

Advantages

All seed plants

Vascular cambium that makes vascular tissue and also makes wood and inner bark in woody plants

Seed plants have the potential to grow tall and produce many branches and reproductive structures.

Learning Outcomes:

Pollen, ovules, seeds

Pollen allows seed plants to disperse male gametophytes. Ovules provide protection and nutrition to female gametophytes and developing embryos. Seeds allow seed plants to reproduce in arid or shady habitats.

Tracheid torus

Fosters water flow in arid or cold conditions

Scales or needle-shaped leaves

Retard water loss from leaf surfaces

Gymnosperms are defined as plants that produce seeds that are exposed rather than enclosed in fruits, as is the case for angiosperms. The word gymnosperm comes from the Greek gymnos, meaning naked (referring to the unclothed state of ancient athletes), and sperma, meaning seed. Most modern gymnosperms are woody plants that occur as shrubs or trees. Conifers, which are widely harvested for wood and produce other valuable materials, are familiar examples. In this section, we will examine the evolution and key features of the gymnosperms.

Conical shape

Sheds snow, preventing damage

Resin

Protects against pathogens and herbivores

Flowers

Foster pollen dispersal, ovule protection, pollination, and seed production

Fruits

Foster seed dispersal

Endosperm

Efficiently provides food to embryo of developing seed

Vessels

Relatively wide diameter fosters water flow

Many secondary compounds

Provide flower colors and fragrances and protect against herbivores

Conifers

Angiosperms

1. Describe how gymnosperms diversified. 2. Identify three gymnosperm phyla, and describe their importance to humans.

Modern Gymnosperms Arose from Woody Ancestors Modern gymnosperms include the famous giant sequoias (Sequoiadendron giganteum) native to the Sierra Nevada mountains of the western U.S. Giant sequoias are among Earth’s largest organisms, weighing as much as 6,000 tons and reaching an amazing 100 m in height. The large size of sequoias and other trees is based on the presence of wood, a tissue composed of numerous pipelike arrays of empty, water-conducting cells whose walls are strengthened by an exceptionally tough polymer known as lignin. These properties enable woody tissues to transport water upward for great distances and also to provide the structural support needed for trees to grow tall and produce many branches and leaves. 

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In modern seed plants, a special tissue known as the vascular cambium produces both thick layers of wood and thinner layers of inner bark. The inner bark transports watery solutions of organic compounds. (The structure and function of the vascular cambium, wood, and inner bark are described in more detail in Chapters 36 and 39.) Vascular cambium, wood, and inner bark help gymnosperms and woody angiosperms to compete effectively for light and other resources needed for photosynthesis. Wood first appeared in a group of ancient seedless plants known as the progymnosperms (from the Greek, meaning before gymnosperms). Woody progymnosperms, such as the fossil plant Archaeopteris, which lived 370 mya, were the first trees that had leafy twigs (Figure 32.2). The vascular tissue of progymnosperms differed from that of earlier vascular plants in being arranged in a ring around a central pith of nonvascular tissue. Seed plants inherited the capacity to make this new arrangement of vascular tissue, which is called a eustele. A eustele contains cells that can develop into a vascular cambium as seedlings grow into saplings. The vascular cambium generates wood, allowing saplings to grow into tall trees. The greatest diversity of gymnosperms occurred during the Mesozoic era, when gymnosperms were the major vegetation present. This period was also known as the Age of Dinosaurs, and gymnosperms are thought to have been the major food for plant-eating

dinosaurs during most of their history. Some groups of gymnosperms became extinct before or as a result of the Cretaceous-Paleogene event (K/T event) about 66 mya. Surviving gymnosperm phyla are the cycads (formally, Cycadophyta); Ginkgo biloba, the only surviving member of a once large phylum termed Ginkgophyta; and conifers plus Gnetales, which comprise about 800 species. These phyla display distinctive reproductive features and play important roles in ecology and human affairs.

Cycads Are Endangered in the Wild but Are Widely Used as Ornamentals Cycads are regarded as the earliest diverging modern gymnosperm phylum, originating more than 300 mya. Nearly 300 cycad species occur today, primarily in tropical and subtropical regions. However, many species of cycads are rare, and their tropical forest homes are increasingly threatened by human activities. Many cycads are listed as endangered, and commercial trade in cycads is regulated by CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora), a voluntary international agreement between governments to protect such species. The structure of cycads is so interesting and attractive that many species are cultivated for use in outdoor plantings or as houseplants. The nonwoody stems of some cycads emerge from the ground much like tree trunks, some reaching 15 m in height, whereas the stems of other cycads are not conspicuous because they are subterranean (Figure 32.3). Cycads display spreading, palmlike leaves (cycad comes from a Greek word meaning palm). Mature leaves of the African cycad Encephalartos laurentianus can reach an astounding 8.8 m in length!

(a) Emergent cycad stem

Figure 32.2  An early forest in which the only trees were the

progymnosperm Archaeopteris.  This illustration was reconstructed from fossil data. Core Skill: Connections  Look ahead to Figure 54.26a–e. In what way did ancient Archaeopteris forests differ from most forests of the present time?

(b) Submergent cycad stem

Figure 32.3  Cycads.  Palmlike foliage and conspicuous seed-

producing cones are features of most cycads. (a) The stems of some cycads emerge from the ground. (b) The stems of other cycads are submerged in the ground, so the leaves emerge at ground level. This image also shows a conspicuous orange conelike structure that bears seeds. a: ©Philippe Psaila/Science Source; b: ©Ed

Reschke/Getty Images



THE EVOLUTION AND DIVERSITY OF MODERN GYMNOSPERMS AND ANGIOSPERMS 667

Root surface Cyanobacteria

(NH3), providing their plant hosts with the nitrogen that is crucial to growth (see Chapter 38). Cycad reproduction is distinctive in several ways. Individual cycad plants produce conspicuous conelike structures that bear either ovules and seeds or pollen (see Figure 32.3b). When mature, both types of reproductive structures emit odors that attract beetles. These insects carry pollen to ovules, where the pollen produces tubes that deliver sperm to eggs.

Ginkgo biloba Is the Last Survivor of a Once Diverse Group

(a) Coralloid roots (b) Coralloid root cross section

Figure 32.4  Coralloid roots of cycads.  (a) Many cycads produce aboveground branching roots that resemble branched corals. (b) This magnified cross section of a coralloid root shows a ring of symbiotic blue-green cyanobacteria, which provide the plant with a form of nitrogen that can be used to make essential cellular compounds. ©Lee W. Wilcox

Concept Check:   Why do the coralloid roots grow aboveground?

In addition to underground roots, which provide anchorage and take up water and minerals, many cycads produce coralloid roots. Such roots extend aboveground and have branching shapes resembling corals (Figure 32.4a). Coralloid roots harbor light-dependent, photosynthetic cyanobacteria within their tissues. The cyanobacteria, which form a bright blue-green ring beneath the root surfaces (Figure 32.4b), convert atmospheric nitrogen (N2) into ammonia

(a) Ginkgo biloba tree

(b) Ginkgo biloba leaf

The beautiful tree Ginkgo biloba (Figure 32.5a) is the single remaining species of a phylum that was much more diverse during the Age of Dinosaurs. G. biloba takes its species name from the two-lobed shape of its leaves, which have unusual forked veins (Figure 32.5b). Widely cultivated modern Ginkgo trees are descended from seeds produced by a tree found in a remote Japanese temple garden and brought to Europe by 17th-century explorers. G. biloba trees are widely planted along city streets because they are ornamental and also tolerate cold, heat, and pollution better than many other trees. In addition, these trees are long-lived— individuals can live for more than a thousand years and grow to 30 m in height. Individual trees produce either ovules and seeds or pollen, based on a sex chromosome system much like that of humans. Ovule-producing trees have two X chromosomes; pollenproducing trees have one X and one Y chromosome. Wind disperses pollen to ovules, where pollen grains germinate to produce pollen tubes. These tubes grow through ovule tissues for several months, absorbing nutrients that are used for sperm development. Eventually the pollen tubes burst, delivering flagellate sperm to egg cells. After fertilization, zygotes develop into embryos, and the ovule integument develops into a fleshy, foul-smelling outer seed coat and a hard, inner seed coat (Figure 32.5c). For streetside or garden plantings, people usually select the pollen-producing trees to avoid the stinky seeds.

(c) Ginkgo biloba seeds

Figure 32.5  Ginkgo biloba.  (a) A Ginkgo biloba tree; (b) fan-shaped leaves with forked veins; and (c) seeds with fleshy, foul-smelling seed coats (because of their fleshy, colorful appearance, mature Ginkgo seeds are often mistaken for fruits). a: ©Karlene V. Schwartz; b: ©Fancy Photography/ Veer/Getty Images; c: ©Topic Photo Agency IN/age fotostock

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Conifers Are the Most Diverse Modern Gymnosperm Lineage The conifers (Figure 32.6) are a lineage of trees named for their seed cones, of which pinecones are familiar examples. Modern conifer families include more than 50 genera. Conifers are particularly common in mountain and high-latitude forests and are important sources of wood and paper pulp. Conifer Reproduction  Conifers produce simple pollen cones and more complex ovule-bearing cones (see step 1 of  Figure 32.7). The ovule cones, also called seed cones, are composed of many short branch systems that bear ovules. Ovules contain female gametophytes, within which eggs develop (see step 3a of Figure 32.7). The pollen cones of conifers have many leaflike structures, each bearing a microsporangium in which meiosis occurs and pollen grains develop (see step 3b of Figure 32.7). When conifer pollen is mature, it is released into the wind, which transports it to ovules. When released from pollen tubes, sperm fuse with eggs, generating zygotes that grow into the embryos within seeds (see steps 4–7 of Figure 32.7). Altogether, it takes nearly 2 years for pines (the genus Pinus) to complete the processes of male and female gamete development, fertilization, and seed development.  Conifer seeds may also display features that aid in dispersal. For example, the seeds of pines and some other conifers develop wings that aid in wind dispersal (Figure 32.8a). Other conifers, such as yew and juniper, produce seeds or cones with bright-colored, fleshy coatings that are attractive to birds, which help to disperse the seeds (Figure 32.8b and c).  Conifer Tracheids  The wood of conifers contains many specialized vascular cells known as tracheids that are adapted for efficient water and mineral conduction even in dry conditions. Like the tracheids of other vascular plants, those of conifers are devoid of cytoplasm and occur in long columns that function like plumbing

pipelines (Figure 32.9a). Tracheid side and end walls possess many thin-walled, circular pits through which water moves both vertically and laterally from one tracheid to another. Conifer pits are unusual in having a porous outer region that lets water flow through and a nonporous, flexible central region called the torus (plural, tori) that functions like a valve (Figure 32.9b).  If conifer tracheids become dry, a common event in arid or cold habitats, they fill with air and are no longer able to conduct water. In this case, the torus presses against the pit opening, sealing it (Figure 32.9c). The torus valve thereby prevents air bubbles from spreading to the next tracheid. This conifer adaptation localizes air bubbles, preventing them from stopping water conduction in other tracheids. The presence of tori in their tracheids helps to explain why conifers have been so successful for hundreds of millions of years.  Conifer wood (and leaves) may also display conspicuous resin ducts, passageways for the flow of syrup-like resin that helps to prevent attack by pathogens and herbivores. Resin that exudes from tree surfaces may trap insects and other organisms, then harden in the air and fossilize, preserving the inclusions in amber. Adaptations to Cold Climates  Many conifers occur in cold climates and thus display numerous adaptations to such environments. Their conical shapes and flexible branches help conifer trees shed snow, preventing heavy snow accumulations from breaking branches. People who use conifers in landscape plantings also value these traits. Conifer leaf shape and structure are adapted to resist damage from drought that occurs in both summer and winter, when liquid water is scarce. Conifer leaves are often scalelike (Figure 32.10a) or needle-shaped (Figure 32.10b); these shapes reduce the area of leaf surface from which water can evaporate. In addition, a thick, waxy cuticle coats conifer leaf surfaces (Figure 32.10c), retarding water loss and attack by disease organisms.  Many conifers are evergreen; that is, their leaves live for more than 1 year before being shed and are not all shed during the same season. Retaining leaves through winter helps conifers start up

Figure 32.6  Representative

conifers.  (a) Many conifers, such as pines, are not deciduous, meaning that they do not lose all their leaves at the same time in the autumn. (b) Some conifers, such as the dawn redwood, are deciduous, meaning that they drop their leaves in the autumn. a: ©Lee W. Wilcox; b: ©Bryan Pickering/Eye Ubiquitous/Corbis/Getty Images

(a) Pine (Pinus ponderosa)

(b) Dawn redwood (Metasequoia glyptostroboides)

3a 2

1

Sporophytes produce 2 types of cones: ovule cones and pollen cones.

In ovule cones, megaspores are produced by meiosis within megasporangia. In pollen cones, microspores are produced by meiosis within microsporangia.

Ovule cone

Cone scale

Megaspore

Scale

Egg (n)

Ovule

Mature sporophyte (2n)

Integument

Megasporangium Meiosis

In ovule cones, megaspores undergo mitosis and produce female gametophytes containing eggs within archegonia. The entire structure, including the outer integuments, is an ovule. Each scale of the cone has 2 ovules; only 1 ovule is shown here.

Female gametophyte (n)

Mitosis

Megasporangium (2n)

Seed coat

Microspores Section of cone Microsporangium

Pollen cone

Archegonium (n)

Pollen grain (n) KEY Haploid Diploid

Seedling 3b Scale Seed

In pollen cones, microspores undergo mitosis and develop into pollen grains, which are young male gametophytes.

Ovule 4

8

Seeds germinate, and embryo sporophytes grow into seedlings.

Sperm

Pollen grains are dispersed into the wind and encounter ovules.

Male gametophyte (n) Embryo (2n)

Mitosis

Fertilization 5

7

The zygote produces an embryo in a seed. Mature seeds are dispersed.

6

The pollen tube delivers sperm to eggs, where fertilization occurs. Only 1 egg per ovule is fertilized and develops.

The pollen grain’s male T gametophyte matures, producing sperm cells in a pollen tube.

Figure 32.7  The life cycle of the genus Pinus.  Core Concept: Structure and Function  This diagram illustrates the entire seed-to-seed growth and development cycle of conifers, illustrating structure-function relationships.

(a) Pine seed

(b) Yew seeds

(c) Juniper cones with seeds

Figure 32.8  Conifer seeds.  (a) Winged, wind-dispersed seed of the genus Pinus. (b) Fleshy-coated, bird-dispersed seeds of yew (Taxus

baccata). (c) Fleshy cones of juniper (Juniperus scopularum) contain one or more seeds and are dispersed by birds. Juniper seeds are used to flavor gin. a: ©Zach Holmes Photography; b: ©Carmen Hauser/Shutterstock; c: ©Ed Reschke/Getty Images Core Skill: Connections  Look ahead to Figure 32.21h. How are wind-dispersed pine seeds similar to wind-dispersed fruits of the angiosperm maple?

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Water Pits Torus Tracheid Torus Tracheid Flexed tori

Air

Porous region (a) Columns of tracheids showing cell walls

(b) Tracheid pits containing tori

Pits open and conducting water

Pits sealed

(c) Tracheid with open pits (left side) and tracheid with sealed pits (right side)

Figure 32.9  Tracheids and tori in conifer wood.  (a) The lignin-rich cell walls of the water-conducting cells called tracheids. (b) Detailed view

of a portion of a tracheid that shows the thin-walled areas known as pits, each with a torus. (c) A water-filled tracheid with open pits and an air-filled tracheid with pits sealed by the flexed tori. Core Concept: Structure and Function  This illustration shows how tori in water-conducting cells of conifers aid survival in arid or cold habitats. (a) Scale-shaped leaves of Eastern red cedar

(a) Scale-shaped leaves of Eastern red cedar

(b) Needle-shaped leaves of pine (b) Needle-shaped leaves of pine (a) Scale-shaped leaves of Eastern red cedar

Thick cuticle Thick cuticle

Photosynthetic cells

Photosynthetic cells

Tracheids

Tracheids Stomata

(c) Stained cross section of pine needle, showing the thick cuticle

Stomata

Figure 32.10  Conifer leaves.  The leaves of conifers are typically shaped as small scales or long needles, with similar internal structure. ©Steven P. Lynch; b: ©Ken Wagner/Phototake; ©Leecuticle W. Wilcox (c) Staineda:cross section of pine needle, showing thec:thick Concept Check:   In what ways are conifer leaves adapted to resist water loss from their surfaces? 

Broad leaf Broad leaf (a) Genus Gnetum



THE EVOLUTION AND DIVERSITY OF MODERN GYMNOSPERMS AND ANGIOSPERMS 671 (a) Genus Gnetum

Photosynthetic stem

Photosynthetic stem

Tiny scaleReproductive like leaves structures

Tiny scalelike leaves

Reproductive structures Broad leaf

Reproductive structures

(b) Genus Ephedra californica (a) Gnetum (b) Ephedra californica

Photosynthetic stem Reproductive structures Tiny scalelike leaves Leaves

Reproductive structures

Reproductive structures

Figure 32.11  Gnetales.  (a) A tropical plant of the genus Gnetum,

displaying broad leaves and reproductive structures. (b) Ephedra californica growing in deserts of North America, showing minuscule Leaves brown leaves on green, photosynthetic stems and reproductive structures. (c) Welwitschia mirabilis growing in the Namib Desert of southwestern Africa, showing long, wind-shredded leaves and reproductive structures. a: ©Robert & Linda Mitchell; b: ©2004 James M. Andre; c:

(c) Welwitschia mirabilis (b) Ephedra californica

©Wildlife GmbH/Alamy Stock Photo

photosynthesis earlier than deciduous trees, which in spring must replace leaves lost during the previous autumn. Evergreen leaves thus provide an advantage in the short growth season of alpine or highlatitude environments. However, some conifers do lose all their leaves in the autumn. The bald cypress (Taxodium distichum)Reproductive of southern structures U.S. floodplains, tamarack (Larix laricina) of northern bogs, and dawn redwood (Metasequoia glyptostroboides; see Figure 32.6b) are examples of deciduous conifers. 

Namib Desert of southwestern Africa, one of the driest places on Earth (Figure 32.11c). A long taproot anchors a stubby stem that barely emerges from the ground. Two very long leaves grow from the stem but are rapidly shredded by the wind into many strips. The plant is thought to obtain most of its water from coastal fog that accumulates on the leaves, explaining how it can grow and reproduce in such a dry place.

Leaves

Gnetales  The conifer clade also includes the Gnetales, an order of three genera, Gnetum, Ephedra, and Welwitschia, that feature distinctive adaptations. Gnetum is unusual among modern gymnosperms in having broad leaves similar to those of many tropical plants ((c) Figure 32.11amirabilis ). Such leaves maximize light capture in dim forest Welwitschia habitats. More than 30 species of the genus Gnetum occur as vines, shrubs, or trees in tropical Africa or Asia. Ephedra, native to arid regions of the southwestern U.S., has tiny brown scalelike leaves and green, photosynthetic stems (Figure 32.11b). These adaptations help the plant conserve water by preventing water loss that would otherwise occur from the surfaces of larger leaves. Ephedra produces secondary metabolites that aid in plant protection but also affect human physiology. Early settlers of the western U.S. used Ephedra to treat colds and other medical conditions. The modern decongestant drug pseudoephedrine is based on the chemical structure of ephedrine, a substance that was named for and originally obtained from Ephedra. Welwitschia has only one living representative species. Welwitschia mirabilis is a strange-looking plant that grows in the coastal

(c) Welwitschia mirabilis

32.3             T  he Evolution and Diversity of Modern Angiosperms Learning Outcomes: 1. List four flower organs and their functions, and explain how each flower part may have first evolved. 2. Describe how diversification of flowers and fruits enhances seed production and dispersal. 3. Name three major types of angiosperm secondary metabolites, and explain how these affect animals.

More than 124 mya, one extinct gymnosperm group, although it’s unclear which one, gave rise to the angiosperms—the flowering plants. Charles Darwin famously referred to the origin of the flowering plants as “an abominable mystery,” one that has not been fully solved even today. Recent geological studies indicate that the rise of angiosperms may be related to a global climate change that brought more humid conditions, arising from the breakup of the supercontinent Pangaea (see Chapter 26). Angiosperms have

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CHAPTER 32

Stamen

Anther

Stigma

Filament

Style Ovary

Pistil (one or more fused carpels)

Figure 32.12  Angiosperm flowers and fruits.  Citrus plants

display the critical innovations of flowering plants: the flowers and fruits shown here and seed endosperm (not shown). ©Bill Ross/Corbis/Getty

Images

Concept Check:   What other trait occurs widely among angiosperms but rarely among other plants?

Perianth

Petal Sepal

Ovules Receptacle Pedicel

Figure 32.13  Generalized flower structure.  Although flowers are retained many structural and reproductive features from ancestral seed plants, but have also evolved several distinctive traits. Flowers and fruits are two of the defining features of angiosperms (Figure 32.12). These two features do not occur in other modern plants. The term angiosperm is from Greek words meaning enclosed seed, which reflects the presence of seeds within fruits. The seed nutritive material known as endosperm is another defining feature of the flowering plants (see Chapters 31 and 40). Flowers, fruits, and seed endosperm are critical innovations that aid reproduction. Flowers foster seed production, fruits favor seed dispersal, and endosperm food helps embryos within seeds grow into seedlings. In addition, most angiosperms possess distinctive water-conducting cells, known as vessels, which are wider than tracheids and therefore increase the efficiency of water flow through plants. Although similar conducting cells occur in some seedless plants and certain gymnosperms, the vessels of angiosperms are thought to have evolved independently. Although humans obtain wood, medicines, and other valuable products from gymnosperms, we depend even more on the angiosperms. Our food, beverages, and spices—flavored by an amazing variety of secondary metabolites—primarily come from flowering plants. People surround themselves with ornamental flowering plants and decorative items displaying flowers or fruit. We also commonly use flowers and fruit in ceremonies. In this section, we will focus on how flowers, fruits, and secondary metabolites played key roles in angiosperm diversification. We will also examine how features of flowers, fruits, and secondary metabolites are used to classify and identify angiosperm species.

Flower Organs Evolved from Leaflike Structures Flowers are complex reproductive structures that are specialized for the efficient production of pollen and seeds. The sexual reproduction process of angiosperms depends on flowers. As the flowering plants diversified, flowers of varied types evolved as reproductive adaptations to differing environmental conditions. To understand this

diverse in size, shape, and color, many have the parts illustrated here.

process, we can start by considering the basic flower parts and their roles in reproduction. Flower Parts and Their Reproductive Roles  Flowers are produced at stem tips, and may contain four types of organs: sepals, petals, pollen-producing stamens, and ovule-producing carpels (Figure 32.13). These flower organs are supported by tissue known as a receptacle, located at the tip of a flower stalk—a pedicel. The functioning of several genes that control flower organ development explains why carpels are the most central flower organs, why stamens surround carpels, and why petals and sepals are the outermost flower organs (refer back to Figure 20.24). Many flowers produce attractive petals that play a role in pollination, the transfer of pollen among flowers. Sepals of many flowers are green and form the outer layer of flower buds. By contrast, the sepals of other flowers look similar to petals, in which case both sepals and petals are known as tepals. Sepals and petals of a flower are collectively known as the perianth. Most flowers have one or more stamens, the structures that produce and disperse pollen. Most flowers also contain a single or multiple carpels, structures that produce ovules. Some flowers lack perianths, stamens, or carpels. Flowers that possess all four types of flower organs are known as complete flowers, and flowers lacking one or more organ types are known as incomplete flowers. Flowers that contain both stamens and carpels are described as perfect flowers, and flowers lacking either stamens or carpels are imperfect flowers. Flowers also differ in the numbers of organs they produce. Some flowers produce only a single carpel, others display several separate carpels, and many possess several carpels that are fused together into a compound structure. Both single and compound carpels are referred to as a pistil (from the Latin pistillum, meaning pestle) because of a resemblance to the device people use to grind materials to powder in



THE EVOLUTION AND DIVERSITY OF MODERN GYMNOSPERMS AND ANGIOSPERMS 673

female gametophyte (see step 5 of Figure 32.14). The latter is the first step in the development of a characteristic angiosperm nutritive tissue known as endosperm. Fed by the endosperm, the zygote develops into an embryo, and the ovule develops into a seed (see steps 6 and 7 of Figure 32.14). Ovaries (and sometimes additional flower parts) develop into fruits.

a mortar (see Figure 32.13). Only one pistil is present in flowers that have only one carpel and in flowers with fused carpels. By contrast, flowers possessing several separate carpels display multiple pistils. Pistil structure can be divided into three regions having distinct functions. The topmost portion of the pistil, known as the stigma, receives and recognizes pollen of the appropriate species or genotype. The elongate middle portion of the pistil is called the style. The lowermost portion of the pistil is the ovary, which encloses and protects ovules. During the flowering plant life cycle, the stigma allows pollen of the appropriate genetic type to germinate, producing a long pollen tube that grows through the style (see steps 1–4 of Figure 32.14). The pollen tube thereby delivers two sperm cells to ovules. In the distinctive angiosperm process known as double fertilization, one sperm fuses with the egg to form a zygote, and the other sperm fuses with other haploid cells of the

Early Flowers  Fossils of whole plants with recognizable flowers and fruits have been identified from geological deposits that are about 124 million years old, though molecular data and fossil pollen grains suggest that angiosperms may have originated earlier. Flowers were a critical innovation that led to extensive angiosperm diversification. Comparative studies of the structures of modern and fossil flowers suggest how modern stamens and carpels might have arisen. Structural comparisons and molecular data indicate that stamens are homologous to gymnosperm microsporophylls, leaflike structures

3 2

In the anther, the microsporangia produce microspores by meiosis. In the ovule, the megasporangium produces megaspores by meiosis, but only 1 survives.

Pollen grains (n) (immature male gametophytes)

Haploid microspores undergo mitosis to produce immature male gametophytes (pollen). The megaspore undergoes mitosis to produce a few-celled female gametophyte.

4

Meiosis

Microspores Anther

1

Pollen germinates on the stigma, producing a pollen tube. This tube delivers 2 sperm to the ovule.

Mitosis

The flowering plant is the diploid sporophyte generation.

Male gametophyte

Ovule

Stigma Two sperm (n) Megasporangium

Integuments

Megaspore precursor in megasporangium

Sporophyte (2n)

Mitosis

Pollen tube

Surviving megaspore (n)

Style

Gametophyte nuclei Embryo (2n) Egg (n) First endosperm cell (3n)

KEY Female gametophyte

7

The embryo germinates into a seedling, or young sporophyte. Endosperm

Seed coat

Double fertilization Zygote (2n)

6

The zygote matures into an embryo. Endosperm is a food source for embryo or seedling development. Embryo and endosperm are enclosed in a seed coat that develops from the ovule integuments.

5

Haploid Diploid

In a double-fertilization process, one sperm fertilizes the egg, and the other fuses with 2 gametophyte nuclei to form the first endosperm cell.

Pollen tube

Figure 32.14  The life cycle of a flowering plant, illustrated by the genus Polygonum.  Flowering plant life cycles differ in length and in the number of cells and nuclei occurring in the female gametophyte, with the seven cells and eight nuclei of Polygonum being common.

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of this hypothesis is the observation that the carpels of some earlydiverging modern plants are leaflike structures that fold over ovules, with the carpel edges stuck together by secretions (see step 2 of Figure 32.15b). During evolution, this folding resulted in carpels that developed specialized regions and completely enclosed ovules (see steps 3 and 4 of Figure 32.15b). Most modern flowers produce carpels whose edges have fused together into a tube whose lower portion (ovary) encloses ovules. Plant biologists hypothesize that such evolutionary change increased ovule protection, which would improve plant fitness. In contrast, flower sepals and petals have no recognizable homologs in modern gymnosperms. These perianth structures are unique

that produce microspores (young pollen). Early fossil flowers and some modern flowers have broad stamens that are leaf-shaped, with elongated, pollen-producing microsporangia on the stamen surface (Figure 32.15a). During angiosperm evolution, the stamens of most modern plants have narrowed to form filaments, or stalks, that elevate anthers, clusters of microsporangia that produce pollen and then open to release it (see steps 2 and 3 of Figure 32.15a). Filaments and anthers are adaptations that foster pollen dispersal. Plant biologists likewise hypothesize that carpels are homologous to gymnosperm megasporophylls, leaflike structures that bear ovules on their surfaces. In early angiosperms, such leaves folded over ovules, protecting them (see step 1 of Figure 32.15b). In support

2

Early stamens were leaflike, with microsporangia on the surface.

1

Front view

Stamens later became narrower.

Microsporangia

3

Eventually, the microsporangia clustered at stamen tips, forming the anther. The rest of the stamen formed an elongated filament.

Stamen

Anther Filament

Anther

Early stamen

Filament Cross section (a) Stamen evolution

Stigma Front view Ovules

Early carpel

Leaf

Fused seam

Style

Secretion Ovules

Compound pistil with multiple carpels

Pistil composed of one carpel

Ovary

Cross section

1

Carpels evolved from leaflike structures whose edges folded over ovules, protecting them.

2

Early carpels folded over ovules, with the seam closed by sticky secretions.

3

Later carpels were completely closed into a tube, by fusion of tissue.

4

Carpels developed specialized regions (stigma, style, and ovary) to form a pistil.

5

In many modern flowers, several to many carpels fuse to form a compound pistil.

(b) Carpel evolution

Figure 32.15  Hypothetical evolutionary origin of stamens, carpels, and pistils.  Plant biologists test these models by searching for new fossils or generating additional molecular data.



THE EVOLUTION AND DIVERSITY OF MODERN GYMNOSPERMS AND ANGIOSPERMS 675

to angiosperms, so plant biologists have long wondered how sepals and petals arose. Recent analyses indicate that the gene expression patterns of the pollen cones of gymnosperms (see Figure 32.7) share features with flower stamens, as expected, but also with the flower perianth. These data suggest that perianth parts originated from stamen-like structures, by loss of sporangia. The first flowers arose when early stamens, carpels, and perianth parts became aggregated into a single structure.

Separate carpels Perianth

Flowering Plants Diversified into Several Lineages, Including Monocots and Eudicots

Nonfunctional stamen

Figure 32.16 presents our current understanding of the relation-

Eudicots

Monocots

Magnoliids and relatives

Star anise and relatives

Water lilies

Amborella

Extinct gymnosperm ancestor

ships among modern angiosperm groups. According to genesequencing studies, the earliest-diverging modern angiosperms are represented by a single species called Amborella trichopoda, a shrub that lives in cloud forests on the South Pacific island of New Caledonia. The flowers of A. trichopoda display hypothesized ancient features. For example, the fairly small flowers have stamens with broad filaments and several separate carpels ( Figure 32.17). A. trichopoda also lacks vessels in the water-conducting tissues, but typical angiosperm vessels are present in later-diverging groups of

Figure 32.16  A phylogenetic tree showing the major modern

angiosperm lineages and examples of whole-genome duplication events.  In a whole-genome duplication event, the genome size doubles. Molecular data indicate that the size of plant genomes underwent major increases at different time points and in particular lineages (only some of which are indicated here). For example, a whole genome duplication occurred before the divergence of Amborella (blue bar), and the genome size tripled (a whole-genome triplication) during the evolution of eudicots (green bar). Plant evolutionary biologists speculate that these duplication and triplication events strongly influenced the diversification of modern angiosperms.

Figure 32.17  Amborella trichopoda flower, similar to a

hypothesized early flower.  This small flower is only about 3–4 mm in diameter. It displays several central, greenish carpels; nonfunctional stamens; and a pink perianth of tepals. This plant species also produces flowers that lack carpels but have many functional stamens. ©Sangtae Kim, Ph.D.

angiosperms, including water lilies, the star anise plant, and other close relatives (see Figure 32.16). Magnoliids, represented by the genus Magnolia, are the next-diverging group. Magnoliids are closely related to two very large and diverse angiosperm lineages: the monocots and the eudicots. Monocots and eudicots are named for differences in the number of embryonic leaves called cotyledons. Monocot embryos possess one cotyledon, whereas eudicots possess two cotyledons. Monocots differ from eudicots in several additional ways (look ahead to Table 36.1). For example, monocots typically have flowers with parts numbering three or some multiple of three (Figure 32.18a). In contrast, eudicot flower parts often occur in fours, fives, or a multiple of four or five (Figure 32.18b).

Core Concept: Evolution Whole-Genome Duplications Influenced the Evolution of Flowering Plants During evolution, whole-genome duplication has occurred in a wide variety of eukaryotes and has happened on multiple occasions during the evolutionary history of plants. For example, a whole-genome duplication event occurred early in the evolution of seed plants (see the red bar in Figure 32.1). Additional examples include duplication of the entire plant genome before the divergence of Amborella (see the blue bar in Figure 32.16) and during eudicot diversification (green bar in Figure 32.16). After such whole-genome duplications, a plant’s genome operates as a diploid system. Although genome sizes vary, the number of genes estimated for plants whose genomes have been studied is about 25,000. Whole-genome duplication has the potential to affect species’ evolutionary pathways because it offers the opportunity for many genes to diverge, forming gene families.

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Figure 32.18  One characteristic difference between monocots and eudicots: flower part number.  (a) Flowers and buds of a lily (genus Lilium), displaying six tepals. (b) A flower and buds of apple (genus Malus), showing five flower petals. Green sepals are visible around the pink buds. a: ©Dudakova Elena/Shutterstock; b: ©Ed Reschke/Getty Images

(a) A monocot with six tepals

Flower Diversification Has Fostered Efficient Seed Production During the diversification of flowering plants, flower evolution has involved several types of changes that foster the transfer of pollen from one plant to another. Effective pollination is essential to efficient seed production because it minimizes the amount of energy plants must expend to accomplish sexual reproduction. Fusion of flower organs, clustering of flowers into groups, and reduction in size of the perianth are some examples of changes leading to effective pollination.

(a) Zinnia flower and butterfly

(b) A eudicot with five petals

Many flowers have fused petals that form floral tubes. Such tubes tend to accumulate sugar-rich nectar that provides a reward for pollinators, animals that transfer pollen among plants. The diameters of floral tubes vary among flowers and are evolutionarily tuned to the feeding structures of diverse animals, which range from the narrow tongues of butterflies to the wider bills of nectarfeeding birds (Figure 32.19). Nectar-feeding bats stick their heads into even larger tubular flowers to lap up nectar with their tongues. Orchids provide another example of ways in which flower parts have become fused; stamens and carpels are fused together into a single reproductive column that is surrounded by attractive tepals

(b) Hibiscus flower and hummingbird

(c) Saguaro cactus flower and bat

Figure 32.19  Flowers whose perianths form nectar-containing floral tubes of different widths that accommodate different pollinators. 

(a) This zinnia is composed of an outer rim of showy flowers and a central disc of narrow tubular flowers that produce nectar. Butterflies, but not other pollinators, are able to reach the nectar by means of their narrow tongues. (b) The hibiscus flower produces nectar in a floral tube whose diameter corresponds to the dimensions of a hummingbird bill. (c) The flower of a saguaro cactus (Carnegiea gigantea) forms a floral tube that is wide enough for nectar-feeding bats to get their heads inside. The cactus flower has been drawn here as if it were transparent, to illustrate bat pollination.



THE EVOLUTION AND DIVERSITY OF MODERN GYMNOSPERMS AND ANGIOSPERMS 677

(Figure 32.20a). This arrangement of flower organs fosters orchid pollination by particular insects and is a distinctive feature of the orchid family.  Many plants produce inflorescences, groups of flowers tightly clustered together, which occur in several types. The sunflower family features a type of inflorescence in which many small flowers are

Tepals

Fused pistil and stamens Tepals (a) An orchid flower with fused pistil and stamens

clustered into a head (Figure 32.20b). The flowers at the center of a sunflower head function in reproduction and lack showy petals, but flowers at the rim have showy petals that attract pollinators. Flower heads allow pollinators to transfer pollen among a large number of flowers at the same time. The grass family features flowers with few or no perianths, which explains why grass flowers are not showy (Figure 32.20c). This adaptation fosters pollination by wind, since petals would only get in the way of such pollen transfer.

Diverse Types of Fruits Function in Seed Dispersal Fruits are structures that develop from ovary walls and function in the dispersal of enclosed seeds. Seed dispersal helps to prevent seedlings from competing with their larger parents for scarce resources such as water and light. Dispersal of seeds also allows plants to colonize new habitats. Diverse fruit types illustrate the many ways in which plants have become adapted for effective seed dispersal. Like flower types, fruit types are useful in classifying and identifying angiosperms. These are just a few examples of the diverse mechanisms that flowering plants use to disperse their seeds.  ∙∙ Many mature angiosperm fruits, such as cherries, grapes, and lemons, are attractively colored, soft, juicy, and tasty (Figure 32.21a–c). Such fruits are adapted to attract animals that consume the fruits, digest the outer portion as food, and eliminate the seeds, thereby dispersing them. Hard seed coats prevent such seeds from being destroyed by the animal’s digestive system. 

(b) A sunflower plant showing inflorescence

∙∙ Strawberries are aggregate fruits, structures consisting of many fruits that all develop from a single flower having multiple pistils (Figure 32.21d). The ovaries of these pistils develop into tiny, single-seeded yellow fruits on a strawberry surface; the fleshy, red, sweet portion of a strawberry develops from a flower receptacle. Aggregate fruits allow a single animal consumer, such as a bird, to disperse many seeds at the same time.  ∙∙ Pineapples (Figure 32.21e) are juicy multiple fruits that develop when many ovaries of an inflorescence fuse together. Such multiple fruits attract relatively large animals that have the ability to disperse seeds for long distances.

(c) Grass flowers lacking showy perianth

Figure 32.20  Evolutionary changes in flower structure.  (a) An

orchid of the genus Cattleya has fused stamens and pistil, and six tepals, one of which is specialized to form a lower lip. (b) An inflorescence (head) of sunflower (genus Helianthus). This inflorescence includes a rim of flowers with conspicuous petals that attract pollinators and an inner disc of flowers that lack attractive perianths. (c) Grass flowers of the grass genus Triticum lack a showy perianth. a: ©Neil Joy/Science Source; b: ©Pixtal/age fotostock; c: ©blickwinkel/Alamy

∙∙ The plant family informally known as legumes is named for its distinctive fruits, dry pods that open down both sides when seeds are mature, thereby releasing them (Figure 32.21f).  ∙∙ Nuts and grains are additional examples of dry fruits. Grains are the characteristic single-seeded fruits of cereal grasses such as rice, corn (maize), barley, and wheat.  ∙∙ Coconut fruits are adapted for dispersal in ocean currents and can float for months before being cast ashore (Figure 32.21g). 

Stock Photo

∙∙ Maple trees produce dry and thus lightweight fruits having wings, features that foster effective wind dispersal (Figure 32.21h). 

Concept Check:   What advantage does the nonshowy perianth of grass flowers provide?

∙∙ Other plants produce dry fruits with surface burrs that attach to animal fur.

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Angiosperms Produce Diverse Secondary Metabolites That Play Important Roles in Plant Structure, Reproduction, and Protection

(a) A fleshy fruit (cherry)

(c) A fleshy fruit (lemon)

(e) A multiple fruit (pineapple)

(b) A fleshy berry fruit (grape)

(d) An aggregate fruit (strawberry)

Secondary metabolism involves the synthesis of organic compounds that are not essential for cell structure and growth in organisms but aid their survival and reproduction. These molecules, called secondary metabolites, are produced by various prokaryotes, protists, fungi, some animals, and all plants, but are most diverse in the angiosperms. About 100,000 different types of secondary metabolites are known, most of which are produced by flowering plants. Because secondary metabolites play essential roles in plant structure, reproduction, and protection, diversification of these compounds has influenced flowering plant evolution. Three major classes of plant secondary metabolites occur: (1) terpenes and terpenoids; (2) phenolics, which include flavonoids and related compounds; and (3) alkaloids (Figure 32.22). About 25,000 types of plant terpenes and terpenoids are constructed from different arrangements of the simple hydrocarbon gas isoprene. Taxol, whose use in the treatment of cancer was noted earlier, is a terpene, as are citronella and a variety of other compounds that repel insects. Rubber, turpentine, rosin, and amber are complex terpenoids that likewise serve important roles in plant biology as well as having useful human applications. Phenolic compounds are responsible for some flower and fruit colors as well as the distinctive flavors of cinnamon, nutmeg, ginger, cloves, chilies, and vanilla. Phenolics absorb UV radiation, thereby preventing damage to a plant's DNA. They also help to defend plants against insects and disease microbes. Some phenolic compounds found in tea, red wine, grape juice, and blueberries are antioxidants that detoxify free radicals, thereby preventing cellular damage. Alkaloids are nitrogen-containing secondary metabolites that often ave potent effects on the animal nervous system. Plants produce at least 12,000 types of alkaloids, and certain species produce many alkaloids. Caffeine, nicotine, morphine, ephedrine, cocaine, and codeine are examples of alkaloids that influence the physiology and behavior of humans and are thus of societal concern. Like flower and fruit structures, secondary metabolites are useful in distinguishing among Earth’s hundreds of thousands of flowering plant species.

(f) Legumes with dry pods (peas)

Figure 32.21  Representative fruit types.  (a–c) The cherry,

grape, and lemon are fleshy fruits adapted to attract animals that consume the fruits and excrete the seeds. (d) Strawberry is an aggregate fruit, consisting of many tiny, single-seeded fruits produced by a single flower. The fruits are embedded in the surface of a fleshy receptacle that is adapted to attract animal seeddispersal agents. (e) Pineapple is a large multiple fruit formed by the aggregation of smaller fruits, each produced by one of the flowers in an inflorescence. (f) Peas produce legumes, fruits that open on two sides to release seeds. (g) Coconut fruits possess a fibrous husk that aids dispersal in water. (h) Maple trees produce dry fruits with wings adapted for wind dispersal. a–e: ©Lee W. Wilcox; f: ©Gloomerique/Getty Images; g: ©foodanddrinkphotos co/age fotostock; h:

(g) Fruit with husk (coconut)

(h) A dry, winged fruit (maple)

©blickwinkel/Alamy Stock Photo

compound.



THE EVOLUTION AND DIVERSITY OF MODERN GYMNOSPERMS AND ANGIOSPERMS 679 Terpene CH3 C

Alkaloid

H C

CH3 C

CH2 H2C

H C

CH2 H2C

CH3 C

H

O

C

H3C

CH2 H2C

Natural rubber (complex terpene)

O

N

N

CH3 H

N

N

CH3 Caffeine

(a) Natural rubber produced by Hevea brasiliensis is an example of a complex terpene. Phenolic

(c) Caffeine produced by Coffea arabica is an example of an alkaloid.

HO H N

O

O

Capsaicin

Figure 32.22  Major types of plant secondary metabolites.  Note that the structures of these plant secondary metabolites differs from that of the primary compounds produced by all cells; primary compounds include sugars and amino acids, described in Chapter 3. The production by plants of terpenes, phenolics, and alkaloids helps to explain how plants survive and reproduce and why plants are useful to humans in so many ways. a: ©Suphatthra China/Shutterstock; b: ©Jonathan Buckley/

(b) Capsaicin extracted from capsicum peppers is an example of a phenolic compound.

GAP Photo/Getty Images; c: ©Science Photo Library/Alamy Stock Photo

Alkaloid

Core Skill: Process of Science O

CH3

N Feature Investigation  | Hillig and Mahlberg Analyzed Secondary Metabolites to Explore N H3C

H

O

N

N

Species Diversification in the Genus Cannabis

The genus Cannabis has long been a source of hemp fiber used for CH3 ropes and fabric. People have also used Cannabis (also known as Caffeine marijuana) in traditional medicine and as a hallucinogenic drug. Cannabis produces THC (tetrahydrocannabinol), a type of alkaloid called a cannabinoid. THC and other cannabinoids are produced in glandular hairs that cover most of the Cannabis plant’s surface but are particularly rich produced in leaves by located the isflowers. THCofmim(c) Caffeine Coffeanear arabica an example an alkaloid. ics compounds known as endocannabinoids, which are naturally produced and act in the animal brain and elsewhere in the body. THC affects humans by binding to receptor proteins in plasma membranes in the same way as natural endocannabinoids do. People sometimes use cannabis to ease pain and other medical conditions. Because humans have subjected cultivated Cannabis plants to artificial selection for so long, plant biologists have been uncertain how cultivated Cannabis species are related to those in the wild. In the past, plants cultivated for drug production were often identified as Cannabis indica, whereas those grown for hemp were typically known as Cannabis sativa. However, these species are difficult to distinguish on the basis of structural features, and the relevance of these names to wild cannabis was unknown. At the same time, species identification has become important for biodiversity studies, agriculture, and law enforcement. For these reasons, plant biologists Karl Hillig and Paul Mahlberg hypothesized that ratios of THC to another cannabinoid known as CBD

(cannabidiol) might aid in defining Cannabis species and identifying plant samples at the species level, as shown in Figure 32.23. To test their hypothesis, the investigators began by collecting Cannabis fruits (containing seeds) from nearly a hundred diverse locations around the world. As shown in step 1 of Figure 32.23, they used the seeds to grow new plants under uniform conditions in a greenhouse. The investigators next extracted cannabinoids, analyzed them by means of gas chromatography (a laboratory technique used to identify components of a mixture), and determined the ratios of THC to CBD. The results, published in 2004, suggested that the wild and cultivated Cannabis samples evaluated in this study could be classified into distinct species: C. sativa, displaying relatively low THC levels, and C. indica, having relatively high THC levels. More recent genetic studies suggest that the genus Cannabis is even more diverse than previously thought. Experimental Questions 1. CoreSKILL » Designing an experiment requires a plan to achieve an adequate number of samples, in order to allow statistical analysis. Hillig and Mahlburg obtained nearly a hundred Cannabis fruit samples from around the world. Why were so many samples needed?  2. Why did Hillig and Mahlberg collect samples from the leaves growing nearest the flowers? 

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Figure 32.23  Hillig and Mahlberg’s analysis of secondary metabolites in the genus Cannabis. (top inset): ©Phil Schermeister/National Geographic/ Getty Images; (middle inset): ©Matthew Kellett/Alamy Stock Photo

GOAL To determine if cannabinoids aid in distinguishing Cannabis species. KEY MATERIALS Cannabis fruits obtained from nearly 100 different worldwide sources. Experimental level

Conceptual level

1

Grow multiple Cannabis plants from seeds under standard conditions in a greenhouse.

Eliminates differential environmental effects on cannabinoid content.

2

Extract cannabinoids from leaves surrounding flowers.

Extracts were made from tissues richest in cannabinoids; this reduces the chance that cannabinoids present in lower levels would be missed.

3

Analyze cannabinoids by gas chromatography. Determine ratios of THC (tetrahydrocannabinol) to CBD (cannabidiol) in about 200 Cannabis plants.

CBD THC

n-eicosane CBDV THCV

Previous data suggested that ratios of THC to CBD might be different in separate species.

R

OH OH Cannabidiol (CBD) (R = C5H11)

CBC CBG

CBGM Time

R O Tetrahydrocannabinol (THC) (R = C5H11 Δ9)

THE DATA Number of isolates

4

OH

30

C. sativa

C. indica

20

Cannabis plants isolated from diverse sources worldwide formed 2 groups—those having relatively high THC to CBD ratios and those having lower THC to CBD ratios. Plants having low THC to CBD ratios, often used as hemp fiber sources, corresponded to the species C. sativa.

10 0 –1.5 –1.0 –0.5 0.0 0.5 1.0

Plants having high THC to CBD ratios, often used as drug sources, corresponded to the species C. indica. 1.5

2.0 2.5 3.0

log10(THC/CBD)

5

CONCLUSION Differing cannabinoid ratios support a concept of 2 Cannabis species.

6

SOURCE Hillig, K.W., and Mahlberg, P.G. 2004. A chemotaxonomic analysis of cannabinoid variation in Cannabis (Cannabaceae). American Journal of Botany 91: 966–975. ©2004 Botanical Society of America. All rights reserved. Used with permission.



THE EVOLUTION AND DIVERSITY OF MODERN GYMNOSPERMS AND ANGIOSPERMS 681

BIO TIPS

THE QUESTION   The study by Hillig and Mahlburg revealed that samples of Cannabis plants from diverse sources varied in their ratios of alkaloids known as cannabinoids. Why did the investigators grow plants from seeds in a greenhouse before conducting their analyses of cannabinoid content? T OPIC  What topic in biology does this question address? The topic is the use of secondary metabolites to differentiate species of plants. More specifically, the question addresses the relative effects of genes and environment on plants’ production of secondary metabolites. I NFORMATION  What information do you know based on the question and your understanding of the topic?  You know from earlier chapters of this textbook that the traits organisms express depend on both genes and environment and that genetically determined traits are used for classifying organisms. In this chapter, you have learned that plants, and flowering plants in particular, produce diverse types of secondary metabolites that play important roles in reproduction and protection. Consequently, you might expect that the ratios of cannabinoids in Cannabis plants reflect environmental conditions, genetic composition, or both. P ROBLEM-SOLVING  S TRATEGY  Design an experiment.  Consider how you might design an experiment to determine how cannabinoid ratios differ among individual plants grown from seeds collected from different sources. Because the seeds came from different sources, they may be from different species of Cannabis, defined by genetic characteristics. In your experiment, you would have to control for possible environmental effects, so that such effects would not mask any differences due to genetics. ANSWER  Growing experimental plants from seeds in a greenhouse under the same (standard) conditions is a way to minimize variation in cannabinoid ratios due to environmental effects. During their development, all of the experimental plants will experience the same conditions of light, moisture, soil minerals, day length, and other factors that affect plant growth and the production of secondary metabolites. Under standardized growth conditions, observed differences in cannabinoid ratios will reflect genetic variation that can be used to classify Cannabis plants into species, as Hillig and Mahlburg were able to do.

32.4     T  he Role of Coevolution in Angiosperm Diversification Learning Outcomes: 1. Explain the concept of coevolution. 2. List examples of coevolution between plants and animal pollinators. 3. List examples of coevolution between plants and animal seed dispersal agents.

The preceding section described how flowering plants are commonly associated with animals in ways that strongly influence plant evolution. Likewise, plants have influenced animal evolution in a diversity-generating process known as coevolution, which is the process by which two or more species of organisms influence each other’s evolutionary pathway. During the diversification of flowering plants, coevolution with animals has been a major evolutionary factor. For example, the diversification of bees about 123 million years ago correlates with the diversification of the eudicots, which today make up three-quarters of all angiosperm species. Coevolution is reflected in the diverse forms of most flowers and many fruits and the many ways that plants accomplish effective pollen and seed dispersal. Human attraction to flowers and fruit also is an example of coevolution. This is because human sensory systems are similar to those of various animals that have coevolved with angiosperms.

Pollination Coevolution Influences the Diversification of Flowers and Animals Animal pollinators transfer pollen from the anthers of one flower to the stigmas of other flowers of the same species. Pollinators thereby foster genetic variation and enhance the potential for evolutionary change among plants. Insects, birds, bats, and other pollinators learn the characteristics of particular flowers, visiting them preferentially. This animal behavior, known as constancy or fidelity, increases the odds that a flower stigma will receive pollen of the appropriate species. Animal pollinators increase the precision of pollen transfer, which reduces the amount of pollen that plants must produce to achieve pollination. By contrast, windpollinated plants must produce much larger amounts of pollen because windblown pollen reaches appropriate flowers by chance. Flowers attract the most appropriate pollinators by means of attractive colors, odors, shapes, and sizes. Secondary metabolites influence the colors and odors of many flowers. Flavonoids, for example, color many blue, purple, or pink flowers. More than 700 types of chemical compounds contribute to floral odors. Most flowers reward pollinators with food: sugar-rich nectar, lipid- and protein-rich pollen, or both. In this way, flowering plants provide an important biological service, providing food for many types of animals. However, some flowers “trick” pollinators into visiting or trap pollinators temporarily, thereby achieving pollination without actually rewarding the pollinator. Examples include flowers that look and smell like dead meat, thereby attracting flies, which are fooled but accomplish pollination anyway. Although many flowers are pollinated by a variety of animals, others have flowers that have become specialized for particular pollinators, and vice versa. These specializations, which have resulted from coevolution, are known as pollination syndromes (Table 32.2). For example, odorless red flowers, such as those of hibiscus (see Figure 32.19b), are attractive to birds, which can see the color red but have a poor sense of smell. By contrast, bees are not typically attracted to red flowers because bee vision does not extend to the red end of the visible light spectrum. Rather, bees are attracted to blue, purple, yellow, and white flowers having sweet odors. If you are allergic to bee stings or just want to reduce the possibility of being stung, avoid dressing in bee-attracting flower colors and wearing flowery fragrances when in locales frequented by bees.

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Table 32.2

Pollination Syndromes

Animal features

Coevolved flower features

Bees Color vision includes ultraviolet (UV), not red

Often blue, purple, yellow, white (not red) colors

Good sense of smell

Fragrant

Require nectar and pollen

Nectar and abundant pollen

Butterflies Good color vision

Blue, purple, deep pink, orange, red colors

Sense odors with feet

Light floral scent

Need landing place

Landing place

Feed with long, tubular tongue

Nectar in deep, narrow floral tubes

Moths Active at night

Open at night; white or bright colors

Good sense of smell

Heavy, musky odors

Feed with long, thin tongue

Nectar in deep, narrow floral tubes

Birds Color vision, includes red

Often colored red

Often require perch

Strong, damage-resistant structure

Poor sense of smell

No fragrance

Feed in daytime

Open in daytime

High nectar requirement

Copious nectar in floral tubes

Hover (hummingbirds)

Pendulous (dangling) flowers

Bats Color blind

Light, reflective colors

Good sense of smell

Strong odors

Active at night

Open at night

High food requirements

Copious nectar and pollen provided

Navigate by echolocation

Pendulous or borne on tree trunks

Core Skill: Modeling  The goal of this modeling challenge is to propose a model that shows a series of steps in the process by which a pollinator accom                   plishes pollination. Modeling Challenge: Table 32.2 lists pollination syndromes, features of animal pollinators and flowers that have coevolved. Pick one of these pollination syndromes and propose a model that shows a series of steps in the pollination process. The model should begin with the pollinator close to, but not touching the flower, and should end with pollination, pollen attachment to the flower stigma. Your model should answer two key questions: Why does the pollinator visit the flower? How does the pollinator deliver pollen to the stigma?

Pollination syndromes are of practical importance in agriculture and in conservation biology. Fruit growers often import colonies of bees to pollinate flowers of fruit crops and thereby increase

Figure 32.24  Brighamia insignis, a plant endangered by the

loss of its pollinator.  The pollinator that coevolved with B. insignis has become extinct, with the result that the plant is unable to produce seeds unless artificially pollinated by humans. ©Garden World Images Ltd/

Alamy Stock Photo

Concept Check:   What kind of animal likely pollinated B. insignis?

crop yields. In recent years, widespread die-offs of bee colonies have become an environmental and agricultural concern. When bee pollinators are not available, growers cannot produce some fruit crops. Some plants have become so specialized to particular pollinators that if the pollinator becomes extinct, the plant becomes endangered. An example is the Hawaiian cliff-dwelling Brighamia insignis (Figure 32.24), whose presumed moth pollinator has become extinct. Humans that hand-pollinate B. insignis are all that stand between this plant and extinction.

Seed-Dispersal Coevolution Influences the Characteristics of Fruits and Animals As in the case of pollination, coevolution between plants and their animal seed-dispersal agents has influenced characteristics of both fruits and the seed-dispersing animals. In addition, flowering plant fruits provide food for animals, an important biological service. For example, many of the plants of temperate forests produce fruits that are attractive to resident birds. Such juicy, sweet fruits have small seeds that readily pass through bird guts. Many plants signal fruit ripeness by undergoing color changes from unripe green fruits to red, orange, yellow, blue, or black (Figure 32.25). Because birds have good color vision, they are able to detect the presence of ripe fruits and consume them before the fruits drop from plants and rot.  Apples, strawberries, cherries, blueberries, and blackberries are examples of fruits whose seed dispersal adaptations have made them attractive food for humans. By contrast, the lipid-rich fruits of Virginia creeper (Parthenocissus quinquefolia) and some other autumn-fruiting plants energize migratory birds but are not tasty to



THE EVOLUTION AND DIVERSITY OF MODERN GYMNOSPERMS AND ANGIOSPERMS 683

Grain Immature ear of teosinte

Mature, shattered ear of teosinte

Nonshattering ear of Z. mays, subspecies mays.

Figure 32.25  Fruits attractive to animal seed-dispersal agents.  Color and odor signals alert coevolved animal species that fruits are ripe, thus favoring the dispersal of mature seeds. ©Beng & Lundberg/naturepl.com

humans. The Virginia creeper’s leaves often turn fall colors earlier than surrounding plants, thereby signaling the availability of nutritious, ripe fruit to high-flying birds. Such lipid-rich fruits must be consumed promptly because they rot easily, in which case seed dispersal cannot occur.

32.5         H  uman Influences on Angiosperm Diversification Learning Outcome:

1. CoreSKILL » Describe how molecular information about modern crop plants is used to infer their evolutionary origin by domestication.

By means of the process known as domestication, which involves artificial selection for traits desirable to humans, ancient humans transformed wild plant species into new crop species. Cultivated bread wheat (Triticum aestivum) was probably among the earliest food crops, having originated more than 8,000 years ago, in what is now southeastern Turkey and northern Syria. Bread wheat originated by a series of steps that included hybridization and whole-genome duplication from wild ancestors (Triticum boeoticum and Triticum dicoccoides).  Among the earliest changes that occurred during wheat domestication was the loss of shattering, the process by which ears of wild grain crops break apart and disperse their grains. A mutation probably caused the ears of some wheat plants to remain intact, a trait that is disadvantageous in nature but beneficial to humans. Nonshattering ears would have been easier for humans to harvest than normal ears. Early farmers probably selected seed stock from plants having nonshattering ears and other favorable traits such as larger grains. These ancient artificial selection processes, together with modern breeding efforts, explain why cultivated wheat differs from its wild relatives in shattering and other properties. The accumulation of these trait differences is why cultivated and wild wheat plants are classified as different species. About 9,000 years ago, people living in what is now Mexico domesticated one type of the native grass known as teosinte

Figure 32.26  Ears and grains of modern corn and its ancestor, teosinte.  This illustration shows that domesticated corn ears are much larger than those of the ancestral grass teosinte. In addition, corn grains are softer and more edible than the grains of teosinte, which are enclosed in a hard casing. Core Skill: Science and Society  The domestication of corn from a wild grass into one of the world’s largest production crops is an amazing feat of artificial selection.

(formally, Zea mays subspecies parviglumis). The domestication process produced a new species, Zea mays subspecies mays, commonly known as corn or maize. The evidence for this pivotal event includes ancient ears that were larger than wild ones and distinctive fossil pollen. Modern ears of corn are much larger than those of teosinte, with many more rows and larger and softer corn grains, and modern corn ears do not shatter, as do those of ancestral teosinte (Figure 32.26). These and other trait changes reflect artificial selection accomplished by humans. An analysis of the corn genome, reported in 2005 by Canadian biologist Stephen Wright, American evolutionary biologist Brandon Gaut, and coworkers, suggests that 1,200 corn genes have been affected by artificial selection. Molecular analyses indicate that domesticated rice (Oryza sativa) originated from ancestral wild species of grasses (Oryza nivara and/ or Oryza rifipogon). As in the cases of wheat and corn, domestication of rice involved loss of ear shattering. Researchers have identified a mutation in domesticated strains of rice that alters the amino acid sequence of a protein that regulates shattering. Ancient humans might have unconsciously selected for this mutation while gathering rice from wild populations, because the mutants would not so easily have shed grains during the harvesting process. Eventually, the nonshattering mutant became a widely planted crop throughout Asia, and today it is the food staple for millions of people. Although humans generated these and other plant species, modern humans have also caused the extinction of plants as the result of habitat destruction and other threats to species. Protecting biodiversity will continue to challenge humans as populations and demands on the Earth’s resources increase. Plant biologists are working to identify one or more molecular sequencing tools for use in barcoding plants, a process that is widely used to identify and catalog animals. The ability to bar code plants, which would enable researchers to quickly analyze the DNA of a species and identify it based on existing barcodes, is important to organizations like CITES and others that monitor international trade in endangered plant species.

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Summary of Key Concepts 32.1  Overview of Seed Plant Diversity ∙∙ Modern seed plants include three phyla of gymnosperms and the angiosperms (Figure 32.1, Table 32.1).

32.2 T  he Evolution and Diversity of Modern Gymnosperms ∙∙ Gymnosperms are plants that produce exposed seeds rather than seeds enclosed in fruits. Gymnosperms originated from seedless woody plants known as progymnosperms (Figure 32.2). ∙∙ The modern gymnosperms include three phyla: cycads, Ginkgo biloba, and the conifers (which include the Gnetales). Nearly 300 species of cycads primarily live in tropical and subtropical regions. Features of cycads include palmlike leaves, nonwoody stems, coralloid roots with cyanobacterial endosymbionts, toxins, and large conelike seed-producing structures (Figures 32.3, 32.4). ∙∙ The tree Ginkgo biloba is the last surviving species of a phylum that was diverse during the Mesozoic, also known as the Age of Dinosaurs. Individual trees produce ovules and seeds or pollen, with a sex chromosome system much like that of humans (Figure 32.5). ∙∙ Conifers have been widespread and diverse members of plant communities for the past 300 million years and are important sources of wood and paper pulp for humans. Reproduction involves simple pollen cones and complex ovule-producing cones. Many conifers display adaptations that aid survival in cold climates. Three genera of Gnetales display distinctive adaptations (Figures 32.6, 32.7, 32.8, 32.9, 32.10, 32.11).

effectiveness of pollination, which enhances seed production (Figures 32.19, 32.20). ∙∙ Fruits are structures that enclose seeds and aid in their dispersal. Fruits occur in many types that foster seed dispersal (Figure 32.21). ∙∙ Angiosperms produce three main groups of secondary metabolites: (1) terpenes and terpenoids; (2) phenolics, which include flavonoids and related compounds; and (3) alkaloids, which play essential roles in plant structure, reproduction, and defense, respectively (Figure 32.22). ∙∙ Hillig and Mahlberg demonstrated the use of particular secondary metabolites in distinguishing species of the societally important genus Cannabis (Figure 32.23).

32.4 T  he Role of Coevolution in Angiosperm Diversification ∙∙ Coevolutionary interactions between flowering plants and animals that serve as pollen- and seed-dispersal agents played a powerful role in the diversification of both angiosperms and animals (Table 32.2, Figures 32.24, 32.25). ∙∙ Human appreciation of flowers and fruits is based on sensory systems similar to those present in the animals with which angiosperms coevolved.

32.5 H  uman Influences on Angiosperm Diversification ∙∙ Humans have produced new crop species by domesticating wild plants. The process of domestication involved artificial selection for traits such as nonshattering ears of wheat, corn, and rice (Figure 32.26).

32.3 T  he Evolution and Diversity of Modern Angiosperms ∙∙ Angiosperms inherited seeds, the capacity to produce wood, and other features from gymnosperm ancestors, but display distinctive features not found in other land plants, including flowers and fruits (Figure 32.12). ∙∙ Flowers foster seed production and are adapted in various ways that aid pollination. The major flower organs are sepals and petals (or tepals), stamens, and carpels, which may occur singly or in fused groups. Both single carpels and compound carpels take a distinctive shape known as a pistil, which displays regions of specialized function. The stigma is a receptive surface for pollen, pollen tubes grow through the style, and ovules develop within the ovary. Pollination is the transfer of pollen from a stamen to a pistil, a process distinct from fertilization. Double fertilization, the production of both a zygote and a nutritive tissue known as endosperm, is a critical innovation of angiosperms. This process allows ovules to develop into seeds containing embryos and endosperm, and ovaries to develop into fruits. Stamens and carpels may have evolved from leaflike structures bearing sporangia (Figures 32.13, 32.14, 32.15). ∙∙ Whole-genome duplications have influenced plant evolution, particularly the diversification of the angiosperms. The two largest and most diverse lineages of flowering plants are the monocots and eudicots (Figures 32.16, 32.17, 32.18). ∙∙ Flower diversification involved evolutionary changes such as fusion of petals, clustering of flowers into inflorescences, and reduction in size of the perianth. These changes improve the

Assess & Discuss Test Yourself 1. What feature(s) must be present for a plant to produce wood? a. a type of conducting system in which vascular bundles occur in a ring around pith b. a eustele c. a vascular cambium d. all of the above e. none of the above 2. Which sequence of critical innovations reflects the order of their appearance in time? a. embryos, vascular tissue, wood, seeds, flowers b. vascular tissue, embryos, wood, flowers, seeds c. vascular tissue, wood, seeds, embryos, flowers d. wood, seeds, embryos, flowers, vascular tissue e. seeds, vascular tissue, wood, embryos, flowers 3. How long have ancient and modern groups of gymnosperms been important members of plant communities? a. 10,000 years, since the dawn of agriculture b. 100,000 years c. 300,000 years d. 65 million years, since the Cretaceous-Paleogene (K/T) event e. 300 million years, since the Coal Age



THE EVOLUTION AND DIVERSITY OF MODERN GYMNOSPERMS AND ANGIOSPERMS 685

4. What similar features do gymnosperms and angiosperms possess that differ from other modern vascular plants? a. Gymnosperms and angiosperms both produce flagellate sperm. b. Gymnosperms and angiosperms both produce flowers. c. Gymnosperms and angiosperms both have tracheids, but not vessels, in their vascular tissues. d. Gymnosperms and angiosperms both produce fruits. e. None of the above statements is true. 5. Which part of a flower receives pollen transported by the wind or a pollinating animal? a. perianth d. pedicel b. stigma e. ovary c. filament 6. The primary function of a fruit is to a. provide food for the developing seed. b. provide food for the developing seedling. c. foster pollen dispersal. d. foster seed dispersal. e. None of the above identifies the primary function of a fruit. 7. Flowers have diversified with regard to a. color. b. number of flower parts. c. fusion of organs. d. aggregation into inflorescences. e. all of the above. 8. Plants of the genus Fuchsia produce deep pink to red flowers that dangle from plants, produce nectar in floral tubes, and have no scent. Based on these features, which animal is most likely to be a coevolved pollinator of these plants? a. bee b. bat c. hummingbird d. butterfly e. moth

9. Which type of plant secondary metabolite is best known for the antioxidant properties of human foods such as blueberries, tea, and grape juice? a. alkaloids b. cannabinoids c. carotenoids d. phenolics e. terpenoids 10. What feature(s) of domesticated grain crops might differ from those of wild ancestors? a. the degree to which ears shatter, allowing for seed dispersal b. grain size c. number of grains per ear d. softness and edibility of grains e. all of the above

Conceptual Questions 1. Make a diagram that shows how plant biologists think flowers arose.  2. Explain why fruits such as apples, strawberries, and cherries are attractive, nutritious, and harmless foods for humans.    3. 

Core Concept: Structure and Function  Compare the structures of an apple flower and a sunflower, explaining how they relate to differences in pollination and seed dispersal. 

Collaborative Questions 1. Where in the world would you have to travel to find wild plants representing all of the gymnosperm phyla, including the three types of Gnetales? 2. How would you go about trying to solve what Darwin called “an abominable mystery,” that is, the identity of the seed plant group that was ancestral to the flowering plants?

CHAPTER OUTLINE

An Introduction to Animal Diversity

33

The variety of life forms on Earth is staggering. Naked mole rats, Heterocephalus glaber, are long-lived rodents that remain cancer free. ©John Visser/Photoshot

N

aked mole rats (Heterocephalus glaber) are a species of rodent that live in arid areas of the Horn of Africa, including Ethiopia, Somalia, and Kenya. Their large protruding teeth are used for digging, and their lips are sealed behind the teeth to keep out soil. Naked mole rats have a unique reproductive process in which only one dominant female, the queen, reproduces. But these rats have an even more intriguing claim to fame. Whereas most species of mice and rats live only 4 years on average, naked mole rats can live for at least 30 years. And they are cancer free! Scientists discovered that the rats produce a polysaccharide called high-molecular-mass hyaluronan, or HMM-HA. Secretion of HMM-HA from mole rat cells causes contact inhibition, preventing the cells from overcrowding and forming tumors. This ability is lost in cancer cells. When researchers inhibited the synthesis of HMM-HA by naked mole rat cells, the cells lost their contact inhibition and tumors formed. From these results, biologists are interested in pursuing this line of research to prevent cancer and extend the life in humans. This is just one example

33.1 Characteristics of Animals 33.2 Animal Classification 33.3 The Use of Molecular Data in Constructing Phylogenetic Trees for Animals  Summary of Key Concepts Assess & Discuss

in which the study of animal diversity could lead to dramatic improvements in human health. Animals constitute the most species-rich kingdom. About 1.3 million species have been found and described, and an estimated 2–5 million more species await discovery and classification. Beyond being members of this kingdom ourselves, humans depend on animals. Many different kinds of animals and their products are part of our diet. Humans also enjoy animal species as companions and depend on other species for tests of lifesaving drugs. We share parts of our genome with other organisms such as fruit flies, nematodes, and zebrafish—all of which are used as model organisms for understanding aspects of human molecular and developmental biology. However, we are also in conflict with animals such as insects that threaten our food supply and transmit deadly diseases. Malaria is transmitted by mosquitoes; sleeping sickness, by tsetse flies; and rabies, by a number of animals, including dogs, raccoons, and bats. With such a huge number and diversity of existing animals and with animals featuring so prominently in our lives, understanding animal diversity is of great importance. Therefore, researchers have spent a great deal of effort in determining the unique characteristics of different taxonomic groups and identifying their evolutionary relationships. Since the time of Carolus Linnaeus in the 1700s, scientists have classified animals based on their morphology, that is, on their physical structure. In the 1990s, animal classifications based on similarities in DNA and rRNA sequences became more common. Quite often, classifications based on morphology and those based on molecular data were similar, but some important differences arose. In this chapter, we will begin by defining the key characteristics of animals and then take a look at the major features of animal body plans that form the basis of classification. We will explore how new molecular data have enabled scientists to revise and refine the animal phylogenetic tree. As more molecular-based evidence becomes available, systematists will likely continue to redraw the tree of animal life. Therefore, as you read this chapter, keep in mind that the classification of animals is now, and will continue to be, a work in progress.



AN INTRODUCTION TO ANIMAL DIVERSITY 687

33.1            Characteristics of Animals Learning Outcomes: 1. List the key characteristics of animals that distinguish them from other organisms. 2. Provide a brief overview of the history of animal life on Earth.

The Earth contains a dazzling diversity of animal species, living in environments from the deep sea to the desert and exhibiting an amazing array of characteristics. Most animals move and eat multicellular prey, and therefore, they are loosely differentiated from species in other kingdoms. However, a single definition of an animal is difficult because they are so diverse that biologists can find exceptions to nearly any given characteristic. Even so, a number of key features can help us broadly characterize the group we call animals (Table 33.1).

Animals Are Multicellular Heterotrophs Animals have several characteristics relating to cell structure, mode of nutrition, movement, and reproduction that collectively distinguish them from other organisms. If we focus on these characteristics, animals can be defined as multicellular heterotrophs with cells that lack cell walls,

Table 33.1   Common Characteristics of Animals Characteristic

Example

Multicellularity

Even relatively simple types of animals such as sponges are multicellular, in contrast to the mostly single-celled eukaryotic microorganisms called protists (see Chapter 28).

Heterotrophs

Animals obtain their food by eating other organisms or their products. This contrasts with plants and algae, most of which are autotrophs and essentially make their own food.

No cell walls

The cells of plants, fungi, bacteria, archaea, and most protists have a rigid cell wall, but animal cells lack a cell wall and are quite flexible.

Nervous tissue

The presence of a nervous system in most animals enables them to respond rapidly to environmental stimuli.

Movement

Most animals have a muscle system, which, combined with a nervous system, allows them to move in their environment.

Sexual reproduction

Most animals reproduce sexually, with small, mobile sperm uniting with a much larger egg to form a fertilized egg, or zygote.

Extracellular matrix

Proteins such as collagen bind animal cells together to give them added support and strength (see Figure 10.1).

Characteristic cell junctions

Animals have characteristic cell junctions, called anchoring, tight, and gap junctions (see Figures 10.7, 10.9, 10.11).

Special clusters of Hox genes

Most animals possess Hox genes, which function in patterning the body axis (see Figures 20.16, 24.15).

Similar rRNA

Animals all have very similar genes that encode for RNA of the small ribosomal subunit (SSU rRNA; see Figure 12.17).

the capacity to move at some point in their life cycle, and the ability to reproduce sexually, with sperm fusing directly with eggs.  Cell Structure  Like some protists, plants, and most fungi, animals are multicellular. However, animal cells lack cell walls and are flexible. This flexibility facilitates movement. Animal cells gain structural support from an extensive extracellular matrix (ECM) that forms strong fibers outside the cell (refer back to Figure 10.1). Additionally, a group of unique cell junctions—anchoring, tight, and gap junctions—play an important role in holding animal cells in place and allowing communication between cells (refer back to Table 10.3). Mode of Nutrition  All animals are heterotrophs; that is, they cannot synthesize their own organic molecules using energy from inorganic substances. Instead, animals must ingest other organisms or their products to sustain life. Many different modes of feeding exist among animals, including suspension feeding (filtering food out of the surrounding water); bulk feeding (eating large food pieces, as done by carnivores and herbivores); and fluid feeding (sucking plant sap or animal body fluids) (Figure 33.1). Although fungi and animals both rely on absorptive nutrition—that is, they secrete enzymes that break down complex materials and absorb the resulting small organic molecules—fungi use external digestion to obtain their nutrients. Animals ingest their food into an internal gut and then break it down using enzymes. Movement  Most animals have muscle cells and nerve cells organized into tissues. Muscle tissue is unique to animals, and most animals are capable of some type of locomotion, the ability to move from place to place, in order to acquire food or escape predators. This ability has led to the development of muscular-skeletal systems, systems of sensory structures, and a nervous system that coordinates movement and prey capture. Sessile species such as barnacles, which stay in one place, use bristled appendages to obtain nearby food. However, in many sessile species, although adults are immobile, the larvae can swim. Reproduction  Nearly all members of the animal kingdom reproduce sexually, although certain insects, fish, and lizard species can reproduce asexually. During sexual reproduction, a small, mobile sperm generally unites with a much larger egg to form a fertilized egg, or zygote. Fertilization may occur internally, which is common in terrestrial species, or externally, which is more common in aquatic species. Similarly, embryos develop inside the mother or outside in the mother’s environment. 

Animal Life Began More Than a Half Billion Years Ago The history of animal life spans over 630 million years, starting at the end of the Proterozoic eon, when multicellular animals emerged (refer back to Figure 26.4). The first animals were invertebrates, animals without a vertebral column, or backbone. A profusion of animal phyla appeared during the Cambrian explosion, 533–525 million years ago (mya), including sponges, jellyfish, corals, flatworms, mollusks, annelid worms, the first arthropods, and echinoderms, plus many phyla that no longer exist today (Figure 33.2).

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(a)

(b)

(c)

Figure 33.1  Modes of animal nutrition.  (a) Suspension feeders, such as these tube worms, filter food particles from the water column.

(b) Grizzly bears and other bulk feeders tear off large pieces of their food and chew it or swallow it whole. (c) Fluid feeders, such as these aphids, suck fluid from their food source. a: ©waldhaeusl.com/age fotostock; b: ©Enrique R Aguirre Aves/Getty Images; c: ©Bartomeu Borrell/age fotostock

The causes of the sudden increase in animal life at that time are not fully understood, but three explanations have been proposed. ∙ Species proliferation may have been related to a warm favorable environment. At the same time, atmospheric and aquatic oxygen levels were increasing, permitting increased metabolic rates, and an ozone layer had developed, blocking out harmful UV radiation and allowing complex life to thrive in shallow water and eventually on land. ∙ The evolution of the Hox gene complex may have permitted much variation in morphology. ∙ As new types of predators evolved, prey developed adaptations that enabled them to avoid their predators, leading to counteradaptations by predators, and so on. This evolutionary “arms race” may have resulted in a proliferation of predator and prey types.

These hypotheses are not mutually exclusive and may well have operated at the same time. Around 520 mya, the first vertebrates, fishes, appeared at roughly the same time as the first plants invaded land. The appearance of land plants introduced a viable food source for any organisms that could utilize them. However, the realm of land and air presented organisms with many challenges. For colonization of land to occur, certain species evolved adaptations that prevented them from drying out and enabled them to breathe, move, and reproduce in the new environment, in much the same way as the plant embryo, leaves, seeds, and other adaptations permitted plants to colonize terrestrial habitats (see Chapter 31). For animal species, such features included lungs and internal fertilization. The development of the amniotic egg, which features a tough, protective shell to prevent drying out, enabled animals to be terrestrial for their entire life cycle. The amniotic egg, which is described in Chapter 35, appeared during the Carboniferous period, about 300 mya, and was responsible for the success of the reptiles, which appeared during this period. Reptiles were to dominate the Earth for many millions of years during the rise and fall of the dinosaurs. Mammals appeared at the same time as dinosaurs, although they were not prevalent. The number and diversity of mammals exploded only after the dinosaurs abruptly died out at the end of the Cretaceous era, about 65 mya.

33.2          Animal Classification Learning Outcomes: 1. Discuss why choanoflagellates are believed to be the closest living relatives of animals. 2. Describe each of the major morphological and developmental features of animal body plans that form the basis of the classification of animals.

Figure 33.2  The profusion of animal life in the Cambrian

period, about 520 mya.  This artist’s reconstruction of marine life shows many different phyla, some of which are now extinct. ©Publiphoto/Science Source

All animals are classified in the domain Eukarya, the supergroup Opisthokonka, and the kingdom Animalia (informally called the animal kingdom) (refer back to  Figure 25.1). Although extremely diverse, most biologists agree that the animal kingdom is monophyletic, meaning that all taxa have evolved from a single common ancestor. Today, scientists recognize about 35 animal phyla. 



AN INTRODUCTION TO ANIMAL DIVERSITY 689

that the first simple animals may have arisen when some of these cells gradually acquired specialized functions—for example, movement or nutrition—while still maintaining coordination with other cells and cell types. As discussed later, evolutionary changes to this simple body plan resulted in critical innovations that led to the more complex body plans found in modern animals.

At first glance, many of the animal phyla seem so distantly related to one another (for example, chordates and jellyfish) that making sense of this diversity with a classification scheme seems very challenging. Fortunately, by carefully examining body features and, more recently, by analyzing molecular data such as DNA sequences, evolutionary biologists have been able to propose models that describe the evolutionary relationships among animals. The model shown in Figure 33.3 describes those relationships for 13 common phyla. In this section, we will explore the major features of animal body plans that form the basis of this animal phylogeny.

Animal Phyla Have Broad Differences Related to Body Plan, Germ Layers, and Features of Embryonic Development

Animals Evolved from a Choanoflagellate-like Ancestor

Prior to the use of molecular data in phylogeny, biologists traditionally classified animal diversity in terms of three main morphological and developmental features of animal body plans:

With the monophyletic nature of the animal kingdom in mind, scientists have attempted to identify the species from which animals most likely evolved. Molecular data indicate that the closest living relative of animals is the flagellated protist known as a choanoflagellate. These tiny, single-celled organisms have a single flagellum surrounded by a collar of cytoplasmic tentacles (refer back to Figure 28.21b).  Some species of choanoflagelles form colonies consisting of many individual organisms on a single stalk. Scientists hypothesize

1. Type of body symmetry 2. Number of germ layers 3. Specific features of embryonic development We will discuss each of these major features of animal body plans next.

Bilateria Protostomia

Deuterostomia

Most with lophophore or trochophore larva Loss of germ layers

Ecdysis Protostome development

Chordata

Echinodermata

Arthropoda

Nematoda

Annelida

Ecdysozoa

Mollusca

Brachiopoda

Bryozoa

Rotifera

Platyhelminthes

Cnidaria

Ctenophora

Porifera

Lophotrochozoa

Deuterostome development, endoskeleton

Bilateral symmetry Gain of mesoderm

Gain of mesoderm

KEY Critical innovations

Gain of two germ layers Multicellularity Common ancestor of animals and choanoflagellates

Figure 33.3  An animal phylogenetic tree based on body plans and molecular data.  Biologists have identified about 35 different animal phyla. We will focus our discussions here and in the next two chapters on the 13 most abundant and recognizable phyla. Core Concept: Evolution  As shown at the bottom of this tree, the first animals evolved from a choanoflagellate-like ancestor.

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(a) Parazoa: no symmetry

(b) Cnidaria: radial symmetry

(c) Bilateria: bilateral symmetry

Figure 33.4  Early divisions in the animal phylogeny.  Animals can be categorized based on body symmetry (a) the absence of symmetry

(Parazoa, the sponges); (b) radial symmetry (the cnidarians); or (c) bilateral symmetry (Bilateria, all other animals). a: ©E Teister/age fotostock; b: ©Gavin

Parsons/Getty Images; c: ©Jens Kuhfs/Getty Images

Symmetry  Animals may be categorized according to the type of symmetry their body displays. Symmetry refers to the existence of balanced proportions of the body on either side of a median plane. Some of the earliest-diverging animals, such as sponges, were asymmetric, meaning they had no plane of symmetry  (Figure 33.4a). Radially symmetric animals can be divided equally by any longitudinal plane passing through the central axis  (Figure 33.4b). Such animals are often circular or tubular in shape, with a mouth at one end, and include cnidarians (jellyfish). Bilaterally symmetric animals, the Bilateria, can be divided along a vertical plane at the midline to create two halves (Figure 33.4c). Thus, a bilateral animal has a left side and a right side, which are mirror images, as well as a dorsal (upper) and a ventral (lower) side, which

1

Zygote

are not identical, and an anterior (head) and a posterior (tail) end. Bilateral symmetry is strongly correlated with both the ability to move through the environment and cephalization—the localization of sensory structures at the anterior end of the body. Such abilities allow animals to encounter their environment initially with their head, which is best equipped to detect and consume prey and to detect and respond to predators and other dangers. Most animals are bilaterally symmetric.   Germ Layers  Fertilization of an egg by a sperm creates a diploid zygote. During the earliest stage of embryonic development, the zygote becomes a multicellular embryo by a process called cleavage— a succession of rapid cell divisions with no significant growth that produces a hollow sphere of cells called a blastula  (Figure 33.5).

Cleavage, or mitotic cell divisions of the zygote, leads to the formation of a hollow ball of cells called the blastula.

Cleavage

Cleavage

2

Gastrulation involves an invagination, or inward folding, of the blastula that creates the gastrula.

Endoderm

Blastula (hollow ball)

Mesoderm

Ectoderm

8-cell stage

Gastrulation

3

Archenteron

Gastrula

Blastopore

In the gastrula, the layer of cells lining the archenteron becomes the endoderm. The cells on the outside of the blastula form the ectoderm. In the Bilateria, a middle layer termed the mesoderm develops between the ectoderm and endoderm.

Figure 33.5  Formation of germ layers.  Note: Radially symmetric animals (cnidarians) do not form mesoderm. Core Skill: Connections  Look back to Figure 25.8. Is the existence of three germ layers in triploblastic animals a shared primitive character or a shared derived character? 



AN INTRODUCTION TO ANIMAL DIVERSITY 691

In all animals except the sponges, the growing embryo then develops different layers of cells, called germ layers. During gastrulation, an area in the blastula folds inward, or invaginates, creating in the process a structure called a gastrula.  The inner layer of cells becomes the endoderm, which lines the primitive digestive tract. The outer layer, or ectoderm, covers the surface of the embryo and differentiates into the epidermis and nervous system. A key difference between Bilateria and most other animals is that the Bilateria develop a third layer of cells, termed the mesoderm, between the ectoderm and endoderm. Mesoderm forms the muscles and most other organs between the digestive tract and the ectoderm. Because the Bilateria have these three distinct germ layers, they are referred to as triploblastic, whereas the cnidarians, which have only ectoderm and endoderm, are termed diploblastic. Interestingly, the mesoderm of the earliest-diverging animals, the ctenophores, probably originated independently of the mesoderm found in bilaterians.

Specific Features of Embryonic Development in the Bilateria  In the Bilateria, a key feature of embryonic development concerns the development of a mouth and anus (Figure 33.6a). In gastrulation, the endoderm forms an indentation, the blastopore, which is the opening of the archenteron to the outside. In protostomes (from the Greek protos, meaning first, and stoma, meaning mouth) (see Figure 33.3), the blastopore becomes the mouth. If an anus is formed in a protostome species, it develops from a secondary opening. In contrast, in deuterostomes (from the Greek deuteros, meaning second), the blastopore becomes the anus, and the mouth is formed from a secondary opening. Protostomes and deuterostomes also differ at the cleavage stage of embryonic development. As mentioned, the earliest stage of embryonic development involves a process known as cleavage (see Figure 33.5). Protostome development is generally characterized by so-called determinate cleavage, in which the fate of each embryonic cell is determined very early (Figure 33.6b). If one of the cells

4-cell embryo Protostomes

Cell excised

Blastopore becomes mouth.

Development arrested Determinate cleavage

Side view

Top view Spiral cleavage

Deuterostomes

4-cell embryo Cell excised

Blastopore becomes anus.

(a) Fate of blastopore

Normal embryo

Normal embryo

Indeterminate cleavage

(b) Fate of embryonic cells

Side view

Top view

Radial cleavage

(c) Cleavage pattern

Figure 33.6  Differences in embryonic development between protostomes and deuterostomes.  (a) In protostomes, the blastopore becomes the mouth. In deuterostomes, the blastopore becomes the anus. (b) Protostomes have determinate cleavage, whereas deuterostomes have indeterminate cleavage. (c) Many protostomes have spiral cleavage, whereas all deuterostomes have radial cleavage. The dashed arrows indicate the direction of cleavage.

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is removed from a four-cell protostome embryo, neither the single cell nor the remaining three-cell mass can form viable embryos, and development is halted. In contrast, deuterostome development in most species is characterized by indeterminate cleavage, in which each cell produced by early cleavage retains the ability to develop into a complete embryo. For example, when one cell is excised from a four-cell sea urchin embryo, both the single cell and the remaining three can go on to form viable embryos. Other embryonic cells compensate for the missing cells. In human embryos, if individual embryonic cells separate from one another early in development, identical twins can result. Another distinguishing feature of the early bilaterian embryo is the cleavage pattern ( Figure 33.6c). In spiral cleavage, the planes of cell cleavage are oblique to the vertical axis of the embryo, resulting in an arrangement in which newly formed upper cells lie centered between the underlying cells. Many protostomes, including mollusks and annelid worms, exhibit spiral cleavage. The coiled shells of some mollusks result from spiral cleavage. Organisms with spiral cleavage are also known as spiralians. In radial cleavage, the cleavage planes are either parallel or perpendicular to the vertical axis of the embryo. This results in tiers of cells, one directly above the other. All deuterostomes exhibit radial cleavage, as do insects and nematodes, suggesting it may have been an ancestral condition.

Body covering (from ectoderm) Coelom (fluid-filled space)

Earthworm Digestive tract (from endoderm)

Tissue layer suspending organs (from mesoderm)

(a) Coelomate Body covering Muscle layer (from ectoderm) (from mesoderm) Pseudocoelom (fluid-filled space)

Nematode Digestive tract (from endoderm) (b) Pseudocoelomate

Additional Morphological Criteria Distinguish the Bilateria In older phylogenetic trees of animal life, classification was also based on morphological features, such as features of body cavities or  the presence of body segmentation. More recent molecular data suggest that although these features are helpful in describing differences in animal structure, they are not as reliable in shedding light on the evolutionary history of animals as previously believed.

Muscle layer (from mesoderm)

Body covering (from ectoderm)

Flatworm

Mesenchyme (from mesoderm)

Muscle layer (from mesoderm)

Digestive tract (from endoderm)

(c) Acoelomate

Body Cavity  A body cavity is an internal space within an animal that houses internal organs. A fluid-filled body cavity is called a coelom. In many animals, the body cavity is completely lined with mesoderm and is called a true coelom. Animals with a true coelom are termed coelomates ( Figure 33.7a ). If the fluid-filled cavity is not completely lined by tissue derived from mesoderm, it is known as a pseudocoelom ( Figure 33.7b). Animals with a pseudocoelom, including rotifers and nematodes, are termed pseudocoelomates. Some animals, such as flatworms, lack a fluid-filled body cavity and are termed acoelomates ( Figure 33.7c). Instead of fluid, this region contains mesenchyme, a tissue derived from mesoderm. A coelom has many important functions, perhaps the most important being that its fluid is relatively incompressible and therefore cushions internal organs such as the heart and intestinal tract, helping to prevent injury from external forces. A coelom also enables internal organs to move and grow independently of the outer body wall. Furthermore, in some soft-bodied invertebrates, such as earthworms, the coelom functions as a hydrostatic skeleton—a fluid-filled body cavity surrounded by muscles that gives support and shape to the body of organisms. Muscle contractions at one part of the body push this

Figure 33.7  Three types of body cavities of bilaterally symmetric animals.  Cross sections of each animal are shown on the right.

Core Skill: Modeling  The goal of this modeling challenge is to draw a phylogenetic tree based on morphological and developmental information. Modeling Challenge: Older phylogenetic trees of animal life were based on developmental and morphological features, such as protostome versus deuterostome development, coelom type, and body segmentation. Let’s consider eight of the phyla described earlier in Figure 33.3 with regard to these three features: Platyhelminthes—protostome, acoelomate, unsegmented; Nematoda and Rotifera—protostome, pseudocoelomate, unsegmented; Mollusca—protostome, coelomate, unsegmented; Annelida and Arthropoda—protostome, coelomate, segmented; Echinodermata—deuterstome, coelomate, unsegmented; and Chordata—deuterostome, coelomate, segmented. Based on these three features, draw a phylogenetic tree for the eight phyla. On your tree, place horizontal black bars to indicate the occurrence of these three critical innovations.



AN INTRODUCTION TO ANIMAL DIVERSITY 693

Annelida

In earthworms, each ring is a distinct segment.

Arthropoda

Chordata

Fishes exhibit segmentation in their backbone.

Lobsters have developed specialized appendages on many segments.

Figure 33.8  Segmentation.  Annelids, arthropods, and chordates all exhibit segmentation.

BIO TIPS

THE QUESTION  Three phyla containing species with obvious segmentation are Annelida, Arthropoda, and Chordata. Are such segmented animals a monophyletic, polyphyletic, or paraphyletic group?

P ROBLEM-SOLVING  S TRATEGY  Make a drawing. One strategy for solving this problem is to draw a simple version of Figure 33.3 with just the names of the phyla and the branches, and then place a star next to each phylum with segmented animals. Next, look at the comparison of monophyletic, polyphyletic, and paraphyletic taxonomic groups shown in Figure 25.5. Decide which pattern best matches your drawing.

Ecdysis

Protostome development

Loss of germ layers

Gain of two germ layers Multicellularity Common ancestor of animals and choanoflagellates

Chordata*

Echinodermata

Arthropoda*

Deuterostome development, endoskeleton

Bilateral symmetry Gain of mesoderm

Gain of mesoderm

Critical innovations

Nematoda

Annelida*

Mollusca

Brachiopoda

Bryozoa

Rotifera

Most with lophophore or trochophore larva

KEY

T OPIC  What topic in biology does this question address? The topic is evolutionary relationships based on segmentation.

Platyhelminthes

Cnidaria

ANSWER Because segmented animals have different common ancestors, the group is polyphyletic.

Porifera

Segmentation  Another feature of the animal body plan is the presence or absence of segmentation. In segmentation, the body is divided into regions called segments. Even though segmentation is a common feature of the Bilateria, its presence is more obvious in some phyla compared to others. In annelids (segmented worms), most segments contain the same set of blood vessels, nerves, and muscles (Figure 33.8). Some segments may differ, such as those containing the brain or sex organs. Segmentation is also evident in arthropods (such as lobsters and insects), but less so in chordates (such as fish and mammals) (Figure 33.8). Most species of chordata are vertebrates, which possess a series of small bones called vertebrae that form the backbone. The repeating pattern of vertebrae indicates segmentation.  The advantage of segmentation is that it allows specialization of body regions. For example, as we will see in Chapter 34, arthropods exhibit a vast degree of specialization of their segments. Many insects have wings and only three pairs of legs, whereas centipedes have no wings and many legs. Crabs, lobsters, and shrimp have highly specialized thoracic appendages that aid in feeding. 

I NFORMATION  What information do you know based on the question and your understanding of the topic? In the question, you are reminded that a taxonomic group can be monophyletic, polyphyletic, and paraphyletic. From your understanding of taxonomy and systematics, discussed in Chapter 25, you may remember that a monophyletic group contains a common ancestor and all of its descendants, a paraphyletic group contains a common ancestor but not all of its descendants, and a polyphyletic group contains groups of species with different common ancestors. You should also remember which phyla are segmented.

ra Ctenophora

fluid toward another part of the body. This type of movement can best be observed in an earthworm. Finally, in some organisms, the fluid in the body cavity also acts as a simple circulatory system.  The presence or absence of a coelom or pseudocoelom was previously used in the construction of animal phylogenies. However, scientists now believe this feature may not be useful in classification because animals that once possessed coeloms may have lost them over long periods of evolutionary time, as is true for the ancestors of flatworms. In addition, the coelom may have arisen twice in animal evolution, once in protostomes and once in deuterostomes.

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Core Concept: Evolution Changes in Hox Gene Expression Control Body Segment Specialization Scientists are beginning to understand the genetic basis for segmentation in animals. As described in Chapter 20, segmentation genes cause an embryo to subdivide into multiple segments, and then Hox genes cause each segment to develop its own unique characteristics. Recent studies have shown that changes in specialization among body segments can be traced to relatively simple changes in Hox genes.  The Hox genes are organized into four clusters of 13 genes, each designated with a number from 1 through 13. Some of these genes are expressed in anterior segments; others are expressed in posterior segments (refer back to Figure 20.17). In the 1990s, Greek molecular biologist Michalis Averof and coworkers showed how relatively simple shifts in the expression patterns of Hox genes along the anteroposterior axis can account for the large variation in arthropod appendage types. More recent work by Averof and colleagues (2010) has shown how specific changes in Hox expression are linked to changes in crustacean maxillipeds— appendages near the mouth that are used for feeding. Maxillipeds arise in the anterior thoracic segments and display a mixture of locomotory and feeding functions. By knocking out Hox genes or expressing Hox genes in an abnormal position, the researchers could change maxillipeds into leglike appendages or transform leglike appendages into maxillipeds. Shifts in the patterns of expression of Hox genes in the embryo along the anteroposterior axis are similarly prominent in vertebrate evolution. In vertebrates, the transition from one type of vertebra to another, for example, from cervical (neck) to thoracic (chest) vertebrae, is controlled by particular Hox genes. The site of the

cervicothoracic boundary appears to be influenced by the HoxC-6 gene (Figure 33.9). Differences in its relative position of expression, which occurs prior to vertebrae development, control neck length in vertebrates. In mice, which have a relatively short neck, the expression of HoxC-6 begins between vertebrae 7 and 8. In chickens and geese, which have longer necks, the expression begins farther back, between vertebrae 14 and 15 or 17 and 18, respectively. The forelimbs also arise at this boundary in all vertebrates. Interestingly, snakes, which essentially have no neck or forelimbs, do not exhibit this boundary, and HoxC-6 expression occurs immediately behind their heads. This, in effect, means that snakes got longer by losing their neck and lengthening their chest. American molecular biologist Sean Carroll has remarked that it is very satisfying to find that the evolution of body forms and novel structures in two of the most successful and diverse animal groups, arthropods and vertebrates, is shaped by the shifting of Hox genes. It also reminds us of one of the core concepts of biology—that evolution often involves descent with modification. Much of the diversity in animal phyla can be seen as modifications to a general body plan.

The Animal Kingdom Encompasses Many Diverse Phyla Table 33.2 summarizes the basic characteristics of the major animal

phyla. In Chapter 34, we will discuss the Ctenophora, Porifera, Cnidaria, Lophotrochozoa, and Ecdysozoa, and also the invertebrate members of Deuterostomia; these are all the animals without a backbone. In Chapter 35, we will turn our attention to the the phylum Chordata, which is the largest group of deuterostomes. These include fishes, amphibians, reptiles, and mammals, which possess a backbone.

Snake

Neck vertebrae No “neck,” no forelimb

Vertebrae: 1 Mouse

2

3

4

5

6

7

8

9 10 11 12 13 14 15 16 17 18 19 20

Hundreds of vertebrae

3

4

5

6

7

8

9 10 11 12 13 14 15 16 17 18 19 20

36 total vertebrae

9 10 11 12 13 14 15 16 17 18 19 20

36 total vertebrae

HoxC-6 Vertebrae: 1

2

HoxC-6

Chicken Vertebrae: 1

2

3

4

5

6

7

8

HoxC-6

Goose Vertebrae: 1

2

3

4

5

6

7

8

9 10 11 12 13 14 15 16 17 18 19 20

44 total vertebrae

HoxC-6

Figure 33.9  Relationship between HoxC-6 gene expression and neck length.  In vertebrates, the transition between neck and trunk vertebrae is controlled by the position of the HoxC-6 gene. In snakes, the expression of this gene is shifted so far forward that a neck does not develop.



AN INTRODUCTION TO ANIMAL DIVERSITY 695

Table 33.2

Summary of the Basic Characteristics of the Major Animal Phyla

Rotifera (rotifers)

Bryozoa and Brachiopoda (bryozoans and brachiopods)

Mollusca (snails, clams, squids)

Annelida Nematoda (segmented (roundworms) worms)

Arthropoda (insects, arachnids, crustaceans)

Echinodermata (sea stars, sea urchins)

Chordata (vertebrates and others)

20,000

2,200

4,800

110,000

18,000

25,000

1,000,000+

7,400

69,730

Cellular; lack Tissue; tissues and lack organs organs

Organs

Organs

Organs

Organs

Organs

Organs

Organs

Organs

Organs

Absent

Bilateral

Bilateral

Bilateral

Bilateral

Bilateral

Bilateral

Bilateral

Bilateral Bilateral larvae, radial adults

Ctenophora (comb Porifera jellies) (sponges)

Cnidaria (hydra, Platyhelanemones, minthes jellyfish) (flatworms)

Estimated number of species

200

8,500

9,000

Level of organization

Tissue; lack organs

Symmetry

Radial

Feature

Radial

Cephalization

Absent

Absent

Absent

Present

Present

Reduced

Present

Present

Present

Present

Absent

Present

Germ layers

Three

Absent

Two

Three

Three

Three

Three

Three

Three

Three

Three

Three

Body cavity, or Coelom

Absent

Absent

Absent

Absent

Pseudocoelom

Coelom

Reduced Coelom

coelom

PseudoCoelom

Reduced coelom

Coelom

Coelom

Obvious segmentation in the adult

Absent

Absent

Absent

Absent

Absent

Absent

Absent

Present

Absent

Present

Absent

Present

33.3                 The Use of Molecular Data in Constructing Phylogenetic Trees for Animals Learning Outcomes: 1. Discuss how molecular data are used to construct and revise phylogenetic trees. 2. List the morphological features of the Ecdysozoa and the Lophotrochozoa.

In Chapter 25 (see Sections 25.2 and 25.3), we considered how molecular data can be used to construct phylogenetic trees. This approach  involves the comparison of genetic data, such as DNA, RNA, and amino acid sequences from different species to estimate their evolutionary relationships based on the degree of similarities between the sequences. More closely related species exhibit fewer sequence differences than distantly related ones.  In Section 33.2, we explored the relationships between major features of animal body plans and animal phylogeny. Early phylogenetic trees for the animal kingdom were based largely on morphological features. In the past few decades, however, major revisions to such trees have occurred when biologists have compared molecular data, such as DNA sequences, with morphological data. The phylogenetic tree shown earlier, in Figure 33.3, is derived from morphological data and also from more recent molecular data.

In this section, we will consider how molecular data are used to refine our understanding of the evolutionary relationships among animals.

The Sequences of SSU rRNA Genes and Hox Genes Are Analyzed to Determine Broad Evolutionary Relationships Among Animals As discussed in Chapter 25, the sequences of some genes change fairly slowly during evolution. Such slowly changing genes are particularly useful for evaluating broad evolutionary relationships, such as comparing phyla. Scientists have often focused on comparing base sequences in the gene that encodes RNA of the small ribosomal subunit (SSU rRNA) (see Chapter 12). SSU rRNA is universal in all organisms, and its base sequence has changed very slowly over long periods of time. We can appreciate this phenomenon by comparing a very small portion of the sequence of the SSU rRNA gene of a sponge, flatworm, seagull, and paramecium (Figure 33.10) in much the same way as we did in Chapter 12 (refer back to Figure 12.17). The three animal sequences are very similar to each other, and all of them differ from that of the paramecium (a protist).  The three animal species shown in Figure 33.10 are members of different phyla. If we compared three different species of sponges with three different species of flatworms, we would find that the sequences from the three species of sponges are more similar to each other than they are to those of the flatworms, and vice versa.

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G AGG T T C GA A G A C GA T C A G A T A CC G T C GT A GT T C C GA C C A T A A A CG A T G Sponge G AGG T T C GA A G A C GA T C A G A T A CC G T C GT A GT T C C A A C C A T A A A CG A T G Flatworm G AGG T T C GA A G A C GA T C A G A T A CC G T C GT A GT T C T G A C C A T A A A CG A T G Seagull G GGG A T C A A A G A C GA T C A G A T A CCG T C GT A GT C T T A A C T A T A A A C T A T A Paramecium Identical in all four species

KEY

Dissimilar in one animal species

Identical in two or three species

Dissimilar in the protist

Figure 33.10  Comparison of small subunit (SSU) rRNA gene sequences from three animals and a protist.  Note the similarities between the animals, even though they are very distantly related within the animal kingdom.

Core Skill: Connections  Look back at Figure 12.17. Which color represents sequences of bases that are the most evolutionarily conserved? 

A second approach for understanding broad evolutionary relationships among animals is to analyze genes that have played a major role in animal diversification. Researchers have studied Hox genes, which are found in cnidarians and bilaterians, to study the evolution of body plans (refer back to Figure 24.15). They hypothesize that the duplication of Hox genes and gene clusters has led to the evolution of more complex animal body forms. Examination of the genes that regulate early developmental differences has provided insight into the evolution of animal development and the mechanisms by which animal body plans have diversified.

Studies using molecular data have resulted in major revisions to phylogenetic trees that were previously based on morphological data. As an example, Figure 33.11 compares the phyla in Protostomia. Figure 33.11a is the current view, which was also shown as part of Figure 33.3. Figure 33.11b is a previous model that was based on morphological data. As described next, the revisions that created our current view of the phylogeny of Protostomia are derived from molecular studies.

Protostomia

Protostomia

Arthropoda

Annelida

Mollusca

Rotifera

Nematoda

Platyhelminthes

Arthropoda

Nematoda

Annelida

Ecdysozoa

Mollusca

Brachiopoda

Bryozoa

Rotifera

Platyhelminthes

Lophotrochozoa

(a) Current view of Protostomia (b) Older model of Protostomia based on morphological data

Figure 33.11  A comparison of a current phylogenetic tree for Protostomia with an older tree based on morphological data.  The current tree shown in (a) is part of the tree shown earlier in Figure 33.3. The model shown in part (b) is no longer accepted.



AN INTRODUCTION TO ANIMAL DIVERSITY 697

Core Skill: Process of Science

Feature Investigation  | Aguinaldo and Colleagues Analyzed SSU rRNA Sequences to

Determine the Taxonomic Relationships of Arthropods to Other Phyla in Protostomia

In 1997, American molecular biologists Anna Marie Aguinaldo, James Lake, and colleagues analyzed the relationships of arthropods to other phyla by sequencing the complete gene that encodes SSU rRNA from a variety of representative phyla (Figure 33.12). Total genomic DNA was isolated using standard techniques and amplified by polymerase chain reaction (PCR; refer back to Figure 21.6). PCR fragments were then subjected to DNA sequencing, a technique also

described in Chapter 21, and the evolutionary relationships among 50 species were examined. The resulting data indicated the existence of a monophyletic clade—the Ecdysozoa—containing the nematodes and arthropods (see step 3 in Figure 33.12 and Figure 33.11a). The hypothesis that nematodes are more closely related to arthropods than previously thought has important ramifications. First, it implies that

Figure 33.12  A revised animal phylogeny based on a comparison of SSU rRNA genes. GOAL To determine the evolutionary relationships among many animal species, especially the relationship of arthropods to other species. KEY MATERIALS Cellular samples from about 50 animals in different taxa. Experimental level

1

Isolate DNA from animals and subject the DNA to polymerase chain reaction (PCR) to obtain enough material for DNA sequencing. PCR is described in Chapter 21.

2 Sequence the amplified

DNA by dideoxy sequencing, also described in Chapter 21.

3 Compare the DNA

sequences and infer phylogenetic relationships using the cladistic approach described in Chapter 25.

4

Conceptual level The goal of PCR is to amplify a region in the SSU rRNA gene.

For more detail, refer back to Figure 21.6.

For more detail, refer back to Figure 21.8.

Lophotrochozoa

C ACCG T A

Ecdysozoa

Dideoxy sequencing, in which DNA strands are separated according to their lengths by subjecting them to gel electrophoresis, is used to determine the base sequence of DNA.

The approach compares traits that are either shared or not shared by different species and creates clades, consisting of a common ancestral species.

THE DATA This process resulted in a large group of DNA sequences that were then analyzed with the use of computer programs.

5

CONCLUSION The arthropods are most closely related to the nematodes, and both phyla are placed in the clade Ecdysozoa. All other protostomes belong to a new clade called the Lophotrochozoa.

4

THE DATA This process resulted in a large group of DNA sequences that were then analyzed with the use of computer programs. CHAPTER 33

698

5

CONCLUSION The arthropods are most closely related to the nematodes, and both phyla are placed in the clade Ecdysozoa. All other protostomes belong to a new clade called the Lophotrochozoa.

6

SOURCE Aguinaldo, A.M. et al. 1997. Evidence for a clade of nematodes, arthropods, and other moulting animals. Nature 387 (6632): 489–493.

two well-researched model organisms, Caenorhabditis elegans (a nematode) and the fruit fly Drosophila melanogaster (an arthropod), are more closely related than had been believed. Second, morphological classification had assumed that arthropods and annelids were closely related to each other based on the presence of segmentation. Molecular data does not support the previous hypothesis that annelids and arthropods form a clade of segmented animals (see Figure 33.11b).

Experimental Questions 1. What was the purpose of the study conducted by Aguinaldo and colleagues?  2. CoreSKILL » What was the major finding of this particular study?  3. What impact does the new view of nematode and arthropod phylogeny have on other areas of research?

The Ecdysozoa and Lophotrochozoa Have Some Distinctive Morphological Features The study by Aguinaldo and colleagues provided evidence for a new clade of molting animals, the Ecdysozoa, consisting of the nematodes and arthropods. According to molecular evidence, the other major protostome clade is the Lophotrochozoa, which encompasses the mollusks, annelids, and several other phyla (see Figure 33.11a). When some morphologists reviewed their data given this new information, they found morphological support for these new groupings. Let’s look at what morphological features make each of these groups unique. The Ecdysozoa is so named because all of its members secrete a nonliving cuticle, an external skeleton (exoskeleton); think of the hard shell of a beetle or that of a crab. As these animals grow, the exoskeleton becomes too small, and the animal molts, or breaks out of its old exoskeleton, and secretes a newer, larger one (Figure 33.13). This molting process is called ecdysis; hence the name Ecdysozoa. Although this group was named for this morphological characteristic, it was first strongly supported as a separate clade by molecular evidence. Similarly, the Lophotrochozoa clade was organized primarily through analyses of molecular data. Its name stems from two morphological features seen in many organisms of this clade: Lopho is derived from the lophophore, a horseshoe-shaped crown of tentacles used for feeding that is present on some phyla in this clade, such as the rotifers, bryozoans, and brachiopods (Figure 33.14a); trocho refers to the trochophore larva, a distinct larval stage characterized by a band of cilia around its middle that is used for swimming (Figure 33.14b). Trochophore larvae are found in several Lophotrochozoa phyla, such as annelid worms and mollusks, indicating their similar ancestry. However, other members of the clade, such as the platyhelminthes, have neither of these morphological features and are classified as lophotrochozoans based strictly on molecular data.

Figure 33.13  Ecdysis.  The dragonfly, shown here emerging from a discarded exoskeleton, is a member of the Ecdysozoa—a clade of animals exhibiting ecdysis, the periodic shedding (molting) and re-formation of the exoskeleton. ©Dwight Kuhn Core Concept: Structure and Function  For animals with exoskeletons, growth and development necessitate molting.



AN INTRODUCTION TO ANIMAL DIVERSITY 699

Lophophore tentacles

Apical tuft of cilia

Anterior

Band of cilia

Anus

Mouth Stomach

Trunk

Anus

∙∙ Segmentation, the division of the body into identical subunits called segments, is an obvious feature of the animal body plan in certain phyla (Figure 33.8). ∙∙ Shifts in the pattern of expression of Hox genes are prominent in evolution. In vertebrates, the transition from one type of vertebra to another is controlled by certain Hox genes (Figure 33.9).

Posterior

(a) Lophophore of a phoronid worm

∙∙ Animals are also classified according to patterns of embryonic development. In protostomes, the blastopore becomes the mouth; in deuterostomes, the blastopore becomes the anus. Most protostomes have spiral cleavage, and all deuterostomes have radial cleavage (Figure 33.6). ∙∙ Animals with a coelom, a body cavity that is completely lined with mesoderm, are termed coelomates. Animals that possess a coelom that is not completely lined by tissue derived from mesoderm are called pseudocoelomates. Those animals lacking a fluid-filled body cavity are termed acoelomates (Figure 33.7).

Mouth

Gut

germ layer termed the mesoderm, which develops between the endoderm and the ectoderm (Figure 33.5).

∙∙ Each animal phylum shows a distinctive set of general characteristics (Table 33.2). (b) Trochophore larva

Figure 33.14  Characteristics of the Lophotrochozoa.  (a) A

lophophore, a crown of ciliated tentacles, generates a current to bring food particles into the mouth. (b) The trochophore larval form is found in several animal lineages.

Summary of Key Concepts 33.1  Characteristics of Animals ∙∙ Animals constitute a very species-rich kingdom, with a number of characteristics that distinguish them from other organisms, including multicellularity, an extracellular matrix, and unique cell junctions, in addition to heterotrophic feeding and internal digestion and the possession of nervous and muscle tissues (Table 33.1). ∙∙ Many different feeding modes are used by animals, including suspension feeding, bulk feeding and fluid feeding (Figure 33.1). ∙∙ The history of animal life on Earth spans over 630 million years. A profusion of animal phyla appeared in the Cambrian explosion (533–525 mya). Animals evolved adaptations to deal with the colonization of land, starting about 520 mya, and the number and diversity of mammals exploded after dinosaurs died out at the end of the Cretaceous period, 65 mya (Figure 33.2).

33.2      Animal Classification ∙∙ The animal kingdom is monophyletic, meaning that all taxa have evolved from a single common ancestor (Figure 33.3). ∙∙ Biologists hypothesize that animals evolved from a choanoflagellate-like ancestor. ∙∙ Animals can be categorized according to their type of symmetry, whether asymmetric (the sponges), radial (the cnidarians and ctenophores), or bilateral (Bilateria, all other animals) (Figure 33.4). ∙∙ The Cnidaria have two embryonic germ layers, the endoderm and the ectoderm, whereas the Bilateria and Ctenophora have a third

33.3     T  he Use of Molecular Data in Constructing Phylogenetic Trees for Animals ∙∙ Phylogenetic trees are constructed and revised by comparing similarities in DNA, RNA, and amino acid sequences among different species (Figure 33.10). ∙∙ Molecular studies resulted in a revision to the animal phylogenetic tree; the protostomes were divided into two major clades: the Ecdysozoa and the Lophotrochozoa (Figures 33.11, 33.12). ∙∙ Members of the Ecdysozoa secrete and periodically shed a nonliving cuticle that is typically an exoskeleton, or external skeleton (Figure 33.13). ∙∙ The Lophotrochozoa are grouped primarily through analyses of molecular data, but some members are distinguished by two morphological features: the lophophore, a crown of tentacles used for feeding, and the trochophore larva, a distinct larval stage (Figure 33.14).

Assess & Discuss Test Yourself 1. Which of the following is not a distinguishing characteristic of animals? a. the capacity to move at some point in the life cycle b. possession of cell walls c. multicellularity d. heterotrophy e. All of the above are characteristics of animals. 2. Which is the correct hierarchy of divisions in the animal kingdom, from most inclusive to least inclusive? a. Protostomia, Ecdysozoa, Bilateria b. Ecdysozoa, Protostomia, Bilateria c. Bilateria, Protostomia, Ecdysozoa d. Protostomia, Bilateria, Ecdysozoa e. none of the above

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3. Bilateral symmetry is strongly correlated with a. the ability to move through the environment. b. cephalization. c. the ability to detect prey. d. a and b. e. a, b, and c. 4.  In triploblastic animals, the inner lining of the digestive tract is derived from the a. ectoderm. b. mesoderm. c. endoderm. d. pseudocoelom. e. coelom. 5. Pseudocoelomates a. lack a fluid-filled cavity. b. have a fluid-filled cavity that is completely lined with mesoderm. c. have a fluid-filled cavity that is partially lined with mesoderm. d. have a fluid-filled cavity that is not lined with mesoderm. e. have an air-filled cavity that is partially lined with mesoderm. 6. Protostomes and deuterostomes can be classified based on a. cleavage pattern. b. destiny of the blastopore. c. whether the fate of the embryonic cells is fixed early during development. d. all of the above. 7. Indeterminate cleavage is found in a. annelids. b. mollusks. c. nematodes. d. vertebrates. e. all of the above. 8. Naturally occurring identical twins are possible only in animals that a. have spiral cleavage. b. have determinate cleavage. c. are protostomes. d. have indeterminate cleavage. e. have spiral and determinate cleavage and are protosomes. 9. Genes involved in the patterning of the body axis, that is, in determining characteristics such as neck length and appendage formation, are called a. small subunit (SSU) rRNA genes. b. Hox genes.

c. metameric genes. d. determinate genes. e. none of the above. 10. A major finding of recent molecular studies is that a. the presence or absence of the mesoderm is not important in phylogeny. b. all animals do not share a single common ancestor. c. body symmetry, whether radial or bilateral, is not an important determinant in phylogeny. d. the echinoderms are not included in the deuterostome clade. e. the presence or absence of a coelom is not important for classification.

Conceptual Questions 1. Fierce debate centers on whether ctenophores or sponges are the earliestdiverging animals. Choanoflagellates, the closest living relatives to animals, appear very similar to the choanocyte cells of sponges. In addition, sponges lack true tissues, although they have distinct types of cells. In contrast, all other animals possess one or more types of tissues. Both the Cnidaria and the Ctenophora are radially symmetric and, until very recently, both were thought to have only two germ layers, endoderm and ectoderm. All other animals are bilaterally symmetric and have three germ layers. Draw an animal phylogenetic tree that illustrated this viewpoint, including Cnidaria and Ctenphora as part of the same phyla, and label the critical innovations. 2. Why was the evolution of a coelom important?    3. 

Core Concept: Evolution  Brachiopods, bryozoans, mollusks, and annelids all exhibit a lophophore or trochophore larvae. Are these monophyletic, paraphyletic, or polyphyletic groups? Explain your answer. Refer back to Figure 25.5 to remind yourself about these terms. 

Collaborative Questions 1. Discuss the many ways that animals can affect humans, both positively and negatively. 2. Summarize how molecular evidence has enabled scientists to refine their views on animal phylogeny.

CHAPTER OUTLINE 34.1 Ctenophores: The Earliest Animals 34.2 Porifera: The Sponges 34.3 Cnidaria: Jellyfish and Other Radially Symmetric Animals 34.4 Lophotrochozoa: The Flatworms, Rotifers, Bryozoans, Brachiopods, Mollusks, and Annelids 34.5 Ecdysozoa: The Nematodes and Arthropods 34.6 Deuterostomia: The Echinoderms and Chordates 34.7 A Comparison of Animal Phyla Summary of Key Concepts Assess & Discuss

The Invertebrates

34

T

What is this organism, and how does it feed? ©Georgie Holland/age fotostock

Deuterostomia

Ecdysozoa

Lophotrochozoa

Cnidaria

Porifera

refinements, and perhaps surprises lay ahead, as the genomes of more and more species are sequenced and compared. Ctenophora

he organism shown in the chapter opening photograph looks like an underwater plant, complete with long leaflike structures and roots. However, you may be surprised to learn that it's an animal, a type of echinoderm called a feather star, which is related to sea stars. Its long arms catch food particles floating in the ocean current, and tiny tube feet pass these particles into special food gutters that run along the center of each arm and empty into the mouth. The number of arms varies from species to species and may reach 200. Feather stars can creep along the ocean floor by means of rootlike projections called cirri. About 550 species of feather stars are in existence today, but some fossil formations are packed with feather star fragments, showing us how successful the group was in the past. The history of animal life on Earth has evolved over hundreds of millions of years. Some scientists suggest that changing environmental conditions, such as a buildup of dissolved oxygen and minerals in the ocean or an increase in atmospheric oxygen, eventually permitted higher metabolic rates and increased the activity of a wide range of animals. Others suggest that with the development of sophisticated locomotor skills, a wide range of predators and prey evolved, leading to an evolutionary “arms race” in which predators evolved powerful weapons and prey evolved more powerful defenses against them. Such adaptations and counteradaptations may have led to a proliferation of different lifestyles and taxa. Also, an increase in the number of Hox genes may have fostered an increase in animal diversity and complexity. In this chapter and the next, we will survey the wondrous diversity of animal life on Earth. In this chapter, we will examine the invertebrates, animals without a backbone, a category that makes up more than 95% of all animal species. We begin by exploring some of the earliest animal lineages, the ctenophores, sponges, and jellyfish. We will then turn to the Lophotrochozoa and Ecdysozoa, the two groups of protostomes introduced in Chapter 33. Finally, we will examine the deuterostomes, focusing here on the echinoderms and the invertebrate members of the phylum Chordata. The animal classification outlined in Chapter 33 (refer back to Figure 33.3) will serve as the basis for our discussion of animal lineages. A simplified version of Figure 33.3 is shown in Figure 34.1. Keep in mind, however, that animal phylogeny is a work in progress, and further revisions,

Protostomia Bilateria

Figure 34.1  An animal phylogeny.  This phylogenetic tree summarizes our current understanding about the evolutionary relationships among animal groups.

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CHAPTER 34

34.1 C  tenophores: The Earliest Animals Learning Outcome: 1. Outline the unique features of ctenophores.

Deuterostomia

Ecdysozoa

Lophotrochozoa

Cnidaria

Porifera

ora a Ctenophora

Ctenophores, also known as comb jellies, constitute the earliest-diverging animal lineage. Comb jellies are a small phylum of about 200 species, all of which are marine and look very much like jellyfish (Figure 34.2). They have on their Protostomia surfaces eight rows of cilia that resemble combs. Based on morBilateria phological data, the ctenophores were once classified as close relatives to cnidarians, which include jellyfish and corals. However, recent molecular analyses have changed this view and placed them farther apart on the animal evolutionary tree.  The name Ctenophora (pronounced teen-o-for'-ah) comes from the Greek ktenos, meaning comb, and phora, meaning bearing. The coordinated beating of the cilia propels the ctenophores. Averaging

about 1–10 cm in length, comb jellies are probably the largest animals to use cilia for locomotion. Most comb jellies possess two long tentacles that secrete a sticky substance onto which small prey adhere. The tentacles are then drawn over the mouth. Digestion occurs in a body cavity called a gastrovascular cavity, and waste and water are eliminated through two anal pores. Prey are generally small and may include tiny crustaceans called copepods and small fishes. Comb jellies are often transported around the world in ships’ ballast water. Mnemiopsis leidyi, a ctenophore species native to the Atlantic coast of North and South America, was accidentally introduced into the Black and Caspian Seas in the 1980s. With a plentiful food supply and a lack of predators, M. leidyi underwent a population explosion and ultimately devastated the local fishing industries. All ctenophores are hermaphrodites  (from the Greek, for the god Hermes and the goddess Aphorodite), possessing both ovaries and testes, and gametes are shed into the water to unite and eventually form a free-swimming larva that is very similar in form to the adult. Nearly all ctenophores exhibit bioluminescence, a phenomenon that results from chemical reactions that give off light. Ctenophores are particularly evident at night. Sometimes, they wash up on shore and make the sand or mud appear luminescent. Like jellyfish, ctenophores have both muscle and nerve cells organized as a diffuse net centralized at an elementary brain. However, the ctenophore nervous system uses different neurotransmitters than those in bilaterians and jellyfish and has different types of synapses. The presence of muscle cells originating from mesoderm suggests that ctenophores share a three-germ-layer embryonic structure with bilaterians. Even so, recent analyses of the genome of the ctenophore M. leidyi suggests that ctenophores lack many of the genes involved in specifying bilaterian mesoderm. In addition, ctenophores lack true Hox genes and possess a ctenophore-specific cleavage program. Finally, many bilaterian neuron-specific genes are absent or not expressed in ctenophores. These findings argue against a linear march of evolutionary forms from more simple animals such as ctenophores and sponges to complex bilaterians. Instead, evolutionary studies suggest that ctenophores were the earliest animals to diverge from a choanoflagellate-like ancestor that was multicellular and had a simple nervous system. Later, the ctenophores evolved their own unique way of forming mesoderm, which is different from the bilaterians. 

34.2       Porifera: The Sponges  Learning Outcomes: 1. Outline the body plan and unique characteristics of sponges. 2. Describe how sponges defend themselves against predators.

Figure 34.2  A ctenophore.  Ctenophores are called comb jellies because the eight rows of cilia on their surfaces resemble combs.

©Matthew J. D’Avella/SeaPics.com

Members of the phylum Porifera (from the Latin, meaning pore bearers), are commonly referred to as sponges. Sponges lack true tissues— groups of cells that have a similar structure and function. However, sponges are multicellular and produce different types of specialized



THE INVERTEBRATES 703

Deuterostomia

Ecdysozoa

Lophotrochozoa

Cnidaria

Porifera

Ctenophora

cells. Even though sponges carry most of the genes that are needed for a functioning nervous system, they have lost the ability to produce neurons during evolution. Biologists have identified approximately 8,000 species of Protostomia sponges, the vast majority of which are marine. Bilateria Sponges range in size from only a few millimeters across to more than 2 m in diameter. Smaller sponges may be radially symmetric, but most have no apparent symmetry. Some sponges have a low, encrusting growth form, whereas others grow tall and erect (Figure 34.3a). Although adult sponges are sessile—that is, anchored in place—the larvae are free-swimming.

Water

(a) Stovepipe sponge

(b) Typical vase shape of sponges

Choanocyte Flagellum

Osculum

Epithelial cell

Collar Nucleus Amoebocyte

Choanocytes Help Circulate Water The body of a sponge looks similar to a vase pierced with small holes or pores (Figure 34.3b). Water is drawn through these pores into a central cavity, the spongocoel, and flows out through the large opening at the top, called the osculum. The water enters the pores by the beating action of the flagella of the choanocytes, or collar cells, that line the spongocoel (Figure 34.3c). In the process, the choanocytes trap and eat small particulate matter and tiny plankton.  A layer of flattened epithelial cells similar to those making up the outer layer of animals in other phyla protects the sponge body. In between the choanocytes and the epithelial cells lies a gelatinous, protein-rich matrix called the mesohyl. Within this matrix are mobile cells called amoebocytes that absorb food from choanocytes, digest it, and carry the nutrients to other cells. Thus, considerable cell-to-cell contact and communication exist in sponges. Sponges are unique among the major animal phyla in using intracellular digestion, the uptake of food particles by cells, as a mode of feeding.

Water Spicule Spongocoel Pore

Mesohyl

Spicule

(c) Cross section of sponge morphology

Figure 34.3  Sponge body plan.  (a) The stovepipe sponge (Aplysina archeri) is a common sponge found on Caribbean reefs. (b) Many sponges have a vaselike shape. (c) A cross section reveals that sponges are multicellular animals, having various cell types but no distinct tissues. a: ©Norbert Probst/age fotostock Concept Check:   If sponges are soft and sessile, why aren’t they eaten by other organisms? 

Sponges Have Mechanical and Chemical Defenses Against Predators Some amoebocytes can form tough skeletal fibers that support the sponge’s body. In many sponges, this skeleton consists of sharp spicules formed of protein, calcium carbonate, or silica. For example, some deep-ocean species, called glass sponges, are distinguished by having needle-like silica spicules that form elaborate lattice-like skeletons. The presence of such tough spicules

may explain why predation of sponges is rare. Other sponges have fibers of a tough protein called spongin that lend skeletal support. Spongin skeletons are still commercially harvested and sold as bath sponges. Many species produce toxic defensive chemicals, some of which are being tested as possible anticancer and anti-inflammatory agents in humans.

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Sponges Reproduce Sexually and Asexually Sponges reproduce through both sexual and asexual means. Like ctenophores, most sponges are hermaphrodites, and thus can produce both sperm and eggs. Gametes are derived from amoebocytes or choanocytes. The eggs remain in the mesohyl, and the sperm are released into the water and carried by water currents to fertilize the eggs of neighboring sponges. Zygotes develop into flagellated swimming larvae that eventually settle on a suitable substrate to become sessile adults. In asexual reproduction, a small fragment or bud may detach and form a new sponge.

Table 34.1

Class and examples (est. number of species)

34.3       Cnidaria: Jellyfish and Other Radially Symmetric Animals Learning Outcomes: 1. Describe the four main classes of cnidarians, and compare and contrast the polyp and medusa body forms. 2. Describe how cnidarians defend themselves and capture prey.

Class characteristics

Hydrozoa: Portuguese man-of-war, Hydra, some corals (2,700)

Mostly marine; polyp stage usually dominant and colonial, reduced medusa stage

Scyphozoa: jellyfish (200)

All marine; medusa stage dominant and large (up to 2 m); reduced polyp stage

Anthozoa: sea anemones, sea fans, most corals (6,000)

All marine; polyp stage dominant; medusa stage absent; many are colonial

Cubozoa: box jellies, sea wasps (20)

All marine; medusa stage dominant; boxshaped

Deuterostomia

Ecdysozoa

Lophotrochozoa

Cnidaria

Porifera

Ctenophora

The members of the phylum Cnidaria (from the Greek knide, meaning nettle, and aria, meaning related to; pronounced nid-air’-e-ah) are mostly found in marine environments, although a few are freshwater species. Cnidaria includes hydra, jellyfish, box jellies, sea anemones, and corals. The cnidarians have only two Protostomia embryonic germ layers: the ectoderm and the endoderm. A gelatinous subBilateria stance called the mesoglea connects the two layers. In jellyfish, the mesoglea is enlarged and forms a transparent jelly, whereas in hydra and corals, the mesoglea is very thin. Most cnidarians have tentacles around the mouth that aid in prey detection and capture. The phylum Cnidaria consists of four classes: Hydrozoa (including the Portuguese man-of-war), Scyphozoa (jellyfish), Anthozoa (sea anemones and corals), and Cubozoa (box jellies). The distinguishing characteristics of these classes are shown in Table 34.1.

Main Classes and Characteristics of the Cnidaria

Cnidarians Exist in Two Different Body Forms Most cnidarians exist in one of two different body forms with an associated lifestyle: the sessile polyp or the motile medusa (Figure 34.4). For example, corals and sea anemones exhibit only the polyp form, and jellyfish exist predominantly in the medusa form. The polyp form has a tubular body with an opening at the oral (top) end that is surrounded by tentacles and functions as both mouth and anus

Mouth/ Tentacle anus

Ectoderm

Bell

Mesoglea Endoderm Gastrovascular cavity The mesoglea is thin in polyps and thick in medusae. Mouth/ anus (a) Polyp

Tentacle

(b) Medusa

Figure 34.4  Polyp and medusa forms of cnidarians.  Both (a) polyp and (b) medusa forms have two layers of cells, an outer layer of ectoderm and an inner layer of endoderm. In between is a layer of mesoglea, which is thin in polyps, such as corals, and thick in medusae, such as most jellyfish. a: Source: Linda Snook, NOAA/CBNMS; b: ©Kick Images/Getty Images

Concept Check:   What are the body forms of the following types of cnidarians: jellyfish, sea anemone, and Portuguese man-of -war? 



THE INVERTEBRATES 705 Gastrodermis Mesoglea Epidermis

Sensory cell Cnidocil Undischarged nematocyst

Discharged nematocyst Filament Stinging cell (cnidocyte)

When triggered, the cnidocyte discharges the nematocyst, which penetrates the prey. (a) Cnidocytes

(b) Portuguese man-of-war

Figure 34.5  Specialized stinging cells of cnidarians, called cnidocytes.  (a) Cnidocytes, which contain stinging capsules called nematocysts, are situated in the tentacles. (b) The Portuguese man-of-war (Physalia physalis) employs cnidocytes that can be lethal to humans. b: ©Nature/UIG/Getty Images Concept Check:   Are cnidocytes recycled for reuse once they have been fired? 

(see Figure 34.4a). The aboral (bottom) end is attached to the substrate. Polyps exist colonially, as in corals, or alone, as in sea anemones. Corals take dissolved calcium and carbonate ions from seawater and precipitate them as limestone underneath their bodies. With some species, this leads to a buildup of limestone deposits. As each successive generation of polyps dies, the limestone remains in place, and new polyps grow on top. Thus, huge underwater limestone deposits called coral reefs are formed (look ahead to Figure 54.26b). The largest of these is Australia’s Great Barrier Reef, which stretches over 2,300 km. Many other extensive coral reefs are known, including the reef system along the Florida Keys. All coral reefs occur in warm water, generally between 20°C and 30°C. The free-swimming medusa form has an umbrella-shaped body with an opening that serves as both mouth and anus located on the concave underside and surrounded by tentacles (see Figure 34.4b). More mobile medusae possess simple sense organs near the bell margin, including organs of equilibrium called statocysts and photosensitive organs known as ocelli. When one side of the bell tips upward, the statocysts on that side are stimulated, and muscle contraction is initiated to right the medusa. The ocelli allow medusae to position themselves in particular light levels.

Cnidarians Have Specialized Stinging Cells One of the unique and characteristic features of the cnidarians is the existence of stinging cells called cnidocytes, which function in defense or the capture of prey (Figure 34.5a). Cnidocytes contain nematocysts, powerful capsules with an inverted coiled and barbed thread. Each cnidocyte has a hairlike trigger called a cnidocil on its surface. When the cnidocil is touched or detects a chemical stimulus, the nematocyst is discharged, and its filament penetrates the prey and injects a small amount of toxin. Small prey are immobilized and passed into the mouth by the tentacles. After discharge, the cnidocyte is absorbed, and a new one grows to replace it. The nematocysts of most cnidarians are not harmful to humans, but those on the tentacles of the larger jellyfish and the Portuguese man-of-war (Figure 34.5b) can cause extreme pain or even death.

34.4 L  ophotrochozoa: The Flatworms, Rotifers, Bryozoans, Brachiopods, Mollusks, and Annelids Learning Outcomes: 1. Describe the unique features of platyhelminthes, rotifers, bryozoans, and brachiopods. 2. Outline the main features and list the major classes of the mollusks. 3. CoreSKILL » Analyze the results of Fiorito and Scotto’s experiments, and explain how they show that octopuses can learn by watching each another. 4. List the advantages of segmentation in the annelids.

As we explored in Chapter 33 (refer back to Figure 33.3), molecular data suggest three clades of bilateral animals: the Lophotrochozoa and the Ecdysozoa (collectively known as the protostomes) and the Deuterostomia. In this section, we will explore the distinguishing characteristics of the Lophotrochozoa, a diverse group that includes taxa that possess either a lophophore (a crown of ciliated tentacles, seen in Bryozoa and Brachiopoda) or a distinct larval stage called a trochophore (Mollusca and Annelida). Also included in this clade are the Platyhelminthes (some of which have trochophore-like larvae) and the Rotifera (which have a lophophore-like feeding device), both of which share molecular similarities with the other members of the Lophotrochozoa.

The Phylum Platyhelminthes Consists of Flatworms with No Coelom Platyhelminthes (from the Greek platy, meaning flat, and helminth, meaning worm), or flatworms, lack a specialized respiratory or

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CHAPTER 34

Ecdysozoa

Deuterostomia

Bryozoa Brachiopoda Mollusca Annelida

Rotifera

Platyhelminthes

Porifera

Cnidaria

Ctenophora

Lophotrochozoa

circulatory system and must respire by diffusion. Thus, no cell can be too far from the surface, making a flattened shape necessary. Flatworms were among the first animals to develop an active predatory lifestyle. However, most species are internal or external parasites.

Flatworm Body Plan  The flatworms are hypothProtostomia esized to be the first bilaterian animals to Bilateria evolve three distinctive embryonic germ layers— ectoderm, endoderm, and mesoderm—with mesoderm replacing the simpler gelatinous mesoglea of cnidarians. For this reason, they are said to be triploblastic. The muscles in flatworms, which are derived from mesoderm, are well developed. The evolution of mesoderm was a critical innovation in animals, leading to the development of more sophisticated organs.  Flatworms lack a coelem—a fluid-filled body cavity in which the gut is suspended. Therefore, they are described as acoelomates. Instead, mesoderm fills the body spaces around the gastrovascular cavity (Figure 34.6). The digestive system of flatworms is incomplete, with only one opening, which serves as both a mouth and an anus, as in cnidarians. Most flatworms possess a muscular pharynx Lophotrochozoa

Ocelli (eyespots)

that may be extended through the mouth. The pharynx opens to a gastrovascular cavity, where food is digested. In large flatworms, the gastrovascular cavity is highly branched to distribute nutrients to all parts of the body. Flatworms have a distinct excretory system consisting of protonephridia, two lateral canals with branches capped by flame cells. Protonephridia are dead-end tubules lacking internal openings. The flame cells, which are ciliated and waft water through the lateral canals to the outside (look ahead to Figure 49.2), primarily function in maintaining osmotic balance between the flatworm’s body and the surrounding fluids. Simple though this system is, its development was key to permitting the movement of animals into freshwater habitats and even moist terrestrial areas. Platyhelminthes are bilaterally symmetrical with a head bearing sensory appendages, the result of the process called cephalization (see Figure 34.6). At the anterior end of some free-living flatworms are light-sensitive eyespots, called ocelli, as well as chemoreceptive and sensory cells that are concentrated in organs called auricles. A pair of cerebral ganglia, clusters of nerve cell bodies, receives input from photoreceptors in eyespots and sensory cells. From the ganglia, a pair of lateral nerve cords running the length of the body allow rapid movement of information from anterior to posterior. In addition, transverse nerves form a nerve net on the ventral surface, similar to that of cnidarians. Thus, flatworms show the beginnings of the more centralized type of nervous system seen throughout much of the rest of the animal kingdom. The Classes of Flatworms  The four classes of flatworms are the Turbellaria, Monogenea, Cestoda (tapeworms), and Trematoda (flukes) (Table 34.2).  ∙∙ Turbellarians are the only free-living class of flatworms and are widespread in lakes, ponds, and marine environments (Figure 34.7a). 

Table 34.2

Auricles

Main Classes and Characteristics of Platyhelminthes Class and examples (est. number of species)

Cerebral ganglia Lateral nerve cords Protonephridia Transverse nerve Gastrovascular cavity

Mostly marine; freeliving flatworms; predatory or scavengers

Monogenea: fish flukes (1,000)

Marine and freshwater; usually external parasites of fish; simple life cycle (no intermediate host)

Cestoda: tapeworms (5,000)

Internal parasites of vertebrates; complex life cycle, usually with one intermediate host; no digestive system; nutrients absorbed across epidermis

Trematoda: flukes (11,000)

Internal parasites of vertebrates; complex life cycle with several intermediate hosts

Pharyngeal chamber Mouth

Pharynx

Figure 34.6  Body plan of a flatworm.  Flatworm morphology is represented by a planarian, a member of the class Turbellaria. Concept Check:   How do flatworms breathe?

Class characteristics

Turbellaria: planarian (3,000)



THE INVERTEBRATES 707

(Figure 34.7b). They have no mouth or gastrovascular cavity and absorb nutrients across the body surface.

(a)

Proglottids Scolex

(b)

Figure 34.7  Flatworms.  (a) Many free-living marine

turbellarians are brightly colored, such as this racing stripe flatworm, Pseudoceros bifurcus, from Bali, Indonesia. (b) A tapeworm, Taenia pisiformis, a member of the class Cestoda. Note the tiny hooks and suckers that make up the scolex. Each segment is a proglottid, which may be filled with eggs.

a: ©Wolfgang Poelzer/age fotostock; b: ©Biophoto Associates/Science Source

 ore Skill: Science and Society  About 1% of U.S. C cattle are infected by beef tapeworms. Consuming beef that is not sufficiently well cooked can lead to infection by these parasites. At least 1,000 hospitalizations a year in the U.S. are due to tapeworm infection, most as a result of eating uncooked pork.

∙∙ Monogeneans are relatively simple external parasites with just one host species (a fish).  ∙∙ Cestodes and trematodes are internally parasitic in humans and other animals and therefore are of great medical and veterinary importance. They possess a variety of organs of attachment, such as hooks and suckers, that enable them to remain embedded within their hosts. For example, cestodes attach to their host by means of an organ at the head end called a scolex

Reproduction in Flatworms  In Platyhelminthes, reproduction is either sexual or asexual. Most species are hermaphroditic but do not fertilize their own eggs. Flatworms can also reproduce asexually by splitting into two parts, with each half regenerating the missing fragment. Flatworm life cycles can be complex. Cestodes often require two different vertebrate host species, such as pigs or cattle, to begin their life cycle and another host, such as humans, to complete their development. Behind the scolex in cestodes is a long ribbon of identical segments called proglottids, which are segments of sex organs that produce thousands of eggs. The proglottids are continually shed in the host’s feces. Human feces passed out onto the ground are eaten with grass by pigs and cattle. Many tapeworms are ingested by humans who consume undercooked, infected meat—hence it is important to cook meat thoroughly. The life cycle of trematodes is typically more complex than that of cestodes, involving multiple hosts. The first host, called the intermediate host, is usually a mollusk, and the final host, or definitive host, is usually a vertebrate, but often a second or even a third intermediate host is involved. In the case of the Chinese liver fluke (Clonorchis sinensis), the adult parasite lives and reproduces in the definitive host, a human (see step 1,  Figure 34.8). Structures, which are sometimes called eggs, contain encapsulated miracidia; these pass from the host via the feces, and then an intermediate host, such as a snail, eats the miracidia, which transform into sporocysts (see steps 2 and 3). The sporocysts asexually produce more sporocysts called rediae, which develop into a free-swimming life stage called cercariae (see steps 4 and 5). In the last stages of the life cycle, cercariae bore their way out of the snail and infect their second intermediate host, fishes, by entering via the gills. Here, the cercariae develop into juvenile flukes and lodge in fish muscle, which the definitive host will eat (see steps 6 and 7). From the small intestine of the definitive host, the juvenile flukes travel to the liver and grow into adult flukes, and the life cycle begins anew. The probability of each trematode stage reaching a suitable host is low, so trematodes produce large numbers of offspring to ensure that some survive. Blood flukes, genus Schistosoma, are the most common parasitic trematodes infecting humans; they cause the disease known as schistosomiasis. Over 200 million people worldwide, primarily in tropical Asia, Africa, and South America, are infected with schistosomiasis. The inch-long adult flukes may live for years in human hosts, and the release of eggs may cause chronic inflammation and blockage in many organs. Untreated schistosomiasis can result in severe damage to the liver, intestines, and lungs and eventually lead to death. Sewage treatment and access to clean water greatly reduce infection rates.

Members of the Phylum Rotifera Have a Pseudocoelom and a Ciliated Crown Members of the phylum Rotifera (from the Latin rota, meaning wheel, and fera, meaning to bear) get their name from their ciliated crown, or corona, which, when beating, looks similar to a rotating wheel

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1 7

Cercariae develop into juvenile flukes and migrate to fish muscle.

If a human eats infected raw fish, juvenile flukes travel to the bile ducts of the liver, where they mature and produce eggs.

Water

Many cercariae

Free-swimming cercariae attach to fish gills, in carp or related species.

5

Eggs are released in feces.

Capsule

Miracidium

Adult fluke

6

2

Rediae develop into free-swimming life stages called cercariae, which break out of a snail’s body.

Many rediae

Egg

Sporocyst

3

Snails eat the eggs, which transform into sporocysts.

Water 4

Sporocysts produce more sporocysts, called rediae, which develop in a snail’s body.

Figure 34.8  The complete life cycle of a trematode.  This figure shows the life cycle of the Chinese liver fluke (Clonorchis sinensis). (Figure 34.9). Most rotifers are microscopic animals, usually less than 1 mm long, and some have beautiful colors. About 2,200 species of rotifers have been identified. They typically inhabit fresh water, with a few marine and terrestrial species. Most often they are bottom-dwelling organisms, living on a pond floor Lophotrochozoa or along lakeside vegetation. The body of the rotifer Protostomia bears a jointed foot with one Bilateria to four toes. Pedal glands in the foot secrete a sticky substance that aids in attachment to a substrate. The internal organs of rotifers lie within a pseudocoelom, a fluid-filled body cavity that is not completely lined with mesoderm. The pseudocoelom serves as a hydrostatic skeleton and as a medium for the internal transport of nutrients and wastes. Rotifers have an alimentary canal, a digestive tract with a separate mouth and anus. For this reason, rotifers can feed more frequently compared to simpler animals that have a single opening to their digestive system, such as cnidarians. The corona of rotifers creates water currents that propel the animal through the water and waft small planktonic organisms or decomposing organic material

Mouth

Ecdysozoa

Deuterostomia

Bryozoa Brachiopoda Mollusca Annelida

Rotifera

Platyhelminthes

Porifera

Cnidaria

Ctenophora

Lophotrochozoa

Corona

Flame bulb Eyespot

Brain Mastax

Digestive gland Protonephridium

Stomach Pseudocoelom Intestine Bladder Anus

Foot

Pedal glands

Toe

Figure 34.9  Body plan of a common rotifer, Philodina genus. toward the mouth. The mouth opens into a circular, muscular pharynx called a mastax, which has jaws for grasping and chewing. The mastax, which in some species can protrude through the mouth to seize small prey, is a structure unique to rotifers. They also have a pair of protonephridia with flame bulbs that collect excretory and digestive waste



THE INVERTEBRATES 709

and drain into a bladder, which passes waste to the anus. The nervous system consists of nerves that extend from the sensory organs, especially the eyespots and some bristles on the corona, to the brain. Reproduction in rotifers is unique. In some species, unfertilized diploid eggs that have not undergone meiotic division develop into females through a process known as parthenogenesis. In other species, some unfertilized eggs develop into females, whereas others develop into males that live only long enough to produce and release sperm that fertilize the eggs. The resultant fertilized eggs form zygotes, which have a thick shell and can survive for long periods of harsh conditions, for example, if a water supply dries up, before developing into new females. Because the tiny zygotes are easily transported, rotifers show up in the smallest of aquatic environments, such as birdbaths or roof gutters.

Zoecium

Lophophore

(a) A bryozoan

Protostomia Bilateria

Deuterostomia

Brachiopoda Mollusca Annelida Ecdysozoa

Bryozoa

Rotifera

Cnidaria

Platyhelminthes

Porifera

Ctenophora

Lophotrochozoa

(b) A brachiopod, the northern lamp shell

Figure 34.10  Bryozoans and brachiopods.  (a) Bryozoans are colonial animals that reside in a nonliving case called a zoecium. (b) Brachiopods, such as this northern lamp shell (Terebratulina septentrionalis), have dorsal and ventral shells. a: ©G. Guenther/age fotostock;

b: ©Gordon MacSkimming/age fotostock

Concept Check:   What are the two main functions of the lophophore? 

Bryozoa and Brachiopoda Have a Lophophore for Feeding and Gas Exchange Lophotrochozoa

Lophophore

The Bryozoa and the Brachiopoda both possess a lophophore, a ciliary feeding device (refer back to Figure 33.14a), and a true coelom (refer back to Figure 33.7a). The lophophore is a circular fold of the body wall bearing tentacles that draw water toward the mouth. Because a thin extension of the coelom penetrates each tentacle, the tentacles also serve as a respiratory organ. Gases diffuse across the tentacles and into or out of the coelomic fluid and are carried throughout the body. Both phyla have a U-shaped alimentary canal, with the anus located near the mouth but outside of the lophophore.

Phylum Bryozoa  The bryozoans (from the Greek bryon, meaning moss, and zoon, meaning animal) are small colonial animals, most of which are less than 0.5 mm long, that can be found on rocks in shallow aquatic environments. They look very much like plants. Within a colony, each animal secretes and lives inside a nonliving exoskeleton called a zoecium that is composed of chitin or calcium carbonate (Figure 34.10a). For this reason, bryozoans have been important reefbuilders. Also, many of them encrust boat hulls and have to be scraped off periodically. About 4,500 species of bryozoans currently exist. They date back to the Paleozoic era, and thousands of fossil forms have been discovered and identified.

Phylum Brachiopoda  Brachiopods (from the Greek brachio, meaning arm, and podos, meaning foot) are marine organisms with two shell halves, much like clams (Figure 34.10b). In clams, however, the shell halves are considered to be left and right sides with the plane of symmetry lying parallel to the site at which the shells join. In contrast, brachiopods have a dorsal and ventral shell, with the plane of symmetry perpendicular to the site at which the shells join. The dorsal and ventral shells of brachiopods are of slightly different sizes and shapes. Brachiopods are bottom-dwelling species that attach to the substrate via a muscular pedicle. Although they are now a relatively small group, with about 300 living species, brachiopods flourished in the Paleozoic and Mesozoic eras—about 30,000 fossil species have been identified. Some of these fossil forms represent organisms that reached 30 cm in length, although their modern relatives are only 0.5–8.0 cm long.

Mollusca Is a Large Phylum Containing Snails, Slugs, Clams, Oysters, Octopuses, and Squids Mollusks (from the Latin mollis, meaning soft) constitute a very large phylum, with over 100,000 living species, including organisms as diverse as snails, clams, octopuses, and chitons. They are an ancient group, as evidenced by the classification of about 35,000 fossil species. Mollusks have considerable economic, aesthetic, and ecological importance to humans. Many serve as sources of food, including scallops, oysters, clams, and squids. A significant industry involves the farming of oysters to produce cultured pearls, and rare and beautiful mollusk shells are extremely valuable to collectors. Snails and slugs can damage vegetables and ornamental plants, and boring mollusks can penetrate wooden ships and wharfs. Mollusks are intermediate hosts to many parasites, and several invasive species have become serious pests. For example, populations of the zebra mussel (Dreissena polymorpha) have been introduced into North America from Asia, probably via ballast water from transoceanic ships. Since their introduction, they have spread rapidly throughout the Great Lakes and an increasing number of inland waterways, adversely impacting native organisms and clogging water intake valves of municipal water-treatment plants around the lakes.

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Mollusk Body Plan  One common feature of mollusks is their soft body, which in many species is found under a protective external shell. Most mollusks are marine, although some have colonized fresh water. Many snails and slugs have moved onto land, but they survive only in humid areas and where the calcium necessary Lophotrochozoa for shell formation is abundant in the soil. The ability Protostomia to colonize freshwater and terrestrial habitats has led to Bilateria a diversification of mollusk body plans. The amazing diversity of mollusks demonstrates how species diversity is related to environmental diversity. Although great variation in morphology occurs between classes, mollusks have a basic body plan consisting of three parts (Figure 34.11).  Ecdysozoa

Deuterostomia

Rotifera

Bryozoa Brachiopoda Mollusca Annelida

Platyhelminthes

Porifera

Cnidaria

Ctenophora

Lophotrochozoa

∙∙ A muscular foot is usually used for movement, and a visceral mass containing the internal organs rests atop the foot.  ∙∙ The mantle, a fold of skin draped over the visceral mass, secretes a shell in those species that form shells.   ∙∙ The mantle cavity houses delicate gills, filamentous organs that are specialized for gas exchange. A continuous current of water, often induced by cilia present on the gills or by muscular pumping, flushes out the wastes from the mantle cavity and brings in new oxygen-rich water. Visceral mass

Gonads

Heart

Coelom

Metanephridium

Stomach

Mantle cavity

Digestive gland

Mantle

Shell

Anus

Foot

Nerve cords

Mouth

Intestine

Gill

Radula

Mollusks are coelomate organisms, but the coelom is confined to a small area around the heart. Most species of mollusks have an open circulatory system with a heart that pumps a body fluid called hemolymph through vessels and into sinuses. Sinuses are open, fluidfilled cavities between the internal organs. The organs and tissues are therefore continually bathed in hemolymph. The sinuses coalesce to form an open cavity known as the hemocoel (blood cavity). From these sinuses, the hemolymph drains into vessels that take it to the gills and then back to the heart. Excretory organs called metanephridia remove nitrogenous and other wastes. Metanephridia have ciliated funnel-like openings inside the coelom that are connected to ducts that lead to the exterior mantle cavity. The pores from the metanephridia discharge wastes into this cavity. The anus also opens into the mantle cavity. The metanephridial ducts may also serve to discharge sperm or eggs from the gonads. The nervous system varies from simple ganglia and nerve chords in most species to much larger brains and sophisticated organs of touch, smell, taste, and vision in octopuses. The mollusk’s mouth may contain a radula, a unique, protrusible, tonguelike organ that has many teeth and is used to eat plants, scrape food particles off rocks, or, if the mollusk is predatory, bore into shells of other species and tear flesh. In the cone shells (genus Conus), the radula is reduced to a few poison-injecting teeth on the end of a long proboscis that is cast about in search of prey, such as a worm or even a fish. Some cone shell species produce a neuromuscular toxin that can kill humans. Other mollusks, particularly bivalves, have lost their radula and are filter feeders that strain water brought in by ciliary currents. Mollusk Shells  Most mollusk shells are complex three-layered structures that are secreted by the mantle and continue to grow as the mollusk grows. Shell growth is often seasonal, resulting in distinct growth lines on the shell, much like tree rings (Figure 34.12a). Using shell growth patterns, biologists have discovered some bivalves that are over 100 years old. The innermost layer of the shells of oysters, mussels, abalone, and other mollusks is a smooth, iridescent lining called nacre, which is commonly known as mother-of-pearl and is often collected from abalone shells for jewelry. Actual pearl production in mollusks, primarily oysters, occurs when a foreign object, such as a grain of sand, becomes lodged between the shell and the mantle, and layers of nacre are laid down around it to reduce the irritation. Reproduction in Mollusks  Most mollusks species have separate sexes, although some exist as hermaphrodites. Gametes are usually released into the water, where they mix and fertilization occurs. In some snails, however, fertilization is internal, with the male inserting sperm directly into the female. Internal fertilization was a critical innovation enabling some snails to colonize land. In many species, reproduction involves the production of a trochophore larva that develops into a veliger, a free-swimming larva that has a rudimentary foot, shell, and mantle (Figure 34.13).

Figure 34.11  The mollusk body plan.  The generalized body plan

of a mollusk includes the characteristic foot, mantle, and visceral mass. Concept Check:   Do molluscan hearts pump blood?

The Major Molluscan Classes  Of the eight molluscan classes, the four most common are the Bivalvia (clams and mussels),



THE INVERTEBRATES 711

(a) A quahog clam, class Bivalvia

(c) A snail, class Gastropoda

(b) A chiton, class Polyplacophora

(d) A nudibranch, class Gastropoda

Figure 34.12  Mollusks.  (a) A bivalve shell, class Bivalvia, with

growth rings. This quahog clam (Mercenaria mercenaria) can live over 20 years. (b) A chiton (Tonicella lineata), a polyplacophoran with a shell made up of eight separate plates. (c) A gastropod, the tree snail, Liguus fasciatus, from the Florida Everglades showing its characteristic coiled shell. (d) A nudibranch (Phyllidia ocellata). The nudibranchs are a gastropod subclass whose members have lost their shell altogether. (e) The highly poisonous blue-ringed octopus (Hapalochlaena lunulata), a cephalopod. a: ©Andrew J. Martinez/Science Source; b: ©Kjell B. Sandved/Science Source; c: ©ImageBROKER/Alamy Stock Photo; d: ©Hal Beral/Corbis /Getty Images; e: ©Richard Merritt FRPS/Getty Images

Polyplacophora (chitons), Gastropoda (snails and slugs), and Cephalopoda (octopuses, squids, and nautiluses) (Table 34.3). ∙∙ Bivalves are freshwater or marine mollusks whose bodies are enclosed within a hinged shell of two valves, or halves. Prominent members of this class include oysters, clams, mussels, and scallops (Figure 34.12a). ∙∙ Polyplacophora are marine mollusks with a shell composed of eight separate plates (Figure 34.12b). Chitons are common in the intertidal zone, an area above water at low tide and under water at high tide, and they creep along when covered by the tide. Feeding occurs by scraping algae off rock surfaces. When the tide recedes, the muscular foot holds the chiton tight to the rock surface, preventing desiccation.

(e) A blue-ringed octopus, class Cephalopoda

∙∙ The class Gastropoda (from the Greek gaster, meaning stomach, and podos, meaning foot) is the largest group of mollusks and encompasses about 75,000 living species, including snails, periwinkles, and limpets (Figure 34.12c). Most gastropods have a one-piece shell, into which the animal can withdraw to escape predators, However, the class also includes species such as slugs and nudibranchs, whose shells have been greatly reduced or completely lost during their evolution (Figure 34.12d). Although gastropods usually occupy marine or freshwater habitats, some species, including snails and slugs, have also colonized land. The 780 species of Cephalopoda (from the Greek kephalo, meaning head, and podos, meaning foot) are the most

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Table 34.3

Major Classes and Characteristics of Mollusks Class and examples (est. number of species)

Figure 34.13  A snail veliger.  Veligers are free-swimming larval

forms of mollusks that look more like adults than the trocophore larvae from which they develop. ©Solvin Zankl/Alamy Stock Photo

morphologically complex of the mollusks and indeed among the most complex of all invertebrates. Most are fast-swimming marine predators that range from organisms just a few centimeters in size to the colossal squid (Mesonychoteuthis hamiltoni), which is known to reach over 13 m in length and 495 kg (1,091 lb) in weight. A cephalopod’s mouth is surrounded by many long arms commonly armed with suckers. All cephalopods have a beaklike jaw that allows them to bite their prey, and some, such as the blue-ringed octopus (Hapalochlaena lunulata), deliver a deadly poison through their saliva (Figure 34.12e).  The foot of some cephalopods has become modified into a muscular siphon. Water drawn into the mantle cavity is quickly expelled through the siphon, propelling the organism forward or backward in a kind of jet propulsion. Such vigorous movement requires powerful muscles and a very efficient circulatory system to deliver oxygen and nutrients to the muscles. Cephalopods are the only mollusks with a closed circulatory system, in which

Class characteristics

Bivalvia: clams, mussels, oysters, scallops (30,000)

Marine or freshwater; shell with two halves or valves; primarily filter feeders with siphons

Polyplacophora: chitons (860)

Marine; eight-plated shell

Gastropoda: snails, slugs, nudibranchs (75,000)

Marine, freshwater, or terrestrial; most with coiled shell, but shell absent in slugs and nudibranchs; radula present

Cephalopoda: octopuses, squids, nautiluses (780)

Marine; predatory, with tentacles around mouth, often with suckers; shell often absent or reduced; closed circulatory system; jet propulsion via siphon

blood flows throughout an animal entirely within a series of vessels. One of the advantages of this type of system is that the heart can pump blood through the tissues rapidly, making oxygen more readily available. The blood of cephalopods contains the copperrich protein hemocyanin for transporting oxygen. Less efficient than the iron-rich hemoglobin of vertebrates, hemocyanin gives the blood a blue color. Cephalopods have a well-developed nervous system and brain that support their active lifestyle. Their sense organs, especially their eyes, are also very well developed. Many cephalopods (with the exception of nautiluses) have an ink sac that contains the pigment melanin; the sac can be emptied to provide a “smokescreen” to confuse predators. In many species, melanin is also distributed in special pigment cells in the skin, which allows for color changes. Octopuses often change color when disturbed, and they can change color rapidly to blend in with their background and escape detection. 

Core Skill: Process of Science

Feature Investigation  | Fiorito and Scotto’s Experiments Showed That Invertebrates Can Exhibit Sophisticated Observational Learning Behavior

The ability to learn by observing the behavior of others has commonly been observed in vertebrates, especially among species that live in social groups. For example, young rhesus macaques (Macaca mulatta) that observed their parents fearfully responding to model snakes also developed a fear of snakes and maintained this fear

for 3 months after observing their parent's behavior. In 1992, Italian researchers Graziano Fiorito and Pietro Scotto set out to test the hypothesis that octopuses (invertebrates) can learn by observing the behavior of other octopuses (Figure 34.14). 



THE INVERTEBRATES 713

Figure 34.14  Observational learning in octopuses. HYPOTHESIS Octopuses can learn by observing another’s behavior. STUDY LOCATION Laboratory setting with Octopus vulgaris collected from the Bay of Naples, Italy. Experimental level

1

Train 2 groups of octopuses, one to attack white balls, one to attack red. These are called the demonstrator octopuses.

2

In an adjacent tank, allow observer octopus to watch trained demonstrator octopus.

Reward choice of correct ball (with fish) and punish choice of incorrect ball (with electric shock). Training is complete when octopus makes no “mistakes” in 5 trials.

Drop balls into the tank of the observer octopus. Test the observer octopus to see if it makes the same decisions as the demonstrator octopus.

4

THE DATA Participant

Conditions a demonstrator octopus to attack a particular color of ball.

Demonstrator

Observer

3

Conceptual level

Observer octopus may be learning the correct ball to attack by watching the demonstrator octopus.

If the observer octopus is learning from the demonstrator octopus, the observer octopus should attack the ball of the same color as the demonstrator octopus was trained to attack.

Observer

Color of ball chosen in 5 trials* Red

White

Observers (watched demonstrator attack red)

4.31

0.31

Observers (watched demonstrator attack white)

0.40

4.10

Untrained (did not watch demonstrations)

2.11

1.94

*Average of 5 trials; data do not always sum to 5, because some trials resulted in no balls being chosen.

5

CONCLUSION Invertebrate animals are capable of learning from watching other individuals behave, in much the same way as vertebrate species learn from watching others.

6

SOURCE Fiorito, G., and Scotto, P. 1992. Observational learning in Octopus vulgaris. Science 256: 545–547.

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P ROBLEM-SOLVING   S TRATEGY  Make a calculation. To solve this problem, you determine percentages of correct responses, initially (on day 1) and after 5 days, for both groups of observer octopuses. For the octopuses that watched a demonstrator trained to attack a red ball, the percentages are as follows.

4.31 Day 1: ​​(​ _________    ​)   ​​ × 100 = 93.3% 4.31 + 0.31

3.88 Day 5: ​​(​ __________       ​)​​ × 100 = 88.6% 3.88 + 0.50 For the octopuses that watched a demonstrator trained to attack a white ball, the percentages are as follows.

4.10 Day 1: ​​(_________ ​     ​)   ​​ × 100 = 91.1% 4.10 + 0.40

3.70 Day 5: ​​(__________    ​     ​)​​ × 100 = 88.1% 3.70 + 0.50

ANSWER The octopuses appeared to retain their learning fairly well, because only a slight drop (less than 5%) was observed after 5 days.

The Phylum Annelida Consists of the Segmented Worms

Annelid Body Plan  The phylum name Annelida is derived from the Latin annulus, meaning little ring. Each ring is a distinct segment of the annelid’s body; adjacent segments are separated by septa (Figure 34.15). Segmentation in the adult confers three advantages:

Deuterostomia

Lophotrochozoa

Ecdysozoa

Annelids are a large phylum with about 18,000 species of segmented worms. The members include freeranging marine worms, tube worms, the familiar earthworm, and leeches. They range in size from less than 1 mm to enormous Australian earthworms that can reach a length of 3 m.

Bryozoa Brachiopoda Mollusca Annelida

I NFORMATION  What information do you know based on the question and your understanding of the topic? In the data of Figure 34.14, you are given the initial frequency of color choices made by the observers. From the question, you know the frequency of color choices made 5 days later.

3. CoreSKILL » Explain the significance of performing the experiment on both observer octopuses and untrained octopuses. 

Rotifera

T OPIC  What topic in biology does this question address? The topic is learning; more specifically it is about learning retention in octopuses.

1. What was the hypothesis tested by Fiorito and Scotto?  2. CoreSKILL » What were the results of the experiment? Did these results support the hypothesis? 

Platyhelminthes

THE QUESTION  To determine if the observer octopuses would retain their learning, Fiorito and Scotto conducted follow-up trials. Five days after their initial testing, the observer octopuses were retested for their ability to choose the correct ball. The observers that had watched a demonstrator that was trained to attack a red ball made the following choices of color: red, 3.88; white, 0.50. The observers that had watched a demonstrator trained to attack a white ball made the following choices: red, 0.50; white, 3.70. Were the observer octopuses retaining their learning after 5 days?

Experimental Questions

Cnidaria

BIO TIPS

likely to attack a red or white ball. These results indicate that one octopus can learn by watching the behavior of another octopus. This was a unexpected finding because many researchers thought that such complex learning would not be found in invertebrate species. It is also surprising because Octopus vulgaris, the species they studied, lives a solitary existence for most of its life.

Porifera

In their experiments, they used a system of reward (a small piece of fish placed behind a ball so that the octopus could not see it) and punishment (a small electric shock for choosing the wrong ball) to train octopuses to attack either a red or a white ball. This type of learning is called classical conditioning (see Chapter 55). Because octopuses are color blind, they must distinguish between the relative brightness of the balls. Octopuses were considered to be trained when they made no mistakes in five trials.  Observer octopuses in adjacent tanks were then allowed to watch the trained octopuses attacking the balls. In step 3, the observer octopuses were themselves tested, as were untrained octopuses that had never watched the demonstrators. As seen in the data, observers nearly always attacked the same color ball as they had observed the demonstrators attacking. In contrast, the untrained octopuses were equally

Ctenophora

714

Lophotrochozoa Protostomia Bilateria

∙∙ Many components of the body are repeated in each segment, including blood vessels, nerves, and excretory and reproductive organs. If the components in one segment fail, those of another segment will still function.



THE INVERTEBRATES 715

Anus

Cuticle Metanephridium

Epidermis Circular muscle Longitudinal muscle

Coelom

Dorsal vessel

Septum (partition)

Intestine Setae Ventral vessel

Nerve cord

Reproduction in Annelids  Sexual reproduction in annelids involves two individuals, often of separate sexes, but sometimes hermaphrodites, which exchange sperm via internal fertilization. In some species, asexual reproduction by fission occurs, in which the posterior part of the body breaks off and forms a new individual.

Clitellum Metanephridium Crop

Pharynx

Pulsating vessels

Cerebral ganglia Mouth

Intestine Gizzard Ventral nerve Setae

Esophagus

a large ventral nerve cord runs down the entire length of the body. The ventral nerve cord is unusual because it contains a few very large nerve cells called giant axons that facilitate high-speed neuronal conduction and rapid responses to stimuli. Annelids have an internal transport system in which the circulatory system and the coelomic fluid both carry nutrients, wastes, and respiratory gases. The circulatory system is closed, with dorsal and ventral vessels connected by pairs of pulsating vessels. The blood of most annelid species contains the respiratory pigment hemoglobin. Respiration occurs directly through the permeable skin surface, which restricts annelids to moist environments. The digestive system is complete and unsegmented, with many specialized regions: mouth, pharynx, esophagus, crop, gizzard, intestine, and anus.

Subpharyngeal ganglion

Figure 34.15  The segmented body plan of an annelid,

as illustrated by an earthworm.  The segmented nature of the worm is apparent internally as well as externally. Individual segments are separated by septa. Concept Check:   What are some of the advantages of segmentation?

∙∙ Annelids possess a fluid-filled coelom that acts as a hydrostatic skeleton. In unsegmented coelomate animals, muscle contractions can distort the entire body during movement. However, such distortion is minimized in segmented animals, which allows for more effective locomotion over solid surfaces. ∙∙ Segmentation permits specialization of some segments, especially at the annelid’s anterior end. Animals with more complex body plans tend to produce a greater variety of specialized segments. All annelids except the leeches have chitinous bristles, called setae, on each segment. In some annelids, these are situated on fleshy, footlike parapodia (from the Greek, meaning almost feet) that are pushed into the substrate to provide traction during movement. In others, the setae are held closer to the body. Many annelid species burrow into soil or into muddy marine sediments and extract nutrients from ingested soil or mud. Some annelids also feed on dead or living vegetation, whereas others are predatory or parasitic. Annelids have a nervous system with a pair of cerebral ganglia that connect to a subpharyngeal ganglion (Figure 34.15). From there,

The Major Annelidan Groups  In 2011, a study by German evolutionary biologist Torsten Struck and colleagues suggested that the phylum Annelida contains two major groups: the Errantia and the Sedentaria. Members of the Errantia have many long setae bristling out of their body and are supported on footlike parapodia (Figure 34.16a). Most of them are free-ranging predators with welldeveloped eyes and powerful jaws. Many are brightly colored. In turn, most species are important prey for fishes and crustaceans. In the Sedentaria, setae are in close proximity to the body wall, which facilitates anchorage in tubes and burrows. The more sedentary lifestyle of the Sedentaria is associated with reductions in head appendages. Within this group, three types of lifestyles are apparent: those of tube worms, earthworms, and leeches.  Tube worms are marine sedentarians that exhibit beautiful tentacle crowns for filtering food items, such as plankton, from the water (Figure 34.16b). The bulk of the worm remains hidden in a tube deep in the mud or sand. Earthworms play a unique and beneficial role in conditioning the soil, primarily due to the effects of their burrows and excretion. Earthworms ingest soil and leaf tissue to extract nutrients and in the process create burrows in the earth. As plant material and soil pass through the earthworm’s digestive system, it is finely ground in the gizzard into smaller fragments. Once excreted, this material—called castings—enriches the soil (Figure 34.16c). Because a worm can eat its own weight in soil every day, worm castings on the soil surface can be extensive. The biologist Charles Darwin was interested in earthworm activity, and his last work, The Formation of Vegetable Mould, through the Actions of Worms, with Observations on Their Habits, was the first detailed study of earthworm ecology. In it, he wrote, “All the fertile areas of this planet have at least once passed through the bodies of earthworms.” Leeches are usually found in freshwater environments, but some are marine species and others are terrestrial species that inhabit warm, moist areas such as tropical forests. They have a fixed number of segments, usually 34, though in most species septa are not present. Most leeches are blood-sucking parasites of vertebrates. Unlike

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(b)

(d)

Figure 34.16  Annelids.  (a) This free-ranging marine worm from Indonesia is a member of the group Errantia. Members of the group Sedentaria include (b) tube worms, (c) earthworms, and (d) leeches. This leech species, Hirudo medicinalis, is sucking blood from a patient to reduce the swelling that can occur after surgery. a: ©WaterFrame/Alamy Stock Photo; b: ©J W Alker/age fotostock; c: ©Colin Varndell/Getty

(a)

(c)

cestode and trematode flatworms, which are internally parasitic and host-specific, leeches are generally external parasites that feed on a broad range of hosts, including fishes, amphibians, and mammals. Leeches have powerful suckers at both ends of the body, and the anterior sucker is equipped with razor-sharp jaws that can bore or slice into the host’s tissues. The salivary secretion (hirudin) acts as an anticoagulant to stop the prey’s blood from clotting and an anesthetic to numb the pain. Leeches can suck up to several times their own weight in blood. They were once used in the medical field in the practice of bloodletting, the withdrawal of often considerable quantities of blood from a patient in the erroneous belief that this would prevent or cure illness and disease. Even today, leeches may be used after surgeries (Figure 34.16d). If the blood vessels are not fully reconnected and excess blood accumulates, a swelling called a hematoma may form. The accumulated blood blocks the delivery of new blood and stops the formation of new vessels. The leeches remove the accumulated blood, and new capillaries are more likely to form.

34.5 E  cdysozoa: The Nematodes and Arthropods Learning Outcomes: 1. List the distinguishing characteristics of nematodes. 2. Describe the arthropod body plan and its major features. 3. Give examples of the arthropod subphyla Chelicerata, Myriapoda, Hexapoda, and Crustacea. 4. List the features that help to account for the diversity of insect species. 5. CoreSKILL » Explain how DNA barcoding can be useful in analyzing and controlling insect populations.

Images; d: ©St. Bartholomew's Hospital/Science Source

The Ecdysozoa is the sister group to the Lophotrochozoa. Although the separation is supported by molecular evidence, the Ecdysozoa is named for a process called  ecdysis, or the periodic molting of the exoskeleton (refer back to Figure 33.13). All ecdysozoans possess a cuticle, a nonliving covering that both supports and protects the animal. Once formed, however, the cuticle typically cannot increase in size, which restricts the growth of the animal inside. The solution for growth is the formation of a new, softer cuticle under the old one. The old one then splits open and is sloughed off, allowing the new, soft cuticle to expand to a bigger size before it hardens.  The evolution of a cuticle was a critical innovation that led to other changes in ecdysoans. A thick cuticle, as in arthropods, impedes the diffusion of oxygen across the skin. Such species acquire oxygen by lungs, gills, or a set of branching, air-filled tubes called tracheae. The ability to shed the cuticle also opened up developmental options for the ecdysozoans. For example, many species undergo complete metamorphosis, changing from a wormlike larva into a winged adult. Animals with internal skeletons cannot do this because growth occurs only by adding more minerals to the existing skeleton. Another significant adaptation is the development of internal fertilization, which permitted species to live in dry environments. A variety of appendages specialized for locomotion evolved in many species, including legs for walking or swimming and wings for flying. Because of these innovations, ecdysozoans are an incredibly successful group. Of the eight ecdysozoan phyla, we will consider the two most common: the nematodes and arthropods. The grouping of nematodes and arthropods is a relatively new concept supported by molecular data, and it implies that the process of molting arose only once in animal evolution. In support of this, certain hormones that stimulate molting have been discovered to exist only in both nematodes and arthropods. 



THE INVERTEBRATES 717

The Phylum Nematoda Consists of Small Pseudocoelomate Worms Covered by a Tough Cuticle The nematodes (from the Greek nematos, meaning thread), also called roundworms, are small, thin worms that range in size from less than 1 mm to about 5 cm (Figure 34.17), although some parasitic species measuring 1 m or more have been found in the placenta of sperm whales. Nematodes are Ecdysozoa ubiquitous organisms that exist in nearly all habitats, Protostomia from the poles to the tropBilateria ics. They are found in the soil, in both freshwater and marine environments, and inside plants and animals as parasites. A shovelful of soil may contain a million nematodes. Over 25,000 species are known, but there are probably at least four times as many undiscovered species. Deuterostomia

Arthropoda

Nematoda

Lophotrochozoa

Cnidaria

Porifera

Ctenophora

Ecdysozoa

Key Features of Nematodes  Nematodes have several distinguishing characteristics. A tough cuticle covers the body. The cuticle is secreted by the epidermis and is made primarily of collagen, a structural protein also present in vertebrates. The cuticle is shed periodically as the nematode grows. Beneath the epidermis are longitudinal muscles but no circular muscles, which means that muscle contraction results in thrashing of the body rather than smoother wormlike movement. The

pseudocoelom functions as both a fluid-filled skeleton and a circulatory system. Diffusion of gases occurs through the cuticle. Nematodes have a complete digestive tract composed of a mouth, pharynx, intestine, and anus. The mouth often contains sharp, piercing organs called stylets, and the muscular pharynx functions to suck in food. Excretion of metabolic waste occurs via two simple tubules that have no cilia or flame cells. Reproduction in Nematodes  Nematode reproduction is usually sexual, with separate males and females, and fertilization takes place internally. Females are generally larger than males and can produce prodigious numbers of eggs, in some cases, over 100,000 per day. In some species, such as Caenorhabditis elegans, both hermaphrodites and males are produced. Hermaphrodites can undergo self fertilization, or they can achieve cross fertilization if they mate with a male. C. elegans has become a model organism for researchers to study the process of development (refer back to Figure 20.1b). Development is easily observed because the organism is transparent and composed of relatively few cells, and the generation time is short. An adult C. elegans has about 1000 somatic cells. Parasitic Nematodes  A large number of nematodes are parasitic in humans and other vertebrates.  ∙∙ The large roundworm Ascaris lumbricoides is a parasite of the small intestine that can reach up to 30 cm in length. Over a billion people worldwide carry this parasite. Although infections are most prevalent in tropical or developing countries, the prevalence of A. lumbricoides is relatively high in rural areas of the southeastern U.S. Eggs pass out in feces and can remain viable in the soil for years, although they require ingestion before hatching into an infective stage. ∙∙ Hookworms (Necator americanus), so named because their anterior end curves dorsally like a hook, are also parasites of the human intestine. The eggs pass out in feces, and recently hatched hookworms can penetrate the skin of a host’s foot to establish a new infection. In areas with modern plumbing, these infections are uncommon. ∙∙ Pinworms (Enterobius vermicularis), although a nuisance, have relatively benign effects on their hosts. The rate of infection in the U.S., however, is staggering: 30% of children and 16% of adults are believed to be hosts. Adult pinworms live in the large intestine and migrate to the anal region at night to lay their eggs, which causes intense itching. The resultant scratching can spread the eggs from the hand to the mouth.  ∙∙ In the tropics, some 250 million people are infected with Wuchereria bancrofti, a fairly large (100 mm) worm that lives in the lymphatic system, blocking the flow of lymph, and, in extreme cases, causing elephantiasis, an extreme swelling of the legs and other body parts (Figure 34.18). Females release tiny, live young called microfilariae, which are transmitted to new hosts via mosquitoes.

Figure 34.17  Scanning electron micrograph of a nematode within a plant leaf. ©Biophoto Associates/Science Source

Concept Check:   Both nematodes and annelids are wormlike in appearance. How are they different? 

The Phylum Arthropoda Contains Species with Jointed Appendages The arthropods (from the Greek arthron, meaning joint, and podos, meaning foot) constitute perhaps the most diverse phylum on Earth, including familiar organisms such as spiders, insects, and crustaceans.

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crustaceans, the exoskeleton is reinforced with calcium carbonate to make it extra hard. The exoskeleton provides protection and also a point of attachment for muscles, all of which are internal. It is also relatively impermeable to water, a feature that may have enabled many arthropods to conserve water and colonize land, in much the same way as a tough seed coat allowed plants to colonize land (see Chapter 31). From this point of view, the development of a hard cuticle was a critical innovation. It also reminds us that the ability to adapt to diverse environmental conditions can itself lead to increased diversity of organisms. Arthropods are segmented, and many of the segments bear jointed appendages. Jointed appendages permit complex movements and functions such as walking, swimming, sensing, breathing, food handling, and reproduction. These appendages are operated by muscles within each segment. In many orders, the body segments have become fused into functional units, or tagmata, such as the head, thorax, and abdomen of an insect (Figure 34.19a). 

Head

Figure 34.18  Elephantiasis in a human leg.  The disease is

caused by the nematode parasite Wuchereria bancrofti, which lives in the lymphatic system and blocks the flow of lymph. ©Noah Seelam/Stringer/

Thorax

Abdomen

Antennae

Getty Images

Ecdysozoa Protostomia Bilateria

Deuterostomia

Arthropoda

Nematoda

Lophotrochozoa

Cnidaria

Porifera

Ctenophora

Ecdysozoa

About three-quarters of all described living species present on Earth are arthropods, and scientists have estimated they are also numerically common, with an estimated 1018 (a billion billion) individual organisms. The huge success of the arthropods, in terms of their sheer numbers and diversity, is related to features that permit these animals to live in all the major areas on Earth, from the poles to the tropics and from marine and freshwater habitats to dry land. These features include an exoskeleton, segmentation, and jointed appendages.

Arthropod Body Plan  The body of a typical arthropod is covered by a hard cuticle, an exoskeleton (external skeleton), made of layers of chitin and protein. The cuticle can be extremely tough in some parts, as in the shells of crabs, lobsters, and even beetles, yet be soft and flexible in other parts, between body segments and segments of appendages, to allow for movement. In the class of arthropods called

Compound eye

Wings

Spiracles (a) External anatomy

Aorta

Crop

Malpighian tubules Stomach Heart

Brain Mouth Hemocoel Digestive cecae

Rectum Nerve ganglia

Ovary

(b) Internal anatomy

Figure 34.19  Body plan of an arthropod, as represented by a grasshopper.

 ore Skill: Connections  Look ahead to Figure 49.5. C Why did the Malpighian tubule system play a key role in the colonization of land by insects and other arthropods? 



THE INVERTEBRATES 719

Pancrustacea

Crustaceans

Hexapods

Myriapods

Chelicerates

In arthropods, cephalization has resulted in a well-defined head, which includes a brain consisting of two or three cerebral ganglia connected to several smaller ventral nerve ganglia. Arthropods have multiple sensory organs, including organs of sight, touch, smell, hearing, and balance. They have compound eyes composed of many independent visual units called ommatidia (singular, ommatidium) (look ahead to Figure 44.13). Together, these lenses render a mosaic-like image of the environment. Some species, particularly some insects, possess additional simple eyes, or ocelli, that are probably only capable of distinguishing light from dark. Like most mollusks, arthropods have an open circulatory system (look ahead to  Figure 48.1a), in which hemolymph is pumped from a tubelike heart into the aorta or short arteries and then into the open sinuses that coalesce to form a cavity called the hemocoel. From the hemocoel, gases and nutrients from the hemolymph diffuse into tissues. The hemolymph flows back into the heart via pores, called ostia, that are equipped with valves. Because the cuticle impedes the diffusion of gases through the body surface, arthropods require special organs that permit gas exchange. In aquatic arthropods, these consist of feathery gills that have an extensive surface area in contact with the surrounding water. Terrestrial species have a highly developed tracheal system (look ahead to Figure 48.18). On the body surface, pores called spiracles provide openings to a series of finely branched air tubes within the body called trachea. The tracheal system delivers oxygen directly to tissues and cells, and the circulatory system does not play a role in gas exchange. The digestive system of arthropods is complex and often includes a mouth, crop, stomach, intestine, and rectum (Figure 34.19b). The stomach has glands called digestive cecae that secrete digestive enzymes. Excretion is accomplished by specialized metanephridia or, in insects and some other taxa, by Malpighian tubules, extensive tubes that extend from the digestive tract into body cavity, where they are surrounded by hemolymph (look ahead to Figure 49.5). Nitrogenous wastes are absorbed by the tubules and emptied into the gut, where the intestine and rectum reabsorb water and salts and the waste is excreted through the anus. This excretory system, allowing the retention of water, was another critical innovation that permitted the colonization of land by arthropods.

Ancestral arthropod

Major Subphyla of Arthropods  The history of arthropod classification is extensive and active. Although many classifications have been proposed, a 1995 study of the mitochondrial DNA of arthropod species by American geneticist Jeffrey Boore and colleagues suggests a phylogeny with five main subphyla: one now-extinct subphyla, Trilobita (trilobites); and four living subphyla, Chelicerata (spiders and scorpions), Myriapoda (millipedes and centipedes), Hexapoda (insects and relatives), and Crustacea (crabs and relatives) (Table 34.4). 

Table 34.4

Main Subphyla and Characteristics of Arthropods Subphyla and examples (est. number of species)

Class characteristics

Chelicerata: spiders, scorpions, mites, ticks, horseshoe crabs, and sea spiders (74,000)

Body usually with cephalothorax and abdomen only; six pairs of appendages, including four pairs of legs, one pair of fangs, and one pair of pedipalps; terrestrial; predatory or parasitic

Myriapoda: millipedes and centipedes (13,000)

Body with head and highly segmented trunk. In millipedes, each segment with two pairs of walking legs; terrestrial; herbivorous. In centipedes, each segment with one pair of walking legs; terrestrial; predatory, poison jaws

Hexapoda: insects such as beetles, butterflies, flies, fleas, grasshoppers, ants, bees, wasps, termites, and springtails (>1 million)

Body with head, thorax, and abdomen; mouthparts modified for biting, chewing, sucking, or lapping; usually with two pairs of wings and three pairs of legs; mostly terrestrial, some freshwater; herbivorous, parasitic, or predatory

Crustacea: crabs, lobsters, shrimp (45,000)

Body of two to three parts; three or more pairs of legs; chewing mouthparts; usually marine

Boore’s research showed that the Trilobita were among the earliest-diverging arthropods. The lineage then split into two groups. One, often referred to as the Pancrustacea, contains the insects and crustaceans. The other, with no overarching name, contains the myriapods and chelicerates. Molecular evidence suggests that insects are more closely related to crustaceans than they are to spiders or millipedes and centipedes. We will take a closer look at insects and crustaceans due to their relative sizes and importance to humans. Subphylum Trilobita: Extinct Early Arthropods  The trilobites were among the earliest arthropods, flourishing in shallow seas of the Paleozoic era, some 500 mya, and dying out about 250 mya. Most trilobites were bottom feeders and were generally 3–10 cm in size, although some reached almost 1 m in length (Figure 34.20). They had three main tagmata: the head, thorax, and tail. Trilobites also had two dorsal grooves that divided the body longitudinally into three lobes—an axial lobe and two pleural lobes—a structural characteristic that gave the subphylum its name. Most of the body segments showed little specialization. In contrast, later-diverging arthropods developed specialized appendages on many segments, including appendages for grasping, walking, and swimming.

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Head

Thorax

Tail Pleural lobe

Axial lobe

Figure 34.20  A fossil trilobite.  About 4,000 fossil species of these early arthropods, including Modocia centralis, shown here, which was about 20 cm long, have been described. ©Sinclair Stammers/Getty Images

Subphylum Chelicerata: The Spiders, Scorpions, Mites, and Ticks  The Chelicerata consists mainly of the class Arachnida, which contains predatory spiders and scorpions as well as the ticks and mites, some of which are blood-sucking parasites that feed on vertebrates. The two other living classes are the Merostomata, the horseshoe crabs (four species), and the Pycnogonida, the sea spiders (1,000 species), both of which are marine, reflecting the group’s marine ancestry. All species have a body consisting of two tagmata: a fused head and thorax, called a cephalothorax, and an abdomen. They also possess six pairs of appendages: the chelicerae, or fangs; a pair of pedipalps, which have various sensory, predatory, or reproductive functions; and four pairs of walking legs. Spider fangs are supplied with venom from poison glands. Most spider bites are harmless to humans, although they are very effective in immobilizing and/or killing their insect prey. Venom from some species, including the black widow (Latrodectus mactans; Figure 34.21a) and the brown recluse (Loxosceles reclusa), are potentially, although rarely, fatal to humans. The toxin of the black widow is a neurotoxin, which interferes with the functioning of the nervous system, whereas that of the brown recluse is hemolytic,

meaning it destroys red blood cells around the bite. After the spider has subdued its prey, it pumps digestive fluid into the tissues via the fangs and sucks out the partially digested meal. Spiders have abdominal silk glands, called spinnerets, and many spin webs to catch prey (Figure 34.22a). The silk is a protein that stiffens after extrusion from the body because the mechanical shearing causes a change in the organization of the protein's structure. Silk is stronger than steel of the same diameter and is more elastic than Kevlar, the material used in bulletproof vests. Each spider family constructs a characteristic size and style of web and can do it perfectly on its first attempt, indicating that web spinning is an innate (instinctual) behavior (see Chapter 55). Spiders also use silk to wrap up prey and to construct egg sacs. Interestingly, spiders that are fed drugged prey spin their webs differently than do undrugged spiders (Figure 34.22b and c). Scorpions (order Scorpionida) are generally tropical or subtropical animals that feed primarily on insects, though they may eat spiders and other arthropods as well as smaller reptiles and mice. Their pedipalps are modified into large claws, and the abdomen tapers into a stinger, which is used to inject venom. Although the venom of most North American species is generally not fatal to humans, that of the Centruroides genus from deserts in the U.S. Southwest and Mexico can be deadly. Fatal species are also found in India, Africa, and other countries. Unlike spiders, which lay eggs, scorpions bear live young that the mother then carries around on her back until they have their first molt (Figure 34.21b). In mites and ticks (order Acari), the two main body segments (cephalothorax and abdomen) are fused and appear as one large segment. Many mite species are free-living scavengers that feed on dead plant or animal material. Other mites are serious pests on crops, and some, like chiggers (Trombicula alfreddugesi), are parasites of humans that spread diseases such as typhus (Figure 34.21c). Chiggers are parasites only on their larval stage. Chiggers do not bore into the skin; their bite and salivary secretions cause skin irritation. Demodex brevis is a hair-follicle mite that is common in animals and humans. The mite is estimated to be present on over 90% of adult humans. Although the mite causes no irritation in most humans,

705.5 μm (a) Black widow spider

(b) Scorpion with young

(c) Chigger mite

(d) Bont ticks

Figure 34.21  Common arachnids.  (a) Female black widow spider (Latrodectus mactans). (b) The Central American black scorpion (Centruroides gracilis) is highly venomous and carries its young on its back. (c) SEM of a chigger mite (Trombicula alfreddugesi) that can cause irritation to human skin and spread disease. (d) These South African bont ticks (Amblyomma hebraeum) are feeding on a white rhinoceros. a: ©George Grall/Getty Images;

b: ©Mark Smith/Science Source; c: ©David Scharf/Science Source; d: ©Roger De LaHarpe/Gallo Images/Corbis/Getty Images

Concept Check:   What is one of the main characteristics distinguishing arachnids from insects?



THE INVERTEBRATES 721

(a) Normal web

(b) Web spun by spider fed with prey containing caffeine

(c) Web spun by spider fed with prey containing marijuana

Figure 34.22  Spider-web construction by normal and drugged spiders. a–c: ©NASA/SPL/Science Source Core Concept: Science and Society  Some scientists have suggested using web-spinning spiders to test substances for the presence of drugs or even to indicate environmental contamination.

Demodex canis causes the skin disease known as mange in domestic animals, particularly dogs. Ticks are larger than mites, and all are ectoparasitic, feeding on the body surface of vertebrates. Their life cycle includes attachment to a host, sucking blood until they are replete, and dropping off the host to molt (Figure 34.21d). Ticks can carry a variety of viral and bacterial diseases, including Lyme disease, a bacterial disease so named because it was first observed in the town of Lyme, Connecticut, in the 1970s. Subphylum Myriapoda: The Millipedes and Centipedes  Myriapods have one pair of antennae on the head and three pairs of appendages that are modified as mouthparts, including mandibles that act like jaws. The millipedes and centipedes, both wormlike arthropods with legs, are among the earliest terrestrial animal phyla known. Millipedes (class Diplopoda) have two pairs of legs per segment, as their class name denotes (from the Latin diplo, meaning two, and podos, meaning feet), not 1,000 legs, as their common name suggests (Figure 34.23a). They are slow-moving herbivores that eat decaying leaves and other plant material. When threatened, the millipede’s response is to roll up into a protective coil. Many millipede species

(a) Two millipedes

(b) A centipede

Figure 34.23  Millipedes and centipedes.  (a) Millipedes have two pairs of legs per segment. (b) The venom of the giant centipede (Scolopendra heros) is known to produce significant swelling and pain in humans. a: ©David Aubrey/Corbis/Getty Images; b: ©Larry Miller/Science Source

also have glands on their underside that can eject a variety of toxic, repellent secretions. Some millipedes are brightly colored, warning potential predators that they can protect themselves. Class Chilopoda (from the Latin chilo, meaning lip, and podos, meaning feet), or centipedes, are fast-moving carnivores that have one pair of walking legs per segment (Figure 34.23b). The head has many sensory appendages, including a pair of antennae and three pairs of appendages modified as mouthparts, including powerful claws connected to poison glands. The venom of some larger species, such as Scolopendra heros, is powerful enough to cause pain in humans. Most species do not have a waxy waterproofing layer on their cuticle and so are restricted to moist environments under leaf litter or in decaying logs, usually coming out at night to actively hunt their prey. Subphylum Hexapoda: Insects and Relatives  Hexapods are sixlegged arthropods. Most are insects, but a few earlier-diverging noninsect hexapods have been identified, including soil-dwelling groups such as collembolans, and molecular studies have shown that these represent a separate but related lineage. Insects are in a class by themselves (Insecta), literally and figuratively. Biologists have classified more species of insects than all other species of animal life combined. Approximately 1 million species of insects have been described thus far, and according to a 2015 estimate by British Entomologist Nigel Stork, 4 million more species await description. At least 90,000  species of insects have been identified in the U.S. and Canada alone. DNA barcoding, which is discussed later in this chapter, can help resolve many taxonomic dilemmas between closely related species. Insects are the subject of an entire field of scientific study, entomology. They are studied in large part because of their significance as pests of the world’s agricultural crops and carriers of some of the world’s most deadly diseases. Insects live in all terrestrial habitats, and virtually all species of plants are fed upon by at least one, usually tens, and sometimes, in the case of large trees, hundreds of insect species. Because approximately one-quarter of the world’s crops are lost annually to insects, researchers are constantly trying to

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find ways to reduce pest densities. Insect pest reduction often involves chemical control (the use of pesticides) or biological control (the use of living organisms). Many species of insects are also important pests or parasites of humans and livestock, both by their own actions and as vectors of diseases such as malaria and sleeping sickness. In contrast, insects also provide us with many types of essential biological services. We depend on insects such as honeybees, butterflies, and moths to pollinate our crops. Bees also produce honey, and silkworms are the source of silk fiber. Despite the revulsion they provoke in us, fly larvae (maggots) are important in the decomposition process of both dead plants and animals. In addition, we use insects in the biological control of other insects. Key Features of Insects  Of paramount importance to the success of insects was the evolution of wings, a feature possessed by no other arthropod and indeed no other living animal except birds and bats. Unlike vertebrate wings, however, insect wings are outgrowths of the body wall cuticle and are not true segmental appendages. This means that insects still have all their walking legs. Insects are thus like the mythological horse Pegasus, which sprouted wings out of its back while retaining all four legs. In contrast, birds and bats have one pair of appendages (arms) modified for flight, which leaves them considerably less agile on the ground. Insects in different orders have also evolved a variety of mouthparts in which the constituent parts, the mandibles and maxillae, are modified for different functions (Figure 34.24). Many of these mouthparts are modified walking appendages and are bilaterally paired. As a result, the jaws of many insects, such as grasshoppers, move in a side-to-side motion, rather than up and down as human jaws do.

(a) Chewing (grasshopper)

(b) Piercing and blood sucking (mosquito)

∙∙ Grasshoppers, beetles, dragonflies, and many others have mouthparts adapted for chewing. ∙∙ Mosquitoes and many plant pests have mouthparts adapted for piercing and sucking. ∙∙ Butterflies and moths have a coiled tongue (proboscis) that can be uncoiled, enabling them to drink nectar from flowers. ∙∙ Some flies have lapping, spongelike mouthparts that sop up liquid food. Their varied mouthparts are adaptations that allow insects to specialize their feeding on virtually anything: plant matter, decaying organic matter, and other living animals. The biological diversity of insects is therefore related to environmental diversity, in this case, the variety of foods that insects eat. Parasitic insects attach themselves to other species, and some insect parasites (called hyperparasites) even feed on other parasites, as noted in a verse sometimes attributed to the 18th-century English poet and satirist Jonathan Swift: Big fleas have little fleas upon their backs to bite ’em; and little fleas have lesser fleas and so, ad infinitum. Major Orders of Insects  The diversity of insects is astounding: Hexapoda is composed of 35 orders, some of which have over 100,000 species. The most common orders are described in Table 34.5.

Proboscis (c) Nectar sucking (butterfly)

(d) Sponging liquid (housefly)

Figure 34.24  A variety of insect mouthparts.  Insect mouthparts have become modified in ways that allow insects to feed by a variety of methods, including (a) chewing (Orthoptera, Coleoptera, and others), (b) piercing and blood sucking (Diptera), (c) nectar sucking (Lepidoptera), and (d) sponging up liquid (Diptera). Concept Check:   Insects have a variety of mouthparts. Name two other key insect adaptations. 



THE INVERTEBRATES 723

Table 34.5

Major Orders and Characteristics of Insects

Order and examples (approx. number of described species)

Order characteristics

Coleoptera: beetles, weevils (400,000)

Two pairs of wings (front pair thick and leathery, acting as wing cases, back pair membranous); armored exoskeleton; biting and chewing mouthparts; complete metamorphosis; largest order of insects

Hymenoptera: ants, bees, wasps (130,000)

Two pairs of membranous wings; chewing or sucking mouthparts; many have posterior stinging organ on females; complete metamorphosis; many species social; important pollinators

Diptera: flies, mosquitoes (120,000)

One pair of wings with hind wings modified into halteres (balancing organs); sucking, piercing, or lapping mouthparts; complete metamorphosis; larvae are grublike maggots in various food sources; some adults are disease vectors

Lepidoptera: butterflies, moths (150,000)

Two pairs of colorful wings covered with tiny scales; long tubelike tongue for sucking; complete metamorphosis; larvae are plant-feeding caterpillars; adults are important pollinators

Hemiptera: true bugs; assassin bug, bedbug, chinch bug, cicada (82,000)

Two pairs of membranous wings; piercing or sucking mouthparts; incomplete metamorphosis; many are plant feeders; some are predatory or blood feeders; vectors of plant diseases

Orthoptera: crickets, grasshoppers (20,000)

Two pairs of wings (front pair leathery, back pair membranous); chewing mouthparts; mostly herbivorous; incomplete metamorphosis; powerful hind legs for jumping

Odonata: damselflies, dragonflies (5,500)

Two pairs of long, membranous wings; chewing mouthparts; large eyes; predatory on other insects; incomplete metamorphosis; nymphs aquatic; considered early-diverging insects

Siphonaptera: fleas (2,400)

Wingless, laterally flattened; piercing and sucking mouthparts; adults are bloodsuckers on birds and mammals; jumping legs; complete metamorphosis; vectors of plague

Phthiraptera: sucking lice (3,000)

Wingless ectoparasites; sucking mouthparts; flattened body; reduced eyes; legs with clawlike tarsi for clinging to skin; incomplete metamorphosis; very host-specific; vectors of typhus

Isoptera: termites (2,300)

Two pairs of membranous wings when present; some stages wingless; chewing mouthparts; social species; incomplete metamorphosis

Core Skill: Modeling  The goal of this modeling challenge is to develop a mathematical model that allows you to estimate the number of insect species on Earth. Modeling Challenge: Some biologists have suggested that we don’t know within an order of magnitude how many species exist on Earth. Because insects represent by far the largest taxa on Earth, the answer to this question is dependent on knowing the number of insect species. Of the insects, the best known are the showy butterflies, with 15,000–20,000 species known worldwide. In Britain, insect diversity is almost completely known, with 67 species of butterflies and a total of 24,043 insect species. Create a mathematical model that allows you to estimate the number of insect species on Earth. (Hint: Look ahead to Section 56.1 and read about the mark-recapture technique if you get stuck.) Can you think of some assumptions your model makes?

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Adult butterfly

Although all insects have six legs, different orders have slightly different wing structures, and many of the orders are based on wing type (their names often include the root pter-, from the Greek pteron, meaning wing).

Fertilized egg

∙∙ In beetles (Coleoptera), only the back pair of wings is functional; the front wings have become protective shell-like coverings under which the back pair folds when not in use.

Caterpillar (larva)

Butterfly emerges from the pupa.

∙∙ Wasps and bees (Hymenoptera) have two pairs of wings that are hooked together and move as one wing. ∙∙ Flies (Diptera) possess only one pair of wings (the front pair); the back pair has been modified into a small pair of balancing organs, called halteres, that act like miniature gyroscopes. ∙∙ Butterflies (Lepidoptera) have wings that are covered in scales (from the Greek lepido, meaning scale); other insects generally have clear, membranous wings.

Pupa (a) Complete metamorphosis

Adult grasshopper

∙∙ In ant and termite colonies, the queen and the drones (males) retain their wings, whereas female individuals called workers have lost theirs. Other orders, such as fleas and lice, are completely wingless. Reproduction and Development of Insects  All insects have separate sexes, and fertilization is internal. During development, the majority (approximately 85%) of insects undergo a change in body form known as complete metamorphosis (from the Greek meta, meaning change, and morph, meaning form) (Figure 34.25a). Animals that undergo complete metamorphosis advance through four stages: egg, larva, pupa, and adult. The dramatic body transformation from larva to adult occurs in the pupa stage. The larval stage is often spent in an entirely different habitat from that of the adult, and larval and adult forms use different food sources. Consequently, they do not compete directly for the same resources. The larval stage, such as a caterpillar, is focused on eating and growth, whereas the adult stage involves sexual reproduction. Most adult insects have wings, allowing them to disperse their fertilized eggs over a larger area.  A smaller percentage of insect species undergo incomplete metamorphosis, in which morphological changes are more gradual (Figure 34.25b). Incomplete metamorphosis has only three stages: egg, nymph, and adult. Young insects, called nymphs, look like miniature adults when they hatch from their eggs, but usually don’t have wings. As they grow and feed, they shed their exoskeleton and replace it with a larger one several times, each time entering a new instar, or stage of growth. When the insects reach their adult size, they have also grown wings. Some insects, such as bees, wasps, ants, and termites, have developed complex social behavior and live cooperatively in underground or aboveground nests. Such colonies exhibit a division of labor, in that some individuals forage for food and care for the brood (workers), others protect the nest (soldiers), and some only reproduce (the queen and drones) (Figure 34.26). Subphylum Crustacea: Crabs, Lobsters, Barnacles, and Shrimp  The crustaceans are common inhabitants of marine environments, although some species live in fresh water and a few are terrestrial. Many species, including crabs, lobsters, crayfish, and shrimp, are

Caterpillar sheds its skin to reveal a green pupa.

Fertilized egg

Nymphs look like miniature adults.

Nymph stages (b) Incomplete metamorphosis

Figure 34.25  Metamorphosis.  (a) Complete metamorphosis,

as illustrated by the life cycle of a monarch butterfly. The adult butterfly has a completely different appearance than the larval caterpillar. (b) Incomplete metamorphosis, as illustrated by the life cycle of a grasshopper. The eggs hatch into nymphs, essentially miniature versions of the adult.

(a) Worker and soldier ants

(b) Queen ant

Figure 34.26  The division of labor in insect societies.  Individuals from the same insect colony may appear very different. Among these army ants (Eciton burchelli) from Paraguay, (a) workers forage for the colony, soldiers (with large mandibles) protect the colony from predators, and (b) the queen produces eggs. a: Source: Alex Wild/myrmecos .net; b: ©Oxford Scientific/Getty Images



THE INVERTEBRATES 725 Cephalothorax (13 segments)

Eye

Abdomen (6 segments)

Carapace

Antennule Antenna Mandible Maxillae Maxillipeds Cheliped (first leg) Swimmerets

Claw

454.5 μm

Walking legs

Figure 34.27  Body plan of a crustacean, as represented by a shrimp.

Core Skill: Connections  Look ahead to Figure 44.8. Where are a crustacean’s organs of balance located? 

economically important food items for humans; smaller species are important food sources for other predators. Crustacean Body Plan  The crustaceans are unique among the arthropods in that they possess two pairs of antennae at the anterior end of the body—the antennule (first pair) and antenna (second pair) (Figure 34.27). In addition, they have three or more sensory and feeding appendages that are modified mouthparts: the mandibles, maxillae, and maxillipeds. These are followed by walking legs and, often, additional abdominal appendages, called swimmerets, and a powerful tail. In some orders, the first pair of walking legs, or chelipeds, is modified to form powerful claws. The head and thorax are often fused together, forming the cephalothorax. In many species, the cuticle covering the head extends over most of the cephalothorax, forming a hard protective covering called the carapace. For growth to occur, a crustacean must shed the entire exoskeleton. Many crustaceans are predators, but others are scavengers, and some, such as barnacles, are filter feeders. Gas exchange typically

(a) Goose barnacles—order Cirripedia

(b) Pill bug—order Isopoda

Figure 34.28  Crustacean larva.  The nauplius, a distinct larval

stage exhibited by most crustaceans, molts several times before reaching maturity. Many of these larvae are less than 0.01 mm long.

©FLPA/D P Wilson/age fotostock

occurs via gills, and crustaceans, like other arthropods, have an open circulatory system. Crustaceans possess two excretory organs: antennal glands and maxillary glands, both modified metanephridia, which open at the bases of the antennae and the maxillae, respectively. Reproduction usually involves separate sexes, and fertilization is internal. Most species carry their eggs in brood pouches under the female’s body. Eggs of most species produce larvae that must go through many different molts prior to assuming adult form. The first of these larval stages, called a nauplius, is very different in appearance from the adult crustacean (Figure 34.28). Crustacean Diversity  Crustacean clades are numerous, but most are small and obscure, although many orders contain important prey items for other marine organisms. For example, copepods are tiny and abundant planktonic crustaceans, which are a food source for filterfeeding organisms and small fish. The clade Cirripedia is composed of the barnacles, crustaceans whose carapace forms calcified plates that cover most of the body (Figure 34.29a). Their legs are modified into feathery filter-feeding structures.

(c) Coral crab—order Decapoda

Figure 34.29  Common crustaceans.  (a) Goose barnacles (Lepas anatifera). (b) Pill bug, or wood louse (Armadillium vulgare). (c) Coral crab (Carpilius maculates). a: ©NHPA/Photoshot; b: ©Miyuki Satake/iStock/Getty Images; c: ©Masa Ushioda/Waterframe/age fotostock

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Malacostraca is the largest class of the crustaceans and is divided into many orders. For example, Euphausiacea are shrimplike krill that grow to about 3 cm and provide a large part of the diet of many whales, seals, penguins, fish, and squid. The order Isopoda contains many small species that are parasitic on marine fishes. Terrestrial isopods, better known as pill bugs, or wood lice, retain a strong connection to water and need to live in moist environments such as leaf litter or decaying logs (Figure 34.29b). When threatened, they curl up into a tight ball, making it difficult for predators to get a grip on them. The most familiar Malacostracan order is Decapoda, which includes the crabs and lobsters, the largest crustacean species (Figure 34.29c). As their name suggests, these decapods have 10 walking legs (five pairs), although the first pair is invariably modified to support large claws. Most decapods are marine, but many are freshwater species, such as crayfish. In hot, moist tropical areas, some species, called land crabs, are terrestrial.

Core Concept: Information

control measures accordingly. For example, tsetse flies transmit tryptosomiasis, a parasitic disease that causes sleeping sickness in humans, and African animal trypanosomiasis, a disease that leads to serious economic losses of livestock. Tsetse flies are hard to track in nature because of their solitary habits and secretive nature, hiding in bushes and waiting for prey to pass by. Capturing tsetse flies and DNA barcoding their blood meals avoids the necessity of costly and difficult field behavioral studies. If cattle are found to be the source of most blood, spraying them with insecticides is an effective control strategy. If wildlife such as buffalo, giraffe, elephants, and warthogs are the source, then trapping devices may be used. Hebert foresees the day when all species can be identified by their DNA barcodes. A huge advantage is that only a small sample of cells is necessary. The sample can come from an adult or immature individual, which is a great help since much insect taxonomy is based solely on adults. Many scientists anticipate the day when handheld field barcoding identification devices will be commonly used. At the moment, barcoding involves a laboratory analysis taking about an hour and costing $2.00 per sample. 

DNA Barcoding: A New Tool for Species Identification

34.6 D  euterostomia: The Echinoderms and Chordates Learning Outcomes: 1. Identify the distinguishing characteristics of echinoderms. 2. Describe the four critical innovations in the body plan of chordates. 3. List the two invertebrate subphyla of Chordata, and explain their relationship to the vertebrates.

Chordata

Echinodermata

Ecdysozoa

Lophotrochozoa

Cnidaria

Porifera

As discussed in Chap­ter 33, the deuterostomes are grouped together because they share similarities in patterns of development (refer back to Figure 33.6). Deuterostomia Molecular evidence also supports a deuterostome clade. All animals in the phylum Chordata (from the Greek chorde, meaning string, referring to the spinal cord), which includes the vertebrates, are deuterostomes. Interestingly, so is one invertebrate group, the Protostomia Deuterostomia phylum Echinodermata, which includes the Bilateria sea stars, sea urchins, and sea cucumbers. Although there are far fewer phyla and species of deuterostomes than Ctenophora

The International Barcoding of Life (IBOL) project, begun in 2003 by Canadian biologist Paul Hebert, is a broad initiative that seeks to create a digital identification system for all life-forms. Hebert made the analogy that the large diversity of products in a grocery store can each be distinguished with a relatively small barcode. Though the diversity of the world’s animal species is considerably larger, he reasoned that all species could be distinguished using their DNA. The complete genome would be too large to analyze rapidly, so Hebert suggested analyzing a small piece of DNA of all species. The DNA sequence he proposed for animals is the first 648 base pairs of a gene called CO1, for cytochrome oxidase, an enzyme in the electron transport chain of mitochondria (refer back to Figure 7.8). All animals have this gene in their mitochondrial DNA. A key observation is that although this part of the CO1 gene varies widely between species, it hardly varies at all between individuals of the same species—only 2%. From a practical perspective, DNA barcoding may be used to analyze and control insect populations For example, about 3,500 species of mosquitoes have been identified, but many of them are hard to tell apart, especially in the field. Some mosquitoes transmit deadly diseases such as malaria and yellow fever and are subject to stringent control measures in many countries. The Mosquito Barcoding Initiative aims to catalog each mosquito species by analyzing the CO1 gene and thereby build up a DNA barcode database. Field researchers will be able to quickly analyze the DNA of some individuals in a given area and identify them based on existing barcodes. Appropriate control measures can then be instigated against a mosquito population if it contains members of a species that is known to be a disease carrier. For blood-feeding insects, scientists can also bar code their blood meals, target their feeding preferences, and optimize

protostomes, the deuterostomes are generally much more familiar to us. After all, we humans are deuterostomes. We will conclude our discussion of invertebrate biology by turning our attention to the invertebrate deuterostomes. In this section, we will explore the phylum Echinodermata and then introduce the phylum Chordata, looking in particular at its distinguishing characteristics and at its two invertebrate subphyla: the cephalochordates, commonly referred to as the lancelets, and the urochordates, also known as the tunicates. We will discuss the subphylum Vertebrata in Chapter 35.

The Phylum Echinodermata Includes Sea Stars and Sea Urchins—Species with a Water Vascular System The phylum Echinodermata (from the Greek echinos, meaning spiny, and derma, meaning skin) consists of a unique grouping of deuterostomes. A striking feature of all echinoderms is their modified radial symmetry. The body of most species can be divided into five parts pointing out from the center. As a consequence, cephalization is absent in most classes. There is no brain and only a simple nervous system consisting of a central nerve ring from which arise radial branches to each limb. The radial symmetry of echinoderms is secondary, present only in adults. The free-swimming larvae have bilateral symmetry and metamorphose into the radially symmetrical adult form. Echinoderm Body Plan  Most echinoderms have an endoskeleton, an internal hard skeleton composed of calcareous plates overlaid by a thin skin (Figure 34.30). The skeleton is covered with spines and jawlike pincers called pedicellariae, the primary purpose of which is to deter settling of animals such as barnacles. These structures can also have poison glands. Echinoderms possess a true coelom, and a portion of the coelom has been adapted to serve as a unique water vascular system, a network of canals that branch into tiny tube feet that function in movement, gas exchange, feeding, and excretion (see inset to Figure 34.30). The water vascular system uses hydraulic power (water pressure generated by the contraction of muscles), which enables the tube feet to extend and contract, allowing echinoderms to move, but only very slowly. Water enters the water vascular system through the madreporite, a sievelike plate on the animal’s surface. From there it flows into the  ring canal in the central disc, into five radial canals, and into the tube feet. At the base of each tube foot is a muscular sac called an ampulla, which stores water. Contractions of the ampullae force water into the tube feet, causing them to straighten and extend. When the foot contacts a solid surface, muscles in the foot contract, forcing water back into the ampulla. Sea stars also use their tube feet in feeding, by exerting a constant, strong pressure on bivalves, whose adductor muscles open and close the shell. The adductor muscles eventually tire, allowing the shell to open slightly. At this stage, the sea star everts its stomach and inserts it into the opening. It then digests its prey, using juices secreted from extensive digestive glands. Sea stars also feed on sea urchins, brittle stars, and sand dollars, prey that cannot easily escape them.

THE INVERTEBRATES 727

Anus Endoskeleton Ring canal Stomach

Dissection to show reproductive system Gonad

Dissection to show digestive system Madreporite

Digestive gland Mouth Radial canal Ampulla

Dissection to show water vascular system Tube feet

Ampulla

Podium

Figure 34.30  Body plan of an echinoderm, as represented

by a sea star.  The arms of this sea star have been dissected to different degrees to show the echinoderm’s various organs. The inset shows a close-up view of the tube feet, part of the water vascular system characteristic of echinoderms. Concept Check:   Echinoderms and chordates are both deuterostomes. What are three defining features of deuterostomes?

Echinoderms cannot osmoregulate, so no species have entered freshwater environments. No excretory organs are present. For some species, both respiration and excretion of nitrogenous waste take place by diffusion across their tube feet. Coelomic fluid circulates around the body. Most echinoderms exhibit autotomy, the ability to intentionally detach a body part, such as a limb, that will later regenerate. In some species, a broken limb can even regenerate into a whole animal. Some sea stars regularly reproduce by breaking in two. Most echinoderms reproduce sexually and have separate sexes. Fertilization is usually external, with gametes shed into the water. Fertilized eggs develop into free-swimming larvae, which become sedentary adults. The Major Echinoderm Classes  Although over 20 classes of echinoderms have been described from the fossil record, only 5 main classes of echinoderms exist today: the Asteroidea (sea stars), Ophiuroidea (brittle stars), Echinoidea (sea urchins and sand dollars), Crinoidea (sea lilies and feather stars), and Holothuroidea (sea cucumbers). The key features of the echinoderms and their classes are listed in Table 34.6, and several members are shown in Figure 34.31.

CHAPTER 34

Ophiuroidea: brittle stars (2,000)

Five long, slender arms; tube feet not used for locomotion; no pedicellariae; browse on sea bottom or filter feed

Echinoidea: sea urchins, sand dollars (1,900)

Spherical (sea urchins) or disc-shaped (sand dollars); no arms; tube feet and moveable spines; pedicellariae present; many feed on seaweeds

Crinoidea: sea lilies and feather stars (700)

Cup-shaped; often attached to substrate via stalk; arms feathery and used in filter feeding; very abundant in fossil record

Holothuroidea: sea cucumbers (1,200)

Cucumber-shaped; no arms; spines absent; endoskeleton reduced; tube feet; browse on sea bottom

(a) Necklace Sea star, Fromia monilis, Baa Atoll, Maldives

(b) Brittle star, Ophiarachna spp., Gulf of Mexico

Chordata

Five arms; tube feet; predatory on bivalves and other echinoderms; eversible stomach

Echinodermata

Asteroidea: sea stars (1,600)

The deuterostomes Deuterostomia consist of two major phyla: the echinoderms and the chordates. As deuterostomes, both phyla share similar developmental traits. In addition, both have an endoskeleton, consisting in the echinoderms of calcareous plates and in chordates, for the most part, of bone. HowProtostomia Deuterostomia ever, the echinoderm Bilateria endoskeleton functions in much the same way as the arthropod exoskeleton, in that an important function is providing protection. The chordate endoskeleton serves a very different purpose. In early-diverging chordates, the endoskeleton is composed of a single flexible rod situated dorsally, deep inside the body. Muscles move this rod, and their contractions cause the back Ecdysozoa

Class characteristics

Lophotrochozoa

Class and examples (est. number of species)

The Phylum Chordata Includes All Vertebrates and Some Invertebrates

Cnidaria

Main Classes and Characteristics of Echinoderms

Porifera

Table 34.6

Ctenophora

728

(c) Sea urchin, Heterocentrotus trigonarius, Hawaii

Figure 34.31  Echinoderms.  (a) Sea star. (b) Brittle star. (c) Sea urchin. (d) Sea lily. (e) Sea cucumber. a: ©ullstein bild/Getty Images; b:

Source: NOAA Okeanos Explorer Program, Gulf of Mexico 2012 Expedition; c: Source: David Burdick/NOAA; d:

(d) Sea Lily, Proisocrinus ruberrimus, Indonesia

(e) Bronze-spot sea cucumber, Holothuria argus.

Source: NOAA Okeanos Explorer Program, INDEX-SATAL 2010; e: ©Poelzer Wolfgang/Alamy Stock Photo



THE INVERTEBRATES 729

Notochord

Dorsal hollow nerve cord Pharyngeal (gill) slits

Postanal tail Muscular segments

Brain

Anus

Mouth Intestine Stomach Heart

Pharynx

Figure 34.32  Chordate characteristics.  The generalized

chordate body plan has four main features: notochord, dorsal hollow nerve cord, pharyngeal slits, and postanal tail.

and tail end to move from side to side, permitting a swimming motion in water. The endoskeleton becomes more complex in different lineages that develop limbs, as we will see in Chapter 35, but it is always internal, with muscles attached. Let’s take a look at the four critical innovations in the body plan of chordates that distinguish them from all other animal life (Figure 34.32):

4. Postanal tail. Chordates possess a postanal tail of variable length that extends posterior to the anal opening. In aquatic chordates such as fishes, the tail is used in locomotion. In terrestrial chordates, the tail may be used for a variety of functions. In virtually all other nonchordate phyla, the anus is at the end of the body. Although few chordates apart from fishes possess all of these characteristics in their adult life, they all exhibit them at some time during development. For example, in adult humans, the notochord becomes the spinal column, and the dorsal hollow nerve cord becomes the central nervous system. However, humans exhibit pharyngeal slits and a postanal tail only during early embryonic development. All the pharyngeal slits, except one, which forms the auditory (Eustachian) tubes in the ear, are eventually lost, and the postanal tail regresses to form the tailbone (the coccyx). The phylum Chordata consists of the invertebrate chordates—the subphylum Cephalochordata (lancelets) and the subphylum Urochordata (tunicates)—along with the subphylum Vertebrata. Although the Vertebrata is by far the largest of these subphyla, biologists have focused on the Cephalochordata and Urochordata for clues as to how the chordate phylum may have evolved. Comparisons of gene sequences for the small subunit rRNA (SSU rRNA) show that these two subphyla are our closest invertebrate relatives (Figure 34.33).

Subphylum Cephalochordata: The Lancelets  The cephalo1. Notochord. Chordates are named for the notochord, a single chordates (from the Greek cephalo, meaning head) look a lot more flexible rod that lies between the digestive tract and the nerve chordate-like than do tunicates. They are commonly referred to as cord. Composed of fibrous tissue encasing fluid-filled cells, lancelets, in reference to their bladelike shape and size, about 5–7 cm the notochord is stiff yet flexible and provides skeletal support in length ( Figure 34.34a). Lancelets are a small subphylum of for all early-diverging chordates. In most chordates, such as 26 species, all marine filter feeders, with 4 species occurring in North vertebrates, a more complex jointed backbone usually replaces American waters. Most of them belong to the genus Branchiostoma. the notochord; its remnants exist only as the soft material within The lancelets live mostly buried in sand, with only the anterior the discs between each vertebrae. end protruding into the water. Lancelets have the four distinguish2. Dorsal hollow nerve cord. Many animals have a long nerve ing chordate characteristics: a clearly discernible notochord (extendcord, but in nonchordate invertebrates, it is a solid tube that lies ing well into the head), dorsal hollow nerve cord, pharyngeal slits, ventral to the alimentary canal. In contrast, the nerve cord in and postanal tail (Figure 34.34b). They are filter feeders, drawing chordates is a hollow tube that develops dorsal to the alimentary canal. In vertebrates, the dorsal hollow nerve cord develops into the brain and spinal cord. C GG C C C C G C CG GG G T C GG C C C AC GG C C T T GG CG G A G - G C C T Human 3. Pharyngeal slits. Chordates, like (vertebrate many animals, have a complete chordate) C GG C C C C G C CG GG G T C GG C C C AC GG C C C T GG CG G A G - C G C T gut, from mouth to anus. However, Lancelet (invertebrate in chordates, slits develop in the chordate) pharyngeal region, close to the mouth, T GG T C T C G G CC C G C C T T T C A - CC GG GC GG CG CC G T T - G G T C that open to the outside. This permits Mollusk (invertebrate) water to enter through the mouth and G T G A A C A T T TG C T A G T C C C T C GGG A T T AC A T T T G A A T C G C T exit via the slits, without having to go Mosquito through the digestive tract. In early(invertebrate) diverging chordates, pharyngeal slits function as a filter-feeding device, Figure 34.33  Comparison of SSU rRNA gene sequences of chordate and nonchordate whereas in later-diverging chordates, species.  Note the many similarities (yellow) and differences (green and red) among the sequences. they develop into gills for gas exchange. In terrestrial chordates, Core Concept: Evolution  The DNA sequence similarities between the invertebrate the slits do not fully form, and they chordates (represented by the lancelet) and the vertebrates (represented by a human) suggest that the former are indeed our closest invertebrate relatives. become modified for other purposes.

730

CHAPTER 34

Dorsal h nerve co Water Incurrent siphon Ciliated pharynx

Postanal

Excurrent siphon

(b) The la

Tunic

Anus Pharyngeal slits (a) Lancelet in the sand

Heart

Intestine

Stomach

Tentacles Mouth

Pharyngeal slits

Notochord

Intestine Atriopore

Water

Muscles

(a) Adult tunicate Excurrent siphon

Dorsal hollow nerve cord

Incurrent siphon

Dorsal hollow nerve cord

Pharyngeal slits

Incurrent siphon

AnusCiliated pharynx Excurrent siphon

Stolons

Postanal tail

Postanal tail Tunic

Notochord

Stomach

Heart

(b) The larval form of the tunicate

(c) Typic (b) BodyAnus plan of the lancelet

Figure 34.34  Lancelets.  (a) A bladelike lancelet. (b) The Pharyngeal slits body

plan of the lancelet clearly displays the four characteristic chordate features. a: ©Natural Visions/Alamy Stock Photo Intestine

Heart

Stomach

water through the mouth and into the pharynx, where it is filtered through the pharyngeal slits. A mucous net across the pharyngeal slits traps food particles, and ciliary action takes the food into the intestine,Stolons while water exits via the atriopore. Gas exchange generally takes place across the body surface. Although the lancelet is usually (a) Adult tunicate sessile, it can leave its sandy burrow and swim to a new spot, using a sequence of serially arranged muscles that appear like chevrons (01 .02.03 .1 .2 .3 .5 1

Low productivity in deserts

2

3 5

10 15 20 30 50

Ocean: Chlorophyll a Concentration (mg/m3)

Minimum

Maximum

Land: Normalized Difference Vegetation Index

across Earth as measured via satellites.  Ocean productivity is determined by measuring chlorophyll concentrations at the ocean’s surface. The normalized difference vegetation index (NDVI) quantifies terrestrial vegetation by measuring the difference between nearinfrared (which vegetation strongly reflects) and red light (which vegetation absorbs). Source: Provided by the SeaWiFS Project, NASA/ Goddard Space Flight Center, and ORBIMAGE

1254

CHAPTER 58

1

Plants and algae capture about 6% of incident sunlight.

3

Spartina and algae

Sunlight

The rest is used in net production of plant biomass.

Insect herbivores take very little of net plant production...

8

Insect herbivores

0.6%

9

0.1%

...and spiders even less.

Spiders 10.1%

22.4%

21.8%

Export by tide

Detritus

6.1% of incident sunlight

77.6%

2

10.7% 4

Most plant and algal material dies and decomposes in place...

Most energy is used in plant cellular respiration.

5

...to be eaten by bacteria...

Bacteria

6

...or nematodes and crabs.

1.0%

Nematodes and crabs

7

The remainder is washed out to sea.

Figure 58.20  Energy-flow diagram for a Georgia salt marsh.  Numbers represent the percentage of gross primary production that flows into different trophic levels or is used in plant respiration. algal cellular respiration. The energy that is accumulated in biomass is 22.4%, and most of the biomass dies in place and rots on the muddy ground, to be consumed by bacteria. Bacteria are the major detritivores in this system, followed distantly by nematodes and crabs, which feed on tiny food particles as they sift through the mud. Some of the dead material is also removed from the system (exported) by the tide. The herbivores take very little of the plant production, around 0.6%, eating only a small proportion of the Spartina and none of the algae. A fraction of herbivore biomass is then consumed by spiders. Overall, if we view the species in ecosystems as transformers of energy, then plants, algae, and cyanobacteria are by far the most important organisms on the planet, other species of bacteria are next, and animals are a distant third.

Summary of Key Concepts ∙∙ The assemblage of many populations of different species in the same location is known as a community. Community ecology explores the factors that influence the number and abundance of these species. An ecosystem is the system formed between communities and their physical environment. Ecosystem ecology addresses the flow of energy and the production of biomass within ecosystems.

58.1  P  atterns of Species Richness and Species Diversity ∙∙ The number of species of most taxa varies according to geographic location, generally increasing from polar areas to tropical areas (Figure 58.1). ∙∙ Different hypotheses for the variation in species richness have been advanced, including the species-time hypothesis, the

species-area hypothesis, and the species-productivity hypothesis (Figures 58.2, 58.3). ∙∙ Species diversity takes into account both species richness and species abundance. The most widely used measure of species diversity is called the Shannon diversity index (Table 58.1).

58.2  S  pecies Richness and Community Stability ∙∙ Community stability is an important concept in ecology. The diversity-stability hypothesis maintains that species-rich communities are more stable than communities with fewer species. Tilman’s field studies, which showed that year-to-year variation in plant biomass decreased with increasing species richness, established a link between diversity and stability (Figure 58.4).

58.3  Succession: Community Change ∙∙ Succession describes the gradual and continuous change in community structure over time. Primary succession refers to succession on a newly exposed site with no prior biological legacy. Secondary succession refers to succession on a site that has supported life but has undergone a disturbance (Figures 58.5, 58.6). ∙∙ Three mechanisms have been proposed for succession. With facilitation, each species facilitates, or makes the environment more suitable for, subsequent species. With inhibition, initial species inhibit later colonists. With tolerance, any species can start the succession, and species replacement is unaffected by previous colonists (Figures 58.7, 58.8).



COMMUNITIES AND ECOSYSTEMS: ECOLOGICAL ORGANIZATION ON LARGE SCALES 1255

58.4  Island Biogeography ∙∙ In the equilibrium model of island biogeography, the number of species on an island tends toward an equilibrium number determined by the balance between immigration and extinction rates (Figure 58.9). ∙∙ The model predicts that the number of species increases with increasing island size, that the number of species decreases with distance from the source pool, and that turnover is high. Support exists for the first two predictions of the model, but experiments on islands in the Florida Keys refuted the third prediction (Figures 58.10, 58.11, 58.12).

58.5  Food Webs and Energy Flow ∙∙ Ecosystem ecology studies the movement of energy and materials through organisms and their communities. Organisms that obtain energy from light or chemicals are primary producers (or autotrophs). Organisms that feed on primary producers are called primary consumers (or herbivores). Organisms that feed on primary consumers are called secondary consumers (or carnivores). Consumers that get their energy from the remains and waste products of organisms are called detritivores (Figure 58.13). ∙∙ Food webs are complex models of interconnected food chains in which multiple links occur between species. Food webs tend to have five or fewer links between top and bottom trophic levels (Figures 58.14, 58.15). ∙∙ Production efficiency measures the percentage of energy assimilated by an organism that becomes incorporated into new biomass. Trophic-level transfer efficiency measures the energy available at one trophic level that is acquired by the level above. These efficiencies can be expressed in the form of ecological pyramids, of which the best known is the pyramid of numbers (Figures 59.16, 59.17).

58.6  Biomass Production in Ecosystems ∙∙ Net primary production (NPP) is gross primary production (GPP) minus the energy released during respiration via photosynthetic organisms. NPP in terrestrial ecosystems is limited primarily by temperature and the availability of water and nutrients. In aquatic ecosystems, it is limited mainly by the availability of light and nutrients (Figures 58.18, 58.19). ∙∙ Secondary production is limited by available primary production, but most primary production goes to detritivores (Figure 58.20).

Assess & Discuss  Test Yourself 1. A community with many individuals but few different species exhibits  a. low abundance and high species complexity. b. high stability. c. low species richness and high abundance. d. high species diversity. e. high abundance and high species richness. 

2. Lake Baikal in Siberia is an ancient unglaciated temperate lake and contains 580 species of bottom-dwelling invertebrates. Great Slave Lake, a comparably sized lake that is at the same latitude in northern Canada and was once glaciated, contains only four bottom-dwelling invertebrate species. This observation supports which of the following hypotheses? a. species-time b. species-area c. species-productivity d. both a and b e. both b and c  3. Which evidence suggests that more diverse communities are more stable than less diverse communities? a. Agricultural land, with fewer species, undergoes less frequent pest outbreaks than natural prairies containing more species. b. In Australia, introduced rabbits frequently assume pest proportions. In Europe, coevolved predators such as foxes prevent rabbit populations from reaching pest proportions. c. Long-term studies of American grasslands show fields with high numbers of plant species vary less in biomass from year to year. d. Both a and b are correct. e. Both b and c are correct.  4. The process of primary succession occurs  a. around a recently erupted volcano. b. on a newly plowed field. c. on a hillside that has suffered a mudslide. d. on a recently flooded riverbank. e. on none of the above.  5. Which of the following represent(s) secondary succession? a. plants growing in cracks in the pavement of a quiet street b. the recovery of vegetation following the 2004 Indonesian tsunami c. the colonization of new sand by beach plants d. the recovery of forests following a wildfire e. both b and d  6. Which is part of MacArthur and Wilson’s equilibrium theory of island biogeography? a. Ŝ is increased by distance from the source pool. b. Ŝ is decreased by island size. c. Ŝ is a balance between immigration and extinction. d. Island size influences immigration rates. e. Distance from the source pool influences extinction rates.  7. As we learned in Chapter 27, some bacteria and archaea are able to use energy from the oxidation of sulphur, iron, or hydrogen. These organisms can be classified as a. heterotrophs. d. both a and b. b. autotrophs. e. both b and c.  c. producers. 8. Which organisms are the most important consumers of energy in a Georgia salt marsh? a. Spartina grass and algae b. insects c. spiders d. crabs e. bacteria  9. Primary production in aquatic systems is limited mainly by  a. temperature and moisture. b. temperature and light. c. temperature and nutrients. d. light and nutrients. e. light and moisture. 

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10. The most highly productive terrestrial ecosystems are  a. deserts. d. savannas. b. prairies. e. tundra.  c. forests.

Conceptual Questions 1. Forest A has 5 tree species with 100 individuals and forest B has 5 tree species with 10 individuals. What is the Shannon diversity index for both forests? Which forest has the higher diversity? What do your answers tell you about the limitations of the Shannon diversity index?  2. At what trophic level does a carrion beetle feed?    3.  

Core Concept: Systems  In the nutrient-poor heathlands of Europe, scotch heather (Calluna vulgaris) and cross-leaved heath (Erica tetralix) are gradually replaced by variegated purple moor grass (Molinia caerulea) and wavy hair grass (Deschampsia flexuosa). Adding C. vulgaris litter or nitrogen fertilizer to the soil speeds up this process. Explain this phenomenon, and identify which mechanism of succession is supported. 

Collaborative Questions 1. List some possible ecological disturbances, their likely frequency in natural communities, and the severity of their effects. 2. Calculate the species diversity (the Shannon diversity index) of the following four communities. Which community has the highest diversity? What is the maximum diversity each community could have? Relative abundance of species Community

Species 1

Species 2

Species 3

1

90

10 

—

2

50

50

—

3

80

10

10 

4

  33.3

  33.3

  33.3

HS

Maximum possible diversity

CHAPTER OUTLINE 59.1 Human Population Growth 59.2 Global Warming and Climate Change 59.3 Pollution and Human Influences on Biogeochemical Cycles 59.4 Pollution and Biomagnification 59.5 Habitat Destruction 59.6 Overexploitation 59.7 Invasive Species Summary of Key Concepts Assess & Discuss

The Age of Humans

59

I

n January 2016, British geoscientist Colin Waters and colleagues proposed formal recognition of a new geological epoch, the Anthropocene, the last and latest epoch of the Quaternary period (refer back to Figure 26.4). Some scientists have argued that the Anthropocene is a popculture term and a political statement, based on the word anthropogenic, meaning resulting from human activity, rather than a new epoch. But support is growing to embrace the Anthropocene, a term coined in the 1980s by American ecologist Eugene Stoermer and later popularized by Dutch atmospheric chemist Paul Crutzen. In the 1970s and 1980s, Crutzen showed how human pollutants can damage the ozone layer, a discovery for which he won the Nobel Prize in Chemistry in 1995, along with Mexican chemist Mario Molina and American chemist Frank Rowland. While agreement is widespread that humans have a profound effect on the global environment, the formal recognition of a new geological time unit is subject to specific criteria. Global-scale changes must be recorded in geological stratigraphic (layered) material, usually rock, and in ice or marine sediments. Waters and colleagues noted the appearance of manufactured items in these sediments, including plastics, concrete, aluminum, and particulates from fossil-fuel combustion. Perhaps the most distinctive new identifiable items in sediments were radioactive elements from the 500 aboveground nuclear blasts that occurred between 1945 and 1963, which created globe-encircling debris. Whether or not the Anthropocene gains wide acceptance in the scientific literature, there is no disputing the immense impacts of humans on natural systems. In this chapter, we will examine some of these impacts, which include global warming, effects on biogeochemical cycles, habitat destruction such as deforestation, the overexploitation of various species via overfishing and overhunting, and the introduction of invasive species to all corners of the globe (see the chapter opening photo of a Burmese python in the Everglades). We will begin the chapter by addressing the huge numbers of humans on the planet and our prodigious rate of population growth.

Burmese python in the Florida Everglades. This species of snake was introduced into the Florida Everglades by humans and has dramatically decreased the populations of several native species. Source: Photo courtesy of National Park Service, Everglades National Park

59.1  Human Population Growth Learning Outcomes: 1. Describe how differences in age structure and human fertility across different countries affect human population growth. 2. Explain the concept of an ecological footprint.

In 2015, the world’s population was estimated to be increasing at the rate of 150 people every minute: about 2 per minute in developed nations and 148 per minute in less-developed nations. In this section, we will examine human population growth trends in more detail and discuss how knowledge of the human population’s age structure and fertility levels can help predict its future growth. We will then investigate the carrying capacity of the Earth for humans and explore how the concept of an ecological footprint, which measures human resource use, can help us determine this carrying capacity.

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Population (billions)

8 7

2011

6

1999

5

1987

Dip corresponds to bubonic plague in 1300s

4 3

Knowledge of a Population’s Age Structure Can Help Predict Its Future Growth The age structure of a population can help to predict future population growth. In all populations, age structure refers to the relative numbers of individuals of each defined age group. This information is commonly displayed as a population pyramid. In West Africa, for example, children younger than age 15 make up nearly half of the population, creating a pyramid with a wide base and narrow top (Figure 59.2a). Even if fertility rates decline, the population is expected to significantly increase as these young people move into childbearing age. The age structure of Western Europe is much more uniform (Figure 59.2b). Even if the fertility rate of young women in Western Europe increases to a level higher than that of their mothers, the annual numbers of births will still be relatively low because of the low number of women of childbearing age.

1974 1960

2

1927

1

1804 C. E.

C. E.

0

20 0

1C . 00 E. 10

70

B. C. E.

00 60 B.C 00 .E. 50 B.C 00 .E. 40 B.C 00 .E. 30 B.C 00 .E. 20 B.C 00 .E. 10 B.C 00 .E.

0

Year

Figure 59.1  The growth pattern of the human population through history.

Human Populations Show Extreme Recent Growth

Human Population Fertility Rates Vary Widely Around the World

Until the beginning of agriculture and the domestication of animals, around 10,000 b.c.e., the average rate of human population growth was very low. With the establishment of agriculture, the world’s population grew to about 300 million by 1 c.e. and to 800 million by the year 1750. Between 1750 and 2011, a relatively short period of human history, the world’s human population surged from 800 million to 7 billion (Figure 59.1). In 2017, the number of humans was estimated at 7.5 billion. Scientists are very interested in determining when and at what size the human population will level off.

Global population growth can be estimated by determining the total fertility rate (TFR), the average number of live births a woman has during her lifetime (Figure 59.3). The total fertility rate differs considerably from one geographic area to another. In Africa, the total fertility rate of 4.6 in 2010 has declined substantially since the 1970s, when it was around 6.7 children per woman. In Latin America and Southeast Asia, the rates declined even more from the 1970s and are now at around 2.1. Canada and most countries in Europe have a TFR of less than 2.0. The TFR was about 1.86 in the U.S. in 2016. In Russia,

Nigeria–2010

Males

Females

Children younger than 15 make up half the population.

15

12

9

6

3

0

3

Population (in millions) (a) Age structure of Nigeria

6

France–2010

Age 100+ 95–99 90–94 85–89 80–84 75–79 70–74 65–69 60–64 55–59 50–54 45–49 40–44 35–39 30–34 25–29 20–24 15–19 10–14 5–9 0–4 9

12

15

Males

Females Bulge of “baby boomers” born 1946–1970

3

2.4

1.8

1.2

0.6

0

0.6

1.2

1.8

2.4

3

Population (in millions) (b) Age structure of France

Figure 59.2  The age structure of human populations in Nigeria and France, as of 2010.  (a) In developing areas of the world such as Nigeria, children comprise the most abundant age group. Population growth is rapid. (b) In the developed countries of Western Europe, the age structure is more evenly distributed. The bulge represents those born in the post–World War II “baby boom,” when birth rates climbed due to stabilization of political and economic conditions. Population growth in developed countries is close to zero. Concept Check:    If the population pyramid in Figure 59.2a was inverted, what would you conclude about the age structure of the population? 



THE AGE OF HUMANS 1259

The Concept of an Ecological Footprint Helps Estimate Carrying Capacity

fertility rates have dropped to 1.61. In China, although the TFR is only 1.6, the population there will still continue to increase until at least 2025 because of the large number of women of reproductive age.  Although the global TFR declined from 4.47 in the 1970s to 2.42 in 2016, this is still greater than the average of 2.3 needed for zero population growth. The replacement rate is slightly higher than 2.0, the number necessary to replace a mother and father, due to natural mortality prior to reproduction. The replacement rate varies globally, from 2.1 in developed countries to between 2.5 and 3.3 in developing countries. The wide variation in fertility rates makes it difficult to predict future population growth. A 2010 United Nations report presented world population projections to the year 2100 for three different growth scenarios: low, medium, and high (Figure 59.4). The three scenarios are based on three different assumptions about fertility rate. Using a low fertility rate estimate of only 1.5 children per woman, the population would reach a maximum of about 8 billion people by 17 16 Population (billions)

15 14

TFR of 2.5 (high) TFR of 2.0 (medium) TFR of 1.5 (low)

15.8

13 12 11

10.0

10 9 8 7

6.1 6 2000 2010 2020 2030 2040 2050 2060 2070 2080 2090 2100 Year

Figure 59.4  Population predictions for 2000–2100, using three different total fertility rates (TFRs).

Core Skill: Science and Society  How TFR is calculated has a great influence on assumptions about how human global population size will change over the next 80 years.

10 9 8 7 6 5 4 3 2 1 0 India

of the world.  Data refer to the average number of children born to a woman during her lifetime.

China

Figure 59.3  Total fertility rates (TFRs) among major regions

Egypt

2005–2010

Mexico

Oceania

Recall from Chapter 56 that carrying capacity refers to the maximum population size that can be sustained by an environment. What is the Earth’s carrying capacity for the human population, and when will it be reached? Estimates vary widely. Much of the speculation on the upper boundary of the world’s population size centers on lifestyle. To use a simplistic example, if everyone on the planet ate meat extensively and drove large cars, then the carrying capacity would be a lot less than if people were vegetarians and used bicycles as their main means of transportation. In the 1990s, Swiss researcher Mathis Wackernagel and his coworkers calculated how much land is needed to support each person on Earth. Everybody has an effect on the Earth, because we consume the land’s resources, including crops, wood, fossil fuels, minerals, and so on. Thus, each person has an ecological footprint—the amount of productive land needed to support a person. The average footprint size for everyone on the planet is about 3 hectares (1 ha = 10,000 m2), but wide variation is found around the globe (Figure 59.5). The ecological footprint of the average Canadian is 7.5 hectares, and it is about 10 hectares for the average American.

World

2.5

Brazil

Latin America & Caribbean

3.3

Japan

Asia Africa

U.K.

2.3

5.0 2.3

1970–1975

5.0

Germany

4.6

Europe

Canada

North America

1.5

Australia

6.7

U.S.

2.0 2.0

2050. A more realistic assumption may be to use the fertility rate estimate of 2.0 or even 2.5; with these rates, the population would continue to rise to 10 billion or almost 16 billion, respectively.

Actual ecological footprint (ha per person)

2.2

Figure 59.5  Ecological footprints of different countries.  The term ecological footprint refers to the amount of productive land needed to support the average individual of that country. Concept Check:    What is your ecological footprint? 

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In most developed countries, the largest component of land use is for energy, followed by food and then forestry. Much of the land needed to provide energy serves to absorb the CO2 emitted by the use of fossil fuels. If everyone required 10 hectares, as the average American does, we would need three Earths to provide us with the needed resources. Many people in less-developed countries use far fewer resources.  Globally, humans are already beyond the Earth’s carrying capacity if we were to live in a sustainable manner. How has this happened? Many people currently live in an unsustainable manner, using more resources than can be regenerated in any given year. Furthermore, a rapidly growing human population contributes to environmental changes on a broad scale including habitat loss for wildlife, overhunting and overfishing, and pollution. As described next, pollution is thought to contribute to climate change on a global scale.

59.2        Global Warming and Climate Change Learning Outcomes: 1. Describe how the greenhouse effect contributes to global warming. 2. Explain how global warming may affect sea levels and precipitation patterns. 3. Predict how climate change will change species distribution patterns.

Global warming refers to an increase in Earth’s average surface temperature. In recent years, ecologists have been investigating how human activities have contributed to global warming. A key impact of global warming is climate change, which is a long-term change in Earth’s climate or a change in climate in a particular region. In most regions on Earth, global warming is expected to increase surface temperatures. However, because global warming can affect ocean currents and the circulation of the atmosphere, some regions may actually become colder or experience seasonal changes such as colder winters. To understand how global warming causes climate change, we will begin by exploring how Earth’s atmosphere acts like the glass panes in a greenhouse, trapping heat inside. By understanding this process, ecologists are better able to predict the future effects of a warming Earth. We will explore how human activities have contributed to global warming and consider some of the potential consequences of climate change, which include rising sea levels, changes in precipitation, and changes in the distributions of species.

The Greenhouse Effect Causes the Earth’s Temperature to Rise The Earth is warmed by the greenhouse effect. In a greenhouse, sunlight penetrates the glass and heats the plants inside. The heat is radiated by the plants but the glass acts to trap the heat inside. Similarly, solar radiation in the form of short-wave energy passes through the atmosphere to heat the surface of the Earth. This energy is then radiated from the Earth’s warmed surface into the atmosphere, but in the

Sunlight

Atmosphere

Minimal heat radiated from Earth escapes into space.

Carbon dioxide Heat

Heat

Longwave infrared radiation Shortwave radiation

Majority of heat radiated from Earth is redirected back to Earth.

Figure 59.6  The greenhouse effect is caused by the insulating

effect of atmospheric carbon dioxide.  Solar radiation, in the form of short-wave energy, passes through the atmosphere to heat the Earth’s surface. Long-wave infrared energy is radiated back into the atmosphere. Most infrared energy is redirected back to Earth by atmospheric gases, including carbon dioxide molecules, causing global temperatures to rise.

form of long-wave infrared radiation. Atmospheric gases absorb much of this infrared energy and radiate it a second time to the Earth’s surface, causing its temperature to rise further (Figure 59.6). The greenhouse effect is important to life on Earth. Without the greenhouse effect, global temperatures would be much lower than they are, perhaps averaging only –17°C compared with the existing average of +15°C. The greenhouse effect is caused by a small group of gases, mainly water vapor, that together make up less than 1% of the total volume of the atmosphere. After water vapor, the four most significant greenhouse gases are carbon dioxide, methane, nitrous oxide, and chlorofluorocarbons (Table 59.1). Ecologists are concerned that human activities are increasing the magnitude of the greenhouse effect, resulting in the gradual elevation of the Earth’s surface temperature. In particular, the burning of fossil fuels appears to be the main culprit of global warming. Fossil fuels such as oil, coal, and natural gas are high in carbon and release carbon dioxide (CO2) into the atmosphere when burned. The atmospheric concentrations of most greenhouse gases have increased since the Industrial Revolution over 200 years ago. Of those increasing, the one that is the greatest contributor to global warming is CO2. As Table 59.1 shows, CO2 has a lower global warming potential per unit of gas (relative absorption) than any other major greenhouse gas, but its concentration in the atmosphere is much higher. An analysis of air trapped in glaciers shows that concentrations of atmospheric CO2 increased from about 280 ppm (parts per million) in the pre-industrial 19th century to 400 ppm in 2015 (Figure 59.7a).  Since 1957, air samples have been collected directly at Mauna Loa, Hawaii, a relatively unpolluted site. The data show a 25%



THE AGE OF HUMANS

Table 59.1

1261

The Major Greenhouse Gases and Their Contribution to Global Warming Carbon dioxide (CO2)

Methane (CH4)

Relative absorption in ppm of increase*

1

21

Nitrous oxide (N2O) 310

Chlorofluorocarbons (CFCs) 10,000

Atmospheric concentration (ppm†)

400

1.75

0.315

0.0005

Contribution to global warming

73%

7%

19%

1%

Percent from natural sources; type of source

20–30%; volcanoes

70–90%; swamps, gas from termites and ruminants

90–100%; soils

0%

Major human-made sources

Fossil-fuel use, deforestation

Rice paddies, landfills, biomass burning, coal and gas exploitation

Cultivated soil, fossil-fuel use, automobiles, industry

Previously manufactured products (for example, aerosol propellants) but now banned in the U.S. and the E.U.

*Relative absorption is the warming potential per unit of gas. †ppm = parts per million

increase in atmospheric CO2 levels in just 58 years, from 313 ppm to 400 ppm during 1957–2015 (Figure 59.7b). In addition, seasonal oscillations in CO2 occur, as seen in the orange line of Figure 59.7b. These types of oscillations differ in the two hemispheres of Earth. The Northern Hemisphere, where Hawaii is located, has greater land area and plant biomass than the Southern Hemisphere. In the northern summer, more CO2 is absorbed by plants and atmospheric CO2 level declines slightly. In the northern winter, less CO2 is absorbed and atmospheric CO2 levels increase.

CO2 concentration (parts per million)

400 380 360 340 320 300

Global Warming Is Expected to Cause Sea Levels to Rise

280 260

1880

1900

1920

1940 Year

1960

1980

1960

1970

1980

1990 Year

2000

2010

(a)

2013

Parts per million

400

380

360

340

320

(b)

2020

Figure 59.7  The increase of atmospheric carbon dioxide. 

(a) Increases in the burning of fossil fuels have caused an increase in atmospheric CO2 since the late 19th century. (b) In air samples taken directly at Mauna Loa, Hawaii, since 1957, CO2 levels have shown consistent increases. Concept Check:    Why does the amount of CO2 fluctuate seasonally in the graph in Figure 59.7b?

To predict the effects of global warming, most scientists focus on a future point, about 2100, when the concentration of atmospheric CO2 will have doubled—that is, increased to about 700 ppm compared with the late-20th-century level of 350 ppm. The 2014 report of the Intergovernmental Panel on Climate Change (IPCC) suggested that if greenhouse gas emissions continue to rise at the same rate, this would lead to a 2–4°C warming by about the end of this century. This increase in temperature might not seem like much, but it is comparable to the warming that ended the last Ice Age. One consequence of global warming is its effect on sea levels due to the melting of glaciers. The term sea level refers to the average level for the surface of one or more of Earth’s oceans. With a 2–4°C warming, sea levels are expected to rise by about 50–60 cm. Sea levels have already risen 10–25 cm over the past century, and seawater entry into coastal forests has killed trees in many areas. An alarming problem is the long time lag between warming temperatures and the time it takes for ice to melt. Even if future temperature increases were prevented, glaciers would continue to melt for many years. For example, the ice sheets of Greenland will take hundreds of years to melt, even though the increase in temperature needed to melt them could be reached in 50–100 years. You might envision this as being similar to an ice cube on a kitchen counter—it takes a while for the ice cube to melt, even though room temperature is considerably above freezing.

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Therefore, even if no greenhouse gases were added to the atmosphere after 2020, at least a quarter of the sea-level rise would still be expected by 2100.

Current and projected ranges of sugar maple

One Effect of Global Warming on Climate Change Is to Alter Precipitation Patterns on Land An increase in global temperatures is also expected to promote climate change and alter global precipitation. Higher temperatures increase evaporation, and warmer air holds more water vapor than cooler air. Global warming will generally lead to more frequent and heavier precipitation. Over the period 1986–2000, the average increase in precipitation over land was 3.5 mm per year. However, over normally dry areas, global warming is expected to increase evaporation of water from Earth’s surface, but the level of moisture in the atmosphere over dry regions may not be high enough to facilitate rain. Therefore, the increased temperatures will likely lead to widespread droughts in desert areas.  We can make the analogy that the atmosphere is like a sponge; warm, moist air allows the sponge to absorb more water, but in dry conditions nothing more can be rung out of the sponge. Northern and southern temperate areas have already shown precipitation increases, as have tropical and subtropical areas. However, desert areas such as the Sahel region south of the Sahara have become drier. In essence, the wet get wetter and the dry get drier.

Climate Change Is Expected to Alter the Distribution of Species Assuming that the previous scenario of climate change is accurate, scientists are beginning to consider the consequences on natural and human-made ecosystems. As most regions on Earth become warmer and a few regions become colder, most plant species cannot easily disperse and move north or south into newly created climatic regions that will be suitable for them. Many tree species take hundreds, even thousands, of years for seed dispersal. Paleobotanist Margaret Davis was among the first to investigate how species’ ranges would be changed in a globally warmed world. She predicted that in the event of a CO2 doubling, many tree species in North America, such as sugar maples, would suffer range contractions because their southern ranges would be eliminated due to higher temperatures (see the yellow areas in  Figure 59.8a). This contraction in the trees’ distribution could be offset by the creation of new favorable habitats in Canada (see the red areas in Figure 59.8a). However, most scientists hypothesize that the climatic zones would shift toward the poles faster than the tree species could either migrate via seed dispersal or evolve to become better adapted to their altered climate. Therefore, the areas shown in red in  Figure 59.8a  are hypothetical and may not be achieved. When Margaret Davis mapped out the future distribution of the sugar maple, Acer saccharum, in a globally warmed world and also took into account changed precipitation patterns, the predicted future area of distribution was considerably less than the prediction taking into account only temperature changes (Figure 59.8b).

Increased temperature and moisture reduction

Increased temperature 0

400 km

Areas where sugar maples would be eliminated Predicted areas where sugar maples do not currently exist but could exist due to climate change

0

400 km

Overlap of areas where sugar maples currently exist and would continue to survive under climate change

Figure 59.8  Possible changes in the ranges of sugar maples

due to climate change.  The map on the left takes into account only temperature changes, whereas the one on the right takes into account temperature and precipitation changes. The yellow shading indicates areas where sugar maples now exist but would not survive due to climate changes associated with a doubling of atmospheric CO2 levels. The red shading indicates areas where sugar maples do not currently exist but would have a favorable climate to exist if CO2 levels doubled. The orange shading indicates the overlap of areas where sugar maples currently exist and those where they could also exist due to climate change. Core Skill: Science and Society  Under a scenario of global warming, changes in both temperature and precipitation patterns need to be considered to understand the future distributions of species.

59.3        Pollution and Human Influences on Biogeochemical Cycles Learning Outcomes: 1. Outline the steps of the carbon cycle, and describe the environmental effects of elevated atmospheric concentrations of CO2. 2. Describe the processes of the water cycle, and explain how they are affected by humans. 3. Describe the role of phosphorus in lake eutrophication. 4. List the five main steps of the nitrogen cycle, and identify the human influences on it.

A unit of energy moves through an ecosystem only once, passing through the trophic levels of a food web from producer to consumer



and dissipating as heat. In contrast, chemical elements such as carbon or nitrogen follow a cycle, moving from the physical environment to organisms and back to the environment, where the cycle begins again. Because the movements of chemicals through ecosystems involve biological, geological, and chemical transport mechanisms, they are termed biogeochemical cycles. Biological mechanisms involve the absorption of chemicals by living organisms and their subsequent release back into the environment. Geological mechanisms include weathering and erosion of rocks and transporting of elements by surface and subsurface drainage. Chemical transport mechanisms include dissolved matter in rain and snow, atmospheric gases, and dust blown by the wind. In addition to the basic building blocks of carbon, hydrogen, and oxygen, the elements required in the greatest amounts by living organisms are phosphorus and nitrogen. In this section, we take a detailed look at the cycles of these nutrients, which can be divided into two broad types: (1) local cycles, such as the phosphorus cycle, which involve elements with no atmospheric mechanism for long-distance transfer, and (2) global cycles, which involve an interchange between the atmosphere and the ecosystem. In our discussion of biogeochemical cycles, we will take a close look at how these cycles are affected by human activities, such as the burning of fossil fuels and the use of fertilizers.

The Carbon Cycle Is Affected by Human Activities Such as the Burning of Fossil Fuels and Deforestation The movement of carbon from the atmosphere into organisms and back again is known as the carbon cycle. The rates of the processes shown in  Figure 59.9 vary greatly. Some carbon becomes locked up in reservoirs with a low turnover rate. For example, a fraction of the material from primary producers is transformed into deposits of coal, natural gas, and oil, which are collectively known as fossil fuels. In addition, much carbon is incorporated into the shells of marine organisms, which eventually form huge limestone deposits on the ocean floor or in terrestrial rocks, where turnover is extremely slow. As a result, rocks and fossil fuels contain the world's largest reserves of carbon.  In contrast, much of the carbon in phototrophs, which include plants, algae, and cyanobacteria, turns over much more rapidly. These organisms acquire CO2 from the atmosphere and incorporate it into the organic matter of their own biomass via photosynthesis. Each year, plants, algae, and cyanobacteria remove approximately oneseventh of the CO2 from the atmosphere. At the same time, respiration and the decomposition of phototrophs recycle a similar amount of carbon back into the atmosphere as CO2. Other natural sources also release significant amounts of CO2 into the atmosphere. These include volcanoes, hot springs, and fires.  Animals can return some CO2 to the atmosphere by respiration and decomposition, but the amount of carbon flowing through this part of the cycle is minimal. Human activities, primarily the burning of fossil fuels, are increasingly causing large amounts of CO2 to enter the atmosphere. In addition, deforestation contributes to elevation of atmospheric CO2 because there is less vegetation to absorb CO2 from the atmosphere. Direct measurements over the past five decades show a steady rise in atmospheric CO2 (see Figure 59.7), a pattern that shows no sign of slowing.  What are the consequences of elevated levels of atmospheric CO2? As discussed in Section 59.2, ecologists have identified a link

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1263

between a rise in atmospheric CO2 and global warming.  Elevated atmospheric CO2 can also increase the acidity of the oceans, mainly near the surface, because carbonic acid is formed when CO2 dissolves in water. Higher acidity inhibits shell growth in marine mollusks, crabs, corals and echinoderms, and can cause reproductive disorders in some fish. Also, as described next, higher CO2 levels may boost plant growth but lower the amount of herbivory.

Atmosphere

Decomposition and respiration

Photosynthesis

Atmospheric CO2

Rocks

Burning of fossil fuels

Respiration

Photosynthesis Soil Plants Algae Deposits of fossil fuels— coal, oil, and natural gas

Sedimentation forms fossil fuels.

Figure 59.9  The carbon cycle.  Each year, plants and algae

remove about one-seventh of the CO2 in the atmosphere. Because the carbon flow due to animal respiration and decomposition is so small, it is not represented. The widths of the arrows indicate the relative contribution of each process to the cycle. Concept Check:    Where are the world's greatest stores of carbon? 

Core Skill: Connections  Refer back to Table 2.2. Carbon is one of just four elements that account for the vast majority of atoms in living organisms. What are the other three, and, therefore, what biogeochemical cycles might be the most important to us? Core Skill: Modeling  The goal of this modeling challenge is to create a model of the carbon cycle by linking reservoirs and processes. Modeling Challenge: Figure 59.9 is a pictorial model of the carbon cycle. In this modeling challenge, you will create a more schematic model of that cycle. Your model should have two types of components. First, reservoirs for carbon should be drawn as boxes with a label in each. For example, one box in your model will be labeled “Atmosphere.” The second component of your model will be arrows that connect the boxes. These arrows represent processes and should also be labeled. For example, one arrow will be labeled “Burning of fossil fuels.” Note: Any given box can be linked to another box by multiple arrows.

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Core Skill: Process of Science

Feature Investigation  | Stiling and Drake’s Experiments with Elevated CO2 Showed

an Increase in Plant Growth but a Decrease in Herbivore Survival

How will forests of the future respond to elevated CO2? To begin to answer such a question, ecologists ideally would enclose large areas of forests with chambers, increase the CO2 content within the chambers, and measure the responses. This has proved to be difficult for two reasons. First, it is hard to enclose large trees in chambers, and second, it is expensive to increase CO2 levels over a large area.  In much of Florida’s forests, trees are small, only 3–5 m high at maturity, because frequent lightning-initiated fires prevent the growth of larger trees. In a discovery-based investigation, ecologists Peter Stiling and Bert Drake were able to increase CO2 levels around patches of forest at the Kennedy Space Center in Cape Canaveral, Florida. In the 1990s, they teamed up with NASA engineers to create 16 circular, open-topped chambers (Figure 59.10). In eight of these, they increased atmospheric CO2 to double the ambient level, from around 350 ppm to 700 ppm, the latter of which is the atmospheric

concentration predicted by the end of the 21st century. The experiments commenced in 1996 and lasted until 2007. The experiment shown in Figure 59.10  focuses on the effects of elevated CO2 on a type of herbivore called a leaf miner, the most common type of herbivore at this site. Because the chambers were open-topped, these insect herbivores could come and go. Censuses were conducted on all species of leaf miners (step 2) and leaves were also examined for damage by leaf miners (step 3). Leaf miner larvae are small enough to burrow between the surfaces of plant leaves, creating leaf mines. These mines result in brown areas, as shown in Figure 59.10, step 3. The analysis of a leaf mine reveals whether a larva survived and emerged, died of nutritional inadequacy, was eaten by predators, or was attacked by parasitoids. As seen in the data in step 4 of Figure 59.10, the mortality of insect herbivores, namely leaf miners, was higher under conditions

Figure 59.10  The effects of elevated atmospheric CO2 on herbivore survival. (photos) ©Peter Stiling GOAL To determine the effects of elevated CO2 on a forest ecosystem; effects on herbivore survival are highlighted here. STUDY LOCATION Patches of forest at the Kennedy Space Center in Cape Canaveral, Florida. Experimental level Erect 16 open-top chambers around native vegetation. Increase CO2 levels from 350 ppm to 700 ppm in half of them.

2

Conduct a yearly count of numbers of insect herbivores per 200 leaves in each chamber.

Expected atmospheric CO2 level is 700 ppm by end of the 21st century. Open-top chambers allow movement of herbivores in and out of chambers.

Number of insect herbivores per 200 leaves

1

Conceptual level

35

Control chambers Elevated CO2 chambers

30 25 20 15 10 5 0

1996

1998

2000

2002

2004

2006

Year

3

Analyze the leaf mines created by leaf miners to determine if the leaf miners survived and emerged, or if they died due to nutritional inadequacy or by the action of predators or parasitoids.

4

THE DATA

Elevated CO2 reduces foliar nitrogen, inhibits normal insect development, and prolongs the feeding time of herbivores, allowing natural enemies greater opportunities to attack them.

by leaf miners to determine if the leaf miners survived and emerged, or if they died due to nutritional inadequacy or by the action of predators or parasitoids.



4

nitrogen, inhibits normal insect development, and prolongs the feeding time of herbivores, allowing natural enemies greater opportunities to attack them. THE AGE OF HUMANS 1265

THE DATA Source of mortality*

Elevated CO2 (% mortality)

Control (% mortality)

10.2

5.0

Predators

2.4

2.0

Parasitoids

10.0

3.2

Nutritional inadequacy

*Data refer only to mortality of larvae within leaves and do not sum to 100%. Mortality of eggs on leaves, pupae in the soil, and flying adults is unknown.

5

CONCLUSION Elevated CO2 increases herbivore mortality.

6

SOURCE Stiling, P., and Cornelissen, T. 2007. How does elevated carbon dioxide (CO2) affect plant-herbivore interactions? A field experiment and meta-analysis of CO2-mediated changes on plant chemistry and herbivore performance. Global Change Biology 13: 1823–1842.

of elevated CO2. This decrease in herbivore survival occurred even though the plants produced more biomass in elevated CO2, because CO2 is limiting to plant growth. (Note: The data for plant biomass increases are not shown in the figure.) Lower leaf miner densities could be attributed to higher mortality rates due to nutritional inadequacy, predators, or parasitoids (see step 3).  Stiling and Drake hypothesized that part of the reason for the decline was that even though plants increased in mass, the existing soil nitrogen was diluted over a greater volume of plant material, so the nitrogen level in leaves decreased. This could have resulted in increased insect mortality by two means. First, poorer leaf quality could directly increase insect death because leaf nitrogen levels may have been too low to support the normal development of the leaf miners. Second, lower leaf quality is expected to increase the amount of time insects need to feed to gain sufficient nitrogen. Increased feeding times, in turn, may lead to increased exposure to natural enemies,

such as predatory spiders and ants and parasitoids (see Figure 57.8), so mortality from natural enemies also increased (see the data of Figure 59.10). Thus, in a world of elevated CO2, plant growth may increase, and herbivory may decrease.

Global Warming and the Interruption of Water Flow by Humans Affect the Water Cycle

world and causing glaciers to melt. On a smaller scale, humans have built structures that affect the flow of moving bodies of water. To increase the amount of available water and to create hydroelectric power, humans have interrupted the water cycle in many ways, most prominently through the use of dams to create reservoirs. Such dams can greatly interfere with the migration of fishes such as salmon and affect their ability to reproduce and survive. Other activities, such as tapping into underground water supplies, or aquifers, for drinking water removes more water than is put back by rainfall and can cause shallow ponds and lakes to dry up and sinkholes to develop, exacerbating local shortages.

The water cycle, also called the hydrological cycle, differs from the cycles of other nutrients in that very little of the water that cycles through ecosystems is chemically changed by any of the cycle’s components (Figure 59.11). This cycle is a physical process, fueled by the Sun’s energy, rather than a chemical one, because it consists of essentially two phenomena: evaporation and precipitation. Even so, the water cycle has important biological components. Over land, 90% of the water that reaches the atmosphere is moisture that has passed through plants and exited from the leaves via evapotranspiration. Only about 2% of the total volume of Earth’s water is found in the bodies of organisms or is held frozen or in the soil. The rest cycles from bodies of water, to the atmosphere, and then to the land and back to bodies of water again. Human activities have altered the water cycle in different ways. As discussed in Section 59.2, climate change may have the greatest effect on the water cycle by altering precipitation patterns around the

Experimental Questions 1. What was the hypothesis of Stiling and Drake’s experiment?  2. CoreSKILL » Explain the purpose of increasing the CO2 levels in only half of the chambers in the experiment and not all of the chambers.  3. CoreSKILL » Imagine that the mortality rates from parasitoids in the eight elevated CO2 chambers were 6%, 11%, 9%, 8%, 13%, 12%, 14%, and 7%, and the rates in the ambient chambers were 1%, 4%, 5%, 2%, 3%, 6%, 1.6%, and 3%. Perform a statistical test to see if mortality from parasitoids was different between elevated and ambient CO2 chambers. 

Fertilizers and Other Pollutants Affect the Phosphorus Cycle Phosphorus has no gaseous phase and thus no atmospheric component; that is, it is not moved by wind. As a result, the phosphorus cycle is viewed as a local cycle even though phosphorus can be transported over long distances by moving water (Figure 59.12). The Earth’s

CHAPTER 59 Solar energy

40

Net movement of water vapor by wind

Precipitation over the land

Evapotranspiration from land Precipitation over the sea Evaporation from the sea

Percolation in soil Runoff and groundwater

Mean annual chlorophyll (mg/m3)

1266

30

20

10

0

0

10

20

30

40

Mean annual total phosphorus (mg/m3)

Figure 59.11  The water cycle.  This cycle is primarily a physical

process, not a chemical one. Solar energy drives the water cycle, causing evaporation of water from the ocean and evapotranspiration from the soil and land plants. The next step is condensation of water vapor into clouds followed by precipitation. The widths of the arrows indicate the relative contribution of each process to the cycle.

Geological uplift Weathering of phosphate rocks Decomposers

Animals Farming

Plants

Runoff Dissolved phosphate

Phosphate in soil (HPO42– H2PO4–) Leaching

Detritus Sedimentation forms new rocks

Figure 59.12  The phosphorus cycle.  Unlike other major

biogeochemical cycles, the phosphorus cycle does not have an atmospheric component and thus cycles only locally. The widths of the arrows indicate the relative contribution of each process to the cycle.

crust is the main storehouse for this element. Weathering and erosion of rocks release phosphorus into the soil. Plants have the metabolic means to absorb dissolved ionized forms of phosphorus, the most important of which occurs as phosphate (HPO42− or H2 PO4−). Herbivores obtain their phosphorus only from eating plants, and carnivores obtain it by eating herbivores or other carnivores. When plants and animals excrete wastes or die, the phosphorus becomes available to decomposers, which release it back to the soil. Leaching and runoff eventually wash much phosphate into aquatic systems, where algae utilize it. Phosphate that is not taken up into the food chain settles to the ocean floor or lake bottom, forming sedimentary rock.

Figure 59.13  The relationship between primary production and

total phosphorus concentration.  As shown in this graph, primary production (measured by chlorophyll concentration) increases linearly with an increase in phosphorus. Each dot represents a different lake.

Phosphorus is commonly a limiting nutrient in aquatic ecosystems. When more phosphorus is added, the growth of algae and aquatic plants can dramatically increase. In lakes, primary production and total phosphorus concentration appear to follow a linear relationship (Figure 59.13). What is the consequence of high primary production? When the algae and plants die, they sink to the bottom, where bacteria decompose them and consume the dissolved oxygen in the water. Dissolved oxygen concentrations can then drop too low for fishes to breathe, killing them. The process by which elevated nutrient levels lead to an overgrowth of algae and the subsequent depletion of water oxygen concentrations is known as eutrophication. Eutrophication is frequently due to the enrichment of water with nutrients derived from human activities, such as fertilizer use and sewage dumping. For example, Lake Erie became eutrophic in the 1960s due to the runoff of fertilizer rich in phosphorus from farms and to the industrial and domestic pollutants released from the many cities along its shores (Figure 59.14a). Fish species such as white fish and lake trout became severely depleted. The U.S. and Canada teamed together to reduce the levels of discharge by 80%, primarily through eliminating phosphorus in laundry detergents and maintaining strict controls on the phosphorus content of wastewater from sewage treatment plants. Fortunately, lake systems have great potential for recovery after phosphorus inputs are reduced, and Lake Erie has experienced fewer algal blooms, clearer water, and a restoration of fish populations (Figure 59.14b).

Fertilizers and Industrial Pollutants Affect the Nitrogen Cycle Nitrogen is an essential component of proteins, nucleic acids, and chlorophyll. Because 78% of the Earth’s atmosphere consists of nitrogen gas (N2), it may seem that nitrogen should not be in short supply for organisms. However, nitrogen is often a limiting factor in



THE AGE OF HUMANS 1267

Denitrifying bacteria produce N2.

ls ue

Nitrogen in atmosphere (N2)

Industri al fi xat ion Burning of fos sil f

Industry Denitrification 5 Animals

Fertilizer runoff Eutrophication

Plants 4

Ammonification

3 Assimilation

Nitrogen 1 fixation Nitrogen-fixing bacteria produce ammonia or ammonium.

Leaching Decomposers

Ammonia (NH3) or Ammonium (NH4+)

Nitrates (NO3‒) Nitrifying bacteria oxidize ammonia or ammonium to nitrate ions. 2 Nitrification

Figure 59.15  The nitrogen cycle.  The five main parts of the

(a) Polluted (eutrophication)

nitrogen cycle are (1) nitrogen fixation, (2) nitrification, (3) assimilation, (4) ammonification, and (5) denitrification. The recycling of nitrogen from dead plants and animals into the soil and then back into plants is of paramount importance because this is the main pathway for nitrogen to enter the soil. The widths of the arrows indicate the relative contribution of each process to the cycle.

as ammonia (NH3). This process, called nitrogen fixation, is a critical component of the five-part nitrogen cycle (Figure 59.15):

(b) Cleared up

Figure 59.14  Phosphorus pollution in Lake Erie.  The lake (a) in the 1960s, when eutrophic and polluted by industrial effluent and fertilizer runoff, and (b) in 2007, after eutrophication was reversed by pollution control laws. a: ©JK Enright/Alamy Stock Photo; b: ©Rolf Hicker Photography/Alamy Stock Photo

ecosystems because N2 molecules must be broken apart before the individual nitrogen atoms can combine with other elements. Because there is a triple bond between its two nitrogen atoms, N2 is very stable, and only certain bacteria can break it apart into usable forms such

1. A few species of bacteria can accomplish nitrogen fixation, that is, convert atmospheric N2 to forms usable by other organisms. The bacteria that fix nitrogen are fulfilling their own metabolic needs, but in the process, they release ammonia (NH3) or ammonium (NH4+), which can be used by some plants. An important group of nitrogen-fixing bacteria, known as rhizobia, live in nodules on the roots of legumes, including peas, beans, lentils, and peanuts, and of some woody plants. Cyanobacteria are important nitrogen fixers in terrestrial and aquatic systems (refer back to Figure 38.12). 2. In the process of nitrification, soil bacteria convert NH3 or NH4+ to nitrate (NO3−), a form of nitrogen commonly used by plants. Bacteria of the genera Nitrosomonas and Nitrococcus first oxidize the forms of ammonia to nitrite (NO2−), after which bacteria of the genus Nitrobacter convert NO2− to NO3−. 3. Assimilation is the process by which inorganic substances are incorporated into organic molecules. In the nitrogen cycle, organisms assimilate nitrogen by taking up NH3, NH4+, and NO3− formed through nitrogen fixation and nitrification and incorporating them into organic molecules. Plants take up these forms of nitrogen through their roots, and animals assimilate nitrogen from the plant tissues they ingest.

CHAPTER 59

4. Ammonia can also be formed in the soil through the decomposition of plants and animals and the release of animal waste. Ammonification is the conversion of organic nitrogen to NH3 and NH4+. This process is carried out by bacteria and fungi. Most soils are slightly acidic, and, because of an excess of H+, the NH3 rapidly gains an additional H+ to form NH4+. Because many soils lack nitrifying bacteria, ammonification is the most common pathway for nitrogen to enter the soil. 5. Denitrification is the reduction of NO3− to N2. Denitrifying bacteria, which are anaerobic and use NO3− in their metabolism instead of O2, perform the reverse of their nitrogen-fixing counterparts by delivering N2 to the atmosphere. This process contributes only a relatively small amount of nitrogen to the atmosphere. Human activities have approximately doubled the rate of nitrogen input to the nitrogen cycle. Industrial fixation of nitrogen for the production of fertilizer makes a major contribution to the pool of nitrogencontaining material in the soils and waters of agricultural regions. As with phosphorus, fertilizer runoff can cause eutrophication of rivers and lakes, and, as the resultant algae die, decomposition by bacteria depletes the oxygen level of the water, resulting in fish kills.  Excess NO3− in surface or groundwater systems used for drinking water is also a health hazard, particularly for infants. In the body, NO3− is converted to NO2−, which then combines with hemoglobin to form methemoglobin, a type of hemoglobin that does not carry oxygen. In infants, the production of large amounts of NO2− can cause methemoglobinemia, a dangerous condition in which the level of O2 carried through the body decreases.  Finally, burning fossil fuels releases not only carbon but also nitrogen in the form of nitrous oxide (N2O), which contributes to air pollution. N2O can react with rainwater to form nitric acid (HNO3), a component of acid rain, which decreases the pH of lakes and streams and increases fish mortality. The release of sulfur from the burning of fossil fuels also contributes to acid rain since the sulfur reacts with rainwater to form highly acidic sulfuric acid.

59.4        Pollution and Biomagnification

the uses of the chemical. The first important application of DDT was in human health programs during and after World War II, particularly as a means of controlling mosquito-borne malaria; at that time, its use in agriculture also began. The global production of DDT peaked in 1970, when 175 million kilograms of the insecticide was manufactured. DDT has several chemical and physical properties that profoundly influence its ecological effect. First, DDT is persistent in the environment. It is not rapidly degraded to other, less toxic chemicals by microorganisms or by physical agents such as light and heat. The typical persistence in soil of DDT is about 10 years, which is two to three times longer than the persistence of many other insecticides. Another important characteristic of DDT is its low solubility in water and its high solubility in fats, or lipids. In the environment, most lipids are present in living tissue. Therefore, because of its high lipid solubility, DDT tends to concentrate in biological tissues. Because biomagnification occurs at each step of a food chain, organisms at higher trophic levels can accumulate especially high concentrations of DDT in their lipids. A typical pattern of biomagnification is illustrated in Figure 59.16, which shows the relative amounts of DDT found in a Lake Michigan food chain. The highest concentration of the insecticide was found in gulls, tertiary consumers that feed on fishes, which are the secondary consumers that eat small insects. An unanticipated effect of DDT on bird species was its interference with the metabolic process of eggshell formation. The result

100

60

DDT (ppm)

1268

40

Learning Outcome: 1. Define biomagnfication, and explain its relationship to pollution.

In Section 59.3, we considered how pollution generated by humans can affect biogeochemical cycles. Certain types of pollutants can also accumulate within the bodies of animals and plants. The tendency of certain chemicals to concentrate in organisms at higher trophic levels in food chains, which is called biomagnification, can cause health and reproductive problems for certain organisms.  The passage of dichlorodiphenyltrichloroethane (DDT), an insecticide used against mosquitoes and agricultural pests, through food chains provides a startling example of biomagnification. DDT was first synthesized by chemists in 1874. In 1939, its insecticidal properties were recognized by Paul Müller, a Swiss scientist who won the 1948 Nobel Prize in Physiology or Medicine for his discovery and subsequent research on

20

0 Bottom mud (0.014 ppm)

Small insects (0.41 ppm)

Fishes (3–6 ppm)

Gulls (99 ppm)

Figure 59.16  Biomagnification in a Lake Michigan food

chain.  The DDT tissue concentration in gulls, a tertiary consumer, was about 240 times that in the small insects sharing the same environment. The biomagnification of DDT in lipids causes its concentration to increase at each successive level in the food chain. The unit ppm is equivalent to 1 mg of DDT per kg of biological material.



THE AGE OF HUMANS 1269

Percentage of species threatened

100

CI

CI H C CCI3

DDT (dichlorodiphenyltrichloroethane) ● Persists in environment ● High solubility in lipids ● Found in high concentrations at higher trophic levels

Figure 59.17  Thinning of eggshells caused by DDT.  Ibis eggs, Texas Gulf Coast. ©George Silk/The LIFE Picture Collection/Getty Images

was thin-shelled eggs that often broke under the weight of incubating birds (Figure 59.17). DDT was responsible for a dramatic decrease in the populations of many birds due to failed reproduction. Relatively high levels of the chemical were also found to be present in some game fishes, which, as a result, became unfit for human consumption. Because of growing awareness of the adverse effects of DDT, most industrialized countries, including the U.S., banned the use of the chemical by the early 1970s. The good news is that following the outlawing of DDT, populations of the most severely affected bird species have recovered. However, had scientists initially possessed a more thorough knowledge of how DDT accumulates in food chains, some of the damage to the bird populations might have been prevented. Biomagnification occurs for other types of molecules that do not break down quickly in the environment and are not excreted efficiently by living organisms. Such substances include mercury, which is emitted from coal-fired power plants, and persistent organic pollutants, or POPs, that are used in herbicides and pesticides. Underwater mining of the ocean floor to extract minerals releases sulfide and selenium that can also biomagnify in food chains. 

59.5        Habitat Destruction Learning Outcomes: 1. Identify the main causes of habitat destruction by humans. 2. Explain why tropical deforestation is a particularly destructive form of habitat loss. 3. Describe how the impact of agriculture causes ecological changes.

Habitat destruction is usually a human-driven process in which a natural habitat is altered in a way that prevents it from supporting the species that were originally present. Organisms that previously occupied the habitat are displaced or unable to survive, thereby reducing biodiversity. Habitat destruction is the primary cause of species extinction, and a high percentage of existing species are threatened

80 60 40 20 0

Habitat destruction

Invasive Pollution species Type of threat

Overexploitation

Figure 59.18  Percentages of plant and animal species

threatened by various causes in the U.S.  Species can suffer from multiple threats, so categories do not sum to 100%. Core Skill: Science and Society  The effects of humans greatly increase the percentage of species threatened with extinction.

by this process (Figure 59.18). Other human-driven practices that are threatening the survival of many species include pollution, which has already been discussed in this chapter, and overexploitation and invasive species, which are described in the last two sections. Habitat destruction includes deforestation, conversion of habitat to agricultural land, urbanization, strip mining, quarrying, and many other forms of land modification. Urbanization, the development of cities on previously natural or agricultural areas, is the most human-dominated and fastest-growing type of land use worldwide, and it devastates the land more severely than nearly any other form of habitat destruction. Freshwater habitats have also suffered via dam construction and river channelization. Wetlands have been drained for agricultural purposes and have been filled in for urban or industrial development. In the U.S., as much as 90% of freshwater marshes have disappeared in states such as Iowa and California, though the national average is approximately 53%. In this section, we will examine the two most widespread and interrelated types of habitat destruction, at least in terms of their influence on species extinctions. These are deforestation and the conversion of land to agricultural purposes.

Deforestation by Humans Threatens the Existence of Many Species Deforestation, the conversion of forested areas to nonforested land, is a prime cause of the extinction of species (Figure 59.19). About onethird of the world’s land surface is covered with forests, and much of this area is at risk of deforestation. Many species live in forests. For example, among North American terrestrial wildlife, about one-quarter of the bird species (272 species) and more than 10% of mammalian species (49 species) have an obligatory relationship with forest cover, meaning that they depend on trees for food and nesting sites. In terms of wildlife use, oaks are among the

1270

CHAPTER 59

Figure 59.19  Deforestation.  Cascade Mountains near Seattle,

Washington, 1906. Source: Library of Congress Prints and Photographs Division [LC-USZ62-67666]

most valuable trees in North America. At least 100 species of birds and mammals include acorns in their diets, and for many species of wildlife, the annual acorn crop is a major determinant of their abundance. Most woodpeckers, as well as many other types of birds, nest in holes that they excavate in trees, and their food usually consists of insects collected on or in trees. The ivory-billed woodpecker (Campephilus principalis), the largest known woodpecker in North America and a former inhabitant of wetlands and forests of the southeastern United States, is presumed to have gone extinct in the 1950s due to destruction of its habitat by heavy logging (Figure 59.20).

Tropical forests, primarily rain forests but also deciduous forests, are among the most species-rich terrestrial habitats and exist primarily in three areas of the globe: Africa, Asia, and Latin America. Latin America contains more than the other two areas combined, with Brazil having the greatest amount of tropical forest of any nation.  The Amazon rain forest has been termed “the lungs of the planet” because it produces more than 20% of the world’s oxygen. Tropical forests, which once covered 14% of the Earth’s dry land, now cover only about 7%. The good news is that rates of tropical deforestation decreased from 0.18% per year in the 1990s to 0.08% annually between 2010 and 2015. Although tropical deforestation occurs for different reasons, clearing land for agriculture has been identified as the prime cause of forest loss. Logging in excess of regrowth is also a significant cause of forest loss, particularly in Asian forests. Collecting wood for fuel can also be important but generally is more of a problem in lightly wooded areas. Finally, the construction of mines, dams, and oil installations is a minor cause of direct deforestation, but the discharge of chemicals and silt into rivers can cause much damage indirectly. The roads built into the regions where logging is being done often open them up to further development. Conservation of tropical forests would not only save many rare species from extinction, it would also benefit humans in several ways. First, many of the world’s crops, including oranges, lemons, bananas, cacao (chocolate), coffee, and vanilla, evolved in tropical rain forests. Rain forests remain a depository of genetic variation that could be used in future breeding of these crops. In addition, rain forests are particularly rich in plants with unusual chemicals that they use in defense (refer back to Chapter 57). Many of these chemicals also have medicinal value. Although many prescription drugs sold worldwide come from plant-derived sources, less than 1% of tropical plants have been tested for their medicinal properties. One estimate has proposed lifetime values for tropical forests at $6,330 per hectare if renewable and sustainable resources such as fruit, rubber, and nuts are harvested. In comparison, forests are worth only $1,000 per hectare for timber and $2,960 per hectare when converted to agricultural grazing land. For these reasons, it seems to make good economic and ecological sense to slow the rate of tropical deforestation.

The Development of Land for Agriculture Causes Adverse Ecological Changes

Figure 59.20  Habitat destruction as an important cause of

species extinction.  The ivory-billed woodpecker, the third-largest woodpecker in the world, is thought to have gone extinct in the southeastern U.S. because of habitat destruction, though some unconfirmed sightings have occurred in the past two decades. ©James T. Tanner/Science Source

No other human endeavor on Earth requires as much land as agriculture. More land has been converted to agriculture since 1945 than in the 18th and 19th centuries combined. The average area of land under crop cultivation worldwide is 11.5%, with an additional 25.8% given over to rangeland for grazing. However, this amount varies substantially among regions (Table 59.2). The planting of crops and the grazing of livestock have produced far-reaching ecological effects on Earth (Figure 59.21). The changes to the land may result in soil erosion, a decrease in soil fertility, flooding, silting of rivers, desertification, and the loss of wildlife habitat. Also, as we have seen, runoff water from agricultural land often contains high levels of nitrogen and phosphorus from fertilizers as well as residual pesticides and manure, all of which contaminate streams and lakes. Some



THE AGE OF HUMANS 1271

Table 59.2         Percentage of Land Area Used for Agricultural Purposes

Continental area

% Cropland

% Pastures

Total

11.5

25.8

37.3

Asia

20.0

33.0

53.0

Central America and the Caribbean

15.6

36.7 

52.3 

Europe

13.1  

7.9

21.0

Middle East and North Africa

7.6

28.1 

35.6 

World

North America

11.4

12.5

23.9 

Oceania

6.2

48.2

54.4 

South America

6.8

28.8

35.6 

Sub-Sahara and Africa

8.1  

33.9

42.0 

4 billion tons of topsoil are washed into U.S. waterways each year, severely impacting the organisms that live there. Topsoil can also be whipped away by wind.

59.6        Overexploitation Learning Outcomes: 1. Outline the main causes of overexploitation of plant and animal populations. 2. Describe examples of the overexploitation of animals and plants. 3. CoreSKILL » Calculate the maximum sustainable yield of a population based on its carrying capacity and per capita rate of increase.

In ecology, overexploitation is the practice in which humans harvest a particular species at a rate that is unsustainable, based on its natural rate of mortality and capacity for reproduction. Overexploitation, particularly the hunting of animals, has been the cause of many extinctions in the past. In this section, we will consider several examples of overexploitation and then examine how ecologists make calculations to determine if overexploitation is occurring.

Many Species Have Gone Extinct or Are Currently Threatened Due to Overexploitation

(a)

With regard to animals, hunting and fishing have been the main practices that facilitate overexploitation. For other groups, such as plants, the ability to identify valuable species and remove them from their native habitats has led to overexploitation. In 2015, a study by Canadian conservation biologist Chris Darimont and colleagues examined the effects of humans as hunters of terrestrial mammals and fishers of marine fishes. They compared 2,125 estimates of exploited animal populations and showed that humans kill adult prey at rates up to 14 times higher than other predators (Figure 59.22). Darimont and colleagues termed humans “super predators” and suggested that, in the long run, this level of hunting and fishing would not be sustainable. As seen in Figure 59.22, humans are predators of species that are considered the top predators in their native environment. For example, humans have greatly decreased the populations of wolves, which are successful predators in many different habitats. Let’s now consider a few examples in which humans have overexploited animals and plants.

(b)

Land Mammals  The list of mammals threatened with extinction or actually driven extinct by hunting is long. In the prairies of North America, hunting diminished populations of buffalo from around 70 million in the 18th century to 1,150 by 1899. Since then, buffalo numbers have rebounded to about 350,000. In Russia, another inhabitant of the prairies, the Eurasian wild horse, also known as the tarpan, (Equus ferus), had been hunted to extinction by the 1860s. Even today, poachers threaten many land mammals. Rhinoceroses have a horn and elephants have tusks that some people believe will cure everything from cancer to hangovers. The black market value for rhino horn in Southeast Asia is about $65,0000 per kilogram, making it more expensive by weight than gold, diamonds, or

Figure 59.21  Modern agriculture and its impact on the

environment.  Modern agriculture has converted vast areas of land into fields for (a) the growing of crops and (b) the grazing of livestock. This conversion results in the destruction of habitat for native species and has a variety of negative ecological effects on soils and bodies of water. a: Source: USDA; b: ©Martial Colomb/Photographer’s Choice/Getty Images

CHAPTER 59

Nonhuman predators

Type of predator Human hunters

Human fishers

15

H Herbivore C Carnivore TP Top predator

Blue

30

Fin

25

Sei

20

Minke

15 10 5

10

5

0

1980

1975

1970

1965

1960

1955

1950

1945

1940

1935

1930

1925

1920

1915

0 1910

Relative rate of exploitation

20

35 Catches (thousands)

1272

Year

Figure 59.23  Sequential decline of whale catches in the Antarctic, showing the strong effect of human predators. AII

H

H C TP Type of prey

C

TP

cocaine. Roughly 100,000 African elephants were poached across the continent between 2010 and 2012. In 2011 alone, poachers killed roughly 1 in every 12 African elephants. Many experts believe that the last of the great woolly mammoth populations were hunted to extinction at the end of the last glacial period about 12,000 years ago.

10. Then the relatively small minke whales (B. acutorostrata), which were ignored in the Southern Ocean until 1971–1972, began to be taken. Since that time, minkes have been the largest component of the southern baleen whale catch. The story has been similar in the Northern Hemisphere. In 1982, the International Whaling Commission (IWC) voted for a moratorium on all commercial whaling. The IWC proposed an end to commercial whaling in 1985–1986, a proposal that did not actually take effect until 1988. The good news is that following the moratorium, the populations of some whales have increased. Blue whales appear to have quadrupled their numbers off the California coast during the 1980s, showing the impact that protection from a predator can have. Steve Palumbi’s laboratory estimated past population sizes of North Atlantic whales by examining mitochondrial DNA sequence variation. Population size estimates for fin and humpback whales suggested that pre-whaling populations were 6–20 times higher than present-day population estimates and that full recovery of whale populations will take another 70–100 years.

Whales  A 2014 estimate of the number of whales killed by industrial harvesting during the last century, 1900–1999, by Roberta Rocha, Director of Science at the New Bedford Whaling Museum in Massachusetts, revealed that nearly three million whales were harvested, in what was the largest cull, in terms of biomass, in human history. The history of whaling in general, and Antarctic whaling in particular, has been characterized by a progression from more valuable or more easily caught species to less attractive ones, as populations of the original targets were depleted (Figure 59.23). In the Antarctic, blue whales (Balaenoptera musculus) dominated the catches through the 1930s, but by the middle 1950s, few were being taken, although the species was not legally protected until 1965. As the populations of blue whales diminished, attention turned to the fin whale (B. physalus) which was originally the most abundant of all whales in the Southern Ocean. By the 1960s, numbers of this species had diminished rapidly. Sei whales (B. borealis) were almost ignored by whalers until the bigger species were no longer available. They were hardly taken at all until about 1958, but then catches increased rapidly and reached a peak of about 20,000 in 1964–1965. Catches declined rapidly thereafter, this time due to the introduction of a catch limit of

Birds  A poignant example of overexploitation was the dodo (Raphus cucullatus), a flightless bird that was native only to the island of Mauritius and had no known predators. A combination of overexploitation and introduced species led to its extinction within 200 years of the arrival of humans. Sailors hunted it for its meat, and the rats and pigs they brought to the island, the latter as a food source, destroyed the dodos’ eggs and chicks in their ground nests. Two abundant species of North American birds, the passenger pigeon and the Carolina parakeet, had been hunted to extinction by the early 20th century. The passenger pigeon (Ectopistes migratorius)  was once the most common bird in North America, probably accounting for over 40% of the entire number of birds (Figure 59.24). Flock sizes were estimated to be over 1 billion birds. It may seem improbable that the most common bird on the continent could be hunted to extinction for its meat, but that is just what happened. The flocking behavior of the birds made them relatively easy targets for hunters, who used special firearms to harvest the birds in quantity. In 1876, in Michigan alone, over 1.6 million birds were killed and sent to markets in the eastern U.S. Similarly, the Carolina

Figure 59.22  Humans as hunters.  The rates at which humans

exploit adult land mammals and marine fish vastly exceed the impacts of other predators. Marine fish of all trophic levels are similarly affected. In contrast, land predators are exploited at much higher rates than herbivores. The term top predator refers to the most successful predator in a given habitat, which also can be a prey to humans. Core Skill: Science and Society  Human hunting and fishing massively impacts populations of herbivores, carnivores, and top predators, compared to the effects of non-human predators.



THE AGE OF HUMANS 1273

Figure 59.24  Overexploitation has caused species

extinctions.  The passenger pigeon, Ectopistes migratorius, which was once among the most abundant bird species on Earth, was hunted to extinction for its meat. ©Topham/The Image Works

(a) 1957

parakeet (Conuropsis carolinensis), the only species of parrot native to the eastern U.S., had been similarly hunted to extinction by the early 1900s. Fishes  Many species of fish are harvested to the degree that the rate of removal exceeds the rate of reproduction. Eventually, these fish populations crash and the fishery collapses. In the case of the Canadian cod fishery, overfishing and collapse came in the early 1990s after hundreds of years of fishing (Figure 59.25). Since that time, the species has not been economically fished. There is hope that the Canadian cod fisheries will eventually recover, but the recovery will be slow because the fish do not spawn until 7 years of age. A 2010 study showed that populations near Newfoundland and Labrador were still only 10% of their original sizes. In the Florida Keys, historical photographs document the reduction of large trophy fish taken over the period 1956–2007 (Figure 59.26). The mean fish size declined from an estimated

(b) early 1980s

900

Yield (thousands of tons)

800 700 600 500 400 300 (c) 2007

200 100 0

Figure 59.26  Change in the sizes of trophy fish caught on Key 1960

1970

1980

1990

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Figure 59.25  Commercial cod fisheries.  Changes in Canadian cod yields from 1960 to 2000.

West charter boats.  (a) 1957, (b) early 1980s, and (c) 2007. a: Source:

From the archives of Monroe County Public Library, Key West, Florida. Photo by Wil-Art Studio/Art Stickel; b: Source: From the archives of Monroe County Public Library, Key West, Florida. Photo by Dale McDonald; c: Photo courtesy Loren McClenachan, Ph.D.

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Quantitative Analysis Ecologists Make Calculations to Determine If Overexploitation Is Occurring For a population that is being harvested by humans, the yield is the number of individuals harvested in a given unit of time. Maximum sustainable yield (MSY) is the largest number of individuals that can be harvested without causing long-term decreases in the population. If the maximum sustainable yield is exceeded on a consistent basis, overexploitation is occurring. According to the logistic equation described in Chapter 56, change in the number of individuals in a population over time, dN/dt, occurs according to the following equation: (K − N) ___ ​​  dN ​​  = rN ​​ _______  ​​    K dt

Figure 59.27  Rothschild’s orchid, Paphiopedilum

rothschildianum.  Overcollection in northern Borneo has pushed this species close to extinction in the wild. ©Matthew Lambley/Alamy Stock Photo

19.9 kg in 1956 to 2.3 kg in 2007! A shift was observed in the types of species caught. In 1956, large groupers (Epinephellus spp.) were commonly landed together with large sharks greater than 2 m. In 2007, small snappers (Lutjanus campechanus and Ocyurus chrysurus) with an average length of 34.4 cm and sharks less than 1 m long were landed. Plants  Many species of valuable plants have also been severely overexploited for human use, including West Indian mahogany (Swietenia mahogani)  in the Bahamas, and Lebanese cedar (Cedrus libani), which in Lebanon has been reduced to a few scattered forest remnants. Rare cacti and orchids have also been threatened by collectors, who seek to own a rare organism or to profit from its sale. Rare orchids are very valuable. A single stem of Rothschild’s orchid (Paphiopedilum rothschildianum), also known as the Gold of Kinabalu, is reported to sell for $5,000 (Figure 59.27). No wonder that after its discovery, this orchid was stripped from the wild in northern Borneo by orchid smugglers, pushing it close to extinction. Plants may also be collected for their medicinal value, real or supposed. In the U.S., American ginseng (Panax quinquefolicus), native to eastern North America, has been sought after to treat the common cold. Plants are so enthusiastically collected by “sang hunters,” who also sell it to Chinese traders, that ginseng has become threatened or endangered in some states. The Botanic Gardens Conservation International Organization has stated that over 400 medical plant species are at risk of extinction because of overcollection and deforestation, including many species of yew tree (genus Taxus), whose bark is used for cancer drugs.

where N is the number of individuals, t is a unit of time, r is the per capita rate of population growth, and K is the carrying capacity. The greatest population growth, and thus the maximum sustainable yield, occurs at the midpoint of the logistic curve, at K/2 (refer back to Figure 56.10). MSY can thus be estimated as MSY = ___ ​​  rK ​​   2 As an example, if K/2 = 10,000 and r = 0.14, then MSY = 1,400. MSY has been extensively used for fisheries management. However, the use of the model has some drawbacks. For example, biologists cannot easily go under water and count the number of individuals. The model also ignores the age and reproductive status of the individuals being harvested. As an alternative, simple models based on data collection from fisheries may be used, which compare costs and revenues and consider MSY (Figure 59.28). The maximum profit (red line) is greater than the profit obtained at MSY (blue line). Why is MSY important to fisheries (and the harvesting of other species)? Let’s assume that total economic costs increase linearly as fishing effort increases. Total revenue also increases with fishing effort, up to a point. After MSY is reached, any increase in effort would result in a decrease in revenue as the fish populations became overfished. The maximum profit is equal to the biggest difference between the cost and revenue curves, and as the red line in Figure 59.28 shows, this occurs below the effort needed to reach the maximum sustainable yield. Why do fisheries become overfished? Most estimates of MSY are nearly always too high, because of overestimates of population size. Furthermore, incremental improvements are made to fishing gear over the years and the same level of effort results in increased catches. Finally, as fish populations decline, the prices inch upward, making it more likely for commercial fishing to keep harvesting them. In the case of the cod industry, the introduction



THE AGE OF HUMANS 1275

Costs or revenue (dollars)

∙ Certain native species may lack defenses against the invasive species. MSY

Profit at MSY Revenue

Maximum profit

Costs Fishing effort

Figure 59.28  Economic fisheries model based on revenue

and costs.  The model assumes that costs increase linearly with effort but revenue reaches a maximum at maximum sustainable yield (MSY). Maximum profit, however, occurs below MSY.

of radar and sonar allowed crews to pursue fish over huge areas. The crews also caught enormous numbers of noncommercial fish, which were discarded. Among these were important prey species for cod, such as capelin. Finally, although undersized cod, which cannot spawn, were returned to the ocean, such discards do not always survive. As the cod populations went into a tailspin, increased effort resulted in more undersized fish being caught and more discarded.

59.7          Invasive Species Learning Outcomes: 1. Define introduced species and invasive species. 2. Compare and contrast invasive species as competitors, as predators, and as pathogens.

As noted in the Feature Investigation of Chapter 54, introduced species are those species moved by humans from their native habitat to another location. Most often, the species are introduced for agricultural or landscaping purposes or as sources of timber, meat, or wool, and they may need humans for their continued survival. In some cases, as with plants, insects, or aquatic species, organisms are unintentionally transported via the movement of cargo by ships or planes. Regardless of the way they have been transported, some introduced species become invasive species, spreading naturally and impacting native species. Why do invasive species become successful in their new habitat? In most cases, they have one or more of the following characteristics. ∙ Invasive species may reproduce rapidly. ∙ They may not have natural enemies in their new habitat.

∙ Invasive species may compete aggressively for resources. ∙ They may tolerate a wide variety of habitat conditions. In the U.S. alone, over 4,500 invasive species have been identified, and 15% cause severe ecological or economic harm.  For example, 142 species of introduced vertebrates have self-sustaining populations in the wild. These include ring-necked pheasants (Phasianus colchicus), which were brought over by hunters, and Burmese pythons (Python molorus), which were introduced by pet owners. Of the 300 most invasive weeds in the U.S., over half were brought in for gardening, horticulture, or landscape purposes. These include purple loosestrife (Lythrum salicaria) and Japanese honeysuckle (Lonicera japonica) in the Northeast, kudzu (Pueraria lobata) in the Southeast, Chinese tallow (Sapium sebiferum)  in the South, and leafy spurge (Euphorbia esula) in the Great Plains. In this section, we will examine how the interactions between invasive and native species may involve competition, predation, and parasitism.

Invasive Species May Compete Against Native Species Ecologists have discovered many examples in which invasive species outcompete native species. For example, placental mammals have been particularly effective competitors in Australia, where introduced feral dogs (Canis lupus, ssp. dingo) are thought to have outcompeted the thylacine (Thylacine cynocephalus), a native marsupial, wolflike animal, in mainland Australia (Figure 59.29a). Sheep introduced for the wool industry appear to successfully compete with a variety of kangaroo species, especially the brush-tailed rock wallaby and larger species, such as the red kangaroo and the western gray kangaroo. Introduced vertebrates are a problem in aquatic environments, too. In California, 48 of 137 species of freshwater fish are nonnative. Of these, 24 are known to have a negative impact on native fish.  Invasive plants are major competitors of native plants throughout the world. In some cases, invasive plants have become so successful that they have produced near monocultures—areas where they exist as the sole plant species. In the U.S. Northeast, purple loosestrife is a strong competitor, choking out other plant species in wetlands (Figure 59.29b). In south Florida, three invasives—Brazilian pepper (Schinus terebinthifolius), Australian pine (Casuarina equisetifolia), and, especially punk-tree (Melaleuca quinquenervia)—are outcompeting native vegetation in the Everglades. 

Invasive Species May Act as Predators Many striking examples of the powerful effects of invasive species have been provided by predator introductions. Sea lampreys (Petromyzon marinus) are primitive, jawless fish that feed by rasping holes in the sides of larger fish species and feeding on their blood. They spawn in freshwater streams, and the juveniles return to salt water (or one of the Great Lakes as a substitute) to develop. Sea lampreys found their way into Lake Ontario in the mid-1800s by way of the Erie Canal (Figure 59.30a). Improvements to the Welland Canal allowed

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(a) Feral dog

(b) Purp Purple loosestrife

Figure 59.29  Introduced species as competitors.  (a) Feral dogs, also called dingoes, are thought to have outcompeted the thylacine in Australia. (b) Introduced plants can choke out native vegetation, as has occurred with purple loosestrife in the U.S. Northeast. a: ©kongsak sumano/123RF; b: ©Reimar Gaertner/Alamy Stock Photo

The sea lamprey invasion of the Great Lakes

300 Population (thousands)

e Superior—1 93 Lak 8 Lak e

—1932 ron Hu

Lake Michiga n— 19 34

First stream treatments for lampreys, 1958

Lampreys enter, 1938

ntario—1800s ke O La Welland Canal Erie Canal 21 19 e— L a k e E ri

250 200

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Path of the invader (a)

(b)

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Figure 59.30  Effects of invasive sea lampreys on the lake trout population in the Great Lakes.  (a) Historical passage of lampreys into the Great Lakes from the Atlantic. (b) Effects of lampreys on the trout population in Lake Superior. Note that detailed records of sea lamprey populations were not available before 1956. a: Source: U.S. Fish and Wildlife Service, Bugwood.org

lampreys to bypass Niagara Falls and colonize the rest of the Great Lakes. In 1921, lampreys were found in Lake Erie and by 1938 they had been found all the way up into Lake Superior. Lake trout (Salvelinus namaycush) were the lampreys’ preferred prey in the Great Lakes. The lake trout fishing industry declined somewhat in the 1940s due to overfishing, but the decline was hastened by the arrival of lampreys (Figure 59.30b). By the 1960s, lake trout catches had been reduced by over 90% of their historic averages, and the fishery collapsed. In the late 1940s, the state of Michigan began control measures for lampreys. Barriers were erected across the mouths of streams to prevent the return of spawning adults, but they were difficult to maintain and were not 100% effective. Attention turned to chemical control of juvenile lampreys, which spend 3–5 years buried in stream

sediments, filter feeding. The chemical TFM (trifluoromethyl nitrophenol) proved effective in controlling juvenile lampreys in streams and was first applied in 1958 to streams feeding into Lake Superior (see Figure 59.30b). These treatments reduced lamprey densities by 90%, and the population of lake trout increased in the 1980s, aided by an active program of restocking. To maintain lamprey control, streams are treated every 3–5 years. Removal of invasive species is time-consuming and costly but may lead to recovery of native prey species. A second example of an invasive species acting as a predator is the Burmese python in the Florida Everglades (see the chapter opening photo). Pythons were likely introduced prior to 1985 and the population has grown exponentially since then. Pythons in Florida



THE AGE OF HUMANS 1277

Density of chestnut trees before chestnut blight

200 1996–1997 (Pre-python)

2

2003–2011 (After python)

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160 120 80 Density after chestnut blight; few survivors

er

40

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Figure 59.31  Effect of invasive Burmese pythons on wildlife

abundance in the Everglades National Park, Florida.  According to roadside surveys, a decline in mammal abundance occurred after pythons became common (2003–2011).

consume a wide range of vertebrate prey, including endangered species such as the wood stork (Mycteria americana) and the Key Largo woodrat (Neotoma floridana). Survey data gathered by counting animals and roadkills showed that raccoons, opossums, and rabbits were often observed during the period 1993–1999, before pythons became common. In the period 2003–2011, when pythons were common, the decline in observations was 99.3% for raccoons, 98.9% for opossums, 94.1% for white-tailed deer, and 87.5% for bobcats (Figure 59.31). No rabbits or foxes were even observed. In south Florida today, these species exist only in locations peripheral to the Everglades, where pythons are rare. 

Some Invasive Species Are Lethal Pathogens A pathogen is an agent that causes disease symptoms in its host. Some pathogens become invasive species when moved to a new geographical location. For example, Chestnut blight (Cryphonectria parasitica) is a fungus from Asia that was accidentally introduced to New York around 1904 from imported Asian chestnut trees (Castanea crenata). At that time, the American chestnut tree (Castanea dentata) was one of the most common trees in the eastern U.S. It was said that a squirrel could jump from one chestnut tree to another all the way from Maine to Georgia without touching the ground. The densest populations of chestnuts occurred in the Appalachian Mountains. Here, humans and wildlife alike feasted on the bountiful supply of nuts. The tree was ingrained in American culture, as in “chestnuts roasting on an open fire.” By the 1950s, however, chestnut blight had significantly reduced the density of American chestnut trees in all areas of the United States, including North Carolina (Figure 59.32). Because at least one tree in four in these forests was a chestnut, the effect was very noticeable, although oaks and hickories replaced chestnuts in the canopy. Eventually, the fungus eliminated nearly all chestnut trees across North America.

Figure 59.32  Effects of an introduced fungus on American

chestnut trees.  The reduction in density of American chestnut trees in North Carolina following the introduction of the fungus Cryphonectria parasitica from Asia shows the severe effect that pathogens can have on their hosts. By the 1950s, this once prevalent species had been virtually eliminated.

Summary of Key Concepts 59.1  Human Population Growth ∙∙ Human population growth has skyrocketed over the last 250 years (Figure 59.1). ∙∙ Differences in the age structure of a population, the relative numbers of individuals in defined age groups, can influence future patterns of population growth (Figure 59.2). ∙∙ The total fertility rate (TFR) is the average number of live births a woman has during her lifetime. TFRs are used to predict the growth of human populations (Figures 59.3, 59.4). ∙∙ The ecological footprint refers to the amount of productive land needed to support each person on Earth (Figure 59.5).

59.2  Global Warming and Climate Change ∙∙ Global warming is an increase in the average surface temperature on Earth. It is expected to result in climate change. ∙∙ The greenhouse effect is the process by which short-wave solar radiation passes through the atmosphere to warm the Earth and is radiated back into the atmosphere as long-wave infrared radiation. Much of this radiation is directed back to Earth’s surface a second time, causing the surface temperature to rise (Figures 59.6). ∙∙ An increase in greenhouse gases, particularly CO2, is intensifying the greenhouse effect, causing climate change (Table 59.1; Figure 59.7). ∙∙ Two consequences of climate change are rising sea levels and changes in precipitation patterns. ∙∙ Ecologists predict that climate change will have a large impact on the distribution of the world’s organisms (Figure 59.8).

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59.3  P  ollution and Human Influences on Biogeochemical Cycles ∙∙ Biogeochemical cycles involve the movement of carbon, phosphorus, nitrogen, and water between the physical environment and organisms. ∙∙ In the carbon cycle, phototrophs incorporate CO2 from the atmosphere into their biomass; decomposition of plants and respiration recycle most of this CO2 back to the atmosphere. Human activities, primarily the burning of fossil fuels, are causing increased amounts of CO2 to enter the atmosphere (Figures 59.9, 59.10). ∙∙ The water cycle is a physical rather than a chemical process because it consists of essentially two phenomena: evaporation and precipitation. Climate change is altering precipitation patterns. In addition, alteration of the water cycle by dams can greatly disrupt migration of fishes such as salmon and trout (Figure 59.11). ∙∙ The phosphorus cycle lacks an atmospheric component and thus is a local cycle. An overabundance of phosphorus can cause the overgrowth of algae and subsequent depletion of oxygen levels, called eutrophication (Figures 59.12, 59.13, 59.14). ∙∙ The nitrogen cycle has five parts: nitrogen fixation, nitrification, assimilation, ammonification, and denitrification. The activities of humans, including the production and use of fertilizers, have altered the nitrogen cycle (Figure 59.15).

59.4  Pollution and Biomagnification ∙∙ Biomagnification is the tendency of certain chemicals to concentrate in higher trophic levels in food chains (Figures 59.16, 59.17).

59.5  Habitat Destruction ∙∙ Habitat destruction involves the conversion of natural habitat to agricultural land, urbanization, the draining of swamps, strip mining, dam destruction, and many other forms of land modification. It is the primary cause of species extinction and is threatening many current species (Figure 59.18). ∙∙ Deforestation—in particular, of tropical forests—threatens many species with extinction because of the high numbers of species that live in forests and the high rate of forest loss (Figures 59.19, 59.20). ∙∙ The planting of crops and the grazing of livestock are among the most important drivers of ecological change. Habitat destruction has changed huge areas of the planet into agricultural areas and rangelands for livestock (Figure 59.21; Table 59.2).

59.6  Overexploitation ∙∙ Overexploitation is the practice in which humans harvest a particular species at a rate that is unsustainable. The overexploitation of plants and animals occurs via hunting, fishing, and removing species from their native habitat. On average, humans decrease prey populations much more than natural predators do (Figure 59.22). ∙∙ Overexploitation has decreased the populations of many species and driven some of them to extinction. Examples include whales, the passenger pigeon, and many species of fishes and plants (Figures 59.23–59.27). ∙∙ The maximum sustainable yield is the largest number of individuals that can be harvested without causing long-term

decreases in the population. Simple economic models suggest that populations should be harvested at levels of maximum profit, which is well below the maximum sustainable yield (Figure 59.28).

59.7  Invasive Species ∙∙ Invasive species are those species introduced into new geographic areas by humans and spread on their own without human support. Invasive species may impact native species as competitors, predators, and pathogens (Figures 59.29–59.32).

Assess & Discuss  Test Yourself 1. The average total fertility rate needed for zero population change across the world is a. 1.7. d. 2.3. b. 1.9. e. 2.5.  c. 2.0. 2. Which anthropogenic gas contributes most to global warming?  a. methane b. chlorofluorocarbons c. carbon dioxide d. nitrogen oxides e. sulfur dioxide  3. The data show that atmospheric carbon dioxide levels have increased by what percentage over the past 58 years? a. 1% d. 25% b. 5% e. 52%  c. 12% 4. Eutrophication is  a. caused by an overabundance of nitrogen, which leads to a decrease in bacteria populations. b. caused by an overabundance of nutrients, which leads to an increase in algal populations. c. usually caused by oil spills. d. normally seen in dry, hot regions of the world. e. accelerated by habitat loss.  5. Human production of fertilizers first impacts which part of the nitrogen cycle?  a. nitrogen fixation d. ammonification b. nitrification e. denitrification  c. assimilation 6. The concentration of certain chemicals, such as DDT, in higher trophic levels is known as a. eutrophication. d. energy transfer. b. biomagnification. e. turnover.  c. biogeochemical cycling. 7. Which is not an example of habitat destruction?  a. deforestation d. draining of wetlands b. agriculture e. overharvesting  c. urbanization 8. The passenger pigeon, once the most common bird in North America, was driven to extinction by  a. pollution. d. invasive species. b. overexploitation. e. all of the above.  c. habitat destruction.



THE AGE OF HUMANS 1279

9. Most recorded extinctions have been caused by  a. invasive species. d. a and b equally. b. habitat destruction. e. a, b, and c equally.  c. overexploitation. 10. Invasive species enter an area through  a. agricultural introductions. b. accidental transportation via ships. c. landscape plants and their pests. d. a and b. e. a, b, and c. 

Conceptual Questions 1. The Earth’s atmosphere consists of 78% nitrogen. Why is nitrogen a limiting nutrient? 

2. Why does maximum sustainable yield occur at the midpoint of the logistic curve and not where the population is at carrying capacity?   3.  

Core Skill: Science and Society  In one family, parents, who were born in 1900, have twins at age 20 but then have no more children. Their children, grandchildren, and so on behave in the same way. In another family, parents, who were also born in 1900, delay reproduction until age 33 but have triplets. Their children and grandchildren behave in the same way. Which family has the most descendants by 2000? What can you conclude? 

Collaborative Questions 1. Discuss what might limit human population growth in the future. 2. As a group, try to predict what effects an atmospheric concentration of 700 ppm of CO2 might have on the environment.

CHAPTER OUTLINE

Biodiversity and Conservation Biology

60

Spix’s macaw (Cyanopsitta spixii). Less than 100 individuals of this species are known to exist in the rain forests of Brazil. ©Patrick Pleul/dpa/picture-alliance/Newscom

I

n 2009, Jeff Corwin, an American conservationist and host for programs on Animal Planet and other television networks, published a book entitled 100 Heartbeats: The Race to Save the Earth’s Most Endangered Species. The Hundred Heartbeat Club had been created earlier by biologist E. O. Wilson to highlight the plight of animal species, such as Spix’s macaw (Cyanopsitta spixii) in Brazil (see the chapter opening photo), the Chinese river dolphin (Lipotes vexillifer), and the Philippine eagle (Pithecophaga jefferyi), that have 100 or fewer individuals left alive (and hence are that number of heartbeats away from extinction). Saving species from extinction is important in its own right, but, as we will see, conservation of biological diversity also has great economic and social value to humankind. Biological diversity, or biodiversity, encompasses the genetic diversity of species, the variety of species, and the different ecosystems they form. The field of conservation biology

60.1 Genetic, Species, and Ecosystem Diversity 60.2 Biodiversity and Ecosystem Function 60.3 Value of Biodiversity to Human Welfare 60.4 Conservation Strategies Summary of Key Concepts Assess & Discuss

uses principles and knowledge from molecular biology, genetics, and ecology to protect and sustain biodiversity. Because it draws from nearly all chapters of this textbook, a discussion of conservation biology is a fitting way to conclude our study of biology. In this chapter, we will begin by examining the questions of what biodiversity is and why it should be conserved and exploring how much biodiversity is needed for ecosystems to function properly. Later, we will consider what is being done to help conserve the world’s endangered plant and animal life. This includes identifying global areas rich in species and establishing parks and refuges of the appropriate size, number, and connectivity. We will also discuss conservation of particularly important types of species and how to restore damaged habitats to a more natural condition. We then examine how captive-breeding programs help to build populations of rare species prior to their release back into the wild. Some programs have also used modern genetic techniques such as cloning to help breed and perhaps eventually increase populations of endangered species.

60.1    G enetic, Species, and Ecosystem Diversity Learning Outcome: 1. List and describe the three levels of biodiversity.

Biodiversity can be examined on three levels: genetic diversity, species diversity, and ecosystem diversity. Each level of biodiversity provides valuable benefits to humanity. Genetic diversity is the amount of genetic variation occurring within and between populations. Without such variation, populations may be unable to respond quickly to changes in environmental conditions, resulting in population decline and even extinction. Maintaining genetic variation in the wild relatives of crops may be vital to the continued success of crop-breeding programs. For example, the café marron (Ramosmania rodriguesii), a wild relative of the coffee plant that is native to a tiny island off the coast of



BIODIVERSITY AND CONSERVATION BIOLOGY 1281

60.2   Biodiversity and Ecosystem Function Learning Outcomes:

1. CoreSKILLS » Create graphical representations of possible relationships between biodiversity level and ecosystem function. 2. Describe experimental evidence that shows how species richness and ecosystem function are linked.

Figure 60.1  Café marron being cultured in London’s Kew

Gardens.  These plants are derived from just one surviving individual found in Mauritius. ©Florapix/Alamy Stock Photo

Mauritius, was assumed to be extinct until 1979, when one surviving tree was identified. Today, cuttings from the tree are being cultured in London’s Kew Gardens (Figure 60.1). The plant may carry genes that could allow coffee to be grown in a wider range of soils and elevations. A second level of biodiversity is  species diversity, the number and relative abundance of species in a community (refer back to Section 58.1). In 1973, the U.S. Endangered Species Act (ESA) was enacted, which was designed to protect both endangered and threatened species. Endangered species are those species that are in danger of extinction throughout all or a significant portion of their range. Threatened species are those species likely to become endangered in the foreseeable future. Many species are currently threatened. According to the International Union for Conservation of Nature and Natural Resources (IUCN), more than 25% of the fish species that live on coral reefs and 22% of all mammals, 12% of birds, and 31% of amphibians are threatened with extinction. In 2000, the World Wildlife Foundation placed Atlantic cod (Gadus morhua)  on the endangered species list as a result of overfishing. Nine of 17 populations of commercially important Chinook salmon (Oncorhynchus tshawytscha) in California and Oregon are listed as endangered or threatened. The last level of biodiversity is ecosystem diversity, the diversity of structure and function within an ecosystem. Conservation has largely focused attention on species-rich ecosystems such as tropical rain forests. Over 120 prescription drugs used to treat malaria, cancer, and other diseases were developed from rain forest plants, yet less than 1% of such plants have been tested for medicinal properties. However, some ecologists have argued that relatively species-poor ecosystems such as prairies are also highly threatened and in equal need of conservation. More than 99% of the original tallgrass prairie in the United States has been converted to agricultural land.

Because biodiversity affects the health of ecosystems, ecologists have explored the question of how much diversity is needed for ecosystems to function properly. In this section, we will examine several models that explore the relationship between ecosystem function and species richness and examine an experimental approach used to study this relationship.

Ecologists Have Proposed Several Models for the Relationship Between Ecosystem Function and Species Richness Because biodiversity affects the health of ecosystems, ecologists have explored the question of how many species are needed for ecosystems to function properly. In doing so, they have described several possible relationships between ecosystem function and species richness. In the 1950s, ecologist Charles Elton proposed the diversity-stability hypothesis, which suggests that species-rich communities are more stable than those with fewer species (refer back to Section 58.2). If we use stability as a measure of ecosystem function, Elton’s hypothesis indicates a linear correlation between ecosystem function and species richness; as the number of different species increases, ecosystem function increases proportionately (Figure 60.2a). Australian ecologist Brian Walker proposed an alternative to this idea, termed the redundancy hypothesis (Figure 60.2b). According to this hypothesis, ecosystem function increases rapidly at fairly low levels of species richness, but then levels off because most additional species are functionally redundant.  Two other alternative ideas relating species richness and ecosystem function have been proposed. The keystone hypothesis (Figure 60.2c) proposes that ecosystem function dramatically rises as species richness approaches its natural level. Finally, the idiosyncratic hypothesis suggests that although ecosystem function can change as the number of species increases or decreases, the amount and direction of change are unpredictable (Figure 60.2d). Determining the correct model(s) for the relationship between ecosystem function and species richness is very important, as our understanding of the effect of species loss on ecosystem function can greatly affect the way we manage our environment. Only relatively recently has the link between ecosystem function and species richness been studied. An early and influential study, conducted by Shahid Naeem and his colleagues in laboratories in England, is described next.

CHAPTER 60

dots represent the end points of a continuum of species richness. The first dot is at the origin, where there are no species and no community services. The second dot represents a natural level of species richness. The relationship is strongest in (a) and weakest in (d).

Ecosystem function

Ecosystem function

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Species richness (b) Redundancy hypothesis

Species richness

Ecosystem function

Ecosystem function

(a) Diversity-stability hypothesis

Species richness (c) Keystone hypothesis

Species richness (d) Idiosyncratic hypothesis

Figure 60.2  Graphical representations of possible relationships

Core Skill: Modeling  The goal of this modeling challenge is to draw a graph showing a different relationship between ecosystem function and species richness, one based on the rivet hypothesis, which was proposed in 1981. Modeling Challenge: In 1981, Paul and Ann Ehrlich proposed a relationship between ecosystem function and species richness called the rivet hypothesis. In this model, species are like the rivets on an airplane. Some species play a small but critical role in keeping the plane, the ecosystem, airborne, while other species do not, and we cannot tell beforehand which species affect the ecosystem function the most. The loss of a single rivet will probably not weaken the plane. However, the loss of few rivets would impair airworthiness. The plane could still function but not at maximum efficiency. Continuing on, the loss of a few more rivets could again be tolerated, but the loss of yet more rivets would prove critical to the airplane’s function. Thus, ecosystem function declines with decreased species richness in a stepwise fashion. Draw a graph that depicts a model for the rivet hypothesis. Use the same format as those in Figure 60.2.

between ecosystem function and species richness.  The two solid

Core Skill: Process of Science

Feature Investigation  | Ecotron Experiments Analyzed the Relationship Between Ecosystem Function and Species Richness

In the early 1990s, American ecologist Shahid Naeem and colleagues used a series of 14 environmental chambers in a facility termed the Ecotron, at Silwood Park, England, to determine how species richness affects ecosystem function. These chambers contained terres-

trial communities that differed only in their level of species richness (Figure 60.3). The number of species in each chamber was manipulated to create high-, medium-, and low-richness ecosystems, each with four trophic levels. The trophic levels consisted of primary

Figure 60.3  Ecotron experiments comparing species richness and ecosystem function. (3): ©Pete Manning, Ecotron Facility, NERC Centre for Population Biology

Concept Check:  What is one of the dangers in interpreting these results? 

HYPOTHESIS Reduced species richness can lead to reduced ecosystem functioning. STARTING LOCATION Ecotron, a controlled environment facility at the Natural Environment Research Council (NERC) Centre for Population Biology, in Silwood Park, England. Experimental level

1

Conceptual level Air exhaust

Construct 14 identical experimental chambers. Irrigation lance Fans Air input

Cooling air for lights Moisture and temperature sensors

Temperature- and humidity-controlled chambers are used to control environmental conditions and allow identical starting conditions in all chambers.



BIODIVERSITY AND CONSERVATION BIOLOGY 1283

2 Add different combinations of species to thecombinations 14 chambers.ofThe different 2 Add species added were based on species to the 14 chambers. The 3 types added of model communities species were based on eachcommunities with 4 trophic 3(food typeswebs), of model levels but with varying (food webs), each with 4degrees trophic of species richness. levels but with varying degrees of species richness.

2° consumers

Subset of high

Subset of medium

Subset of high

Subset of medium

The three diagrams to the left eachthree represent a single chamber. The diagrams to the left Circles represent species, and each represent a single chamber. lines connecting represent Circles represent them species, and bioticconnecting interactions among the species. lines them represent Note that each lower-biodiversity biotic interactions among the species. community is alower-biodiversity subset of its Note that each higher-diversity counterpart community is a subset of its and that all community types have 4 higher-diversity counterpart and trophic levels. that all community types have 4 trophic levels.

2° 1° consumers 1° consumers 1° producers 1° producers Detritivores Detritivores Biodiversity

High

Medium

Low

Biodiversity High Number of 6 chambers Number of analyzed 6

Medium 4

Low 4

4 chambers analyzed Species present in all 3 systems Speciespresent presentin inall 2 systems Species 3 systems Speciespresent presentin in2most diverse system only Species systems

4

Species present in most diverse system only

3 Measure and analyze a range of processes, including and analyze vegetation a range of 3 Measure cover and nutrient processes, includinguptake. vegetation

Measurements help determine how each different type community Measurements help of determine how functions. each different type of community

4 THE DATA 4 THE DATA

functions.

Percent change in vegetation cover Percent change in vegetation cover

cover and nutrient uptake.

16 16

Plant productivity is linked to community diversity as measured Plant productivity is linked to by the percent change in vegetation community diversity as measured cover initial conditions. by the from percent change in vegetation cover from initial conditions. Data reveal that low-diversity communities have lower vegetation Data reveal that low-diversity cover and thus arelower less productive communities have vegetation than high-diversity communities. cover and thus are less productive

12 12 8 8 High species richness Medium species richness High species richness Low species richness Medium species richness

4 4 0 20 0 20

65 65

Low species richness 110 155 Day 110 155

than high-diversity communities. 200 200

Day

5 5 6 6

CONCLUSION Increases in species richness lead to increases in ecosystem function. In this case, increased plant species richness results in greater vegetation CONCLUSION Increases in speciescover. richness lead to increases in ecosystem function. In this case, increased plant species richness results in greater vegetation cover. SOURCE Naeem, S., et al. 1994. Declining biodiversity can alter the performance of ecosystems. Nature 368: 734–737. SOURCE Naeem, S., et al. 1994. Declining biodiversity can alter the performance of ecosystems. Nature 368: 734–737.

producers (annual plants), primary consumers (insects, snails, and slugs), secondary consumers (parasitoids that fed on the herbivores), and detritivores (earthworms and soil insects). The experiment ran for just over 6 months, and species were added only after the trophic level below them was established. For example, parasitoids were not added until herbivores were abundant.

Researchers monitored and analyzed a range of measures of ecosystem function, including community respiration, decomposition, nutrient retention rates, and community productivity. The data shown in step 4 of Figure 60.3 focus only on community productivity. The result was that community productivity, expressed as percent change in vegetation cover (the amount of ground covered

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by leaves of plants), increased as species richness increased. This productivity increase occurred because plant species of different heights could utilize light at different levels of the plant canopy. A larger ground cover also meant a larger plant biomass and greater community productivity, and increased decomposition and nutrient uptake rates. For the first time, ecologists had provided an experimental demonstration that a loss of species richness can alter or impair the functioning of an ecosystem.

Experimental Questions

Field Experiments Have Explored the Relationship Between Species Richness and Ecosystem Function

greater variety of plant root lengths could utilize nutrients at different levels of the soil (Figure 60.4b). Furthermore, the frequency of invasive plant species (species not originally planted in the plots) decreased with increased plant species richness (Figure 60.4c). Although Tilman’s results show a relationship between species richness and ecosystem function, they also suggest that most of the advantages of increasing richness come with the first 5–10 species, beyond which adding more species appears to have little to no effect. These data support the redundancy hypothesis (see Figure 60.2b). Confirmation of the redundancy hypothesis is also observed on a larger scale. The productivity of temperate forests on different continents is roughly the same, despite different numbers of tree species being present: 729 species in East Asia, 253 in North America, and 124 in Europe. The presence of more tree species may ensure a supply of “backups,” should some of the most productive species die off from insect attack or disease. This effect was seen following the demise of the American chestnut tree. Disease devastated this species, and its presence in forests dramatically decreased by the mid-20th century (refer back to Figure 59.32). The forests filled in with other species

In the mid-1990s, David Tilman and colleagues performed experiments in the field to determine how species richness affected proper ecosystem functioning. Tilman’s previous experiments had suggested that species-rich grasslands were more stable (that is, they were more resistant to the ravages of drought and recovered from drought more quickly) than species-poor grasslands (refer back to Figure 58.4). In subsequent experiments, Tilman’s group sowed multiple plots, each 3 m by 3 m and having comparable soils, with seeds of 1, 2, 4, 6, 8, 12, or 24 species of prairie plants. Exactly which species were sown into each plot was determined randomly from a pool of 24 native species. The treatments were replicated 21 times, for a total of 147 plots.  The results showed that plots with more species had increased productivity, expressed as a percentage of plant cover (the amount of ground covered by leaves of plants) than plots with fewer species  (Figure 60.4a). More species-rich plots also used more nutrients, such as nitrate (NO3−), than lower richness plots because a

1. What was the goal of Naeem and colleagues in their experiment at Silwood Park, England?  2. What was the hypothesis tested by the researchers?  3. CoreSKILL » How did the researchers test for ecosystem functioning?  4. CoreSKILL » Which relationship between species richness and ecosystem function do these results support? (Refer to Figure 60.2.)

65 0.40 60

50 45 40 35 30 25

0.35

NO3– NO3–

0.30 0.25 0.20 0.15

Number of external invading species

Nitrate in rooting zone (mg/kg)

55 Total plant cover (%)

Centaurea maculosa

8

6

4

2

0.10 0

5 10 15 20 25 Plant species richness

(a) Plant cover increased with more species.

0

5 10 15 20 25 Plant species richness

(b) Available nitrate decreased with more species.

Figure 60.4  The relationship of species richness to ecosystem function.

0

5

10

15

20 25

Plant species richness (c) Invasive species decreased with more species.



BIODIVERSITY AND CONSERVATION BIOLOGY 1285

and continued to function as before in terms of nutrient cycling and gas exchange. However, although the forests continued to function without the American chestnuts, some important changes occurred. For example, the loss of chestnuts deprived bears and other animals of an important source of food and may have affected their reproductive capacity and hence the size of their populations.

60.3  V  alue of Biodiversity to Human Welfare Learning Outcomes: 1. Outline the benefits of biological diversity to human welfare.

Why should biodiversity be a concern? American biologists Paul Ehrlich and E. O. Wilson have suggested that the loss of biodiversity should be an area of great concern for at least three reasons: 1. Humans depend on plants, animals, and microorganisms for a wide range of foods, medicines, and industrial products. 2. Ecosystems provide an array of essential services, such as clean air and water. 3. Humans have an ethical responsibility to protect what are our only known living companions in the universe. In this section, we examine some of the primary reasons why it is so important to preserve biodiversity.

Society Benefits Economically from Biodiversity Many different sectors of society benefit from biodiversity. Three key sectors are the pharmaceutical, agricultural, and the natural products industries. Pharmaceutical Industry  The pharmaceutical industry is heavily dependent on plant, animal, fungal, and bacterial products for source material. Worldwide prescription drug sales are forecast to be $1 trillion in 2020. 

(a)

(b)

An estimated 50,000–70,000 plant species are used in traditional and modern medicine. About 25% of the prescription drugs in the U.S. alone are derived from plants, and the 2015 market value of such drugs was estimated to be $374 billion, accounting for a little less than half the global pharmaceutical market.  Many medicines come from plants found only in tropical rain forests. These include quinine, a drug from the bark of the cinchona tree (Cinchona officinalis), which is used for treating malaria, and vincristine, a drug derived from rosy periwinkle (Catharanthus roseus), which is a treatment for leukemia and Hodgkin's disease (Figure 60.5a).  Animal products have also been important to the pharmaceutical industry. For example, the venom of the gila monster (Heloderma suspectum), one of only two venomous lizards in the world, is being used to treat people who are resistant to conventional treatment for type 2 diabetes, a disease that may affect 30% of Americans at some point in their lives. A protein from the South American pit viper (Bothrops jacara) may help control human blood pressure. Tarantula venom may be helpful in treating neurological disorders such as Parkinson’s disease. Fungi and soil bacteria have provided an important reservoir of drugs. In 1928, Scottish scientist Alexander Fleming discovered that a fungus of the genus Penicillium produces penicillin, one of the first and most widely used antibiotics. In 1964, a group of Canadian scientists traveled to Easter Island and identified a drug produced by a soil bacterium that suppresses immune reactions in human. It is used to prevent organ rejection in transplants and as a coating on heart stents. The drug was named rapamycin after the indigenous name of Easter Island, which is Rapa Nui. Agriculture  Although humans depend on only about 20 plant species to provide 90% of the world’s food, wild relatives of these crops provide a useful reservoir of genetic material for developing pest-resistant varieties or strains that can grow in marginal areas. A gene from longstamen rice (Oryza longistaminata), a grass species from Africa, has been integrated into the genome of commercially grown rice (O. sativa) to confer resistance to rice blight disease (Figure 60.5b). In the 1970s, infusion of genetic material from wild corn in Mexico

(c)

Figure 60.5  Societal benefits from biodiversity.  (a) Bark of the cinchona tree (Cinochona officinalis), a plant found only in tropical rain forests,

is used to produce quinine, an effective treatment for malaria. (b) A gene from longstamen rice (Oryza longistaminata), native to Africa, was used to reduce rice blight disease in rice, O. sativa, native to Asia. (c) Commercial fishing for salmon is an important part of the economy in the U.S. Pacific Northwest. a: ©Heather Angel/Natural Visions; b: ©Arterra Picture Library lamy Stock Photo; c: ©Joshua Roper/Alamy Stock Photo

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was used to protect commercially grown U.S. corn from a leaf fungus, which had killed 15% of the crop. Lake Placid mint (Dicerandra frutescens), native only in central Florida, produces a powerful insect-repelling chemical that may have benefits for crop protection. Another endangered species, buffalo clover (Trifolium stoloniferum), has high protein content and is a perennial, making it of high potential value as a forage crop.  Natural Products Industry  Many products that are used by humans are harvested from plant species growing in their native environments. Biodiversity is important for the maintenance of those native environments. Natural plant products include wood, rubber, and dietary supplements. The forest products industry manufactures o​ ver $2​00 billion in products in the U.S. annually. Maple syrup, nuts, blueberries and algae are all harvested in addition to the trees themselves. Interestingly, a relatively new commercial crop is made by the flowering shrub Parthenium argentartum. It produces high amounts of natural rubber and grows in the deserts of the Southwest U.S., adding economic value to marginal lands.  Animals, too, have great commercial value in the natural products industry. Salmon fishing in the Pacific Northwest supports over 60,000 jobs and injects over $1 billion into the economy (Figure 60.5c). In the U.K., the sea fish catch is worth over $500 million annually. Exploitation of wild animals, often known as bushmeat, in Africa is a major source of animal protein for more than a billion of the world's poorest people. Game birds, especially pheasants and ducks, are often shot in North America and Europe.

Natural Ecosystems Provide Essential Services to Humans Beyond the direct economic gains from biodiversity, humans benefit enormously from the essential services that natural ecosystems provide (Table 60.1). For example, forests soak up carbon dioxide, maintain soil fertility, and retain water, helping to prevent or minimize flooding. Estuaries provide water filtration and protect rivers and coastal shores from excessive erosion. Prochlorococcus, an abundant ocean-dwelling genus of cyanobacteria, was discovered only in 1986, yet it is estimated to produce about 20% of the oxygen we breathe. Other ecosystem functions include the maintenance of populations of natural predators to regulate pest outbreaks and of reservoirs of pollinators to pollinate crops and other plants. In addition, approximately 75% of the 100,000 chemicals released into the environment can be degraded by living organisms. The loss of biodiversity can disrupt an ecosystem’s ability to carry out such functions. In the 1990s, farmers in India began using the anti-inflammatory drug diclofenac to reduce pain and fever in their livestock. They could hardly anticipate that vultures scavenging on dead carcasses would accumulate large doses of the drug and die of renal failure. But the consequences did not stop there. Following a 97% reduction in vulture numbers over a 14-year period, the population of feral dogs exploded, because of the greater availability of uneaten carcasses. The incidence of rabies in humans increased, with estimates of an additional 48,000 people dying over the 14-year time span. The loss of the scavenging services of the vultures was estimated to cost India $24 billion. A 2014 paper in the journal Global Environmental Change by economist Robert Costanza and colleagues made an attempt to calculate the monetary value of ecosystems to various economies (in 2007

Table 60.1

Examples of the World’s Ecosystem Services

Service

Example

Atmospheric gas supply

Regulation of carbon dioxide, ozone, and oxygen levels

Climate regulation

Regulation of carbon dioxide, nitrogen dioxide, and methane levels

Disturbance regulation

Storm protection; flood control

Water regulation

Regulation of hydrological flows

Water supply

Irrigation; water for industry

Erosion control

Retention of topsoil; reduction of accumulation of sediments in lakes

Soil formation

Soil formation processes

Nutrient cycling

Nitrogen, phosphorus, and carbon cycles

Waste treatment

Sewage purification

Pollination

Pollination of crops

Biological control

Pest population regulation

Wilderness and refuges

Habitat for wildlife

Food production

Crops; livestock

Raw materials

Fossil fuels; timber

Genetic resources

Medicines; genes for plant resistance

Recreation

Ecotourism; outdoor recreation

Cultural

Aesthetic and educational value

dollars). They came to the conclusion that, at the time, the world’s ecosystems were worth more than $124 trillion a year, nearly twice the gross national product of the world’s economies combined ($75.2 trillion in 2007 dollars).

Ethical Reasons Underlie the Conservation of Biodiversity Arguments can also be made against the loss of biodiversity on ethical grounds. As only one of many species on Earth, many people have argued that we have no right to destroy other species and the environment around us. John Muir, the founder of the Sierra Club, thought that natural areas had spiritual value and should be preserved rather than used as a source of natural products. This idea, which became known as the preservationist ethic, contrasts with the resource conservation ethic, which focuses on management of natural areas to allow the wisest current and future use of natural resources. In the United States, California condors (Gymnogyps californianus) and grizzly bears (Ursus arctos) have little economic value to people yet we assign them enough value that we preserve the habitats they live in. American philosopher Tom Regan suggests that animals should be treated with respect because they have a life of their own and therefore have value apart from anyone else’s interests. American law professor Christopher Stone, in an influential 1972 article titled “Should Trees Have Standing?” has argued that entities such as nonhuman natural objects, like trees or lakes, should be given legal rights just as corporations are treated as individuals for certain purposes. In 1984, E. O. Wilson proposed the concept known as biophilia: Humans have innate attachments with other species and natural habitats because of our close association with them over millions of years.



BIODIVERSITY AND CONSERVATION BIOLOGY

60.4  Conservation Strategies Learning Outcomes: 1. List and describe the criteria that conservation biologists use to identify areas for protection. 2. Explain how the principles of island biogeography and landscape ecology are used to create nature preserves. 3. Describe different approaches that conservation biologists use to protect individual species. 4. Define restoration ecology, and describe the approaches used to restore degraded ecosystems and populations of species. 5. Describe the advantages and disadvantages of using cloning as a conservation strategy to help save endangered species.

As discussed in Chapter 59, the activities of humans have had many negative effects that threaten biodiversity and ecosystems. The goal of conservation biologists is to manage natural resources with the aim of protecting species, their habitats, and ecosystems. In their efforts to maintain the diversity of life on Earth, these biologists are active on many fronts.  We begin this section by discussing how conservation biologists identify the global areas most in need of conservation. We will then examine some of the factors that must be considered when designing nature preserves, also called parks. These factors include the size and shape of the preserve and the ability of species to move from one nature preserve to another. In some cases, efforts are aimed at protecting species that have a great ecological impact; in others, they are aimed at protecting species, such as the panda bear, which are recognizable and garner support from humans. We will then explore the topic of  habitat restoration—the full or partial repair or replacement of biological habitats and/or their populations that have been degraded or destroyed. Such restoration may involve captive breeding programs to reestablish populations of threatened species in the wild. Finally, we will discuss how genetic cloning may be used as an additional tool to help conserve endangered species.

Conservation Seeks to Establish Protected Areas Currently, about 15.4% of global land area is under some form of environmental protection. More than 217,155 separate areas and 3.4% of the global ocean area are protected, with more being added daily. Conservation biologists often must make decisions regarding which habitats should be protected. Many conservation efforts have focused on saving habitats in so-called megadiversity countries, because they often have the greatest number of species. However, more recent strategies have promoted preservation of certain key areas with the highest levels of unique species or the preservation of representative areas of all types of habitat, even relatively speciespoor areas. Megadiversity Countries  One strategy of targeting areas for conservation is to identify megadiversity countries, those countries with the greatest numbers of species. Using the number of plants, vertebrates, and selected groups of insects as criteria, American biologist Russell Mittermeier and colleagues determined that just 17 countries are home to nearly 70% of all known species. Brazil, Indonesia, and

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Colombia top the list, followed by Australia, Peru, Mexico, Madagascar, China, and nine other countries. The megadiversity country approach suggests that conservation efforts should be focused on the most biologically rich countries. However, although megadiversity areas may contain the most species, they do not necessarily contain the greatest number of unique species. The mammal species list for Peru is 344, and for Ecuador, it is 271; of these, however, 208 species are common to both countries. Areas Rich in Endemic Species  Another approach for setting conservation priorities—one adopted by the organization Conservation International—takes into account the number of species that are endemic; that is, they are found only in a particular place or region. This approach suggests that conservationists focus their efforts on biodiversity hot spots, regions that are biologically diverse and under threat of destruction. To qualify as a biodiversity hot spot, a region must meet two criteria: (1) It must contain at least 1,500 species of vascular plants as endemic species, and (2) it must have lost at least 70% of its original habitat. Vascular plants were chosen as the primary group of organisms to determine whether or not an area qualifies as a hot spot, mainly because most other terrestrial organisms depend on them to some extent. Conservationists Norman Myers, Russell Mittermeier, and colleagues identified 34 biodiversity hot spots that together occupy a mere 2.3% of the Earth’s surface but contain 150,000 endemic plant species, or 50% of the world’s total (Figure 60.6). This approach proposes that protecting such hot spots will prevent the extinction of a larger number of endemic species than would protecting areas of a similar size elsewhere. The main argument against using hot spots as the criterion for targeting conservation efforts is that the areas richest in endemic species—tropical forests—would receive the majority of attention and funding, perhaps at the expense of protecting other areas. Representative Habitats and Crisis Ecoregions  In a third approach to prioritizing areas for conservation, some conservation biologists have argued that we need to conserve representatives of all major habitats. Prairies are a case in point. An example is the Pampas region of South America, which is arguably the most threatened habitat on the continent because of rapid conversion of its natural grasslands to ranch land and agriculture (Figure 60.7). The Pampas does not compare well in richness or endemics with the rain forests, but it is a unique area that, without preservation efforts, could disappear. By selecting habitats that are most distinct from those already preserved, many areas that are threatened but not biologically rich may be preserved in addition to the less immediately threatened, but richer, tropical forests. With regard to representative habitats, habitat loss has been most extensive in temperate grasslands and tropical and temperate deciduous forests, where, in each case, over 50% of the land has been converted to other uses, such as agriculture. At the same time, very little, less than 10%, of these habitats have been protected. Such habitats are thus termed crisis ecoregions.  Last of the Wild  The final approach to conservation involves preservation of regions of the world relatively untouched by humans.

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California Floristic Province

Madrean pine-oak woodlands

Mesoamerica Polynesia/ Micronesia

Choco/ Darien/ Western Ecuador Central Chile

Mediterranean Basin IranoAnatolian Caucasus

Mountains of Central Asia

South Central Japan China Caribbean Horn of IndoBurma Himalaya Philippines Eastern Africa Brazil’s Afromontane Cerrado Wallacea Western Tropical Ghats and Melanesian Islands West Andes Sri Lanka African Sundaland New forests Caledonia Madagascar Succulent Coastal Brazil’s Karoo Southwest forests Atlantic Cape Australia of Eastern Forest Floristic New Zealand Province Africa

Figure 60.6  Location of the major biodiversity hot spots.  Hot spots have high numbers of endemic species. Different colors distinguish the biodiversity hot spots. 

for conservationists because of their relatively intact communities. These wild areas include the tundra and boreal forests of Russia and Canada as well as some desert biomes and tropical forests.

Preserve Design Incorporates Principles of Island Biogeography and Landscape Ecology After identifying areas to preserve, conservationists must determine the size, arrangement, and management of the protected land. Among the questions conservationists ask is whether one large preserve is preferable to an equivalent area composed of smaller preserves. Ecologists also need to determine whether nature preserves should be close together or far apart and whether or not they should be connected by strips of suitable habitat to allow the movement of plants and animals between them.

Figure 60.7  The Pampas, Argentina.  This habitat is not rich in species but is threatened due to conversion to ranch land and agriculture. The guanaco, shown here, is a characteristic grazer of pampas grass. ©Vicki Fisher/Alamy Stock Photo Scientists have mapped out the extent of the human footprint on the globe. The areas of the Earth that fall within the lowest 10% of the human-affected areas have been termed the “last of the wild.” Such areas, because they are relatively pristine, offer a great opportunity

The Role of Island Biogeography  According to the equilibrium model of island biogeography (refer back to Section 58.4), the biodiversity on an island tends toward an equilibrium number that is determined by the balance between two factors: immigration rates and extinction rates. This theory has been applied to nature preserves because, in essence, they are islands in a sea of human-altered habitat.  One question for conservationists is how large a protected area should be (Figure 60.8a). According to island biogeography, the number of species should increase with increasing area (the speciesarea effect). Thus, a larger area would mean that a larger number of species would be protected. In addition, larger preserves have other benefits. For example, they are beneficial for organisms that require



BIODIVERSITY AND CONSERVATION BIOLOGY 1289

Better

Worse

(a) Large or small

(b) Single large or several small

(c) Linked or separate

(d) Round or oblong

Figure 60.8  The theoretical design of nature preserves.  (a) A larger preserve holds more species and has low extinction rates. (b) A given area should be fragmented into as few pieces as possible. (c) Maintaining or creating corridors between fragments may also enhance dispersal. (d) Circular-shaped areas minimize the amount of edge effects. The labels “Better” and “Worse” refer to theoretical principles generated by the equilibrium model of island biogeography, but empirical data have not supported all the predictions. Concept Check:  What are some of the potential risks in connecting preserved areas with movement corridors? 

large spaces, including migrating species and species with extensive territories, such as lions and tigers. A related question is whether it is preferable to protect a single, large preserve or several smaller ones (Figure 60.8b). This question is called the SLOSS debate (for single large or several small). Proponents of a single, large preserve claim that a larger preserve is better able to protect more species and larger populations than an equal area divided into small areas. According to island biogeography, a larger block of habitat should support more species than several smaller blocks. However, many empirical studies suggest that multiple small sites of equivalent area will contain more species, because a series of small sites is more likely to contain a broader variety of habitats than one large site. Looking at a variety of sites, American conservationists Jim Quinn and Susan Harrison concluded that animal life was richer in collections of small preserves than in a smaller number of larger ones. In their study, having more habitat types outweighed the effect of larger area size on species richness. In addition, another benefit of a series of smaller preserves is a reduction of extinction risk by a single event such as a wildfire or the spread of disease. The Role of Landscape Ecology  Landscape ecology is an area of ecology that examines the spatial arrangement of communities and ecosystems in a geographic area. Landscape ecologists have suggested that small preserves should be linked together by movement corridors, thin strips of land that permit the movement of species between preserved patches (Figure 60.8c). Such corridors ideally facilitate movements of organisms that are vulnerable to predation outside their natural habitat or have poor powers of dispersal between habitat patches. In this way, if a population in one small preserve experiences a disaster, immigrants from neighboring populations can more easily recolonize it. This avoids the need for humans to physically move new plants or animals into an area. Several types of habitat function as movement corridors, including hedgerows (a linear patch of shrubs and small trees), which facilitate movement and dispersal of species between forest fragments (Figure 60.9). In China, corridors of habitat have been established to

link small, adjacent populations of giant pandas. However, some disadvantages are associated with movement corridors. Corridors also can facilitate the spread of disease, invasive species, and fire between small preserves. Finally, nature preserves are often designed to minimize edge effects, the special physical conditions that exist at the boundaries, or edges, of ecosystems. Habitat edges, particularly those between a natural habitat such as a forest and developed land, are often different in physical characteristics from the habitat core. For example, the center of a forest is shaded by trees and has less wind and light than

Hedgerows

Figure 60.9  Movement corridors.  ©Andrew Parker/Alamy Stock Photo Concept Check:  How do these European hedgerows act as movement corridors?

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As we have seen, many conservation biologists consider broad global issues when deciding which habitats are more important to preserve, as well as more local issues concerning the sizes, shapes, and interconnectedness of preserves. When establishing and managing nature preserves, they may take a single-species approach to their conservation efforts, which focuses on saving species that are deemed particularly important. As with habitat conservation, different approaches are used to identify the species that are most important.

ecosystem. For example, corals are good indicators of marine processes such as siltation—the accumulation of sediments transported by water. Because siltation reduces the availability of light, the abundance of many marine organisms decreases in such situations, with corals among the first to display a decline in health. Coral bleaching is also an indicator of climate change. Polar bears (Ursus maritimus) are thought to be a mammalian indicator species of global climate change (Figure 60.10a). Most scientists are in agreement that global warming is causing the ice in the Arctic to melt earlier in the spring than in the past. Because polar bears rely on the ice to hunt for seals, the earlier breakup of the ice is leaving the bears less time to feed and build the fat that enables them to sustain themselves and their young. A U.S. Geological Survey study concluded that future reduction of Arctic ice could result in a loss of two-thirds of the world’s polar bear population within 50 years. In May 2008, the polar bear was listed as a threatened species under the U.S. Endangered Species Act (ESA).

Indicator Species  Some conservation biologists have suggested that certain organisms can be monitored as indicator species, those species whose status provides information on the overall health of an

Umbrella Species  Umbrella species are those whose habitat requirements are so large that protecting them would protect many other species existing in the same habitat. The Northern spotted owl

the forest edge, which is unprotected. Many forest-adapted animals therefore shy away from forest edges and prefer forest centers. For this reason, circular preserves are generally preferable to oblong ones, because the amount of edge is minimized (Figure 60.8d).

The Single-Species Approach Focuses Conservation Efforts on One Species in a Particular Habitat

(a) Indicator species: polar bear

(b) Umbrella species: northern spotted owl

(c) Flagship species: Florida panther

(d) Keystone species: American beaver

Figure 60.10  Indicator, umbrella, flagship, and keystone species.  (a) Polar bears have been called an indicator species with respect to global climate change. (b) The northern spotted owl is considered an umbrella species for the old-growth forest in the Pacific Northwest. (c) The Florida panther has become a flagship species for Florida. (d) The American beaver, a keystone species, creates large dams across streams, and the resultant lakes provide habitats for a great diversity of species. a: ©Robert E. Barber/Alamy Stock Photo; b: Source: John & Karen Hollingsworth/U.S. Fish & Wildlife Service; c: Source: Larry Richardson, US Fish & Wildlife Service; d: ©Wildlife/Alamy Stock Photo



BIODIVERSITY AND CONSERVATION BIOLOGY 1291

(Strix occidentalis) of the Pacific Northwest is considered to be an important umbrella species (Figure 60.10b). A pair of birds needs at least 800 hectares of old-growth forest for survival and reproduction, so maintaining healthy owl populations helps to ensure survival of many other forest-dwelling species. In the southeastern U.S., the red-cockaded woodpecker (Picoides borealis) is often seen as that region’s equivalent of the Northern spotted owl because it requires large tracts of old-growth long-leaf pine (Pinus palustris), including old diseased trees in which it can excavate its nests. Flagship Species  In the past, conservation resources were often allocated to a flagship species, a single large or instantly recognizable species. Such species were typically chosen because they were attractive and thus more readily engendered support from the public for their conservation. The concept of the flagship species, typically a charismatic vertebrate such as the American buffalo (Bison bison), has often been used to raise awareness for conservation in general. The giant panda (Ailuropoda melanoleuca) is the World Wildlife Fund’s emblem for endangered species, and the Florida panther (Puma concolor) has become a symbol of the state’s conservation campaign (Figure 60.10c). Keystone Species  A different conservation strategy focuses on keystone species, species within a community that have a role out of proportion to their abundance or biomass. The beaver, a relatively small animal, can have a dramatic impact on a community by building a dam and flooding an entire river valley (Figure 60.10d). The resultant lake may become a home to fish species, wildfowl, and aquatic vegetation. A decline in the number of beavers may have serious ramifications for the remaining community members, promoting fish die-offs, waterfowl loss, and the death of vegetation adapted to waterlogged soil. American ecologist John Terborgh considers tropical palm nuts and figs to be keystone plant species because they produce fruit during otherwise fruitless times of the year and are thus critical resources for tropical forest fruit-eating animals, including primates, rodents, and many birds. Together, these fruit eaters account for as much as

(a) Complete restoration

(b) Rehabilitation

three-quarters of the tropical forest animal biomass. Without the fruit trees, widespread extinction of these animals could occur.

Habitat Restoration Attempts to Improve Degraded Habitats Another aspect of conservation efforts is improving the quality of a previously degraded habitat. As noted at the beginning of this section, habitat restoration is the full or partial repair or replacement of biological habitats and/or their populations that have been degraded or destroyed. It can focus on complete restoration, rehabilitation, or replacement of a habitat, and it can involve returning species to the wild following captive breeding. Types of Habitat Restoration  In complete restoration, conservation biologists attempt to return a habitat to its composition and condition prior to the disturbance. For example, under the leadership of American ecologist Aldo Leopold, the University of Wisconsin pioneered the restoration of prairie habitats as early as 1935, converting agricultural land back to species-rich prairies (Figure 60.11a). The second approach of habitat restoration aims to return the habitat to something similar to, but a little less than, full restoration, a goal called rehabilitation. In Florida, phosphate mining involves removing a layer of topsoil, mining the phosphate-rich layers, returning the topsoil, and then replanting the area. Unfortunately, species such as cogongrass (Imperata cylindrica), an invasive Southeast Asian species, may invade these disturbed areas. Even so, the restoration serves to revegetate the area (Figure 60.11b). The third approach to repairing a habitat, termed replacement, makes no attempt to restore what was originally present but instead replaces the original ecosystem with a different one. Ecosystem replacement is particularly useful for places in which the terrain has been substantially altered by past human activities. It would be nearly impossible to re-create the original landscape of an area that was mined for stone or gravel. In these situations, however, wetlands or lakes may be created in the open pits (Figure 60.11c).

(c) Ecosystem replacement

Figure 60.11  Habitat restoration.  (a) The University of Wisconsin pioneered the practice of complete restoration of agricultural land to native prairies. (b) In Florida, complete restoration after phosphate mining is not usually possible. After topsoil is replaced, invasive species such as cogongrass often grow, resulting in habitat rehabilitation rather than complete restoration. (c) This old limestone mine in Crimea has been flooded to provide a valuable freshwater habitat, replacing the ecosystem that was originally present. a: ©University of Wisconsin-Madison Arboretum; b: Courtesy of DL Rockwood, School of Forest Resources and Conservation, University of Florida, Gainesville, FL; c: ©Vladimir Mulder/Shutterstock

Core Skill: Science and Society  Restoration of human-degraded habitats can lead to recovery of habitat and increased biodiversity.

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Reintroductions and Captive Breeding  Reintroducing species into areas where they previously existed is a valuable conservation strategy that can re-establish populations in areas where they once occurred (look back at the opening photograph in  Chapter 56). Captive breeding, the propagation of animals and plants outside their natural habitat to produce stock for subsequent release into the wild, has proved valuable in reestablishing breeding populations following extinction or near extinction. Zoos, aquariums, and botanical gardens often play a key role in captive breeding, propagating species that are highly threatened in the wild. Several classic programs illustrate the value of captive breeding and reintroduction. The peregrine falcon (Falco peregrinus) had become extinct in nearly all of the eastern U.S. by the mid-1940s, a decline that was linked to the effects of DDT (refer back to Figure 59.16). In 1970, American biologist Tom Cade gathered falcons from other parts of the country to start a captive breeding program at Cornell University. Since then, the program has released thousands of birds into the wild, and in 1999, the peregrine falcon was removed from the list of endangered species.  A captive breeding program is also helping to save the California condor (Gymnogyps californicus) from extinction. At a cost of $35 million, this species conservation project is the most expensive one ever undertaken in the U.S. In the 1980s, the population had dropped to only 22 known condors, some in captivity and some in the wild. Scientists made the decision to capture the remaining wild birds in order to protect and breed them (Figure 60.12a). By 2016, the captive population numbered 167 individuals, and 268 birds were living in the coastal mountains of California; northern Baja California, Mexico; the Grand Canyon area of Arizona; and Zion National Park, Utah (Figure 60.12b). A milestone was reached in 2003, when a pair of captive-reared California condors bred in the wild.

Can Cloning Save Endangered Species? The use of reproductive cloning to clone endangered species is a new method that may eventually help bolster populations of captive-bred

(a) A condor chick being fed using a puppet

species. In 1997, geneticist Ian Wilmut and colleagues at Scotland’s Roslin Institute announced to the world that they had cloned a sheep, the now-famous Dolly, from mammary cells of an adult ewe. Since then, interest has arisen among conservation biologists about whether the same technology might be used to save species on the verge of extinction.  Scientists were encouraged that in January 2001, an Iowa farm cow called Bessie gave birth to a cloned Asian gaur (Bos gaurus), an endangered species. The gaur, an oxlike animal native to the jungles of India and Burma, was cloned from a single skin cell taken from a dead animal. To clone the gaur, scientists removed the nucleus from a cow’s egg and replaced it with a nucleus from the gaur’s cell. The treated egg was then placed into the cow’s uterus. Unfortunately, the gaur died from dysentery 2 days after birth, although scientists believe this was unrelated to the cloning procedure.  More recently, other endangered or extinct species have been cloned. In 2003, another type of endangered wild cattle, the Javan banteng (Bos javanicus), was successfully cloned (Figure 60.13). In 2005, clones of the African wildcat (Felis libyca) successfully produced wildcat kittens. This is the first time that clones of a wild species have bred. In 2009, a cloned Pyrenean ibex (Capra pyrenaica) was born but lived only 7 minutes due to physical defects in the lungs. The last wild Pyrenean ibex died in Spain in 2000. Other candidates for cloning include the Sumatran tiger (Panthera tigris) and the giant panda. Brazil plans to clone eight of its endangered species. Cloning long-extinct animals such as the woolly mammoth (Mammuthus primigenius) or Tasmanian tiger (Thylacinus cynocephalus) would be more difficult due to a lack of fully preserved DNA. Despite the promise of cloning, a number of issues remain unresolved: 1. Scientists would have to develop an intimate knowledge of different species’ reproductive cycles. For sheep and cows, this was routine, based on the vast experience in breeding these species, but eggs of different species, even if they could be

(b) A released captive-bred condor

Figure 60.12  Captive breeding programs.  The California condor (Gymnogyps californicus), the largest bird in the U.S., with a wingspan of nearly 3 m, has been bred in captivity in California. (a) A researcher at the San Diego Wild Animal Park feeds a chick with a puppet so that the birds will not become habituated to the presence of humans. (b) This captive-bred condor soars over the Grand Canyon. Note the tag on the underside of its wing. a: ©Charlie Neuman/San Diego Union-Tribune/ZUMA Press/Alamy Stock Photo; b: ©Simpson/Photri Images/Alamy Stock Photo



BIODIVERSITY AND CONSERVATION BIOLOGY 1293

Figure 60.13  Cloning an endangered species.  In 2004, this 8-month-old cloned Javan banteng (Bos javanicus) made its public debut at the San Diego Zoo. ©Yvette Cardozo/Alamy Stock Photo Core Concept: Information  Reproductive cloning utilizes a somatic cell, which contains the complete DNA or genetic blueprint of the animal that is to be cloned. The somatic cell is fused with an oocyte that has had its nucleus removed.

harvested, often require different nutritive media in laboratory cultures. 2. Because it is desirable to use natural mothers for gestation of cloned animals, scientists will have to identify surrogate females of similar but more common species that can carry the fetus to term. 3. Some argue that cloning does not address the root causes of species loss, such as habitat fragmentation or poaching, and that resources would be better spent elsewhere—for example, in preserving the remaining habitat of endangered species. 4. Cloning from a limited number of sources might not be able to increase the genetic variation of a species. However, if cells were obtained from many different deceased animals—for example, from their skin—these clones could theoretically reintroduce lost genes back into the population. Many biologists believe that while cloning may have a role in conservation, it is only part of the solution and we need to address what made the species go extinct before attempting to restore it.

Preserving Biodiversity Is an Important Goal for Human Societies As we saw in Section 60.3, biodiversity is of great value to human welfare. Therefore, conservation is clearly a matter of great importance, and a failure to value and protect our natural resources adequately could be a grave mistake. Some authors, most recently American ecologist and geographer Jared Diamond, have investigated why many societies of the past—including Angkor Wat, Easter Island,

and the Mayans—collapsed or vanished, leaving behind monumental ruins. Diamond has concluded that the collapse of these societies occurred partly because people inadvertently destroyed the ecological resources on which their societies depended.  Modern nations such as Rwanda face similar issues. The country’s population density is the highest in Africa, and it has a limited amount of land that can be used for growing crops. By the late 1980s, the need to feed a growing population had led to the wholesale clearing of Rwanda’s forests and wetlands, with the result that little additional land was available to farm. Increased population pressure, along with food shortages fueled by environmental scarcity, were likely contributing factors in igniting the genocide of 1994. As we hope you have seen throughout this textbook, an understanding of biology is vital to learning and helping to solve many of society’s problems. The study of biology has a huge potential for improving people’s lives and society at large. Biology offers the opportunity to unlock new diagnoses and treatments for diseases, to improve nutrition and food production, and to maintain biological diversity.

Summary of Key Concepts 60.1        Genetic, Species, and Ecosystem Diversity ∙∙ Biodiversity represents diversity at three levels: genetic diversity, species diversity, and ecosystem diversity. Conservation biology uses knowledge from molecular biology, genetics, and ecology to protect biological diversity (Figure 60.1).

60.2  Biodiversity and Ecosystem Function ∙∙ Four models describe the relationship between ecosystem function and species richness: the diversity-stability, redundancy, keystone, and idiosyncratic hypotheses (Figure 60.2). ∙∙ Laboratory and field experiments have shown that increased species richness results in increased ecosystem function and support the redundancy hypothesis (Figures 60.3, 60.4).

60.3  Value of Biodiversity to Human Welfare ∙∙ The preservation of biodiversity has been justified because of its economic value, because of the value of services that ecosystems provide, and on ethical grounds (Figure 60.5, Table 60.1).

60.4  Conservation Strategies ∙∙ Habitat conservation strategies commonly target megadiversity countries, countries with the largest number of species; biodiversity hot spots, areas with the largest number of endemic species, or those unique to the area; representative habitats including crisis ecoregions, areas that represent the major habitats; and “last of the wild,” or pristine areas that have not been severely affected by human activities (Figures 60.6, 60.7). ∙∙ Conservation biologists employ many strategies in protecting biodiversity. Principles of the equilibrium model of island biogeography and landscape ecology are used in the theory and practice of preserve design (Figure 60.8, 60.9).

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∙∙ The single-species approach focuses conservation efforts on indicator species, umbrella species, flagship species, or keystone species (Figure 60.10). ∙∙ Habitat restoration seeks to repair or replace populations and their habitats. Three basic approaches to habitat restoration are complete restoration, rehabilitation, and ecosystem replacement (Figure 60.11). ∙∙ Captive breeding is propagating animals or plants outside their natural habitat and reintroducing them to the wild. Cloning of endangered species has been accomplished on a very small scale and, despite its limitations, may eventually have a role in conservation biology (Figures 60.12, 60.13).

Assess & Discuss Test Yourself 1. Which of the following best describes an endangered species?  a. a species that is likely to become extinct in a portion of its range b. a species that has disappeared in a particular community but is present in other natural environments c. a species that is extinct d. a species that is in danger of becoming extinct throughout all or a significant portion of its range e. Both b and d are true of endangered species.  2. In 1977, Rafael Guzman, a Mexican biologist, discovered a previously unknown wild relative of corn that is resistant to many of the viral diseases that infect domestic corn. Agriculturalists believe that crossbreeding the wild corn with domestic corn could improve current corn crops. In this case, biodiversity is important at which level? a. ecosystem b. species c. genetic d. community e. both a and b  3. The idea that humans have an innate attachment to other life-forms, put forth by E. O. Wilson, is known as  a. biodiversity. b. biophilia. c. the call of the wild. d. biotheology. e. the “last of the wild.”  4. The research conducted by Tilman and colleagues demonstrated that  a. as diversity increases, productivity increases. b. as diversity decreases, productivity increases. c. areas with higher diversity demonstrate less efficient use of nutrients. d. increases in species richness lead to an increase in invasive species. e. increased diversity results in increased susceptibility to disease.  5. Which hypothesis best describes the idea that a small decline in species richness results in a large drop in ecosystem function?  a. Diversity-stability hypothesis b. Redundancy hypothesis c. Keystone hypothesis d. Idiosyncratic hypothesis e. Community hypothesis 

6. According to the equilibrium model of island biogeography, which type of preserve would contain the most species? a. One large park b. Several small parks with a combined area equal to that of a large park c. Several small parks connected by a movement corridor d. A circular park e. All of the above  7. Saving endangered habitats, such as the Argentine Pampas, focuses on  a. saving genetic diversity. b. saving keystone species. c. conservation in a megadiversity country. d. preserving an area rich in endemic species. e. preserving a representative habitat.  8. Biodiversity hot spots are those areas rich in  a. species. b. habitats. c. rare species. d. biodiversity. e. endemic species.  9. Over time, dark forms of the peppered moth (Biston betularia) became more common in polluted environments because predators were less able to detect them on trees darkened by soot. These moths are regarded by many as a(n) a. keystone species. b. indicator species. c. umbrella species. d. flagship species. e. endangered species.  10. After being used for mining, what was once a deciduous forest is replaced by grassland to be used for public recreation. This process is known as a. complete restoration. b. rehabilitation. c. ecosystem replacement. d. bioremediation. e. habitat repair. 

Conceptual Questions 1. What is the value of increased biodiversity for human society?  2. Distinguish among the following as bases for strategies to conserve biodiversity: megadiversity countries, biodiversity hot spots, crisis ecoregions, and “last of the wild.”  3.

 ore Concept: Systems Describe how the following C hypotheses link species richness with ecosystem function: diversity-stability, redundancy, keystone, and idiosyncratic. 

Collaborative Questions 1. Discuss the differences between indicator species, umbrella species, flagship species, and keystone species. 2. You are called upon to design a park with maximum biodiversity in a tropical country. What are your recommendations?

Appendix A Periodic Table of the Elements MAIN–GROUP ELEMENTS

MAIN–GROUP ELEMENTS

1 1

H 1.008

2

Period

3

4

7

Atomic mass (average mass of all isotopes)

2 3A (13)

4A (14)

5A (15)

6A (16)

7A (17)

He 4.003

3

4

5

6

7

8

9

10

Be

B

C

N

O

F

Ne

6.941

9.012

10.81

12.01

14.01

16.00

19.00

20.18

11

12

13

14

15

16

17

18

Na

Mg

Al

Si

P

S

Cl

Ar

22.99 19

K

TRANSITION ELEMENTS

24.31

3B (3)

4B (4)

5B (5)

6B (6)

7B (7)

20

21

22

23

24

25

Ca

Sc

Ti

V

Cr

Mn

(8)

8B (9)

26

27

Fe

Co

(10)

1B (11)

2B (12)

28

29

30

31

32

33

34

35

36

Ni

Cu

Zn

Ga

Ge

As

Se

Br

Kr

40.08 44.96 47.88 50.94 52.00 54.94 55.85 58.93 58.69

63.55 65.41

26.98 28.09 30.97 32.07 35.45 39.95

69.72 72.61

74.92 78.96 79.90 83.80

37

38

39

40

41

42

43

44

45

46

47

48

49

50

51

52

53

54

Rb

Sr

Y

Zr

Nb

Mo

Tc

Ru

Rh

Pd

Ag

Cd

In

Sn

Sb

Te

I

Xe 131.3

85.47 87.62 6

Symbol

Li

39.10 5

2A (2)

8A (18)

Atomic number

88.91

91.22

92.91

95.94

(98)

101.1

102.9

106.4

107.9

112.4

114.8

118.7

121.8

127.6

126.9

55

56

57

72

73

74

75

76

77

78

79

80

81

82

83

84

85

86

Cs

Ba

La

Hf

Ta

W

Re

Os

Ir

Pt

Au

Hg

Tl

Pb

Bi

Po

At

Rn

132.9

137.3

138.9

178.5

180.9

183.9

186.2

190.2

192.2

195.1

197.0

(210)

(222)

87

88

89

104

105

106

107

108

109

Fr

Ra

Ac

Rf

Db

Sg

Bh

Hs

Mt

110

111

112

113

(223)

(226)

(227)

(263)

(262)

(266)

(267)

(277)

(268)

Ds

Rg

Uub

Uut

(281)

(272)

200.6 204.4 207.2 209.0 (209)

(285)

APPENDIX A

Metals (main-group) Metals (transition) Metals (inner transition) Metalloids Nonmetals

1A (1)

(?)

114

115

116

117

118

Fl

Uup

Lv

Uus

Uuo

(289)

(288)

(293)

(291)

(?)

INNER TRANSITION ELEMENTS 6

7

Lanthanides

Actinides

58

59

60

61

62

63

64

65

66

67

68

69

70

71

Ce

Pr

Nd

Pm

Sm

Eu

Gd

Tb

Dy

Ho

Er

Tm

Yb

Lu

140.1

140.9

144.2

(145)

150.4

152.0

157.3

158.9

162.5

164.9

167.3

168.9

173.0

175.0

90

91

92

93

94

95

96

97

98

99

100

101

102

103

Th

Pa

U

Np

Pu

Am

Cm

Bk

Cf

Es

Fm

Md

No

Lr

(242)

(243)

(247)

(247)

(251)

(252)

(257)

(258)

(259)

(260)

232.0 (231)

238.0 (237)

 The complete Periodic Table of the Elements.  Group numbers are different in some cases from those presented in Figure 2.5, because of the inclusion of transition elements. In some cases, the average atomic mass has been rounded to one or two decimal places, and in others only an estimate is given in parentheses due to the short-lived nature or rarity of those elements. The symbols and names of some of the elements between 112–118 are temporary until the chemical characteristics of these elements become better defined. Element 117 is currently not confirmed as a true element, and little is known about element 118. The International Union of Pure and Applied Chemistry (IUPAC) has recently proposed adopting the name copernicium (Cp) for element 112 in honor of scientist and astronomer Nicolaus Copernicus.

A-1

Appendix B Answer Key Answers to Collaborative Questions can be found on the website.

Chapter 1

Concept Checks Figure 1.3  The herd is at the population level. Figure 1.6  Natural selection is a process that leads to evolution. Figure 1.8  A tree of life suggests that all living organisms evolved from a single ancestor by vertical descent with mutation. A web of life assumes that both vertical descent and horizontal gene transfer have been important mechanisms in the evolution of new species.

APPENDIX B

Figure 1.9  The genome stores the information used to make proteins. In and of itself, the genome is merely DNA. The traits of cells and organisms are largely determined by the structures and functions of the thousands of different proteins they produce. Figure 1.11  Taxonomy helps us appreciate the unity and diversity of life. Organisms that are closely related evolutionarily are placed in smaller groups. Figure 1.14  A researcher can compare the results from the experimental group and the control group to determine if a single variable is causing a particular outcome in the experimental group. Figure 1.15  After the CFTR gene was identified by discovery-based science, researchers realized that this gene was similar to other genes that encoded proteins that were already known to be transport proteins. This provided an important clue about the likely function of the CFTR gene.

Core Skills: Connections Figure 1.10  Fungi are more closely related to animals.

Feature Investigation Questions 1. In discovery-based science, a researcher does not need to have a preconceived hypothesis. Experimentation is conducted in the hope that it may have practical applications or may provide new information that will lead to a hypothesis. By comparison, hypothesis testing occurs when a researcher forms a hypothesis that makes certain predictions. Experiments are conducted to see if those predictions are correct. In this way, the hypothesis may be accepted or rejected. 2. This strategy may be described as a five-stage process: 1. Observations are made regarding natural phenomena. 2. These observations lead to a hypothesis that tries to explain the phenomena. A useful hypothesis is one that is testable because it makes specific predictions. 3. Experimentation is conducted to determine if the predictions are correct. 4. The data from the experiment are analyzed. 5. The hypothesis is accepted or rejected. 3. In an ideal experiment, the control and experimental groups differ by only one factor. Biologists apply statistical analyses to their data to determine if the outcomes for the control and experimental groups are likely to differ because of the single variable that is different between the two groups. This provides an objective way to accept or reject a hypothesis.

Test Yourself

1. d  2. a  3. b  4. c  5. d  6. b  7. d  8. d  9. a  10. b

A-2

Conceptual Questions 1. Evolution applies only to populations, whereas the other four core concepts could apply to individuals and to populations. 2. The unity among different species occurs because modern species have evolved from a group of related ancestors. Some of the traits in those ancestors are also found in modern species, which thereby unites them. The diversity is due to the variety of environments on the Earth. Each species has evolved to occupy its own unique environment. For every species, many traits are evolutionary adaptations to survival in a specific environment. For this reason, evolution also promotes diversity. 3. Students should rephrase the concepts in their own words.

Chapter 2

Concept Checks Figure 2.4  An electron shell is a region outside the nucleus of an atom occupied by electrons of a given energy level. More than one orbital can be found within an electron shell. An orbital may be spherical or dumbbell-shaped and contains up to two electrons. Figure 2.11  Strand separation requires energy, because the DNA strands are held together by a large number of hydrogen bonds. Although each hydrogen bond is weak, the collective strength of such bonds in a molecule of DNA adds up to a considerable amount. Figure 2.17  The oil will be in the centers of the soap micelles.

Core Skills: Connections

Figure 2.20  At a pH of 5.0, the H+ concentration would be 10–5 M, as can be seen in Figure 2.20 and can also be calculated with the equation pH = –log10[H+]. (From this information, you can also determine that the OH– concentration must be 10–9 M, because the product of the H+ and OH– concentrations must be equal to 10–14 M.)

Feature Investigation Questions 1. Scientists were aware that atoms contained charged particles. Many believed that the positive charges and mass were evenly distributed throughout the atom. 2. Rutherford was testing the hypothesis that atoms are composed of positive charges evenly distributed throughout the atom. Based on this model of the structure of the atom, α particles, which are positively charged nuclei of helium atoms, should be slightly deflected as they pass through gold foil, due to the presence of positive charges spread throughout the foil. 3. Instead of showing slight deflection as they passed through the gold foil, the majority, 98%, of the α particles passed directly through the foil without deflection. Less than 2% of them showed deflection, and a much smaller percentage bounced back from the gold foil. Rutherford suggested that since most of the α particles passed unimpeded through the gold foil, most of the volume of atoms is empty space. Rutherford also proposed that the bouncing back of some of the α particles indicated that most of the positively charged particles in an atom were concentrated in a compact area. These results ran counter to the hypothesized model.

Test Yourself

1. b  2. b  3. b  4. d  5. e  6. e  7. e  8. c  9. c  10. e



APPENDIX B

1. Covalent bonds are bonds in which atoms share electrons. A nonpolar covalent bond is one between two atoms of similar electronegativities, such as two carbon atoms. A hydrogen bond is a weak interaction that forms when a hydrogen atom in a polar molecule becomes electrically attracted to an electronegative atom. The van der Waal dispersion forces are temporary, weak interactions, resulting from random electrical forces generated by the changing distributions of electrons in the outer shells of nearby atoms. The strong attraction between two oppositely charged atoms forms an ionic bond. 2. Within limits, bonds within molecules can rotate and thereby change the molecules’ shapes. This is important because it is the shape of a molecule that determines, in part, the ability of that molecule to interact with other molecules. Also, when two molecules do interact through such forces as hydrogen bonds, the shape of one or both molecules may change as a consequence. The change in shape is often part of the mechanism by which signals are sent within and between cells. 3. When two or more atoms react with each other to form a new substance, that new substance often has emergent properties that are quite different from the starting materials. A good example of emergent properties at the molecular level occurs in the formation of sodium chloride (NaCl), a solid white crystalline compound that is very important for most living organisms. In their elemental states, sodium is a soft, highly reactive metal and chlorine is a toxic gas. When they combine through ionic bonds, the two elements produce a completely new and harmless substance found in all the world’s oceans and soils. Another example from this chapter is water, a liquid that is vital for all life but which is formed from two gases, hydrogen and oxygen, with very different properties.

Chapter 3

Concept Checks Figure 3.5  One reason is that the binding of a molecule to an enzyme depends on the spatial arrangements of the atoms in that molecule. Enantiomers have different spatial relationships and are mirror images of each other. Therefore, one may bind very tightly to an enzyme and the other may not be recognized at all. Figure 3.6  Recall from Figure 3.4 that the reverse of a dehydration reaction is a hydrolysis reaction, in which a molecule of water is added to the molecule being broken down, resulting in the formation of monomers. Figure 3.10  Hydrogenation is the addition of hydrogens to double-bonded carbon atoms, changing them from unsaturated to saturated. This causes the resulting fat to have a higher melting point and thus be solid at room temperature. Figure 3.14  The process would produce 71 water molecules, one less than the number of amino acids in the polypeptide. Figure 3.18  If the primary structure of protein 1 were altered in this way, the changes would, in turn, most likely alter the secondary and tertiary structures of protein 1. Therefore, it is possible that the precise fit between proteins 1 and 2 would no longer be possible and the two proteins would lose the ability to interact. Figure 3.23  Yes. The opposite strand must be complementary to the first strand, because A must be paired with T, and G with C. For instance, if a portion of the first strand has the sequence AATGCA, the opposite strand for that portion will be TTACGT.

Core Skills: Connections Figure 3.7  Cellulose is believed to be the most abundant organic molecule on Earth. In addition to being part of plant cells, it is also found in many other organisms, including many protists.

Feature Investigation Questions 1. Anfinsen was testing the hypothesis that the information necessary for determining the three-dimensional shape of a protein is contained within the protein itself. In other words, the chemical characteristics of the amino acids that make up a protein determine the protein’s three-dimensional shape. 2. The urea disrupts hydrogen and ionic bonds that are necessary for protein folding. The β-mercaptoethanol breaks the S−S bonds that form between certain amino acids of the same polypeptide. Both substances cause the polypeptide to unfold, disrupting the three-dimensional shape.

3. Anfinsen removed the urea and β-mercaptoethanol from the ribonuclease by size-exclusion chromatography. After removing these substances, Anfinsen discovered that the protein refolded into its proper three-dimensional shape and became functional again. This was important because the solution at that point contained only the protein and lacked any other cellular material that could possibly assist in protein folding. This demonstrated that the protein could refold itself into the functional conformation.

Test Yourself

1. b  2. e  3. e  4. a  5. c  6. b  7. e  8. d  9. b  10. b

Conceptual Questions 1. Isomers are molecules with the same chemical formula but with different structures and arrangements of their atoms. There are two major types of isomers: structural isomers and stereoisomers. Because many chemical reactions in biology depend on the actions of enzymes, which are often highly specific with respect to the spatial arrangement of atoms in a molecule, one isomer of a pair may have biological functions, and the other may not. 2. Saturated fatty acids are saturated with hydrogens and have only single (C−C) bonds, whereas unsaturated fatty acids have one or more double (C=C) bonds. The double bonds in unsaturated fatty acids alters the shape, resulting in one or more kinks in the chain. Saturated fatty acids are unkinked and are better able to stack tightly together. Fats containing saturated fatty acids have a higher melting point than those containing mostly unsaturated fatty acids; consequently, saturated fats tend to be solids at room temperatures, and unsaturated fats are usually liquids at room temperature. 3. The structures of all these macromolecules determine their functions. For example, the structure of a protein determines its three-dimensional shape. This, in turn, allows a protein to interact specifically with certain other molecules. Also, protein domains have specific structures that determine their functions. A single protein may have multiple domains, allowing that protein to perform a fairly complex function, such as activating genes in response to hormone binding. Likewise, the structures of different lipids determine such functional characteristics as male/female differences, cellular membrane formation, and energy storage. The different structures of polysaccharides determine their usefulness as energy stores or as components of plant cell walls.

Chapter 4

Concept Checks Figure 4.2  These vents release hot gases from the interior of the Earth. Organic molecules can form in the temperature gradient between the extremely hot vent water and the cold water that surrounds the vent. Figure 4.3  A liposome is more similar to today’s cells, which are surrounded by a membrane that is composed of a phospholipid bilayer. Figure 4.4  Chemical selection occurs when certain molecules, such as RNAs, have properties that provide advantages and therefore cause them to increase in number relative to other molecules in the same environment. Figure 4.5  You would use an electron microscope. A light microscope does not have good enough resolution. Figure 4.7  The primary advantage is that it gives an image of the 3-D surface of an object. Figure 4.11  Centrioles: Not found in plant cells; their role is not entirely clear, but they are found in the centrosome, which is where microtubules are anchored. Chloroplasts: Not found in animal cells; function in photosynthesis. Cell wall: Not found in animal cells; important in cell shape. Central vacuole: Not found in animal cells; site that provides storage and regulates cell volume. Figure 4.16  Both dynein and microtubules are anchored in place. Using ATP as a source of energy, dynein tugs on microtubules. Because the microtubules are anchored, they bend in response to the force exerted by dynein. Figure 4.19  The nuclear matrix, located inside the nucleus, serves to organize the chromosomes into chromosome territories. Figure 4.22  The protein is synthesized into the ER and then travels through the cis, medial, and trans Golgi before being secreted. Figure 4.26  Of these three functions, membrane transport is probably the most important to metabolism because it determines which molecules can enter the cell

APPENDIX B

Conceptual Questions

A-3

A-4

APPENDIX B

and participate in metabolism and which products of metabolism are exported from the cell. Figure 4.28  The invaginations increase the surface area where ATP synthesis takes place, thereby increasing the amount of ATP synthesis. Figure 4.33  The signal sequence of such a protein is recognized by SRP, which halts translation. The growing polypeptide and its ribosome are then transferred to the ER membrane, where translation resumes.

motor protein is activated. If the motor protein is fixed in place and the filament is free to move, this will cause the filament to move when the motor protein is activated. If both the motor protein and the filament are fixed in place, the activation of the motor protein will cause the filament to bend. 3. ATP synthesis occurs along the inner mitochondrial membrane. The invaginations of this membrane greatly increase its surface area, thereby allowing for a greater amount of ATP synthesis.

Figure 4.34  If chaperone proteins were not present in the cytosol, the protein destined for the mitochondrial matrix would start to fold, which might prevent it from passing through the channels in the outer and inner mitochondrial membranes. Normally, a protein is threaded through these channels in an unfolded state.

Chapter 5

Core Skills: Connections

Figure 5.6  Phospolipids are transferred to the other leaflet of the ER membrane via enzymes called flippases.

Figure 4.3  Phospholipids are amphipathic molecules; they have a polar end (the head) and a nonpolar end (the two fatty acid tails). Phospholipids form a bilayer such that the heads interact with water, whereas the tails are shielded from the water. This is an energetically favorable structure. Figure 4.10  Alternative splicing produces proteins with slightly different structures, because they have certain regions that have different amino acid sequences. The functions of such proteins are often similar, but specialized for the cell type in which they are expressed. Figure 4.12  The surfaces of structures involved with gas exchange are highly convoluted. This provides them with much greater surface areas, thereby facilitating the movement of gases through the surfaces.

APPENDIX B

Figure 4.15  The type of movement shown in part (b) of Figure 4.15 occurs during muscle contraction. Figure 4.20  During cell division, the chromosomes condense and form more compact structures. Figure 4.30  These processes are similar in that DNA replication occurs and then the mitochondrion or bacterial cell splits in two. They are different in that bacteria have cell walls and such a wall must form between the two daughter cells, which does not occur when mitochondria divide.

Feature Investigation Questions 1. In a pulse-chase experiment, radioactive material is provided to cells in a single administration. This is referred to as the pulse. After a few minutes, a large amount of nonradioactive material is provided to the cells to “chase away” the ability to use the radioactive material. The researchers were attempting to determine the movement of proteins through the different compartments of a cell. Radioactive amino acids were used to label the proteins and enable the researchers to visualize where the proteins were at different times. 2. Pancreatic cells produce large numbers of proteins that they then secrete. Thus, these cells provide researchers with an ideal system for studying protein movement through a cell. 3. Using electron microscopy, the researchers found that the proteins, labeled with radioactivity, were first found in the ER of the cells. Later the radioalabeled proteins moved to the Golgi and then into vesicles near the plasma membrane. The researchers concluded that proteins move through several cellular compartments before they are secreted from a cell. Also, the movement of proteins through these compartments is not random but follows a particular pathway: ER, Golgi, secretory vesicles, plasma membrane, and, finally, extracellular environment.

Test Yourself

1. d 2. d 3. a 4. b 5. e 6. a 7. e 8. e 9. a The protein would go there first, because targeting to the ER occurs cotranslationally. 10. c It is true that they all carry out metabolism, but so do eukaryotic cells.

Conceptual Questions 1. Stage 1: Nucleotides and amino acids were produced prior to the existence of cells. Stage 2: Nucleotides and amino acids became polymerized to form DNA, RNA, and proteins. Stage 3: Polymers became enclosed in membranes. Stage 4: Polymers enclosed in membranes evolved cellular properties. 2. If the motor protein is bound to a cargo and can walk along a cytoskeletal filament that is fixed in place, this will cause movement of the cargo when the

Concept Checks Figure 5.7  The most common feature causing a transmembrane segment to form is a stretch (about 20) of amino acids that mostly have hydrophobic (nonpolar) side chains. Figure 5.13  Water will move from outside to inside, from the lower to the higher concentration. Figure 5.15  The purpose of gating is to regulate the function of channels, allowing them to be open or closed. Figure 5.21  The protein coat allows the budding process at the surface of the Golgi membrane to form a vesicle.

Core Skills: Connections Figure 5.5  Transmembrane proteins called cell adhesion molecules bind to each other to promote cell-to-cell adhesion. In addition, they can bind to filaments in the extracellular matrix, such as collagen fibers, thereby causing a cell to adhere to the extracellular matrix. Figure 5.10  Leucine would be more likely to cross an artificial phospholipid bilayer because it is more hydrophobic than lysine. Figure 5.11  Gradients of sodium and potassium ions are important for the conduction of action potentials.

Feature Investigation Questions 1. Most cells allow movement of water across the cell membrane by passive diffusion. However, it was noted that certain cell types had a much higher rate of water movement, indicating that something different was occurring in these cells. 2. The researchers identified water channels by characterizing proteins that are present in red blood cells and kidney cells but not other types of cells. Red blood cells and kidney cells have a faster rate of water movement across the membrane than other cell types. These cells are more likely to have water channels. By identifying proteins that are found in both of these types of cells but not in other cells, the researchers were identifying possible candidate proteins that function as water channels. In addition, CHIP28 had a structure that resembled other known channel proteins. Agre and his associates experimentally created multiple copies of the gene that produces the CHIP28 protein and then artificially transcribed the genes to produce many mRNAs. The mRNAs were injected into frog oocytes where they could be translated to make the CHIP28 proteins. After altering the frog oocytes by introducing the CHIP28 mRNAs, the researchers compared the rate of water transport in the altered oocytes versus normal frog oocytes. This procedure allowed them to introduce the candidate protein into a cell type that normally does not have the protein present. 3. After artificially introducing the candidate protein into the frog oocytes, the researchers found that the experimental oocytes took up water at a much faster rate in a hypotonic solution as compared to the control oocytes. The results indicated that the presence of the CHIP28 protein did increase water transport into cells.

Test Yourself

1. c  2. c  3. b  4. d  5. b  6. e  7. d  8. e  9. e  10. c

Conceptual Questions 1. See Figure 5.1 for the type of drawing you should have made. The membrane is considered a mosaic of lipid, protein, and carbohydrate molecules. The membrane exhibits properties that resemble a fluid because lipids and proteins can move relative to each other within the plane of the membrane.



APPENDIX B

3. The lipid bilayer, channels, and transporters cause the plasma membrane to be selectively permeable. This allows a cell to take up needed nutrients from its extracellular environment and to export waste products into the environment.

Chapter 6

Concept Checks

Figure 6.2  The solution of dissolved Na+ and Cl– has more entropy. A salt crystal is very ordered, whereas the ions in solution are much more disordered. Figure 6.4  If a large amount of ADP was broken down, the cell would not be able to synthesize as much ATP, which is made by the attaching a phosphate to ADP. The ATP cycle would be inhibited. Figure 6.5 Lowering EA speeds up the rate. When the activation energy is lower, it takes less time for reactants to reach the transition state, where a reaction can occur. Lowering EA does not affect the direction of a reaction. Figure 6.7  At a substrate concentration of 0.5 mM, the reaction catalyzed by enzyme A would have the higher velocity. That reaction would be very near its Vmax, whereas enzyme B’s reaction would be well below its Vmax. Figure 6.14  Protein degradation eliminates proteins that are worn out, misfolded, or no longer needed by the cell. Such proteins could interfere with normal cell function. In addition, the recycling of amino acids saves the cell energy.

Core Skills: Connections Figure 6.9  If RNase P did not function properly, ptRNAs could not be converted to their mature forms. The ptRNAs would be too large to fit into the sites on the ribosome. Therefore, translation would be inhibited. Figure 6.13  Feedback inhibition prevents the excessive breakdown of carbohydrates and thereby prevents the excessive synthesis of ATP. Cells don’t waste energy making ATP if they don’t need it.

Feature Investigation Questions

Chapter 7

Concept Checks Figure 7.3  The molecules that donate phosphates are 1,3-bisphosphoglycerate and phosphoenolpyruvate. Figure 7.6  For each acetyl group that is oxidized, the main products are 2 CO2, 3 NADH, 1 FADH2, and 1 GTP. Figure 7.8  The protein complex is called cytochrome oxidase because it removes electrons from (oxidizes) cytochrome c. Figure 7.10  No. The role of the electron transport chain is to produce an H+ electrochemical gradient, which is what drives ATP synthase. If the H+ electrochemical is made another way, such as by bacteriorhodopsin, ATP synthase can still make ATP. Figure 7.14  The advantage is that cells can use the same enzymes to metabolize different kinds of organic molecules. This saves energy because it would require a lot of energy to make many different enzymes, which are composed of proteins.

Core Skills: Connections Figure 7.2  Glycolytic muscle fibers rely on glycolysis for their ATP needs. Because glycolysis does not require oxygen, such muscle fibers can function without oxygen. Figure 7.4  FDG is radiolabeled so it can be specifically detected by a PET scan.

Feature Investigation Questions 1. The researchers attached an actin filament to the γ subunit of ATP synthase. The actin filament was fluorescently labeled, so the researchers could determine if the actin filament moved when viewed under a fluorescence microscope. 2. When functioning in the hydrolysis of ATP, the actin filament was seen to rotate. The actin filament was attached to the γ subunit of ATP synthase. The rotational movement of the filament was the result of the rotational movement of the γ subunit. In the control part of the experiment, no ATP was added to stimulate enzyme activity. In the absence of ATP, no movement was observed. 3. No, the counterclockwise rotation observed by the researchers is the opposite of what would be expected inside mitochondria. During the experiment, the ATP synthase was not functioning to synthesize ATP but instead was running backward and hydrolyzing ATP.

1. RNase P has both a protein and an RNA subunit. To determine which subunit has catalytic function, it was necessary to purify them individually and then see which one was able to cleave ptRNA.

Test Yourself

2. The experimental strategy was to incubate RNase P or subunits of RNase P with ptRNA and then do gel electrophoresis to determine if ptRNA had been cleaved to a mature tRNA and a 5′ fragment. The control without the protein subunit was used to determine if the RNA alone could catalyze the cleavage. The control without the RNA subunit was used to determine if some other factor in the experiment (for instance, Mg2+ or protein) was able to cleave the ptRNA.

Conceptual Questions

3. The critical results occurred when the researchers incubated the purified RNA subunit at high Mg2+ concentrations with the ptRNA. Under these conditions, the ptRNA was cleaved. These results indicated that the RNA subunit has catalytic activity. A high Mg2+ concentration is needed to keep it catalytically active in the absence of the protein subunit.

Test Yourself

1. e  2. b  3. b  4. c  5. a  6. c  7. b  8. e  9. e  10. a

Conceptual Questions 1. Exergonic reactions are spontaneous. They proceed in a particular direction. An exergonic reaction could be slow or fast. By comparison, an endergonic reaction is not spontaneous. It will not proceed in a particular direction unless free energy is supplied. An endergonic reaction can be fast or slow.

1. a  2. b  3. b  4. c  5. a  6. c  7. b  8. d  9. d  10. b

1. The purpose of the electron transport chain is to pump H+ across the inner mitochondrial membrane to establish an H+ electrochemical gradient. When H+ flow back across the membrane through ATP synthase, ATP is synthesized. 2. The movement of H+ through the contact site between the c and a subunits causes the γ subunit to rotate. As it rotates, it sequentially alters the conformation of the β subunits, where ATP is made. This causes (1) ADP and Pi to bind with moderate affinity, (2) ADP and Pi to bind very tightly such that ATP is made, and (3) ATP to be released. 3. The phases of glucose metabolism are regulated in a variety of ways. For example, key enzymes in glycolysis and the citric acid cycle are regulated by the availability of their substrates and by feedback inhibition. The electron transport chain is regulated by the ATP/ADP ratio. Such regulation ensures that a cell does not waste energy making ATP when it is in sufficient supply. Also, the production of too much NADH is potentially harmful because at high levels it has the potential to haphazardly donate its electrons to other molecules and promote the formation of free radicals, highly reactive chemicals that damage DNA and cellular proteins.

Chapter 8

Concept Checks

2. During feedback inhibition, the product of a metabolic pathway binds to an allosteric site on an enzyme that acts earlier in the pathway. The product inhibits this enzyme, thereby preventing the overaccumulation of the product.

Figure 8.3  The Calvin cycle can occur in the dark as long as sufficient CO2, ATP, and NADPH are present in the stroma.

3. Recycling of amino acids and nucleotides conserves a great deal of energy. Cells don’t have to remake these building blocks, which would require a large amount of energy.

Figure 8.5  To become more stable by dropping down to a lower energy level, a photoexcited electron can release energy in the form of heat, release energy in the form of light, or transfer energy to another electron by resonance energy transfer.

Figure 8.4  Gamma rays have higher energy than radio waves.

APPENDIX B

2. Integral membrane proteins can contain transmembrane segments that cross the membrane, or they may contain lipid anchors. Peripheral membrane proteins are noncovalently bound to integral membrane proteins or to the polar heads of phospholipids.

A-5

A-6

APPENDIX B

Figure 8.7  Having different pigment molecules allows plants to absorb a wider range of wavelengths of light.

Chapter 9

Figure 8.8  ATP and NADPH are produced in the stroma. O2 is produced in the thylakoid lumen.

Concept Checks

Figure 8.9  Linear electron flow produces equal amounts of ATP and NADPH. However, plants usually need more ATP than NADPH. Cyclic photophosphorylation allows plants to make just ATP, thereby increasing the relative amount of ATP.

Figure 9.1  It is glucose. Figure 9.3  Endocrine signals are more likely to exist for a longer period of time. Their longer existence is necessary because these signals, called hormones, travel relatively long distances to reach their target cells. Therefore, they must exist long enough to get to their destinations.

Figure 8.10  Because these two proteins are homologous, this means that the genes that encode them were derived from the same ancestral gene. Therefore, the amino acid sequences of these two proteins are expected to be very similar, though not identical. Because the amino acid sequence of a protein determines its structure, two proteins with similar amino acid sequences would be expected to have similar structures. Figure 8.12  An electron has the highest amount of energy just after its energy has been boosted by light in photosystem I. Figure 8.13  NADPH reduces organic molecules and makes them more able to form C─C and C─H bonds. Figure 8.16  The arrangement of cells in C4 plants makes the level of CO2 high and the level of O2 low in the bundle-sheath cells. Figure 8.17  When there is plenty of moisture and it is not too hot, C3 plants are more efficient. However, under hot and dry conditions, C4 and CAM plants have the advantage because they lose less water and avoid photorespiration.

Core Skills: Connections APPENDIX B

Figure 8.2  Two guard cells make up one stoma.

Feature Investigation Questions 1. The researchers were attempting to determine the biochemical pathway of the process of carbohydrate synthesis via photosynthesis. The researchers wanted to identify different molecules produced over time to determine the steps of the biochemical pathway. 2. The purpose for using 14C-labeled CO2 was to label the different carbon molecules produced during the biochemical pathway. The researchers could “follow” the carbon molecules from the radiolabeled CO2 that were incorporated into the organic molecules during photosynthesis. The radioactive isotope provided the researchers with a method of labeling the different molecules. The purpose of the experiment was to determine the steps in the biochemical pathway of photosynthesis. By examining samples from different times after the introduction of the labeled carbon source, the researchers were able to determine which molecules were produced first and, thus, distinguish products of the earlier steps of the pathway from products of later steps of the pathway. The researchers used two-dimensional paper chromatography to separate the different molecules from each other. After being separated, the different molecules were identified by various chemical methods. 3. Calvin and his colleagues were able to determine the biochemical process that incorporates CO2 into organic molecules during photosynthesis. The researchers were able to identify the biochemical steps and the molecules produced at these steps of what is now called the Calvin cycle.

Test Yourself

1. c  2. c  3. c  4. a  5. b  6. b  7. c  8. b  9. e  10. c

Conceptual Questions 1. The two stages of photosynthesis are the light reactions and the Calvin cycle. The key products of the light reactions are ATP, NADPH, and O2. The key product of the Calvin cycle is carbohydrates. The initial product is G3P, which is used to make sugars and other organic molecules. 2. NADPH is used during the reduction phase of the Calvin cycle. It donates its electrons to 1,3-BPG. 3. At the level of the biosphere, the role of photosynthesis is to incorporate carbon dioxide into organic molecules. These organic molecules can then be broken down, by autotrophs and by heterotrophs, to make ATP. The organic molecules made during photosynthesis are also used as starting materials to synthesize a wide variety of organic molecules and macromolecules that are made by cells.

Figure 9.4  The effect of a signaling molecule is to cause a cellular response. Most signaling molecules do not enter the cell. Therefore, to exert an effect, they must alter the conformation of a receptor protein, which, in turn, stimulates an intracellular signal transduction pathway that leads to a cellular response. Figure 9.7  The α subunit has to hydrolyze its bound GTP to GDP and Pi. This changes the conformation of the α subunit so that it can reassociate with the β/γ dimer. Figure 9.12  The signal transduction pathway begins with activation of the G protein and ends with the activated subunits of protein kinase A . The cellular response involves the phosphorylation of target proteins, which changes their function in some way. Figure 9.13  Depending on the protein involved, phosphorylation can activate or inhibit protein function. Phosphorylation of phosphorylase kinase and glycogen phosphorylase activates their function, whereas phosphorylation inhibits glycogen synthase. Figure 9.14  Signal amplification allows a single signaling molecule to affect many proteins within a cell, thereby amplifying a cellular response. Figure 9.18  The initiator caspase is part of the death-inducing signaling complex. It is directly activated when a cell receives a death signal. The initiator caspase then activates the executioner caspase, which cleaves various cellular proteins and thereby causes the destruction of the cell.

Core Skills: Connections Figure 9.2  Light is sensed by the cells on the illuminated side of the shoot tip and they send auxin to cells on the nonilluminated side, which accumulate more auxin, causing them to elongate. Figure 9.5  Most receptors and enzymes bind their ligands noncovalently and with high specificity. Enzymes, however, convert their ligands (which are reactants) into products, whereas receptors undergo a conformational change due to the binding of their ligands. Figure 9.10  The GTP-bound form of Ras is active and promotes cell division. To turn the signal transduction pathway off, Ras hydrolyzes GTP to GDP and Pi. If this cannot occur due to a mutation of Ras, the pathway will be continuously on, and uncontrolled cell division (cancer) will result.

Feature Investigation Questions 1. Compared with control rats, those injected with prednisolone alone would be expected to have a decrease in the number of adrenal cortex cells because prednisolone suppresses ACTH synthesis. Therefore, apoptosis would be higher. By comparison, rats injected with prednisolone + ACTH would have a normal number of cells because the addition of ACTH would compensate for the effects of prednisolone. The rats injected with ACTH alone would be expected to have a greater number of cells; apoptosis would be inhibited. 2. Yes, injection of both prednisolone and ACTH probably inhibited the ability of the rats to make their own ACTH. Even so, they were given ACTH by the injection, so they didn’t need to make their own ACTH to prevent apoptosis. 3. The lowest level of apoptosis would occur in the rats given ACTH alone, because they could make their own ACTH plus they were given ACTH. With such high levels of ACTH, they probably had the lowest level of apoptosis; it was already known that ACTH promotes cell division.

Test Yourself

1. d  2. c  3. d  4. e  5. a  6. c  7. e  8. e  9. e  10. b

Conceptual Questions 1. Cells need to respond to a changing environment, and cells need to communicate with each other. 2. In the first stage, a signaling molecule binds to a receptor, causing receptor activation. In the second stage, one type of signal is transduced, or converted to a different signal inside the cell. In the third stage, the cell responds in some way to the signal, possibly by altering the activity of enzymes, structural



APPENDIX B

3. Cell signaling allows cells to respond to environmental changes. For example, if a yeast cell is exposed to glucose, cell signaling will allow it to adapt to that change and utilize glucose more readily. Likewise, cell signaling allows plants to grow toward light. In addition, cells in a multicellular organism respond to changes in signaling molecules, such as hormones, and thereby coordinate their activities.

Chapter 10

Concept Checks Figure 10.1  The four functions of the ECM in animals are strength, structural support, organization, and cell signaling. Figure 10.2  The extension sequences of procollagen prevent large fibers from forming intracellularly. Figure 10.3  The proteins would become more linear, and the fiber would come apart. Figure 10.4  GAGs are highly negatively charged molecules that tend to attract positively charged ions and water. The high water content gives the ECM a gel-like character, which makes it difficult to compress. Figure 10.7  Adherens junctions and desmosomes are cell-to-cell junctions, whereas hemidesomosomes and focal adhesions are cell-to-ECM junctions. Figure 10.10  In contrast to the result shown in Figure 10.10, the lanthanum would be on the side of the cell layer facing the digestive tract. You would see it on that side of the cell layer up to the tight junction, but not on the other side of the tight junction. Figure 10.13  Middle lamellae are similar to anchoring junctions and desmosomes in that they also function in cell-to-cell adhesion. However, their structures are quite different. Middle lamellae are composed primarily of negatively charged polysaccharides that interact with divalent cations. By comparison, anchoring junctions and desmosomes hold cells together via proteins such as cadherins and integrins. Figure 10.15  Connective tissue has the most extensive ECM. Figure 10.17  Dermal tissue is found on the surfaces of leaves, stems, and roots.

Core Skills: Connections Figure 10.9  If tight junctions did not exist, substances in the lumen of your intestine might directly enter your blood. This could be potentially harmful if you consumed something with a toxic molecule in it. Likewise, materials from blood could be lost by diffusing into the lumen of your small intestine. Figure 10.14  Plasmodesmata facilitate the movement of nutrients in a cell-to-cell manner. This is called symplastic transport.

Feature Investigation Questions 1. The purpose of this study was to determine the sizes of molecules that can move through gap junctions from one cell to another. 2. The researchers used fluorescent dyes to visibly monitor the movement of material from one cell to an adjacent cell through the gap junctions. First, single layers of rat liver cells were cultured. Next, fluorescent dyes with molecules of various masses were injected into particular cells. The researchers then used fluorescence microscopy to determine whether or not the dyes were transferred from one cell to the next. 3. The researchers found that molecules with masses less than 1,000 daltons (Da) could pass through the gap junction channels. Molecules with masses larger than 1,000 Da could not pass through the gap junctions. Further experimentation revealed variation in gap-junction channel size among different cell types. However, the upper limit of the gap-junction channel size was determined to be around 1,000 Da.

Test Yourself

1. e  2. c  3. b  4. e  5. e  6. d  7. e  8. d  9. e  10. a

Conceptual Questions 1. The primary cell wall is synthesized first between the two newly made daughter cells. It is relatively thin and allows cells to expand and grow. The secondary cell wall is made in layers by the deposition of cellulose fibrils and other components. In many cell types, it is relatively thick.

2. Cadherins and integrins are both integral membrane proteins that function as cell adhesion molecules. They also can function in cell signaling. Cadherins bind one cell to another cell, whereas integrins bind a cell to the extracellular matrix. Cadherins require calcium ions to function, but integrins do not. 3. Cell junctions are important in the proper arrangement of cells in a multicellular organism. In animals, for example, cells junctions allow cells to recognize and bind to each other. This is very important during embryonic development. In addition, cell junctions adhere cells to the extracellular matrix. Likewise, in plants, the cell wall and middle lamella are important in forming connections between plant cells that gives plants their correct morphology and function.

Chapter 11

Concept Checks Figure 11.4  Cytosine is found in both DNA and RNA. Figure 11.5  The phosphate is attached to the 5′ carbon in a DNA nucleotide. Figure 11.11  The expected fractions would be 1/8 half-heavy and 7/8 light. Figure 11.15  The oxygen in a new phosphoester bond comes from the sugar. Figure 11.17  The lagging strand is made discontinuously in the direction opposite to the movement of the replication fork. Figure 11.19  When primase is synthesizing a primer in the lagging strand, it moves from left to right in this figure. After it is done making a primer, it needs to hop to the opening of the replication fork to make a new primer. This movement is from right to left in this figure. Figure 11.21  Telomerase uses an RNA sequence that it contains as a template to make the DNA repeat sequence. Figure 11.24  Proteins hold the bases of the radial loop domains in place.

Core Skills: Connections Figure 11.1  When a bacterium dies, it may release some of its DNA into the environment. Such DNA can be taken up via transformation by living bacteria, even bacteria of other species. If the DNA that is taken up encodes an antibiotic resistance gene, the gene may be incorporated into the genome of the living bacterium and make it resistant to an antibiotic. Figure 11.25  If chromosomes did not become very compact, they might get tangled up with each other during cell division, which would prevent their even distribution into the two daughter cells.

Feature Investigation Questions 1. Previous studies had indicated that mixing different strains could lead to transformation, or the changing of a strain into a different one. Griffith had shown that mixing heat-killed type S with living type R bacteria would result in the transformation of the type R to type S. Though mutations could cause a change of identity of certain strains, the type R to type S transformation was not due to mutation but was more likely due to the transmission of a biochemical substance between the two strains. Griffith recognized this and referred to the biochemical substance as the “transformation principle.” If Avery, MacCleod, and McCarty could determine the biochemical identity of this “transformation principle,” they could identify the genetic material for the bacteria. 2. A DNA extract contains DNA that has been purified from a sample of cells. 3. The researchers could not verify that the DNA extract was completely pure, that is, lacking small amounts of contaminating molecules, such as proteins and RNA. The researchers were able to treat the extract with enzymes to degrade proteins (using protease), RNA (using RNase), or DNA (using DNase). Eliminating the proteins or RNA did not alter the transformation of the type R to type S strains. Only the enzymatic degradation of DNA disrupted the transformation, indicating that DNA is the genetic material.

Test Yourself

1. a  2. b  3. d  4. d  5. b  6. c  7. b  8. d  9. d  10. c

Conceptual Questions 1. The genetic material must contain the information necessary to construct an entire organism. The genetic material must be accurately copied and transmitted from parent to offspring and from cell to cell during cell division in multicellular organisms. The genetic material must contain differences that can account for the known variation within each species and among different species.

APPENDIX B

proteins, or transcription factors. When the estrogen receptor is activated, the second stage, signal transduction, does not occur because the estrogen receptor is an intracellular receptor that directly activates the transcription of genes to elicit a cellular response.

A-7

A-8

APPENDIX B Griffith discovered something called the transformation principle, and his experiments showed the existence of biochemical genetic information. In addition, he showed that this genetic information can move from one individual to another of the same species. In his experiments, Griffith took heat-killed type S bacteria and mixed them with living type R bacteria and injected them into a live mouse, which died after the injection. By themselves, these two strains would not kill the mouse, but when they were put together, the genetic information from the heat-killed type S bacteria was transferred into the living type R bacteria, thus transforming the type R bacteria into type S.

2. Since DNA is double stranded, 560 nucleotides form 280 bp. With 10 bp per turn, this DNA double helix will have 28 complete turns. 3. In a DNA double helix, the two strands hydrogen-bond with each other according to the AT/GC rule. This provides the basis for DNA replication. In addition, as described in later chapters, hydrogen bonding between complementary bases is the basis for the transcription of RNA, which is needed for gene expression. The sequence of bases within DNA strands have the function of storing information such as the sequence of amino acids within a polypeptide.

Chapter 12

Concept Checks Figure 12.1  A person with two defective copies of phenylalanine hydroxylase would have phenylketonuria.

ability of cells to catalyze just one reaction in this pathway, thereby suggesting that a single gene encodes a single enzyme. 2. Each of these 20 enzymes catalyzes the attachment of a specific amino acid to a specific tRNA molecule. 3. During transcription, a DNA strand is used as a template for the synthesis of RNA. Most genes encode mRNAs, which contain the information to make polypeptides. During translation, an mRNA binds to a ribosome and a polypeptide is made, which becomes a unit within a functional protein.

Chapter 13

Concept Checks Figure 13.1  The binding of an ncRNA to DNA or another RNA could be inhibited by the formation of a stem-loop, because it would interfere with base pairing. Figure 13.4  HOTAIR binds to the target gene because a segment of the RNA in HOTAIR is complementary to the target gene. Figure 13.6  RISC binds to an mRNA because the miRNA is complementary to the mRNA. The miRNA and mRNA hydrogen bond to each other.

Core Skills: Connections

APPENDIX B

Figure 12.2  The ability to convert ornithine into citrulline is missing.

Figure 13.7  In eukaryotes, proteins that are destined for the ER, Golgi, vacuoles, lysosomes, or secretion need SRP to reach their proper locations. In bacteria and archaea, proteins that are secreted need SRP.

Figure 12.3  The usual direction of flow of genetic information is from DNA to RNA to protein, though exceptions occur.

Feature Investigation Questions

Figure 12.9  The ends of protein-encoding genes do not have a poly T region that acts as a template for the synthesis of a poly A tail. Instead, the poly A tail is added to the pre-mRNA after transcription by an enzyme that attaches many adenine nucleotides in a row. Figure 12.11  A protein-encoding gene would still be transcribed into RNA if the start codon was missing. However, it would not be translated properly into a polypeptide. Figure 12.19  A region near the 5′ end of the mRNA is complementary to a region of rRNA in the small subunit. These complementary regions hydrogen bond with each other to promote the binding of the mRNA to the small ribosomal subunit.

Core Skills: Connections Figure 12.5  Both DNA and RNA polymerase use a DNA strand as a template and connect nucleotides to each other in a 5′ to 3′ direction based on the complementarity of base pairing. One difference is that DNA polymerase needs a pre-existing strand, such as a RNA primer, to begin DNA replication, whereas RNA polymerase can begin the synthesis of RNA on a bare template strand. Another key difference is that DNA polymerase connects deoxyribonucleotides, whereas RNA polymerase connects ribonucleotides. Figure 12.15  The attachment of an amino acid to a tRNA is an endergonic reaction. ATP provides the energy to drive this reaction.

Feature Investigation Questions 1. A triplet mimics mRNA because it can cause a specific tRNA to bind to the ribosome. This was useful to Nirenberg and Leder because it allowed them to correlate the binding of a tRNA carrying a specific amino acid with a triplet sequence. 2. The researchers were attempting to match codons with appropriate amino acids. By radiolabeling one amino acid in each of the 20 tubes for each codon, the researchers were able to identify the correct relationship by detecting which tube produced radioactivity on the filter. 3. For the AUG triplet, the filter would have shown radioactivity when methionine was radiolabeled. Even though AUG acts as the start codon, it also codes for the amino acid methionine. The other three codons act as stop codons and do not code for an amino acid. In these cases, the researchers would not have detected radioactivity on any of the filters.

Test Yourself

1. b  2. a  3. d  4. e  5. e  6. e  7. d  8. d  9. d  10. b

Conceptual Questions 1. Confirmation of their one gene/one enzyme hypothesis came from studies involving arginine biosynthesis. Biochemists had already established that particular enzymes are involved in a pathway to produce arginine. Intermediates in this pathway are ornithine and citrulline. Mutants in single genes disrupted the

1. The mex-3 mRNA corresponds to the sense strand. 2. The researchers began with a copy of the mex-3 gene in a plasmid. When RNA polymerase and nucleotides were added, the sense strand of mex-3 mRNA was made. They also modified this plasmid by placing the promoter on the opposite side of the mex-3 coding sequence. When RNA polymerase and nucleotides were added, the antisense strand of mex-3 mRNA was made. 3. The mixture of sense and antisense mex-3 mRNA was the most effective at causing the degradation of mex-3 mRNA.

Test Yourself

1. e  2. a  3. e  4. c  5. d  6. d  7. e  8. a  9. c  10. d

Conceptual Questions 1. HOTAIR: scaffold, guide SRP RNA: scaffold, alterer of protein function miRNA: guide crRNA: guide 2. RNA interference is the phenomenon in which an miRNA or an siRNA silences the expression of an mRNA. The double-stranded pre-miRNA or pre-siRNA is cleaved by dicer into a smaller double-stranded RNA that associates with RISC. One of the RNA strands is then degraded, so that only a short single-stranded miRNA or siRNA that recognizes an mRNA is found within RISC. This miRNA or siRNA guides RISC to the mRNA and causes it to be silenced. 3. The structure of HOTAIR provides a scaffold for the binding of two histonemodifying complexes. The structure is also complementary to GA-rich sequences next to certain target genes, such as the HoxD gene, and HOTAIR thereby guides the histone-modifying complexes to those genes. Such genes are then covalently modified, which causes them to be repressed.

Chapter 14

Concept Checks Figure 14.2  Gene regulation causes each type of cell to express its own unique set of proteins, which, in turn, are largely responsible for the morphology and function of that type of cell. Figure 14.6 The lacZ, lacY, and lacA genes are under the control of the lac promoter. Figure 14.7  Negative control refers to the action of a repressor protein, which inhibits transcription when it binds to the DNA. Inducible refers to the action of a small effector molecule. When it is present, it promotes transcription.



APPENDIX B

Figure 14.16  When an activator interacts with mediator, it causes RNA polymerase to proceed to the elongation stage of transcription. Figure 14.18  Some histone modifications enhance transcription, whereas others inhibit it. Figure 14.21  The advantage of alternative splicing is that it allows a single gene to encode two or more polypeptides. This enables organisms to have smaller genomes, which are more efficient and easier to package into a cell. Figure 14.22  When iron levels rise in the cell, the iron binds to IRP and removes it from the mRNA that encodes ferritin. This results in the rapid translation of ferritin protein, which can store excess iron. Unfortunately, ferritin storage does have limits, so iron poisoning can still occur if too much is ingested.

Core Skills: Connections

Figure 15.8  UvrC and UvrD are responsible for removing the damaged DNA. UvrC makes cuts on both sides of the damage, and then UvrD removes the damaged region. Figure 15.9  The Sun produces UV light and other harmful radiation that can damage DNA. This person has a defect in the nucleotide excision repair system. Therefore, her DNA is more likely to suffer mutations, which can cause pigmentation changes and other effects on the skin. Figure 15.11  Growth factors turn on a signal transduction pathway that ultimately leads to cell division. Figure 15.14  The type of cancer associated with this translocation is leukemia, which is a cancer of blood cells. The fused gene is expressed in white blood cells because it has the bcr promoter. The abnormal fusion protein promotes cancer in these cells. Figure 15.15  Checkpoints prevent cell division if a genetic abnormality is detected. This mechanism helps to properly maintain the genome by minimizing the possibility that a cell harboring a mutation will divide to produce two daughter cells.

Figure 14.10  In eukaryotic cells, cAMP acts as a second messenger in signal transduction pathways.

Figure 15.16  Cancer would not occur if both copies of the Rb gene and both copies of the E2F gene were rendered inactive due to mutations. An activated copy of the E2F gene is needed to promote cell division.

Figure 14.19  A nucleosome is composed of DNA wrapped around an octamer of histone proteins.

Core Skills: Connections

Feature Investigation Questions 1. The first observation was the identification of rare bacterial strains that showed constitutive expression of the lac operon. Normally, the lac genes are expressed only when lactose is present. These mutant strains expressed the genes continuously. The researchers also observed that some of these strains had mutations in the lacI gene. These two observations were key to the development of hypotheses explaining the relationship between the lacI gene and the regulation of the lac operon. 2. The correct hypothesis is that the lacI gene encodes a repressor protein that inhibits the operon. 3. The researchers introduced an F′ factor into the mutant strain that carried the wild-type lacI gene. In this merozygote, the cells that contained the F′ factor had both a mutant and a normal copy of the lacI gene. In the merozygote with an F′ factor with a normal copy of the lacI gene, regulation of the lac operon was restored. The researchers concluded that the normal lacI gene produced adequate amounts of a diffusible protein that could interact with the operator site on the chromosomal DNA as well as the F′ factor DNA and regulate transcription.

Test Yourself

1. d  2. b  3. c  4. c  5. c  6. d  7. c  8. c  9. d  10. c

Conceptual Questions 1. In an inducible operon, the presence of a small effector molecule causes transcription to occur. An example is the lac operon, which is induced with allolactose. In repressible operons, a small effector molecule inhibits transcription. An example is the trp operon, which is represssed by high levels of tryptophan. The effects of these small molecules are mediated through regulatory proteins that bind to the DNA. 2. a. regulatory protein; b. small effector molecule; c. segment of DNA; d. small effector molecule; and e. regulatory protein. 3. Gene regulation offers key advantages, such as (1) proteins are made only when they are needed; (2) proteins are made in the correct cell type; and (3) proteins are made at the correct stage of development. These advantages are important for reproduction and sustaining life.

Chapter 15

Concept Checks Figure 15.1  At neutral pH, glutamic acid is negatively charged. Perhaps the negative charges repel each other and prevent hemoglobin proteins from aggregating into fiber-like structures. Figure 15.3  This trait is due to a mutation that occurred in a somatic cell, so it cannot be transmitted to the individual’s offspring. Figure 15.6  A thymine dimer is harmful because it can cause an error in DNA replication that results in a mutation.

Figure 15.11  Drugs that inhibit protein kinases may be used to combat cancer if they target the protein kinases that are overactive in certain forms of cancer.

Feature Investigation Questions 1. Some biologists believed that heritable traits may be altered by physiological events. This view suggests that mutations may be stimulated by certain needs of the organism. Others believed that mutations are random. If a mutation had a beneficial effect that improved survival and/or reproductive success, it would be more likely to be maintained in the population through natural selection. 2. The Lederbergs were testing the hypothesis that mutations are random events. 3. When the researchers looked at the locations on the secondary plates of colonies that were resistant to the bacteriophages, the pattern was the same on the two plates. This indicates that the mutation that allowed the colonies to be resistant to the virus occurred on the master plate. Thus, the mutation occurred randomly and was not caused by exposure to the virus.

Test Yourself

1. d  2. d  3. d  4. e  5. d  6. b  7. b  8. b  9. c  10. e

Conceptual Questions 1. Random mutations are more likely to be harmful than beneficial. The genes within each species have evolved to work properly. They have functional promoters, coding sequences, terminators, and so on, that are all needed for expression. Mutations are more likely to disrupt these sequences. For example, mutations within the coding sequence may produce early stop codons, frameshift mutations, and missense mutations that result in a nonfunctional polypeptide. On rare occasions, however, mutations are beneficial; they may produce a gene that is expressed better than the original gene or produce a polypeptide that functions better. 2. A spontaneous mutation originates within a living cell. It may be due to spontaneous changes in nucleotide structure, errors in DNA replication, or alterations of the structure of DNA by products of normal metabolism. The causes of induced mutations originate from outside the cell. They may be physical agents, such as UV light or X-rays, or chemicals that act as mutagens. Both spontaneous and induced mutations may cause a harmful phenotype such as a cancer. In many cases, induced mutations are avoidable if the individual can prevent exposure to the environmental agent that acts as a mutagen. 3. Mutations may alter the expression of a gene and/or alter the function of a protein encoded by a gene. In many cases, such changes are harmful because a gene may not be expressed at the correct level, or the protein may not function as well as the normal (nonmutant) protein.

Chapter 16

Concept Checks Figure 16.1  Chromosomes are readily seen when they are compacted in a dividing cell. By adding such a drug, the researchers increase the percentage of cells that are actively dividing. Figure 16.2  Interphase consists of the G1, S, and G2 phases of the cell cycle.

APPENDIX B

Figure 14.11  In the case of bacterial metabolism of sugars, the repressor keeps the lac operon turned off unless lactose is present in the environment. The activator allows the bacterium to choose between glucose and lactose.

A-9

A-10

APPENDIX B

Figure 16.8  The astral microtubules, which extend away from the chromosomes, are important for positioning the spindle apparatus within the cell. The polar microtubules project into the region between the two poles. Polar microtubules that overlap with each other play a role in the separation of the two poles. Kinetochore microtubules are attached to kinetochores at the centromeres and are involved in sorting the chromosomes.

Figure 17.7  The genotype was Pp. To produce white offspring, which are pp, the original plant had to have at least one copy of the p allele. Because it had purple flowers, it also had to have one copy of the P allele. So, its genotype must have been Pp.

Figure 16.9  Cytokinesis in both animal and plant cells follows mitosis and separates a mother cell into two daughter cells. In animal cells, cytokinesis involves the formation of a cleavage furrow, which constricts like a drawstring to separate the cells. In plants, the two daughter cells are separated by a cell plate, which forms a cell wall between them.

Figure 17.11  There are four possible ways that the chromosomes can align, and eight different types of gametes (ABC, abc, ABc, abC, Abc, aBC, AbC, aBc) can be produced.

Figure 16.14  The purpose of meiosis in animals is to produce gametes. These gametes combine during fertilization to produce a diploid organism. Following fertilization, the purpose of mitosis is to produce a multicellular organism. Figure 16.16  Inversions and reciprocal translocations do not affect the total amount of genetic material.

Core Skills: Connections Figure 16.3  Checkpoint proteins prevent cancer by checking the integrity of the genome. If abnormalities in DNA structure are detected or if a chromosome is not properly attached to the spindle apparatus, the checkpoint protein will delay cell division until the problem is fixed. If it cannot be fixed, the checkpoint protein will initiate the process of apoptosis, thereby killing a cell that may harbor mutations. This prevents the proliferation of cells that have the potential to be cancerous.

Feature Investigation Questions APPENDIX B

1. Researchers had demonstrated that the binding of progesterone to receptors in oocytes caused the cells to advance from the G2 phase of the cell cycle to mitosis. It appeared that progesterone acted as a signaling molecule for advancement through the cell cycle. 2. The researchers proposed that progesterone acted as a signaling molecule that led to the synthesis of molecules that cause the oocyte to advance through the cell cycle and achieve maturation. To test their hypothesis, donor eggs were exposed to progesterone for either 2 or 12 hours. Control donor oocytes were not exposed to progesterone. Cytosol from each treatment was then transferred to recipient oocytes. The researchers recorded whether or not the recipient oocytes underwent maturation. 3. The oocytes that were exposed to the progesterone for only 2 hours did not induce maturation in the recipient oocytes, whereas the oocytes that were exposed to progesterone for 12 hours did induce maturation in the recipient oocytes. The researchers suggested that a time span greater than 2 hours is needed to accumulate the proteins that are necessary to promote maturation.

Test Yourself

1. b  2. e  3. b  4. e  5. c  6. a  7. c  8. d  9. b  10. c

Conceptual Questions 1. In diploid species, chromosomes are present in pairs, one from each parent, and contain similar gene arrangements. Such chromosomes are homologous. When DNA is replicated, two identical copies are created, and these are sister chromatids. 2. There are four copies. A karyotype shows homologous chromosomes that come in pairs. Each member of the pair has replicated to form a pair of sister chromatids. Therefore, four copies of each gene are present. See the inset to Figure 16.1. 3. Mitosis is a process that produces two daughter cells with the same genetic material as the original daughter cell. In the case of plants and animals, this allows a fertilized egg to develop into a multicellular organism composed of many, genetically identical cells.

Chapter 17

Concept Checks Figure 17.4  The stamens are removed from the purple flower to prevent self-fertilization. Figure 17.5  The reason why offspring of the F1 generation exhibit only one variant of each character is because one trait is dominant over the other. Figure 17.6  The ratio of alleles (T to t) is 1:1. The reason why the phenotypic ratio is 3:1 is because T is dominant to t.

Figure 17.8  If the linked assortment hypothesis had been correct, the ratio would have been 3 yellow, round to 1 green, wrinkled.

Figure 17.12  No. If two parents are affected with the disease, they would have to be homozygous for the mutant allele if it’s recessive. Two homozygous parents would produce all affected offspring, barring rare mutations. If they produce an unaffected offspring, then the mutant allele is not recessive. Figure 17.13  All affected offspring having at least one affected parent suggests a dominant pattern of inheritance. Figure 17.14  The person is a female. In mammals, the presence of the Y chromosome causes maleness. Therefore, lacking a Y chromosome, a person with a single X chromosome develops into a female. Figure 17.18  No. You need a genetically homogenous population to study the norm of reaction. A wild population of squirrels is not genetically homogenous, so it could not be used. Figure 17.19  The recessive allele is the result of a loss-of-function mutation. In a Ccpp individual, the enzyme encoded by the P gene is defective.

Core Skills: Connections Figure 17.9  Sexual reproduction is the process in which two haploid gametes (for example, sperm and egg) combine with each other to begin the life of a new individual. Each gamete contributes one set of chromosomes. The resulting zygote has chromosomes that occur in pairs (one from each parent). The members of each pair are called homologs of each other; they carry the same types of genes. Figure 17.10  Alleles segregate, or go into separate cells, during the process of meiosis. Meiosis begins with a diploid mother cell that has pairs of genes, which may be found in different alleles. During meiosis, these pairs of genes separate and end up in different haploid cells. Therefore, each haploid cell has only one copy of each gene. In other words, each haploid cell has only one allele of a given gene.

Feature Investigation Questions 1. Morgan was testing the hypothesis of use and disuse. This hypothesis suggests that if a structure is not used, over time, it will diminish and/or disappear. Morgan was originally testing to see if flies reared in the dark would lose some level of eye development. 2. When the F1 individuals were crossed, only male F2 offspring expressed the white eye color. At this time, Morgan was aware of sex chromosome differences between male and female flies. He realized that because males only possess one copy of X-linked genes, this would explain why only F2 males exhibited the recessive trait. 3. In a cross between a white-eyed male and a female that is heterozygous for the white and red alleles, 1/2 of the female offspring would have white eyes. Also, a cross between a white-eyed male and a white-eyed female would yield all offspring with white eyes.

Test Yourself

1. c 2. b. Mendel’s law of segregation refers to the separation of the two alleles into separate cells. Meiosis is the nuclear division process that produces haploid cells. During the first meiotic division, a diploid cell divides to produce haploid cells. This is the phase in which the two alleles segregate, or separate, from each other. 3. d  4. c  5. e  6. d. Half of the males will be affected, but only half of the children will be males, so you multiply: 0.5 x 0.5 = 0.25, or 25%.  7. d  8. d  9. d  10. c

Conceptual Questions 1. Two affected parents having an unaffected offspring would rule out recessive inheritance. If two unaffected parents have an affected offspring, dominant inheritance is ruled out. However, it should be noted that this answer assumes that no new mutations are happening. In rare cases, a new mutation could cause or alter these results. For recessive inheritance, two affected parents could have an unaffected offspring if the offspring had a new mutation that converted the recessive allele to the dominant allele. Similarly for dominant inheritance, two unaffected parents could have an affected offspring if the offspring inherited a new mutation that was dominant. Note: New mutations are expected to be very rare.



APPENDIX B

3. The environment is necessary for the expression of genes. For example, organic molecules and energy are needed for transcription and translation. In addition, environmental factors influence the outcomes of traits. For example, sunlight can cause a tanning response, thereby affecting the darkness of the skin.

Chapter 18

Concept Checks Figure 18.1  Only the allele inherited from the father would be expressed in the offspring. Because he is heterozygous, half of the offspring would be normal size and half would be dwarf. Figure 18.3  The Barr body is much more compact than the other X chromosome in the cell. This compaction prevents most of the genes on the Barr body from being expressed. Figure 18.7  The gene is located in the chloroplast DNA. In this species, chloroplasts are transmitted from parent to offspring via eggs but not via sperm. Figure 18.10  Crossing over occurred during oogenesis in the heterozygous female of the F1 generation to produce the recombinant offspring of the F2 generation. Figure 18.11  One strategy would be to begin with two true-breeding parental strains: alal dpdp and al+ al+ dp + dp+ and cross them to get F1 heterozygotes, al+ al dp+ dp. Then testcross female F1 heterozygotes to male alal dpdp homozygotes. In the F 2 generation, the recombinant offspring would be al+ al dpdp and alal dp+ dp, and the nonrecombinants would be al+ al dp+ dp, and alal dpdp.

Core Skills: Connections Figure 18.6  The evolutionary origin of these organelles is an ancient endosymbiotic relationship. Mitochondria are derived from purple bacteria, and chloroplasts are derived from cyanobacteria.

Feature Investigation Questions 1. Bateson and Punnett were testing the hypothesis that the gene pairs that influence flower color and pollen shape would assort independently of each other. The two traits were expected to show a pattern consistent with Mendel’s law of independent assortment. 2. The expected results were a phenotypic ratio of 9:3:3:1. The researchers expected 9/16 of the offspring would have purple flowers and long pollen, 3/16 of the offspring would have purple flowers and round pollen, 3/16 of the offspring would have red flowers and long pollen, and 1/16 of the offspring would have red flowers and round pollen. 3. Though all four of the expected phenotypes were seen, they were not in the predicted ratio of 9:3:3:1. The number of individuals with the phenotypes found in the parental generation (purple flowers and long pollen or red flowers and round pollen) was much higher than expected. Bateson and Punnett suggested that the gene controlling flower color was somehow coupled with the gene that controls pollen shape. This would explain why these traits did not always assort independently.

Test Yourself

1. e  2. d  3. c  4. a  5. a  6. e  7. e  8. d  9. c  10. c

Conceptual Questions 1. Epigenetics is the study of mechanisms that lead to changes in gene expression that can be passed from cell to cell and are reversible, but do not involve a change in the sequence of DNA. Not all epigenetic changes are passed from parent to offspring. For example, a cigarette smoker could acquire an epigenetic change in a lung cell; this change would not be passed to offspring. 2. A Barr body is an X chromosome in the somatic cells of female mammals that has undergone X-chromosome inactivation. It is highly compacted. This compaction prevents the expression of most X-linked genes. 3. Epigenetics alters the way that genes are expressed, and thereby can affect an individual’s traits. Such traits, in turn, may affect reproduction.

Chapter 19

Concept Checks Figure 19.5  The advantage of the lytic cycle is that the phage can make many copies of itself and proliferate. However, sometimes the growth conditions may not be favorable to make new phages. The advantage of the lysogenic cycle is that the prophage can remain latent until conditions become favorable to make new phages. Figure 19.10  The loop domains are held in place by proteins that bind to the DNA at the bottoms of the loops. The proteins also bind to each other. Figure 19.11  Bacterial chromosomes and plasmids are similar in that they are both circular DNA molecules. However, bacterial chromosomes are usually much longer than plasmids and carry many more genes. Also, bacterial chromosomes tend to be more compacted due to the formation of loop domains and DNA supercoiling. Figure 19.12  In 16 hours, there will be 32 doublings. So, 232 = 4,294,967,296. (The actual number would be much less because the cells would deplete the growth media and grow more slowly than the maximal rate.) Figure 19.15  Yes. The two strains would have mixed together, allowing them to conjugate. Therefore, there would have been colonies on the plates. Figure 19.16  During conjugation, only one strand of the DNA from an F factor is transferred from the donor to the recipient cell. The single-stranded DNA in both cells is then used as a template to create double-stranded F factor DNA in both cells. Figure 19.18  Transduction is not a normal part of the phage life cycle. It is a mistake in which a piece of the bacterial chromosome is packaged into a phage coat and is then transferred to another bacterial cell.

Core Skills: Connections Figure 19.4  Viral release occurs via a budding process in which a membrane vesicle is formed that surrounds the capsid. Similarly, exocytosis involves the formation of a membrane vesicle that encloses some type of cargo. Figure 19.9  A nucleoid is not a membrane-bound organelle. It is simply a site where a bacterial chromosome is found. A cell nucleus in a eukaryotic cell has an envelope with a double membrane. Figure 19.17  Griffiths was able to show that genetic material was transferred to type R bacteria, which converted them to type S. This occurred via transformation. Later, Avery, MacLeod, and McCarty determined that DNA was the material that was being transferred.

Feature Investigation Questions 1. Lederberg and Tatum were testing the hypothesis that genetic material could be transferred from one bacterial strain to another. 2. The experimental growth medium lacked particular amino acids and biotin. The mutant strains were unable to synthesize these particular substances. Therefore, they were unable to grow due to the lack of the necessary nutrients. The two strains used in the experiment each lacked the ability to make two essential nutrients necessary for growth. The appearance of colonies growing on the experimental growth medium indicated that some bacterial cells had acquired the functional genes in place of the two mutations they carried. By acquiring these functional genes, they gained the ability to synthesize the essential nutrients. 3. Davis placed samples of the two bacterial strains in different arms of a U-tube. A filter allowed the free movement of the liquid in which the bacterial cells were suspended, but prevented actual contact between the bacterial cells. After incubating the strains taken from the U-tube, Davis found that gene transfer did not take place. He concluded that physical contact between cells of the two strains was required for gene transfer.

Test Yourself

1. c  2. e  3. c  4. b  5. e  6. a  7. d  8. d  9. b  10. c

Conceptual Questions 1. Viruses are similar to living cells in that they contain a genetic material that provides a blueprint to make new viruses. However, viruses are not composed of cells, and by themselves, they do not carry out metabolism, use energy, maintain homeostasis, or even reproduce. A virus or its genetic material must be taken up by a living cell to replicate. 2. Conjugation involves direct physical contact between two bacterial cells in which a donor cell transfers a strand of DNA to a recipient cell.

APPENDIX B

2. The individual probabilities are as follows: AA = 0.25; bb = 0.5; CC = 0.5; and Dd = 0.5. These are determined by making small Punnett squares. We use the product rule to calculate the probability of AAbbCCDd = (0.25)(0.5)(0.5)(0.5) = 0.03125, or 3.125%.

A-11

A-12

APPENDIX B

Transformation occurs when a bacterium takes up a DNA fragment from the environment, which may have come from a dead bacterium. Transduction occurs when a bacteriophage that has infected a bacterial cell breaks up the chromosome, and a fragment of bacterial chromosomal DNA is incorporated into a newly made bacteriophage. It then transfers this fragment of DNA to a recipient bacterial cell. 3. Horizontal gene transfer is the transfer of genes from an organism to another organism that is not the offspring of the first organism. These acquired genes sometimes promote survival and therefore may have an evolutionary advantage. Such genes may even lead to the formation of new species. From a medical perspective, an important example of horizontal gene transfer is when one bacterium acquires a resistance gene from another bacterium and becomes resistant to an antibiotic. This phenomenon is making it increasingly difficult to treat a wide variety of bacterial diseases.

Chapter 20

2. Both types of genes encode transcription factors that bind to the DNA and regulate the expression of other genes. The effects of Hox genes determine the characteristics of certain regions of the body, whereas the myoD gene is cell-specific—it causes a cell to become a skeletal muscle cell. 3. Maternal effect genes control the formation of body axes, such as the anteroposterior and dorsoventral axes. Next, the segmentation genes divide the embryo into segments, though visible segments are lost in many animal species at later stages of development. Finally, the homeotic genes determine the characteristics of each segment.

Chapter 21

Concept Checks

Figure 20.4  If apoptosis did not occur, the fingers would be webbed.

Figure 21.3  The insertion of chromosomal DNA into the vector disrupts the lacZ gene, thereby preventing the expression of β-galactosidase. The functionality of lacZ can be determined by providing the growth medium with a colorless compound, X-Gal, which is cleaved by β-galactosidase into a blue dye. Bacterial colonies containing recircularized vectors form blue colonies, whereas colonies containing recombinant vectors carrying a segment of chromosomal DNA will be white.

Figure 20.8  The larva would have anterior structures at both ends and would lack posterior structures such as a spiracle.

Figure 21.5  The 600-bp fragment will be closer to the bottom. Smaller pieces travel faster through the gel.

Figure 20.9  The Bicoid protein functions as a transcription factor that promotes the formation of anterior structures. Its function is highest in the anterior end of the zygote.

Figure 21.6  The primers are complementary to sequences at each end of the DNA region to be amplified.

Figure 20.14  The last abdominal segment would have legs!

Figure 21.8  If a ddNTP is added to a growing DNA strand, the strand can no longer grow because the 3′ —OH group, the site of attachment for the next nucleotide, is missing.

Concept Checks Figure 20.3  Cell division and cell migration are common in the early stages of development, whereas cell differentiation and apoptosis are more common as tissues and organs start to form.

APPENDIX B

Figure 20.18  Stem cells can divide, and the daughter cells can differentiate into specific cell types. Figure 20.20  Hematopoietic stem cells are multipotent. Figure 20.24  The pattern would be sepal, petal, stamen, stamen. Figure 20.23  Stem cells in plants are found in meristems, which are located at the tips of roots and shoots.

Core Skills: Connections Figure 20.5  Some cell surface receptors recognize signals that convey positional information. After the signal binds to this type of receptor, a signal transduction pathway is activated that may cause a cell to divide, migrate, differentiate, or undergo apoptosis. Figure 20.17  As the number of Hox genes increases, the body plan of the animal becomes more complex.

Feature Investigation Questions 1. The researchers were interested in the factors that cause cells to differentiate. In this particular study, they were attempting to identify the gene(s) involved in the differentiation of muscle cells. 2. Using genetic technology, the researcher compared the gene expression in cells that could differentiate into muscle cells with the gene expression in cells that could not differentiate into muscle cells. Though many genes were expressed in both, the researchers were able to identify three genes that were expressed in muscle cell lines that were not expressed in nonmuscle cell lines. 3. Again, using genetic technology, each of the candidate genes was introduced into a cell that normally did not give rise to skeletal muscle. This procedure was used to test whether or not the gene played a key role in muscle cell differentiation. If the genetically engineered cell gave rise to muscle cells, the researchers would have evidence that that particular candidate gene was involved in muscle cell differentiation. Of the three candidate genes, only one was shown to be involved in muscle cell differentiation. When the MyoD gene was expressed in fibroblasts, these cells differentiated into skeletal muscle cells.

Test Yourself

1. c  2. d  3. e  4. b  5. c  6. e  7. a  8. a  9. b  10. d

Conceptual Questions 1. a. This abnormality is consistent with a mutation in a segmentation gene, such as a gap gene. b. This abnormality is consistent with a mutation in a homeotic gene because the characteristics of a particular segment have been changed.

Figure 21.9  A fluorescent spot identifies a cDNA that is complementary to a particular DNA sequence. Because the cDNA was generated from mRNA, the fluorescence identifies a gene that has been transcribed in a particular cell type under a given set of conditions. Figure 21.10  The sgRNA is composed of two different components of the bacterial defense system, crRNA and tracrRNA, which have been linked together. Figure 21.12  One reason is that more complex species tend to have more genes. A second reason is that species vary with regard to the amount of repetitive DNA sequences in their genomes. Figure 21.18  Retrotransposons. A single retrotransposon can be transcribed into multiple copies of RNA, which can be converted to DNA by reverse transcriptase, and inserted into multiple sites in the genome.

Core Skills: Connections Figure 21.2  Plasmids are small, circular DNA molecules that exist independently of the bacterial chromosome. They have their own origin of replication. Many plasmids carry genes that convey some type of selective advantage to the host cell, such as antibiotic resistance. Figure 21.14  The proteins produced by family members at early stages of development (embryonic and fetal stages) have a higher affinity for oxygen than the proteins produced in an adult. This allows the embryo and fetus to obtain oxygen from the mother’s bloodstream.

Feature Investigation Questions 1. The goal of the experiment was to sequence the entire genome of Haemophilus influenzae. By conducting this experiment, the researchers would have information about genome size and the types of genes the bacterium has. 2. If you divide 20 by 4.1, this equals 4.9. The value of 4.9 represents m in the equation: P = e−m. If you substitute 4.1 for m into the equation and solve for P. the probability P equals 0.0074 or 0.74%. Therefore, only 0.74% would be left unsequenced, which is less than 1%. 3. The researchers were successful in sequencing the entire genome of the bacterium. The genome size was determined to be 1,830,137 base pairs, with a predicted 1,743 structural genes. The researchers were also able to predict the function of many of these genes. More importantly, the results were the first complete genomic sequence of a living organism.



APPENDIX B

Test Yourself

Test Yourself

Conceptual Questions

Conceptual Questions

1. A ddNTP is missing an oxygen at the 3′ position. This prevents the further growth of a DNA strand, thereby causing chain termination. 2. a. yes b. No, it’s only one chromosome in the nuclear genome. c. Yes, it’s corn’s nuclear genome. Corn also has a mitochondrial genome and a chloroplast genome. d. yes 3. The genome contains the information for the production of cellular proteins; it is a blueprint. The production of proteins is largely responsible for determining cellular characteristics, which, in turn, are largely responsible for determining an organism’s traits. In addition, the genome also encodes many non-coding RNAs that perform a variety of different functions.

Chapter 22

Concept Checks Figure 22.2  A single organism does not evolve. Populations may evolve from one generation to the next due to differences in reproductive success. Figure 22.7  Due to a changing global climate, the island fox became isolated from the mainland species. Over time, natural selection resulted in adaptations for the population on the island and eventually resulted in a new species with characteristics that are somewhat different from those of the mainland species. Figure 22.8  Many answers are possible. One example is the wing of a bird and the wing of a bat. Figure 22.11  The magnitudes of traits are changing. For example, in the breeds of dogs, the lengths of legs, body size, and so on, are quite different. Artificial selection is often aimed at changing the relative sizes of body parts or the amount of something, such as oil content. Figure 22.14  Orthologs have similar gene sequences because they are derived from the same ancestral gene. The sequences are not identical because after the species diverged, each one accumulated different random mutations that changed their sequences. Figure 22.16  Humans have one large chromosome 2, but this chromosome is divided into two separate chromosomes in the other three species. In chromosome 3, the banding patterns among humans, chimpanzees, and gorillas are very similar, but the orangutan has a large inversion that flips the arrangement of bands in the centromeric region.

Core Skills: Connections

1. d  2. d  3. b  4. b  5. b  6. d  7. c  8. d  9. d  10. e

1. Some random mutations result in a phenotype with greater reproductive success. If this occurs, natural selection results in a greater proportion of such individuals in succeeding generations. 2. The process of convergent evolution produces two different species from different lineages that show similar characteristics because they occupy similar environments. An example is the long snout and tongue of both the giant anteater, found in South America, and the echidna, found in Australia. These structures enable these animals to feed on ants, but the two structures evolved independently. These observations support the idea that evolution results in adaptations to particular environments. 3. Homologous structures are two or more structures that are similar because they are derived from a common ancestor. An example is the set of bones that is found in the human arm, turtle arm, bat wing, and whale flipper. The forearms in these species have been modified to perform different functions. This supports the idea that all of these animals evolved from a common ancestor by descent with modification.

Chapter 23

Concept Checks Figure 23.3  Over the short run, alleles that confer better fitness in the warmer climate would be favored and increase in frequency, perhaps enhancing diversity. Over the long run, however, an allele that confers high fitness in the homozygous state may become monomorphic, thereby reducing genetic diversity. Figure 23.4  Stabilizing selection eliminates alleles that result in phenotypes that deviate significantly from the average phenotype. For this reason, it tends to decrease genetic diversity. Figure 23.6  If malaria was eradicated, there would be no selective advantage for the heterozygote. The HS allele would eventually be eliminated because the HSHS homozygote has a lower fitness. Directional selection would occur. Figure 23.7  Courtship songs are likely to be part of intersexual selection. Such traits are likely to be involved in mate choice. Figure 23.11  The bottleneck effect tends to decrease genetic diversity. This may eliminate adaptations that promote survival and reproductive success. Therefore, the bottleneck effect makes it more difficult for a population to survive. Figure 23.13  Migration results in gene flow, which tends to make the allele frequencies in neighboring populations more similar to each other. It also promotes genetic diversity by introducing new alleles into populations.

Core Skills: Connections

Figure 22.15  The three mechanisms of horizontal gene transfer between bacterial species are conjugation, transformation and transduction.

Figure 23.12  There are lots of possibilities. The idea is that you are changing one codon to another codon that specifies the same amino acid. For example, changing a codon from GGA to GGG is likely to be neutral because both codons specify glycine.

Feature Investigation Questions

Feature Investigation Questions

1. The island has a moderate level of isolation but is located near enough to the mainland to have some migrants. The island is an undisturbed habitat, so the researchers would not have to consider the effects of human activity on the study. Finally, the island had an existing population of ground finches that would serve as the subjects of the study over many generations. 2. First, the researchers were able to show that beak depth is a genetic trait that has variation in the population. Second, the depth of the beak is an indicator of the types of seeds the birds can eat. The birds with larger beaks can eat larger and drier seeds; therefore, changes in the types of seeds available could act as a selective force on the bird population. During the study period, annual changes in rainfall occurred, which affected the seed sizes produced by the plants on the island. In the drier year, fewer small seeds were produced, so the birds would have to eat larger, drier seeds. 3. The researchers found that following the drought in 1977, the average beak depth in the finch population increased. This indicated that birds with larger beaks were better able to adapt to the environmental changes due to the drought and produce more offspring. This is direct evidence of the phenomenon of natural selection.

1. The males of the two species of cichlids used in the experiment are distinguishable by coloration, and the researchers were testing the hypothesis that the females make mate choices based on this variable. 2. Individual females were placed in an aquarium that also contained one male from each species. The males were held in separate enclosures to limit their movement but allow the female to see each of the males. The researchers recorded the courtship behavior between the female and males and the number of positive encounters between the female and each of the different males. This procedure was conducted under normal lighting and under monochromatic lighting that obscured the coloration differences between the males of the two species. Comparing the behavior of the females under normal light conditions and monochromatic light conditions allowed the researchers to determine the importance of coloration in mate choice. 3. The researchers found that the female was more likely to select a mate from her own species in normal light conditions. However, under monochromatic light conditions, the species-specific mate choice was not observed. Females were as likely to choose males of the other species as they were males of their own species. This indicated that coloration is an important factor in mate choice in these species of fish.

APPENDIX B

1. d  2. b  3. b  4. b  5. c  6. e  7. e  8. a  9. c  10. e

A-13

A-14

APPENDIX B

Test Yourself

1. d  2. c  3. c  4. e  5. b  6. c  7. b  8. d  9. b  10. a

Conceptual Questions 1. The frequency of the disease is a genotype frequency because it represents individuals with the disease. If we let q2 represent the genotype frequency, then q equals the square root of 0.04, which is 0.2. If q = 0.2, then p = 1 –q, which is 0.8. The frequency of heterozygous carriers is 2pq, which is 2(0.8) (0.2) = 0.32, or 32%.

APPENDIX B

2. Directional selection—In this pattern of natural selection, individuals with an extreme phenotype are more likely to survive and reproduce. As a result, the extreme phenotype will become predominant in the population. In addition to selecting for a certain phenotype, the opposite extreme phenotype is removed from the gene pool. Stabilizing selection—This pattern of natural selection favors individuals with intermediate phenotypes, whereas individuals with extreme phenotypes are less likely to reproduce. Stabilizing selection tends to prevent major changes in the phenotypes prevalent in populations. Disruptive selection—This pattern of natural selection favors both extremes and removes the intermediate phenotype. It is also known as diversifying selection. Balancing selection—This pattern of natural selection results in a balanced polymorphism in which two or more alleles are stably maintained in a population. It can occur as a result of heterozygote advantage, as with the sickle cell allele, or negative frequency-dependent selection, as in certain prey populations. Sexual selection—This is a type of natural selection that is directly associated with reproductive success. It can occur by any of the previous four mechanisms. Male coloration in African cichlids is an example. 3. Genetic drift involves random changes in the genetic composition of a population from one generation to the next. Neutral changes in DNA sequences may happen randomly, and these are most likely to accumulate in a population due to genetic drift. This is evolution at the level of DNA, but it does not act upon phenotype.

Chapter 24

Concept Checks Figure 24.1  There are a lot of possibilities. Certain grass species look quite similar. Elephant species look very similar. And so on. Figure 24.3  Temporal isolation is an example of a prezygotic isolating mechanism. Because the two species breed at different times of the year, hybrid zygotes are not produced. Figure 24.5  Hybrid sterility is a type of postzygotic isolating mechanism. A hybrid is produced by the interbreeding of the two species, but it is sterile. Figure 24.11  The offspring would inherit 16 chromosomes from G. tetrahit and anywhere from 8 to 16 from the hybrid. So it would have 24 to 32 chromosomes. The hybrid parent would always pass on the 8 chromosomes that are found in pairs. With regard to the 8 chromosomes not found in pairs, it could pass on 0 to 8 of them. Figure 24.12  The insects on a particular type of host plant would tend to breed with each other, and natural selection would favor the development of traits that are an advantage for feeding on that host. Over time, the accumulation of genetic changes may lead to reproductive isolation between the populations of insects feeding on different hosts. Figure 24.14  If the Gremlin gene was underexpressed, less gremlin protein would be produced. Because the gremlin protein inhibits apoptosis, more cell death would occur, and the result would probably be smaller feet, possibly not webbed.

Feature Investigation Questions 1. Podos hypothesized that the morphological changes in the beaks would also affect the birds’ songs. A male bird’s song is an important component for mate choice. If changes in the beak alter the song, reproductive ability will be affected. Podos suggested that changes in the beak morphology could thus lead to reproductive isolation among the finches. 2. Podos first caught male birds in the field and collected data on beak size. The birds were banded for identification and released. Later, the banded birds’ songs were recorded and analyzed for range of frequencies and trill rates. The results were then compared with similar data from other species of birds to determine if beak size constrained the frequency range and trill rate of the song. 3. The results of the study did indicate that natural selection acting on beak size due to changes in diet could lead to changes in song. Considering the importance of bird song to mate choice, the changes in the songs could also lead to reproductive isolation. The phrase “by-product of adaptation” refers to changes in phenotype that are not directly acted on by natural selection. In the case of the Galápagos finches, the changes in beak size were directly related to diet; however, as a consequence of that selection, the song pattern was also altered. The change in song pattern was a by-product.

Test Yourself

1. b  2. b  3. e  4. d  5. c  6. a  7. b  8. d  9. c  10. c

Conceptual Questions 1. Prezygotic isolating mechanisms prevent the formation of a zygote. An example is mechanical isolation, the incompatibility of genitalia. Postzygotic isolating mechanisms act after the formation of the zygote. An example is inviability of the hybrid that develops. (Other examples shown in Figure 24.2 are also correct.) Postzygotic mechanisms are more costly because some energy is expended for the formation of a zygote and its subsequent growth. 2. The concept of gradualism suggests that each new species evolves continuously over long spans of time (Figure 24.13a). The principal idea is that large phenotypic differences that produce new species are due to the accumulation of many small genetic changes. According to the concept of punctuated equilibrium (Figure 24.13b), species exist relatively unchanged for many generations. During this period, the species is in equilibrium with its environment. These long periods of equilibrium are punctuated by relatively short periods during which evolution occurs at a far more rapid rate. This rapid evolution is caused by relatively few genetic changes. 3. One example involves the Hox genes, which control morphological features along the anteroposterior axis in animals. An increase in the number of Hox genes during evolution is associated with an increase in body complexity and may have spawned many different animal species.

Chapter 25

Concept Checks Figure 25.2  A phylum is broader than a family. Figure 25.3  Yes. They can have many common ancestors, depending on how far back you go in the tree. For example, dogs and cats have a common ancestor that gave rise to mammals, and an older common ancestor that gave rise to vertebrates. The most recent common ancestor is the point at which two species diverged from each other.

Figure 24.17  The tip of the mouse’s tail might have a mouse eye!

Figure 25.4  An order is a smaller taxon that would have a more recent common ancestor.

Core Skills: Connections

Figure 25.9  A hinged jaw is the character common to the salmon, lizard, and rabbit, but not to the lamprey.

Figure 24.2  Female choice is a prezygotic isolating mechanism. Figure 24.7  The Hawaiian Islands have many different ecological niches that can be occupied by birds. The founding population evolved to occupy those niches, thereby evolving into many different species of honeycreepers. Figure 24.15 The Hox genes expressed along the anteroposterior axis during early embryonic development are homeotic genes. In insects that contain discrete body segments, each Hox gene determines the structures that will ultimately form in those segments. Although more complex animals such as mammals do not display discrete segments, the expression of the Hox genes controls what structures will form along the anteroposterior axis.

Figure 25.10  The change of G2 to A is common to species A, B, and C, but not to species G. Figure 25.12  The kiwis are found in New Zealand. Surprisingly, however, kiwis are more closely related to Australian and African flightless birds than they are to moas, which were found in New Zealand. Figure 25.15  Monophyletic groups are defined on the assumption that a particular group of species descended from a common ancestor. If horizontal gene transfer has occurred, not all of the genes carried by the species in such a group were inherited from the common ancestor, thus muddling the concept of monophyletic groups.



APPENDIX B

A-15

Core Skills: Connections

Core Skills: Connections

Figure 25.1  The domains Bacteria and Archaea have organisms with prokaryotic cells.

Figure 26.7  First, the process of membrane invagination created the nuclear envelope. Second, endocytosis may have enabled an ancient archaeon to take up a bacterial cell. Over time, bacterial genes were transferred to the nucleus, which gave rise to the eukaryotic nuclear genome. An engulfed bacterial cell eventually became a mitochondrion, and an engulfed cyanobacterial cell became a chloroplast in algae and plants.

Feature Investigation Questions 1. Molecular paleontology is the sequencing and analysis of DNA obtained from extinct species. Tissue samples from specimens of extinct species may contain DNA molecules that can be extracted, amplified, and sequenced. The DNA sequences can then be compared with those of living species to study evolutionary relationships between modern and extinct species. The researchers extracted DNA from tissue samples of moas, extinct flightless birds that lived in New Zealand. The DNA sequences from the moas were compared with the DNA sequences of modern species of flightless birds to determine the evolutionary relationships of this particular group of birds. 2. The researchers compared the DNA sequences of the extinct moas and modern kiwis of New Zealand to the emu and cassowary of Australia and New Guinea, the ostrich of Africa, and rheas of South America. All of the birds are flightless. By selecting these birds, the researchers could look for similarities between flightless birds over a large geographic area. 3. The DNA sequences were very similar among the different species of flightless birds. Interestingly, the sequences of the kiwis of New Zealand were more similar to those of the modern species of flightless birds found on other landmasses than they were to those of the moas found in New Zealand. The researchers constructed a new phylogenetic tree that suggests that kiwis are more closely related to the emu, cassowary, and ostrich than to moas. Also, based on the results of this study, the researchers suggested that New Zealand was colonized twice by ancestors of flightless birds. One ancestor gave rise to the now-extinct moas. The other ancestor gave rise to the kiwis.

Test Yourself

1. c  2. d  3. e  4. d  5. b  6. d  7. b  8. b  9. c  10. e

Conceptual Questions 1. The scientific name of every species has two parts, which are the genus name and the species epithet. The genus name is always capitalized, but the species name is not. Both names are italicized. An example is Canis lupus. 2. If neutral mutations occur at a relatively constant rate, they act as a molecular clock with which to measure evolutionary time. Genetic diversity between species that is due to neutral mutations gives an estimate of the time elapsed since the last common ancestor. A molecular clock can provide a timescale for a phylogenetic tree. 3. Morphological analysis focuses on structural features of extinct and modern species. Many traits are analyzed to obtain a comprehensive picture of how species may be related. Convergent evolution leads to similar traits that arise independently in different species as they adapt to similar environments. Convergent evolution can, therefore, cause errors if a researcher assumes that a particular trait arose only once and that all species having the trait have the same common ancestor.

Chapter 26

Concept Checks Figure 26.2  In a sedimentary rock formation, the layer at the bottom is usually the oldest. Figure 26.3  For this time frame, you could analyze the relative amounts of potassium-40 and argon-40, rubidium-87 and strontium-87, uranium-235 and lead-207, or uranium-238 and lead-206. Figure 26.9  Most animal species, including fruit flies, fishes, and humans, exhibit bilateral symmetry. Figure 26.16  Defining features of primates are grasping hands, forward-facing eyes to facilitate binocular vision, a large brain, digits with flat nails instead of claws, and complex social behavior including well-developed parental care.

Figure 26.13  Two key features are mammary glands and hair. Mammals also have specialized teeth, external ears, enlarged skulls that harbor highly developed brains, and four-chambered hearts. Mammals are typically endothermic.

Test Yourself

1. c  2. e  3. a  4. d  5. e  6. c  7. b  8. a  9. d  10. d

Conceptual Questions 1. The relative ages of fossils can be determined by their locations in a sedimentary rock formation. Older fossils are found in lower layers. A common way to determine the ages of fossils is via radiometric dating, which is often conducted on a sample of igneous rock from the vicinity of the fossil. A radioisotope is an unstable isotope of an element that decays spontaneously, releasing radiation at a constant rate. The half-life is the length of time required for a radioisotope to decay to exactly one-half of its initial quantity. To determine the age of an igneous rock (and that of a fossil found near it), scientists can measure the amounts of a given radioisotope and its decay product. 2. The process of membrane invagination led to formation of the nuclear envelope. In addition, endocytosis may have enabled an ancient archaeon to take up a bacterial cell. Over time, bacterial genes were transferred to the nucleus, which gave rise to the eukaryotic nuclear genome. An engulfed bacterial cell eventually became a mitochondrion, and an engulfed cyanobacterial cell became a chloroplast in algae and plants. 3. Several examples are described in this chapter. In some cases, catastrophic events like volcanic eruptions and glaciers caused mass extinctions, which allowed new species to evolve and flourish. In other cases, changing environmental conditions (for example, changes in temperature and moisture) played key roles. One interesting example is adaptation to terrestrial environments. Plant species evolved seeds that are desiccation resistant, whereas animal species evolved eggs with shells. Mammalian species evolved internal gestation.

Chapter 27

Concept Checks Figure 27.11  The motion of the stiff filament of a prokaryotic flagellum is more like that of a propeller shaft than the flexible arms of a human swimmer. Figure 27.15  Endospores allow bacterial cells to survive treatments and environmental conditions that would kill ordinary cells.

Core Skills: Connections Figure 27.6  Like the bacterium Magnetospirillum magnetotacticum, birds such as homing pigeons and migratory fishes such as rainbow trout have the capacity to sense and respond to magnetic fields. Figure 27.12  The microscopic protist Giardia intestinalis uses flagella to move within the human small intestine.

Feature Investigation Questions 1. Many bacteria are known to produce organic compounds that function as antibiotics, which are potential food sources for chemoheterotrophic bacteria. 2. Researchers isolated and cultivated bacteria from different types of soils, then grew the cultured bacteria on media that contained one of several common types of antibiotics as the only source of organic food.

Test Yourself

1. c  2. b  3. c  4. d  5. a  6. a  7. b  8. e  9. d  10. d

Conceptual Questions 1. Small cell size and simple division processes allow many bacteria to increase in number much more rapidly than eukaryotes can. This rapid population growth helps to explain why food can spoil so quickly and why infections can spread very rapidly within the body. Other factors also influence these rates.

APPENDIX B

Figure 25.13  There are lots of possibilities. The changes need to be ones that change one codon to another codon that specifies the same amino acid. For example, changing a codon from GGA to GGG is likely to be neutral because both codons specify glycine.

A-16

APPENDIX B

2. Pathogen populations naturally display genetic variation in their susceptibility to antibiotics. When such populations are exposed to antibiotics, even if only a few cells are initially resistant, the number of resistant cells will eventually increase and such cells could come to dominate natural populations. 3. Humans and cyanobacteria. When humans pollute natural waters with high levels of fertilizers originating from sewage effluent or crop field runoff, cyanobacterial populations are able to grow large enough to produce harmful blooms.

Chapter 28

Concept Checks Figure 28.7  After food particles are collected in a feeding groove, they are enclosed by membrane vesicles and then digested by enzymes. Figure 28.9  The intestinal parasite Giardia intestinalis is transmitted from one person to another via fecal wastes, whereas the urogenital parasite Trichomonas vaginalis can be transmitted by sexual activity. Figure 28.17  Flagellar hairs function like oars, helping to pull the cell through the water. Figure 28.18  Kelps are harvested for use in the production of industrially useful materials. In addition, they nurture fishes and other wildlife of economic importance.

APPENDIX B

Figure 28.21  Genes that encode cell adhesion and extracellular matrix proteins are likely essential to modern choanoflagellates’ ability to attach to surfaces, where they feed. Similar proteins are involved in the formation of multicellular tissues in animals. Evolutionary biologists would say that ancient choanoflagellates were preadapted for the later evolution of multicellular tissues in early animals. Figure 28.24  Cysts allow protists to survive conditions that are not suitable for growth. One such condition would be the dry or cold environment outside a parasitic protist’s warm, moist host tissues. Figure 28.29  Gametes of Plasmodium falciparum undergo fusion to produce zygotes while in the mosquito host.

Chapter 29

Concept Checks Figure 29.4  Fungal hyphae growing into a substrate having a much higher solute concentration will tend to lose cell water to the substrate, a process that could inhibit fungal growth. This process explains how drying or salting foods helps to protect them from fungal degradation and thus preserves them. Figure 29.6  You might filter the air entering the patient’s room and limit the entry of visitors and materials that could introduce fungal spores from the outside environment.

Core Skills: Connections Figure 29.7 The Saccharomyces cerevisiae genome is only 12 million base pairs in size, relatively small for a eukaryote. Figure 29.10  Amanitin, by interfering with the function of RNA polymerase II, inhibits transcription in eukaryotic cells, including those of humans.

Feature Investigation Questions 1. Plants growing on soils with temperatures up to 65°C would be expected to have fungal endophytes that aid in heat stress tolerance. 2. The investigators cured some of their Curvularia protuberata cultures of an associated virus; then they compared the survival of plants infected with fungal endophytes that had virus versus fungal endophytes lacking virus under conditions of heat stress. Only plants infected with fungal endophytes that possessed the virus were able to survive growth on soils with a high temperature. 3. The fungus C. protuberata might be used to confer heat stress tolerance to crop plants, as the investigators demonstrated in tomato.

Test Yourself

1. c  2. b  3. a  4. b  5. a  6. d  7. b  8. c  9. e  10. a

Conceptual Questions

Figure 28.5  In sponges, amoebocytes, which move similarly to amoeboid protists, carry food to other cells.

1. Fungi are like animals in being heterotrophic, having absorptive nutrition, and storing surplus organic compounds in their cells as glycogen. Fungi are like plants in having rigid cell walls and reproducing by means of walled spores that are dispersed by wind, water, or animals.

Feature Investigation Questions

2. Toxic or hallucinogenic compounds likely help to protect the fungi from organisms that would consume them.

Core Skills: Connections

1. Natural growths of this alga were already known to resist microbial attack and breakdown. 2. This process is commonly used to release tough fossils from rock.

Test Yourself

1. c  2. a  3. b  4. b  5. e  6. b  7. e  8. d  9. b  10. c

Conceptual Questions 1. Protists are amazingly diverse, reflecting the occurrence of extensive adaptive radiation after the origin of eukaryotic cells, widespread occurrence of endosymbiosis, and adaptation to many types of moist habitats, including the tissues of animals and plants. As a result of this extensive diversity, protists cannot be classified into a single kingdom or phylum. 2. Several protists, including the apicomplexans Cryptosporidium parvum and Plasmodium falciparum and the kinetoplastids Leishmania major and Trypanosoma brucei, cause many cases of illness around the world, but few treatments are available, and organisms often evolve drug resistance. Genomic data allow researchers to identify metabolic features of these parasites that are not present in humans and are therefore good targets for development of new drugs. An example is provided by metabolic pathways of the apicoplast, a reduced plastid that is present in cells of the genus Plasmodium. Because the apicoplast plays essential metabolic roles in the protist but is absent from humans, drugs that disable apicoplast metabolism would kill the parasite without harming the human host. 3. Most protist cells cannot survive outside moist environments, but cysts have tough walls and dormant cytoplasm, allowing them to persist in habitats that are unfavorable for growth. While cysts play important roles in the asexual reproduction and survival of many protists, they also allow protist parasites such as Entamoeba histolytica (the cause of amoebic dysentery) to spread to human hosts who consume food or water that has been contaminated with cysts. Widespread contamination can cause illness or disease in thousands of people at a time.

3. Many fungi degrade organic compounds, thereby contributing to decomposition, which recycles materials. Some fungi trap and consume the bodies of small animals, such as nematodes. Some fungi cause diseases of plants or animals, which also helps to control populations in nature.

Chapter 30

Concept Checks Figure 30.15  Mycorrhizal fungi provide their plant partners with water and minerals absorbed from a much larger volume of soil than plant roots can exploit on their own.

Feature Investigation Questions 1. Investigators fed the experimental mice germ-free food so that microbes normally found in food would not be present, allowing the effects of the fecal transplants to be more easily detected. In this way, the investigators removed a potentially confounding factor from their experiment. 2. Microbes from healthy children enabled the mice receiving them to grow larger than mice receiving microbes from stunted children. This outcome was a first clue that the microbes directly affected child growth, a connection that was established by additional studies.

Test Yourself

1. c  2. d  3. c  4. c  5. b  6. e  7. e  8. b  9. c  10. d

Conceptual Questions 1. Ice microbiomes include colored surface films of algae that absorb solar radiation, thereby reducing the amount reflected into space. The absorption of solar radiation has a warming effect on the physical environment, but could also influence other organisms present. Soil microbiomes contain diverse prokaryotic and eukaryotic species, including nitrogen-fixing bacteria and mycorrhizal fungi that aid plant growth.



APPENDIX B

3. Mycorrhizal fungi, which are components of many plant root microbiomes, mobilize and transport phosphorus and other minerals to plant roots. This improves the plant’s ability to obtain minerals from the environment.

Chapter 31

Concept Checks Figure 31.5  Wind speed varies, so if the sporangium released all the spores at the same time and there were little or no wind, the spores would not travel very far and the resulting offspring might have to compete with the parent plant for scarce resources. Releasing spores gradually means that some spores may encounter strong gusts of wind that will carry them long distances, reducing competition with the parent. Figure 31.12  During the Carboniferous period (Coal Age), atmospheric oxygen levels reached historically high levels, enough to supply the large needs of giant insects, which obtain oxygen by diffusion. Figure 31.17  Larger sporophytes are able to capture more resources for use in producing larger numbers of progeny and therefore increase the fitness of ferns and seed plants. Figure 31.22  Although some angiosperm seeds, such as those of corn and coconut, contain abundant endosperm, many angiosperm embryos consume most or all of the nutritive endosperm during their development. Figure 31.24  Because the lacy integument of R. heinzelinii does not completely enclose the megasporangium, it probably did not function to protect the megasporangium before fertilization or act as an effective seed coat after fertilization, as do the integuments of modern seed plants. However, the lacy integument of R. heinzelinii might have retained the megasporangium on the parent sporophyte during the period of time when nutrients flowed from parent to developing ovule and seed. That function would prevent megasporangia from dropping off the parent plant before fertilization occurred, allow the parent plant to provide nutrients needed during embryo development, and allow seeds time to absorb and store more nutrients from the parent. Such a function would illustrate how one mutation having a positive reproductive benefit can lay the foundation for subsequent mutations that confer additional fitness. R. heinzelinii illustrates a first step in the multistage evolutionary process that gave rise to modern seeds.

Core Skills: Connections Figure 31.23  Like the plant seed, the amniotic egg characteristic of many animals provides protection and nutrients to the developing embryo.

Feature Investigation Questions 1. The experimental goals were to determine the rate at which organic molecules produced by gametophyte photosynthesis were able to move into sporophytes and to investigate the effect of sporophyte size on the amount of organic molecules transferred from the gametophyte. 2. The investigators shaded sporophytes with blackened glass tubing to ensure that all of the radioactive organic molecules detected in sporophytes at the end of the experiment came originally from the gametophytes. 3. The investigators measured the amount of radioactivity in gametophytes and sporophytes, and in sporophytes of different sizes. These measurements indicated the relative amounts of labeled organic compounds that were present in different plant tissues.

Test Yourself

1. c  2. d  3. d  4. e  5. b  6. a  7. c  8. e  9. c  10. b

Conceptual Questions 1. Streptophyte algae, particularly the complex genera Chara and Coleochaete, share many features of structure, reproduction, and biochemistry with land plants. Examples include cell division similarities, plasmodesmata, and sexual reproduction by means of flagellate sperm and eggs. 2. Bryophytes are well adapted for sexual reproduction when water is available for fertilization. Their green gametophytes efficiently transfer nutrients to developing embryos, enhancing their growth into sporophytes. Their sporophytes are able to produce many genetically diverse spores as the result of meiosis and effectively disperse these spores by means of wind. 3. Vascular tissues allow tracheophytes to effectively conduct water from roots to stems and to leaves. Waxy cuticle helps prevent loss of water by evaporation

through plant surfaces. Stomata allow plants to achieve gas exchange under moist conditions and help them avoid losing excess water under arid conditions.

Chapter 32

Concept Checks Figure 32.4  The nitrogen-fixing cyanobacteria that often occur within the coralloid roots of cycads are photosynthetic organisms that require light. If coralloid roots grew underground, the cyanobacteria would not receive enough light to survive. Figure 32.10  Ways in which conifer leaves are adapted to resist water loss include low surface area/volume ratio, needle or scale shape, thick surface coating of waxy cuticle, and stomata that are recessed and are therefore less exposed to drying winds. Figure 32.12  Relatively wide vessels are commonly present in the water transport tissues of angiosperms and much less commonly in other plants. The vessels occasionally found in nonangiosperms are thought to have evolved independently from those of angiosperms. Figure 32.20  A large, showy perianth would not be useful to grass plants because they are wind pollinated; such a perianth would interfere with pollination in grasses. By not producing a showy perianth, grasses increase the chances of successful pollination and save resources that would otherwise be consumed during perianth development. Figure 32.24  The flower characteristics of Brighamia insignis shown in this figure (white color and deep, narrow nectar tubes) are consistent with pollination by a moth (see Table 32.2).

Core Skills: Connections Figure 32.2  Modern forests are dominated by seed plants, gymnosperms and angiosperms, whereas nonseed plants dominated Archaeopteris forests. Figure 32.8  The wind-dispersed seeds of the gymnosperm pine resemble the winddispersed fruits of the angiosperm maple in having winglike structures that enhance transport in air.

Feature Investigation Questions 1. The investigators obtained many samples from around the world because they wanted to increase their chances of finding as many species as possible. 2. Although cannabinoids are produced in glandular hairs that cover the plant surface, these compounds are most abundant on leaves near the flowers. Collecting such leaves reduces the chances that compounds might be missed by the analysis.

Test Yourself

1. d  2. a  3. e  4. e  5. b  6. d  7. e  8. c  9. d  10. e

Conceptual Questions 1. Refer to Figure 30.15 to see how plant biologists think stamens and pistils might have evolved from leaves that bore sporangia. Then consider how green leaves surrounding stamens and pistils might have been transformed into petals, sepals, or tepals. 2. Apple, strawberry, and cherry plants coevolved with animals that use the fleshy, sweet portion of the fruits as food and excrete the seeds, thereby dispersing them. Humans have sensory systems similar to those of the animal seed-dispersal agents and likewise are attracted by the same colors, odors, and tastes. 3. Unlike an apple flower, a sunflower is not a single flower, but rather is an inflorescence, a group of flowers. A pollinator visiting a compact inflorescence such as a sunflower head may be able to pollinate many flowers at the same time, thereby potentially producing many seeds per pollinator visit. Likewise, a seed disperser agent might be able to disperse more seeds per plant.

Chapter 33

Core Skills: Connections Figure 33.5  A shared derived character. Figure 33.10 Yellow.

Feature Investigation Questions 1. The researchers sequenced the complete gene that encodes small subunit rRNA from a variety of representative phyla of animals to determine their phylogenetic relationships, particularly the relationships of arthropods to other phyla.

APPENDIX B

2. One example of a host is the common, abundant nearshore green alga Cladophora, whose microbiota include nitrogen-fixing bacteria that aid host growth and obtain oxygen and organic molecules from the host.

A-17

APPENDIX B

2. The results indicated a monophyletic clade containing arthropods and nematodes. This clade was called the Ecdysozoa. The results of this study indicated that nematodes are more closely related to arthropods than was previously believed. 3. The fruit fly, Drosophila melanogaster, and the nematode, Caenorhabditis elegans, have been widely studied to understand early development. Under the traditional phylogeny, these two species were not considered to be closely related, so similarities in development were assumed to have arisen early in animal evolution. With the closer relationship indicated by this study, these similarities may have evolved after the divergence of the Ecdysozoan clade. This puts into question the applicability of studies of these organisms to the understanding of human biology.

Test Yourself

1. b  2. c  3. e  4. c  5. c  6. d  7. d  8. d  9. b  10. e

Figure 34.6  Having no specialized respiratory or circulatory system, flatworms obtain oxygen by diffusion. A flattened shape ensures that no cells are too far from the body surface. Figure 34.10  The lophophore functions as (1) a ciliary feeding device and (2) a respiratory organ. Figure 34.11  Technically, the hearts of most mollusks pump hemolymph into vessels and then into tissues. The hemolymph collects in open, fluid-filled cavities called sinuses, which flow into the gills and then back to the heart. This is known as an open circulatory system. Only closed circulatory systems pump blood, as occurs in the cephalopods.

Most with lophophore or trochophore larva

Ecdysis Protostome development

Radial symmetry

Bilateral symmetry Gain of mesoderm Tissues Multicellularity

KEY Critical innovations

Deuterostome development, endoskeleton

Common protist ancestor of animals and choanoflagellates

Chordata

Figure 34.30  In embryonic development, deuterostomes show radial cleavage and indeterminate cleavage, and the blastopore becomes the anus. (In protostomes, cleavage is spiral and determinate, and the blastopore becomes the mouth.)

Echinodermata

Bryozoa

Rotifera

Platyhelminthes

Figure 34.3  Sponges aren’t eaten by other organisms because they produce toxic chemicals and contain needle-like silica spicules that are hard to digest.

Figure 34.24  Two other key insect adaptations are the development of wings and an exoskeleton that reduced water loss and aided in the colonization of land.

Arthropoda

Concept Checks

Cnidaria and Ctenophora

APPENDIX B

Chapter 34

Figure 34.21  All arachnids have a body consisting of two tagmata: a cephalothorax and an abdomen. Insects have three tagmata: head, thorax, and abdomen.

Nematoda

3. They are paraphyletic since the group contains a common ancestor but not all of its descendants.

Figure 34.17  An annelid is segmented and possesses a true coelom, whereas a nematode is unsegmented and has a pseudocoelom. In addition, nematodes molt, but annelids do not.

Annelida

2. The coelom cushioned the internal organs in fluid, preventing injury from external forces. In addition, the coelom enabled the internal organs to grow and move independently of the outer body wall. Finally, in some invertebrates, the coelom acts as a hydrostatic skeleton that supports the body and permits movement.

Mollusca

1. See Figure below.

Porifera

Figure 34.5  Cnidocytes are not reused. New ones form to replace the discharged ones.

Figure 34.15  Some advantages of segmentation are organ duplication, minimization of body distortion during movement, and specialization of some segments.

Conceptual Questions

Choanoflagellates

Figure 34.4  The dominant life stages are jellyfish: medusa; sea anemone: polyp; Portuguese man-of-war: polyp (in a large floating colony).

Brachiopoda

A-18



APPENDIX B

Figure 34.19  Because most species can excrete urine that is isoosmotic or hyperosmotic to the body fluids. Figure 34.27  These organs, called statocysts, are located at the base of the antennules.

Feature Investigation Questions 1. The researchers tested the hypothesis that an octopus can learn by observing the behavior of another octopus. 2. The results indicated that the observer learned by watching the training of the other octopus. The observer was much more likely to choose the same color ball that the demonstrator was trained to attack. These results support the hypothesis that octopuses can learn by observing the behavior of others. 3. The untrained octopuses had no prior exposure to the demonstrators. The results indicated that these octopuses were as likely to attack the white ball as the red ball. No preference for either color was indicated. The untrained octopuses acted as a control. This is an important factor to ensure that the results from the trials using observers indicate a response to learning and not an existing preference for a certain color.

Test Yourself

Figure 35.14  Besides the amniotic egg, other critical innovations in amniotes are thoracic breathing; internal fertilization; a thicker, less permeable skin; and more efficient kidneys. Figure 35.16  Snakes evolved from tetrapod ancestors but subsequently lost their limbs. Some species have tiny vestigial limbs. Figure 35.20  Adaptations in birds to reduce body weight for flight include a lightweight skull, reduction of organ size (including smaller gonads outside of breeding season), and a lack of a urinary bladder and teeth. Also female birds have one ovary and can carry relatively few eggs.

Core Skills: Connections Figure 35.5  No, an examination of Figure 35.1 shows that “fishy” organisms include an ancestral population and some of its descendants, but not all of them. The “fish” are thus a paraphyletic group. To be a monophyletic group, the fish would have to include the tetrapods as well. Therefore, there is no true monophyletic group that corresponds to the popular name “fish.” Figure 35.17  Both crocodilians and birds and mammals have four-chambered hearts and care for their young. Figure 35.26  None. The bloodstreams of fetus and mother are brought into close contact in the placenta, but they do not mix.

Feature Investigation Questions

1. b  2. d  3. d  4. d  5. b  6. c  7. b  8. a  9. c  10. b

1. The researchers were interested in determining the role of Hox genes in controlling limb development in mice.

Conceptual Questions

2. The researchers bred mice that were homozygous for certain mutations in specific Hox genes. This allowed the researchers to determine the function of individual genes.

1. The five main feeding methods used by invertebrate animals are (1) suspension feeding, (2) decomposition, (3) herbivory, (4) predation, and (5) parasitism. Suspension feeding is usually used to filter out food particles from the water. A great many phyla, including sponges, rotifers, bryozoans, brachiopods, some mollusks, some echinoderms and tunicates, are filter feeders. Decomposers usually feed on dead material such as animal carcasses or dead leaves. For example, many fly and beetle larvae feed on dead animals, and earthworms consume dead leaves from the surface of the Earth. Earthworms and crabs also sift through soil or mud, eating the substrate and digesting the soil-dwelling bacteria, protists, and dead organic material. Herbivores eat plants or algae and are especially common in the arthropoda. Adult moths and butterflies also consume nectar. Snails are also common plant feeders. Predators feed on other animals, killing their prey, and may be active hunters or sit-and-wait predators. Many scorpions and spiders actively pursue their prey, whereas web-spinning spiders ambush their prey using webs. Parasites also feed on other animals but do not normally kill their hosts. Endoparasites, which includes flukes, tapeworms, and nematodes, live inside their hosts. Ectoparasites (ticks and lice) live on the outside of their hosts. 2. Gametes would dry out on land, and internal fertilization prevents this from happening. Also, water facilitates the movement of gametes, reducing the need for internal fertilization. 3. Complete metamorphosis has four stages: egg, larva, pupa, and adult. The larval stage is often spent in an entirely different habitat from that of the adult, and larval and adult forms utilize different food sources. Incomplete metamorphosis has only three stages: egg, nymph, and adult. Young insects, called nymphs, look like miniature adults when they hatch from their eggs.

Chapter 35

Concept Checks Figure 35.1  Vertebrates (but not invertebrates) usually possess a (1) notochord; (2) dorsal hollow nerve chord; (3) pharyngeal slits; (4) postanal tail, exhibited by all chordates; (5) vertebral column; (6) cranium; and (7) endoskeleton of cartilage or bone. Figure 35.7  Ray-finned fishes (but not sharks) have a (1) bony skeleton; (2) mucuscovered skin; (3) swim bladder; and (4) operculum covering the gills. Figure 35.8  Both lungfishes and coelocanths are Sarcopterygii, having lobe fins. Figure 35.11  The advantages for animals that moved onto land included an oxygenrich environment and a bonanza of food in the form of terrestrial plants and the insects that fed on them. Figure 35.13  No. Caecilians and some salamanders give birth to live young.

3. The researchers found that homozygous mutants developed limbs of shorter length compared to limbs of the wild-type mice. The reduced length was due to the lack of development of particular bones in the limb, specifically, the radius, ulna, and some carpels. These results indicated that simple mutations in a few genes could lead to dramatic changes in limb development.

Test Yourself

1. b  2. e  3. d  4. e  5. a  6. d  7. d  8. c  9. c  10. a

Conceptual Questions 1. Both vertebrates and arthropods have external limbs that move when the attached muscles contract or relax. The difference is that arthropods have external skeletons, with the muscles attached internally, whereas vertebrates have internal skeletons with the muscles attached externally. 2. Endothermy (warm-bloodedness) probably evolved independently in both birds and mammals. If the common ancestor of reptiles and birds were endothermic, the chances are that all reptiles would be endothermic. 3. Probably. Both birds and reptiles lay amniotic eggs and possess scales, though these only cover the legs in birds. Birds and crocodilians also share a four-chambered heart. Finally, birds share many skeletal similarities with certain dinosaurs.

Chapter 36

Concept Checks Figure 36.8  Having stomata located on the darker and cooler lower epidermis helps reduce water loss from the leaf. Figure 36.12  A twig having five sets of bud scale scars is likely to be approximately 6 years old. Figure 36.17  Cactus stems are green and photosynthetic; they play the role served by the leaves of most plants and make the organic compounds. Figure 36.21  A woody stem such as a tree trunk builds up a thicker layer of wood than inner bark in part because older tracheids and vessel element walls are not lost during shedding of bark, which is the case for secondary phloem. In addition, plants typically produce a greater volume of xylem than phloem tissue per year, in part because vessel elements are relatively wide. A large volume of water-conducting tissue helps plants maintain a large amount of internal water. Figure 36.24  Lateral roots are produced from internal meristematic tissue because roots do not produce axillary buds like those from which shoot branches develop. Internal production of branch roots helps to prevent them from shearing off as the root tip grows through abrasive soil.

APPENDIX B

Core Skills: Connections

A-19

A-20

APPENDIX B

Chapter 37

Core Skills: Connections Figure 36.5  Apical-basal polarity of the plant body resembles anterior-posterior polarity in the animal body.

Concept Checks Figure 37.4  Auxin efflux carriers could be located on the upper sides of root cells, thereby allowing auxin to move upward in roots.

Figure 36.9  Plant cells often possess a large vacuole, whereas vacuoles in animal cells are relatively small.

Figure 37.6  Once a callus has been formed from a single plant having desirable characteristics using plant tissue culture, the callus can be divided into many small calluses. A grower can transfer these to separate containers having the appropriate hormone mixtures to induce root and shoot growth, then transplant the young plant clones to soil. In this way, the grower can produce many identical plants.

Figure 36.11  There is no difference among eukaryotes with respect to the structure of microtubules.

Feature Investigation Questions 1. The advantages of using natural plants include the opportunity to avoid influencing plants with unnatural environmental factors, such as artificial light, and the exposure of all experimental plants to similar growth conditions. In addition, the investigators studied the leaves of some large trees, which would be hard to accommodate in a greenhouse.

Figure 37.9  The triple response of a seedling to internally produced ethylene serves to protect the delicate apical meristem from damage as the seedling pushes upward through the soil. Figure 37.11  The inactive conformation of phytochrome would absorb the red light in the sunlight, thereby converting the molecule into the active conformation.

2. Pinnately veined leaves were splinted to prevent their breaking, since they were cut at the single main vein, which has both support and conducting functions.

Figure 37.12  Exposing plants to brief periods of darkness during the daytime will have no effect on flowering because flowering is determined by night length.

3. The researchers measured leaf water conduction at two or more places on each leaf because the effect of cutting a vein might have affected some portions of leaves more than others.

Test Yourself

Figure 37.14  Yes, just as shoots exhibit negative gravitropism in upward growth, roots are capable of using negative phototropism to grow downward, because light decreases with depth in the soil.

1. d  2. c  3. b  4. a  5. c  6. a  7. d  8. e  9. b  10. e

Figure 37.19  The immunity effect is relatively long-lasting in both cases.

Conceptual Questions

Feature Investigation Questions

APPENDIX B

1. Hypothetically, auxin enhances the rate at which cell membrane proton pumps acidify the plant cell wall, thereby allowing cells to extend. Although the evidence for acid effects on cell-wall extension is strong, the molecular basis of possible auxin effects on proton pumps is not as yet clear.

1. If overall plant architecture were bilaterally symmetrical, plants would be shaped like higher animals, with a distinct front (ventral surface) and back (dorsal surface). Bilaterally symmetrical plants would have a reduced ability to deploy branches and leaves in a way that would fill available lighted space and would thus be unable to take optimal photosynthetic advantage of their habitats.

2. A small number of seedling tips could display atypical responses for a variety of reasons. The investigators actually performed the experiment with many replicate seedling tips (coleoptiles), in order to gain confidence that the responses are general.

2. If leaves were generally radially symmetrical (shaped like spheres or cylinders), they would not have the maximal ability to absorb sunlight, and they would not be able to optimally disperse excess heat from their surfaces. 3. Although tall herbaceous plants exist (palms and bamboo are examples), the additional support and water-conducting capacity that are provided by secondary xylem allow woody plants to grow tall.

Test Yourself

1. c  2. c  3. a  4. e  5. d  6. d  7. c  8. d  9. d  10. d

BioTIPS page 762 HYPOTHESIS Light destroys auxin on lit side of shoot tips, causing unequal auxin distribution. Unlit side should grow more than lit side. STARTING MATERIALS Corn seedlings. Experimental level

1

Darkgrown tip

Collect auxin into agar blocks from: A dark-grown tips B tips grown with directional light

Auxin diffusion

Conceptual level Directional light-grown tip

A

2

Place agar blocks on right side of decapitated shoots.

B

Agar block

Darkgrown Shoot

A

3

THE DATA Darkgrown

4 26

A

Lightgrown

26 B

Lightgrown

Light

If light destroys auxin on one side, less auxin will enter the block.

If the block on the right side has less auxin, it will cause less bending.

B

CONCLUSION Similar bending demonstrates that light did not destroy auxin in the directionally lit shoot tip. If it had, less auxin would have been present in the agar block in B, and the degree of bending would have been less. The hypothesis described under conceptual level (above) is incorrect.



APPENDIX B

1. Behavior is defined as the response of a living thing to a stimulus. Therefore, because plants display many kinds of responses to diverse stimuli, they display behavior. 2. Many kinds of disease-causing bacteria and fungi occur in nature, and these organisms evolve very quickly, producing diverse elicitors. Thus, plants must maintain various types of resistance genes, each having many alleles. 3. Talking implies a conversation with “listeners” who detect a message and respond to it. Thus, plants that exude volatile compounds that attract enemies of herbivores could be interpreted as “talking” to those enemies. The message is “Hey, you guys, there’s food for you over here.” In addition, research has revealed that some plants near those under attack respond to volatile compounds by building up defenses. “Talking” to other plants does not enhance the “talker’s” fitness. But the ability to “listen” enhances the “listener’s” fitness, because it can take preemptive actions to prevent attack.

Chapter 38

Concept Checks Figure 38.5  Plastids that are clustered near the nucleus should have more rubisco than plastids at the periphery. Figure 38.6  Chlorosis is not always a sign of iron deficiency; it can be a symptom of a deficiency of any of several mineral nutrients, including zinc in corn. Figure 38.10  Mineral leaching occurs more readily in sandy soils than in clay soils. Figure 38.12  Soil crusts containing nitrogen-fixing cyanobacteria increase soil fertility, fostering the growth of larger plants that stabilize soils against erosion and provide forage for animals. Figure 38.13  Oxygen, which makes up 21% of Earth’s present atmosphere, can bind to the active site of nitrogenase, thereby inactivating it.

Core Skills: Connections Figure 38.20  Both the tapeworm and the dodder obtain organic food from a host, an animal or a plant, respectively.

Feature Investigation Questions 1. SDQ1 expression is induced by phosphorus deficiency. This gene fosters replacement of plastid phospholipids with sulfur-containing lipids, thereby reducing the plant’s phosphorus requirement. 2. They used genetic engineering techniques to place a reporter gene under the control of the SQD1 promoter, so that when SQD1 was expressed, the reporter gene was expressed also. After growing plants in nutrient solutions containing various levels of phosphorus, they removed sample leaves and treated them with a compound that turns blue when the reporter gene is expressed. When they saw blue leaves, the investigators could infer (1) that the plants from which those leaves had been taken were beginning to experience phosphorus deficiency and (2) that application of fertilizer at this point could prevent damage to the plants.

Test Yourself

1. e  2. a  3. c  4. b  5. e  6. c  7. d  8. d  9. a  10. b

Conceptual Questions 1. Agricultural experts are concerned that adding excess fertilizer to crop fields increases the costs of crop production. Ecologists are concerned that excess fertilizers will wash from crop fields into natural waters and cause harmful overgrowths of cyanobacteria, algae, and aquatic plants. Methods for closely monitoring crop nutrient needs so that only the appropriate amount of fertilizer is applied would help to allay both groups’ concerns. 2. Use Figure 38.18 as a reference. A first arrow could be drawn from a root to rhizobia in the soil, and the arrow labeled “flavonoids.” A second arrow could be drawn from rhizobia to roots and labeled “Nod factors.” A third arrow from rhizobia to roots could be labeled “infection proteins.” A fourth arrow from roots to rhizobia could be labeled “nodulins” and the resulting nodule environmental conditions, which influence the formation of bacterioids. A fifth arrow could represent the flow of fixed nitrogen from bacterioids to plant. A sixth arrow could represent the flow of organic compounds from plant to bacteroids. 3. Tropical plants often partner with microbes that provide essential mineral nutrients. Such partnerships include nitrogen-fixing bacteria that may live

within plant roots and/or mycorrhizal fungi that harvest minerals from decaying organisms and transport the minerals to plant root tissues.

Chapter 39

Concept Checks Figure 39.5  When placed in pure water, a turgid cell having a water potential of 1.0 will lose water, because 1 is greater than 0. When placed in pure water, a plasmolyzed cell having a water potential of –1.0 MPa will gain water. When placed in pure water, a flaccid cell having a water potential of –0.5 MPa will gain water. This is because water moves from a region of higher water potential to a region of lower water potential, and 0 is greater than –0.5. Figure 39.11  You would likely see stained rings or helical ribbons extending up the insides of the walls of extensible tracheids. You would not see staining at the ends of tracheids, where they connect to form long tubes. Figure 39.12  The large perforations in vessel element end walls allow an air bubble to extend from one element to another, thereby clogging a vessel and preventing water flow through it. In contrast, the much smaller pores in the end walls of tracheids do not allow water to flow as efficiently as it does through vessels, but these smaller pores also retard the movement of air bubbles. As a result, an air bubble will be confined to a single tracheid where it can do little harm. Figure 39.13  Root pressure can help to reverse an embolism, thereby restoring water flow through the plant xylem. Figure 39.15  The evaporation of water has a powerful cooling effect because it dissipates heat so effectively. Water has the highest heat of vaporization of any known liquid. Figure 39.16  You could model a stomatal guard cell with an elongate balloon by partially inflating it, then attaching thick tape along one side to represent thickened inner walls and circles of string or thin tape to represent radial cellulose, then adding more air to the balloon. The balloon should curve as it expands, just as a guard cell does when the stomatal pore opens. Two such balloons could be used to model both guard cells and the stomatal pore. Figure 39.19  In the ocotillo’s desert habitat, times of drought and availability of water sufficient to support the development and photosynthetic function of leaves do not occur as predictably as in temperate forests. For this reason, ocotillo leaf abscission is not amenable to the evolution of genetic mechanisms that allow leaf drop to be precisely timed in anticipation of the onset of drought.

Core Skills: Connections Figure 39.8  Tight junctions in the intestinal epithelium of animals and Casparian strips in walls of endodermal cells of plant roots both form a tight seal, preventing movement of materials from one location to another. Figure 39.21  Stomatal guard cell and phloem companion cell development both begin with an unequal cell division.

Feature Investigation Questions 1. Replicates provide reproducibility, and controlled growth conditions reduce the effects of environment. 2. Leaf temperature indicates degree of evaporation through open stomata.

Test Yourself

1. c  2. b  3. e  4. d  5. a  6. e  7. d  8. e  9. a  10. c

Conceptual Questions 1. In the case of plant fertilizers, more is not better, because the ion concentration of overfertilized soil may become so high as to draw water from plant cells. In this case, the cells would be bathed in a hypertonic solution and would likely lose water to the solution. If plant cells lose too much water, they will die. 2. When the natural vegetation is removed, transpiration stops, so water is not transported from the ground to the atmosphere, where it may be an important contributor to local rainfall. Extensive removal of plants actually changes local climates in ways that reduce agricultural productivity and human survival. 3. When mineral ion concentrations in the soil are lower than those within root cells, root-hair plasma membranes take up nutrient ions by active transport, which requires energy in the form of ATP. So the plant rooted in soil of lower mineral concentration will likely expend more ATP during nutrient uptake.

APPENDIX B

Conceptual Questions

A-21

A-22

APPENDIX B

Chapter 40

Concept Checks Figure 40.3  Some flowers lack some of the major flower parts. Figure 40.4  By having its stamens clustered around the pistil, the hibiscus flower increases the chance that a pollinator will both pick up pollen and deliver pollen from another hibiscus flower in the same visit. Figure 40.7  The absence of showy petals often correlates with wind pollination, because large petals would interfere with the shedding of pollen in the wind. Figure 40.10  The rim flowers of Gerbera inflorescences have bilateral symmetry, conferred by expression of a CYCLOIDEA-like gene. Rim flowers also possess showy petals that attract pollinators, but lack pollen-producing stamens. By contrast, central flowers display radial symmetry, lack showy petals, and possess pollen-producing stamens. Figure 40.12  The maximum number of cells in a mature male gametophyte of a flowering plant is three: a tube cell and two sperm cells. Figure 40.14  Female gametophytes are not photosynthetic and cannot produce their own organic food. Enclosed within ovules, female gametophytes lack direct access to the outside environment. Carpels contain veins of vascular tissue that bring nutrients from sporophytic tissue to ovules. Figure 40.16  An embryo in which the TOPLESS genes were nonfunctional would have two roots and no shoots. Figure 40.17  During their maturation, the cotyledons of eudicot seeds absorb the nutrients originally present in the endosperm.

APPENDIX B

Core Skills: Connections Figure 40.1  The gametophyte generation of a flowering plant is small, nonphotosynthetic, and haploid. Figure 40.15  The plant pollen tube is analogous in function to a human penis in that both structures accomplish internal fertilization. The plant pollen tube grows long enough to deposit sperm at the micropyle within the body of the female gametophyte, much as a male animal’s penis deposits sperm within the female’s body. In both cases, sperm are more likely to survive and accomplish fertilization than if they were deposited outside the female body.

Feature Investigation Questions 1. The large flowers of this lily enabled investigators to more easily mark petals and record the positions of marks over time. 2. Time-lapse video reduced the amount of time investigators would have to spend recording changes in the positions of petal marks.

Test Yourself

1. a  2. b  3. d  4. b  5. d  6. e  7. b  8. c  9. d  10. c

Conceptual Questions 1. Pollen grains are vulnerable to mechanical damage and microbial attack during the journey through the air from the anthers of a flower to a stigma. Sporopollenin is an extremely tough polymer that helps to protect pollen cells from these dangers. 2. The embryos within seeds are vulnerable to mechanical damage and microbial attack after they are dispersed. Seed coats protect embryos from these dangers and also help to prevent seeds from germinating until conditions are favorable for seedling survival and growth. 3. Flower diversity is an evolutionary response to diverse pollination circumstances. For example, plants such as oak and corn that are wind-pollinated produce flowers having a poorly developed perianth. If the flowers of such plants had large, showy perianths, they would get in the way of pollen dispersal or acquisition. On the other hand, flowers that are pollinated by animals often have diverse shapes and attractive petals of differing colors or fragrances that have coevolved with different types of animal pollinators.

Chapter 41

Concept Checks Figure 41.8  Surface area is important to any living organism that needs to exchange materials with the environment. A good example of a high surface area/volume ratio is that of most tree leaves. This high ratio makes leaves ideally suited for such processes as light absorption (required for photosynthesis; see Chapter 8) and the exchange of gases and water with the environment.

Figure 41.13  In nature, an animal such as a horse would have the same type of response shown here if threatened by a predator. Upon sensing the presence of the predator, the horse’s respiratory and circulatory systems would begin increasing their activities in preparation for the possibility that the horse might have to flee or defend itself. The increase would occur even before the horse began to flee. Figure 41.14  Blood, including plasma and blood cells, would leak out of the blood vessel into the interstitial space. The fluid level of the bloodstream would decrease, and that of the interstitial space near the site of the injury would increase. Eventually the blood that entered the interstitial space would be degraded by enzymes, resulting in the characteristic skin appearance of a bruise. If the injury were very severe, the fluid level in the blood could decrease to a point where the various tissues and organs of the body would not receive sufficient nutrients and oxygen to function normally. Figure 41.15  A decrease in intracellular fluid volume, like that shown in the middle panel in Figure 41.15, will result in an increase in intracellular solute concentration (likewise, an increase in intracellular fluid volume will decrease intracellular solute concentrations). Such a change may have drastic consequences for cell function. For example, some solutes, like Ca2+ and certain other ions, are toxic to cells at high concentrations. Figure 41.16  No, obligatory exchanges must always occur, but animals can minimize obligatory losses through modifications in behavior. For example, terrestrial animals that seek shade on a hot, sunny day reduce evaporative water loss. As another example, reducing activity minimizes water loss due to respiration. Figure 41.18  Humans cannot survive by drinking seawater because we do not possess specialized salt glands to rid ourselves of the excess sodium and other ions we would ingest with the seawater. The human kidneys cannot eliminate that much salt. The high blood concentrations of sodium and other ions would cause changes in cellular membrane potentials, disrupting vital functions of electrically excitable tissue such as cardiac muscle and nerve tissue.

Core Skills: Connections Figure 41.6  Note that both the stomach and the small intestine depicted in Figures 41.6 and 46.6 contain layers of muscle wrapped around a lumen. Although you will learn later that the stomach and intestine have many different functions, this similarity in anatomy suggests that both of these organs may perform the functions of mechanically breaking apart chunks of food and propelling the food from one region to another. Figure 41.11  Negative feedback may occur at the molecular level. It is a common feature of some enzymatic pathways, such as the metabolic one depicted in Figure 6.13.

Feature Investigation Questions 1. Symptoms of prolonged, heavy exercise include fatigue, muscle cramps, and even occasionally seizures. Fatigue results from the reduction in blood flow to muscles and other organs. Muscle cramps and seizures are the results of imbalances in plasma ion concentrations. Cade and his colleagues hypothesized that maintaining a normal balance of water and ions would prevent these problems from occurring, and that if water and ion concentrations were maintained, athletic performance should not decrease as rapidly with prolonged exercise. 2. To test their hypothesis, the researchers created a drink that would restore the correct proportions of water and ions lost by the athletes during exercise. If the athletes consumed the drink, they should not experience as much fatigue or muscle cramping, and thus their performance should be enhanced compared with that of a control group of athletes that drank only water. 3. Gatorade and many similar sports drinks are beneficial in replacing the ions and water lost in perspiration during exercise. These drinks also typically contain sugar that is meant to provide energy for someone who is being very active. Given that a person at rest or one who is exercising lightly would not be expected to perspire very much, a logical hypothesis is that sports drinks are not beneficial in such cases. A small degree of perspiration will not create a significant ion imbalance. Also, as a rule, consuming sugary drinks should be avoided because of their links to weight gain and dental disease. Thus, to a person at rest or engaging in only light exercise, the benefits of such drinks are minimal and may be outweighed by their potential negative effects.

Test Yourself

1. c  2. c  3. d  4. b  5. c  6. c  7. d  8. b  9. e  10. e

Conceptual Questions 1. Structure and function are related in that the function of a given organ, for example, depends in part on the organ’s size, shape, and cellular and tissue arrangement. Clues about a physical structure’s function can often be obtained by examining the structure’s form. For example, the extensive surface area of a moth’s antennae suggests that the antennae are important in detecting the presence of airborne



APPENDIX B

2. Homeostasis is the ability of animals to maintain a stable internal environment by adjusting physiological processes, despite changes in the external environment. Examples include maintenance of ion and water balance, pH of body fluids, and body temperature. Some animals conform to their external environment to achieve homeostasis, but others regulate their internal environment themselves. 3. Maintaining homeostasis requires continual supplies of energy. Animals consume food, and the energy from that food helps sustain activities that maintain physiological variables such as body temperature, water and ion homeostasis, and synthesis of complex molecules. Without this energy, it would be difficult or impossible for animals to maintain many important biological processes within a narrow range despite changes in the environment.

potentials occur along the dendrites and cell body. If a graded potential reaches the threshold potential at the axon hillock, an action potential results. This is a change in the membrane potential that is of a constant value and is propagated from the axon hillock to the axon terminal. 2. An increase in extracellular Na+ concentration would slightly depolarize neurons, thereby changing the resting membrane potential. This effect would be minimal, however, because the resting membrane is not very permeable to Na+. However, the shape of the action potentials in such neurons would be a little steeper, and the peak a little higher, because the electrochemical gradient favoring Na+ entry into the cell through voltage-gated channels would be greater. 3. Neurons are among the most highly complex cells in an animal’s body, with numerous extensions of the cell body. These extensions provide considerable surface area that allows for an extraordinary number of cell-to-cell contacts with other neurons and other types of cells, making them ideally suited for intercellular communication. In addition, myelin sheaths provide a structure that speeds up electric signaling along the axon, further facilitating intercellular communication.

Chapter 42

Chapter 43

Concept Checks

Concept Checks

Figure 42.4  Many reflexes, such as the knee-jerk reflex, cannot be prevented once started. Others, however, can be controlled to an extent. Open your eyes widely and gently touch your eyelashes. A reflex that protects your eye will tend to make you close your eyelid. However, you can overcome this reflex with a bit of difficulty if you need to, for example, when you are putting in contact lenses.

Figure 43.4  Not necessarily. Brain mass is not the sole determinant of intelligence or the ability to perform complex tasks. The degree of folding of the cerebral cortex is also important. Figure 43.6  A spinal nerve is composed of axons of both afferent and efferent neurons.

Figure 42.9  When the K+ channels opened (at 1 msec), the Na+ channels would still be opened, so the part of the curve that slopes downward would not occur as rapidly, and perhaps the cell would not be able to restore its resting potential.

Figure 43.7  The major symptom experienced by patients undergoing a lumbar puncture is headache, in part because the brain is no longer cushioned adequately by CSF. Within 24–48 hours, however, the CSF is replenished to normal levels.

Figure 42.11  Saltatory conduction allows an action potential to move faster down an axon. This effect is especially important for long axons, such as those that carry signals from the spinal cord to distant muscles.

Figure 43.11  It was in her right hand.

Core Skills: Connections

Figure 43.1  As defined in Chapter 33, animals are multicellular heterotrophs (cannot make their own food) whose cells lack a cell wall. Most animals have a nervous system, muscles, and the abilities to move about during at least some phase of their life cycle and to reproduce sexually.

Figure 42.6  Electrochemical ion gradients function in neuronal signaling, ATP synthesis, muscle contraction, osmotic regulation, and transport of organic molecules across membranes. Figure 42.7  Water molecules move through membrane channels called aquaporins.

Feature Investigation Questions 1. Loewi was aware that electrical stimulation of the vagus nerve associated with heart muscle slowed down the rate of heart contractions in a frog. Also, he knew that electrical stimulation of other nerves associated with the frog heart produced the opposite result. If the effects of the different nerves on heart muscle were mediated directly by electrical activity only, the heart muscle cells would have no way to distinguish between stimulatory and inhibitory signals. Loewi hypothesized that nerves released chemicals onto heart muscle cells and that it was these different chemicals that produced the varied effects on the heart. 2. The results could also have been explained as a chemical having been released into the bathing medium from heart 1. The stimulated vagus nerve might have caused the muscle cells to release a chemical that was then capable of inhibiting heart 2. This may have been unlikely, but Loewi’s experiment did not rule it out. A control experiment might have been to electrically stimulate heart 1 directly, by applying current to the muscle itself and not indirectly via the vagus nerve. If Loewi’s hypothesis was correct, this control experiment would result in no effect on heart 2. 3. If the vagus nerve released acetylcholine, and it was this neurotransmitter that slowed the rate of beating of heart 2 in Loewi’s experiment, then simply adding acetylcholine to the medium of a resting heart should produce the same effect as Loewi observed in his experiment. Alternatively, repeating Loewi’s experiment but with the addition of an acetylcholine receptor blocker to heart 2, should decrease or eliminate the response.

Test Yourself

1. c  2. d  3. d  4. e  5. b  6. d  7. b  8. e  9. a  10. e

Conceptual Questions 1. In a graded potential, a weak stimulus causes a small change in the membrane potential, whereas a strong stimulus produces a greater change. Graded

Core Skills: Connections

Feature Investigation Questions 1. Gaser and Schlaug hypothesized that repeated exposure to musical training would increase the size of certain areas of the brain associated with motor, auditory, and visual skills. All three skills are commonly used in reading and performing musical pieces. The researchers used MRI to examine the areas of the brain associated with motor, auditory, and visual skills in three groups of individuals: professional musicians, amateur musicians, and nonmusicians. The researchers found that certain areas of the brain were larger in the professional musicians compared to the other groups, and larger in the amateur musicians compared to the nonmusicians. 2. Schmithorst and Holland found that, when exposed to music, certain regions of the brains of musicians were activated differently compared with those regions in the brains of nonmusicians. This study supports the hypothesis that there is a difference in the brains of musicians versus nonmusicians. The experiment conducted by Gaser and Schlaug compared the size of certain regions of the brain among professional musicians, amateur musicians, and nonmusicians. Schmithorst and Holland, however, were also able to detect functional differences between musicians and nonmusicians. 3. A trained athlete might be expected to show greater development of brain areas devoted to motor skills. For example, athletes who engage in repetitive activities such as tennis and badminton have been found to have greater volumes of motor and balance regions including the cerebellum. Someone deaf from birth might be predicted to have decreased development of auditory regions such as those in the temporal lobe. However, it is not necessarily this simple. For example, MRI studies sometimes but not always reveal differences in cell number in the temporal lobes of deaf versus hearing subjects, but there is generally significantly less development of fiber tracts (white matter) in this region in the brains of deaf persons. Therefore, the size of a brain structure (that is, the number of neurons) by itself may not always be predictive of function.

Test Yourself

1. b  2. a  3. c  4. c  5. c  6. b  7. e  8. b  9. a  10. d

APPENDIX B

chemicals. Likewise, any structure that contains a large surface area for its volume is likely involved in some aspect of signal detection, cell-cell communication, or transport of materials within the animal or between the animal and the environment. Surface area increases by a power of 2, and volume increases by a power of 3 as an object enlarges; this means that in order to greatly increase surface area of a structure such as an antenna, without occupying enormous volumes, specializations must be present (such as folds) to package the structure in a small space.

A-23

A-24

APPENDIX B

Conceptual Questions 1. All animals with nervous systems have reflexes, which allow rapid behavioral responses to changes in the environment. When a cnidarian senses a tactile stimulus, its nerve net responds immediately and the animal reflexively contracts nearly all of its muscles, making the animal a smaller target. This behavior protects the animal from predators. When you hear a loud, unexpected, and frightening sound (such as a firecracker), you hunch your shoulders and slightly lower your head; this reflex protects you from danger by minimizing exposure of your neck and head to danger. Dilation of the pupils of the eyes in darkness, and constriction of the pupils in bright light, are reflexes that help us see in the dark and protect our retinas in bright light. Reflexes are particularly adaptive because they occur rapidly, typically with very few synapses involved, and without the need for conscious thought. 2. White matter consists of the myelinated axons that are bundled together in large tracts in the central nervous system and which connect different CNS regions. The lipid-rich myelin gives the tracts a whitish appearance. In contrast, gray matter consists of the cell bodies, dendrites, and some unmyelinated axons of neurons in the CNS. 3. The activities of animal nervous systems are replete with examples of new properties emerging from complex interactions. For example, you learned about reflexes in this chapter, which are behaviors that emerge from interactions between individual neurons that form communication circuits between the peripheral and central nervous systems. You also learned about “higher” functions of nervous systems, such as conscious thought, which also emerges from the interactions between many individual cells, each of which is in communication with up to hundreds of thousands of other cells. Individually, the cells cannot “think,” but networked together in elaborate ways, they enable a person to think, remember, plan ahead, and interpret the environment.

APPENDIX B

Chapter 44

Concept Checks Figure 44.3  To think about the touch sensations you are aware of, let’s take the example of sitting in a chair reading this textbook while holding it on your lap. You are aware of the constant weight of the book, the brush of the pages on your fingertips as you turn a page, a gentle breeze that may be circulating in your environment, the deep pressure from regularly adjusting your posture in your chair, an itch you may have on your skin, and the heat or cold of the room. Even a simple exercise such as this one is filled with stimuli of numerous types and durations. Figure 44.7  Waves of fluid (perilymph) movement caused by sound pressure on the tympanic membrane result in vibration of the basilar membrane. Figure 44.9  The orientation of the canals permits animals to detect circular or angular movement of the head in three different planes. The fluid in a canal that is oriented in the same plane as the plane of movement will respond maximally to the movement. For example, the canal that is oriented horizontally will show the greatest response to horizontal movements, while the other two canals will not respond as much. Overall, by comparing the signals from the three canals, the brain can interpret the motion in three dimensions. Figure 44.11  By comparing the intensity of signals from both sides of its head, a pit viper can determine the direction from which the heat is coming and thus localize its prey. Figure 44.18  Because red-green color blindness is caused by a sex-linked recessive gene, males require only a single defective allele on an X chromosome, whereas females require two defective alleles, one on each X chromosome. Figure 44.21  Photoreceptors synapse with bipolar cells, which in turn form synapses with ganglion cells. Figure 44.26  Salt is a vital nutrient needed to maintain plasma membrane potentials and fluid balance in animals’ bodies. Sugar provides glucose and other monosaccharides, important energy-yielding compounds. Sour (acidic) foods, like citrus fruits, provide nutrients and important antioxidants (vitamin C, for example) that protect against disease. Bitter substances are often toxic, and their bad taste discourages animals from eating them.

Core Skills: Connections Figure 44.1  The term sensory receptor refers to a type of cell that can respond to a particular type of stimulus. The term membrane receptor refers to a protein within a cell membrane that binds a ligand, thereby generating signals that initiate a cellular response. Figure 44.4  Cilia are cell extensions that contain in their internal structure microtubules and motor proteins that cause them to beat, or move, in a coordinated fashion. Stereocilia are membrane projections that are not motile, but instead are deformed by the movements of surrounding fluids. Figure 44.8  Statoliths are also found in the roots and shoots of plants. They serve as a gravity-detection mechanism that results in roots growing downward and shoots upward.

Figure 44.16  The microvilli of the photoreceptor in the compound eye of insects and the outer segments of the rod and cone in the vertebrate eye share membrane adaptations that increase their surface area, making them better able to detect photons.

Feature Investigation Questions 1. One possibility is that many different types of odor molecules might bind to one or just a few types of receptor proteins, with the brain responding differently depending on the number or distribution of the activated receptors. The second hypothesis is that organisms can make a large number of receptor proteins, each type binding a particular odor molecule or group of odor molecules. According to this hypothesis, it is the type of receptor protein, and not the number or distribution of receptors, that is important for olfactory sensing. The researchers extracted mRNA molecules from the olfactory receptor cells of the nasal epithelium of rats. They then used this mRNA to identify genes that encoded G-protein-coupled receptors. 2. The results of the experiment conducted by Buck and Axel support the hypothesis that animals discriminate between different odors based on having a variety of receptor proteins that recognize different odor molecules. Current research suggests that each olfactory receptor cell has a single type of receptor protein that is specific to particular odor molecules. Because most odors are due to multiple chemicals that activate many different types of odor receptor proteins, the brain detects odors based on the combination of the activated receptor proteins. Odor seems to be discriminated by many olfactory receptor proteins, which are in the membrane of separate olfactory receptor cells. 3. Among other things, animals use odors to detect potential sources of food, shelter, mates, and danger. Discerning between the odors of food versus potentially toxic material is key to the survival of many animals (think, for example, how we recognize fresh milk and spoiled milk). Many animals also use olfaction in finding shelter; some birds, for example, can distinguish the odors produced by particular beneficial plants that they use to build their nests. These plants have natural pathogen-killing properties and help maintain a healthier nest site. Odor preference also plays an important role in animals finding mates via the release of pheromones, particularly animals that live in dark environments such as nocturnal animals. The ability to discern the odors of different predators even when the predator may not be close enough to hear, or may not be in sight, is a huge survival advantage for many animals, who generally can differentiate such odors from those of nonthreatening species.

Test Yourself

1. d  2. c  3. b  4. c  5. e  6. e  7. b  8. b  9. d  10. b

Conceptual Questions 1. Sensory transduction is the process by which incoming stimuli are converted into neural signals. An example is the generation of signals in the retina when a photon of light strikes a photoreceptor. Perception is an awareness of the sensations that are experienced. An example is realizing what a particular visual image is. 2. Structurally, single-lens and compound eyes both have a lens, photoreceptors, light-absorbing pigmented cells, and structures with extensive surface areas. Functionally, both types of eye are capable of sensing the intensity of light, as well as distinguishing between wavelengths of light (color). In both cases, also, information from the eye is sent to the brain. 3. Of the various senses, the sense of olfaction (smell) is least important for the survival of humans. As diurnal animals, we rely largely on our visual sense. Sounds are a critical way to learn about impending danger, such as a car horn, but also provide our major means of communication. Other senses, such as the ability to sense pain, have acutely important functions from time to time. Olfaction, though often a pleasurable sense and at times a protective one (think of the smell of spoiled food), nonetheless provides little survival advantage to us. In fact, many people spend much of their lives with greatly diminished olfactory abilities, whether from chronic allergies or other problems, and are not hindered in any significant way. The story is very different for animals such as nocturnal mammals, which rely very heavily on olfaction to find food, locate mates, and avoid predators.

Chapter 45

Concept Checks Figure 45.1  In addition to not needing to shed their skeletons periodically, animals with endoskeletons can use their skin as an efficient means of heat transfer (and, to an extent in amphibians, water transfer). In addition, the body surface of such animals is often a highly sensitive sensory organ.



APPENDIX B

Core Skills: Connections

Figure 45.10  Voltage-gated Ca2+ channels exist in the terminals of all axons that communicate by chemical signaling (neurotransmitter release). In those cases, depolarization of the axon terminal opens Ca2+ channels, allowing Ca2+ to enter the terminal and trigger exocytosis of stored vesicles containing neurotransmitter molecules.

Feature Investigation Questions 1. PPAR-δ is a transcription factor that regulates the expression of genes that enable cells to more efficiently burn fat instead of glucose for energy. 2. Evans hypothesized that if PPAR-δ were highly activated in mice, the mice would lose weight because of the high level of fat metabolism. Evans and his coworkers developed transgenic mice with highly activated PPAR-δ. Then they fed the transgenic mice and a group of wild-type mice high-fat diets. They then compared the weights of the two groups of mice to determine if the change in PPAR-δ activity affected weight. The weights of the transgenic mice were considerably lower than those of the wild-type mice. These results supported the hypothesis that highly activated PPAR-δ would lead to lower weight gain due to fat metabolism. Interestingly, the researchers also discovered that the transgenic mice could perform prolonged exercise for a much longer time than the wild-type mice. The muscle tissue of the transgenic mice was more specialized for long-term exercise. 3. Based on the mean body weight prior to the switch in diet, the wild-type and transgenic mice should weigh approximately 49–50 g and 33–34 g, respectively, at the conclusion of the study. Current dietary recommendations suggest that people consume no more than about 30% of their daily calories from fat, and that most of that fat should be in the form of unsaturated fat. According to the Centers for Disease Control and Prevention, the average consumption of fat in the U.S. amounts to roughly 33% of daily calories; however, that is an average and many individuals consume far more fat than that each day.

Test Yourself

1. b  2. e  3. d  4. b  5. e  6. c  7. a  8. e  9. c  10. e

Conceptual Questions 1. Exoskeletons are on the outside of an animal’s body, and endoskeletons are inside the body. Both function in support and protection, but only exoskeletons protect an animal’s outer surface. Exoskeletons must be shed when an animal grows, whereas endoskeletons grow with an animal. 2. Animals can fly, glide, swim, walk, hop, jump, crawl, and be moved by water or air currents. For animals adapted to it, swimming and flying are energetically less costly than moving on land. In all cases, however, friction due to contact with land or drag due to the resistance of water or air requires energy to overcome. 3. The use of energy released by the hydrolysis of ATP is fundamental to skeletal muscle function and locomotion. Recall that ATP must be hydrolyzed during the cross-bridge cycle for skeletal muscle cells to shorten. Energy is also used to maintain calcium ion balance in the sarcoplasmic reticulum and is expended in all forms of locomotion. The amount of energy expended by animals during locomotion reflects how well they are adapted to the environment in which they must move.

Chapter 46

Concept Checks Figure 46.4  Sauropod dinosaurs were herbivores that probably had a gizzard-type structure in which stones helped to grind up coarse vegetation. Such stones would have become smooth after months or even years of tumbling around in the gizzard. Some of these sauropods are known to have lacked the sort of grinding teeth characteristic of modern mammalian herbivores, and thus a gizzard would have functioned in their digestion much as it does in modern birds. Figure 46.7  A gallbladder stores bile and releases it precisely when it is needed, in response to a meal, which is particularly useful for animals that consume large or infrequent meals. In the absence of a gallbladder, bile flows into the intestine continuously and cannot be increased to match the amount or timing of food intake.

Core Skills: Connections Figure 46.8  Transmembrane transport processes such as facilitated diffusion and secondary active transport are not unique to animals, and one or more types occur in virtually all cells.

Figure 46.11  CCK inhibits stomach activity. This is an example of negative feedback. The arrival of chyme in the small intestine stimulates secretion of CCK, which promotes digestion. At the same time, CCK inhibits contraction of the smooth muscles of the stomach so that the entry of chyme into the small intestine is slowed down. This allows time for controlled digestion and absorption of nutrients in the small intestine, and prevents the intestine becoming overfilled with chyme. Simultaneously, CCK inhibits acid production by the stomach so that the pH of the small intestine does not become dangerously low before bicarbonate ions are able to neutralize it.

Feature Investigation Questions 1. The surprising observations that some people with gastritis or ulcers have living bacteria (H. pylori) in their stomachs and that administering bacteria-killing compounds provided some relief from the symptoms led to the hypothesis that H. pylori infection is a cause of ulcers in humans. 2. The results did support the hypothesis. However, the results also clearly indicated that not all ulcers are due to H. pylori infection. 3. A combined treatment with bismuth and an antibiotic seems to be the most effective treatment. It is apparent, however, that even in individuals with continued H. pylori infections, some ulcers will heal on their own. In the absence of bismuth-antibiotic therapy, though, the likelihood of a recurrence of a new ulcer is much greater.

Test Yourself

1. d  2. e  3. d  4. c  5. c  6. a  7. d  8. c  9. e  10. e

Conceptual Questions 1. Digestion is the breaking down of large molecules into smaller ones by the action of enzymes and acid. Absorption is the transport of ions and small molecules, including those that do not require digestion, across the epithelial cells of the alimentary canal and from there into the extracellular fluid of an animal. 2. The crop is a dilation of the esophagus, which stores and softens food. The gizzard contains swallowed pebbles that help pulverize food. Both of these functions are adaptations that assist digestion in birds, which do not have teeth and therefore do not chew food. Humans, like many animals, can chew food before swallowing. 3. The small intestine contains layers of smooth muscle whose contractions help mix the contents of the intestine; this mixing facilitates digestion by bringing enzymes and food molecules into contact. Tight junctions along the apical membranes of the epithelium prevent enzymes from leaking out of the intestine. The surface area available for absorption is greatly increased by the folding of the epithelium to form villi and by the presence of microvilli, making up the brush border. The epithelial cells have digestive enzymes on their apical membranes; this ensures that the final steps of digestion will release products at the cell surface, where they can be quickly absorbed. The small intestine also contains neurons that, when activated by stretching of the intestine, signal the stomach to temporarily relax so that the intestine can process chyme in small amounts.

Chapter 47

Concept Checks Figure 47.6  Nearly all animals today show a similar relationship between body mass and metabolic rate, and there is no reason why that should not always have been true. Thus, the tiny 1-foot-tall ancestral horse Eohippus most likely had a higher BMR than do today’s larger horses. Figure 47.9  Humans are homeothermic endotherms. We maintain our body temperature within a very narrow range, and we supply our own body heat.

Core Skills: Connections Figure 47.3  Exocytosis involves the fusion of intracellular vesicles with the plasma membrane, resulting in the release of the vesicle contents into the extracellular fluid. See Figure 5.21 for a general description and Figure 42.13 for a specific example unique to animal cells.

Feature Investigation Questions 1. Scientists were interested in knowing how animals regulate their body mass around a particular level, even though many animals experience changes in food supply throughout the year. This observation seemed to indicate that a mechanism existed within the body that monitored when fuel stores were higher or lower than normal and that initiated changes in behavior and metabolism to compensate.

APPENDIX B

Figure 45.3  If a tendon is torn, the attachment of a muscle to a bone is reduced or lost. Therefore, when that muscle contracts, it will not be able to move the bone, at least not as much as usual.

A-25

A-26

APPENDIX B

2. The ob mice lost weight and ate less during the experimental procedure. This confirmed that something in the bloodstream of the wild-type mice was regulating body weight but was missing in the ob mice. When the unknown factor crossed into the bloodstream of the ob mice, it caused them to lose weight. In another group of parabiosed mice, however, the wild-type mice lost weight, but the db mice did not. Coleman concluded that these obese mice were not able to respond to the chemical signal that regulates body weight, even though they made the signal themselves and it was active in their parabiosed wild-type partners. It is now known that db mice produce leptin and ob mice do not; however, db mice are not sensitive to leptin and consequently they failed to lose weight in Coleman’s experiment. 3. When parabiosed, leptin from db mice will enter the circulation of ob mice. The ob mice will lose weight as a consequence. The db mice will continue to gain weight because they remain insensitive to leptin.

and the forces generated during locomotion would probably collapse the tracheoles. Finally, diffusion of oxygen from the surface of the body to the deepest regions of a human-sized insect would take far too long to support the metabolic demands of internal structures. Figure 48.19  As the lungs expand, the pressure within them decreases, as defined by Boyle’s law. This permits air to flow into the lungs. Figure 48.25  An increase in the blood concentration of HCO3− would favor the reaction HCO3– + H+ → H2CO3 → CO2 + H2O. This would reduce the H+ concentration of the blood, thereby raising the pH; the CO2 formed as a result would be exhaled. These changes would shift the hemoglobin curve to the left of the usual position.

Core Skills: Connections

Test Yourself

Figure 48.4  Immune defenses are found in most living organisms. Many bacteria produce antibacterial secretions that kill other bacteria. Plants, as shown in Figures 37.17 through 37.19, have a wide array of pathogen-fighting mechanisms.

Conceptual Questions

Figure 48.17  Countercurrent exchange is an efficient means of heat transfer between arteries and veins, such as those near the skin surface of the legs of a wading bird. Heat from the descending arteries is transferred to surrounding veins, which return the warm blood to the heart, preventing heat loss through the skin to the water.

1. c  2. a  3. d  4. c  5. a  6. c  7. e  8. c  9. c  10. e

APPENDIX B

1. Insulin acts on adipose and skeletal muscle cells to facilitate the diffusion of glucose from extracellular fluid into the cells’ cytosol. This is accomplished by increasing the translocation of proteins called glucose transporters (GLUTs) from the cytosol to sites within the plasma membrane of insulin-sensitive cells. Insulin also inhibits glycogenolysis and gluconeogenesis in the liver, which decreases the amount of glucose secreted into the blood by the liver. Insulin is required for glucose transport because like many other polar molecules, glucose cannot move across the lipid bilayer of a plasma membrane by simple diffusion. The inhibitory effects of insulin on liver function help to ensure that liver glycogen stores will be spared for the postabsorptive period. 2. Appetite is controlled by a satiety center in the brain that receives signals from the stretched stomach and intestines after a meal. When digestion and absorption are complete, the stomach and intestines return to their original size, and the brain no longer perceives that the animal feels “full.” In addition, appetite is controlled by leptin, a hormone secreted by adipose cells in direct proportion to the amount of fat stored in an animal’s body. When leptin concentrations in the blood are high, appetite is suppressed. When leptin concentrations are low, as occurs when an animal is losing weight, appetite is increased. The presence of a hormone that is released into the blood in proportion to fat mass in the body allows the brain to monitor the amount of energy stored in the body. A decrease in the concentration of leptin in the blood, for example, is the mechanism that communicates to the brain that fat stores are lower than normal. This initiates the sensation of hunger, which encourages an animal to seek food. 3. Countercurrent exchange is a mechanism for retaining body heat. The physical arrangement (structure) of arteries and veins in an animal’s body can contribute to the very important function of thermoregulation. As warm blood travels through arteries down a bird’s leg, for example, heat moves by conduction from the artery to adjacent veins carrying cooler blood in the other direction, toward the heart. By the time the arterial blood reaches the tip of the leg, its temperature has dropped considerably, decreasing the amount of heat loss to the environment, while the heat is returned to the body’s core via the warmed veins.

Chapter 48

Concept Checks Figure 48.1  Open circulatory systems evolved prior to closed systems. However, this does not mean that open systems are in some way “primitive” compared to closed circulatory systems. It is better to think of open systems as being ideally suited to the needs of those animals that have them. Arthropods are an incredibly successful order of animals, having the greatest number of species and inhabiting virtually every ecological niche on Earth. Clearly, their type of circulatory system has not hindered the success of arthropods. Figure 48.6  The aorta and all arteries branching from it carry oxygenated blood. Figure 48.8  The left and right ventricles pump blood through the semilunar valves into the aorta and the pulmonary trunk, respectively. Figure 48.12  No, erythrocytes never leave the blood vessels unless a vessel is cut. Figure 48.18  Several factors probably limit insect body size, but the respiratory system most likely is one of them. If an insect grew to the size of a human, for example, the trachea and tracheoles would be so large and extensive that there would be little room for any other internal organs in the body! Also, the mass of the animal’s body

Figure 48.26  The brainstem includes the midbrain, pons, and medulla oblongata. See Figure 43.9 for an illustration of the major parts of the human brain.

Feature Investigation Questions 1. Since glucocorticoids stimulate production of surfactant by lung tissues, injections of glucocorticoids to a pregnant woman should induce surfactant production by the lungs of the fetus. This indeed happens; the glucocorticoids cross into the fetal circulation from the mother, and stimulate surfactant in the fetus. Once born, even though the baby is premature, its lungs are relatively more mature and are able to remain open. 2. The oxygen levels achieved after surfactant therapy were all improved compared to the pre-treatment levels, but some babies actually had far higher values than is normal for a healthy baby. This was because at first all the babies were being ventilated with a mixture of gas that was very high in oxygen (much higher than is found in air); when their lung function improved, this mixture resulted in very high blood oxygen levels until the oxygen mixture was reduced. The differences in outcomes between babies likely reflected the degree of overall health of the individual babies; some were born slightly less prematurely than others. 3. Blood CO2 levels were increased in the sick infants because lung ventilation is important not just for obtaining O2, but for eliminating CO2. If ventilation is compromised in any person, for any reason, blood levels of CO2 inevitably increase.

Test Yourself

1. b  2. c  3. b  4. a  5. d  6. a  7. a  8. b  9. b  10. b

Conceptual Questions 1. Closed circulatory system: In a closed circulatory system, the blood is contained within tubes called blood vessels and is transported by a pump called the heart. All of the nutrients and oxygen that tissues require are delivered directly to them by the blood vessels. Advantages of a closed circulatory system are that different parts of an animal’s body can receive blood flow in proportion to each part’s metabolic requirements at any given time. Due to its efficiency, a closed circulatory system allows organisms to become larger. Open circulatory system: In an open circulatory system, the organs are bathed in hemolymph that ebbs and flows into and out of the heart(s) and body cavity, rather than having blood directed to all cells by increasingly smaller vessels. As in a closed circulatory system, there are a pump and blood vessels, but these two structures are less developed and less complex than those in a closed circulatory system. Partly as a result, the sizes of organisms such as mollusks and arthropods are generally relatively small, although exceptions do exist. 2. Carbon dioxide, hydrogen ions, and heat are produced by metabolism; the more active a cell is, the more of these products it generates. Because these products, in turn, reduce the ability of hemoglobin to bind oxygen (in other words facilitate the unloading of oxygen), more active regions of an animal’s body obtain more oxygen in proportion to their metabolic demand at that time. 3. Hemoglobin is a protein with quaternary structure (see Chapter 3) in which the different subunits cooperate to bind up to a total of four oxygen molecules. It is the structure of the subunits and their relationship to each other that contributes to their ability to bind O2 and to the nonlinear relationship of the oxygen-hemoglobin dissociation curve. In addition, however, interactions



APPENDIX B

Chapter 49

Concept Checks Figure 49.2  Secretion of substances into the tubules is advantageous because it increases the amounts of the substances that are removed from the body by the excretory organs. The increase in amounts is important, because many substances that get secreted are potentially toxic. Filtration, though efficient, is limited by the volume of fluid that can leave the capillaries and enter the excretory tubule.

Core Skills: Connections Figure 49.8  A brush border composed of microvilli is also present along the epithelial cell layer of the vertebrate small intestine (as shown in Figure 46.6). In the intestine, the brush border serves to increase the absorption of nutrients. In both the intestine and the proximal tubules of nephrons, therefore, a brush border provides extensive surface area for the transport of substances between a lumen and the epithelial cells (and from there to extracellular fluid). Figure 49.10  Epithelial cells like those in the distal tubule and cortical collecting duct can distribute proteins between the apical and basolateral sides of the plasma membrane. In this way, the Na+/K+-ATPase pumps that are stimulated by aldosterone are present and active only on one side of the cells, the basolateral surfaces. If the pumps were activated on the apical surfaces of the cells, aldosterone would not be able to promote reabsorption of Na+ and water, because Na+ would also be transported from the cells into the lumen.

How others maintain Ca2+ balance without dietary or sunlight-derived active vitamin D remains uncertain. Figure 50.12 Na+ and K+ balance is of vital importance for most animals because of the critical role these ions play in nervous system and muscle function. It is more the rule than the exception that such important physiological variables are under multiple layers of control. This control grants a high degree of fine-tuning capability so that these ions—and other similarly important substances—rarely exceed or fall below the normal range of concentration for a given animal. Figure 50.13  The great height of the twin on the left clearly indicates that his condition arose prior to puberty. Figure 50.15  Because 20-hydroxyecdysone is a steroid hormone, you would predict that its receptor would be intracellular. All steroid hormones interact with receptors located either in the cytosol or, more commonly, in the nucleus. The hormone-receptor complex then acts to promote or inhibit transcription of one or more genes. The receptor for 20-hydroxyecdysone is indeed found in cell nuclei.

Core Skills: Connections Figure 50.3  When dopamine is secreted from an axon terminal into a synapse, from which it diffuses into a postsynaptic cell, it is considered a neurotransmitter. When it is secreted from an axon terminal into the extracellular fluid, from which it diffuses into the blood, it is considered a hormone. Figure 50.7  In addition to the pancreas, certain other organs in an animal’s body may contain both exocrine and endocrine tissue or cells. For example, you learned in Chapters 46 and 47 that the vertebrate alimentary canal is composed of several types of secretory cells. Some of these cells release hormones into the blood that regulate the activities of the pancreas and other structures, such as the gallbladder. Other cells of the alimentary canal secrete exocrine products such as acids or mucus into the lumen of the canal that directly aid in digestion or act as a protective coating, respectively.

Feature Investigation Questions

Test Yourself

1. Banting and Best based their procedure on a condition that results when the pancreatic duct is blocked. The exocrine cells will deteriorate in a pancreas that has an obstructed duct; however, the islet cells are not affected. The researchers proposed to experimentally replicate the condition to isolate the cells suspected of secreting the glucose-lowering factor. From these cells, they assumed they would be able to extract the substance of interest without contamination or degradation due to exocrine products.

Conceptual Questions

2. The extracts obtained by Banting and Best did contain insulin, the glucoselowering factor, but were of low strength and purity. Collip developed a procedure to obtain a more purified extract with a higher concentration of insulin.

Figure 49.13  Countercurrent exchange is important in heat regulation in endotherms, in oxygen diffusion from the water into the blood across the gills of fishes, and in solute and water reabsorption in the loop of Henle in the mammalian kidney.

1. e  2. e  3. a  4. c  5. c  6. e  7. d  8. a  9. e  10. b

1. Nitrogenous wastes are the breakdown products of the metabolism of proteins and nucleic acids. They can be ammonia and ammonium ions, urea, or uric acid. The predominant type of waste excreted depends in part on an animal’s environment. For example, aquatic animals typically excrete ammonia and ammonium ions, whereas many terrestrial animals excrete primarily urea and uric acid. Urea and uric acid are less toxic than the other types but require energy to be synthesized. Urea and uric acid also result in less water being excreted, an adaptation that is especially useful for organisms that must conserve water, such as many terrestrial species. 2. The three processes are filtration, reabsorption, and secretion. During filtration, an organ acts like a sieve or filter, removing some of the water and small solutes from the blood, interstitial fluid, or hemolymph, while excluding blood cells and large solutes such as proteins. Reabsorption is the process whereby epithelial cells of an excretory organ recapture useful solutes that were filtered. Secretion is the process whereby epithelial cells of an excretory organ transport unneeded or harmful solutes from the blood to the excretory tubules for elimination. Some substances such as glucose and amino acids are reabsorbed but not secreted, while some other substances such as toxic compounds are not reabsorbed and are secreted. Still other substances, namely proteins, are not filtered at all. 3. The respiratory system eliminates CO2, the major waste product of metabolism produced by animals. The digestive system eliminates certain solid wastes from ingested food. The urinary system eliminates soluble wastes other than CO2.

Chapter 50

Concept Checks Figure 50.10  Not all mammals use the energy of sunlight to synthesize vitamin D. Many animals, such as those that inhabit caves or that are strictly nocturnal, rarely are exposed to sunlight. Some of these animals get their vitamin D from dietary sources.

3. Normally, the concentration of glucose in a mammal’s blood is never high enough to exceed the ability of the kidneys to reabsorb it all from the filtrate (refer back to Chapter 49 for details about filtration). However, like all transport processes, reabsorption of glucose from the kidney filtrate has a finite capacity that depends on the number of transporter molecules and their inherent rate of activity. In untreated diabetes, the blood concentration of glucose becomes so high that it exceeds the capacity of the kidney nephrons to fully reabsorb it from the filtrate. Consequently, some glucose appears in the urine.

Test Yourself

1. b  2. e  3. b  4. d  5. b  6. e  7. c  8. d  9. b  10. d

Conceptual Questions 1. Leptin acts in the hypothalamus to reduce appetite and increase metabolic rate. Because adipose tissue is typically the most important and abundant source of stored energy in an animal’s body, the ability to relay information to the appetite and metabolism centers of the brain about the amount of available adipose tissue is a major benefit. In this way, the brain’s centers can indirectly monitor the minute-to-minute energy status in the body. A decrease in leptin, for example, indicates a decrease in adipose tissue—as might occur during a fast. Removal of the leptin signal causes appetite to increase and metabolism to decrease, thereby conserving energy. The presence of an appetite and the subjective sensations associated with hunger motivate an animal to seek food at the expense of other activities, such as seeking shelter, finding a mate, and so on. 2. Type 1 diabetes mellitus is characterized by insufficient production of insulin due to the immune system destroying the insulin-producing cells of the pancreas. In type 2 diabetes mellitus, insulin is still produced by the pancreas (at least for a time), but adipose and muscle cells do not respond normally to the insulin.

APPENDIX B

of hemoglobin with other molecules, such as CO2, change the structure of hemoglobin in such a way that its properties change. Under such conditions, hemoglobin is less able to bind O2 and consequently it releases the gas. Any molecule that binds to hemoglobin will alter its structure and change its properties; these revert to the original state once the bound molecules are released. A particularly dramatic example of the relationship between the structure and function of hemoglobin is that which occurs in sickle cell disease, due to a mutation that changes the structure of the protein.

A-27

A-28

APPENDIX B

3. Insulin acts to lower blood glucose concentrations, for example, after a meal, whereas glucagon elevates blood glucose, for example, during fasting. Insulin acts by stimulating the insertion of glucose transporters (GLUTs) into the cell membrane of muscle and fat cells. Glucagon acts by stimulating glycogenolysis in the liver. If a high dose of glucagon were injected into an mammal, including a human, the blood concentration of glucagon would increase rapidly. This would stimulate increased glycogenolysis, resulting in blood glucose concentrations that were above normal.

Chapter 51

Concept Checks Figure 51.12  Pregnancy and subsequent lactation require considerable energy and, therefore, nutrient ingestion. Consuming the placenta provides the female with a rich supply of protein and other important nutrients.

Core Skills: Connections Figure 51.10  In addition to its other functions, the placenta must serve the function of the lungs for the fetus. Arteries always carry blood away from the heart; veins carry blood to the heart. Blood leaving the heart of the fetus and traveling through arteries to the placenta is deoxygenated. As blood leaves the placenta and returns to the heart, the blood has become oxygenated as oxygen diffuses from the maternal blood into fetal blood. That oxygenated blood then gets pumped from the fetal heart through other arteries to the rest of the fetus’s body.

APPENDIX B

Figure 51.11  Positive feedback also occurs during ovulation in the ovarian cycle (see Figure 51.9). Stimulation of an ovarian follicle by LH causes growth of the follicle and the release of estradiol, which further stimulates LH, which causes more follicle activity, and so on until ovulation occurs.

Feature Investigation Questions 1. Using Daphnia pulex, Paland and Lynch compared the accumulation of mitochondrial mutations between sexually reproducing populations and asexually reproducing populations. 2. Of all the mutations observed in the populations, 17.7% were either moderately or mildly deleterious and all of these persisted in the asexually reproducing species, whereas only 4.4% persisted in sexually reproducing species. Thus, populations of asexually reproducing species were about four times more likely to retain a deleterious mutation. 3. Sexual reproduction allows for mixing of the different alleles of genes with each generation, thereby increasing genetic variation within the population. This increased variation could prevent the accumulation of deleterious alleles in the population.

Test Yourself

1. d  2. c  3. e  4. a  5. d  6. c  7. b  8. c  9. c  10. e

Conceptual Questions 1. External fertilization results in exposure of gametes to predation and other environmental dangers. Many animals have evolved the ability to lay enormous numbers of eggs to compensate for these dangers. 2. Cells of the hypothalamus produce two important hormones that regulate reproduction. GnRH stimulates the anterior pituitary gland to release two gonadotropic hormones, LH and FSH. These two hormones regulate the production of gonadal hormones and development of gametes in both sexes. In addition, increased secretion of GnRH contributes to the initiation of puberty. The mammalian hypothalamus also produces oxytocin, a hormone that is stored in the posterior pituitary gland and that acts to stimulate uterine contractions during labor and milk release during lactation. 3. Sexual reproduction requires that males and females of a species produce different gametes and that these gametes come into contact with each other. Thus, males and females must expend energy to locate mates. Also, the production of very large numbers of gametes may be necessary to increase the likelihood that the eggs are fertilized. These costs are outweighed by the genetic diversity afforded by sexual reproduction.

Chapter 52

Concept Checks Figure 52.2  Although swelling is one of the most obvious manifestations of inflammation, it has no significant adaptive value of its own. It is a consequence of fluid

leaking out of blood vessels into the interstitial space. It can, however, contribute to pain sensations, because the buildup of fluid may cause distortion of connective tissue structures such as tendons and ligaments. Pain, while obviously unpleasant, is an important signal that alerts many animals to an injury and serves as a reminder to protect the injured site. Figure 52.10  Both B-cell and T-cell receptors have transmembrane domains, a constant region, and a variable region that binds a specific antigen. Figure 52.14  Because an animal may encounter the same type of pathogen many times during its life, having a secondary immune response means that future infections will be fought off much more efficiently.

Feature Investigation Questions 1. The amino acid sequence of Toll protein shared similarities with a portion of a protein known to be involved in immune responses in vertebrates. In addition, activation of Toll protein and the vertebrate immune protein (a cytokine receptor) resulted in the generation of some of the same intracellular signals. These findings suggested that in addition to its characterized role in embryonic development, Toll may also be important in immune functions in flies. 2. No, Toll protein is not a receptor that recognizes pathogen-associated molecular patterns (PAMPs) expressed on microbial surfaces, and thus it is distinguishable from Toll-like receptors in vertebrates. Toll is, however, a transmembrane protein that binds to extracellular signals; these signals arise, however, not from the microbes themselves but rather from proteins that are endogenous to flies and that are generated during infections. 3. Yes, the results of the survival study clearly implicated Toll as a protein required for the induction of antimicrobial proteins and the ability to withstand fungal infection. Thus, the investigators’ hypothesis was supported.

Test Yourself

1. e  2. b  3. c  4. c  5. a  6. e  7. b  8. a  9. d  10. b

Conceptual Questions 1. Innate immunity is present at birth and is found in all animals. These defenses recognize general, conserved features common to a wide array of pathogens and include internal defenses involving phagocytes and other cells. Adaptive immunity develops after an animal has been exposed to a particular antigen. The responses include humoral and cell-mediated defenses. Adaptive immunity appears to be largely restricted to vertebrates. Unlike innate immunity, in adaptive immunity, the response to an antigen is greatly increased if an animal is exposed to that antigen again at some future time. 2. Bacteria are single-celled prokaryotes that lack a true nucleus but are capable of reproducing on their own. Viruses are nucleic acids packaged in a protein coat; they require a host cell to reproduce. Eukaryotic parasites include certain fungi, protists and worms. 3. An immunoglobulin consists of four interlinked polypeptides, two heavy chains and two light chains, held together by disulfide bonds. Each immunoglobulin contains within its structure a constant region that is the same from one molecule to another within a given immunoglobulin class, and a variable region. The amino acid sequence of the variable region is what distinguishes one immunoglobulin from another and allows that region to specifically bind a particular antigen.

Chapter 53

Concept Checks Figure 53.6  Most of these receptors are located in or associated with blood vessels supplying the brain, a vital organ that among other functions controls many of the compensatory responses to changes in blood pressure or blood oxygen levels. Other receptors are located in the aorta, the first major vessel to leave the heart. Thus, blood pressure and gases are monitored in the general circulation and also specifically in the circulation entering the brain.

Core Skills: Connections Figure 53.3  Stretch-sensitive receptors are widespread in animal bodies. The familiar knee-jerk response is a reflex triggered by the stretch of receptors located in tendons in the knee. Other examples include stretch receptors in muscles that provide feedback information on an animal’s posture and movement,



APPENDIX B

A-29

receptors in the stomach that relay a sense of fullness when the stomach is stretched after eating, and receptors in the urinary bladder that signal when the bladder is full.

Chapter 54

Figure 53.11  Positive feedback also occurs during the ovarian cycle in mammals at the time of ovulation (see Figure 51.9) and during the process of birth in mammals (see Figure 51.11).

Figure 54.6  Cold water suppresses the ability of the coral-building organisms to secrete their calcium carbonate shell.

1. Muscular movements help propel blood from veins in the limbs back to the heart. The increased venous return helps restore blood pressure by providing additional blood for the heart to pump. It is also possible that the unusually large decrease in pressure that occurred in the denervated dogs upon standing activated other, slower mechanisms that increased blood pressure independently of the two sets of baroreceptors described here. For example, although it was not described in the chapter, most animals including mammals have additional sets of baroreceptors in other organs that appear to play a smaller role in the control of blood pressure. 2. By testing the animals in a quiet, isolated room, the investigators reduced the possibility of other complicating variables that might cause a change in blood pressure. For example, stressful sounds or smells, or the sight of unfamiliar investigators might activate neural pathways associated with fight-or-flight responses, and these could raise blood pressure independently of baroreceptor input. 3. To ascertain the relative contributions of different baroreceptors to the responses shown by the animals in this experiment, the investigators could denervate the carotid or aortic baroreceptors independently, leaving the other set intact. This would allow a direct comparison of the effectiveness of each set of baroreceptors.

Test Yourself

1. b  2. d  3. a  4. c  5. a  6. c  7. e  8. e  9. c  10. e

Conceptual Questions 1. Animals in nature are confronted with many types of homeostatic challenges that often require integrated responses by multiple organ systems. For example, a bird flying at a high altitude over a mountain range faces the challenge of obtaining sufficient oxygen from the air. In such a situation, a bird might increase its breathing rate, adjust its cardiac output, or both; indeed, both of these changes and several others do occur. Similarly, fish that migrate between fresh and salt water, such as salmon, alter the function of their respiratory and urinary systems to help compensate for the changes in ion and water movement across the gills due to moving from one environment to another. Yet another common example of a challenge to homeostasis is starvation, during which the nervous, endocrine, urinary, and digestive systems will help maintain glucose homeostasis by processes such as gluconeogenesis. 2. Light-headedness can occur in some people when donating blood, which is essentially a carefully controlled hemorrhage. Initially, as the homeostatic processes described in this chapter are just beginning, there is a period of instability with respect to blood pressure control. While lying or sitting down, this is rarely noticeable, but when the person stands, gravity counteracts the movement of blood through limb veins back to the heart, causing a sudden decrease in pressure. Fainting does not usually occur, however, because the baroreceptor reflex responds immediately to this sudden change in pressure, and within seconds the heart rate and cardiac output are increased due to the actions of the sympathetic nervous system. The phenomenon of light-headedness can actually happen any time a person stands up after reclining, even under ordinary circumstances, but it is more noticeable when a person’s blood volume is reduced such as after donating blood. 3. All of the homeostatic responses to hemorrhage described in this chapter require energy. Increasing the activity of any muscle, including that of the heart and the respiratory muscles, requires a considerable increase in expenditure of energy (ATP). Activity of the nervous system, so vital to the compensatory response to hemorrhage, requires continual ATP production and hydrolysis to maintain ion concentration gradients across the plasma membrane of neurons; without the maintenance of these gradients, there could be no flow of current along a neuron. Many of the transport processes in the kidneys also require ATP to drive the ion pumps that move ions across membranes and that create osmotic gradients for the movement of water.

Figure 54.9  In some areas when fire is prevented, fuel, in the form of old leaves and branches, can accumulate. When a fire eventually occurs, it can be so large and hot that it destroys everything in its path, even reaching high into the tree canopy. Figure 54.14  Acid soils are low in essential plant and animal nutrients such as calcium and nitrogen and are lethal to some soil microorganisms that are important in decomposition and nutrient cycling. Figure 54.16  This band is due to increasing cloudiness and rain in the tropics, which maintain fairly constant temperatures across a relatively wide latitudinal range. Figure 54.22  Soil conditions can also influence biome type. Nutrient-poor soils, for example, may support vegetation different from that of the surrounding area. Figure 54.23 Taiga.

Core Skills: Connections Figure 54.13  Plants cannot readily absorb salty water because of its highly negative water potential.

Feature Investigation Questions 1. Most believed that invasive species succeed in new environments because of the lack of natural enemies and that diseases and predators present in the original environment controlled the growth of the population. When a species is introduced into a novel environment, the natural enemies are usually absent. This allows for an unchecked increase in the population of the invasive species. 2. Callaway and Aschehoug were able to demonstrate through a controlled experiment that the presence of C. diffusa, an invasive species, reduced the biomass of three other native species of grasses by releasing allelochemicals. Similar experiments using species of grasses that are found in the native region of C. diffusa indicated that these species have evolved defenses against the allelochemicals. 3. The activated charcoal helped to remove the allelochemical(s) from the soil. The researchers conducted this experiment to provide further evidence that the chemical(s) released by C. diffusa was reducing the biomass of the native Montana grasses. With the removal of the chemical(s) by the addition of the charcoal, the researchers observed an increase in biomass of the native Montana grasses compared with the experiments lacking the charcoal. 4. Researchers could measure the biomass of C. diffusa. Because C. diffusa is invasive in the U.S., effects of native North American grasses on C. diffusa would be expected to be weak. Conversely, C. diffusa is not invasive in Eurasia so strong effects of Eurasian grasses on C. diffusa should be observed, and this is what researchers found.

Test Yourself

1. b  2. a  3. b  4. b  5. a  6. a  7. d  8. d  9. a  10. c

Conceptual Questions 1. Mountains are cooler than valleys because of adiabatic cooling. Air at higher altitudes expands because of decreased pressure. As it expands, air cools, at a rate of 10°C for every 1,000 m in elevation. As a result, mountain tops can be much cooler than the plains or valleys that surround them. 2. First, lightning strikes from electrical storms are usually more frequent in prairies than in deserts. Second, the vegetation in a prairie is more continuous and the biomass more extensive than in a desert, so fires burn more frequently and for longer periods. 3. Florida is a peninsula that is surrounded by the Atlantic Ocean and the Gulf of Mexico. Differential heating between the land and the sea creates onshore sea breezes on both the east and west coasts. These breezes often drive clouds across the whole peninsula, bringing heavy rain.

Chapter 55

Concept Checks Figure 55.3  In operant conditioning a behavior is reinforced by a reward or punishment. In classical conditioning, an involuntary response comes to be associated with a stimulus that did not originally elicit the response, as with Pavlov’s dogs salivating at the sound of a metronome.

APPENDIX B

Feature Investigation Questions

Concept Checks

A-30

APPENDIX B

Figure 55.5  The ability to sing the same distinctive song must be considered innate behavior because the cuckoo has had no opportunity to learn its song from its parents.

Figure 56.13  It has lost the ability to produce viable seeds but it makes thousands of fully formed plantlets, borne on its leaves.

Figure 55.7  Tinbergen manipulated pinecones, but not all digger wasp nests are surrounded by pinecones. You could manipulate branches, twigs, stones, and leaves to determine the necessary size and dimensions of objects that digger wasps use as landmarks.

Feature Investigation Questions

Figure 55.8  Monarch migration is an unusual example because the return trip involves several different generations: One generation overwinters in Mexico, but these individuals lay eggs and die on the return journey, and their offspring continue the return trip. Figure 55.15  The individuals in the center of the group are less likely to be attacked than those on the edge of the group. This advantage is referred to as the geometry of the selfish herd. Figure 55.18  All the larvae in the group are likely to be the progeny of one egg mass from one adult female moth. The death of one caterpillar in the cluster teaches a predator to avoid preying on caterpillars with that warning pattern and thus benefits the caterpillar’s close kin.

Core Skills: Connections Figure 55.3  Prey species converge on the color patterns displayed by toxic, badtasting, or dangerous species to reinforce predators’ avoidance of them. Figure 55.4  According to studies of humans and other animals, learning a task increases the size of brain regions that are associated with learning and memory.

Feature Investigation Questions APPENDIX B

1. Tinbergen observed the activity of digger wasps as they prepared to leave the nest. Each time, the wasp hovered and flew around the nest for a period of time before leaving. Tinbergen suggested that during this time, the wasp was making a mental map of the nest site. He hypothesized that the wasp was using characteristics of the nest site, particularly landmarks, to help relocate it. 2. Tinbergen placed pinecones around the nest of the wasps. When the wasps left the nest, he removed the pinecones from the nest site and set them up in the same pattern a distance away, constructing a sham nest. For each trial, the wasps would go directly to the sham nest, which had the pinecones around it. This indicated to Tinbergen that the wasps identified the nest based on the pinecone landmarks. 3. No, but Tinbergen also conducted an experiment to determine if the wasps were responding to the visual cue of the pinecones or the chemical cue of the pinecone scent. The results of this experiment indicated that the wasps responded to the visual cue of the pinecones and not their scent.

Test Yourself

1. d  2. d  3. d  4. c  5. c  6. d  7. b  8. c  9. a  10. c

Conceptual Questions 1. The donation of the male’s body to the female is the ultimate nuptial gift. It is possible that this meal enables the females to produce more eggs. In this way, the male benefits because its genes will be passed on to future generations. 2. Certainty of paternity influences degree of parental care. With internal fertilization, certainty of paternity is relatively low. With external fertilization, eggs and sperm are deposited together, and paternity is more certain. This explains why males of some species, such as mouth-breeding cichlid fish, are more likely to engage in parental care. 3. Alarm calling calls attention to the caller, so if no relatives are present, females bolt into their warren to escape a predator. However, daughters and sisters are kin and may pass on copies of a female’s genes, so alarm calls are frequently made when these relatives are present.

Chapter 56

Concept Checks Figure 56.3  In a half-empty classroom, the distribution is often clumped because friends sit together. Figure 56.6  (a) type III, (b) type II Figure 56.12  Only density-dependent factors have this stabilizing tendency.

Core Skills: Connections Figure 56.3  Uniform. Territorial marking is likely to keep cheetahs well separated from each other.

1. It became apparent that the sheep population was declining. Some individuals thought that the decline in the population was due to the negative effect of increased wolf predation on population growth. This idea led to the suggestion of culling the wolf population to reduce the level of predation on the sheep. 2. The survivorship curve is similar to a typical type I survivorship curve, which would suggest that survival is high among young and reproductively active members of the population and that mortality rates are higher for older members of the population. One difference between the actual survivorship curve and a typical type I curve is that the mortality rate of very young sheep was higher in the actual curve and then leveled off after the second year. This suggests that very young and older sheep are at greater risk from predation. 3. It was concluded that wolf predation was not the primary reason for the drop in the sheep population. It appeared that wolves prey on the vulnerable members of the population and not on the healthy, reproductively active members. The Park Service determined that several cold winters may have had a more important effect on the sheep population than wolf predation did. Based on these conclusions, the Park Service ended its wolf-control program.

Test Yourself

1. b  2. e  3. b  4. c  5. c  6. b  7. b  8. c  9. d  10. c

Conceptual Questions 1. It increases. Instead of recapturing 5 tagged fish, you will recapture only 4. Population size is now estimated as 50 × 40/4 = 2,000/4 = 500. Your population size estimate has increased to 500 when, in fact, it is more likely that 400 fish occur in the lake. 2. When population sizes are low (N = 100), (K – N)/K is so small that growth is low. (1,000−100) dN ​​ = (0.1)(100) × _________ ​​​ ___ ​​   ​​    1,000 dt dN ​​​ ___ ​​ = 9 dt At medium values of N, (K – N)/K is closer to a value of 1, and population growth is relatively large. If K = 1,000, N = 500, and r = 0.1, then (1,000−100) dN ​ ​= (0.1)(500) × ___________ ​​​ ___ ​​   ​​    1,000 dt dN ​ ​= 25 ​​​ ___ dt By comparing these two examples with that shown in Section 56.3, we see that growth is small at high and low values of N and is greatest at immediate values of N. Growth is greatest when N = K/2. However, when expressed as a percentage, growth is greatest at low population sizes. Where N = 100, percentage growth = 9/100 = 9%. Where N = 500, percentage growth = 25/500 = 5%, and where N = 900, percentage growth = 9/100 = 1%. 3. In the ponds that dry out, species would tend to be semelparous, producing all their offspring in a single reproductive event while water is present. In the permanently wet ponds, species would be iteroparous, reproducing repeatedly over the course of a lifetime.

Collaborative Questions 2. a) λ = 1,200 / 1,000 = 1.2 b) After 5 years, N5 = N0λ5  =   (1,000) (1.2)5   = 2,488

Chapter 57

Concept Checks Figure 57.2  Individual vultures often fight one another over small carcasses. These interactions constitute intraspecific interference competition. Figure 57.6  In 1974, Tom Schoener examined segregation in a more wideranging literature review of over 80 species, including slime molds, mollusks, and insects, as well as birds. He found segregation by habitat occurred in the majority



APPENDIX B

Figure 57.8  Omnivores, such as bears, can feed on both plant material, such as berries, and animals, such as salmon. Thus, omnivores may act as either predators or herbivores, depending on what they are feeding on. Figure 57.9  Batesian mimicry has a positive effect for the mimic, and the model is unaffected, so it is a +/0 relationship, like commensalism. Müllerian mimicry has a positive effect on both species, so it is a +/+ relationship, like mutualism. Figure 57.11  Invertebrate herbivores can eat around mechanical defenses; therefore, chemical defenses are probably most effective against these herbivores. Figure 57.16  It’s an example of facultative mutualism, because both species can live without the other. Figure 57.19  Fertilizer increases plant quality and hence herbivore density, which, in turn, increases the density of spiders. This is bottom-up control.

Core Skills: Connections Figure 57.9  Most mollusks are heavily armored. However, sea slugs have lost their shells. These species are aposematically colored, advertising a poisonous body. In addition, some octopuses are poisonous, and most can eject an inky chemical “smokescreen.” Figure 57.11  Red hot chili peppers. Figure 57.13  Dodder, Cuscuta pentagona, is another important parasitic plant. Figure 57.17  Red.

Feature Investigation Questions 1. The two species of barnacles can be found in the same intertidal zone, but there is a distinct difference between the realized niches of these species. Chthamalus stellatus is found only in the upper intertidal zone. Semibalanus balanoides is found only in the lower tidal zone. 2. Connell moved rocks with young Chthamalus from the upper intertidal zone into the lower intertidal zone to allow Semibalanus to colonize the rocks. After the rocks were colonized by Semibalanus, he removed Semibalanus from one side of each rock and returned the rocks to the lower intertidal zone. This procedure allowed Connell to observe the growth of Chthamalus in the presence and the absence of Semibalanus. 3. Connell observed that Chthamalus was more resistant to desiccation than Semibalanus. Though Semibalanus was the better competitor in the lower intertidal zone, that species was at a disadvantage in the upper intertidal zone when water levels were low. This fact allowed Chthamalus to flourish and outcompete Semibalanus in a different region of the intertidal zone.

Test Yourself

1. d  2. c  3. b  4. d  5. c  6. b  7. d  8. b  9. b  10. c

Conceptual Questions 1. Yes, it is possible that by removing parasites from a neighbor, a primate may be reducing the likelihood of the parasite spreading to infect it. You scratch my back, I’ll scratch yours, and together we will both be better off. 2. There are at least three factors that might limit losses due to pest damage to crops. First, plants possess an array of defensive chemicals, including alkaloids, phenolics, and terpenes. Second, many herbivore populations are reduced by the action of natural enemies. Third, the low nutritive value of plants ensures that herbivore populations remain low and unlikely to affect plant populations. While we can’t easily increase the levels of defensive chemicals in many crop plants or reduce their nutritive value, we can introduce more natural enemies of plant pests. We see evidence for this in the use of biological controls.

Chapter 58

Concept Checks Figure 58.3  The species richness of trees doesn’t increase in the mountainous areas of the West because rainfall in the western U.S. is low compared to that in the East. Figure 58.5  Walking from the current edge of the glacier to the mouth of the inlet, an ecologist is walking backward in ecological time to communities that originated hundreds of years ago. Figure 58.8  Competition features more prominently. Although early colonists tend to make the habitat more favorable for later colonists, it is the later colonists who outcompete the earlier ones, and this fuels species change.

Figure 58.10  At first glance, the change looks small, but the data are plotted on a log scale. On this scale, an increase in bird richness from 1.2 to 1.6 equals an increase from 16 to 40 species, a change of over 100%. Figure 58.14  It depends on the trophic level of their food, whether dead vegetation or dead animals. Many decomposers feed at multiple trophic levels.

Core Skills: Connections Figure 58.9  The model helps conservationists design the best shaped and optimally placed nature reserves in a “sea” of developed land. Figure 58.13  Cyanobacteria.

Feature Investigation Questions 1. Simberloff and Wilson were testing the three predictions of the equilibrium theory of island biogeography. One prediction suggested that the number of species should increase with increasing island size. Another prediction suggested that the number of species should decrease with increasing distance of the island from the source pool. Finally, the researchers were testing the prediction that the turnover of species on islands should be considerable. 2. Simberloff and Wilson used the information gathered from the species survey to determine whether the same types of species recolonized the islands or the colonizing species were random. 3. Island distance to the mainland affected species richness with near islands having higher numbers of species than distant islands. However, species turnover was low on all islands and was unaffected by island distance from the mainland.

Test Yourself

1. c  2. a  3. c  4. a  5. e  6. c  7. e  8. a  9. d  10. c

Conceptual Questions 1. The value of the Shannon diversity index is 1.609 for both forests. By this measure, diversity is equal in the two forests. The index is unable to discriminate between communities that have different species abundances but the same relative proportions of species. An observer would be more likely to encounter a variety of trees in forest A than in forest B. 2. Carrion beetles are decomposers. They feed on dead animals such as mice, at trophic level 3 or 4. Mice generally feed on vegetative material (trophic level 1) or crawling arthropods (trophic level 2), so mice themselves feed at trophic level 2 or 3. 3. C. vulgaris litter enriches the soil with nitrogen, facilitating the growth of the grasses. Adding fertilizer also increases soil nitrogen. The mechanism of succession operating in this case is facilitation.

Chapter 59

Concept Checks Figure 59.2  The conclusion would be that were very few juveniles in the population and many mature adults. The population would be in decline. Figure 59.5  Many different ecological footprint calculators are available on the Internet. Does altering inputs such as type of transportation, amount of meat eaten, or amount of waste generated make a difference? Figure 59.7  Hawaii lies north of the equator. The Northern Hemisphere has greater land area and plant biomass than the Southern Hemisphere, so in the northern summer more CO2 is used up by plants and atmospheric CO2 level declines slightly. In the northern winter, less CO2 is absorbed and atmospheric CO2 levels increase. Figure 59.9  The greatest stores are in rocks and fossil fuels.

Core Skills: Connections Figure 59.9  The other three elements are oxygen, hydrogen, and nitrogen. Therefore, the water and nitrogen cycles are very important to humans.

Feature Investigation Questions 1. The researchers wanted to learn the effects of increased carbon dioxide levels on the forest ecosystem: the effects on primary production as well as on other trophic levels in the ecosystem. 2. By increasing the carbon dioxide levels in only half of the chambers, the researchers were maintaining the control treatment necessary in all scientific studies.

APPENDIX B

of the examples, 55%. The second most common form of segregation was by food type, 40%.

A-31

A-32

APPENDIX B

By maintaining equal numbers of control and experimental treatments, the researchers could compare data to determine what effects the experimental treatment had on the ecosystem. 3. t14 = 5.667, P < 0.001; x1 = 10.00, s.d = 2.93; x2 = 3.20, s.d = 1.72

Feature Investigation Questions 1. The researchers hoped to replicate terrestrial communities that differed only in their level of species richness. This would allow the researchers to determine the relationship between species richness and ecosystem function.

Test Yourself

2. The hypothesis was that ecosystem function was directly related to species richness. If species richness increased, the hypothesis suggested that ecosystem function should increase.

Conceptual Questions

3. The researchers tested for ecosystem functioning by monitoring community respiration, decomposition, nutrient retention rates, and productivity. All of these indicate the efficiency of nutrient production and use in the ecosystem.

1. d  2. c  3. d  4. b  5. a  6. b  7. e  8. b  9. b  10. e

1. Nitrogen molecules have a triple bond, making them hard to break apart. Only a few species of bacteria can break apart atmospheric nitrogen and fix nitrogen. The excess ammonia, NH3, or ammonium, NH4+, that they produce in this way gradually accumulates and can be used by plants. 2. Maximum sustainable yield represents the number of individuals that can be removed from a population without affecting population growth. This is rather like removing the interest from a bank account and not touching the principal. Maximal sustainable yield occurs at the steepest point of the growth curve, which is at the midpoint of the logistic curve. 3. The family whose members have triplets has 27 descendants in 2000, compared to 32 for the family whose members have twins. Delaying reproduction can slow population growth.

Chapter 60 APPENDIX B

Concept Checks Figure 60.3  It is possible that the results are driven by what is known as a sampling effect. As the numbers of species in the community increase, so does the likelihood of including a “superspecies,” a species with exceptionally large individuals that would use up resources. In communities with higher diversity, care has to be taken that increased species richness is driving the results, not the increased likelihood of including a superspecies. Figure 60.8  Corridors might also promote the movement of invasive species or the spread of fire between areas. Figure 60.9  The hedgerows act as habitat corridors because they permit species movement between forest fragments.

4. The redundancy hypothesis.

Test Yourself

1. d  2. c  3. b  4. a  5. c  6. a  7. e  8. e  9. b  10. c

Conceptual Questions 1. Increased species diversity increases ecosystem function. Ecosystem functions such as nutrient cycling, regulation of atmospheric gases, pollination of crops, pest regulation, water purity, storm protection, and sewage purification are all likely to be increased by increased species diversity. In addition, increased plant species diversity increases likely availability of new medicines for humans. 2. Megadiversity countries are those with the greatest number of species. Biodiversity hot spots conserve the greatest numbers of endemic species. Crisis ecoregions are those areas of the Earth which represent distinct biome types, such as temperate grasslands and tropical deciduous forests, but have undergone substantial habitat loss. “Last of the wild” areas are relatively pristine areas such as much tundra and taiga, deserts, and some tropical rainforests. 3. The diversity-stability hypothesis suggests a linear correlation between species richness and ecosystem function; as diversity increases, ecosystem function increases proportionately. The redundancy hypothesis suggests that ecosystem function increases rapidly at lower levels of species richness but then levels off, as additional species are functionally redundant. The keystone hypothesis suggests that ecosystem function is low at low levels of species richness and only rises substantially as species richness approaches high levels. The idiosyncratic hypothesis suggests that there is no predictable relationship between species richness and ecosystem function.

1000 Genomes Project  ​ ​An international research effort to establish the level of human genetic variation. 20-hydroxyecdysone  ​ ​A hormone produced by the prothoracic glands of arthropods that stimulates molting. 30-nm fiber  ​ ​Nucleosome units organized into a more compact structure that is 30 nm in diameter. 5′ cap  ​ ​The 7-methylguanosine structure at the 5′ end of most mature mRNAs in eukaryotes.

A

ABC model  ​ ​A model for flower development in which three classes of genes, called A, B, and C, govern the formation of sepals, petals, stamens, and carpels. More recently, a fourth class, called the E genes, was found to be required for this process.  abiotic  ​ ​The term used to describe interactions between organisms and their nonliving environment. abscisic acid  ​ ​One of several plant hormones that help a plant cope with environmental stress. absolute refractory period  ​ ​The period during an action potential when the inactivation gate of the voltagegated sodium channel is closed; during this time, it is impossible to generate another action potential. absorption spectrum  ​ ​A diagram that depicts the wavelengths of electromagnetic radiation that are absorbed by a pigment. absorption  ​ ​The process in which ions, water, and small molecules diffuse or are transported out of the alimentary canal into an animal’s body fluids. absorptive nutrition  ​ ​The process whereby an organism uses enzymes to digest organic materials and absorbs the resulting small food molecules into its cells. absorptive state  ​ ​One of two alternating phases in the utilization of nutrients; occurs when ingested nutrients enter the blood from the gastrointestinal tract. The other phase is the postabsorptive state. accommodation  ​ ​In the vertebrate eye, the process in which contraction and relaxation of the ciliary muscles adjust the lens according to the angle at which light enters the eye. acetylcholinesterase  ​ ​An enzyme located on membranes of postsynaptic cells that respond to the neurotransmitter acetylcholine, such as in muscle fibers in a neuromuscular junction; breaks down excess acetylcholine released into the synaptic cleft. acid hydrolase  ​ ​A hydrolytic enzyme found in lysosomes that functions at acidic pH and uses a molecule of water to break a covalent bond. acid rain  ​ ​Precipitation with a pH of less than 5.6; results from the burning of fossil fuels. acid  ​ ​A molecule that releases hydrogen ions (H+) in solution. acidic  ​ ​A solution that has a pH below 7. acoelomate  ​ ​An animal that lacks a fluid-filled body cavity. acquired antibiotic resistance  ​ ​The common phenomenon in which a previously susceptible strain of bacteria becomes resistant to a specific antibiotic. acquired immunodeficiency syndrome (AIDS)  ​ ​A disease caused by the human immunodeficiency virus (HIV) that weakens the immune system of infected individuals. acrocentric  ​ ​A chromosome in which the centromere is near one end. acromegaly  ​ ​A condition in which a person’s growth hormone level is abnormally elevated after puberty, causing many bones to thicken and enlarge.

acrosomal reaction  ​ ​An event in fertilization in which enzymes released from a sperm’s acrosome break down the outer layers of an egg cell, allowing the entry of the sperm cell’s nucleus into the egg cell. acrosome  ​ ​A special structure at the tip of a sperm’s head containing proteolytic enzymes that help break down the protective outer layers of the egg cell at fertilization. actin filament  ​ ​A thin type of protein filament composed of actin proteins that forms part of the cytoskeleton and supports the plasma membrane; plays a key role in cell strength, shape, and movement. actin  ​ ​A cytoskeletal protein, found in the thin filaments of myofibrils. action potential  ​ ​An electrical signal along a cell’s plasma membrane; occurs in animal neuron axons and muscle cells and in some plant cells. action spectrum  ​ ​The rate of photosynthesis plotted as a function of the wavelength of light. activation energy  ​ ​An initial input of energy in a chemical reaction that allows the molecules to get close enough to cause a rearrangement of bonds. activator  ​ ​A transcription factor that binds to DNA and increases the rate of transcription. active immunity  ​ ​An animal’s ability to fight off a pathogen to which it has been previously exposed. Active immunity can develop as a result of natural infection or artificial immunization. active site  ​ ​The location in an enzyme where a chemical reaction takes place. active transport  ​ ​The transport of a substance across a membrane from an area of low concentration to one of higher concentration with the aid of a transport protein; requires an input of energy. adaptations  ​ ​Changes in populations of living organisms that are the result of natural selection and that increase their ability to survive and reproduce in their environment. adaptive immunity  ​ ​A specific immune defense that develops only after an animal is exposed to a foreign substance; believed to be unique to vertebrates. adaptive radiation  ​ ​The process whereby a single ancestral species evolves into a wide array of descendant species that differ greatly in their habitat, form, or behavior. adenine (A)  ​ ​A purine base found in DNA and RNA. adenosine triphosphate (ATP)  ​ ​A molecule that is a common energy source for all cells. adenylyl cyclase  ​ ​An enzyme in the plasma membrane that synthesizes cAMP from ATP. adherens junction  ​ ​A mechanically strong type of cell junction between animal cells that is organized into bands. The cells are connected to each other via cadherins, and the cadherins are linked to actin filaments on the inside of the cells. adhesion  ​ ​The ability of two different substances to bind to each other; the ability of water to be attracted to, and thereby adhere to, a surface that is not electrically neutral. adiabatic cooling  ​ ​The process in which increasing elevation produces a decrease in air temperature due to lowered air pressure. adventitious root  ​ ​A root that is produced on the surfaces of stems (and sometimes leaves) of vascular plants; also, roots that develop at the bases of stem cuttings. aerenchyma  ​ ​Spongy plant tissue with large air spaces. aerobic respiration  ​ ​A type of cellular respiration in which O2 is consumed and CO2 is released.

aerotolerant anaerobe  ​ ​A microorganism that does not use oxygen but is not poisoned by it either. afferent arteriole  ​ ​Blood vessel that carries blood into a glomerulus of the vertebrate kidney. affinity  ​ ​The degree of attraction between an enzyme and its substrate(s). aflatoxins  ​ ​Fungal toxins that cause liver cancer and are a major health concern worldwide. age structure  ​ ​The relative numbers of individuals of each defined age group in a population. age-specific fertility rate  ​ ​The rate of offspring production for females of a certain age; used to calculate how a population grows. akinete  ​ ​A thick-walled, food-filled cell produced by certain bacteria or protists that enables them to survive unfavorable conditions in a dormant state. aldosterone  ​ ​A steroid hormone made by the adrenal glands that regulates salt and water balance in vertebrates. algae (singular, alga)  ​ ​A term that applies to about 10 phyla of protists, including mostly photosynthetic and some nonphotosynthetic species; often also includes cyanobacteria. alimentary canal  ​ ​In animals, the single elongated tube of a digestive system, with an opening at either end through which food and eventually wastes pass from one end to the other. alkaline  ​ ​A solution with a pH above 7. allantois  ​ ​One of the four extraembryonic membranes in the amniotic egg. It serves as a disposal sac for metabolic wastes. allele frequency  ​ ​The number of copies of a particular allele in a population divided by the total number of alleles for that gene in that population. allele  ​ ​A variant form of a gene. allelochemical  ​ ​A powerful plant chemical, often a root exudate, that kills other plant species. allelopathy  ​ ​The suppression of growth of one species due to the release of toxic chemicals by another species. allergy  ​ ​Hypersensitivity reaction to an environmental antigen (an allergen) that is otherwise a harmless or relatively harmless substance. allopatric speciation  ​ ​A form of speciation that occurs when a population becomes geographically isolated from other populations and evolves into one or more new species. allopatric  ​ ​The term used to describe species occurring in different geographic areas. alloploid  ​ ​An organism having at least one set of chromosomes from two or more different species. allosteric site  ​ ​A site on an enzyme where a molecule can bind noncovalently and affect the enzyme’s function. alternation of generations  ​ ​The phenomenon that occurs in plants and some protists in which the life cycle alternates between multicellular diploid organisms, called sporophytes, and multicellular haploid organisms, called gametophytes. alternative splicing  ​ ​The splicing of pre-mRNA in more than one way to allow the production of two or more different polypeptides from the same gene. altruism  ​ ​Behavior that appears to benefit others at a cost to oneself. alveolus (plural, alveoli)  ​ ​1. Saclike structures in the lungs where gas exchange occurs. 2. Saclike cellular features of the protists known as alveolates. Alzheimer’s disease (AD)  ​ ​The leading worldwide cause of dementia; characterized by a loss of memory and intellectual and emotional function.

G-1

GLOSSARY

Glossary

G-2 GLOSSARY

GLOSSARY

AM  ​  ​See arbuscular mycorrhizae.   amensalism  ​ ​One-sided competition between species, in which the interaction is detrimental to one species but not to the other. Ames test  ​ ​A test that helps ascertain whether or not an agent is a mutagen by using a strain of a bacterium, Salmonella typhimurium. amino acid  ​ ​Any of the monomers that are linked to form a protein. Amino acids have a common structure in which a carbon atom, called the α-carbon, is linked to an amino group (─NH2) and a carboxyl group (─COOH), as well as to a hydrogen atom and a side chain that distinguishes the particular amino acid. aminoacyl site (A site)  ​ ​One of three sites for tRNA binding in the ribosome during translation; the other two are the peptidyl site (P site) and the exit site (E site). The A site is where incoming tRNA molecules bind to the mRNA (except for the initiator tRNA). aminoacyl tRNA  See charged tRNA. aminoacyl-tRNA synthetase  ​ ​An enzyme that catalyzes the attachment of amino acids to tRNA molecules. ammonification  ​ ​The conversion of organic nitrogen to NH3 and NH4+ during the nitrogen cycle. amnion  ​ ​The innermost of the four extraembryonic membranes in the amniotic egg. It protects the developing embryo in a fluid-filled sac called the amniotic cavity. amniotes  ​ ​A group of tetrapods with amniotic eggs that includes turtles, lizards, snakes, crocodiles, birds, and mammals. amniotic egg  ​ ​A type of egg produced by amniotes that contains the developing embryo and the four separate extraembryonic membranes that it produces: the amnion, the yolk sac, the allantois, and the chorion. amoeba (plural, amoebae)  ​ ​A protist that moves by pseudopodia, which involves extending cytoplasm into filaments or lobes. amoebocyte  ​ ​A mobile cell within a sponge’s mesophyl that absorbs food from choanocytes, digests it, and carries the nutrients to other cells. amphibian  ​ ​An ectothermic, vertebrate animal that metamorphoses from a water-breathing to an airbreathing form but must return to the water to reproduce. amphipathic  ​ ​Refers to molecules containing a hydrophobic (water-fearing) region and a hydrophilic (water-loving) region. amplicon analysis  ​ ​A comparison of amplicons (amplified sequences) present in a particular DNA sample to reference sequences in a database. amplicon  ​ ​Any gene region for which many copies have been made (amplified) from a DNA sample with the use of specific primer sequences in polymerase chain reaction (PCR). ampulla (plural, ampullae)  ​ ​1. A muscular sac at the base of each tube foot of an echinoderm; used to store water. 2. A bulge in the walls of the semicircular canals of the mammalian inner ear; important for sensing circular motions of the head. amygdala  ​ ​An area of the limbic system of the vertebrate forebrain known to be critical for understanding and remembering emotional situations. amylase  ​ ​A digestive enzyme in saliva and the pancreas involved in the digestion of carbohydrates. anabolic reaction  ​ ​A metabolic pathway that involves the synthesis of larger molecules from smaller precursor molecules. Such reactions usually require an input of energy. anabolism  ​ ​A metabolic pathway that results in the synthesis of cellular molecules and macromolecules; requires an input of energy. anaerobic respiration  ​ ​The breakdown of organic molecules in the absence of oxygen by using a final electron acceptor that is something other than oxygen.

anaerobic  ​ ​Refers to an environment that lacks oxygen or a process that occurs in the absence of oxygen; a form of metabolism that does not require oxygen. anagenesis  ​ ​The pattern of speciation in which a single species is transformed into a different species over the course of many generations. analogous structure  ​ ​A structure that is the result of convergent evolution. Such structures have arisen independently, two or more times, because species have occupied similar types of environments on Earth. anaphase  ​ ​The phase of mitosis during which the sister chromatids separate from each other and move to opposite poles; the poles themselves also move farther apart. anatomy  ​ ​The study of the structures of living things. anchoring junction  ​ ​A type of junction between animal cells that attaches cells to each other and to the extracellular matrix (ECM). androgens  ​ ​Steroid hormones produced by the male testes (and, to a lesser extent, the adrenal glands) that affect most aspects of male reproduction. aneuploidy  ​ ​Alteration of the number of a particular chromosome present in an organism or cell, so the total number of chromosomes is not an exact multiple of a set. angiosperm  ​ ​A flowering plant. The term means enclosed seed, which reflects the presence of seeds within fruits. animal pole  ​ ​In triploblast organisms, the pole of the egg with less yolk and more cytoplasm. Animalia  ​ ​A eukaryotic kingdom of the domain Eukarya. animals  ​ ​Multicellular heterotrophs with cells that lack cell walls. Most animals have nerves, muscles, the capacity to move at some point in their life cycle, and the ability to reproduce sexually, with sperm fusing directly with eggs. anion  ​ ​An ion that has a net negative charge. annual  ​ ​A plant that dies after producing seed during its first year of life. antagonist  ​ ​Two or more muscles that produce oppositely directed movements at a joint. anterior  ​ ​Refers to the end of an animal where the head is found. anteroposterior axis  ​ ​In bilateral animals, one of the three axes along which the adult body pattern is organized; the others are the dorsoventral axis and the left-right axis. anther  ​ ​The uppermost part of a flower stamen, consisting of a cluster of four sporangia that produce and release pollen. antheridia  ​ ​Spherical or elongate gametangia that produce sperm in plants. anthropogenic  ​ ​Caused by humans or their activities; the term comes from the Greek anthropogenes, meaning “born of man,” and is often applied to environmental pollution originating from human activity. anthropoidea  ​ ​A group of primates that includes the monkeys and the hominoidea; these species are largerbrained, diurnal, and have opposable thumbs. antibiotic  ​ ​A chemical, usually made by microorganisms, that inhibits the growth of certain other microorganisms. antibody  ​ ​A protein secreted by plasma cells that is part of the immune response; antibodies travel all over the body to reach antigens identical to those that stimulated their production, combine with these antigens, and then guide an attack that eliminates the antigens or the cells bearing them. anticodon  ​ ​A three-base sequence in tRNA that is complementary to a codon in mRNA. antidiuretic hormone (ADH)  ​ ​A polypeptide hormone secreted by the posterior pituitary that acts on kidney cells to decrease urine production.

antigen  ​ ​Any foreign molecule that the host does not recognize as self and that triggers a specific immune response. antigen-presenting cells (APCs)  ​ ​Cells of a vertebrate’s acquired immune system that complex antigen with class II MHC proteins, leading to helper T cell activation. antiparallel  ​ ​The arrangement in DNA where one strand runs in the 5´ to 3´ direction and the other strand is oriented in the 3´ to 5´ direction. antiporter  ​ ​A type of transporter that binds two or more ions or molecules and transports them in opposite directions across a membrane. anus  ​ ​The opening at the posterior end of the alimentary canal through which solid wastes are expelled. aorta  ​ ​In vertebrates, a large blood vessel that exits a ventricle of the heart and leads to the systemic circulation. apical meristem  ​ ​In plants, a group of actively dividing cells at a growing tip. apical region  ​ ​The region of a plant seedling that produces the leaves and flowers. apical-basal polarity  ​ ​An architectural feature of plants in which they display an upper, apical pole and a lower, basal pole; the shoot apical meristem occurs at the apical pole, and the root apical meristem occurs at the basal pole. apical-basal-patterning genes  ​ ​A category of genes that are important in early stages of plant development during which the apical and basal axes are formed. apomixis  ​ ​A natural asexual reproductive process in which plant fruits and seeds are produced within flowers in the absence of fertilization. apoplast  ​ ​The continuum of water-filled cell walls and intercellular spaces in a plant. apoplastic transport  ​ ​The movement of solutes along cell walls and in the spaces between cells. apoptosis  ​ ​Programmed cell death. apoptosome  ​ ​A complex of proteins that promotes apoptosis via the intrinsic pathway by activating caspases.  aposematic coloration  ​ ​Warning coloration that advertises an organism’s unpalatable taste. aquaporin  ​ ​A transport protein in the form of a channel that allows the rapid diffusion of water across the cell membrane. aqueous solution  ​ ​A solution made with water. aquifer  ​ ​An underground water supply. arbuscular mycorrhizae  ​ ​Associations between plant cells, often root cells of vascular plants, and fungi that form highly branched hyphae. Archaea  ​ ​One of the three domains of life; the other two are Bacteria and Eukarya. archaea  ​ ​When not capitalized, refers to a species within the domain Archaea. archegonia (singular, archegonium)  ​ ​Flask-shaped gametangia that each enclose a single egg cell in plants. archenteron  ​ ​A cavity formed in an animal embryo during gastrulation that will become the organism’s digestive tract. area hypothesis  ​ ​The proposal that larger areas contain more species than smaller areas because they can support larger populations and a greater range of habitats. artery  ​ ​A blood vessel that carries blood away from the heart. artificial selection  See selective breeding. asci (singular, ascus)  ​ ​Fungal sporangia shaped like sacs that produce and release sexual ascospores. ascocarp  ​ ​The type of fruiting body produced by ascomycete fungi. ascomycetes  ​ ​A phylum of fungi that produce sexual spores in saclike asci located at the surfaces of fruiting bodies known as ascocarps.

ascospore  ​ ​The type of sexual spore produced by fungi in the phylum Ascomycota. aseptate  ​ ​The condition of not being partitioned into smaller cells; usually refers to fungal cells. asexual reproduction  ​ ​A reproductive strategy that occurs when offspring are produced from a single parent, without the fusion of gametes from two parents. The offspring are therefore clones of the parent. assimilation  ​ ​During the nitrogen cycle, the process by which plants and animals incorporate the NH3, – NH4+, and NO3 formed through nitrogen fixation and nitrification. assisted reproductive technologies (ART)  ​ ​A collection of procedures used to produce a pregnancy by artificial mechanisms. association  ​ ​A statistical result in which changes in two variables follow a pattern. associative learning  ​ ​A change in behavior due to the development of an association between a stimulus and a response. asthma  ​ ​A disease in which the smooth muscles around the bronchioles contract more than usual, decreasing airflow in the lungs. AT/GC rule  ​ ​Refers to the phenomenon that an A in one DNA strand always hydrogen-bonds with a T in the opposite strand, and a G in one strand always hydrogen-bonds with a C. atherosclerosis  ​ ​The condition in which plaques cause the arteries to narrow and harden and large plaques may occlude (block) the lumen of an artery. atmospheric pressure  ​ ​The pressure exerted by the gases in the air on the body surfaces of animals. atom  ​ ​The smallest functional unit of matter that forms all chemical substances and cannot be further broken down into other substances by ordinary chemical or physical means. atomic mass  ​ ​An atom’s mass relative to the mass of other atoms. By convention, the most common form of carbon, which has six protons and six neutrons, is assigned an atomic mass of exactly 12. atomic nucleus  ​ ​The center of an atom; contains protons and neutrons. atomic number  ​ ​The number of protons in an atom. ATP synthase  ​ ​An enzyme that utilizes the energy stored in a H+ electrochemical gradient for the synthesis of ATP via chemiosmosis. ATP-dependent chromatin remodeling complex  ​ ​A collection of proteins that alters chromatin structure. atrial natriuretic peptide (ANP)  ​ ​A polypeptide hormone secreted from the atria of the heart whenever blood levels of sodium increase; ANP causes a loss of Na+ in the urine (natriuresis) by decreasing sodium reabsorption in the renal tubules. atrioventricular (AV) node  ​ ​Specialized cardiac cells in most vertebrates that sit near the junction of the atria and ventricles and conduct the electrical events from the atria to the ventricles. atrioventricular (AV) valve  ​ ​A one-way valve into a ventricle of the vertebrate heart through which blood moves from an atrium. atrium  ​ ​In the heart, a chamber to collect blood from the tissues. atrophy  ​ ​A reduction in the size of a structure, such as a muscle. audition  ​ ​The ability to detect and interpret sound waves; present in vertebrates and arthropods. autoimmune disease  ​ ​In humans and many other vertebrates, a disorder in which the body’s normal state of immune tolerance breaks down, with the result that immune responses are directed against the body’s own cells and tissues. autonomic nervous system  ​ ​The division of the peripheral nervous system that regulates homeostasis and organ function.

autophagosome  ​ ​A double-membrane structure enclosing cellular material destined to be degraded; produced by the process of autophagy. autophagy  ​ ​A process whereby cellular material, such as a worn-out organelle, becomes enclosed in a double membrane and is degraded. autosomes  ​ ​All of the chromosomes found in the cell nucleus of eukaryotes except for the sex chromosomes. autotomy  ​ ​In echinoderms, the ability to detach a body part, such as a limb, that will later regenerate. autotroph  ​ ​An organism that has metabolic pathways that use energy from either inorganic molecules or light to make organic molecules. auxin efflux carrier  ​ ​One of several types of PIN proteins, which transport auxin out of plant cells. auxin influx carrier (AUX1/LAX)  ​ ​A plasma membrane protein that transports auxin into plant cells. auxin-responsive genes  ​ ​Plant genes that are regulated by the hormone auxin. auxins  ​ ​A group of plant hormones; considered to be “master” plant hormones because they influence plant structure, development, and behavior in many ways. avirulence gene (Avr gene)  ​ ​A gene in a plant pathogen that encodes a virulence-enhancing elicitor, which causes plant disease. axillary bud  ​ ​A bud that occurs in the axil, the upper angle where a twig or leaf emerges from a stem. axillary meristem  ​ ​A meristem produced in the axil, the upper angle where a twig or leaf emerges from a stem. Axillary meristems generate axillary buds, which can produce flowers or branches. axon hillock  ​ ​The part of the axon closest to the cell body; typically where an action potential begins. axon terminal  ​ ​The end of an axon, which conveys electrical or chemical messages to other cells. axon  ​ ​An extension of the plasma membrane of a neuron that is involved in sending signals to neighboring cells. axoneme  ​ ​An internal structure of eukaryotic flagella and cilia that contains microtubules, the motor protein dynein, and linking proteins.

B

B cell  ​ ​A type of lymphocyte that participates in acquired immune responses. bacilli (singular, bacillus)  ​ ​Rod-shaped prokaryotic cells. backbone  ​ ​The linear arrangement of phosphates and sugar molecules in a DNA or RNA strand. Bacteria  ​ ​One of the three domains of life; the other two are Archaea and Eukarya. bacterial colony  ​ ​A clone of genetically identical cells formed from a single bacterium by repeated cell divisions. bacteriophage  ​ ​A virus that infects bacteria. bacteroid  ​ ​A modified bacterial cell of the type known as rhizobia present in mature root nodules of some plants. balanced polymorphism  ​ ​The phenomenon in which two or more alleles are kept in balance and maintained in a population over the course of many generations. balancing selection  ​ ​A type of natural selection that maintains genetic diversity in a population. balloon angioplasty  ​ ​A common treatment to restore blood flow through an artery. A thin tube with a tiny, inflatable balloon at its tip is threaded through the artery to the diseased area; inflating the balloon compresses the plaque against the arterial wall, widening the lumen. baroreceptor reflex  ​ ​The rapid, involuntary compensatory response of vertebrates to a change in blood pressure; the pressure is detected by baroreceptors, which signal the brainstem to

initiate changes in the activity of autonomic neurons. This, in turn, influences the function of structures of the circulatory system in such a way as to correct for a deviation of blood pressure beyond the normal range. baroreceptor  ​ ​A pressure-sensitive region within the walls of certain arteries that contains the endings of nerve cells; these regions sense and help to maintain blood pressure in the normal range for an animal. Barr body  ​ ​A highly condensed X chromosome present in the cells of female mammals. basal body  ​ ​A site at the base of flagella or cilia from which microtubules grow. Basal bodies are anchored on the cytosolic side of the plasma membrane. basal metabolic rate (BMR)  ​ ​The metabolic rate of an animal under resting conditions, in a postabsorptive state, and at a standard temperature. basal nuclei  ​ ​Clusters of neuronal cell bodies in the vertebrate forebrain that surround the thalamus and lie beneath the cerebral cortex; involved in planning and learning movements. basal region  ​ ​The region of a plant seedling that produces the roots. basal transcription  ​ ​A low level of transcription resulting from the action of the core promoter alone. base pair  ​ ​The structure in which two bases in opposite strands of DNA  are held together by hydrogen bonding to each other. base substitution  ​ ​A mutation that involves the substitution of a single base in the DNA for another base. base  ​ ​1. A molecule that when dissolved in water lowers the H+ concentration. 2. A component of nucleotides that is a single or double ring of carbon and nitrogen atoms. basidia  ​ ​Club-shaped cells that produce sexual spores in the fruiting bodies of basidiomycete fungi. basidiocarp  ​ ​The type of fruiting body produced by fungi in the phylum Basidiomycota. basidiomycetes  ​ ​A phylum of fungi whose sexual spores are produced on the surfaces of club-shaped structures (basidia). basidiospore  ​ ​A sexual spore of fungi in the phylum Basidiomycota. basilar membrane  ​ ​A component of the mammalian ear that vibrates back and forth in response to sound and bends the stereocilia in one direction and then the other. basophil  ​ ​A type of leukocyte that secretes the anticlotting factor heparin at the site of an infection, which helps flush out the infected site; basophils also secrete histamine, which attracts infection-fighting cells and proteins. Batesian mimicry  ​ ​The mimicry of an unpalatable species (the model) by a palatable one (the mimic). behavior  ​ ​The observable response of an organism to an external or internal stimulus. behavioral ecology  ​ ​A subdiscipline of organismal ecology that focuses on how the behavior of an individual organism contributes to its survival and reproductive success, which, in turn, eventually affects the population density of the species. benign tumor  ​ ​A precancerous mass of abnormal cells. bidirectional replication  ​ ​The process in which DNA replication proceeds outward from the origin in opposite directions. biennial  ​ ​A plant that does not reproduce during the first year of life but may reproduce within the following year. Bilateria  ​ ​Bilaterally symmetric animals. bile salts  ​ ​A group of substances produced in the liver that solubilize dietary fat and increase its accessibility to digestive enzymes. bile  ​ ​A substance produced by the liver that contains bicarbonate ions, cholesterol, phospholipids, a number

GLOSSARY

GLOSSARY G-3

G-4 GLOSSARY

GLOSSARY

of organic wastes, and a group of substances derived from cholesterol and collectively termed bile salts. Bile emulsifies fats so that they can be absorbed by the small intestine. binary fission  ​ ​The process of cell division in bacteria and archaea in which one cell divides into two cells. binocular (or stereoscopic) vision  ​ ​A type of vision in animals having two eyes located at the front of the head; the overlapping images coming into both eyes are processed together in the brain to form one perception. Binocular vision enables depth perception. binomial nomenclature  ​ ​The standard format for scientific naming of species. Each species has a genus name and a specific epithet. biochemistry  ​ ​The study of the chemistry of living organisms. biodiversity crisis  ​ ​The idea that there is currently an elevated loss of species on Earth, far beyond the normal historical extinction rate of species. biodiversity hot spots  ​ ​Regions that are biologically diverse and under threat of destruction. biodiversity  ​ ​The variety of life-forms that exist now and existed in the past. biofilm  ​ ​An aggregation of microorganisms that secrete adhesive mucilage, thereby gluing themselves to surfaces. biogeochemical cycle  ​ ​The continuous movement of a nutrient such as nitrogen, carbon, sulfur, or phosphorus from the physical environment to organisms and back. biogeographic region  ​ ​One of six geographic regions into which the world’s biota can be divided: Nearctic, Palearctic, Neotropical, Ethiopian, Oriental, and Australian. biogeography  ​ ​The study of the geographic distribution of extinct and living species. biological control  ​ ​The use of an introduced species’ natural enemies to control its proliferation. biological diversity  See biodiversity. biological evolution  ​ ​A heritable change in a population of organisms from one generation to the next.  biological membrane  ​ ​Any membrane made by living cells; can be the plasma membrane or an internal membrane that surrounds an organelle. biological nitrogen fixation  ​ ​Nitrogen fixation that is performed in nature by certain prokaryotes. biological species concept  ​ ​An approach used to distinguish species, which states that a species is a group of individuals whose members have the potential to interbreed with one another in nature to produce viable, fertile offspring but cannot successfully interbreed with members of other species. biology  ​ ​The study of life. bioluminescence  ​ ​A phenomenon in living organisms in which chemical reactions give off light rather than heat. biomagnification  ​ ​The increase in the concentration of a substance in living organisms from lower to higher trophic levels in a food chain. biomass  ​ ​A quantitative estimate of the total mass of living matter in a given area, usually measured in grams or kilograms per square meter. biome  ​ ​A major type of habitat characterized by distinctive plant and animal life. bioremediation  ​ ​The use of living organisms, usually microbes or plants, to detoxify polluted habitats such as dump sites or oil spills. biosphere  ​ ​The regions on the surface of the Earth and in the atmosphere where living organisms exist. biosynthetic reaction  ​ ​Also called an anabolic reaction; a chemical reaction in which small molecules are used to synthesize larger molecules. biotic  ​ ​The term used to describe interactions among organisms.

biparental inheritance  ​ ​An inheritance pattern in which both the male and female gametes contribute organellar genes to the offspring. bipedal  ​ ​Having the ability to walk on two feet. bipolar cells  ​ ​Cells in the vertebrate eye that make synapses with photoreceptors and relay responses to the ganglion cells. bivalent  ​ ​Homologous pairs of sister chromatids that are associated with each other, lying side by side. blade  ​ ​The flattened portion of a leaf. blastocoel  ​ ​A cavity formed in a cleavage-stage vertebrate embryo (blastula); provides a space into which cells of the future digestive tract will migrate. blastocyst  ​ ​The mammalian counterpart of a blastula. blastoderm  ​ ​A flattened disc of dividing cells in the embryo of animals that undergo incomplete cleavage; occurs in birds and some fishes. blastomeres  ​ ​The two half-size daughter cells produced by each cell division during cleavage. blastopore  ​ ​A small opening created when a band of tissue invaginates during gastrulation. It forms the primary opening of the archenteron to the outside. blastula  ​ ​An animal embryo at the stage where it has an outer epithelial layer and an inner cavity, forming a hollow sphere of cells. blood pressure  ​ ​The force exerted by blood on the walls of blood vessels; blood pressure is responsible for moving blood through the vessels. blood  ​ ​A fluid connective tissue in animals consisting of cells and (in mammals) cell fragments suspended in a solution of water containing dissolved nutrients, proteins, gases, and other molecules. body mass index (BMI)  ​ ​A method of assessing body fat and health risk that involves calculating the ratio of weight compared with height; weight in kilograms is divided by the square of the height in meters. Bohr effect  ​ ​The effect of CO2 and H+ on the affinity of hemoglobin for oxygen (that is, on the oxygenhemoglobin dissociation curve). bone  ​ ​A relatively hard component of the vertebrate skeleton; a living, dynamic tissue composed of organic materials and minerals. bottleneck effect  ​ ​A change in allele frequencies due to genetic drift in a population that has been dramatically reduced in size; this effect can reduce the genetic diversity of the population. Bowman’s capsule  ​ ​A saclike structure that houses the glomerulus at the beginning of the tubular component of a nephron in the mammalian kidney. brain  ​ ​Organ of the central nervous system of animals that functions to process and integrate information. brainstem  ​ ​The part of the vertebrate brain composed of the medulla oblongata, the pons, and the midbrain. brassinosteroid  ​ ​One of several plant hormones that help a plant to cope with environmental stress. bronchi (singular, bronchus)  ​ ​Tubes branching from the trachea and leading into the lungs. bronchiole  ​ ​A thin-walled, small tube branching from the bronchi and leading to the alveoli in mammalian lungs. bronchodilator  ​ ​A compound that binds to receptors on the plasma membranes of smooth muscle cells of the bronchioles of the lung and causes the muscle cells to relax, thereby widening the bronchioles and easing breathing. brown adipose tissue  ​ ​A specialized tissue in small mammals such as hibernating bats, small rodents living in cold environments, and many newborn mammals, including humans, that can help to generate heat and maintain body temperature. brush border  ​ ​The collective name for the microvilli in the small intestine and the proximal tubules of the kidneys in vertebrates. bryophytes  ​ ​Liverworts, mosses, and hornworts, the modern nonvascular land plants.

buccal pumping  ​ ​A form of breathing in which animals take in water or air into their mouths, then raise the floor of the mouth, creating a positive pressure that pumps water or air across the gills or into the lungs; found in fishes and amphibians. bud  ​ ​A miniature plant shoot having a dormant shoot apical meristem. budding  ​ ​A form of asexual reproduction in which a portion of the parent organism pinches off to form a complete new individual. buffer  ​ ​An acid-base pair that minimizes pH fluctuations in the fluids of living organisms. Buffers can raise or lower pH as needed. bulk flow  ​ ​The mass movement of liquid in a plant caused by pressure, gravity, or both.

C

C3 plant  ​ ​A plant that adds CO2 to RuBP to produce 3PG, a three-carbon molecule. C4 plant  ​ ​A plant that uses PEP carboxylase to initially fix CO2 into a four-carbon molecule and later uses rubisco to fix CO2 into simple sugars; this mechanism is an adaptation to hot, dry environments. cadherin  ​ ​A cell adhesion molecule found in animal cells that promotes cell-to-cell adhesion. calcitonin  ​ ​A hormone that plays a role in Ca2+ homeostasis in some vertebrates. calorie  ​ ​The amount of heat required to raise the temperature of 1 gram of water 1°C. The Calorie (dietary unit) is equivalent to a kilocalorie, or 1,000 calories. Calvin cycle  ​ ​The second stage in the process of photosynthesis. During this cycle, ATP is used as a source of energy and NADPH is used as a source of high-energy electrons, driving the synthesis of carbohydrates using CO2. CAM (crassulacean acid metabolism) plants  ​ ​ C4 plants that open their stomata at night to take up CO2. Cambrian explosion  ​ ​An event during the Cambrian period (543–490 mya) in which there was an abrupt increase (on a geological scale) in the diversity of animal species. camouflage  ​ ​The blending of an organism with the background of its habitat. cAMP  See cyclic adenosine monophosphate. canopy  ​ ​The uppermost layer of tree foliage in a forest. CAP site  ​ ​One of two regulatory sites near the lac promoter; this site is a DNA sequence recognized by the catabolite activator protein (CAP). capillary  ​ ​A tiny thin-walled vessel that is the site of gas and nutrient exchange between the blood and interstitial fluid. capping  ​ ​The process in which 7-methylguanosine is covalently attached at the 5´ end of pre-mRNAs of eukaryotes. capsid  ​ ​A protein coat enclosing a virus’s genome. capsule  ​ ​A very thick, gelatinous glycocalyx produced by certain strains of bacteria that may help them avoid being destroyed by an animal’s immune (defense) system. carapace  ​ ​The hard protective cuticle covering the cephalothorax of a crustacean. carbohydrate  ​ ​A carbon-containing organic molecule often represented by the general formula, Cn(H2O)n; carbohydrates include starches, sugars, and cellulose. carbon fixation  ​ ​A process in which carbon from inorganic CO2 is incorporated into an organic molecule such as a carbohydrate. carcinogen  ​ ​An agent that increases the likelihood of developing cancer, usually a mutagen. carcinoma  ​ ​A cancer of epithelial cells.

cardiac angiography  ​ ​A medical procedure used to visualize the coronary arteries and check for the presence of disease. cardiac cycle  ​ ​The events that produce a single heartbeat, which can be divided into two phases: diastole and systole. cardiac muscle  ​ ​A type of muscle tissue, found only in hearts, in which physical and electrical connections between individual cells enable many of the cells to contract simultaneously. cardiac output (CO)  ​ ​The amount of blood the heart pumps per unit time, usually expressed in units of L/min. carnivore  ​ ​An animal that consumes animal flesh or fluids. carotenoid  ​ ​A type of photosynthetic or protective pigment found in plastids that imparts a color that ranges from yellow to orange to red. carpel  ​ ​A flower shoot organ that produces ovules that contain female gametophytes. carrying capacity (K)  ​ ​The upper boundary for a population size in a given environment. Casparian strips  ​ ​Ribbon-like structures in the walls of endodermal cells of plant roots, composed of suberin and phenolic polymers; prevent apoplastic transport of solutes into vascular tissues. caspase  ​ ​An enzyme that functions as a protease when it is activated during apoptosis. catabolic reaction  ​ ​A metabolic pathway in which a molecule is broken down into smaller components, usually releasing energy. catabolism  ​ ​A metabolic pathway that results in the breakdown of larger molecules into smaller molecules. Such reactions are often exergonic. catabolite activator protein (CAP)  ​ ​An activator protein for the lac operon. catabolite repression  ​ ​In bacteria, a process whereby transcriptional regulation is influenced by the presence of a preferred energy source (glucose). catalase  ​ ​An enzyme within peroxisomes that breaks down hydrogen peroxide to water and oxygen gas. catalyst  ​ ​An agent that speeds up the rate of a chemical reaction without being permanently changed or consumed during the reaction. cataract  ​ ​An accumulation of protein in the lens of the eye; causes blurring and poor night vision. cation exchange  ​ ​With regard to soil, the process in which hydrogen ions replace mineral cations on the surfaces of clay particles. cation  ​ ​An ion that has a net positive charge. cDNA library  ​ ​A type of DNA library in which the inserts are derived from cDNA. cDNA  See complementary DNA. cecum  ​ ​The first portion of a vertebrate’s large intestine. cell adhesion molecule (CAM)  ​ ​A membrane protein found in animal cells that promotes cell adhesion. cell adhesion  ​ ​A vital function of the cell membrane that allows cells to bind to each other. Cell adhesion is critical in the formation of multicellular organisms and provides a way to convey positional information between neighboring cells. cell biology  ​ ​The study of individual cells and their interactions with each other. cell body  ​ ​A part of a neuron that contains the cell nucleus and other organelles. cell communication  ​ ​The process by which cells can detect, interpret, and respond to signals in their environment. In multicellular organisms, cell communication is also needed to coordinate cellular activities within the whole organism. cell cycle  ​ ​A series of events that leads to cell division. For eukaryotes, it involves a series of phases in which a cell divides by mitosis or meiosis. cell differentiation  ​ ​The process by which cells become specialized into particular types.

cell division  ​ ​The process of cell reproduction, in which one cell divides into two cells. cell junctions  ​ ​Specialized structures that adhere cells to each other and to the ECM. cell nucleus  ​ ​The membrane-bound area of a eukaryotic cell in which the genetic material is found. cell plate  ​ ​In plant cells, a structure that forms a cell wall between the two daughter cells during cytokinesis. cell signaling  ​ ​A vital function of the plasma membrane in which cells sense changes in their environment and communicate with each other. cell surface receptor  ​ ​A receptor found in the plasma membrane that enables a cell to respond to different kinds of extracellular signaling molecules. cell theory  ​ ​A theory that states that all organisms are made of cells, cells are the smallest units of living organisms, and new cells come from pre-existing cells by cell division. cell wall  ​ ​A relatively rigid, porous structure located outside the plasma membrane of prokaryotic, plant, fungal, and certain protist cells; provides support and protection. cell  ​ ​The simplest unit of a living organism. cell-free translation system  ​  ​See in vitro translation system. cell-mediated immunity  ​ ​A type of acquired immunity in which cytotoxic T cells directly attack and destroy infected body cells, cancer cells, or transplanted cells. cell-to-cell communication  ​ ​A form of cell communication that occurs between two different cells. cellular respiration  ​ ​A process by which living cells obtain energy from organic molecules and release waste products. cellular response  ​ ​Adaptation at the cellular level that involves a cell responding to signals in its environment. cellulose  ​ ​The main macromolecule of the cell wall of plants and many algae; a linear polymer made of thousands of glucose monomers. central cell  ​ ​In the female gametophyte of a flowering plant, a large cell that contains two nuclei; after double fertilization, it forms the first cell of the nutritive endosperm tissue. central dogma  ​ ​Refers to the steps of gene expression at the molecular level: DNA is transcribed into mRNA, and mRNA is translated into a polypeptide. central nervous system (CNS)  ​ ​In vertebrates, the brain and spinal cord. central region  ​ ​The region of a plant seedling that produces stem tissue. central vacuole  ​ ​An organelle that often occupies 80% or more of the volume of a plant cell and stores a large amount of water, enzymes, and inorganic ions. central zone  ​ ​The area of a plant shoot meristem where undifferentiated stem cells are maintained. centrioles  ​ ​A pair of structures within the centrosome of animal cells. Most plant cells and many protists lack centrioles. centromere  ​ ​The region where the two sister chromatids are tightly associated; the centromere is an attachment site for kinetochore proteins. centrosome  ​ ​A single structure often near the nucleus of a eukaryotic cell that forms a nucleating site for the growth of microtubules; also called a microtubuleorganizing center. cephalization  ​ ​The localization of sensory structures at the anterior end of an animal’s body. cerebellum  ​ ​The part of the vertebrate hindbrain, along with the pons, responsible for monitoring and coordinating body movements. cerebral cortex  ​ ​The surface layer of gray matter that forms the outer part of the cerebrum of the vertebrate brain.

cerebral ganglia  ​ ​A paired structure in the head of invertebrates that receives input from sensory cells and controls motor output. cerebrospinal fluid  ​ ​Fluid that exists in ventricles within the central nervous system and surrounds the exterior of the brain and spinal cord; it absorbs physical shocks to the brain resulting from sudden movements or blows to the head. cerebrum  ​ ​A region of the vertebrate forebrain that is responsible for the higher functions of conscious thought, planning, and emotion, as well as control of motor function. channel  ​ ​A transmembrane protein that forms an open passageway for the facilitated diffusion of ions or molecules across a membrane. chaperone  ​ ​A protein that keeps another protein in an unfolded state during the process of post-translational sorting. character displacement  ​ ​The tendency for two species to diverge in morphology and thus resource use because of competition. character state  ​ ​A particular variant of a given character. character  ​ ​A characteristic of an organism, such as the appearance of seeds, pods, flowers, or stems in the garden pea. charged tRNA  ​ ​A tRNA with its attached amino acid; also called aminoacyl tRNA. checkpoint protein  ​ ​A protein that senses if a cell is in the proper condition to divide and prevents it from progressing through the cell cycle if it is not. checkpoint  ​ ​One of three critical regulatory points found in the cell cycle of eukaryotic cells. At these checkpoints, a variety of proteins act as sensors to determine if a cell is in the proper condition to divide. chemical equilibrium  ​ ​A state of a chemical reaction in which the rate of formation of products equals the rate of formation of reactants. chemical evolution  ​ ​The process by which a population of molecules changes over time to become a new population with a different chemical composition. chemical mutagen  ​ ​A chemical that causes mutations. chemical potential energy  ​ ​The potential energy contained within atoms and the bonds between atoms. chemical reaction  ​ ​A process in which one or more substances are changed into other substances. chemical selection  ​ ​The process that occurs when a chemical within a mixture has special properties or advantages that cause it to increase in amount. May have played a key role in the formation of an RNA world. chemical synapse  ​ ​A synapse in which a chemical called a neurotransmitter is released from an axon terminal and acts as a signal from the presynaptic to the postsynaptic cell. chemiosmosis  ​ ​A process for making ATP in which energy stored in an ion electrochemical gradient is used to make ATP from ADP and Pi. chemoautotroph  ​ ​An organism able to use energy obtained by chemical modifications of inorganic compounds to synthesize organic compounds. chemoheterotroph  ​ ​An organism that must obtain organic molecules both for energy and as a carbon source. chemoreceptor  ​ ​A sensory receptor in animals that responds to specific chemical compounds. chitin  ​ ​A tough, nitrogen-containing, polysaccharide polymer that forms the external skeleton of many insects and crustaceans and is found in the cell walls of fungi. chlorophyll a  ​ ​A type of chlorophyll pigment found in plants, algae, and cyanobacteria. chlorophyll b  ​ ​A type of chlorophyll pigment found in plants, green algae, and some other photosynthetic organisms.

GLOSSARY

GLOSSARY G-5

G-6 GLOSSARY

GLOSSARY

chlorophyll  ​ ​A photosynthetic green pigment found in the chloroplasts of plants, algae, and some bacteria. chloroplast genome  ​ ​The chromosome found in chloroplasts. chloroplast  ​ ​A semiautonomous organelle found in plant and algal cells that carries out photosynthesis. chlorosis  ​ ​The yellowing of plant leaves caused by any of various mineral deficiencies. choanocyte  ​ ​A specialized cell of sponges that functions to trap and eat particulate matter and plankton. cholecystokinin (CCK)  ​ ​A hormone released by cells of the small intestine in vertebrates; stimulates release of pancreatic enzymes into the small intestine and contraction of the gallbladder. chondrichthyans  ​ ​Members of the clade Chondrichthyes, including sharks, skates, and rays. chorion  ​ ​One of the four extraembryonic membranes in the amniotic egg. It provides gas exchange between the embryo and the surrounding air. chorionic gonadotropin  ​ ​An LH-like hormone made by a layer of cells around the blastocyst and by the placenta that maintains the corpus luteum. chromatin  ​ ​The complex of DNA and proteins that makes up eukaryotic chromosomes. chromosome territory  ​ ​A distinct area where each chromosome is located within the cell nucleus of eukaryotic cells; chromosome territories do not overlap. chromosome theory of inheritance  ​ ​An explanation of how the steps of meiosis account for the inheritance patterns observed by Mendel. chromosome  ​ ​A discrete unit of genetic material composed of DNA and associated proteins. Eukaryotes have chromosomes in their cell nuclei and in plastids and mitochondria. chylomicron  ​ ​Large fat droplet coated with amphipathic proteins that perform an emulsifying function similar to that of bile salts; chylomicrons are formed in intestinal epithelial cells from absorbed fats in the diet. chyme  ​ ​A solution of water, ions, molecular fragments of proteins, nucleic acids, and carbohydrates, droplets of fat, and various other small molecules produced in the vertebrate stomach. cilia (singular, cilium)  ​ ​Cell appendages that have the same internal structure as flagella and function like flagella to facilitate cell movement; cilia are shorter and more numerous than are flagella. ciliate  ​ ​A protist that moves by means of cilia, which are tiny hairlike extensions that occur on the outside of cells and have the same internal structure as flagella. circadian rhythm  ​ ​Internal biological clock that occurs in plants, animals, and other organisms. circulatory system  ​ ​All of the structures in an animal’s body that contribute to the movement of blood or hemolymph throughout the body; in vertebrates includes the heart, blood vessels, and blood. cis/trans isomers  ​ ​Organic molecules with the same chemical composition but existing in two different configurations determined by the positions of hydrogen atoms on the two carbons of a C=C double bond. When the hydrogen atoms are on the same side of the double bond, it is called a cis isomer; when on the opposite sides of the double bond, it is a trans isomer. cis-acting element  ​ ​A DNA segment that must be adjacent to the gene(s) that it regulates cis-effect  ​ ​The effect on gene regulation that is mediated by a cis-acting element. cisternae  ​ ​Flattened, fluid-filled tubules of the endoplasmic reticulum. citric acid cycle  ​ ​A cycle that results in the breakdown of carbohydrates to CO2; also known as the Krebs cycle.

clade  ​ ​A group of species consisting of a common ancestral species and all of its descendant species. cladistic approach  ​ ​An approach used to construct a phylogenetic tree by comparing shared primitive and shared derived characters among different species. cladistics  ​ ​The classification of species based on evolutionary relationships. cladogenesis  ​ ​The splitting or diverging of one species into two or more species. cladogram  ​ ​A phylogenetic tree constructed by using a cladistic approach. clasper  ​ ​An extension of the pelvic fin of a chondrichthyan, used by the male to transfer sperm to the female. class  ​ ​In taxonomy, a subdivision of a phylum. classical conditioning  ​ ​A type of associative learning in which an involuntary response comes to be associated positively or negatively with a stimulus that did not originally elicit the response. cleavage furrow  ​ ​In animal cells, an area that constricts like a drawstring to separate the cells during cytokinesis. cleavage  ​ ​A succession of rapid cell divisions with no significant growth that produces a hollow sphere of cells called a blastula. climate change  ​ ​A long-term change in Earth’s climate or change in climate in a particular region. climate  ​ ​The prevailing weather pattern of a given region. climax community  ​ ​A distinct end point of succession. clonal deletion  ​ ​One of two mechanisms that explain why normal individuals lack active lymphocytes that respond to self components; in this case, T cells with receptors capable of binding self proteins are destroyed by apoptosis. clonal inactivation  ​ ​One of two mechanisms that explain why normal individuals lack active lymphocytes that respond to self components; in this case, the process occurs outside the thymus and causes potentially selfreacting T cells to become nonresponsive. clonal selection  ​ ​The process by which an antigenstimulated lymphocyte divides and forms a clone of cells, each of which recognizes that particular antigen. closed circulatory system  ​ ​A circulatory system in which blood flows throughout an animal entirely within a series of vessels and is kept separate from the interstitial fluid. closed conformation  ​ ​Chromatin that cannot be transcribed into RNA. clumped  ​ ​The term used to refer to the most common pattern of dispersion within a population, in which individuals are gathered in small groups. cnidocil  ​ ​On the surface of a cnidocyte, a hairlike trigger that detects stimuli. cnidocyte  ​ ​A characteristic feature of cnidarians; a stinging cell that functions in defense or the capture of prey. coacervates  ​ ​Droplets that form spontaneously from the association of charged polymers such as proteins, carbohydrates, or nucleic acids surrounded by water. coactivator  ​ ​A protein that increases the rate of transcription but does not directly bind to the DNA itself. cocci  ​ ​Sphere-shaped prokaryotic cells. cochlea  ​ ​A coiled structure in the inner ear of mammals that contains the auditory receptors (organ of Corti). coding sequence  ​ ​The region of a gene or a DNA molecule that encodes the information for the amino acid sequence of a polypeptide. coding strand  ​ ​The DNA strand opposite to the template (or noncoding strand). codominance  ​ ​The phenomenon in which a single individual expresses two alleles. codon  ​ ​A sequence of three nucleotide bases that specifies a particular amino acid or a stop codon; codons function during translation.

coefficient of relatedness (r)  ​ ​The probability that any two individuals will share a copy of a particular gene. coelom  ​ ​A fluid-filled body cavity in an animal. coelomate  ​ ​An animal with a true coelom. coenzyme  ​ ​An organic molecule that temporarily binds to an enzyme and participates in the chemical reaction that the enzyme catalyzes, but is left unchanged when the reaction is completed. coevolution  ​ ​The process by which two or more species of organisms influence each other’s evolutionary pathway. cofactor  ​ ​Usually an inorganic ion that temporarily binds to the surface of an enzyme and promotes a chemical reaction. cognitive learning  ​ ​The ability to solve problems with conscious thought and without direct environmental feedback. cohesion  ​ ​The ability of like molecules to noncovalently bind to each other; the attraction of water molecules for each other. cohesion-tension theory  ​ ​The explanation for longdistance water transport in plants as the combined effect of the cohesion of water and evaporative tension. cohort  ​ ​A group of organisms of the same age. coleoptile  ​ ​A protective sheath that encloses the first bud of the epicotyl in a mature monocot embryo. coleorhiza  ​ ​A protective envelope that encloses the young root of a monocot. colinearity rule  ​ ​The phenomenon whereby the order of homeotic genes along the chromosome correlates with their expression along the anteroposterior axis of the body. collagen  ​ ​A protein secreted from animal cells that forms large fibers in the extracellular matrix. collenchyma cell  ​ ​A type of flexible plant cell that makes up the tissue called collenchyma. collenchyma  ​ ​A plant ground tissue that provides support to plant organs. colligative property  ​ ​A property of a solution that depends only on the total number of dissolved solute particles. colon  ​ ​A part of a vertebrate’s large intestine consisting of three relatively straight segments—the ascending, transverse, and descending portions. The terminal portion of the descending colon is S-shaped, forming the sigmoid colon, which empties into the rectum. combinatorial control  ​ ​The phenomenon whereby a combination of many factors determines the expression of any given gene. commensalism  ​ ​An interaction that benefits one species and leaves the other unaffected. communication  ​ ​The use of specially designed visual, chemical, auditory, or tactile signals to modify the behavior of others. community ecology  ​ ​The study of how populations of species interact and form functional communities. community  ​ ​An assemblage of populations of different species that live in the same place at the same time. compartmentalization  ​ ​A characteristic of eukaryotic cells, in which many membrane-bound organelles separate the cell into different regions. Cellular compartmentalization allows a cell to carry out specialized chemical reactions in different places. competent  ​ ​The term used to describe bacterial strains that have the ability to take up DNA from the environment. competition  ​ ​An interaction that affects two or more species negatively, as they compete over food or other resources. competitive exclusion principle  ​ ​The idea that two species with the same resource requirements cannot occupy the same niche. competitive inhibitor  ​ ​A molecule that binds noncovalently to the active site of an enzyme and inhibits the ability of the substrate to bind.

complement  ​ ​The family of plasma proteins that provides a means for extracellular killing of microbes without prior phagocytosis. complementary DNA (cDNA)  ​ ​DNA molecules that are made using mRNA as a starting material. complementary  ​ ​The characteristic of the two strands of DNA that is due to the specific base pairing that occurs between nucleic acids: A pairs only with T (in DNA) or U (in RNA), and G pairs only with C. complete flower  ​ ​A eudicot flower that possesses all four types of flower whorls or a monocot flower that has tepals, androecium, and gynoecium. complete metamorphosis  ​ ​During development in the majority of insects, a dramatic change in body form from larva to a very different looking adult. compound eye  ​ ​A type of image-forming visual organ in arthropods and some annelids consisting of several hundred to several thousand light detectors called ommatidia. compound  ​ ​A molecule composed of two or more different elements. concentration gradient  ​  ​See transmembrane gradient. concentration  ​ ​The amount of a solute dissolved in a unit volume of solution. condensation reaction  ​ ​A chemical reaction in which two or more molecules are combined into one larger molecule by covalent bonding, with the loss of a small molecule. condom  ​ ​A sheathlike membrane worn over the penis; in addition to their contraceptive function, condoms significantly reduce the risk of contracting and transmitting sexually transmitted diseases. conduction  ​ ​The process in which the body surface loses or gains heat through direct contact with cooler or warmer substances. cones  ​ ​1. Photoreceptors found in the vertebrate eye; they are less sensitive to low levels of light but can detect color. 2. The reproductive structures of coniferous plants. congenital hypothyroidism  ​ ​A condition characterized by poor differentiation of the central nervous system due to a failure of neurons to become myelinated in fetal development; results in profound mental defects. conidia  ​ ​A type of asexual reproductive cell produced by many fungi. conifers  ​ ​A phylum of gymnosperm plants, Coniferophyta. conjugation  ​ ​A type of gene transfer between bacteria that involves a direct physical interaction between two bacterial cells. connective tissues  ​ ​Groups of cells that connect, anchor, and support the structures of an animal’s body; include blood, adipose (fat-storing) tissue, bone, cartilage, loose connective tissue, and dense connective tissue. connexon  ​ ​A channel that forms gap junctions in vertebrates, consisting of six connexin proteins in one cell aligned with six connexin proteins in an adjacent cell. conservation biology  ​ ​The study that uses principles and knowledge from molecular biology, genetics, and ecology to protect and sustain the biological diversity of life. conservative mechanism  ​ ​In this incorrect model for DNA replication, both parental strands of DNA remain together (are conserved) following DNA replication. The two newly made daughter strands are also joined together. constant region  ​ ​The portion of the amino acid sequence in the heavy and light chains that is identical in all immunoglobulins of a given class. constitutive gene  ​ ​An unregulated gene that has a relatively constant level of expression in all conditions over time.

contig  ​ ​A contiguous sequence of DNA fragments that consists of overlapping pieces of chromosomal DNA. continental drift  ​ ​The process by which, over the course of billions of years, the major landmasses, known as the continents, have shifted their positions, changed their shapes, and, in some cases, become separated from each other. contraception  ​ ​The use of methods to prevent fertilization or implantation of a fertilized egg. contractile vacuole  ​ ​A small, membrane-enclosed, water-filled compartment that eliminates excess liquid from the cells of certain protists. contrast  ​ ​In microscopy, relative differences in the lightness, darkness, or color between adjacent regions in a sample. control group  ​ ​The sample in an experiment that is treated just like an experimental group except that it is not subjected to one particular variable. convection  ​ ​The transfer of heat by the movement of air or water next to the body. convergent evolution  ​ ​The process whereby two different species from different lineages independently develop similar characteristics because they occupy similar environments. core promoter  ​ ​Refers to the TATA box and the transcriptional start site of a eukaryotic proteinencoding gene. corepressor  ​ ​A small effector molecule that binds to a repressor protein to inhibit transcription. cork cambium  ​ ​A secondary meristem in a plant that produces cork tissue. cornea  ​ ​A thin, clear layer on the front of the vertebrate eye; also part of the lens of ommatidia in compound eyes. corona  ​ ​The ciliated crown of members of the phylum Rotifera. coronary artery bypass  ​ ​A common treatment to restore blood flow through a coronary artery. A small piece of healthy blood vessel is removed from one part of the body and surgically grafted onto the coronary circulation in order to bypass the diseased artery. coronary artery disease  ​ ​A condition that occurs when plaques form in the coronary arteries. corpus callosum  ​ ​The major tract that connects the two hemispheres of the cerebrum. corpus luteum  ​ ​A structure that develops from a ruptured follicle following ovulation; it is responsible for secreting hormones that stimulate the development of the uterus during pregnancy. cortex  ​ ​The area of a plant stem or root beneath the epidermis that is largely composed of parenchyma tissue. cortical reaction  ​ ​An event in fertilization in which IP3 and Ca2+ produce barriers to more than one sperm cell binding to and uniting with an egg. cortisol  ​ ​A glucocorticoid hormone made in the adrenal cortex. cotranslational sorting  ​ ​The sorting process in which the synthesis of certain eukaryotic proteins begins in the cytosol and then halts temporarily until the ribosome has become bound to the ER membrane. cotyledon  ​ ​An embryonic seed leaf. countercurrent exchange  ​ ​1. An arrangement of water and blood flow in which water enters a fish’s mouth and flows between the lamellae of the gills in the opposite direction to blood flowing through the lamellar capillaries. 2. The transfer of heat between blood flowing in opposite directions in arteries and veins under the skin of vertebrates; regulates heat loss to the environment. countercurrent multiplication system  ​ ​The mechanism by which the loop of Henle in the vertebrate kidney reabsorbs salts and water along it length. covalent bond  ​ ​A chemical bond in which two atoms share a pair of electrons.

CpG island  ​ ​A cluster of CpG sites. C and G refer to the bases cytosine and guanine in DNA, and p refers to a phosphodiester linkage between the nucleotides containing those bases. cranial nerve  ​ ​A nerve in the peripheral nervous system that is directly connected to the brain. cranium  ​ ​A protective bony or cartilaginous housing that encases the brain of a craniate. crisis ecoregions  ​ ​Representative habitats that are at greatest risk because of extensive habitat loss and lack of conservation or protection.  CRISPR-Cas system  ​ ​A system found in bacteria and archaea composed of noncoding RNAs and proteins that provides defense against bacteriophages, viruses, and transposons. CRISPR-Cas technology  ​ ​An experimental technique to introduce mutations into genes. cristae  ​ ​Projections of the highly invaginated inner membrane of a mitochondrion. critical innovations  ​ ​New features that foster the diversification of phyla. critical period  ​ ​A limited period of time during development in which many animals acquire speciesspecific patterns of behavior. crop  ​ ​A storage organ that is a dilation of the lower esophagus; found in most birds and many invertebrates, including insects and some worms. cross-bridge cycle  ​ ​During muscle contraction, the sequence of events that occurs between the time when a cross-bridge binds to a thin filament and when it is set to repeat the process. cross-bridge  ​ ​A region of myosin molecules that extends from the surface of each thick filament toward a thin filament in skeletal muscle. cross-fertilization  ​ ​Fertilization that involves the union of a female gamete and a male gamete from different individuals. crossing over  ​ ​The exchange of genetic material between homologous chromosomes during meiosis; allows for increased variation in the genetic information that each parent may pass to the offspring. cross-pollination  ​ ​The process in which a stigma receives pollen from a different plant of the same species. cryosphere  ​ ​Earth’s icy environments. cryptochrome  ​ ​A type of blue-light receptor in plants and protists. CT scan  ​ ​Computerized tomography, which is an X-ray technique used to examine the structure of bones and soft tissues, including the brain. C-terminus  ​ ​The location of the last amino acid in a polypeptide; also known as the carboxyl end. cupula  ​ ​A gelatinous structure within the lateral line organ of fishes that detects changes in water movement. cuticle  ​ ​A waxy surface coating that helps to reduce water loss from plant surfaces. Also, a nonliving covering that serves to both support and protect an animal. cycads  ​ ​A phylum of gymnosperm plants, referred to formally as Cycadophyta. cyclic adenosine monophosphate (cAMP)  ​ ​A small molecule that is produced from ATP and acts as a second messenger. cyclic AMP (cAMP)  See cyclic adenosine monophosphate. cyclic electron flow  See cyclic photophosphorylation. cyclic photophosphorylation  ​ ​During photosynthesis, a pattern of electron flow in the thylakoid membrane that is cyclic and generates only ATP. cyclin  ​ ​A protein responsible for advancing a cell through the phases of the cell cycle by binding to a cyclin-dependent kinase. cyclin-dependent kinase (cdk)  ​ ​A protein responsible for advancing a cell through the phases of the cell

GLOSSARY

GLOSSARY G-7

G-8 GLOSSARY cycle. Its function is dependent on the binding of a cyclin. cyst  ​ ​A unicellular or multicellular structure that often has a thick, protective wall and can remain dormant through periods of unfavorable climate or low food availability. cytogenetics  ​ ​The field of genetics that involves the microscopic examination of chromosomes. cytokines  ​ ​A family of proteins that function in both innate and acquired immune defenses by providing a chemical communication network that synchronizes the components of the immune response. cytokinesis  ​ ​The division of the cytoplasm to produce two distinct daughter cells. cytokinin  ​ ​A type of plant hormone that promotes cell division. cytosine (C)  ​ ​A pyrimidine base found in DNA and RNA. cytoskeleton  ​ ​In eukaryotes, a network within the cytosol consisting of three different types of protein filaments called microtubules, intermediate filaments, and actin filaments. cytosol  ​ ​The region of a eukaryotic cell that is inside the plasma membrane and outside the organelles. cytotoxic T cell  ​ ​A type of lymphocyte that travels to the location of its target, binds to the target by combining with an antigen on it, and directly kills the target via secreted chemicals.

D

GLOSSARY

dalton (Da)  ​ ​A measure of atomic mass. One dalton equals one-twelfth the mass of a carbon atom. daughter strand  ​ ​The newly made strand in DNA replication. day-neutral plant  ​ ​A plant that flowers regardless of the night length, as long as day length meets the minimal requirements for plant growth. deafness  ​ ​Hearing loss, usually caused by damage to the hair cells within the cochlea. death receptor  ​ ​A type of cell surface receptor found in eukaryotic cells that can promote apoptosis when it becomes activated. decomposer  ​ ​An organism that gets its energy from the remains and waste products of other organisms. defecation  ​ ​The expulsion of feces that occurs through the anus of an animal’s digestive canal. defensive mutualism  ​ ​A mutually beneficial interaction often involving an animal defending a plant or herbivore in return for food or shelter. deforestation  ​ ​The conversion of forested areas by humans to nonforested land. degenerate  ​ ​The characteristic of the genetic code that more than one codon can specify the same amino acid. dehydration reaction  ​ ​A type of condensation reaction in which a molecule of water is lost. deletion  ​ ​A type of mutation in which a segment of chromosomal material has been removed. demographic transition  ​ ​The shift in birth and death rates accompanying human societal development. demography  ​ ​The study of birth rates, death rates, age distributions, and the sizes of populations. dendrite  ​ ​A treelike extension of the plasma membrane of a neuron that receives electrical signals from other neurons. dendritic cell  ​ ​A type of cell derived from bone marrow stem cells that plays an important role in innate immunity; these cells are scattered throughout most tissues, where they perform various macrophage-like functions. denitrification  ​ ​The reduction of nitrate (NO3–) to gaseous nitrogen (N2). density-dependent factor  ​ ​A mortality factor whose influence increases with the density of the population.

density-independent factor  ​ ​A mortality factor whose influence is not affected by changes in population density. deoxynucleoside triphosphates  ​ ​Individual nucleotides with three phosphate groups. deoxyribonucleic acid (DNA)  ​ ​One of two types of nucleic acids; the other is ribonucleic acid (RNA). A DNA molecule consists of two strands of nucleotides coiled around each other to form a double helix, held together by hydrogen bonds according to the AT/GC rule. deoxyribose  ​ ​A five-carbon sugar found in DNA. depolarization  ​ ​The change in the membrane potential that occurs when a cell membrane becomes less polarized, that is, less negative inside the cell relative to the surrounding fluid. dermal tissue  ​ ​The covering on various parts of a plant. desertification  ​ ​The process by which an area becomes more desert-like, usually as a result of overstocking with domestic animals that can greatly reduce grass coverage through overgrazing. desmosome  ​ ​A mechanically strong type of cell junction between animal cells that typically occurs in spotlike rivets. determinate cleavage  ​ ​In animals, a characteristic of protostome development in which the fate of each embryonic cell is determined very early. determinate growth  ​ ​Growth that is of limited duration, such as the growth of flowers or of animal bodies. determined  ​ ​Refers to a cell that has committed to become a particular cell type. detritivore  ​ ​An organism that gets its energy from consuming detritus. detritus  ​ ​Unconsumed plants that die and decompose, along with the dead remains of animals and animal waste products. deuterostome  ​ ​An animal whose development exhibits radial, indeterminate cleavage and in which the blastopore becomes the anus; includes echinoderms and vertebrates. development  ​ ​In biology, a series of changes in the state of a cell, tissue, organ, or organism; the underlying process that gives rise to the structures and functions of living organisms. developmental genetics  ​ ​A field of study aimed at understanding how gene expression controls the process of development. diaphragm  ​ ​A large muscle that subdivides the thoracic cavity from the abdomen in mammals; contraction of the diaphragm enlarges the thoracic cavity during inhalation. diarrhea  ​ ​A common intestinal disorder arising from ingested microbes or other causes; usually runs its course within one or two days but, in serious cases, can require hospitalization. diastole  ​ ​The first phase of the cardiac cycle, in which the ventricles fill with blood coming from the atria through the open AV valves. dideoxy chain-termination method  ​ ​A method for determining the sequence of bases in DNA that utilizes dideoxynucleotide triphosphates as reagents. dideoxy sequencing  See dideoxy chain-termination method. differential gene regulation  ​ ​The phenomenon in which the expression of genes differs under various environmental conditions and in specialized cell types. digestion  ​ ​The process of breaking down nutrients in food into smaller molecules that can be absorbed across the intestinal epithelia and directly used by cells. digestive system  ​ ​In animals, the long tube through which food is processed. In a vertebrate, this system consists of the alimentary canal plus several associated structures.

dihybrid  ​ ​Refers to an offspring that is a hybrid with respect to two traits. dikaryotic mycelium  ​ ​A fungal body that is made of cells that each possess two genetically distinct nuclei. dimorphic fungi  ​ ​Fungi that exist in two different morphological forms. dinosaur  ​ ​A term, meaning terrible lizard, used to describe some of the extinct reptiles preserved as fossils. dioecious  ​ ​Refers to plants that produce staminate and carpellate flowers on separate plants. diploblastic  ​ ​Having two distinct germ layers—ectoderm and endoderm—but not mesoderm. diploid   ​ ​Containing two sets of chromosomes; designated as 2n. diploid-dominant species  ​ ​Species in which the diploid organism is the multicellular organism in the life cycle. Animals are an example. direct repair  ​ ​A type of DNA repair in which an enzyme finds an incorrect structure in the DNA and directly restores the correct structure. directional selection  ​ ​A pattern of natural selection that favors individuals at one extreme of a phenotypic distribution. directionality  ​ ​In a DNA or RNA strand, refers to the orientation of the sugar molecules within that strand. Can be 5′ to 3′ or 3′ to 5′. disaccharide  ​ ​A carbohydrate composed of two monosaccharides. discovery science  ​ ​The collection and analysis of data without the need for a preconceived hypothesis; also called discovery-based science. discovery-based science  ​ ​The collection and analysis of data without the need for a preconceived hypothesis; also called discovery science. discrete trait  ​ ​A trait with clearly defined phenotypic variants. dispersion  ​ ​The extent to which individuals in a population are clustered together or spread out. dispersive mechanism  ​ ​In this incorrect model for DNA replication, segments of parental DNA and newly made DNA are interspersed in both strands following the replication process. dispersive mutualism  ​ ​A mutually beneficial interaction often involving plants and pollinators that disperse their pollen, and plants and fruit eaters that disperse the plant’s seeds. dissociation constant  ​ ​An equilibrium constant for the formation and dissociation of a ligand and a protein, such as a receptor or an enzyme. distal tubule  ​ ​The segment of the renal tubule through which fluid flows into one of the many collecting ducts in the kidney. disulfide bridge  ​ ​Covalent chemical bond formed between two sulfhydryl groups on cysteine side chains in a protein; important in the tertiary structure of proteins. diversifying selection  ​ ​A pattern of natural selection that favors the survival of two or more different genotypes that produce different phenotypes. diversity-stability hypothesis  ​ ​The proposal that species-rich communities are more stable than those with fewer species. DNA (deoxyribonucleic acid)  ​ ​The genetic material that provides a blueprint for the organization, development, and function of living things. DNA helicase  ​ ​An enzyme that uses ATP to separate DNA strands during DNA replication. DNA library  ​ ​A collection of recombinant vectors, each containing a particular fragment of DNA from a given organism. DNA ligase  ​ ​An enzyme that catalyzes the formation of a covalent bond between nucleotides in adjacent DNA fragments to complete the replication process.

DNA methylation  ​ ​A process in which methyl groups are attached to cytosines in DNA. DNA methyltransferase  ​ ​An enzyme that attaches methyl groups to bases in DNA. DNA microarray  ​ ​A technology used to monitor the expression of thousands of genes simultaneously. DNA polymerase  ​ ​An enzyme responsible for covalently linking nucleotides together during DNA replication. DNA primase  ​ ​An enzyme that synthesizes a primer for DNA replication. DNA replication  ​ ​The process by which DNA is copied. The original DNA strands are used as templates for the synthesis of new DNA strands DNA sequencing  ​ ​A procedure used to determine the base sequence of DNA. DNA supercoiling  ​ ​A process that compacts a chromosome through twisting of the DNA molecule to form additional coils. DNA topoisomerase  ​ ​An enzyme that alleviates DNA supercoiling during DNA replication. DNA transposon  ​ ​A type of transposable element that moves as a DNA molecule. DNase  ​ ​An enzyme that digests DNA. domain  ​ ​1. A defined region of a protein with a distinct structure and function. 2. One of the three major categories of life: Bacteria, Archaea, and Eukarya. domestication  ​ ​A process that involves artificial selection of plants or animals for traits desirable to humans. dominant species  ​ ​A species that has a large effect in a community because of its high abundance or high biomass. dominant  ​ ​Refers to the trait that is displayed in a heterozygote. dormancy  ​ ​A phase of metabolic slowdown in a plant or a seed. dorsal hollow nerve cord  ​ ​A hollow tract of nervous tissue that lies dorsal to the notochord and alimentary canal and which in vertebrates develops into the spinal cord and brain. dorsal  ​ ​Refers to the upper side of an animal. dorsoventral axis  ​ ​In bilateral animals, one of the three axes along which the adult body pattern is organized; the others are the anteroposterior axis and the leftright axis. dosage compensation  ​ ​The phenomenon in which the expression of X-linked genes is equalized between males and females; in mammals, the inactivation of one X chromosome in the female reduces the number of expressed copies (doses) of X-linked genes from two to one. double bond  ​ ​A bond that occurs when the atoms of a molecule share two pairs of electrons. double fertilization  ​ ​In angiosperms, the process in which two different fertilization events occur, producing both a zygote and the first cell of a nutritive endosperm tissue. double helix  ​ ​Two strands of DNA hydrogen-bonded with each other. In a DNA double helix, two DNA strands are twisted together to form a structure that resembles a spiral staircase. Down syndrome  ​ ​A human disorder caused by the inheritance of three copies of chromosome 21. droplet organelle  ​ ​An organelle that is not surrounded by a membrane but exists as a droplet formed by liquid-liquid phase separation. Duchenne muscular dystrophy  ​ ​An inherited, X-linked recessive disorder of humans causing muscle weakness and muscle degeneration. duodenum  ​ ​The first part of the vertebrate small intestine, arising from the stomach. duplication  ​ ​A type of mutation in which a section of a chromosome occurs two or more times.

dynamic instability  ​ ​The oscillation of a single microtubule between growing and shortening phases; important in many cellular activities, including the sorting of chromosomes during cell division.

E

Ecdysis  ​ ​The process by which an animal molts, or breaks out of its old exoskeleton, and secretes a newer, larger one. Ecdysozoa  ​ ​A clade of molting animals that encompasses the arthropods and nematodes. echolocation  ​ ​The phenomenon in which certain species listen for echoes of high-frequency sound waves in order to determine the distance and location of an object. ecological footprint  ​ ​The amount of productive land needed to support each person on Earth. ecological species concept  ​ ​An approach used to distinguish species; considers a species within its native environment and states that each species occupies its own ecological niche. ecology  ​ ​The study of interactions among organisms and between organisms and their environments. ecosystem diversity  ​ ​The diversity of structure and function within an ecosystem. ecosystem  ​ ​The biotic community of organisms in an area, as well as the abiotic environment affecting that community. ecosystems ecology  ​ ​The study of the flow of energy and cycling of nutrients among organisms within a community and between organisms and the environment. ecotypes  ​ ​Genetically distinct populations adapted to their local environments. ectoderm  ​ ​In animals, the outermost layer of cells formed during gastrulation that covers the surface of the embryo and differentiates into the epidermis and nervous system. ectomycorrhizae  ​ ​Beneficial associations between temperate forest trees and soil fungi that coat their roots. ectoparasite  ​ ​A parasite that lives on the outside of the host’s body. ectotherm  ​ ​An animal that largely depends on the environment to warm its body. ectothermic  ​ ​Dependent on external heat as the main source of body heat. edge effect  ​ ​A special physical condition that exists at the boundary, or edge, of an area of habitat. effective number of species  ​ ​The number of equally abundant species needed to obtain the same diversity index as that observed in a dataset of interest in which all species are not equally abundant. It is a measure of diversity that converts values from species diversity indices into equivalent numbers of species. effective population size  ​ ​The number of individuals that contribute genes to future populations, often smaller than the actual population size. effector cell  ​ ​A cloned lymphocyte that carries out the attack response during an acquired immune response. effector  ​ ​A molecule that directly influences a cellular response; in a homeostatic control system in animals, a structure that compensates for a deviation of a physiological variable from its set point. efferent arteriole  ​ ​A blood vessel that carries blood away from a glomerulus of the vertebrate kidney. egestion  ​ ​In animals, the process of eliminating undigested material from the body. egg cells  ​ ​Female haploid gametes in species that reproduce sexually. egg  ​ ​The mature female gamete; also called an ovum. ejaculation  ​ ​The movement of semen through the urethra by contraction of muscles at the base of the penis.

elastin  ​ ​A protein that makes up elastic fibers in the extracellular matrix of animals. electrical synapse  ​ ​A synapse that directly passes electric current from the presynaptic to the postsynaptic cell via gap junctions. electrocardiogram (ECG or EKG)  ​ ​A record of the electrical impulses generated by the cells of the heart during the cardiac cycle. electrochemical gradient  ​ ​The combined effect of both an electrical and a chemical gradient across a membrane; determines the direction in which ions will move. electrogenic pump  ​ ​A pump that generates an electrical gradient across a membrane. electromagnetic receptor  ​ ​A sensory receptor in animals that detects radiation within a wide range of the electromagnetic spectrum, including visible, ultraviolet, and infrared light, as well as electrical and magnetic fields in some animals. electromagnetic spectrum  ​ ​All possible wavelengths of electromagnetic radiation, from relatively short wavelengths (gamma rays) to much longer wavelengths (radio waves). electron microscope  ​ ​A microscope that uses an electron beam for illumination. electron shell  ​ ​The region around an atom’s nucleus where electrons reside; larger atoms have more electron shells than smaller atoms. electron transport chain (ETC)  ​ ​A group of protein complexes and small organic molecules within the inner membranes of mitochondria and chloroplasts and the plasma membrane of prokaryotes. The components accept and donate electrons to each other in a linear manner and produce an H+ electrochemical gradient. electron  ​ ​A negatively charged particle found in orbitals around an atomic nucleus. electronegativity  ​ ​A measure of an atom’s ability to attract electrons in a bond with another atom. element  ​ ​A pure substance composed of only one kind of atom. elicitor  ​ ​A protein produced by bacterial and fungal pathogens that promotes virulence. elongation factor  ​ ​A protein that is needed for polypeptide synthesis during the elongation stage of translation. elongation  ​ ​The second stage in transcription or translation, where RNA strands or polypeptides are made, respectively. embryo  ​ ​The early stages of development in a multicellular organism during which the organization of the organism is largely established. embryogenesis  ​ ​The process by which embryos develop from single-celled zygotes by mitotic divisions. embryonic development  ​ ​The process by which a fertilized egg is transformed into an organism with distinct physiological systems and body parts. embryonic germ cell (EG cell)  ​ ​A cell in the early mammalian embryo that later gives rise to sperm or egg cells. These cells are pluripotent. embryonic stem cell (ES cell)  ​ ​A cell in the early mammalian embryo that can differentiate into almost every cell type of the body. These cells are pluripotent. embryophytes  ​ ​The land plants. emerging virus  ​ ​A virus that has arisen recently or has recently shown a greater probability of causing infection. emphysema  ​ ​A progressive disease characterized by a loss of elastic recoil ability of the lungs, usually resulting from chronic tobacco smoking. empirical thought  ​ ​Thought that relies on observation to form an idea or hypothesis, rather than trying to understand life from a nonphysical or spiritual point of view.

GLOSSARY

GLOSSARY G-9

G-10 GLOSSARY

GLOSSARY

emulsification  ​ ​A process during digestion that disrupts large lipid droplets into many tiny droplets, thereby increasing their total surface area and providing greater exposure to lipase action. enantiomer  ​ ​One of a pair of stereoisomers that exist as mirror images. endangered species  ​ ​Those species that are in danger of extinction throughout all or a significant portion of their range. endemic  ​ ​Refers to species that are naturally found only in a particular place or region. endergonic  ​ ​Refers to chemical reactions that require an addition of free energy and do not proceed spontaneously. endocrine disruptor  ​ ​A chemical found in polluted water and soil that resembles a natural hormone; a common example are chemicals that resemble estrogen and can bind to estrogen receptors in animals. endocrine glands  ​ ​Structures that contain epithelial cells that secrete hormones into the bloodstream, where they circulate throughout the body. endocrine system  ​ ​All the endocrine glands and other organs containing hormone-secreting cells. endocytosis  ​ ​A process in which the plasma membrane invaginates, or folds inward, to form a vesicle that brings substances into the cell. endoderm  ​ ​In animals, the innermost layer of cells formed during gastrulation; lines the gut and gives rise to many internal organs. endodermis  ​ ​In vascular plants, a thin cylinder of root tissue that forms a barrier between the root cortex and the central core of vascular tissue. endomembrane system  ​ ​A network of membranes that includes the nuclear envelope, the endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, peroxisomes, and plasma membrane. endomycorrhizae  ​ ​Partnerships between plants and fungi in which the fungal hyphae grow into the spaces between root cell walls and plasma membranes. endoparasite  ​ ​A parasite that lives inside the host’s body. endoplasmic reticulum (ER)  ​ ​A convoluted network of membranes in a cell’s cytoplasm that forms flattened, fluid-filled tubules, or cisternae. endoskeleton  ​ ​An internal hard skeleton covered by soft tissue; present in echinoderms and vertebrates. endosperm  ​ ​A nutritive tissue that increases the efficiency with which food is stored and used in the seeds of flowering plants. endospore  ​ ​A structure with a tough coat that is produced inside of certain bacteria and then released when the enclosing bacterial cell dies and breaks down. endosporic gametophyte  ​ ​A plant gametophyte that grows within the confines of microspore or megaspore walls. endosymbiosis theory  ​ ​A theory that mitochondria and chloroplasts originated from bacteria that took up residence within primordial eukaryotic cells. endosymbiosis  ​ ​A symbiotic relationship in which the smaller species (the symbiont) lives inside the larger species (the host). endosymbiotic  ​ ​Describes a relationship in which one organism (the endosymbiont) lives inside another (the host). endotherm  ​ ​An animal that generates most of its body heat by metabolic processes. endothermic  ​ ​Capable of generating body heat through metabolism. energy flow  ​ ​The movement of energy through an ecosystem. energy intermediate  ​ ​A molecule such as ATP or NADH that stores energy and is used to drive endergonic reactions in cells.

energy  ​ ​The ability to promote change or do work. enhancer  ​ ​A regulatory element in eukaryotes that increases the rate of transcription when bound by an activator protein. enthalpy (H)  ​ ​The total energy of a system. entomology  ​ ​The scientific study of insects. entropy  ​ ​The degree of disorder of a system. environmental science  ​ ​The application of ecology to real-world problems. enzyme  ​ ​A protein that acts as a catalyst to speed up a chemical reaction in a cell. enzyme-linked receptor  ​ ​A receptor found in all living species that typically has two important domains: an extracellular domain, which binds a signaling molecule, and an intracellular domain, which has a catalytic function. enzyme-substrate complex  ​ ​The structure produced by binding an enzyme and its substrate(s). eosinophil  ​ ​A type of phagocyte found in large numbers in mucosal surfaces lining the gastrointestinal, respiratory, and urinary tracts, where they fight off parasitic infections. epicotyl  ​ ​The portion of an embryonic plant stem with two tiny leaves in a first bud; located above the point of attachment of the cotyledons. epidermis  ​ ​A layer of dermal tissue on the surfaces of leaves, stems, and roots that helps protect a plant from damage. epigenetic inheritance  ​ ​An epigenetic change that is passed from parent to offspring. An example is genomic imprinting. epigenetics  ​ ​The study of mechanisms that lead to changes in gene expression that can be passed from cell to cell and are reversible, but do not involve a change in the sequence of DNA. epilimnion  ​ ​The upper layer of water in a lake, usually warm and containing high levels of dissolved oxygen. epimutation  ​ ​A heritable change in gene expression that does not alter the sequence of DNA. episome  ​ ​A plasmid or viral genome that can integrate into a host chromosome or can replicate independently. epistasis  ​ ​A gene interaction in which the alleles of one gene mask the expression of the alleles of another gene. epithalamus  ​ ​A region of the vertebrate forebrain that includes the pineal gland. epithelial tissue  ​ ​In animals, a sheet of densely packed cells that covers the body, covers individual organs, or lines the walls of various cavities inside the body. epitope  ​ ​An antigenic determinant; the polypeptide fragment of an antigen that is complexed to an MHC protein and presented to a helper T cell. equilibrium model of island biogeography  ​ ​A model that explains the process of succession on new islands, proposing that the number of species on an island tends toward an equilibrium number that is determined by the balance between immigration rates and extinction rates. equilibrium potential  ​ ​The membrane potential at which the flow of an ion is at equilibrium, with no net movement in either direction. equilibrium  ​ ​1. In a chemical reaction, occurs when the rate of the forward reaction is balanced by the rate of the reverse reaction. 2. In a population, the situation in which the population size stays the same. ER lumen  ​ ​A single compartment enclosed by the ER membrane. ER signal sequence  ​ ​A sorting signal in a polypeptide that is usually located near the N-terminus and is recognized by SRP (signal recognition particle), allowing the polypeptide to be directed to the ER membrane. erythrocyte  ​ ​A cell that serves the critical function of transporting oxygen throughout an animal’s body; also known as a red blood cell.

erythropoietin (EPO)  ​ ​A hormone made by the liver and kidneys in response to any situation where additional red blood cells are required. esophagus  ​ ​In animals, the tubular structure that forms a pathway from the pharynx to the stomach. essential amino acid  ​ ​An amino acid that is required in the diet of many animals. essential element  ​ ​In plants, a chemical element that is required for metabolism, sometimes by functioning as an enzyme cofactor. essential fatty acid  ​ ​An unsaturated fatty acid, such as linoleic acid, that cannot be synthesized by animal cells and must therefore be consumed in the diet. essential nutrient  ​ ​In animals, a compound that cannot be synthesized from any ingested or stored precursor molecule and so must be obtained in the diet in its complete form. In plants, those substances needed to complete reproduction while avoiding the symptoms of nutrient deficiency. estradiol  ​ ​The major estrogen in many vertebrates, including humans. estrogens  ​ ​Steroid hormones produced by the ovaries that affect most aspects of female reproduction. ethology  ​ ​Scientific studies of animal behavior. ethylene  ​ ​A plant hormone that is particularly important in coordinating plant developmental and stress responses. euchromatin  ​ ​The less condensed regions of a chromosome; areas that are capable of gene transcription. eudicots  ​ ​One of the two largest lineages of flowering plants in which the embryo possesses two seed leaves. Eukarya  ​ ​One of the three domains of life; the other two are Bacteria and Archaea. eukaryote  ​ ​A member of the domain Eukarya. The distinguishing feature of eukaryotes is cell compartmentalization, including a cell nucleus; eukaryotes include protists, fungi, plants, and animals. eukaryotic  ​ ​Refers to organisms having cells with internal compartments that serve various functions; includes all members of the domain Eukarya. euphyll  ​ ​A leaf with branched veins. euploid  ​ ​Refers to an organism that has a chromosome number that is a multiple of a chromosome set (1n, 2n, 3n, etc.). eusociality  ​ ​An extreme form of altruism in social insects in which the vast majority of females, known as workers, do not reproduce. Instead, they help one reproductive female (the queen) raise offspring. eustele  ​ ​In plants, a ring of vascular tissue arranged around a central pith of nonvascular tissue; typical of progymnosperms, gymnosperms, and angiosperms. eutherian  ​ ​A placental mammal; a member of the clade Eutheria. eutrophic  ​ ​Waters that contain relatively high levels of nutrients such as phosphate or nitrogen and typically exhibit high levels of primary productivity and low levels of biodiversity. eutrophication  ​ ​The process by which elevated nutrient levels in a body of water lead to an overgrowth of algae or aquatic plants and a subsequent depletion of water oxygen concentrations when these photosynthesizers decay. evaporation  ​ ​The conversion of water from the liquid to the gaseous state at normal temperatures. Animals use evaporation as a means of losing excess body heat. evapotranspiration rate  ​ ​The rate at which water moves into the atmosphere through the processes of evaporation from the soil and other surfaces and transpiration of plants. evo-devo   See evolutionary developmental biology. evolution  ​ ​A heritable change in a population of organisms from one generation to the next.  evolutionarily conserved  ​ ​The term used to describe homologous DNA sequences that are very similar or identical between different species.

evolutionary developmental biology  ​ ​The field of biology that compares the development of different organisms in an attempt to understand relationships between organisms and the mechanisms that bring about evolutionary change; referred to as evo-devo. evolutionary lineage concept  ​ ​An approach used to distinguish species; states that a species is derived from a single distinct lineage and has its own evolutionary tendencies and historical fate. excitation-contraction coupling  ​ ​The sequence of events by which an action potential in the plasma membrane of a muscle fiber leads to cross-bridge activity. excitatory postsynaptic potential (EPSP)  ​ ​The response to an excitatory neurotransmitter that depolarizes the postsynaptic membrane; the depolarization brings the membrane potential closer to the threshold potential that would trigger an action potential. excretion  ​ ​In animals, the process of expelling waste or harmful materials from the body. excretory system  ​ ​All of an animal’s organs (such as gills, lungs, kidneys, and, in some animals, the body surface) that function to remove soluble wastes generated from metabolism. excurrent siphon  ​ ​A structure in a tunicate used to expel water from the body exercise  ​ ​Any physical activity that increases an animal’s metabolic rate. exergonic  ​ ​Refers to chemical reactions that release free energy and occur spontaneously. exocrine gland  ​ ​A gland in which epithelial cells secrete chemicals into a duct, which carries those molecules directly to another structure or to the outside surface of the body. exocytosis  ​ ​A process in which material inside a cell is packaged into vesicles and excreted into the extracellular environment. exon  ​ ​A portion of RNA that is found in the mature mRNA molecule after splicing is finished. exoskeleton  ​ ​An external skeleton made primarily of chitin that surrounds and protects most of the body surface of animals such as insects. expansin  ​ ​A protein that occurs in the plant cell wall and fosters cell enlargement. experimental group  ​ ​The sample in an experiment that is subjected to some type of variation that does not occur for the control group. exploitation competition  ​ ​Competition in which organisms compete indirectly through the consumption of a limited resource. exponential growth  ​ ​Rapid population growth that occurs when the per capita growth rate remains above zero. extant  ​ ​Refers to a species that is still in existence. extensor  ​ ​A muscle that straightens a limb at a joint. external fertilization  ​ ​Fertilization that occurs in aquatic environments, when eggs and sperm are released into the water in close enough proximity for fertilization to occur. extinct  ​ ​Refers to a species that existed in the past, but has died out. extinction  ​ ​The end of the existence of a species or a group of species. extracellular fluid  ​ ​The fluid in an organism’s body that is outside of the cells. extracellular matrix (ECM)  ​ ​A network of material that is secreted from animal cells and forms a complex meshwork outside of cells. The ECM provides strength, support, and organization. extranuclear inheritance  ​ ​In eukaryotes, the transmission of genes that are located outside the cell nucleus. extremophile  ​ ​An organism that occurs primarily in extreme habitats.

extrinsic pathway  ​ ​One of two different pathways for apoptosis that involves the activation of death receptors. eye  ​ ​The visual organ in animals that detects light and sends signals to the brain. eyecup  ​ ​A visual organ in flatworms that detects light and its direction but does not form an image.

F

F factor  ​ ​A fertility factor, or type of bacterial plasmid that plays a role in bacterial conjugation. F1 generation  ​ ​The first generation of offspring in a genetic cross. F2 generation  ​ ​The second generation of offspring in a genetic cross. facilitated diffusion  ​ ​A mechanism of passive transport in which a transport protein provides a passageway for a substance to cross a membrane from an area of higher concentration to one of lower concentration. facilitation  ​ ​A mechanism for succession in which a species facilitates or makes the local environment more suitable for subsequent species. facultative anaerobe  ​ ​A microorganism that can use oxygen in aerobic respiration, obtain energy via anaerobic fermentation, or use inorganic chemical reactions to obtain energy. facultative mutualism  ​ ​An interaction between mutualistic species that is beneficial but not essential to the survival and reproduction of either species. falsifiable  ​ ​Refers to a hypothesis that can be shown to be incorrect based on additional observations or experimentation. family  ​ ​In taxonomy, a subdivision of an order. fast fiber  ​ ​A skeletal muscle fiber containing myosin with higher ATPase activity. fast-glycolytic fiber  ​ ​A skeletal muscle fiber that has high myosin ATPase activity but cannot make as much ATP as an oxidative fiber because its source of ATP is glycolysis; best suited for rapid, intense actions. fast-oxidative fiber  ​ ​A skeletal muscle fiber that has high myosin ATPase activity and can make large amounts of ATP; used for long-term actions. fate  ​ ​The ultimate morphological features that a cell or a group of cells will adopt. feedback inhibition  ​ ​A type of regulation in which the product of a metabolic pathway inhibits an enzyme that acts early in the pathway, thus preventing the overaccumulation of the product. feedforward regulation  ​ ​The process by which an animal’s body begins preparing for a change in some variable before it even occurs. female gametophyte  ​ ​A haploid multicellular plant generation that produces one or more eggs but does not produce sperm cells. female-enforced monogamy hypothesis  ​ ​The hypothesis that a male is monogamous due to various actions employed by his female mate. fermentation  ​ ​The breakdown of organic molecules to produce energy without any net oxidation of an organic molecule. fertilization  ​ ​The union of two gametes, such as an egg cell with a sperm cell, to form a zygote. fertilizer  ​ ​A soil addition that enhances plant growth by providing essential elements. fetus  ​ ​The maturing embryo after the eighth week of gestation in humans. fever  ​ ​An increase in an animal’s body temperature, typically due to infection. fiber  ​ ​A type of tough-walled plant cell that provides support. fibrous root system  ​ ​The root system of monocots, which consists of multiple adventitious roots that grow from the stem base.

fight-or-flight response  ​ ​The response of vertebrates to real or perceived danger; associated with increased activity of the sympathetic branch of the autonomic nervous system. filament  ​ ​1. The elongate portion of a flower’s stamen; contains vascular tissue that delivers nutrients from parental sporophytes to anthers. 2. In fishes, a part of the gills. filtrate  ​ ​In the process of filtration in an excretory system, the material that passes through the filter and enters the excretory organ for either further processing or excretion. filtration  ​ ​The passive removal of water and small solutes from the blood during the production of urine. finite rate of increase  ​ ​In ecology, the ratio of a population size from one year to the next. fitness  ​ ​The relative likelihood that a genotype will contribute to the gene pool of the next generation as compared with other genotypes. fixed action pattern (FAP)  ​ ​An animal behavior that, once initiated, will continue until completed. fixed nitrogen  ​ ​Atmospheric nitrogen that has been combined with another element into a substance that can be used by plants. An example is ammonia, NH3. flaccid  ​ ​Refers to a plant cell in which the concentration of solutes is the same as that in the external fluid environment. A flaccid cell has a water content higher than a plasmolyzed cell, but lower than a turgid cell. flagella (singular, flagellum)  ​ ​Relatively long cell appendages that facilitate cellular movement or the movement of extracellular fluids. flagellate  ​ ​A protist that uses one or more flagella to move in water or cause water motions useful in feeding. flagship species  ​ ​A single large or instantly recognizable species. flame cell  ​ ​A cell that exists primarily to maintain osmotic balance between an organism’s body and surrounding fluids; present in flatworms. flexor  ​ ​A muscle that bends a limb at a joint. flower  ​ ​A reproductive shoot; a short stem branch bearing reproductive organs instead of leaves. flowering plants  ​ ​The angiosperms, which produce ovules within the protective ovaries of flowers. The ovules develop into seeds, and the ovaries develop into fruits, which function in seed dispersal. fluidity  ​ ​A property of biological membranes in which individual molecules remain in close association yet have the ability to move rotationally or laterally within the plane of the membrane. Membranes are semifluid. fluid-mosaic model  ​ ​The accepted model of a biological membrane; its basic framework is the semifluid phospholipid bilayer with a mosaic of proteins. Carbohydrates may be attached to the lipids or proteins. focal adhesion  ​ ​A mechanically strong type of cell junction that connects an animal cell to the extracellular matrix (ECM). follicle-stimulating hormone (FSH)  ​ ​A gonadotropin that stimulates follicle development. follicular phase  ​ ​The first half of the human ovarian cycle, in which a cohort of immature follicles begin to grow and differentiate. food chain  ​ ​A linear depiction of energy flow between organisms, with each organism feeding on and deriving energy from the preceding organism. food web  ​ ​A complex model of interconnected food chains in which there are multiple links among different species. food-induced thermogenesis  ​ ​A rise in an animal’s metabolic rate and heat production for a few hours after eating. foot  ​ ​In mollusks, a muscular structure usually used for movement.

GLOSSARY

GLOSSARY G-11

G-12 GLOSSARY

GLOSSARY

forebrain  ​ ​One of three major divisions of the vertebrate brain; the other two divisions are the midbrain and the hindbrain. fossil fuel  ​ ​A fuel formed in the Earth from protist, plant, or animal remains, such as coal, petroleum, or natural gas. fossil  ​ ​Recognizable preserved remains of past life on Earth. founder effect  ​ ​Genetic drift that occurs when a small group of individuals separates from a larger population and establishes a colony in a new location. fovea  ​ ​A small area on the retina directly behind the lens, where an image is most sharply focused. frameshift mutation  ​ ​A mutation that involves the addition or deletion of a number of nucleotides that is not a multiple of three and alters the reading frame of a protein-encoding gene. Frank-Starling law of the heart  ​ ​A law that states the strength of a heart contraction (beat) is related to the amount of blood that had filled the heart chambers prior to the contraction. Increased return of blood to the heart will increase the subsequent strength of a heart contraction. free energy (G)  ​ ​The amount of a system’s energy that is available and can be used to promote change or do work. free radical  ​ ​A molecule containing an atom with a single, unpaired electron in its outer shell. A free radical is unstable and interacts with other molecules by removing electrons from their atoms. frequency  ​ ​For a sound wave, the number of complete wavelengths that occur in 1 second, measured in hertz (Hz). frontal lobe  ​ ​One of four lobes of the cerebral cortex of the human brain; important in a variety of functions, including judgment and conscious thought. fruit  ​ ​A structure that develops from flower parts, encloses seeds, and fosters seed dispersal in the environment. fruiting bodies  ​ ​The visible fungal reproductive structures that are composed of densely packed hyphae that typically grow out of the substrate. functional genomics  ​ ​Genomic methods aimed at studying the expression of a genome. functional group  ​ ​A group of atoms with a characteristic chemical structure that exhibits particular properties. Each functional group exhibits the same properties in all molecules in which it occurs. functional magnetic resonance imaging (fMRI)  ​ ​A technique used to determine changes in brain activity while a person is performing specific tasks. fundamental niche  ​ ​The optimal range of conditions in which a particular species functions best. Fungi  ​ ​A eukaryotic kingdom of the domain Eukarya. fungus-like protists  ​ ​Heterotrophic protists that often resemble true fungi in having threadlike, filamentous bodies and absorbing nutrients from their environment.

G

G protein  ​ ​An intracellular protein that binds guanosine triphosphate (GTP) and guanosine diphosphate (GDP) and participates in intracellular signaling pathways. G1 phase  ​ ​The first gap phase of the cell cycle. G2 phase  ​ ​The second gap phase of the cell cycle. gallbladder  ​ ​In many vertebrates, a small sac underneath the liver that is a storage site for bile; allows the release of large amounts of bile to be precisely timed to the consumption of fats. gametangia  ​ ​Specialized structures produced by some fungi and many land plants in which developing gametes are protected by a jacket of tissue. gamete  ​ ​A haploid cell that is involved with sexual reproduction, such as a sperm or egg cell.

gametogenesis  ​ ​The formation of gametes. gametophyte  ​ ​In plants and many multicellular protists, the haploid stage that produces gametes by mitosis. ganglion cells  ​ ​Cells in the vertebrate eye whose axons extend into the optic nerve. gap gene  ​ ​A type of segmentation gene; a mutation in this type of gene may cause several adjacent segments to be missing in the larva. gap junction  ​ ​A type of junction between animal cells that provides a passageway for intercellular transport. gas exchange  ​ ​The process of moving oxygen and carbon dioxide in opposite directions between the environment and blood and between blood and cells. gastrin  ​ ​A hormone secreted by cells of the vertebrate stomach that stimulates smooth muscle contraction and acid production by stomach cells. gastrovascular cavity  ​ ​In certain invertebrates such as cnidarians, a body cavity with a single opening to the outside; it functions as both a digestive system and circulatory system. gastrula  ​ ​A stage of an animal embryo that is the result of gastrulation and has three cellular layers: the ectoderm, endoderm, and mesoderm. gastrulation  ​ ​In animals, a process in which an area in the blastula invaginates and folds inward, creating different embryonic cell layers called germ layers. gated  ​ ​A property of many channels that allows them to open and close to control the movement of solutes across a membrane. gel electrophoresis  ​ ​A technique used to separate macromolecules by applying an electric field that causes them to migrate through a gel matrix. gene cloning  ​ ​The process of making multiple copies of a particular gene. gene expression  ​ ​Gene function either at the level of traits or at the molecular level. gene family  ​ ​A group of homologous genes within a single species that carry out related functions. gene flow  ​ ​A transfer of alleles into or out of a population that occurs when fertile individuals migrate between populations having different allele frequencies. gene interaction  ​ ​The phenomenon in which a single trait is controlled by two or more genes, each of which has two or more alleles. gene pool  ​ ​All of the alleles for every gene in a population. gene regulation  ​ ​The ability of cells to control the expression of their genes. gene transfer  ​ ​The process by which genetic material is transferred from one bacterial cell to another. gene  ​ ​A unit of heredity.  At the molecular level, a gene is an organized unit of base sequences in a DNA strand that can transcribed into RNA and ultimately results in the formation of a functional product. general lineage concept  ​ ​A widely accepted approach used to distinguish species; states that each species is a population of an independently evolving lineage. general transcription factors (GTFs)  ​ ​Five different proteins that play a role in initiating transcription at the core promoter of protein-encoding genes in eukaryotes. generative cell  ​ ​In a seed plant, one of the cells resulting from the division of a microspore; a generative cell divides to produce two sperm cells. genetic code  ​ ​A code that specifies the relationship between the sequence of bases in the codons found in mRNA and the sequence of amino acids in a polypeptide. genetic diversity  ​ ​The amount of genetic variation occurring within and between populations. genetic drift  ​ ​The random change in a population’s allele frequencies from one generation to the next that is attributable to chance. It occurs more quickly in small populations.

genetic map  ​ ​A chart that shows the linear arrangement of genes along a chromosome. genetic mapping  ​ ​The use of genetic crosses to determine the linear order of genes that are linked to each other along the same chromosome. genetics  ​ ​The branch of biology that deals with inheritance. genome centric metagenomics  ​ ​The process of assembling whole microbial genomes from metagenomic DNA sequences. genome  ​ ​The complete genetic material of an organism or species. genomic imprinting  ​ ​A phenomenon in which a segment of DNA is imprinted, or marked, during egg or sperm formation in a way that affects gene expression throughout the life of the individual who inherits that DNA. genomic library  ​ ​A type of DNA library in which the inserts are derived from chromosomal DNA. genomics  ​ ​Techniques that are used to analyze the DNA sequence of the entire genome of a species. genotype frequency  ​ ​In a population, the number of individuals with a given genotype divided by the total number of individuals. genotype  ​ ​The genetic composition of an individual. genus (plural, genera)  ​ ​In taxonomy, a subdivision of a family. geological timescale  ​ ​A timeline of the Earth’s history and major events from its origin about 4.55 bya to the present. germ layer  ​ ​An embryonic cell layer such as ectoderm, mesoderm, or endoderm. germ line  ​ ​Cells that give rise to gametes, such as egg and sperm cells. germination  ​ ​In plants, the process in which an embryo absorbs water, becomes metabolically active, and grows out of the seed coat, producing a seedling. giant axon  ​ ​A very large axon in certain species such as squids that facilitates high-speed neuronal conduction and rapid responses to stimuli. gibberellic acid  ​ ​A type of gibberellin, a plant hormone. gibberellin  ​ ​A plant hormone that stimulates both cell division and cell elongation. gills  ​ ​Specialized filamentous organs in aquatic animals that are used to obtain oxygen and eliminate wastes. ginkgos  ​ ​A phylum of gymnosperms; formally known as Ginkgophyta. gizzard  ​ ​The muscular portion of the stomach of birds and some reptiles that is capable of grinding food into smaller fragments. glaucoma  ​ ​A condition in which drainage of aqueous humor in the eye becomes blocked and the pressure inside the eye increases. If untreated, this pressure damages cells in the retina and leads to irreversible loss of vision. glia  ​ ​Cells that surround the neurons; a major class of cells in nervous systems that perform various functions. global warming  ​ ​A gradual elevation of the Earth’s average surface temperature caused by an increasing greenhouse effect. glomerular filtration rate (GFR)  ​ ​The rate at which a filtrate from plasma is formed in all the glomeruli of the vertebrate kidneys. glomerulus  ​ ​A cluster of interconnected, fenestrated capillaries in the renal corpuscle of the kidney; the site of filtration in the kidney. glucagon  ​ ​A hormone secreted by the pancreas of an animal that stimulates the processes of glycogenolysis, gluconeogenesis, and the synthesis of ketones in the liver. gluconeogenesis  ​ ​A mechanism for maintaining blood glucose level in which enzymes in the liver convert noncarbohydrate precursors into glucose, which is then secreted into the blood.

glucose sparing  ​ ​A metabolic adjustment that reserves the glucose produced by the liver for use by the nervous system. glycocalyx  ​ ​1. An outer viscous covering surrounding a bacterium that traps water and helps protect the bacterium from drying out. 2. A carbohydrate-rich zone on the surface of animal cells; also called a cell coat. glycogen  ​ ​A polysaccharide found in animal cells (especially liver and skeletal muscle) and sometimes called animal starch; also, the major carbohydrate storage of fungi. glycogenolysis  ​ ​A mechanism for maintaining blood glucose level by breaking down stored glycogen by hydrolysis, yielding molecules of glucose, which are then secreted into the blood. glycolipid  ​ ​A lipid that has carbohydrate attached to it. glycolysis  ​ ​A metabolic pathway that breaks down glucose to pyruvate. glycolytic fiber  ​ ​A skeletal muscle fiber that has relatively few mitochondria but possesses both a high concentration of glycolytic enzymes and a large store of glycogen. glycoprotein  ​ ​A protein that has a carbohydrate attached to it. glycosaminoglycan  ​ ​The most abundant type of polysaccharide in the extracellular matrix (ECM) of animals, consisting of repeating disaccharide units that give a gel-like character to the ECM. glycosidic bond  ​ ​A covalent bond formed between two sugar molecules via a dehydration reaction. glycosylation  ​ ​The covalent attachment of a carbohydrate to a protein or lipid, producing a glycoprotein or glycolipid, respectively. glyoxysome  ​ ​A specialized organelle within plant seeds that contains enzymes needed to convert fats to sugars. gnathostomes  ​ ​All vertebrate species that possess jaws. Golgi apparatus  ​ ​A stack of flattened, membranebound compartments that performs three overlapping functions: secretion, processing, and protein sorting. gonads  ​ ​The testes in males and the ovaries in females, where the gametes are formed. G-protein-coupled receptor (GPCR)  ​ ​A common type of receptor found in the cells of eukaryotic species that interacts with G proteins to initiate a cellular response. graded potential  ​ ​A depolarization or hyperpolarization of a neuron’s plasma membrane that varies with the strength of a stimulus. gradualism  ​ ​A concept suggesting that species evolve continuously over long spans of time. grain  ​ ​The characteristic single-seeded fruit of cereal grasses such as rice, corn, barley, and wheat. granum  ​ ​A structure composed of stacked membranebound thylakoids within a chloroplast. gravitropism  ​ ​Plant growth in response to the force of gravity. gray matter  ​ ​Brain tissue that consists of neuronal cell bodies, dendrites, and some unmyelinated axons. gross primary production (GPP)  ​ ​The measure of biomass production by photosynthetic organisms; equivalent to the carbon fixed during photosynthesis. ground tissue  ​ ​Type of tissue that makes up most of the body of a plant and has a variety of functions, including photosynthesis, storage of carbohydrates, and support. Ground tissue can be subdivided into three types: parenchyma, collenchyma, and sclerenchyma. group selection  ​ ​A premise that attempts to explain altruism by claiming that natural selection produces outcomes beneficial for the whole group or species rather than for individuals. growth factors  ​ ​A signaling molecule in animals that promotes cell division.

growth hormone (GH)  ​ ​A hormone produced in vertebrates by the anterior pituitary gland; GH acts on the liver to produce insulin-like growth factor-1 (IGF-1). growth  ​ ​An increase in weight or size. guanine (G)  ​ ​A purine base found in DNA and RNA. guard cell  ​ ​A specialized plant cell that allows epidermal pores (stomata) to close when conditions are too dry and to open under moist conditions, allowing the entry of CO2 needed for photosynthesis. gustation  ​ ​The sense of taste. guttation  ​ ​The phenomenon in which droplets of water form at the edges of leaves as the result of root pressure. gymnosperm  ​ ​A plant that produces seeds that are exposed rather than seeds enclosed in fruits.

H

H+ electrochemical gradient  ​ ​A transmembrane gradient for H+ composed of both an electrical gradient and a concentration difference for H+ across a membrane. habitat destruction  ​ ​A usually human-driven process in which a natural habitat is altered in a way that prevents it from supporting the species that were originally present. habitat restoration  ​ ​The full or partial repair or replacement of biological habitats and/or their populations that have been damaged. habituation  ​ ​The form of nonassociative learning in which an organism learns to ignore a repeated stimulus. hair cell  ​ ​A mechanoreceptor in animals that is a specialized epithelial cell with deformable stereocilia. half-life  ​ ​1. In the case of organic molecules in a cell, refers to the time it takes for 50% of the molecules to be broken down and recycled. 2. In the case of radioisotopes, the time it takes for 50% of the atoms to decay and emit radiation. halophyte  ​ ​A plant that can tolerate higher than normal salt concentrations and can occupy coastal salt marshes or saline deserts. Hamilton’s rule  ​ ​The proposal that an altruistic gene will be favored by natural selection when rB > C, where r is the coefficient of relatedness of the donor (the altruist) to the recipient, B is the benefit received by the recipient, and C is the cost incurred by the donor. haplodiploid system  ​ ​A genetic system in which females develop from fertilized eggs and are diploid but males develop from unfertilized eggs and are haploid. haploid  ​ ​Containing one set of chromosomes; designated as 1n. haploid-dominant species  ​ ​Species in which the haploid organism is the multicellular organism in the life cycle. Examples include fungi and some protists. haplorrhini  ​ ​Larger-brained diurnal species of primates, including tarsiers, monkeys, gibbons, orangutans, gorillas, chimpanzees, and humans. Hardy-Weinberg equation  ​ ​An equation (p2 + 2pq + q2 = 1) that relates allele and genotype frequencies; the equation predicts an equilibrium if no new mutations are formed, no natural selection occurs, the population size is very large, the population does not migrate, and mating is random. heartburn  ​ ​More properly called gastroesophageal reflux; the movement of acidic stomach contents upward into the esophagus, typically causing pain. heat capacity  ​ ​The amount of heat required to raise the temperature of an entire object or amount of substance. heat of fusion  ​ ​The amount of heat energy that must be withdrawn or released from a substance to cause it to change from the liquid to the solid state.

heat of vaporization  ​ ​The heat required to vaporize 1 mole of any substance at its boiling point under standard pressure. helper T cell  ​ ​A type of lymphocyte that assists in the activation and function of B cells and cytotoxic T cells. hematocrit  ​ ​The volume of blood that is composed of red blood cells, usually between 35% and 65% in vertebrates. hemidesmosome  ​ ​A mechanically strong type of cell junction that connects an animal cell to the extracellular matrix (ECM). hemiparasite  ​ ​A parasitic organism that photosynthesizes, but lacks a root system to draw water and thus depends on its host for that function. hemispheres  ​ ​The two halves of the cerebrum. hemizygous  ​ ​Having only one copy of a particular gene; a male mammal is hemizygous for an X-linked gene. hemocyanin  ​ ​A copper-containing pigment that binds oxygen and gives blood or hemolymph a bluish tint. hemodialysis  ​ ​A medical procedure used to artificially perform the kidneys’ function. hemoglobin  ​ ​An iron-containing protein that reversibly binds to oxygen and is found within the cytosol of red blood cells. hemolymph  ​ ​Mixed fluid found in one body compartment (hemocoel) in an animal; present in many invertebrates. hemorrhage  ​ ​A loss of blood from a ruptured blood vessel. herbaceous plant  ​ ​A plant that produces little or no wood and is composed mostly of primary vascular tissues. herbivore  ​ ​An animal that eats only plants. herbivory  ​ ​A form of species interaction in which herbivores feed on plants. heritable  ​ ​A property of DNA, which means that it can be passed from cell to cell and from parent to offspring. hermaphrodites  ​ ​In animals, individuals that possess both ovaries and testes. heterochromatin  ​ ​The highly compacted regions of chromosomes that are usually transcriptionally inactive because of their tight conformation. heterochrony  ​ ​Differences among species in the rate or timing of developmental events. heterospory  ​ ​In plants, the production of two different types of spores: microspores and megaspores; microspores produce male gametophytes, and megaspores produce female gametophytes. heterotherm  ​ ​An animal that has a body temperature that varies widely with environmental temerature; both ectotherms and endotherms may be heterotherms. heterotroph  ​ ​Organisms that cannot produce their own organic molecules by using energy from inorganic sources or light; they must obtain one or more organic compounds from their environment. heterotrophic  ​ ​Requiring organic food from the environment. heterozygote advantage  ​ ​A phenomenon in which a heterozygote has a higher fitness than either corresponding homozygote. heterozygous  ​ ​An individual with two different alleles of the same gene. highly repetitive sequence  ​ ​A DNA sequence that is repeated tens of thousands or even millions of times throughout a genome. hindbrain  ​ ​One of three major divisions of the vertebrate brain; the other two divisions are the midbrain and the forebrain. hippocampus  ​ ​The area of the limbic system of the vertebrate forebrain that functions in establishing memories for spatial locations, facts, and the sequence of events.

GLOSSARY

GLOSSARY G-13

G-14 GLOSSARY

GLOSSARY

histone acetyltransferase  ​ ​An enzyme that attaches acetyl groups to the amino terminal tails of histone proteins. histone code hypothesis  ​ ​The idea that the pattern of histone modification is recognized by proteins and thus plays a role in the expression of eukaryotic genes. histone variant  ​ ​A histone protein that has a slightly different amino acid sequence than that of a standard histone protein. histones  ​ ​A group of proteins involved in the formation of nucleosomes, which aid in the compaction of eukaryotic DNA. holobiont  ​ ​The combination of a host organism and its microbiome. holoblastic cleavage  ​ ​A complete type of cell cleavage in certain animals in which the entire zygote is bisected into two equal-sized blastomeres. hologenome  ​ ​The combined genomes of a host organism and its microbiome. holoparasite  ​ ​A parasitic organism that lacks chlorophyll and is totally dependent on a host plant for its water and nutrients. homeobox  ​ ​A 180-bp sequence within the coding sequence of a homeotic gene. homeodomain  ​ ​A region of a homeotic protein that functions in binding to the DNA. homeostasis  ​ ​The process whereby living organisms regulate their cells and bodies to maintain relatively stable internal conditions. homeostatic control system  ​ ​A system designed to regulate particular variables in an animal’s body, such as body temperature; consists of a set point, sensor, integrator, and effectors. homeotherm  ​ ​An animal that maintains its body temperature within a narrow range. homeotic gene  ​ ​A gene that specifies the developmental fate of a particular segment or region of an animal’s body. hominin  ​ ​A species of humans, whether extant or extinct. hominoidea (hominoid)  ​ ​A group of primates that includes gibbons, orangutans, gorillas, chimpanzees, and humans, as well as all of their recent ancestors. homolog  ​ ​A member of a pair of chromosomes in a diploid organism. homologous genes  ​ ​Genes derived from the same ancestral gene that have accumulated random mutations that make their sequences slightly different. homologous structures  ​ ​Structures that are similar to each other because they are derived from the same ancestral structure. homology  ​ ​A similarity that occurs due to descent from a common ancestor. homozygous  ​ ​An individual with two identical copies of an allele. horizontal gene transfer  ​ ​A process in which an organism incorporates genetic material from another organism without being the offspring of that organism. hormone  ​ ​In animals, a chemical signal that is produced in a gland or other structure and released into the blood or hemolymph, where it acts on distant target cells. In plants, a signaling molecule that is important in coordination of plant development or plant response to the environment. hornworts  ​ ​A phylum of bryophytes; formally known as Anthocerophyta. host cell  ​ ​1. A cell that is infected by a virus, fungus, or bacterium. 2. A eukaryotic cell that contains photosynthetic or nonphotosynthetic endosymbionts. host plant resistance  ​ ​The ability of plants to prevent herbivory via either chemical or mechanical defenses. host range  ​ ​The number of species and cell types that a virus or bacterium can infect. host  ​ ​A larger organism that provides an environment that is occupied by one or more smaller organisms or viruses. 

hot spot  ​ ​A human-impacted geographic area with a large number of endemic species. To qualify as a hot spot, a region must contain at least 1,500 species of endemic vascular plants and have lost at least 70% of its original habitat. Hox genes  ​ ​In animals, a class of homeotic genes involved in pattern formation in early embryos. Human Genome Project  ​ ​A 13-year international effort coordinated by the U.S. Department of Energy and the National Institutes of Health that characterized and sequenced the entire human genome. human immunodeficiency virus (HIV)  ​ ​A retrovirus that is the causative agent of acquired immune deficiency syndrome (AIDS). humoral immunity  ​ ​A type of acquired immunity in which plasma cells secrete antibodies that bind to antigens. hybrid zone  ​ ​An area where two populations can interbreed. hybridization  ​ ​The process in which two individuals of the same species with different characteristics are bred or crossed to each other; the offspring are referred to as hybrids. hydrocarbon  ​ ​Molecules with predominantly hydrogen– carbon bonds. hydrogen bond  ​ ​A weak chemical attraction between a hydrogen atom in a polar molecule and an electronegative atom in another polar molecule. hydrolysis reaction  ​ ​A chemical reaction that utilizes water to break apart other molecules. hydrophilic  ​ ​Refers to molecules that contain ionic and/ or polar covalent bonds and will dissolve in water. hydrophobic  ​ ​Refers to molecules that do not have partial charges and therefore are not attracted to water molecules. Such molecules are composed predominantly of carbon and hydrogen and are relatively insoluble in water. hydrostatic skeleton  ​ ​A fluid-filled body cavity in certain soft-bodied invertebrates that is surrounded by muscles and provides support and shape. – hydroxide ion  ​ ​An anion with the formula OH . hyperpolarization  ​ ​The change in the membrane potential that occurs when the cell membrane becomes more polarized. hypersensitive response (HR)  ​ ​A plant’s local defensive response to pathogen attack. hypertension  ​ ​High blood pressure. hyperthermophile  ​ ​An organism that thrives in extremely hot temperatures. hypertonic  ​ ​When the concentration of solutes outside the cell is higher and causes a cell to shrink due to osmosis of water out of the cell. hypha  ​ ​A microscopic, branched filament of the body of a fungus. hypocotyl  ​ ​The portion of an embryonic plant stem located below the point of attachment of the cotyledons. hypolimnion  ​ ​The layer of cold, dense water at the bottom of a lake, often with low levels of dissolved oxygen. hypothalamus  ​ ​A part of the vertebrate brain located ventral to the thalamus; it controls functions related to growth, reproduction, and metabolism among others, and regulates many basic behaviors such as eating and drinking. hypothesis testing  ​ ​Also known as the scientific method, a strategy for formulating and testing the validity of a hypothesis. hypothesis  ​ ​In biology, a proposed explanation for a natural phenomenon that is based on previous observations or experimental studies. hypotonic  ​ ​When the concentration of solutes outside the cell is lower and causes a cell to swell due to the uptake of water via osmosis.

I

idiosyncratic hypothesis  ​ ​The idea that ecosystem function changes as the number of species increases or decreases but that the amount and direction of change are unpredictable. immune system  ​ ​The cells and organs within an animal’s body that contribute to immune defenses. immune tolerance  ​ ​The process by which the body distinguishes between self and nonself components. immunity  ​ ​The ability of an animal to ward off internal threats, including harmful microorganisms, foreign molecules, and abnormal cells such as cancer cells. immunoglobulin (Ig)  ​ ​A Y-shaped protein with two heavy chains and two light chains that provides immunity to foreign substances; antibodies are a type of immunoglobulin. immunological memory  ​ ​The immune system’s ability to produce a secondary immune response. imperfect flower  ​ ​A flower that lacks either stamens or carpels. implantation  ​ ​The first event of pregnancy, when the blastocyst embeds within the uterine endometrium. imprinting  ​ ​1. Learning that occurs during a brief critical period and establishes a long-lasting behavioral response to a specific object or individual, such as recognition and bonding to a parent. 2. In genetics, the marking of DNA that occurs differently between males and females. in vitro translation system  ​ ​A mixture of components isolated from cells that is capable of synthesizing polypeptides if mRNA is added.  inactivation gate  ​ ​A string of amino acids that juts out from a channel protein into the cytosol and blocks the movement of ions through the channel. inborn error of metabolism  ​ ​A genetic defect that produces an inability to metabolize a certain compound. inbreeding depression  ​ ​The phenomenon whereby inbreeding produces homozygotes that are less fit, thereby decreasing the reproductive success of a population. inbreeding  ​ ​Mating between genetically related individuals. inclusive fitness  ​ ​The term used to designate the total number of copies of genes passed on through one’s relatives, as well as one’s own reproductive output. incomplete dominance  ​ ​The phenomenon in which a heterozygote that carries two different alleles exhibits a phenotype that is intermediate between the phenotypes of the corresponding homozygous individuals. incomplete flower  ​ ​A flower that lacks one or more of the four flower whorls. incomplete metamorphosis  ​ ​During development in some insects, a gradual change in body form from a nymph into an adult. incurrent siphon  ​ ​A structure in a tunicate used to draw water through the mouth. indeterminate cleavage  ​ ​In animals, a characteristic of deuterostome development in which each cell produced by early cleavage retains the ability to develop into a complete embryo. indeterminate growth  ​ ​Growth in which plant shoot apical meristems continuously produce new stem tissues and leaves, as long as conditions remain favorable. indicator species  ​ ​A species whose status provides information on the overall health of an ecosystem. indirect calorimetry  ​ ​A method of determining metabolic rate in which the rate at which an animal uses oxygen is measured. individualistic model  ​ ​A view of the nature of a community that considers it to be an assemblage of

GLOSSARY G-15 integrase  ​ ​An enzyme, sometimes encoded by viruses, that catalyzes the integration of the viral genome into a host-cell chromosome. integrator  ​ ​The part of a homeostatic control system, typically a nucleus in the brain, in which the value of a variable is compared to a set point. integrin  ​ ​A cell adhesion molecule found in animal cells that connects cells to the extracellular matrix. integument  ​ ​In plants, a leaflike structure that encloses the sporangium to form an ovule. interference competition  ​ ​Competition in which organisms interact directly with one another by physical force or intimidation. interferon  ​ ​A protein that generally inhibits viral replication inside host cells. intermediate filament  ​ ​A type of protein filament of the cytoskeleton of animal cells that helps maintain cell shape and rigidity. intermediate-disturbance hypothesis  ​ ​The proposal that moderately disturbed communities are more diverse than undisturbed or highly disturbed communities. internal fertilization  ​ ​Fertilization that occurs in terrestrial animals, in which sperm are deposited within the reproductive tract of the female during copulation. interneuron  ​ ​A type of neuron that forms interconnections between other neurons. internode  ​ ​The region of a plant stem between adjacent nodes. interphase  ​ ​The portion of the cell cycle consisting of the G1, S, and G2 phases, during which the chromosomes are decondensed and found in the nucleus. intersexual selection  ​ ​Sexual selection between members of the opposite sex. interspecies hybrid  ​ ​The offspring resulting from the interbreeding of members of two different species. interspecific competition  ​ ​Competition between individuals of different species. interstitial fluid  ​ ​The fluid that surrounds cells. intertidal zone  ​ ​The area where the land meets the sea, which is alternately submerged and exposed by the daily cycle of tides. intracellular fluid  ​ ​The fluid inside cells. intrasexual selection  ​ ​Sexual selection that occurs via competition between members of the same sex for the opportunity to mate with individuals of the opposite sex. intraspecific competition  ​ ​Competition between individuals of the same species. intrauterine device (IUD)  ​ ​A small object that is placed in the uterus and interferes with the endometrial preparation required for acceptance of the blastocyst; used as a form of contraception. intrinsic pathway  ​ ​A pathway leading to apoptosis that initially involves internal DNA damage.  intrinsic rate of increase  ​ ​The maximum value of the per capita growth rate, which is attained when conditions are optimal for population growth. introduced species  ​ ​A species moved by humans from a native location to another location. intron  ​ ​Intervening DNA sequences that are found in between the coding sequences of genes. invasive species  ​ ​Introduced species that spread on their own, often outcompeting native species for space and resources. inverse density-dependent factor  ​ ​A mortality factor whose influence decreases as population size increases. inversion  ​ ​A type of mutation that involves a change in the direction of the genetic material along a single chromosome. invertebrate  ​ ​An animal that lacks a backbone (vertebrae). iodine-deficient goiter  ​ ​An overgrown thyroid gland that is incapable of making thyroid hormone due to a lack of dietary iodine.

ion  ​ ​An atom or molecule that gains or loses one or more electrons and acquires a net electric charge. ionic bond  ​ ​The bond that occurs when a cation binds to an anion. ionotropic receptor  ​ ​One of two types of postsynaptic receptors, the other being a metabotropic receptor. Consists of a ligand-gated ion channel that opens in response to binding of a neurotransmitter. iris  ​ ​The circle of pigmented smooth muscle and connective tissue that is responsible for eye color. iron regulatory element (IRE)  ​ ​A response element within the ferritin mRNA to which the iron regulatory protein binds. iron regulatory protein (IRP)  ​ ​An RNA-binding protein that regulates the translation of the mRNA that encodes ferritin. islets of Langerhans  ​ ​Spherical clusters of endocrine cells that are scattered throughout the pancreas; the cells secrete insulin or glucagon, among other hormones. isomers  ​ ​Two or more molecules with the same chemical formula but different structures and characteristics. isotonic  ​ ​Condition in which the solute concentrations on both sides of a plasma membrane are equal, which does not cause a cell to shrink or swell. isotope  ​ ​A form of an element that contains a different number of neutrons from the element’s other isotopes. iteroparity  ​ ​The pattern of repeated reproduction at intervals throughout an organism’s life cycle.

J

joint  ​ ​The juncture where two or more bones of a vertebrate endoskeleton come together. juvenile hormone  ​ ​A hormone made in arthropods that inhibits maturation from a larva into a pupa.

K

karyogamy  ​ ​The process of nuclear fusion. karyotype  ​ ​A photographic representation of the chromosomes from an actively dividing cell. kcal (kilocalorie)  ​ ​One thousand calories; the amount of heat energy required to raise the temperature of 1 kg of water by 1°C. ketones  ​ ​Small compounds generated from fatty acids. Ketones are made in the liver and released into the blood during prolonged fasting to provide an important energy source for many tissues, including the brain. keystone hypothesis  ​ ​The idea that ecosystem function plummets as soon as biodiversity declines from its natural levels. keystone species  ​ ​A species within a community that has a role out of proportion to its abundance or biomass. kidney  ​ ​The major excretory organ found in all vertebrates. kin selection  ​ ​Selection for behavior that lowers an individual’s own fitness but enhances the reproductive success of a relative. kinesis  ​ ​A movement in response to a stimulus, but one that is not directed toward or away from the source of the stimulus. kinetic energy  ​ ​Energy associated with movement. kinetic skull  ​ ​A characteristic of lizards and snakes in which the joints between various parts of the skull are extremely mobile. kinetochore  ​ ​A group of proteins that bind to a centromere and are necessary for sorting the chromosomes. kingdom  ​ ​A taxonomic group; the second largest division after domain. KM  ​ ​The substrate concentration at which an enzymecatalyzed reaction is half of its maximal value.

GLOSSARY

species coexisting primarily because of similarities in their physiological requirements and tolerances. induced fit  ​ ​The phenomenon that occurs when a substrate(s) binds to an enzyme and the enzyme undergoes a conformational change that causes the substrate(s) to bind more tightly to the enzyme. induced mutation  ​ ​A mutation brought about by environmental agents that enter the cell and then alter the structure of DNA. inducer  ​ ​A small effector molecule that increases the rate of transcription of a gene. inducible operon  ​ ​A type of operon for which the presence of a small effector molecule causes transcription to increase. induction  ​ ​1. In development, the process by which a cell or group of cells governs the developmental fate of neighboring cells. 2. In molecular genetics, refers to the process by which transcription has been turned on by the presence of a small effector molecule. industrial nitrogen fixation  ​ ​The human activity of producing nitrogen fertilizers. infertility  ​ ​The inability to produce viable offspring. inflammation  ​ ​An innate local response to infection or injury characterized by local redness, swelling, heat, and pain. inflorescence  ​ ​A tightly clustered group of flowers produced by a plant. infundibular stalk  ​ ​The thin piece of tissue that physically connects the hypothalamus to the pituitary gland. ingestion  ​ ​In animals, the act of taking food into the body. ingroup  ​ ​In a cladogram, the group whose evolutionary relationships are of interest. inheritance  ​ ​The transmission of characteristics from parent to offspring. inhibition  ​ ​A mechanism for succession in which early colonists exclude subsequent colonists. inhibitory postsynaptic potential (IPSP)  ​ ​The response to an inhibitory neurotransmitter that hyperpolarizes the postsynaptic membrane; this hyperpolarization reduces the likelihood of an action potential. initiation factor  ​ ​A protein that facilitates the interactions between mRNA, the first tRNA, and the ribosomal subunits during the initiation stage of translation. initiation  ​ ​The first stage in the process of transcription or translation. innate immunity  ​ ​The body’s defenses that are present at birth and act against any foreign material in much the same way, regardless of that material’s specific identity; these defenses include the skin and mucous membranes, plus various cellular and chemical defenses. innate  ​ ​The term used to describe behaviors that seem to be genetically programmed. inner bark  ​ ​The thin layer of secondary phloem that transports watery solutions of organic compounds in a woody stem. inner segment  ​ ​The part of the vertebrate photoreceptors (rods and cones) that contains the cell nucleus and cytoplasmic organelles. inorganic chemistry  ​ ​The study of the nature of atoms and molecules, with the exception of those that contain rings or chains of carbon. insulin  ​ ​A hormone found in animals that regulates metabolism in several ways, primarily by regulating the blood glucose concentration. insulin-like growth factor-1 (IGF-1)  ​ ​A hormone in mammals that stimulates the elongation of bones, especially during puberty. integral membrane protein  ​ ​A protein such as a transmembrane protein or a lipid-anchored protein that cannot be released from the membrane unless the membrane is dissolved with an organic solvent or detergent.

G-16 GLOSSARY knowledge  ​ ​The awareness and understanding of information. Koch’s postulates  ​ ​A series of steps used to determine whether a particular organism causes a specific disease. K-selected species  ​ ​A species whose life history strategy shows a low rate of per capita population growth but good competitive ability.

L

GLOSSARY

labor  ​ ​The strong rhythmic contractions of the uterus that serve to deliver a fetus during childbirth. lac repressor  ​ ​A repressor protein that regulates the lac operon. lac operon  ​ ​An operon in the genome of E. coli that contains the genes for the proteins that allow the bacterium to metabolize lactose. lacteal  ​ ​A lymphatic vessel in the center of each intestinal villus; lipids are absorbed by the lacteals, which eventually empty into the circulatory system. lagging strand  ​ ​During DNA replication, a DNA strand made as a series of small Okazaki fragments that are subsequently connected to each other to form a continuous strand. lamellae (singular, lamella)  ​ ​Platelike structures in the internal gills of fishes that branch from structures called filaments; gas exchange occurs here. larva  ​ ​A free-living organism that is morphologically very different from the embryo and adult. larynx  ​ ​The segment of the respiratory tract that contains the vocal cords. latent  ​ ​The term used to describe a prophage or provirus that remains inactive for a long time. lateral line system  ​ ​Microscopic sensory organs in fishes and some toads that allows them to detect movement in surrounding water. lateral meristem  See secondary meristem. leaching  ​ ​The dissolution and removal of inorganic ions as water percolates through materials such as soil. leading strand  ​ ​During DNA replication, a DNA strand made in the same direction that the replication fork is moving. The strand is synthesized as one long continuous molecule. leaf abscission  ​ ​The process by which a leaf drops after the formation of an abscission zone. leaf primordia  ​ ​Small outgrowths that occur at the sides of a shoot apical meristem and develop into young leaves. leaf vein  ​ ​In plants, a bundle of vascular tissue in a leaf. leaflet  ​ ​1. Half of a phospholipid bilayer. 2. A portion of a compound leaf. learning  ​ ​The ability of an animal to make modifications to a behavior based on previous experience; the process by which new information is acquired. leaves  ​ ​Flattened plant organs that emerge from stems and typically function in photosynthesis. left-right axis  ​ ​In bilaterally symmetric animals, the left and right sides of the body. leghemoglobin  ​ ​A protein found in legume plants that helps to regulate local oxygen concentrations around rhizobial bacteroids in root nodules. legume  ​ ​A member of the pea (bean) family; also the distinctive fruit of such a plant. lek  ​ ​A designated communal courting area used by certain species of animals. lens  ​ ​1. A structure of the eye that focuses light. 2. The glass components of a light microscope or the electromagnetic parts of an electron microscope that allow the production of magnified images of microscopic structures. lentic  ​ ​Refers to a freshwater habitat characterized by standing water.

lenticels  ​ ​Passages in the outer bark of a woody plant stem that allow inner stem tissues to accomplish gas exchange. leptin  ​ ​A hormone produced by adipose cells in proportion to fat mass; controls appetite and metabolic rate. leukocyte  ​ ​A cell that develops from the marrow of certain bones of vertebrates; all leukocytes (also known as white blood cells) perform vital functions that defend the body against infection and disease. lichen  ​ ​A complex mutualistic association between fungi and other microbes, including photosynthetic green algae or cyanobacteria. Liebig’s law of the minimum  ​ ​The principle that states that species’ biomass or abundance is limited by the scarcest factor. life cycle  ​ ​The sequence of events that characterize the steps of development of the individuals of a given species. life table  ​ ​A table that provides data on the numbers of living individuals in various age classes in a population and their relative fertilities. ligand  ​ ​An ion or molecule that binds to a protein, such as an enzyme or a receptor. ligand•receptor complex  ​ ​The structure formed when a ligand and its receptor bind noncovalently to each other. ligand-gated ion channel  ​ ​A type of cell surface receptor that binds a ligand and functions as an ion channel. Ligand binding either opens or closes a channel. light microscope  ​ ​A microscope that utilizes light for illumination. light reactions  ​ ​The first of two stages in the process of photosynthesis. During the light reactions, photosystem II and photosystem I absorb light energy and produce ATP, NADPH, and O2. light-harvesting complex  ​ ​A component of photosystem II and photosystem I composed of several dozen pigment molecules that are anchored to proteins in the thylakoid membrane of a chloroplast. The role of these complexes is to absorb photons of light. lignin  ​ ​A tough polymer that adds strength and decay resistance to cell walls of tracheids, vessel elements, and other cells of plants. limbic system  ​ ​In the vertebrate forebrain, the areas involved in the formation and expression of emotions; also plays a role in learning, memory, and the perception of smells. limiting factor  ​ ​A factor whose amount or concentration limits the rate of a biological process or a chemical reaction. line transect  ​ ​A sampling technique used by plant ecologists in which the number of plants located along a length of string are counted. lineage  ​ ​A series of species that forms a line of descent. linear electron flow  ​ ​In the light reactions of photosynthesis, the movement of electrons from PSII to PSI and ultimately to NADP+ to form NADPH.  linkage group  ​ ​A group of genes that usually stay together during meiosis. linkage  ​ ​The phenomenon in which two genes close together on the same chromosome are transmitted as a unit. lipase  ​ ​The major fat-digesting enzyme, secreted by the pancreas. lipid raft  ​ ​In a membrane, a group of lipids, sometimes including associated proteins, that float together as a unit in a larger sea of lipids. lipid  ​ ​A molecule composed predominantly of hydrogen and carbon atoms. Lipids are nonpolar and therefore very insoluble in water. They include fats (triglycerides), phospholipids, waxes, and steroids. lipid-anchored protein  ​ ​A type of integral membrane protein that is attached to the membrane via a lipid molecule.

lipid-exchange protein  ​ ​A protein that extracts a lipid from one membrane, diffuses through the cell, and inserts the lipid into another membrane. lipolysis  ​ ​The enzymatic breakdown of triglycerides into fatty acids and either monoglycerides or glycerol. lipopolysaccharides  ​ ​Lipids with covalently bound polysaccharides; prevalent in the thin, outer envelope that encloses the cell walls of Gram-negative bacteria. liposome  ​ ​A vesicle surrounded by a phospholipid bilayer. liquid-liquid phase separation  ​ ​The phenomenon in which aggregated solutes, such as proteins and RNA molecules, separate from the bulk solvent, and form a droplet. liver  ​ ​An organ in vertebrates that performs diverse metabolic functions and is the site of bile production. liverworts  ​ ​A phylum of bryophytes; formally called Hepatophyta. loam  ​ ​A type of soil that contains a mixture of sand, silt, and clay and is ideal for plant cultivation. lobe-finned fishes  ​ ​Fishes in which the fins are part of the body; the fins are supported by skeletal extensions of the pectoral and pelvic areas. locomotion  ​ ​The movement of an animal from place to place. locus  ​ ​The physical location of a gene on a chromosome. logistic equation  ​ ​An equation that relates the growth of a population to the carrying capacity, K, of its environment. logistic growth  ​ ​The pattern in which the growth of a population typically slows down as the population size approaches the carrying capacity. long-day plant  ​ ​A plant that flowers in spring or early summer, when the night period is shorter (and thus the day length is longer) than a defined period. long-term potentiation (LTP)  ​ ​The long-lasting strengthening of the connection between neurons that is believed to be part of the mechanism of learning and memory. loop domain  ​ ​In bacteria, a chromosomal segment that is folded into a loop by attachment to proteins; a means of compacting a bacterial chromosome. loop of Henle  ​ ​A segment of the renal tubule of the kidney containing a sharp hairpin-like loop that contributes to reabsorption of ions and water and that consists of a descending limb coming from the proximal tubule and an ascending limb leading to the distal tubule. lophophore  ​ ​A horseshoe-shaped crown of tentacles used for feeding in several invertebrate species. Lophotrochozoa  ​ ​A clade of animals that encompasses the mollusks, annelids, and several other phyla; they are distinguished by two morphological features: the lophophore, a crown of tentacles used for feeding, and the trochophore larva, a distinct larval stage. lotic  ​ ​Refers to a freshwater habitat characterized by running water. lumen  ​ ​The internal space or hollow cavity of an organelle or an organ, such as the endoplasmic reticulum, the stomach, or a blood vessel. lung  ​ ​In terrestrial vertebrates, internal paired structures used to bring O2 into the circulatory system and remove CO2. lungfishes  ​ ​The Dipnoi; fish with primitive lungs that live in oxygen-poor freshwater swamps and ponds. luteal phase  ​ ​The phase of the human ovarian cycle that begins after ovulation and during which a corpus luteum is formed. luteinizing hormone (LH)  ​ ​A gonadotropin that controls the production of sex steroids in both males and females. lycophyll  ​ ​A relatively small leaf having a single unbranched vein; produced by lycophytes. lycophytes  ​ ​Members of a phylum (Lycopodiophyta) of vascular land plants whose leaves are lycophylls.

lymphatic system  ​ ​A system of vessels along with a group of organs and tissues where most leukocytes reside. The lymphatic vessels collect excess interstitial fluid and return it to the blood. lymphocyte  ​ ​A type of leukocyte that is responsible for specific immunity; may be either a B cell or a T cell. lysogenic cycle  ​ ​A type of viral reproductive cycle consisting of integration of phage DNA into that of a bacterium, prophage replication, and excision. lysosome  ​ ​A small organelle found in animal cells that contains acid hydrolases that degrade molecules and macromolecules. lytic cycle  ​ ​A type of viral reproductive cycle in which the production and release of new phages lyses the host cell.

M

M phase  ​ ​The phase of the cell cycle consisting of the sequential events of mitosis and cytokinesis. macroalgae  ​ ​Photosynthetic protists that can be seen with the unaided eye; also known as seaweeds. macroevolution  ​ ​Evolutionary changes that produce new species and groups of species. macromolecule  ​ ​Many molecules bonded together to form a polymer. Carbohydrates, proteins, and nucleic acids (for example, DNA and RNA) are important macromolecules found in living organisms. macronutrient  ​ ​An element required by plants in amounts of at least 1 g/kg of plant dry matter. macroparasite  ​ ​A parasite that lives in a host but releases infective juvenile stages outside the host’s body. macrophage  ​ ​A large phagocyte capable of engulfing viruses and bacteria. macular degeneration  ​ ​An eye condition in which photoreceptor cells in and around the macula (which contains the fovea of the retina) are lost; one of the leading causes of blindness in the U.S. madreporite  ​ ​A sievelike plate on the surface of an echinoderm through which water enters the water vascular system. magnetic resonance imaging (MRI)  ​ ​An imaging method that relies on the use of magnetic fields and radio waves to visualize the internal structure of an organism’s body. magnification  ​ ​The ratio between the size of an image produced by a microscope and the object’s actual size. major depressive disorder  ​ ​A neurological disorder characterized by feelings of despair and sadness, resulting from an imbalance in neurotransmitter levels in the brain. major groove  ​ ​A wider groove that spirals around the DNA double helix; provides a location where a protein can bind to a particular sequence of bases and affect the expression of a gene. major histocompatibility complex (MHC)  ​ ​A gene family that encodes the plasma membrane self proteins that must be complexed with an antigen for T-cell recognition to occur. male gametophyte  ​ ​A haploid multicellular plant life cycle stage that produces sperm. male-assistance hypothesis  ​ ​A hypothesis to explain the existence of monogamy that maintains that males remain with females to help them rear their offspring. malignant tumor  ​ ​A growth of cells that has progressed to the cancerous stage. Malpighian tubules  ​ ​Delicate projections from the digestive tract of insects and some other taxa that function as an excretory organ. mantle cavity  ​ ​The chamber in a mollusk mantle that houses delicate gills. mantle  ​ ​In mollusks, a fold of skin draped over the visceral mass that secretes a shell in those species that form shells.

many-eyes hypothesis  ​ ​The idea that increased group size decreases predators’ success because of increased detection of predators. map distance  ​ ​The distance between genes along chromosomes, which is calculated as the number of recombinant offspring divided by the total number of offspring times 100. map unit (mu)  ​ ​A unit of distance on a chromosome equivalent to a 1% recombination frequency. marker genes  ​ ​Genes that mark, or indicate, the occurrence of particular metabolic functions in organisms. mark-recapture technique  ​ ​The capture and tagging of animals so they can be released and recaptured, allowing an estimate of population size. marsupial  ​ ​A member of a group of seven mammalian orders and about 280 species found in the clade Metatheria. mass extinction  ​ ​An event in which many species become extinct at the same time. mass-specific BMR  ​ ​The amount of energy expended per gram of body mass in the resting condition. mast cell  ​ ​A type of cell derived from bone marrow stem cells that occurs throughout connective tissues and plays an important role in innate immunity. mastax  ​ ​The circular muscular pharynx in the mouth of rotifers. mate-guarding hypothesis  ​ ​The hypothesis that a male is monogamous to prevent his mate from being fertilized by other males. maternal effect gene  ​ ​A gene for which only the mother’s gene product affects the phenotype of the resulting offspring. maternal inheritance  ​ ​A phenomenon in which offspring inherit particular genes only from the female parent (through the egg). matrotrophy  ​ ​In plants, the phenomenon in which zygotes remain enclosed within gametophyte tissues, where they are sheltered and fed. matter  ​ ​Anything that has mass and takes up space. mature mRNA  ​ ​In eukaryotes, transcription produces a longer RNA, called pre-mRNA, which undergoes certain modifications before it exits the nucleus; mature mRNA is the final functional product. maximum likelihood  ​ ​One method used to evaluate a phylogenetic tree based on an evolutionary model. maximum sustainable yield (MSY)  ​ ​The largest number of individuals that can be removed without causing long-term decreases in the population. mean fitness of the population  ​ ​The average reproductive success of members of a population. mechanoreceptor  ​ ​A sensory receptor in animals that transduces mechanical energy such as pressure, touch, stretch, movement, and sound. mediator  ​ ​A large protein complex that plays a role in initiating transcription at the core promoter of proteinencoding genes in eukaryotes. medulla oblongata  ​ ​The part of the vertebrate hindbrain that coordinates many processes that maintain homeostasis, such as breathing. medusa  ​ ​A type of cnidarian body form that is motile and usually floats mouth down. megadiversity countries  ​ ​Those countries with the greatest numbers of species; used in targeting areas for conservation. megaspore  ​ ​In seed plants and some seedless plants, a large spore that produces a female gametophyte within the spore wall. meiosis I  ​ ​The first division of meiosis in which homologous chromosomes are separated into different cells. meiosis II  ​ ​The second division of meiosis in which sister chromatids are separated into different cells. meiosis  ​ ​The process by which haploid cells are produced from a cell that was originally diploid.

Meissner corpuscle  ​ ​A specialized receptor that senses touch and light pressure and lies just beneath the skin surface of an animal. membrane attack complex (MAC)  ​ ​A multi-unit protein formed by the activation of complement proteins; the complex creates water channels in the microbial plasma membrane and causes the microbe to swell and burst. membrane potential  ​ ​The difference between the electric charges outside and inside a cell; also called a potential difference (or voltage). membrane transport  ​ ​The movement of ions or molecules across a biological membrane. membrane vesicle  ​ ​A small sphere enclosed by a membrane. memory cell  ​ ​A cloned lymphocyte that remains poised to recognize a returning antigen; a component of acquired immunity. memory  ​ ​The ability to retain, retrieve, and use previously learned information. Mendelian inheritance  ​ ​The inheritance patterns of genes that segregate and assort independently. Mendel’s law of independent assortment  ​ ​The alleles of different genes assort independently of each other during the process that gives rise to gametes. Mendel’s law of segregation  ​ ​The two alleles of a gene separate (segregate) from each other during the process that gives rise to gametes, so every gamete receives only one allele. meninges  ​ ​Three layers of sheathlike membranes that cover and protect the brain and spinal cord. meningitis  ​ ​A potentially life-threatening infectious disease in which the meninges become inflamed. menopause  ​ ​The event during which a woman permanently stops having ovarian cycles. menstrual cycle  ​ ​The cyclical changes that occur in the uterus in parallel with the ovarian cycle in a female mammal; also called the uterine cycle. menstruation  ​ ​A period of bleeding at the beginning of the uterine cycle in a female mammal. meristem  ​ ​In plants, a region of undifferentiated cells (stem cells) that produces new tissue by cell division. meroblastic cleavage  ​ ​An incomplete type of cell cleavage in which only the region of the egg containing cytoplasm at the animal pole undergoes cell division; occurs in birds and some fishes. merozygote  ​ ​A bacterial cell that contains an F′ factor. mesoderm  ​ ​In animals, a layer of cells formed during gastrulation that develops between the ectoderm and endoderm; gives rise to the skeleton, muscles, and much of the circulatory system. mesoglea  ​ ​A gelatinous substance between the epidermis and the gastrodermis in cnidarians. mesohyl  ​ ​A gelatinous, protein-rich matrix in between the choanocytes and the epithelial cells of a sponge. mesophyll  ​ ​The internal tissue of a plant leaf; the site of photosynthesis. messenger RNA (mRNA)  ​ ​RNA that contains the information to specify a polypeptide with a particular amino acid sequence. metabolic cycle  ​ ​A biochemical cycle in which particular molecules enter while others leave; the process is cyclical because it involves a series of organic molecules that are regenerated with each turn of the cycle. metabolic pathway  ​ ​In living cells, a coordinated series of chemical reactions in which each step is catalyzed by a specific enzyme. metabolic rate  ​ ​The total energy expenditure of an organism per unit of time. metabolism  ​ ​The sum of all bodily activities and chemical reactions that occur within an organism. Also, a specific set of chemical reactions occurring at the cellular level.

GLOSSARY

GLOSSARY G-17

G-18 GLOSSARY

GLOSSARY

metabolome  ​ ​Collection of information about the types and abundances of molecules, such as sugars and fatty acids, produced by metabolism in a single organism. metabotropic receptor  ​ ​A G-protein-coupled receptor that initiates a signaling pathway in response to a neurotransmitter. One of two types of postsynaptic receptors, the other being an ionotropic receptor. metacentric  ​ ​Refers to a chromosome in which the centromere is near the middle. metagenome  ​ ​The genomes of all the organisms present in a sample. metagenomics  ​ ​A field of study that seeks to identify and analyze the collective microbial genomes contained in a community of organisms, including those not easily cultured in the laboratory. meta-metabolome  ​ ​Collection of information about the types and abundances of molecules, such as sugars and fatty acids, produced by metabolism by an entire microbiome. metamorphosis  ​ ​The process in which a pupal or juvenile organism changes into a mature adult with very different characteristics. metanephridia  ​ ​Excretory filtration organs found in a variety of invertebrates, including annelids. metaphase plate  ​ ​A plane halfway between the poles of the spindle apparatus on which the sister chromatids align during metaphase in mitosis. metaphase  ​ ​The phase of mitosis during which the chromosomes are aligned along the metaphase plate. metaproteome  ​ ​All the proteins produced by all the members of a microbiome. metastasis  ​ ​The process by which cancer cells spread from their original location to distant parts of the body. metatranscriptome  ​ ​A collection of all the mRNAs present in an environmental sample, that is, all of the mRNAs produced by all of the organisms sampled from a particular place at a particular time. methanogens  ​ ​Several groups of anaerobic archaea that convert CO2, methyl groups, or acetate to methane, and release it from their cells. methanotroph  ​ ​An aerobic bacterium that consumes methane. methyl-CpG-binding protein  ​ ​A protein that binds methylated DNA sequences and inhibits transcription. micelle  ​ ​A sphere formed from the aggregation of long amphipathic molecules when they are mixed with water. The polar regions are on the surface and in contact with water and the nonpolar regions are in the center.  microbiome  ​ ​A particular assemblage of microbes (including their genes) that are associated with a defined environment. microbiota  ​ ​Collections of microbial life cataloged by amplicon analysis. microcystin  ​ ​A type of toxin produced by some cyanobacteria, including the genus Microcystis. microevolution  ​ ​Changes in a population’s gene pool, such as changes in allele frequencies, from generation to generation. microfilament  See actin filament. micrograph  ​ ​An image taken with the aid of a microscope. micronutrient  ​ ​An element required by plants in amounts equal to or less than 0.1 g/kg of plant dry matter; also known as a trace element. microparasite  ​ ​A parasite that multiplies within its host, usually within the cells. micropyle  ​ ​A small opening in the integument of a seed plant ovule through which a pollen tube grows. microRNAs (miRNAs)  ​ ​Small RNA molecules, typically 22 nucleotides in length, that are transcribed from endogenous eukaryotic genes and  silence the expression of specific mRNAs by inhibiting translation.

microscope  ​ ​A magnification tool that enables researchers to visualize the structures and inner workings of cells. microspore  ​ ​In seed plants and some seedless plants, a relatively small spore that produces a male gametophyte within the spore wall. microtubule  ​ ​A type of hollow protein filament composed of tubulin proteins that is part of the cytoskeleton and is important for cell shape, organization, and movement. microvilli  ​ ​Small projections of the plasma membranes of epithelial cells in the small intestine and many other absorptive cells. midbrain  ​ ​One of three major divisions of the vertebrate brain; the other two divisions are the hindbrain and the forebrain. middle lamella  ​ ​An extracellular layer in plants composed primarily of carbohydrate; cements adjacent plant cell walls together. migration  ​ ​Long-range seasonal movement of animals in order to feed or breed. mimicry  ​ ​The resemblance of an organism (the mimic) to another organism (the model). mineral  ​ ​An inorganic ion required by a living organism for normal cellular functioning. mineralization  ​ ​The general process by which phosphorus, nitrogen, CO2, and other minerals are released from organic compounds. minor groove  ​ ​A groove that spirals around the DNA double helix but is smaller than the major groove. missense mutation  ​ ​A base substitution that changes a single amino acid in a polypeptide. mitochondrial genome  ​ ​The chromosome found in mitochondria. mitochondrial matrix  ​ ​A compartment inside the inner membrane of a mitochondrion. mitochondrial pathway  ​  ​See intrinsic pathway. mitochondrion  ​ ​A semiautonomous organelle found in eukaryotic cells that supplies most of a cell’s ATP. mitosis  ​ ​In eukaryotes, the process in which nuclear division results in two nuclei, each of which receives the same complement of chromosomes. mitotic cell division  ​ ​A process whereby a eukaryotic cell divides to produce two new cells that are genetically identical to the original cell. mitotic spindle  ​ ​The structure responsible for organizing and sorting the chromosomes during mitosis; also called the mitotic spindle apparatus. mixotroph  ​ ​An organism that is able to use photoautotrophy as well as phagotrophy or osmotrophy to obtain organic nutrients. model organism  ​ ​An organism studied by many different researchers so that they can compare their results and determine scientific principles that apply more broadly to other species. model-based learning  ​ ​An educational approach in which students evaluate or generate models as a way to enhance their understanding of scientific concepts and improve their criticalthinking skills. moderately repetitive sequence  ​ ​A DNA sequence that is repeated a few hundred to several thousand times in a genome. molar  ​ ​A term used to describe a solution’s molarity; a 1 molar solution contains 1 mole of a solute dissolved in enough water to make 1 L of solution. molarity  ​ ​The number of moles of a solute dissolved in 1 L of water. mole  ​ ​The amount of any substance that contains the same number of particles as there are atoms in exactly 12 g of carbon. molecular biology  ​ ​A field of study spawned largely by genetic technology that allows researchers to study the structure and function of the molecules of life.

molecular clock  ​ ​A method for estimating evolutionary time; based on the observation that neutral mutations occur at a relatively constant rate. molecular evolution  ​ ​The process of evolution at the level of genes and proteins. molecular formula  ​ ​A representation of a molecule that consists of the chemical symbols for all of the atoms present and subscripts that indicate how many of those atoms are present. molecular homologies  ​ ​Similarities at the molecular level that indicate that living species evolved from a common ancestor or interrelated group of ancestors. molecular mass  ​ ​The sum of the atomic masses of all atoms in a molecule. molecular systematics  ​ ​A field of study that involves the analysis of genetic data, such as DNA and amino acid sequences, to identify and study genetic homologies and construct phylogenetic trees. molecule  ​ ​Two or more atoms that are connected by chemical bonds. monoclonal antibodies  ​ ​Antibodies of a specific type that are derived from a single clone of cells. monocots  ​ ​One of the two largest lineages of flowering plants in which the embryo possesses a single seed leaf. monocular vision  ​ ​A type of vision in animals that have eyes on the sides of the head; the animal sees a wide area at one time, though depth perception is reduced. monocyte  ​ ​A type of phagocyte that circulates in the blood for only a few days, after which it enters an organ or tissue and develops into a macrophage. monoecious  ​ ​Refers to plants that produce carpellate and staminate flowers on the same plant. monogamy  ​ ​A mating system in which each individual mates exclusively with one partner over at least a single breeding cycle. monohybrid  ​ ​The F1 offspring, also called single-trait hybrids, of true-breeding parents that differ with regard to a single character. monomer  ​ ​An organic molecule that can be used to form a larger molecule (polymer) consisting of many repeating units of the monomer. monomorphic gene  ​ ​A gene that exists predominantly as a single allele in a population. monophagous  ​ ​The term used to describe parasites that feed on one or a few closely related species. monophyletic group  ​ ​A group of species, a taxon, that is a clade. monosaccharide  ​ ​A simple sugar, such as a pentose or hexose. monotreme  ​ ​A member of the mammalian order Monotremata, which consists of five species found in Australia and New Guinea: the duck-billed platypus and four species of echidna. morphogen  ​ ​A molecule that imparts positional information and promotes developmental changes at the cellular level. morphology  ​ ​The structure or form of a body part or an entire organism. morula  ​ ​An early stage in a mammalian embryo in which physical contact between cells is maximized by compaction. mosaic  ​ ​An individual with somatic regions that are genetically different from each other. mosses  ​ ​A phylum of bryophytes; formally called Bryophyta. motility  ​ ​The ability of a cell to move or change position within its environment. motor end plate  ​ ​The region of a skeletal muscle cell that lies beneath an axon terminal at the neuromuscular junction. motor neuron  ​ ​A neuron that sends signals away from the central nervous system and elicits some type of response from a gland, muscle or other structure.

motor protein  ​ ​A type of cellular protein that uses ATP as a source of energy to promote movement; consists of three domains called the head, hinge, and tail. movement corridor  ​ ​Thin strips of habitat that may permit the movement of individuals between larger habitat patches. mRNA  See messenger RNA. Müllerian mimicry  ​ ​A type of mimicry in which two or more noxious species converge to look the same, thus reinforcing the basic distasteful design. multicellular  ​ ​Describes an organism consisting of more than one cell, particularly when cell-to-cell adherence and signaling processes and cellular specialization can be demonstrated. multiple alleles  ​ ​The phenomenon in which a gene has three or more alleles in a natural population. multiple sclerosis (MS)  ​ ​A disease in which the patient’s own body attacks and destroys myelin as if it were a foreign substance; impairs the function of myelinated neurons that control movement, speech, memory, and emotion. multipotent  ​ ​Refers to a stem cell that can differentiate into several cell types, but far fewer than a pluripotent cell can. muscle fiber  ​ ​Individual cell within a muscle. muscle tissue  ​ ​Bundles of muscle fibers (cells) that are specialized to contract when stimulated and thus generate a force that facilitates movement or exerts pressure . muscular dystrophy  ​ ​A group of diseases associated with progressive degeneration of skeletal and cardiac muscle fibers. mutagen  ​ ​An agent known to cause mutation. mutant allele  ​ ​An allele that has been altered by mutation. mutation  ​ ​A heritable change in the genetic material of an organism. mutation  ​ ​A heritable change in the genetic material. mutualism  ​ ​A symbiotic interaction in which both species benefit. mycelium  ​ ​A fungal body composed of microscopic branched filaments known as hyphae. mycorrhizae (singular, mycorrhiza)  ​ ​Associations between the hyphae of certain fungi and the roots of seed plants. myelin sheath  ​ ​In the nervous system, an insulating layer made up of specialized glial cells wrapped around the axons. myocardial infarction (MI)  ​ ​The death of cardiac muscle cells, which can occur if a region of the heart is deprived of blood for an extended time. myofibril  ​ ​Rodlike collection of myofilaments within a muscle fiber (cell); contains thick and thin filaments. myoglobin  ​ ​An oxygen-binding protein that provides an intracellular reservoir of oxygen for muscle fibers. myosin  ​ ​A motor protein found abundantly in muscle cells and also in other cell types.

N

NAD+  ​ ​Nicotinamide adenine dinucleotide; an organic molecule that functions as an energy intermediate. It combines with two electrons and H+ to form NADH. NADPH  ​ ​Nicotinamide adenine dinucleotide phosphate; an energy intermediate that provides the energy and electrons to drive the Calvin cycle during photosynthesis. natural killer (NK) cell  ​ ​A type of leukocyte that participates in both innate and acquired immunity; recognizes general features on the surface of cancer cells or any virus-infected cells. natural selection  ​ ​The process that eliminates those individuals that are less likely to survive and reproduce in a particular environment, while allowing

other individuals with traits that confer greater reproductive success to increase in numbers. nauplius  ​ ​The first larval stage in a crustacean. navigation  ​ ​A mechanism of migration that involves the ability not only to follow a compass bearing but also to set or adjust it. negative control  ​ ​Transcriptional regulation by repressor proteins. negative feedback loop  ​ ​A homeostatic mechanism in animals in which a change in the variable being regulated brings about responses that move the variable in the opposite direction. negative frequency-dependent selection  ​ ​A pattern of natural selection in which the fitness of a genotype decreases when its frequency becomes higher; the result is balanced polymorphism. negative pressure filling  ​ ​The process by which reptiles, birds, and mammals ventilate their lungs. nekton  ​ ​Free-swimming animals in the open ocean that can swim against currents to locate food. nematocyst  ​ ​In a cnidarian, a powerful capsule with an inverted coiled and barbed thread that functions to immobilize small prey. nephron  ​ ​One of several million single-cell-thick tubules that are the functional units of the mammalian kidney. Nernst equation  ​ ​The formula that gives the equilibrium potential for an ion at any given concentration gradient: E = 60 mV log10([Xextracellular]/[Xintracellular]). nerve net  ​ ​Interconnected neurons with no central control organ. nerve  ​ ​A structure found in the peripheral nervous system that is composed of multiple myelinated axons bound by connective tissue; carries information to or from the central nervous system. nervous system  ​ ​Coordinated circuits of cells that sense internal and environmental changes and transmit signals that enable an animal to respond in an appropriate way. nervous tissue  ​ ​Networks of cells (neurons) that receive, generate, and conduct electrical signals throughout an animal’s body. net primary production (NPP)  ​ ​Gross primary production minus the energy lost in plant cellular respiration. net reproductive rate  ​ ​The population growth rate per generation. neural crest  ​ ​In vertebrates, a group of embryonic cells derived from ectoderm that disperse throughout the embryo and contribute to the development of the skeleton and other structures, including peripheral nerves. neural tube  ​ ​In chordates, a structure formed from ectoderm located dorsal to the notochord; all neurons and their supporting cells in the central nervous system originate from neural precursor cells derived from the neural tube. neurogenesis  ​ ​The production of new neurons by cell division. neurohormone  ​ ​A hormone made in and secreted by neurons whose cell bodies are in the hypothalamus. neuromodulator  ​ ​Another term for a neuropeptide, which is a neurotransmitter that can alter or modulate the response of a postsynaptic neuron to other neurotransmitters. neuromuscular junction  ​ ​The contact point between an axon terminal of a motor neuron and a skeletal or cardiac muscle fiber. neuron  ​ ​A highly specialized cell found in nervous systems of animals that communicates with other cells by electrical or chemical signals. neuroparasitology  ​ ​The study of how parasites control the nervous systems of their hosts. neuroscience  ​ ​The scientific study of nervous systems.

neurulation  ​ ​The embryological process responsible for initiating central nervous system formation. neutral theory of evolution  ​ ​Theory proposing that most genetic variation in a population is due to the accumulation of neutral mutations that have attained high frequencies in the population via genetic drift. neutral variation  ​ ​Changes in genes and proteins that result from genetic drift and do not have an effect on reproductive success. neutron  ​ ​A neutral particle found in the nucleus of an atom. neutrophil  ​ ​A phagocyte that is the most abundant type of leukocyte; neutrophils engulf bacteria by endocytosis. niche  ​ ​The unique set of habitat resources a species requires as well as its effect on the ecosystem. nitrification  ​ ​The conversion by soil bacteria of –  ammonia (NH3) or ammonium (NH4+) to nitrate (NO3 ), a form of nitrogen commonly used by plants. nitrogen fixation  ​ ​A specialized metabolic process in which certain prokaryotes use the enzyme nitrogenase to convert inert atmospheric nitrogen gas (N2) into ammonia (NH3); also, the industrial process by which humans produce NH3 fertilizer from N2. nitrogenase  ​ ​An enzyme used in the biological process of fixing nitrogen. nitrogen-limitation hypothesis  ​ ​The proposal that organisms select food based on its nitrogen content. nociceptor  ​ ​A sensory receptor in animals that responds to extreme heat, cold, and pressure, as well as to certain molecules such as acids; also known as a pain receptor. Nod factor  ​ ​Nodulation factor; a substance produced by nitrogen-fixing bacteria in response to flavonoids secreted from the roots of potential host plants. Nod factors bind to receptors in plant root membranes, starting a process that allows the bacteria to invade roots. node  ​ ​1. The region of a plant stem from which one or more leaves, branches, or buds emerge. 2. The branch points in a phylogenetic tree. nodes of Ranvier  ​ ​Exposed areas along the axons of myelinated neurons that contain many voltage-gated Na+ channels and are the sites of regeneration of action potentials. nodule  ​ ​A small swelling on a plant root that contains nitrogen-fixing bacteria. nodulin  ​ ​One of several plant proteins that foster root nodule development. non-coding RNA (ncRNA)  ​ ​An RNA molecule that does not encode the amino acid sequence of a polypeptide. noncompetitive inhibitor  ​ ​A molecule that binds noncovalently to an enzyme at a location that is outside the active site and inhibits the enzyme’s function. non-Darwinian evolution  ​ ​The idea that much of the modern variation in gene sequences is explained by neutral variation rather than adaptive variation. nondisjunction  ​ ​An event in which the chromosomes do not separate properly during cell division. nonpolar covalent bond  ​ ​A strong bond formed between two atoms of similar electronegativities in which electrons are shared between the atoms. nonrandom mating  ​ ​The phenomenon that occurs when individuals choose their mates based on their genotypes or phenotypes. nonrecombinant  ​ ​An offspring whose combination of traits has not changed from the true-breeding parental generation. nonsense mutation  ​ ​A mutation that changes a normal codon into a stop codon; this causes translation to be terminated earlier than expected, producing a truncated polypeptide.

GLOSSARY

GLOSSARY G-19

G-20 GLOSSARY

GLOSSARY

nonshivering thermogenesis  ​ ​An increase in an animal’s metabolic rate that is not due to increased muscle activity; occurs primarily in brown adipose tissue. norm of reaction  ​ ​The phenotype range that individuals with a particular genotype exhibit under differing environmental conditions. notochord  ​ ​A defining characteristic of all chordate embryos; a flexible rod that lies between the digestive tract and the nerve cord. N-terminus  ​ ​The location of the first amino acid in a polypeptide; also known as the amino end. nuclear envelope  ​ ​A double-membrane structure that encloses the cell’s nucleus. nuclear genome  ​ ​The chromosomes found in the nucleus of a eukaryotic cell. nuclear lamina  ​ ​A collection of protein fibers that line the inner nuclear membrane; part of the nuclear matrix. nuclear matrix  ​ ​A filamentous network of proteins that is found inside the nucleus and lines the inner nuclear membrane. The nuclear matrix serves to organize the chromosomes. nuclear pore  ​ ​A passageway for the movement of molecules and macromolecules into and out of the nucleus; formed where the inner and outer nuclear membranes make contact with each other. nucleic acid  ​ ​An organic macromolecule composed of nucleotides. The two types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). nucleoid  ​ ​The site in a bacterial cell where the genetic material (DNA) is located. nucleolus  ​ ​A droplet organelle in the nucleus of nondividing cells where ribosome assembly occurs. nucleosome  ​ ​A structural unit of eukaryotic chromosomes composed of an octamer of histones (eight histone proteins) wrapped with DNA. nucleosome-free region (NFR)  ​ ​In eukaryotes, a site in the chromatin in which the DNA is not wrapped around histone proteins to form nucleosomes. nucleotide excision repair (NER)  ​ ​A common type of DNA repair system that removes (excises) and repairs a region of the DNA where damage has occurred. nucleotide  ​ ​An organic molecule having three components: one or more phosphate groups, a fivecarbon sugar (either deoxyribose or ribose), and a single or double ring of carbon and nitrogen atoms known as a base. nucleus (plural, nuclei)  ​ ​1. In cell biology, an organelle found in eukaryotic cells that contains most of the cell’s genetic material. 2. In chemistry, the region of an atom that contains protons and neutrons. 3. In neurobiology, a group of neuronal cell bodies in the brain that are involved in a particular function. nutrient  ​ ​Any substance that is taken in by a living organism and is required for survival, growth, development, tissue repair, or reproduction. nutrition  ​ ​The process of consuming and using nutrients.

O

obligate aerobes  ​ ​Organisms that require oxygen for survival. obligatory mutualism  ​ ​An interaction in which two mutualistic species cannot live without each other. occipital lobe  ​ ​One of four lobes of the cerebral cortex of the human brain; controls aspects of vision and color recognition. ocelli  ​ ​Photosensitive organs found in some animal species. octet rule  ​ ​The observation that many atoms are most stable when their outermost shell is full, with eight electrons.

Okazaki fragments  ​ ​Short segments of DNA synthesized in the lagging strand during DNA replication. olfaction  ​ ​The sense of smell. olfactory bulbs  ​ ​Part of the limbic system of the forebrain of vertebrates; the olfactory bulbs carry information about odors to the brain. oligodendrocytes  ​ ​Glial cells that produce the myelin sheath around neurons in the central nervous system. oligotrophic  ​ ​The term used to describe aquatic systems that are low in nutrients such as phosphate and combined nitrogen and are consequently low in primary productivity and biomass, but typically high in species diversity. ommatidium (plural, ommatidia)  ​ ​A visual unit in the compound eye of arthropods and some annelids that functions as a separate photoreceptor capable of forming an independent image. omnivore  ​ ​An animal that consumes both plants and animals for food. oncogene  ​ ​A type of mutant gene derived from a proto-oncogene. An oncogene is overactive, thus contributing to uncontrolled cell growth and promoting cancer. one-gene/one-enzyme hypothesis  ​ ​An early hypothesis by Beadle and Tatum that suggested that one gene encodes one enzyme. It was later modified. oocyte  ​ ​In animals, a cell that undergoes meiosis to produce an egg cell. oogenesis  ​ ​Gametogenesis in a female animal, resulting in the production of an egg cell. oogonium (plural, oogonia)  ​ ​In animals, the diploid germ cell that gives rise to the female gamete, the egg. open circulatory system  ​ ​In animals, a circulatory system in which hemolymph, which does not differ from the interstitial fluid, flows throughout the body and is not confined to special vessels. open complex  ​ ​A separation between the two DNA strands that occurs near the promoter during transcription; also called a transcription bubble. open conformation  ​ ​Chromatin that can be transcribed into RNA. operant conditioning  ​ ​A form of behavior modification; a type of associative learning in which an animal’s behavior is reinforced by a consequence, either a reward or a punishment. operator  ​ ​A DNA sequence in bacteria that is recognized by activator or repressor proteins that regulate the level of gene transcription. operculum  ​ ​A protective flap that covers the gills of a bony fish. operon  ​ ​A set of two or more genes in bacteria that are under the transcriptional control of a single promoter. opsin  ​ ​A protein that is a component of visual pigments in the vertebrate eye. opsonization  ​ ​The process by which an antibody binds to a pathogen and provides a means to link the pathogen with a phagocyte. optic disc  ​ ​In vertebrates, the point on the retina where the optic nerve leaves the eye. optic nerve  ​ ​A structure of the vertebrate eye that carries electrical signals to the brain. optimal foraging  ​ ​The concept that in a given circumstance, an animal seeks to obtain the most energy possible with the least expenditure of energy. optimality theory  ​ ​The theory that predicts that an animal should behave in a way that maximizes the benefits of a behavior minus its costs. orbital  ​ ​The region surrounding the nucleus of an atom where the probability is high of finding a particular electron. order  ​ ​In taxonomy, a subdivision of a class. organ of Corti  ​ ​Coiled structure in the vertebrate ear responsible for detecting sound.

organ system  ​ ​Different organs that work together to perform an overall function or functions in an organism. organ  ​ ​A collection of two or more tissues that performs a specific function or set of functions. organelle  ​ ​A subcellular structure or membrane-bound compartment with its own unique structure and function. organic chemistry  ​ ​The study of carbon-containing molecules. organic farming  ​ ​The production of crops without the use of commercial inorganic fertilizers, growth substances, and pesticides. organic molecule  ​ ​A carbon-containing molecule, so named because such molecules were first discovered in living organisms. organism  ​ ​A living thing that maintains an internal order that is separated from the environment. organismal ecology  ​ ​The study of the ways in which individual organisms meet the challenges of their biotic and abiotic interactions within their environments. organismic model  ​ ​A view of the nature of a community that considers it to be equivalent to a superorganism; individuals, populations, and communities have a relationship to each other that resembles the associations found between cells, tissues, and organs. organizing center  ​ ​A group of cells in a plant shoot meristem that ensures the proper organization of the meristem and preserves the correct number of actively dividing stem cells. organogenesis  ​ ​The developmental stage during which cells and tissues form organs in animal embryos. orientation  ​ ​A mechanism of migration in which animals have the ability to follow a compass bearing and travel in a straight line. origin of replication  ​ ​A site within a chromosome that serves as a starting point for DNA replication. orthologs  ​ ​Homologous genes found in different species. osmoconformer  ​ ​An animal whose osmolarity conforms to that of its environment. osmolarity  ​ ​The solute concentration of an aqueous solution, expressed as milliosmoles/liter (mOsm/L). osmoregulator  ​ ​An animal that maintains stable internal ion concentrations and osmolarities, even when living in water whose osmolarity is very different from that of its body fluids or living on land. osmosis  ​ ​The movement of water across a membrane to balance solute concentrations. Water diffuses from a solution that is hypotonic (lower solute concentration) into a solution that is hypertonic (higher solute concentration). osmotic adjustment  ​ ​The process by which a plant cell modifies the solute concentration of its cytosol. osmotroph  ​ ​An organism that relies on osmotrophy (uptake of small organic molecules) as a mechanism of nutrition. osmotrophy  ​ ​The process of feeding by absorbing small organic molecules. osteichythan  ​ ​A clade that includes all vertebrates with a bony skeleton. osteomalacia  ​ ​Bone deformation in adults due to inadequate mineral intake or absorption from the small intestine. osteoporosis  ​ ​A disease in which the mineral and organic components of bone are reduced. otolith  ​ ​Granules of calcium carbonate found in the gelatinous substance that embeds hair cells in the vertebrate ear. outer bark  ​ ​Protective layers of mostly dead cork cells that cover the outside of woody stems and roots. outer segment  ​ ​The highly convoluted plasma membranes found in the rods and cones of the eye. outgroup  ​ ​In a cladogram, a species or group of species that does not exhibit one or more shared derived characters found in the ingroup.

ovarian cycle  ​ ​The events beginning with the development of an ovarian follicle, followed by release of a secondary oocyte, and concluding with formation and subsequent degeneration of a corpus luteum. ovary  ​ ​1. In animals, the female gonad where eggs are formed. 2. In plants, the lowermost portion of the pistil that encloses and protects the ovules. overexploitation  ​ ​The practice in which humans harvest a particular species at a rate that is unsustainable, based on its natural rate of mortality and capacity for reproduction. oviduct  ​ ​A thin tube with undulating fimbriae (finger-like structures) that is connected to the uterus and extends out to the ovary; also called the Fallopian tube. oviparous  ​ ​Refers to an animal whose young hatch from eggs laid outside the mother’s body. ovoviparous  ​ ​Refers to an animal that retains fertilized eggs covered by a protective sheath or other structure within the body, where the young hatch. ovulation  ​ ​The process by which a mature oocyte is released from an ovary. ovule  ​ ​In a seed plant, a megaspore-producing sporangium with enclosing structures known as integuments. oxidation  ​ ​The removal of one or more electrons from an atom or molecule; occurs during the breakdown of small organic molecules. oxidative fiber  ​ ​A skeletal muscle fiber that contains numerous mitochondria and has a high capacity for oxidative phosphorylation. oxidative phosphorylation  ​ ​A process during which NADH and FADH2 are oxidized to make more ATP via the phosphorylation of ADP. oxygen-hemoglobin dissociation curve  ​ ​A curve that represents the relationship between the partial pressure of oxygen and the binding of oxygen to hemoglobin proteins. oxytocin  ​ ​A hormone secreted by the posterior pituitary gland that stimulates contractions of the smooth muscles in the uterus of a pregnant mammal, facilitating the birth process; after birth, it is important in milk secretion.

P

P generation  ​ ​The parental generation in a genetic cross. P protein  ​ ​Phloem protein; the proteinaceous material used by plant phloem as a response to wounding. pacemaker  See sinoatrial (SA) node. Pacinian corpuscle  ​ ​A specialized receptor that is located deep beneath the surface of an animal’s skin and responds to deep pressure or vibration. pair-rule gene  ​ ​A type of segmentation gene; a mutation in this gene may cause alternating segments or parts of segments to be absent. paleontologist  ​ ​A scientist who studies fossils. palisade parenchyma  ​ ​Photosynthetic ground tissue of the plant leaf mesophyll that consists of closely packed, elongate cells adapted to efficiently absorb sunlight. palmate  ​ ​A type of leaf vein pattern in which veins radiate outward, resembling an open hand. pancreas  ​ ​In vertebrates, an elongated gland located behind the stomach that secretes digestive enzymes and a fluid rich in bicarbonate ions. paracrine signaling  ​ ​A type of cellular communication in which molecules are released into the interstitial fluid and act on nearby cells. paralogs  ​ ​Homologous genes within a single species. paraphyletic group  ​ ​A group of species that contains a common ancestor and some, but not all, of its descendants. parapodia  ​ ​Fleshy, footlike structures in the Errantia, a type of Annelid worm, that are pushed into the substrate to provide traction during movement.

parasite  ​ ​An organism that feeds on another organism, called the host, for a relatively long time, but does not normally kill it outright. parasitism  ​ ​A symbiotic association in which one organism feeds off another but does not normally kill it. parasympathetic division  ​ ​The division of the autonomic nervous system that is involved in maintaining and restoring body functions. parathyroid hormone (PTH)  ​ ​A hormone that acts on bone to stimulate the activity of cells that dissolve the mineral part of bone. parenchyma cell  ​ ​A type of plant cell that is thin-walled and alive at maturity. parenchyma  ​ ​A plant ground tissue that is composed of parenchyma cells. parental strand  ​ ​The original strand in DNA replication. parietal lobe  ​ ​One of four lobes of the cerebral cortex of the human brain; receives and interprets sensory input from visual and somatic pathways. parthenogenesis  ​ ​An asexual process in which an offspring develops from an unfertilized egg. partial pressure  ​ ​The individual pressure of each gas in the air; the sum of these pressures is known as atmospheric pressure. particulate inheritance  ​ ​The idea that the determinants of hereditary traits are transmitted in discrete units, or particles, from one generation to the next. passive immunity  ​ ​A type of acquired immunity that confers protection against disease through the direct transfer of antibodies from one individual to another. passive transport  ​ ​The diffusion of a solute across a membrane in a process that is energetically favorable and does not require an input of energy. paternal inheritance  ​ ​A pattern in which only the male gamete contributes particular organellar genes to the offspring. pathogen  ​ ​A virus or microorganism that causes disease symptoms in its host. pathogen-associated molecular pattern (PAMP)  ​ ​Any general molecular feature common to many pathogens that triggers an innate immune response. pattern formation  ​ ​The process that gives rise to a plant or animal with a particular body structure. pedal glands  ​ ​Glands in the foot of a rotifer that secrete a sticky substance that aids in attachment to the substrate. pedicel  ​ ​1. A flower stalk. 2. A narrow, waistlike point of attachment between the body parts of spiders and some insects. pedigree analysis  ​ ​An examination of human traits over several generations in a family as a way to deduce the pattern of inheritance. peer-review process  ​ ​A procedure in which experts in a particular area evaluate papers submitted to scientific journals. pelagic zone  ​ ​The open ocean, where the water depth averages 4,000 m and nutrient concentrations are typically low. penis  ​ ​A male external accessory sex organ found in many animals that is involved in copulation. pentadactyl limb  ​ ​A limb ending in five digits. pepsin  ​ ​An active enzyme in the stomach that begins the digestion of protein. peptide bond  ​ ​The covalent bond between a carboxyl and amino group that links amino acids in a polypeptide. peptidoglycan  ​ ​A polymer composed of carbohydrates crosslinked with peptides that is an important component of the cell walls of most bacteria. peptidyl site (P site)  ​ ​One of three sites for tRNA binding in the ribosome during translation; the other two are the aminoacyl site (A site) and the exit site (E site). The P site holds the tRNA carrying the growing polypeptide chain.

peptidyl transfer reaction  ​ ​During translation, the transfer of the polypeptide from the tRNA in the P site to the amino acid at the A site. per capita growth rate  ​ ​The per capita birth rate minus the per capita death rate; the rate that determines how a population grows over any time period. perception  ​ ​An awareness of the sensations that are experienced. perennial  ​ ​A plant that lives for more than 2 years, often producing seeds each year after it reaches reproductive maturity. perfect flower  ​ ​A flower that has both stamens and carpels. perianth  ​ ​The term that refers to flower petals and sepals collectively. pericarp  ​ ​The wall of a plant’s fruit. pericycle  ​ ​A cylinder of plant tissue that has cell division (meristematic) capacity and encloses the root vascular tissue. periderm  ​ ​The outer layers of a woody stem, composed of cork cambium, layers of cork tissue produced by the cork cambium, and associated parenchyma cells, together forming outer bark. peripheral membrane protein  ​ ​A protein that is noncovalently bound to a region of an integral membrane protein that projects out from the membrane or noncovalently bound to the polar head group of phospholipids. peripheral nervous system (PNS)  ​ ​In vertebrates, all nerves and ganglia outside the brain and spinal cord. peripheral zone  ​ ​The area of a plant shoot meristem that contains dividing cells that will eventually differentiate into plant structures. periphyton  ​ ​Communities of microorganisms that are attached by mucilage to underwater surfaces such as rocks, sand, and plants. peristalsis  ​ ​In animals, the rhythmic, spontaneous waves of muscle contractions that propel food through the digestive system. peritubular capillaries  ​ ​A capillary near the junction of the cortex and medulla that surrounds the renal tubule of the mammalian kidney. permafrost  ​ ​A layer of permanently frozen soil found in tundra. peroxisome  ​ ​A relatively small organelle that is found in all eukaryotic cells and that catalyzes detoxifying reactions. personalized medicine  ​ ​A medical practice in which information about a patient’s genotype is used to individualize the person’s medical care. petal  ​ ​A flower organ that usually serves to attract insects or other animals for pollen transport. petiole  ​ ​A stalk that connects a leaf to the stem of a plant. pH  ​ ​The mathematical expression of a solution’s hydrogen ion (H+) concentration, defined as the negative logarithm to the base 10 of the H+ concentration. phage  See bacteriophage. phagocyte  ​ ​A cell capable of phagocytosis; phagocytes provide nonspecific defense against pathogens that enter the body. phagocytosis  ​ ​A type of endocytosis that involves the formation of a membrane vesicle, called a phagosome, or phagocytic vacuole, which engulfs a particle such as a bacterium. phagotroph  ​ ​An organism that specializes in phagotrophy (particle feeding) by means of phagocytosis as a mechanism of nutrition. pharyngeal slit  ​ ​A defining characteristic of all chordate embryos. In early-diverging chordates, pharyngeal slits develop into a filter-feeding device, and in some advanced chordates, they form gills. pharynx  ​ ​A portion of the vertebrate alimentary canal; also known as the throat.

GLOSSARY

GLOSSARY G-21

G-22 GLOSSARY

GLOSSARY

phenotype  ​ ​The characteristics of an organism that are the result of the expression of its genes. pheromone  ​ ​A powerful chemical attractant used to manipulate the behavior of others. phloem loading  ​ ​The process of conveying sugars to sieve-tube elements for long-distance transport. phloem  ​ ​A specialized conducting tissue in a plant’s stem. phoresy  ​ ​A form of commensalism in which individuals of one species use individuals of a second species for transportation. phosphodiester linkage  ​ ​Refers to a double linkage (two phosphoester bonds) that holds together adjacent nucleotides in DNA and RNA strands. phosphodiesterase  ​ ​An enzyme that breaks a bond in cAMP to form AMP. phospholipid bilayer  ​ ​The basic framework of a biological membrane, consisting of two layers of phospholipids. phospholipid  ​ ​A type of lipid that is similar in structure to a triglyceride, but with the third hydroxyl group of glycerol linked to a phosphate group instead of a fatty acid; a key component of biological membranes. phosphorylation  ​ ​The attachment of a phosphate to a molecule. photic zone  ​ ​A fairly narrow zone close to the surface of an aquatic environment, where light is sufficient to allow photosynthesis to occur. photoautotroph  ​ ​An organism that uses the energy from light to make organic molecules from inorganic sources. photoheterotroph  ​ ​An organism that is able to use light energy to generate ATP but must take in organic compounds from the environment as a source of carbon. photon  ​ ​One of the discrete particles that make up light. A photon is massless and travels in a wavelike pattern. photoperiodism  ​ ​A plant’s ability to measure and respond to the amount of light and day length; used as a way of detecting seasonal change. photophosphorylation  ​ ​The process by which the light reactions of photosynthesis produce ATP.  photopsin  ​ ​Any of several types of visual pigments in the cone cells of the vertebrate eye. photoreceptor  ​ ​A specialized sensory receptor in an animal that responds to visible light energy; in plants, molecules that respond to light. photorespiration  ​ ​The metabolic process occurring in C3 plants when the enzyme rubisco combines with O2 instead of CO2 and produces only one molecule of 3PG instead of two, thereby reducing photosynthetic efficiency. photosynthesis  ​ ​The process whereby light energy is captured by plant, algal, or photosynthetic bacterial cells and is used to synthesize organic molecules from CO2 and H2O (or H2S). photosystem I (PSI)  ​ ​A distinct complex of proteins and pigment molecules in chloroplasts that absorbs light during the light reactions of photosynthesis. photosystem II (PSII)  ​ ​A distinct complex of proteins and pigment molecules in chloroplasts that absorbs light and also generates oxygen from water during the light reactions of photosynthesis. phototropin  ​ ​The main blue-light sensor involved in positive phototropism in plants. phototropism  ​ ​The tendency of a plant to grow toward a light source. phylogenetic tree  ​ ​A diagram that describes the evolutionary relationships among various species, based on the information available to and gathered by systematists. phylogeny  ​ ​The evolutionary history of a species or group of species. phylum (plural, phyla)  ​ ​In taxonomy, a subdivision of a kingdom. physical mutagen  ​ ​A physical agent, such as ultraviolet light, that causes mutations.

physical systems  ​ ​Physical environments, such as oceans, ice, fresh waters, and soils, that serve as habitats for microbiomes. physiological ecology  ​ ​A subdiscipline of organismal ecology that investigates how organisms are physiologically adapted to their environment and how the environment impacts the distribution of species. physiology  ​ ​The study of the functions of living things. phytochrome  ​ ​A red-light and far-red-light receptor in plants. phytoplankton  ​ ​Microscopic photosynthetic protists that float in water or actively move through it. pigment  ​ ​A molecule that can absorb light energy. pili (singular, pilus)  ​ ​Threadlike surface appendages that allow bacteria to attach to each other during conjugation or to move across surfaces. piloting  ​ ​A mechanism of migration in which an animal moves from one familiar landmark to the next. pinnate  ​ ​A type of leaf vein pattern in which veins appear feather-like. pinocytosis  ​ ​A type of endocytosis that involves the formation of membrane vesicles from the plasma membrane as a way for cells to internalize the extracellular fluid. pistil  ​ ​A flower structure that may consist of a single carpel or multiple, fused carpels and is differentiated into stigma, style, and ovary. pit  ​ ​A thin-walled circular area in a plant cell wall where secondary wall materials such as lignin are absent and through which water moves. pituitary giant  ​ ​A person who has a tumor of the GH-secreting cells of the anterior pituitary gland and thus produces excess GH during childhood and, if untreated, during adulthood; the person can grow very tall before growth ceases after puberty. pituitary gland  ​ ​A multilobed endocrine gland sitting directly below the hypothalamus of the brain. placenta  ​ ​A structure in humans and other eutherian mammals that connects the developing young to the mother’s uterine wall and allows the transfer of nutrients and gases. placental transfer tissues  ​ ​In plants, nutritive tissues that aid in the transfer of nutrients from maternal parent to embryo. plant tissue culture  ​ ​A laboratory process to produce thousands of identical plants having the same desirable characteristics. plant  ​ ​A multicellular eukaryotic organism that is usually photosynthetic (having plastids), primarily lives on land, and has cells with a cell wall containing cellulose. Plantae  ​ ​A eukaryotic kingdom of the domain Eukarya. plaques  ​ ​1. Deposits of lipids, fibrous tissue, and smooth muscle cells that may develop inside arterial walls. 2. A bacterial biofilm that may form on the surfaces of teeth. plasma cell  ​ ​A cell that synthesizes and secretes antibodies. plasma membrane  ​ ​The biological membrane that separates the internal contents of a cell from its external environment. plasma  ​ ​The fluid part of blood that contains water and dissolved solutes. plasmid  ​ ​A small circular piece of DNA that exists separately from the bacterial chromosome in many strains of bacteria; plasmids are also found in some eukaryotic cells, such as yeast, and can be used as vectors in cloning experiments. plasmodesma (plural, plasmodesmata)  ​ ​A membranelined, ER-containing channel that connects the cytoplasm of adjacent plant cells. plasmogamy  ​ ​The fusion of the cytoplasm between two gametes. plasmolysis  ​ ​The shrinkage of algal or plant cytoplasm that occurs when water leaves the cell by osmosis,

with the result that the plasma membrane no longer presses on the cell wall. plastid  ​ ​A general name given to organelles found in plant and algal cells that are bound by two or more membranes and contain DNA and large amounts of either chlorophyll (in chloroplasts), carotenoids (in chromoplasts), or starch (in amyloplasts). platelets  ​ ​Cell fragments in the blood of mammals that play a crucial role in the formation of blood clots. pleiotropy  ​ ​The phenomenon in which a mutation in a single gene can have multiple effects on an individual’s phenotype. pleural sac  ​ ​A double layer of thin, moist connective tissue that encases each lung. pluripotent  ​ ​Refers to the ability of embryonic stem cells to differentiate into almost every cell type of the body. point mutation  ​ ​A mutation that affects only a single base pair within DNA or that involves the addition or deletion of a single base pair to a DNA sequence. polar covalent bond  ​ ​A covalent bond between two atoms that have different electronegativities; the shared electrons are closer to the nucleus of the atom of higher electronegativity than to the nucleus of the atom of lower electronegativity. This distribution of the shared electrons around the atoms creates a polarity, or difference in electric charge, across the molecule. polar transport  ​ ​The process whereby auxin flows primarily downward in shoots. pole  ​ ​A structure of the spindle apparatus defined by each centrosome. pollen grain  ​ ​The immature male gametophyte of a seed plant. pollen tube  ​ ​In seed plants, a long, thin tube produced by a pollen grain that delivers sperm to the ovule. pollen  ​ ​In seed plants, tiny male gametophytes enclosed by sporopollenin-containing microspore walls. pollination syndromes  ​ ​The pattern of coevolved traits between particular types of flowers and their specific pollinators. pollination  ​ ​The process in which pollen grains are transported to an angiosperm flower or a gymnosperm cone primarily by means of wind or animal pollinators. pollinator  ​ ​An animal that carries pollen between angiosperm flowers or cones of gymnosperms. poly A tail  ​ ​A string of adenine nucleotides at the 3′ end of most mature mRNAs in eukaryotes. polyandry  ​ ​A mating system in which one female mates with several males, but males mate with only one female. polycistronic mRNA  ​ ​An mRNA that contains the coding sequences for two or more protein-encoding genes. polygenic  ​ ​Refers to a trait for which several or many genes contribute to the outcome. polygyny  ​ ​A mating system in which one male mates with several females in a single breeding season, but females mate with only one male. polymer  ​ ​A large molecule formed by linking many smaller molecules called monomers. polymerase chain reaction (PCR)  ​ ​A technique to make many copies of a gene in vitro; primers are used that flank the region of DNA to be amplified. polymorphic gene  ​ ​A gene that commonly exists as two or more alleles in a population. polymorphism  ​ ​The presence of two or more variations of a character (trait) within a population. polyp  ​ ​A type of cnidarian body form that is sessile and occurs mouth up. polypeptide  ​ ​A molecule consisting of a linear sequence of amino acids; the term denotes structure. polyphagous  ​ ​Parasites that feed on many host species.

polyphyletic group  ​ ​A group of species that consists of members of several evolutionary lines and does not include the most recent common ancestor of the included lineages. polyploid  ​ ​Refers to an organism or cell that has three or more sets of chromosomes. polyploidy  ​ ​The condition in which a cell or organism has three or more sets of chromosomes. polysaccharide  ​ ​A long carbohydrate polymer formed of many monosaccharides linked together. polysome  ​ ​The complex of a single mRNA and multiple ribosomes. pons  ​ ​The part of the vertebrate hindbrain that, along with the cerebellum, has an integrative motor function; it also plays a role in regulating breathing. population density  ​ ​The number of organisms of a given species in a given unit area or volume. population ecology  ​ ​The study of how populations grow and what factors promote or limit growth. population genetics  ​ ​The study of genes and genotypes in a population. population  ​ ​A group of individuals of the same species that occupy the same environment and (for sexually reproducing organisms) can interbreed with one another. portal vein  ​ ​A vein that not only collects blood from capillaries—like all veins—but also forms another set of capillaries, as opposed to returning the blood directly to the heart. positional information  ​ ​Information regarding a cell’s location relative to other cells that is conveyed by morphogens and cell-to-cell contacts. positive control  ​ ​Transcriptional regulation by activator proteins. positive feedback loop  ​ ​In animals, a mechanism that accelerates or amplifies a process, leading to what is sometimes called an explosive system. postabsorptive state  ​ ​One of two alternating phases in the utilization of nutrients; occurs when the gastrointestinal tract is empty of nutrients and the body’s own stores must supply energy. The other phase is the absorptive state. postanal tail  ​ ​A defining characteristic of all chordate embryos; a tail of variable length that extends posterior to the anal opening. posterior  ​ ​Refers to the rear (tail) end of an animal. postsynaptic cell  ​ ​The cell that receives the electrical or chemical signal sent from a neuron. post-translational sorting  ​ ​The uptake of proteins into the nucleus, mitochondria, chloroplasts, or peroxisomes that occurs after the protein is completely made in the cytosol (that is, completely translated). postzygotic isolating mechanism  ​ ​A mechanism that prevents interbreeding by blocking the development of a viable and fertile individual after fertilization has taken place. potential energy  ​ ​The energy that a substance possesses due to its structure or location. power stroke  ​ ​In muscle, a conformation change in the myosin cross-bridge that results in binding between myosin and actin and the movement of the actin filament. prebiotic soup  ​ ​The medium formed by the slow accumulation of organic molecules in the early oceans over a long period of time prior to the existence of life. predation  ​ ​An interaction in which the action of a predator results in the death of its prey. prediction  ​ ​An expected outcome based on a hypothesis that can be shown to be correct or incorrect through observation or experimentation. pregnancy  ​ ​The time during which a developing embryo or fetus grows within the uterus of the mother; also known as gestation.

preinitiation complex  ​ ​The assembled structure consisting of RNA polymerase II and transcription factors (GTFs) at the TATA box prior to transcription of eukaryotic protein-encoding genes. pre-mRNA  ​ ​In eukaryotes, the mRNA transcript before any biochemical modifications are made to it. pressure potential  ​ ​The component of water potential due to hydrostatic pressure. pressure-flow hypothesis  ​ ​Explains sugar translocation in plants as a process driven by differences in turgor pressure between cells of a sugar source, where sugar is produced, and cells of a sugar sink, where sugar is consumed. presynaptic cell  ​ ​The neuron that sends an electrical or chemical signal to another cell. prezygotic isolating mechanism  ​ ​A mechanism that blocks interbreeding by preventing the formation of a zygote. primary active transport  ​ ​A type of transport that involves pumps that directly use energy to transport a solute against a gradient. primary cell wall  ​ ​In plants, a relatively thin and flexible cell wall that is synthesized first between two newly made daughter cells. primary consumer  ​ ​An organism that obtains its food by eating primary producers; also called a herbivore. primary electron acceptor  ​ ​The molecule to which a high-energy electron from an excited pigment molecule such as P680* is transferred during photosynthesis. primary endosymbiosis  ​ ​The process by which a eukaryotic host cell acquires prokaryotic endosymbionts. Mitochondria and the plastids of green and red algae are examples of organelles that originated via primary endosymbiosis. primary growth  ​ ​Plant growth that occurs from primary meristems and produces primary tissues and organs of diverse types. primary immune response  ​ ​The immune response to an initial exposure to an antigen. primary meristem  ​ ​A meristematic tissue that increases plant length and produces new organs. primary oocyte  ​ ​In animals, a cell that undergoes meiosis to begin the process of egg production. primary plastid  ​ ​A plastid that originated from a prokaryote as the result of primary endosymbiosis. primary producers  ​ ​Autotrophs such as plants, algae, and photosynthetic bacteria that use sunlight and form the basis of the food chain. primary production  ​ ​Production by autotrophs, normally green plants. primary spermatocyte  ​ ​In animals, a cell that undergoes meiosis to begin the process of sperm production. primary structure  ​ ​The linear sequence of amino acids of a polypeptide; one of four levels of protein structure. primary succession  ​ ​Succession on newly exposed sites that were not previously occupied by soil and vegetation. primary vascular tissue  ​ ​Plant tissue composed of xylem and phloem; a conducting tissue of nonwoody plants. principle of parsimony  ​ ​The concept that the preferred hypothesis is the one that is the simplest. principle of species individuality  ​ ​A view of the nature of a community in which each species is distributed according to its physiological needs and population dynamics; most communities intergrade continuously, and competition does not create distinct vegetational zones. prion  ​ ​An infectious protein that causes disease by inducing the abnormal folding of other protein molecules. probability  ​ ​The chance that an event will have a particular outcome.

probiotic treatment  ​ ​The introduction of one or more microbial strains into the microbiome of a host organism, usually to improve health. proboscis  ​ ​The coiled tongue of a butterfly or moth, which can be uncoiled, enabling the insect to drink nectar from flowers. processivity  ​ ​The characteristic of DNA polymerase that keeps it from falling off the template stand as it is synthesizing a new daughter strand.  producer  ​ ​An organism that synthesizes the organic compounds used by other organisms for food. product rule  ​ ​The probability that two or more independent events will occur is equal to the product of their individual probabilities. product  ​ ​The end result of a chemical reaction. production efficiency  ​ ​The percentage of energy assimilated by an organism that becomes incorporated into new biomass. productivity hypothesis  ​ ​The proposal that greater production by plants results in greater overall species richness. progesterone  ​ ​A hormone secreted by the female ovaries that plays a key role in pregnancy. progymnosperms  ​ ​An extinct group of plants having wood but not seeds, which evolved before the gymnosperms. prokaryotic cell  ​ ​Refers to a cell lacking a membraneenclosed nucleus and cell compartmentalization; includes the cells from all members of the domains Bacteria and Archaea. prokaryotic  ​ ​Refers to organisms having cells lacking a membrane-enclosed nucleus and cell compartmentalization; includes all members of the domains Bacteria and Archaea. prometaphase  ​ ​The phase of mitosis during which the nuclear envelope completely fragments into vesicles and the mitotic spindle is fully formed. promiscuous  ​ ​In ecology, a term for animals that have many different sexual mates. promoter  ​ ​A sequence of DNA within a gene that controls when and where transcription begins. proofreading  ​ ​The ability of DNA polymerase to identify a mismatched nucleotide and remove it from the daughter strand. prophage  ​ ​The DNA of a phage that has become integrated into a bacterial chromosome. prophase  ​ ​The phase of mitosis during which the chromosomes condense and the nuclear membrane begins to vesiculate. proplastid  ​ ​A type of unspecialized structure from which a plastid is derived. prosthetic group  ​ ​A small molecule that is permanently attached to the surface of an enzyme and aids in the enzyme’s function. protease  ​ ​An enzyme that cuts proteins into smaller polypeptides. proteasome  ​ ​A protein complex that provides the primary pathway for protein degradation in archaea and eukaryotic cells. protein kinase cascade  ​ ​The sequential activation of multiple protein kinases. protein kinase  ​ ​An enzyme that transfers a phosphate group from ATP to a specific amino acid in a protein. protein phosphatase  ​ ​An enzyme responsible for removing phosphate groups from proteins. protein subunit  ​ ​An individual polypeptide within a functional protein; most functional proteins are composed of two or more polypeptides. protein  ​ ​A functional unit composed of one or more polypeptides. Each polypeptide is composed of a linear sequence of amino acids. protein-encoding gene  ​ ​A gene that serves as a template to make an mRNA molecule that contains the information to specify a polypeptide with a particular

GLOSSARY

GLOSSARY G-23

G-24 GLOSSARY

GLOSSARY

amino acid sequence; most genes are protein-encoding genes. protein-protein interactions  ​ ​The specific interactions between proteins that occur during many critical cellular processes. proteoglycan  ​ ​A long, linear core protein with many GAGs attached to it; found in the ECM. proteolysis  ​ ​A processing event within a cell in which enzymes called proteases cut proteins into smaller polypeptides. proteome  ​ ​The complete complement of proteins that a cell is currently making or an organism can make. proteomics  ​ ​Techniques used to analyze and compare proteomes. prothoracicotropic hormone (PTTH)  ​ ​A hormone produced in certain invertebrates that stimulates a pair of endocrine glands called the prothoracic glands. Protista  ​ ​Formerly a eukaryotic kingdom. Protists are now placed into seven eukaryotic supergroups. protobiont  ​ ​The term used to describe the first nonliving structure that could have evolved into a living cell. proton  ​ ​A positively charged particle found in the nucleus of an atom. The number of protons in an atom is called the atomic number and defines each type of element. protonephridia  ​ ​Simple excretory organs found in flatworms that are used to filter out wastes and excess water. proto-oncogene  ​ ​A normal gene that, if mutated, can become an oncogene. protostome  ​ ​An animal whose development exhibits spiral determinate cleavage and in which the blastopore becomes the mouth; includes mollusks, annelid worms, and arthropods. protozoa  ​ ​A term commonly used to describe diverse heterotrophic protists. proventriculus  ​ ​The glandular portion of the stomach of a bird. provirus  ​ ​Viral DNA that has become integrated into a chromosome of the host cell. proximal tubule  ​ ​The segment of the renal tubule in the kidney that drains Bowman’s capsule. proximate cause  ​ ​A specific genetic and physiological mechanism that underlies a behavior. pseudocoelomate  ​ ​An animal with a pseudocoelom. pteridophytes  ​ ​A phylum of vascular plants having euphylls, but not seeds; formally called Pteridophyta. pulmonary arteries  ​ ​The arteries that bring blood from the right ventricle to the lungs in animals with a double circulation. pulmonary circulation  ​ ​The circuit in a double circulation in which blood is pumped from the right side of the heart to the lungs to pick up oxygen from the atmosphere and release carbon dioxide. pump  ​ ​A transporter that directly couples its conformational changes to an energy source, such as ATP hydrolysis. punctuated equilibrium  ​ ​A concept that suggests that the tempo of evolution is more sporadic than gradual. Species rapidly evolve into new species followed by long periods of equilibrium with little evolutionary change. Punnett square  ​ ​A common method for predicting the outcome of simple genetic crosses. pupa  ​ ​A developmental stage in some insects that undergo metamorphosis; occurs between the larval and adult stages. pupil  ​ ​A small opening in the eye of a vertebrate that transmits different patterns of light emitted from or reflected off objects in the animal’s field of view. purine  ​ ​Either of the bases adenine (A) and guanine (G), which have a fused double ring of carbon and nitrogen atoms. pyramid of biomass  ​ ​A graphic representation of trophic levels in a food web in which the organisms at each trophic level are weighed.

pyramid of energy  ​ ​A graphic represention of trophic levels in a food web in which rates of energy production are used rather than biomass. pyramid of numbers  ​ ​A graphic representation of trophic levels in a food web in which the number of individuals decreases at each trophic level, with a huge number of individuals at the base and fewer individuals at the top. pyrimidine  ​ ​Any of the bases thymine (T), cytosine (C), and uracil (U), which have a single ring of carbon and nitrogen atoms.

Q

quadrat  ​ ​A sampling device used by plant ecologists consisting of a square frame that often encloses an area of 0.25 m2. quantitative trait  ​ ​A trait that shows continuous variation over a range of phenotypes. quaternary structure  ​ ​The association of two or more polypeptides to form a protein; one of four levels of protein structure. quorum sensing  ​ ​A mechanism by which prokaryotic cells are able to communicate by chemical means when they reach a critical population size.

R

radial cleavage  ​ ​A mechanism of animal development in which the cleavage planes are either parallel or perpendicular to the vertical axis of the embryo. radial loop domain  ​ ​A loop of chromatin, often 25,000 to 200,000 base pairs in size, that is anchored to the nuclear matrix. radial pattern  ​ ​A characteristic of the body plan of plants in which root and shoot cells form concentric rings. radial symmetry  ​ ​1. In plants, an architectural feature in which embryos display a cylindrical shape, which is retained in the stems and roots of seedlings and mature plants. In addition, new leaves or flower parts are produced in circular whorls, or spirals, around shoot tips. 2. In animals, an architectural feature in which the body can be divided into symmetrical halves by many different longitudinal planes along a central axis. radiation  ​ ​The emission of electromagnetic waves from the surfaces of objects; a means of heat exchange in animals. radicle  ​ ​An embryonic root, which extends from the hypocotyl in eudicot seeds. radioisotope  ​ ​An isotope found in nature that is inherently unstable and usually does not exist for long periods of time. Such isotopes decay and emit energy in the form of radiation. radiometric dating  ​ ​A process for estimating the age of a fossil by analyzing the decay of radioisotopes within the accompanying rock. radula  ​ ​A unique, protrusible, tonguelike organ in a mollusk that has many teeth and is used to eat plants, scrape food particles off rocks, or bore into shells of other species. rain shadow  ​ ​An area on the side of a mountain that is sheltered from the wind and experiences less precipitation. random sampling error  ​ ​The deviation between the observed and the expected outcomes due to random chance. random  ​ ​The rarest pattern of dispersion within a population, in which the location of individuals lacks a pattern. rate-limiting step  ​ ​The slowest step in a reaction pathway.

ray-finned fishes  ​ ​The Actinopterygii, which includes all bony fishes except the coelacanths and lungfishes. reabsorption  ​ ​In the production of urine, the process in which useful solutes in the filtrate are recaptured and transported back into the body fluids of an animal. reactant  ​ ​A substance that participates in a chemical reaction and becomes changed by that reaction. reading frame  ​ ​Refers to the way in which codons are read during translation, in groups of three bases beginning with the start codon. realized niche  ​ ​The actual range of an organism in nature. receptacle  ​ ​The enlarged region at the tip of a flower peduncle to which flower parts are attached. receptor potential  ​ ​The membrane potential in a sensory receptor cell of an animal. receptor tyrosine kinase  ​ ​A type of enzyme-linked receptor found in animals and choanoflagellates that can attach phosphate groups to tyrosines in the receptor itself or in other cellular proteins. receptor  ​ ​1. A cellular protein that recognizes a signaling molecule and becomes activated or inhibited in response to it. 2. A structure capable of detecting changes in the environment of an animal, such as a touch receptor. receptor-mediated endocytosis  ​ ​A common type of endocytosis in which a receptor in the membrane is specific for a given cargo. recessive  ​ ​Refers to a trait that is masked by the presence of a dominant trait in a heterozygote. reciprocal cross  ​ ​A cross in which the sexes and phenotypes are reversed compared to another cross. reciprocal translocation  ​ ​A type of mutation in which two different types of chromosomes exchange pieces, thereby producing two abnormal chromosomes carrying translocations. recombinant DNA technology  ​ ​The use of laboratory techniques to bring together fragments of DNA from multiple sources. recombinant vector  ​ ​A vector containing a piece of chromosomal DNA. recombinant  ​ ​An offspring that has a different combination of traits from the true-breeding parental generation. recombination frequency  ​ ​The frequency of crossing over between two genes. rectum  ​ ​The last segment of the large intestine of vertebrates that ends at the anus, the posterior opening of the alimentary canal to the external environment. redox reaction  ​ ​A type of reaction in which an electron that is removed during the oxidation of an atom or molecule is transferred to another atom or molecule, which becomes reduced; short for a reductionoxidation reaction. reduction  ​ ​The addition of one or more electrons to an atom or molecule. reductionism  ​ ​An approach that involves reducing complex systems to simpler components as a way to understand how the system works. In biology, reductionists study the parts of a cell or organism as individual units. redundancy hypothesis  ​ ​The proposal that ecosystem function increases rapidly at fairly low levels of species richness, but then levels off because most additional species are redundant. reflex arc  ​ ​A simple circuit that allows an organism to respond rapidly to inputs from sensory neurons and consists of only a few neurons. regeneration  ​ ​A form of asexual reproduction in which a complete organism forms from a fragment of an animal’s body. regulatory element  ​ ​In eukaryotes, a DNA sequence that is recognized by regulatory transcription factors and regulates the expression of genes.

GLOSSARY G-25 respiratory pigment  ​ ​A large protein that contains one or more metal atoms that bind to oxygen. respiratory system  ​ ​All components of the body that contribute to the exchange of gas between the external environment and cells of the body; in mammals, includes the nose, mouth, airways, and lungs and the muscles and connective tissues that encase these structures within the thoracic (chest) cavity. resting potential  ​ ​The difference in charges across the plasma membrane in an unstimulated neuron. rest-or-digest response  ​ ​The response of vertebrates to situations associated with nonstressful states, such as feeding; mediated by the parasympathetic branch of the autonomic nervous system. restriction enzyme  ​ ​An enzyme that recognizes a particular DNA sequence and cleaves the DNA backbone at two sites. restriction point  ​ ​A point in the cell cycle in which a cell has become committed to divide. reticular formation  ​ ​An array of nuclei in the brainstem of vertebrates that plays a major role in controlling states such as sleep and arousal. retina  ​ ​A sheetlike layer of photoreceptors at the back of the vertebrate eye. retinal  ​ ​A derivative of vitamin A that is capable of absorbing light energy; a component of visual pigments in the vertebrate eye. retrotransposon  ​ ​A type of transposable element that moves via an RNA intermediate. retrovirus  ​ ​An RNA virus that utilizes reverse transcription to produce viral DNA that can be integrated into a chromosome of the host cell. reverse transcriptase  ​ ​A viral enzyme that catalyzes the synthesis of viral DNA starting with viral RNA as a template. rhizobia  ​ ​A general term for nitrogen-fixing bacteria associated with plant roots. rhodopsin  ​ ​The visual pigment in the rods of the vertebrate eye. ribonucleic acid (RNA)  ​ ​One of two classes of nucleic acids; the other is deoxyribonucleic acid (DNA). RNA consists of a single strand of nucleotides. ribose  ​ ​A five-carbon sugar found in RNA. ribosomal RNA (rRNA)  ​ ​An RNA that forms part of ribosomes, which provide the site where translation occurs. ribosome  ​ ​A structure composed of proteins and rRNA that is the site where translation of mRNAs and synthesis of polypeptides occurs. ribozyme  ​ ​A biological catalyst that is an RNA molecule. rickets  ​ ​A condition in children characterized by bone deformations due to inadequate mineral intake or malabsorption in the small intestine. ring canal  ​ ​A structure in the central disc in the water vascular system of echinoderms. RNA interference (RNAi)  ​ ​Refers to a type of mRNA silencing; miRNA or siRNA interferes with the proper expression of an mRNA. RNA modification  ​ ​The biochemical modification of an RNA.  RNA polymerase  ​ ​The enzyme that synthesizes strands of RNA during gene transcription. RNA splicing  See splicing. RNA world  ​ ​A hypothetical period on primitive Earth when both the information needed for life and the catalytic activity of living cells were contained solely in RNA molecules. RNA  See ribonucleic acid. RNA-induced silencing complex (RISC)  ​ ​A complex consisting of miRNA or siRNA and proteins; mediates RNA interference. RNase  ​ ​An enzyme that digests RNA. rod  ​ ​Type of photoreceptor found in the vertebrate eye that is very sensitive to low-intensity light but does

not readily discriminate different colors. Rods are useful mostly at night, and they send signals to the brain that generate a black-and-white visual image. root apical meristem (RAM)  ​ ​The region of rapidly dividing cells at the tip of a plant root. root hair  ​ ​A specialized, long, thin root epidermal cell that functions to absorb water and minerals, usually from soil. root pressure  ​ ​Osmotic pressure within roots that causes water to rise for some distance through a plant stem, under conditions of high soil moisture or low transpiration. root system  ​ ​The collection of roots and root branches produced by root apical meristems. root  ​ ​A plant organ that provides anchorage in the soil and also fosters efficient uptake of water and minerals. root-shoot axis  ​ ​The general body pattern of plants in which the root grows downward and the shoot grows upward. rough endoplasmic reticulum (rough ER)  ​ ​The part of the ER whose outer surface is studded with ribosomes; this region plays a key role in the initial synthesis and sorting of proteins that are destined for the ER, Golgi apparatus, lysosomes, vacuoles, plasma membrane, or outside of the cell. r-selected species  ​ ​A species whose life history strategy shows a high rate of per capita population growth but poor competitive ability. rubisco  ​ ​The enzyme that catalyzes the first step in the Calvin cycle, in which CO2 is incorporated into an organic molecule. Ruffini corpuscle  ​ ​A specialized receptor that is located beneath the surface of the skin of mammals and responds to deep pressure and vibration. ruminants  ​ ​Animals such as sheep, goats, llamas, and cows that have complex stomachs consisting of several chambers.

S

S phase  ​ ​The DNA synthesis phase of the cell cycle. saltatory conduction  ​ ​The conduction of an action potential along an axon in which the action potential is regenerated at each node of Ranvier instead of along the entire length of the axon. sarcoma  ​ ​A tumor of connective tissue such as bone or cartilage. sarcomere  ​ ​One complete unit of the repeating pattern of thick and thin filaments within a myofibril. sarcoplasmic reticulum  ​ ​A specialized form of endoplasmic reticulum in a muscle fiber that is the source of the increase in cytosolic calcium involved in muscle contraction. satiety  ​ ​A feeling of fullness. saturated fatty acid  ​ ​A fatty acid in which all the carbons are linked by single covalent bonds. scanning electron microscopy (SEM)  ​ ​A type of microscopy that utilizes an electron beam to produce an image of the three-dimensional surface of a biological sample. Schwann cells  ​ ​The glial cells that form myelin on axons that travel outside the brain and spinal cord. science  ​ ​In biology, the observation, identification, experimental investigation, and theoretical explanation of natural phenomena. scientific method  ​ ​A series of steps to test the validity of a hypothesis. This approach often involves a comparison between control and experimental groups. scientific model  ​ ​In biology, a conceptual, mathematical, or physical depiction of a real-world phenomenon sclereid  ​ ​A star- or stone-shaped plant cell having a tough, lignified cell wall.

GLOSSARY

regulatory sequence  ​ ​In the regulation of transcription, a DNA sequence that functions as a binding site for regulatory transcription factor proteins, which influence the rate of transcription. regulatory transcription factor  ​ ​A protein that binds to DNA, usually in the vicinity of a promoter, and affects the rate of transcription of one or more nearby genes. relative abundance  ​ ​The frequency of occurrence of the species in a community. relative refractory period  ​ ​The period near the end of an action potential when voltage-gated potassium channels are still open; during this time a new action potential can be generated if a stimulus is sufficiently strong to raise the membrane potential to threshold. relative water content (RWC)  ​ ​The property often used to gauge the water content of a plant organ or entire plant; RWC integrates the water potential of all cells within an organ or plant and is thus a measure of relative turgidity. release factor  ​ ​A protein that recognizes a stop codon in the termination stage of translation and promotes the termination of translation. renal corpuscle  ​ ​A filtering component in the nephron of the mammalian kidney. renal tubule  ​ ​The major portion of the mammalian nephron, consisting of three major segments with specialized functions. repeatable  ​ ​A characteristic of an experiment that yields similar results when conducted on multiple occasions.  repetitive sequence  ​ ​DNA sequences that are present in many copies in a genome. replica plating  ​ ​A technique in which a replica of bacterial colonies is transferred from one petri plate to a new petri plate. replication fork  ​ ​The area where two DNA strands have separated and new strands are being synthesized. replication  ​ ​1. The copying of DNA strands. 2. The performing of experiments several or many times. repressible operon  ​ ​A type of operon for which a small effector molecule inhibits transcription. repressor  ​ ​A transcription factor that binds to DNA and inhibits transcription. reproduction  ​ ​The generation of offspring by sexual or asexual means. reproductive isolating mechanisms  ​ ​Mechanisms that prevent interbreeding between different species. reproductive isolation  ​ ​A criterion for identifying a species; the circumstances and mechanisms that collectively prevent a species from interbreeding with other species. reproductive success  ​ ​The likelihood that an individual will contribute fertile offspring to the next generation. resistance (R)  ​ ​The tendency of blood vessels to slow the flow of blood through their lumens. resistance gene (R gene)  ​ ​A plant gene that has evolved as part of a defense system in response to pathogen attack. resolution  ​ ​In microscopy, the ability to observe two adjacent objects as distinct from one another; a measure of the clarity of an image. resonance energy transfer  ​ ​The process by which energy (not an electron itself) can be transferred to adjacent pigment molecules during photosynthesis. resource partitioning  ​ ​The differentiation of niches, both in space and time, that enables similar species to coexist in a community. resource-based mutualism  ​ ​A mutually beneficial interaction in which both species receive a benefit in the form of resource transfer of energy and nutrients. respiration  See gas exchange. respiratory centers  ​ ​Several nuclei in the brainstem in vertebrates that initiate expansion of the lungs. respiratory chain  See electron transport chain.

G-26 GLOSSARY

GLOSSARY

sclerenchyma  ​ ​A rigid plant ground tissue composed of tough-walled fibers and sclereids. sea level  ​ ​The average level for the surface of one or more of Earth’s oceans. second messengers  ​ ​Small molecules or ions that relay signals inside the cell after an extracellular signaling molecule (a first messenger) has activated a cell surface receptor. secondary active transport  ​ ​A type of membrane transport that involves the utilization of a pre-existing gradient to drive the active transport of another solute. secondary cell wall  ​ ​A thick rigid plant cell wall that is synthesized and deposited between the plasma membrane and the primary cell wall after a plant cell matures and has stopped increasing in size. secondary consumer  ​ ​An organism that eats primary consumers; also called a carnivore. secondary endosymbiosis  ​ ​A process that occurs when a eukaryotic host cell acquires a eukaryotic endosymbiont having a primary plastid. secondary growth  ​ ​Plant growth that occurs from secondary meristems and increases the girth of woody plant stems and roots. secondary immune response  ​ ​An immediate and heightened production of additional specific antibodies against the particular antigen that previously elicited a primary immune response. secondary meristem  ​ ​A meristem in woody plants forming a ring of actively dividing cells that encircle the stem. secondary metabolite  ​ ​Molecules that are produced by secondary metabolism. secondary oocyte  ​ ​In animals, the large haploid cell that is produced when a primary oocyte completes meiosis I during oogenesis. secondary phloem  ​ ​The inner bark of a woody plant. secondary plastid  ​ ​A plastid that has originated by the endosymbiotic incorporation of a eukaryotic cell containing a primary plastid into a eukaryotic host cell. secondary production  ​ ​The measure of production of heterotrophs and decomposers. secondary spermatocytes  ​ ​In animals, the haploid cells produced when a primary spermatocyte undergoes meiosis I during spermatogenesis. secondary structure  ​ ​The bending or twisting of a region of a protein into an α helix or β sheet; one of four levels of protein structure. secondary succession  ​ ​Succession on a site that has previously supported life but has undergone a disturbance. secondary xylem  ​ ​In plants, a type of secondary vascular tissue that is also known as wood. secretin  ​ ​A hormone released by cells of the small intestine in vertebrates; stimulates release of bicarbonate ions from the pancreas into the small intestine. secretion  ​ ​1. The export of a substance from a cell. 2. In the production of urine, the process in which some solutes are actively transported into the tubules of the excretory organ; this supplements the amount of a solute that would normally be removed by filtration alone. secretory pathway  ​ ​A pathway for the movement of larger substances, such as carbohydrates and proteins, from the ER to the outside of a cell. secretory vesicle  ​ ​A membrane vesicle carrying different types of materials that fuses with the cell’s plasma membrane to release the contents extracellularly. seed coat  ​ ​A hard, tough covering that develops from the ovule’s integuments and protects a plant embryo. seed plant  ​ ​The informal name for gymnosperms and angiosperms. seed  ​ ​A reproductive structure having specialized tissues that enclose a plant embryo; produced by

gymnosperms and flowering plants, usually as the result of sexual reproduction. segmentation gene  ​ ​A gene that controls the segmentation pattern of an animal embryo. segmentation  ​ ​The organization of an animal’s body into clearly defined regions. segment-polarity gene  ​ ​A type of segmentation gene; a mutation in this gene causes portions of segments to be missing and cause adjacent regions to become mirror images of each other. selectable marker  ​ ​A gene whose presence can allow organisms (such as bacteria) to grow under a certain set of conditions. For example, an antibiotic-resistance gene is a selectable marker that allows bacteria to grow in the presence of the antibiotic. selective breeding  ​ ​Programs and procedures designed to modify traits in domesticated species. selective permeability  ​ ​The property of membranes that allows the passage of certain ions or molecules but not others. selective serotonin reuptake inhibitors (SSRIs)  ​ ​Drugs used to treat major depressive disorder that act by increasing concentrations of serotonin in the brain. self-compatibility (SC)  ​ ​The reproductive state of plants that can serve as both mother and father to their progeny. self-fertilization  ​ ​Fertilization that involves the union of a female gamete and male gamete from the same individual. self-incompatibility (SI)  ​ ​Reproductive state of a plant that prevents the germination of pollen that is genetically too similar to its pistil. self-pollination  ​ ​The process in which pollen from the anthers of a flower is transferred to the stigma of the same flower or between flowers of the same plant. self-splicing  ​ ​The phenomenon in which an rRNA or a tRNA catalyzes the removal of its own intron(s). semelparity  ​ ​A reproductive pattern in which organisms produce all of their offspring in a single reproductive event. semen  ​ ​A mixture containing fluid and sperm that is released during ejaculation. semicircular canal  ​ ​Structures of the vertebrate ear that can detect a range of motions of the head. semiconservative mechanism  ​ ​The correct model for DNA replication; double-stranded DNA is half conserved following replication, resulting in new double-stranded DNA containing one parental strand and one daughter strand. semifluid  ​ ​A property of biological membranes in which movement of membrane components occurs only in two dimensions. semilunar valve  ​ ​One-way valve into the aorta or pulmonary trunk through which blood is pumped from the left or right ventricle, respectively. seminiferous tubule  ​ ​A tightly packed tubule in the testis, where spermatogenesis takes place. sense  ​ ​A system in an animal that consists of specialized cells that respond to a specific type of chemical or physical stimulus and send signals to the central nervous system, where the signals are received and interpreted. sensor  ​ ​A structure such as a sensory receptor or a nucleus in the brain that detects a signal in a homeostatic control system. sensory neuron  ​ ​A neuron that detects or senses information from the outside world, such as light, sound, touch, and heat; sensory neurons also detect internal body conditions such as blood pressure and body temperature. sensory receptor  ​ ​In animals, a specialized cell whose function is to receive sensory inputs. sensory transduction  ​ ​The process by which incoming stimuli are converted into neural signals.

sepal  ​ ​A flower structure that is often green and is part of the outer layer of a bud. septum (plural, septa)  ​ ​A cross wall; examples include the cross walls that divide the hyphae of most fungi into many small cells and the structure that separates the old and new chambers of a nautilus. set point  ​ ​The normal value for a controlled variable, such as blood pressure, in an animal. setae  ​ ​Chitinous bristles in the integument of many invertebrates. sex chromosomes  ​ ​A distinctive pair of chromosomes that are different in males and females of some species and determine the sex of an individual. sex pili  ​ ​Hairlike structures made by bacterial F + cells that bind specifically to F – cells. sex-linked gene  ​ ​A gene that is found on one sex chromosome but not on the other. sexual dimorphism  ​ ​A pronounced difference in the morphologies of the two sexes within a species. sexual reproduction  ​ ​A process in which two haploid gametes unite in a fertilization event to produce a cell called a zygote. sexual selection  ​ ​A type of natural selection that is directed at certain traits of sexually reproducing species that make it more likely for individuals to find or choose a mate and/or engage in successful reproduction. Shannon diversity index (HS)  ​ ​A means of measuring the diversity of a community, using the formula HS = –Σpi ln pi. shared derived character  ​ ​A character that is shared by two or more species or taxa and originated in their most recent common ancestor. shared primitive character  ​ ​A character that is shared by two or more different taxa and inherited from ancestors older than their last common ancestor. shattering  ​ ​The process by which ears of wild grain crops break apart and disperse seeds. shell  ​ ​A tough, protective covering on an amniotic egg that is impermeable to water and prevents the embryo from drying out. shivering thermogenesis  ​ ​Rapid muscle contractions in an animal, without any locomotion, in order to raise body temperature. shock  ​ ​A condition in which the vertebrate circulatory system cannot provide sufficient delivery of blood containing oxygen and nutrients to the vital organs of the body, resulting in cell death and decreased function of those organs. shoot apical meristem (SAM)  ​ ​The region of rapidly dividing cells at the tip of a plant shoot. shoot system  ​ ​The collection of plant organs produced by shoot apical meristems. shoot  ​ ​The portion of a plant consisting of stems and leaves. short stature  ​ ​A condition characterized by stunted growth; formerly called pituitary dwarfism. short-day plant  ​ ​A plant that flowers only when the night length is longer than a defined period. shotgun DNA sequencing  ​ ​A strategy for sequencing an entire genome by randomly sequencing many different DNA fragments. sickle cell disease  ​ ​A disease due to a mutation in a hemoglobin gene that results in sickle-shaped red blood cells that are less able to move smoothly through capillaries and can block blood flow, resulting in pain and cell death of the surrounding tissue. sieve plate pore  ​ ​One of many perforations in a plant’s sieve plate. sieve plate  ​ ​The perforated end wall of a mature sievetube element. sieve-tube elements  ​ ​A component of the phloem tissues of flowering plants; thin-walled cells arranged end to end to form pipes.

sigma factor  ​ ​A protein that recognizes the promoter in a bacterial gene and binds RNA polymerase to the promoter. sign stimulus  ​ ​In animals, a trigger that initiates a fixed action pattern of behavior. signal recognition particle (SRP)  ​ ​A protein-RNA complex that recognizes the ER signal sequence of a polypeptide, pauses translation, and directs the ribosome to the ER to complete translation. signal transduction pathway  ​ ​A group of proteins that convert an initial signal to a different signal inside a cell. signal  ​ ​Regarding cell communication, an agent that influences the properties of cells. silencer  ​ ​A regulatory element in eukaryotes that prevents transcription of a given gene when bound by a repressor protein. silent mutation  ​ ​A gene mutation that does not alter the amino acid sequence of the polypeptide, even though the base sequence has changed. simple diffusion  ​  When a substance moves across a membrane from a region of high concentration to a region of lower concentration by passing directly through the phospholipid bilayer. simple Mendelian inheritance  ​ ​The inheritance pattern of traits affected by a single gene that is found in two variants, one of which is completely dominant over the other. simple translocation  ​ ​A type of mutation in which a single piece of chromosome is attached to another chromosome. single-factor cross  ​ ​A cross in which an experimenter follows the variants of only one character. single-lens eye  ​ ​Type of eye found in vertebrates and some invertebrates that has only one lens, as opposed to compound eyes with many lenses. single-nucleotide polymorphism (SNP)  ​ ​A type of genetic variation in a population in which a particular gene sequence varies at a single nucleotide. single-strand binding protein  ​ ​A protein that binds to both of the single strands of parental DNA and prevents them from re-forming a double helix during DNA replication. sinoatrial (SA) node  ​ ​A collection of modified cardiac cells in the right atrium of most vertebrates that spontaneously and rhythmically generates action potentials that spread across the entire atria; also known as the pacemaker of the heart. sister chromatids  ​ ​The two duplicated chromatids that are still joined to each other after DNA replication. skeletal muscle  ​ ​A type of muscle tissue that is attached by tendons to bones in vertebrates and to the exoskeleton of invertebrates. skeleton  ​ ​A structure that serves one or more functions related to support, protection, and locomotion. sliding filament mechanism  ​ ​The process by which a muscle fiber shortens during muscle contraction. SLOSS debate  ​ ​In conservation biology, the debate over whether it is preferable to protect one single, large preserve or several smaller ones. slow fiber  ​ ​A skeletal muscle fiber containing myosin with low ATPase activity. slow-oxidative fiber  ​ ​A skeletal muscle fiber that has a low rate of myosin ATPase activity but has the ability to make large amounts of ATP; used for prolonged, regular movement. small effector molecule  ​ ​A molecule that affects gene transcription by binding to a regulatory transcription factor, causing a conformational change in that protein. small intestine  ​ ​In vertebrates, the part of the alimentary canal that leads from the stomach to the large intestine

(or to the anus or cloaca in animals that lack a large intestine) and that carries out nearly all digestion of food and absorption of food nutrients and water. small-interfering RNAs (siRNAs)  ​ ​RNA molecules that are usually from outside sources and are processed to a small size (22 nucleotides). They are usually a perfect match to pre-existing mRNAs and cause their degradation. smooth endoplasmic reticulum (smooth ER)  ​ ​The part of the ER whose outer surface is not studded with ribosomes. This region is continuous with the rough ER and functions in diverse metabolic processes such as detoxification, carbohydrate metabolism, accumulation of calcium ions (Ca2+), and synthesis and modification of lipids. smooth muscle  ​ ​A type of muscle tissue that surrounds and forms part of the lining of hollow organs and tubes in vertebrate bodies; it is not under conscious control. solute potential  ​ ​The component of water potential due to the presence of solute molecules. solute  ​ ​A substance dissolved in a liquid. solution  ​ ​A liquid that contains one or more dissolved solutes. solvent  ​ ​The liquid in which a solute is dissolved. somatic cell  ​ ​The type of cell that constitutes all cells of an animal or plant body except those that give rise to gametes. somatic embryogenesis  ​ ​The production of plant embryos from body (somatic) cells. somatic nervous system  ​ ​The division of the peripheral nervous system that senses external environmental conditions and controls skeletal muscles. sorting signal  ​ ​A short amino acid sequence in a protein that directs the protein to its correct location in a cell; also known as a traffic signal. source pool  ​ ​The pool of species on the mainland that is available to colonize an island. spatial summation  ​ ​Occurs when two or more postsynaptic potentials are generated at one time along different regions of the dendrites and their depolarizations and hyperpolarizations sum together to initiate an action potential. speciation  ​ ​The formation of new species. species concept  ​ ​A way of defining the concept of a species and/or of providing an approach to distinguish one species from another species diversity  ​ ​A measure of biological diversity that incorporates both the number of species in an area and the relative distribution of individuals among species. species interactions  ​ ​The various ways in which a species can interact with other species, such as predation, competition, parasitism, mutualism, and commensalism; part of the study of population ecology. species richness  ​ ​The numbers of species in a community. species  ​ ​In taxonomy, a subdivision of a genus. Each species is a group of related organisms that share a distinctive set of attributes in nature and (for sexually reproducing species) are capable of interbreeding. species-area effect  ​ ​The relationship between the amount of available area and the number of species present. species-area hypothesis  ​ ​The proposal that larger areas contain more species than smaller ones because they can support larger populations and a greater range of habitats. species-productivity hypothesis  ​ ​The proposal that greater production by plants results in greater overall species richness. species-time hypothesis  ​ ​The proposal that temperate regions have less species-rich communities than tropical ones because they are younger.

specific heat  ​ ​The amount of energy required to raise the temperature of 1 gram of a substance by 1°C. sperm  ​ ​Refers to a male gamete that is generally smaller than the female gamete (egg). spermatids  ​ ​In animals, haploid cells produced when the secondary spermatocytes undergo meiosis II; these cells eventually differentiate into sperm cells. spermatogenesis  ​ ​Gametogenesis in a male animal, resulting in the production of sperm. spermatogonium (plural, spermatogonia)  ​ ​In animals, a diploid germ cell that gives rise to the male gamete, the sperm. spermatophytes  ​ ​All of the living and extinct phyla of seed-producing plants. spicules  ​ ​Needle-like structures that are made of protein, calcium carbonate, or silica and form lattice-like skeletons in sponges, possibly helping to reduce predation. spinal cord  ​ ​In chordates, the structure that connects the brain to all areas of the body and together with the brain constitutes the central nervous system. spinal nerve  ​ ​A nerve that connects the peripheral nervous system and the spinal cord. spiracle  ​ ​One of several pairs of pores on the body surface of insects through which air enters and exits the body. spiral cleavage  ​ ​A mechanism of animal development in which the planes of cell cleavage are oblique to the axis of the embryo. spirilli  ​ ​Rigid, spiral-shaped prokaryotic cells. spirochaetes  ​ ​Flexible, spiral-shaped prokaryotic cells. spliceosome  ​ ​A complex of several subunits known as snRNPs that removes introns from eukaryotic premRNA. splicing  ​ ​The process in which introns are removed from an RNA molecule, such as a pre-mRNA, and the remaining exons are connected to each other.  spongin  ​ ​A tough protein that lends skeletal support to a sponge. spongocoel  ​ ​A central cavity in the body of a sponge. spongy parenchyma  ​ ​Photosynthetic ground tissue of the plant leaf mesophyll that contains rounded cells separated by abundant air spaces. spontaneous mutation  ​ ​A mutation resulting from some abnormality in a biological process. sporangia (singular, sporangium)  ​ ​Structures that produce and disperse the spores of plants, fungi, or protists. spore  ​ ​A haploid, typically single-celled reproductive structure of fungi and plants. A spore is able to grow into a new fungal mycelium or plant gametophyte in a suitable location. sporophyte  ​ ​The diploid generation of plants or multicellular protists that have a sporic life cycle; this generation produces haploid spores by the process of meiosis. sporopollenin  ​ ​A tough material found in the walls of plant spores that helps to prevent cellular damage during transport in air. spring overturn  ​ ​The mixing of lake water as ice melts and storms churn up water from the bottom. stabilizing selection  ​ ​A pattern of natural selection that favors the survival of individuals with intermediate phenotypes. stamen  ​ ​A flower organ that produces the male gametophytes, pollen. standing crop  ​ ​The total biomass in an ecosystem at any one point in time. starch  ​ ​A polysaccharide composed of repeating glucose units that is produced by the cells of plants and some algal protists. Starling forces  ​ ​The forces that influence the movement of water into and out of capillaries in animals; they are the osmotic imbalance between the plasma and

GLOSSARY

GLOSSARY G-27

G-28 GLOSSARY

GLOSSARY

the interstitial fluid and the hydrostatic pressure of the blood entering and exiting the capillary. start codon  ​ ​A three-base sequence—usually AUG— that specifies the first amino acid in a polypeptide. statocyst  ​ ​An organ of equilibrium found in many invertebrate species. statolith  ​ ​1. Tiny granules of sand or other dense objects located in a statocyst that aid equilibrium in many invertebrates. 2. In plants, a starch-heavy plastid that allows both roots and shoots to detect gravity. stem cell  ​ ​A cell that divides in such a way that one daughter cell can remain a stem cell and the other can differentiate into a specialized cell type. Stem cells supply the cells that constitute the bodies of all animals and plants. stem  ​ ​A plant organ that contains vascular tissue and produces buds, leaves, branches, and reproductive structures. stereocilia  ​ ​Deformable projections from epithelial cells called hair cells that are bent by movements of fluid or other stimuli. stereoisomers  ​ ​Isomers with identical bonding relationships, but different spatial positioning of their atoms. sternum  ​ ​The breastbone of a vertebrate. steroid  ​ ​A lipid containing four interconnected rings of carbon atoms; functions as a hormone in animals and plants. stigma  ​ ​In a flower, the topmost portion of the pistil, which receives and recognizes pollen of the appropriate species or genotype. stomach  ​ ​A saclike organ in some animals that most likely evolved as a means of storing food; it partially digests some of the macromolecules in food and regulates the rate at which its contents empty into the small intestine. stomata (singular, stoma or stomate)  ​ ​Pores on plant surfaces that can be closed to retain water or open to allow the entry of CO2 (needed for photosynthesis) and the exit of O2 and water vapor. stop codon  ​ ​One of three three-base sequences—UAA, UAG, and UGA—that signals the end of translation; also called a termination codon or codon. strain  ​ ​Within a given species, a lineage that has genetic differences compared to another lineage. strand  ​ ​A structure of DNA (or RNA) formed by the covalent linkage of nucleotides in a linear manner. strepsirrhini  ​ ​Smaller species of primates, including bush babies, lemurs, and pottos. streptophyte algae  ​ ​The green algae that are closely related to land plants (embryophytes). streptophyte  ​ ​Land pants (embryophytes) and their close relatives among the green algae. stretch receptor  ​ ​A type of mechanoreceptor found widely in an animal’s organs and muscle tissues that can be distended. stroke volume (SV)  ​ ​The amount of blood ejected with each beat, or stroke, of the heart. stroma  ​ ​The fluid-filled region of the chloroplast between the thylakoid membrane and the inner membrane. stromatolite  ​ ​A layered calcium carbonate structure generally produced by cyanobacteria living in an aquatic environment. strong acid  ​ ​An acid that completely dissociates into ions when added to water. structural formula  ​ ​A type of chemical formula for molecules in which each covalent bond is represented by a line indicating a pair of shared electrons. structural isomers  ​ ​Isomers that contain the same atoms but in different bonding relationships. style  ​ ​In a flower, the elongate portion of the pistil through which the pollen tube grows. stylet  ​ ​A sharp, piercing organ in the mouth of nematodes and some insects.

submetacentric  ​ ​Refers to a chromosome in which the centromere is off center. subsidence zones  ​ ​Areas of high pressure that are the sites of the world’s tropical deserts because the subsiding air is relatively dry, having released all of its moisture over the equator. subspecies  ​ ​A subdivision of a species; this designation is used when two or more geographically restricted groups of the same species differ, but not enough to warrant their placement into separate species. substrate  ​ ​1. The reactant molecules that bind to an enzyme at the active site and participate in a chemical reaction. 2. The organic compounds such as soil or rotting wood that fungi use as food. substrate-level phosphorylation  ​ ​A method of synthesizing ATP that occurs when an enzyme directly transfers a phosphate from an organic molecule to ADP. succession  ​ ​The gradual and continuous change in species composition of a community over time. sugar sink  ​ ​The plant tissues or organs in which more sugar is consumed than is produced by photosynthesis. sugar source  ​ ​The plant tissues or organs that produce more sugar than they consume in respiration. supergroup  ​ ​One of the seven subdivisions of the domain Eukarya. surface area-to-volume (SA/V) ratio  ​ ​The ratio between a structure’s surface area and the volume in which the structure is contained. surface tension  ​ ​A measure of how difficult it is to break the interface between a liquid and air. surfactant  ​ ​A mixture of proteins and amphipathic lipids produced in type II alveolar cells that prevents the collapse of the alveoli by reducing surface tension in the lungs. survivorship curve  ​ ​A graphical plot of the numbers of surviving individuals for each age class in a population. suspensor  ​ ​A short chain of cells at the base of an early angiosperm embryo that provides anchorage and nutrients. swim bladder  ​ ​A gas-filled, balloon-like structure that helps a fish remain buoyant in the water even when it is completely stationary. symbiosis  ​ ​An intimate association between two or more organisms of different species. sympathetic division  ​ ​The division of the autonomic nervous system that is responsible for rapidly activating body systems to provide immediate energy in response to danger or stress. sympatric speciation  ​ ​A form of speciation that occurs when members of a species that initially occupy the same habitat within the same range diverge into two or more different species even though there are no physical barriers to interbreeding. sympatric  ​ ​The term used to describe species occurring in the same geographic area. symplast  ​ ​All of a plant’s protoplasts (the cell contents without the cell walls) and plasmodesmata. symplastic transport  ​ ​The movement of a substance from the cytosol of one cell to the cytosol of an adjacent cell via membrane-lined channels called plasmodesmata. symplesiomorphy  See shared primitive character. symporter  ​ ​A type of transporter that binds two or more ions or molecules and transports them in the same direction across a membrane; also called a cotransporter. synapomorphy  See shared derived character. synapse  ​ ​A junction where an axon terminal meets another neuron, a muscle cell, or a gland cell and through which an electrical or chemical signal passes. synapsis  ​ ​The process of forming a bivalent.

synaptic cleft  ​ ​The extracellular space between a neuron and a receiving cell. synaptic plasticity  ​ ​A change in strength of the connection between two neurons, which occurs as a result of learning. synergids  ​ ​In the female gametophyte of a flowering plant, the two cells adjacent to the egg cell that help to import nutrients from maternal sporophyte tissues. synthetic microbiomes  ​ ​Microbiomes generated by mixing cultures of beneficial microbial species. systematics  ​ ​The study of biological diversity and evolutionary relationships among species, both extant and extinct. systemic acquired resistance (SAR)  ​ ​A whole-plant defensive response to a pathogen attack. systemic circulation  ​ ​The circuit of a double circulation in which blood is pumped from the left side of an animal’s heart to the body to drop off O2 and nutrients and pick up CO2 and wastes. The blood then returns to the right side of the heart. systems biology  ​ ​A field of study in which researchers investigate living organisms in terms of their underlying networks—groups of structural and functional connections—rather than their individual molecular components. systole  ​ ​The second phase of the cardiac cycle, in which the ventricles contract and eject the blood through the open semilunar valves.

T

T cells  ​ ​A type of lymphocyte that directly kills infected, mutated, or transplanted cells. tagmata  ​ ​Functional units composed of fused body segments. taproot system  ​ ​The root system of eudicots, consisting of one main root with many branch roots. taste buds  ​ ​Structures located in the mouth and tongue of vertebrates that contain the sensory cells, supporting cells, and associated neuronal endings that contribute to taste sensation. TATA box  ​ ​One of three features found in  promoters of many protein-encoding genes in eukaryotes; the others are the transcriptional start site and regulatory elements. taxis  ​ ​A directed movement in response to a stimulus, either toward or away from the stimulus. taxon  ​ ​A group of species that are evolutionarily related to each other. In taxonomy, each species is placed into several taxons that form a hierarchy from large (domain) to small (genus). taxonomy  ​ ​The field of biology that is concerned with the theory, practice, and rules of classifying living and extinct species and also viruses. telocentric  ​ ​Refers to a chromosome in which the centromere is at the end. telomerase  ​ ​An enzyme that catalyzes the replication of the telomere. telomere  ​ ​A region at the ends of eukaryotic chromosomes where a specialized form of DNA replication occurs. telophase  ​ ​The phase of mitosis during which the chromosomes decondense and the nuclear membrane re-forms. temperate phage  ​ ​A bacteriophage that can follow either a lysogenic or a lytic cycle. template strand  ​ ​The DNA strand that is used as a template for RNA synthesis or DNA replication. temporal lobe  ​ ​One of four lobes of the cerebral cortex of human brain; necessary for language, hearing, and some types of memory. temporal summation  ​ ​Occurs when two or more postsynaptic potentials arrive at the same location in a

dendrite in quick succession and their depolarizations and hyperpolarizations sum together to initiate an action potential. tepal  ​ ​A flower perianth part that cannot be distinguished by appearance as a petal or a sepal. termination codon  See stop codon. termination  ​ ​The final stage of transcription, in which the RNA dissociates from the DNA, or of translation, in which the polypeptide is released from the ribosome. terminator  ​ ​A sequence of DNA within a gene that specifies the end of transcription. territory  ​ ​A fixed area in which an individual or group excludes other members of its own species, and sometimes other species, by aggressive behavior or territory marking. tertiary consumer  ​ ​An organism that feeds on secondary consumers; also called a secondary carnivore. tertiary endosymbiosis  ​ ​The acquisition by eukaryotic protist host cells of plastids from cells that possess secondary plastids. tertiary plastid  ​ ​A plastid acquired by the incorporation into a host cell of an endosymbiont having a secondary plastid. tertiary structure  ​ ​The three-dimensional shape of a single polypeptide; one of four levels of protein structure. testable  ​ ​Refers to a hypothesis that can be accepted or rejected based on experimentation. testcross  ​ ​(1) A cross to determine if an individual with a dominant phenotype is a homozygote or a heterozygote. (2) Also, a cross to determine if two different genes are linked. testis (plural, testes)  ​ ​In animals, the male gonad, where sperm are produced. testosterone  ​ ​The primary androgen in many vertebrates, including humans. tetraploid  ​ ​Refers to an organism or cell that has four sets of chromosomes. tetrapod  ​ ​A vertebrate animal having four legs or leglike appendages. thalamus  ​ ​A region of the vertebrate forebrain that plays a major role in relaying sensory information to appropriate parts of the cerebrum and, in turn, sending outputs from the cerebrum to other parts of the brain. theory  ​ ​In biology, a broad explanation of some aspect of the natural world that is substantiated by a large body of evidence. Biological theories incorporate observations, hypothesis testing, and the laws of other disciplines such as chemistry and physics. A theory makes valid predictions. thermocline  ​ ​The thin transitional zone in a lake that separates the epilimnion from the hypolimnion thermodynamics  ​ ​The study of energy interconversions. thermoreceptor  ​ ​A sensory receptor in animals that responds to cold and heat. theropods  ​ ​A group of bipedal saurischian dinosaurs. thick filament  ​ ​A section of the repeating pattern in a myofibril composed almost entirely of the motor protein myosin. thigmotropism  ​ ​Touch responses in plants. thin filament  ​ ​A section of the repeating pattern in a myofibril that contains the cytoskeletal protein actin, as well as two other proteins—troponin and tropomyosin—that play important roles in regulating contraction. thoracic breathing  ​ ​Breathing in which coordinated contractions of muscles expand the rib cage, creating a negative pressure to suck air in and then forcing it out later; used by amniotes. thoraco-abdominal pump  ​ ​In mammals, the mechanical effect of breathing movements on the return of blood from veins in the abdomen to the thorax where the

heart is located; increased depth and rate of breathing results in pressure differences between the two body compartments that favors flow of blood into the chest; also called the respiratory pump. threatened species  ​ ​Those species that are likely to become endangered in the foreseeable future. threshold concentration  ​ ​The concentration above which a morphogen exerts its effects but below which it is ineffective. threshold potential  ​ ​The membrane potential, typically around –55 to –50 mV, which is sufficient to trigger an action potential in an electrically excitable cell such as a neuron. thylakoid lumen  ​ ​The fluid-filled compartment within a thylakoid. thylakoid membrane  ​ ​A membrane within the chloroplast that forms many flattened, fluidfilled tubules that enclose a single, convoluted compartment. It contains chlorophyll and is the site where the light-dependent reactions of photosynthesis occurs. thylakoid  ​ ​A flattened, fluid-filled tubule found in cyanobacterial cells and the chloroplasts of photosynthetic protists and plants; the location of the light reactions of photosynthesis. thymine (T)  ​ ​A pyrimidine base found in DNA. thymine dimer  ​ ​A site in DNA where two adjacent thymine bases become covalently crosslinked to each other; may cause a mutation when the DNA strand is replicated. thyroxine (T4)  ​ ​A weakly active thyroid hormone that contains iodine and helps regulate metabolic rate; it is converted by cells into the more active triiodothyronine (T3). tidal ventilation  ​ ​A type of breathing in mammals in which the lungs are inflated with air and then the chest muscles and diaphragm relax and recoil back to their original positions as an animal exhales. During exhalation, air leaves via the same route that it entered during inhalation, and no new oxygen is delivered to the airways at that time. tight junction  ​ ​A type of junction between animal cells that forms a tight seal between adjacent cells and thereby prevents material from leaking between the cells. tissue  ​ ​A part of an animal or plant consisting of a group of cells having a similar structure and function, for example, muscle tissue. tolerance  ​ ​A mechanism for succession in which any species can start the succession, but the eventual climax community is reached in a somewhat orderly fashion; early species neither facilitate nor inhibit subsequent colonists. Toll-like receptors (TLRs)  ​ ​Receptor proteins that recognize nonspecific antigens in microbes; a key part of the innate immune response. topsoil  ​ ​The uppermost layer of a soil. torus (plural, tori)  ​ ​The nonporous, flexible central region of a conifer pit that functions like a valve. total fertility rate  ​ ​The average number of live births a female has during her lifetime. total peripheral resistance (TPR)  ​ ​The sum of all the resistance in all the arterial vessels of the systemic circulation. totipotent  ​ ​Refers to the ability of a fertilized egg to produce all of the cell types in the adult organism or the ability of unspecialized plant cells to regenerate an adult plant. toxins  ​ ​Compounds that have adverse physiological effects in living organisms; often produced by various protist and plant species. trace element  ​ ​An element that is essential for normal growth and function of living organisms but is required in extremely small quantities.

trachea  ​ ​1. A sturdy tube arising from the spiracles of an insect’s body; involved in respiration. 2. The name of the tube leading to the lungs of air-breathing vertebrates. tracheal system  ​ ​The respiratory system of insects, consisting of a series of finely branched air tubes called tracheae; air enters and exits the tracheae through spiracles, which are pores on the body surface. tracheary elements  ​ ​Water-conducting cells in plants that, when mature, are always dead and empty of cytosol; include tracheids and vessel elements. tracheid  ​ ​A type of dead, lignified plant cell in xylem that conducts water, along with dissolved minerals and hormones; also provides structural support. tracheophytes  ​ ​A term used to describe vascular plants. tract  ​ ​A parallel bundle of myelinated axons in the central nervous system. traffic signal  See sorting signal. trait  ​ ​An identifiable characteristic; usually refers to a variant. transcription factor  ​ ​A protein that influences the ability of RNA polymerase to transcribe genes. transcription  ​ ​The process that produces an RNA copy of a gene. transcriptional start site  ​ ​The site in a eukaryotic promoter where transcription begins. transcriptome  ​ ​A collection of all the mRNA sequences produced by a single organism under defined conditions. transduction  ​ ​A type of gene transfer between bacteria in which a virus infects a bacterial cell and then a newly made virus subsequently transfers some of that cell’s DNA to another bacterium. trans-effect  ​ ​In both prokaryotes and eukaryotes, a form of genetic regulation that can occur even though two DNA segments are not physically adjacent. The action of the lac repressor on the lac operon is a trans-effect. transepithelial transport  ​ ​The process of moving molecules across an epithelium, such as across the intestinal cells of animals. transfer RNA (tRNA)  ​ ​An RNA that carries amino acids and is used to translate mRNA into polypeptides. transformation  ​ ​A type of gene transfer between bacteria in which a segment of DNA from the environment is taken up by a competent cell and incorporated into the bacterial chromosome. transition state  ​ ​In a chemical reaction, a state in which the original bonds have stretched to their limit; once this state is reached, the reaction can proceed to the formation of products. transitional form  ​ ​An organism that provides a link between earlier and later forms in evolution. translation  ​ ​The process of synthesizing a specific polypeptide on a ribosome. translocation  ​ ​1. A type of mutation in which one segment of a chromosome becomes attached to a different chromosome. 2. A process in plants in which phloem transports substances from a source to a sink. transmembrane gradient  ​ ​A situation in which the concentration of a solute is higher on one side of a membrane than on the other. transmembrane protein  ​ ​A protein that has one or more regions that are physically embedded in the hydrophobic region of a membrane’s phospholipid bilayer. transmembrane transport  ​ ​The export of material from one cell into the intercellular space and then into an adjacent cell. transmission electron microscopy (TEM)  ​ ​A type of microscopy in which a beam of electrons is transmitted through a biological sample to form an image on a photographic plate or screen.

GLOSSARY

GLOSSARY G-29

G-30 GLOSSARY

GLOSSARY

transpiration  ​ ​The process by which water evaporates from the aerial parts of plants, usually via the stomata of leaves. transport protein  ​ ​A transmembrane protein that provides a passageway for the movement of ions and hydrophilic molecules across the phospholipid bilayer. transporter  ​ ​A transmembrane protein that binds a solute and undergoes a conformational change to allow the movement of the solute across a membrane; also called a carrier. transposable element (TE)  ​ ​A segment of DNA that can move from one site to another within a genome. transposase  ​ ​An enzyme that facilitates transposition. transposition  ​ ​The process in which a short segment of DNA, a transposable element, moves to a new site in a genome. transverse tubules (T-tubules)  ​ ​Invaginations of the plasma membrane of skeletal muscle fibers that open to the extracellular fluid and conduct action potentials from the outer surface of the fibers to the myofibrils. trichome  ​ ​A projection, often hairlike, from the epidermal tissue of a plant that offers protection from excessive light, ultraviolet radiation, extreme air temperature, or attack by herbivores. triglyceride  ​ ​A molecule composed of three fatty acids linked by ester bonds to a molecule of glycerol; also known as a triacylglycerol. triiodothyronine (T3)  ​ ​A thyroid hormone that contains iodine and helps regulate metabolic rate. triplet  ​ ​A group of three bases that functions as a codon. triploblastic  ​ ​Having three distinct germ layers: endoderm, ectoderm, and mesoderm. triploid  ​ ​Refers to an organism or cell that has three sets of chromosomes. trochophore larva  ​ ​A distinct larval stage of many invertebrate phyla. trophectoderm  ​ ​The outer layer of cells in a developing mammalian blastocyst; continuous with the ectoderm layer. trophic level  ​ ​Each feeding level in a food chain. trophic-level transfer efficiency  ​ ​The amount of energy at a trophic level that is acquired by the trophic level above and incorporated into biomass. tropism  ​ ​In plants, a growth response that is dependent on a stimulus that occurs in a particular direction. tropomyosin  ​ ​A rod-shaped protein that plays an important role in regulating muscle contraction. troponin  ​ ​A small globular-shaped protein that plays an important role in regulating muscle contraction through its ability to bind Ca2+. trp operon  ​ ​An operon of E. coli that encodes enzymes required to make the amino acid tryptophan, a building block of cellular proteins. true-breeding line  ​ ​A strain that continues to exhibit the same trait after several generations of self-fertilization or inbreeding. trypsin  ​ ​A protease involved in the breakdown of proteins in the small intestine. tubal ligation  ​ ​A means of contraception that involves the cutting and sealing of a woman’s oviducts, thereby preventing movement of a fertilized egg into the uterus. tube cell  ​ ​In a seed plant, one of the cells resulting from the division of a microspore; produces the pollen tube to deliver sperm to the female gametophyte. tube feet  ​ ​Echinoderm structures that function in movement, gas exchange, feeding, and excretion. tumor  ​ ​An abnormal overgrowth of cells. tumor-suppressor gene  ​ ​A gene that when normal (that is, not mutant) encodes a protein that prevents cancer; however, when a mutation eliminates its function, cancer may occur. tunic  ​ ​A nonliving structure that encloses a tunicate, made of protein and a cellulose-like material called tunicin.

turgid  ​ ​Refers to a plant cell whose cytosol is so full of water that the plasma membrane presses right up against the cell wall; as a result, a turgid cell is firm or swollen. turgor pressure  See osmotic pressure. two-factor cross  ​ ​A cross in which an experimenter simultaneously follows the inheritance of two different characters. type 1 diabetes mellitus (T1DM)  ​ ​A disease in which the pancreas does not produce sufficient insulin; as a result, extracellular glucose cannot cross plasma membranes, and glucose accumulates to very high concentrations in the blood. type 2 diabetes mellitus (T2DM)  ​ ​A disease in which the pancreas produces sufficient insulin, but the cells of the body lose much of their ability to respond to insulin.

U

ubiquitin  ​ ​A small protein in eukaryotic cells that is covalently attached to an unwanted protein, which directs the protein to a proteasome for degradation. ulcer  ​ ​An erosion of the wall of the alimentary canal; typically occurs in the lower esophagus, stomach, or duodenum. ultimate cause  ​ ​The reason a particular behavior evolved, in terms of its effect on reproductive success. umbrella species  ​ ​A species whose habitat requirements are so large that protecting it would protect many other species existing in the same habitat. uniform  ​ ​A pattern of dispersion within a population in which individuals maintain a certain minimum distance between themselves to produce an evenly spaced distribution. uniporter  ​ ​A type of transporter that binds a single ion or molecule and transports it across a membrane. unipotent  ​ ​Refers to a stem cell found in an adult organism that can produce daughter cells that differentiate into only one cell type. unsaturated fatty acid  ​ ​A fatty acid that contains one or more C=C double bonds. unsaturated  ​ ​The property of certain lipids that contain one or more C=C double bonds. upwelling  ​ ​In the ocean, a process that carries mineral nutrients from the bottom waters to the surface. uracil (U)  ​ ​A pyrimidine base found in RNA. urea  ​ ​A nitrogenous waste commonly produced in many terrestrial species, including mammals. uremia  ​ ​A condition characterized by the retention of urea and other waste products in the blood; typically results from kidney disease. uric acid  ​ ​A nitrogenous waste produced by birds, insects, and most reptiles. urine  ​ ​The part of the filtrate formed in the kidney that remains after all reabsorption of solutes and water is complete. uterine cycle  See menstrual cycle. uterus  ​ ​A small, pear-shaped organ capable of enlarging and specialized for carrying a developing fetus in female mammals.

V

vaccination  ​ ​The injection into the body of small quantities of weakened or dead pathogens, resulting in the development of immunity to those pathogens without causing disease. vacuole  ​ ​Specialized compartments found in eukaryotic cells that function in storage, the regulation of cell volume, and degradation. vagina  ​ ​The birth canal of female mammals; also functions to receive sperm during copulation.

vaginal diaphragm  ​ ​A barrier method of preventing fertilization in which a diaphragm is placed in the upper part of the vagina just prior to intercourse; blocks movement of sperm to the cervix. valence electron  ​ ​An electron in the outermost shell of an atom that is available to share with other atoms. Such electrons allow atoms to form chemical bonds with each other. van der Waals dispersion forces  ​ ​Attractive forces between molecules in close proximity to each other, caused by the variations in the distribution of electron density around individual atoms. variable region  ​ ​A unique domain within an immunoglobulin that serves as the antigen-binding site. vasa recta capillaries  ​ ​Capillaries surrounding the renal tubules in the medulla of the kidney. vascular bundle  ​ ​A cluster of primary plant vascular tissues that appears round or oval in cross section. vascular cambium  ​ ​A secondary meristematic tissue of seed plants that produces both wood and inner bark. vascular plants  ​ ​A broad category of plants distinguished by internal water and nutrientconducting (vascular) tissues that also provide structural support vascular tissue  ​ ​A complex plant tissue composed of interconnected cells that form conducting vessels for water, minerals, and organic compounds. vasectomy  ​ ​A surgical procedure in men that severs the vas deferens, thereby preventing the release of sperm at ejaculation. vasoconstriction  ​ ​A decrease in blood vessel radius; an important mechanism for directing blood flow away from specific regions of the body. vasodilation  ​ ​An increase in blood vessel radius; an important mechanism for directing blood flow to specific regions of the body. vasotocin  ​ ​A peptide hormone that is responsible for regulating salt and water balance in the blood of nonmammalian vertebrates. vector  ​ ​A type of DNA that acts as a carrier of a DNA segment that is to be cloned. vegetal pole  ​ ​In triploblast organisms, the pole of the egg where the yolk is most concentrated. vegetative growth  ​ ​The production of new nonreproductive tissues by the shoot apical meristem and root apical meristem during seedling development and growth of mature plants. vegetative reproduction  ​ ​A form of asexual reproduction that involves nonreproductive parts of plants. vein  ​ ​1. In animals, a blood vessel that returns blood to the heart. 2. In plants, a bundle of vascular tissue in a leaf. veliger  ​ ​In mollusks, a free-swimming larva that has a rudimentary foot, shell, and mantle. venation  ​ ​Leaf vein patterns. ventilation  ​ ​The process of bringing oxygenated water or air into contact with a respiratory organ such as gills or lungs. ventral  ​ ​Refers to the lower side of an animal. ventricle  ​ ​In the heart, a chamber that pumps blood out of the heart. vernalization  ​ ​The process in which certain species of plants require an exposure to cold temperatures in order to flower. vertebrae  ​ ​Interlocking bony or cartilaginous structures forming a column that provides support and also protects the nerve cord, which lies within the column’s tubelike structure. vertebrate  ​ ​An animal with a backbone. vertical evolution  ​ ​A type of evolution in which genetic changes occur in a series of related species that form a lineage; species evolve from pre-existing species by the accumulation of mutations.

GLOSSARY G-31 volt  ​ ​A unit of measurement of potential difference in charge (electrical force), such as the difference between the interior and exterior of a cell. voltage-gated ion channels  ​ ​Ion channels that open and close in response to changes in voltage across a cell membrane.

W

water potential  ​ ​The potential energy of water. water vascular system  ​ ​A network of canals in which water pressure generated by the contraction of muscles enables extension and contraction of the tube feet, allowing echinoderms to move slowly. water  ​ ​The liquid form of H2O. wavelength  ​ ​The distance from one peak to the next in a sound wave or light wave. weak acid  ​ ​An acid that only partially dissociates into ions when added to water. weathering  ​ ​The physical and chemical breakdown of rock. white matter  ​ ​Brain tissue that consists of myelinated axons that are bundled together in large numbers to form tracts. whole metagenomic sequencing (WMS)  ​ ​Base sequencing of all of the DNA present in a sample. whorls  ​ ​In a flower, concentric rings of sepals and petals (or tepals), stamens, and carpels. wild-type allele  ​ ​A prevalent allele in a population. wood  ​ ​A secondary plant tissue composed of numerous pipelike arrays of empty, water-conducting cells whose walls are strengthened by an exceptionally tough polymer known as lignin. woody plant  ​ ​A type of plant that produces both primary and secondary vascular tissues.

X

X inactivation center (Xic)  ​ ​A short region on the X chromosome known to play a critical role in X inactivation. X-chromosome inactivation (XCI)  ​ ​A process that causes an X chromosome to become highly compacted and silences the genes that it carries.

X-linked gene  ​ ​A gene found on the X chromosome but not on the Y. xylem  ​ ​A specialized conducting tissue in plants that transports water, minerals, and some organic compounds.

Y

yeast  ​ ​A unicellular fungus that may reproduce by budding. yield  ​ ​The number of individuals harvested in a given unit of time. yolk sac  ​ ​One of the four extraembryonic membranes in the amniotic egg. The yolk sac encloses a stockpile of nutrients, in the form of yolk, for the developing embryo.

Z

Z scheme  ​ ​A model depicting the series of energy changes of an electron during the light reactions of photosynthesis. The electron absorbs light energy twice, resulting in an energy curve with a zigzag shape. zero population growth  ​ ​The situation in which no changes in population size occur. zombie parasite  ​ ​A parasite that infects its host and is then able to control that host’s behavior.  zona pellucida  ​ ​The glycoprotein covering that surrounds a mature oocyte. zone of elongation  ​ ​The area above the root apical meristem of a plant where cells extend by water uptake, thereby dramatically increasing root length. zone of maturation  ​ ​The area above the zone of elongation in a plant root where most root cell differentiation and tissue specialization occur. zooplankton  ​ ​Aquatic organisms drifting in the open ocean or fresh water; includes minute animals consisting of some worms, copepods, tiny jellyfish, and the small larvae of invertebrates and fishes. zygospore  ​ ​A dark-pigmented, thick-walled, multinucleate spore that matures within the zygosporangium of zygomycete fungi during sexual reproduction. zygote  ​ ​A diploid cell formed by the fusion of two haploid gametes.

GLOSSARY

vessel element  ​ ​A type of plant cell in xylem that conducts water, along with dissolved minerals, hormones, and certain organic compounds. vessel  ​ ​In a plant, a water-conducting structure made up of aligned vessel elements. vestibular system  ​ ​The organ of balance in vertebrates, located in the inner ear next to the cochlea. vestigial structure  ​ ​An anatomical feature that has no current function but resembles a structure of a presumed ancestor. vibrios  ​ ​Comma-shaped prokaryotic cells. villi (singular, villus)  ​ ​Finger-like projections extending from the inner surface into the lumen of the vertebrate small intestine; these are specializations that aid in digestion and absorption. viral envelope  ​ ​A structure enclosing a viral capsid that consists of a membrane derived from the plasma membrane of the host cell and embedded with virally encoded spike glycoproteins. viral genome  ​ ​The genetic material of a virus. viral reproductive cycle  ​ ​The series of steps that results in the production of new viruses during a viral infection. viral vector  ​ ​A type of vector used in cloning experiments that is derived from a virus. viroid  ​ ​An RNA molecule that infects plant cells. virulence  ​ ​The ability of a pathogen to infect its host and cause disease. virulent phage  ​ ​A bacteriophage that follows only the lytic cycle. virus  ​ ​A small infectious particle that consists of nucleic acid enclosed in a protein coat. Some viruses also have a viral envelope derived from the plasma membrane of the host cell. visceral mass  ​ ​In mollusks, a structure that rests atop the foot and contains the internal organs. vitamin D  ​ ​A vitamin that is converted into a hormone in the body; regulates the calcium level in the blood through an effect on intestinal transport of calcium ions. vitamin  ​ ​An organic nutrient that serves as a coenzyme for a metabolic or biosynthetic reaction. viviparous  ​ ​Refers to an animal whose embryos develop within the uterus, receiving nourishment from the mother via a placenta. Vmax  ​ ​The maximal velocity, or rate, of an enzymecatalyzed reaction.

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Page numbers followed by f denote figures; those followed by t denote tables.

A

A. See adenine. A band, 955 ABA receptor protein, 831–32f, 831–33 ABC model, of flower development, 431 abiotic factors: effects of, on organisms, 1155t in environment, 1152 abiotic interactions, 1149 abiotic synthesis, 70 abl gene, 316 ABO blood groups, 365, 365t abomasum, 978 aboveground plant microbiomes, 633 abscisic acid: and plant behavior, 786t, 792, 797 in plant reproduction, 852 water stress and, 831–32 abscission, 792 absolute refractory periods, 890 absorption: of amino acids, 982, 982f into blood and lymph, 979 defined, 970, 971f of digested carbohydrates, 980–81, 981f of fat, 983–84, 983f of nutrients, 974–75, 975f, 984, 992–93, 992f in small intestine, 978–79, 979f of vitamins, minerals, and water, 984 absorption spectra, 169, 169f absorptive nutrition, 606, 608f absorptive state: blood glucose concentration in, 996 defined, 992 energy sources in, 994t nutrients in, 992–93, 992f regulation of, 994–97, 995f, 997f Acacia collinsii, 1230f acacia trees, 1f, 1230, 1230f Acanthodii, 738 Acanthoplegma genus, 591f Acanthuridae, 978 Acari, 720 accessory organs, of digestive systems, 979–80, 980f accommodation, in single-lens eye, 936f accuracy, of DNA replication, 236 ACE (angiotensin-converting enzyme) inhibitors, 1f Acer saccharum: and climate change, 1262, 1262f leaf abscission in, 833 transport in, 828 Acetabularia, 583f acetaldehyde, 161 acetylcholine (ACh): and baroreceptors, 1135 and cell communication, 196

discovery of, 896–98, 897f and muscular-skeletal systems, 960 in response to hemorrhage, 1134 size and structure of, 895 acetylcholinesterase, 960 acetyl CoA: in citric acid cycle, 151, 152f in pyruvate oxidation, 150–51, 150f N-Acetylgalactosamine, 365 acetyl groups: in citric acid cycle, 152f in pyruvate oxidation, 150–51, 150f acetylsalicylic acid, 127 Acheta domesticus (house cricket), 2t acid hydrolases, 94 acidic soils, 42, 1159, 1159f acidic solutions, 42, 42f acidity, 1159–60 acid rain, 1160 acid reflux, 986 acids: defined, 41 and hydrogen ion concentration, 41 plant nutrition, 806 stomach, 986 Acinonyx jubatus, 1190, 1190f acoelomates, 692, 692f acquired antibiotic resistance, 411 acquired immune deficiency syndrome (AIDS), 399–400, 637, 1128–29, 1128f acquired immunity, 1108 See also adaptive immunity acrocentric chromosomes, 342, 342f acromegaly, 1077 acrosomal reaction, 1089, 1089f acrosomes, 1089 ACTH (adrenocorticotropic hormone), 197 actin, in skeletal muscles, 955–57 actin filaments: and cell communication, 186 and cell junctions, 209 in cytoskeleton, 84–85, 85t Actinistia and actinisians, 741, 742f Actinobacteria, 568, 812 actinomorphic flowers, 845 Actinomycetes, 574–75 Actinopterygii, 738, 741, 741f action potentials, 889–92 all-or-none operation of, 889–90, 890f in baroreceptors, 1133, 1134 changes occurring during, 890f depolarization phase, 889 electrical properties of neurons, 885 in hearing, 930, 931f in heart, 1017–18 peak of, 890f and plant behavior, 796, 796f and plant nutrition, 815 propagation of, 891–92, 891f, 892f refractory periods, 890 repolarization phase, 889–90 and sensory stimulus strength, 926

in skeletal muscle, 954, 958 action spectra, 169, 169f Actitis macularia, 1198 activation, of cellular receptors, 186–91f activation domain, 64 activation energy, 131, 132f activators, 285 eukaryotic, of transcription, 294–95, 296f, 298, 299f of lac operon, 291–93, 292f active carbon, 1151 active immunity, 1126 active sites, of enzymes, 132, 139 active transport: in animal bodies, 873 defined, 113, 114f in digestive systems, 974–75, 975f in plant cells, 820, 820f and transmembrane gradient, 115 transport proteins for, 120–21, 121f active trapping mechanisms, 815 acyl transferase, 112f Acyrthosiphon pisum, 507 AD (Alzheimer disease), 279, 922–23, 923f adaptation phase (CRISPR-Cas system), 275–76, 277f, 278 adaptations: to local environments, 506–8 and natural selection, 482 See also evolution adaptive immunity, 1115–26 cell-mediated immunity, 1117–18, 1117f, 1121–23, 1122f, 1124f defined, 1108 example, 1123–24, 1125f humoral immunity, 1117–21, 1117f, 1119–21f immunological memory in, 1125–26, 1126f lymphocytes, 1116–17, 1116f lymphoid organs, tissues, and cells in, 1115–16, 1116f and self molecules, 1124–25 adaptive radiation, 502–3 adenine (A): in DNA, 224 molecular structure of, 64, 65 adenosine diphosphate. See ADP. adenosine monophosphate (AMP). See cAMP. adenosine triphosphate. See ATP. adenoviruses, 393, 394, 394f adenylyl cyclase, 192, 193f ADH. See antidiuretic hormone. adherens junctions, 208, 209f adhesion: cell, 96, 96f in long-distance plant transport, 828f of water, 40f, 41 adhesive proteins: in connective tissue, 863 in extracellular matrix, 204, 204t

adiabatic cooling, 1162 adipose tissue, 999 as connective tissue, 863f in endocrine system, 1060f leptin secretion in, 1073 ADP (adenosine diphosphate): from ATP hydrolysis, 129–30, 129f in citric acid cycle, 153 in cross-bridge cycle, 957 in oxidative phosphorylation, 153, 155 adrenal cortex, 197, 198f, 1060f, 1067, 1068 adrenal glands, 1060f, 1067–68, 1068f, 1069t adrenaline. See epinephrine. adrenal medulla, 1060f, 1067, 1068 adult-onset diabetes. See type 2 diabetes mellitus. adults, structures of, 418, 419f adventitious roots, 767, 785 Aedes genus, 399 aeration, soil, 806–7, 806f, 807f aerenchyma, 797 aerobic exercise, 962 aerobic respiration, 146 See also citric acid cycle; glycolysis; oxidative phosphorylation aerotolerant anaerobes, 573 afferent arterioles, 1047–49, 1141f afferent neurons, 883–84 afferent vessels, 1026 affinity: of enzymes, 133 of GLUTs for glucose, 995 of hemoglobin for oxygen, 1034–35, 1035f, 1036f of receptors, 196 aflatoxins, 610 African apes, 630, 631f African cichlids, 487–89, 508 African clawed tree frog, 414 African forest elephants, 516 African savanna elephants, 516 African violets, 855 African wildcat, 1292 Afrotheria, 757 Agalychnis callidryas, 746f agar, 787 agave plants, 1205f Agave shawii, 1205f age, and sexual selection, 487 age classes, 1205 Age of Amphibians, 745 Age of Dinosaurs, 546 Age of Fishes, 546 Age of Mammals, 547 age-specific fertility, 1208–9 age structure, of populations, 1258, 1258f aggregation, and flower symmetry, 845, 846 aggression, in visual communication, 1191, 1191f aging, 790

I-1

INDEX

Index

I-2 INDEX

INDEX

Agouti gene, 379–80 Agre, Peter, 117–19, 1053, 1054 agriculture: artificial selection in, 470–71, 470f, 471f biodiversity benefits to, 1285, 1286 impact of, on ecosystems, 1270–71, 1271f, 1271t legume-rhizobia symbioses, 813 and plant behavior, 797 and plant nutrition, 804, 806f, 808–11, 814 and species interactions, 1227, 1227f Agrobacterium tumefaciens, 446, 565, 577f, 578 agrochemicals, 831–33 Agropyron cristatum, 1151, 1151f Agropyron spicata, 1150–51, 1151f Agrostis capillaris, 484–85 Aguinaldo, Anna Marie, 697, 698 A horizon (soil), 805 AIDS (acquired immune deficiency syndrome), 399–400, 637, 1128–29, 1128f Ailuropoda melanoleuca, 1291 Aintegumenta gene, 431 air: composition of, 1024 in sandy soil, 806, 807, 807f airborne pathogens, 784 air-breathing vertebrates, lungs of, 1027, 1028f air bubbles, in plant vessels, 827–28 air flow, in ventilation, 1028, 1029f air pollution. See pollution. air sacs, of birds, 751, 751f air tubes, of insects and mammals, 865–66, 866f akinetes, 572, 572f alarm calling, 1195 albatross, 1204f albinism, 348 alders, 142f, 1241 alder trees, 812 aldosterone: evolution of, 1076–77 and ions in kidney filtrate, 1051–52, 1052f in response to hemorrhage, 1140, 1141f and sodium/potassium ion concentrations, 1076 alertness, and midbrain, 910, 912 Aleuria aurantia, 615 Alexandrium catenella, 590f alfalfa, 507 algae: agar and, 787 body types of, 582, 583f central vacuole of, 94f chytrids and, 611, 612f inheritance patterns and, 381–82 in intertidal zone, 1242–43, 1243f light as limiting resource for, 1158, 1159f microbiome, 623, 623f movement of, 86, 87f origin of, 545

phosphorus and eutrophication, 1266, 1267f photosynthesis in, 165–66, 166f plant nutrition and, 808 reproduction of, 651, 651f supergroup containing, 586–89 volvocine, 543 See also seaweeds algal blooms, 1253 alimentary canal: of birds, 977, 977f defined, 970 digestion in, 974 erosion of, 986–87 functional regions of, 975–76, 976f modeling of, 978 nervous and endocrine system control of, 984–85, 985f in response to hemorrhage, 1143 structural division of, 984 alkaline soils, 1159, 1159f alkaline solutions, 42, 42f alkaloids, as plant defense, 1227, 1227f alkaptonuria, 245 allantois, 746, 747f allele frequency: and Hardy-Weinberg equation, 479–80 and microevolution, 481 and migration, 492 natural selection and, 482 in population genetics, 479 alleles: codominance and multiple, 365, 365t in epistasis, 366–67, 367f and genes, 351–52, 352f linkages of, 386–87, 387f segregation of, 352–53, 352f, 356f and selective breeding, 469 allelochemicals, 1150–51, 1151f allelopathy, 1218 allergens, 1127 allergies: and asthma, 1039 immune systems and, 1127–28, 1128f to pollen, 849 Alligator mississippiensis (alligators), 360, 748–49, 749f, 925 Allis, David, 297 allolactose, 286, 287 allopatric speciation, 502–4, 509, 1221– 22, 1222t alloploid organisms, 506 allopolyploids, 506 allosteric sites, 134, 139 allosterism, 1035 Alnus genus, 812 Alnus sinuata, 142f, 1241 Alper, Tikvah, 402 alpha cells, 1069 alpha particles, 25–26 α subunits, G protein, 192, 193, 193f α-carbons, 56 α chains, 204, 205 α-globin genes, 451, 1097 α-glucose, 50, 50f α helices, 59f, 60 α-ketoglutarate, 139, 152f

α-ketoglutarate dehydrogenase, 153 α-proteobacteria, 99 α-tropomyosin, 300, 300f alprazolam, 899 alternation of generations, 643 in flowering plants, 761, 761f, 840, 840f life cycles and, 340f, 341 in plants, 651, 651f protists with, 597, 598f alternative splicing, 251 gene regulation and, 299–301, 300f, 301t in plasma cells, 1118 altitude: homeostatic response to change in, 1143, 1144 and pressure exerted by gases, 1024–25 Altman, Sidney, 135–37 altruism, 1193–96, 1194f, 1195f Alu gene sequence, 452–54 aluminum ions, plant transport of, 824 Alveolata supergroup, 589–90, 589f, 590f alveoli: of protists, 589, 590f in respiratory system, 1028, 1029f, 1030–31, 1040 Alzheimer, Alois, 922 Alzheimer disease (AD), 279, 922–23, 923f amacrine cells, 941 Amanita muscaria, 611f Amanita virosa, 610 AM (arbuscular mycorrhizae) fungi, 633, 634f Amazon rain forest, 164 Amblyomma hebraeum, 720f Amborella trichopoda, 675, 675f Ambrosia genus, 849 Ambulocetus genus, 466 amenorrhea, 1084, 1105 amensalism, 1217 American alligator, 360, 749f American avocet, 752f American buffalo, 1291 American chestnut, 1277, 1277f, 1282 American crocodile, 749f American Foundation for the Blind, 947 American ginseng, 1274 American redstart, 1232 American woodcock, 942, 942f Ames, Bruce, 311 Ames test, 311–12, 311f amines: biogenic, 895 as hormones, 1059, 1061–62 amino acids: absorption of, 982, 982f in absorptive state, 992f, 993 in charging of tRNAs, 257, 258f coding sequence, codons, anticodons and, 253, 253f essential, 971–72 gene mutations and sequence of, 305–6, 306f genetic code and, 252, 252t mRNA and, 252–53, 252f

as neurotransmitters, 896, 896t in polypeptides, 58, 58f in proteins, 56–58, 57f and receptor activation, 188 aminoacyl-tRNA, 257 aminoacyl-tRNA synthetases, 257, 258f amino group: in amino acids, 56, 57, 57f molecular structure of, 46 2-aminopurine, 310 amino terminal tails, histone protein, 297, 297f Amish population, founder effect in, 491 ammonia: in Miller and Urey experiments, 70–71 molecular shape of, 35f as nitrogenous wastes, 1050, 1050f and plant nutrition, 808, 813 in water, 41 ammonification, 1267f, 1268 ammonium cyanate, 45, 46 ammonium ions, as nitrogenous wastes, 1050, 1050f amnion, 746, 747f amniotes, 746–52 amniotic eggs of, 746–47, 747f birds, 749–52 and mammals, 752 reptiles, 747–49 amniotic eggs, 546, 746–47, 747f amoebae, 116, 583–84, 584f Amoebozoa and amoebocytes, 591, 703 amphibians: baroreceptors of, 1135 characteristics of, 744–46 circulatory systems of, 1012, 1014, 1023 cleavage-stage embryos of, 1100, 1100f, 1101 digestive system of, 975 endocrine system of, 1077 endoskeletons of, 952 gastrulation in, 1101–3, 1102f genome size of, 449 locomotion by, 964 nitrogenous wastes from, 1044 origins of, 546 respiratory systems of, 1025 sensory systems of, 937 and shared derived characters of reptiles, lobe-finned fish, 736 amphipathic molecules, 37, 38f in membranes, 107 phospholipids as, 54–55 Amphiprion ocellaris, 12 amplicon analysis, of microbiome, 624f, 625, 626f amplicons, 625 amplitude, of sound waves, 948 ampR gene, 436, 437 ampullae, 727, 727f, 932 amygdala, 914–15 amylase: for carbohydrate digestion, 980–81, 981f in saliva, 976 amyloplasts, 98

amyotrophic lateral sclerosis, 966 anabolic reactions: ATP use for, 155 defined, 137 requirements and function of, 139 anabolism, defined, 84 anaerobic environments, defined, 159–60 anaerobic respiration, 159–60, 160f anagenesis, 519 analogous structures, 468 anaphase I (meiosis), 336, 339f anaphase II (meiosis), 339f anaphase (mitosis), 331, 332, 333f anatomical homologies, 471–72, 471f, 472t See also homologies anatomy, defined, 13, 13f anchoring junctions, 208, 208t, 209f ancient DNA analysis, 527–29 Andersen, Dorothy, 16 androgens, 1058 and cell communication, 186–87 misuse of, 1080 receptors for, 63, 64f, 1062 and reproduction, 1080, 1092 in reproduction, 1092 synthesis and function of, 1061f anemones, 731f anemotaxis, 1185 aneuploidy, 343–45, 343f, 344f, 345t Anfinsen, Christian, 61–63 angiosperms, 672 origins of, 547 overview, 647, 647f See also flowering plants angiotensin-converting enzyme (ACE) inhibitors, 1f angiotensin II (AII), 1140 animal bodies, 859–80 eukaryotic parasites in, 1109 and exoskeletons, 951–52 homeostasis in, 867–79, 868t innate immunity and surfaces of, 1109–10 internal fluids of, 872–78 organization of, 859–65, 865t and structure and function relationships, 865–67, 866f, 867f summary, 879–80 animal cells: bacterial and plant cells vs., 102, 103t cell junctions of, 208–12, 208t cell structure and function of (See eukaryotic cells) compartments in, 84f cytokinesis in, 332, 334f extracellular matrix of, 203–6, 204t, 206t genetic material in, 382f GLUT proteins of, 995–96 ligand-gated ion channels in, 189 meiosis in, 338–39f microtubules in, 84 mitosis in, 331, 332–33f nucleus and endomembrane system of, 88f osmosis in, 115, 116, 116f

semiautonomous organelles of, 96f structure of, 80f transmembrane proteins in, 111, 111f animal development, 1096–1104 of amphibians, 745, 745f of cerebral cortex, 916 development in plants vs., 429 embryonic development (See embryonic development; metamorphosis) fertilization process (See fertilization) of insects, 724, 724f of nervous system, 904–6, 907f and pregnancy/birth in mammals, 1096–99, 1096f, 1097t, 1098f summary, 1106–7 animal diversity, 686–700 characteristics of animals, 687, 687t, 688f classification, 688–95, 695t and molecular data for phylogenetic trees, 695–99 summary, 699 animal embryos: and adult structures, 418, 419f cleavage-stage, 1099–1101 defined, 414 development of (See embryonic development) and female reproductive tract structure, 1093, 1093f gastrulation in, 1101–3, 1102f hormones in preparation for, 1095 pattern formation in, 417, 418, 418f in pregnancy, 1096–97 Animalia (Animal kingdom), 517, 518, 605, 688, 694–95, 695t animal models, in physiological studies, 998 animal pole, of embryo, 1110, 1110f animal reproduction, 687, 1084–95 in amphibians, 745, 745f in annelids, 715 asexual, 1085–86, 1085f in bony fishes, 741 in chondrichthyans, 740 elimination of harmful mutations in populations, 1086–87 and endocrine systems, 1079–80 fertilization, 1089–90, 1089f in flatworms, 707 gametogenesis, 1087–89, 1088f human reproductive system, 1090–95 in insects, 724, 724f in mollusks, 710, 712f in nematodes, 717 overview, 1084–87 and pregnancy/birth in mammals, 1096–99, 1096f, 1097t, 1098f public health issues related to, 1104–6, 1105f sexual reproduction, 1085–87 summary, 1106, 1107 animals: advantages of hearing for, 930–31 bodies of (See animal bodies) body plan axes in, 415, 415f

and carnivorous plants, 801, 814–15, 815f cells of (See animal cells; eukaryotic cells) characteristics of, 687, 687t, 688f characteristics of phyla of, 731, 731t chromosome number changes in, 343–45, 344f, 345t classification of (See animal diversity) and coevolution of plants, 681–83, 682f, 682t, 683f consumption of, 971 defined, 687 developmental genetics, 418–29, 426t, 428–29f development of (See animal development) in Eukarya, 9, 10f evolution of color vision in, 938–39, 939f and evolution of plants, 650, 650f fungal disease in, 617–18, 617f, 618f gametophyte production in, 340 and heat exchange between environment, 1003–4, 1003f, 1004f homeotic genes of, 423–24, 424f host-associated microbiomes in, 633–37 Hox genes and body complexity of, 510 locomotion in, 964–66, 965f microbiomes of, 638, 639f nervous system and environmental adaptations by, 905, 906f nitrogenous waste production by, 1044–45, 1044f nutrition for, 970–74t origins of life for, 544–46 pattern formation in, 415, 417–24 phylogeny of, 701, 701f pollination via, 841, 843, 845 reproduction in (See animal reproduction) sex determination in, 359–60, 360f sexual reproduction in, 340, 341f in systems with environments, 861 tissues of, 215–16, 215f used in pharmaceutical industry, 1284 vestigal structures in, 471, 472t See also specific animals anions, defined, 34 aniridia, 413 Anisotremus taeniatus, 502 Anisotremus virginicus, 502 Anna’s hummingbird, 752f Annelida and annelids: characteristics of, 695t, 714–16, 715f, 716f, 731f excretory systems of, 1046, 1046f nervous system of, 905, 906f segmentation, 693, 693f annual plants, 763 Anodorhynchus hyacinthinus, 752f Anopheles genus, 599 ANP (atrial natriuretic peptide), 1076 antagonists, muscle, 954 Antarctica, microbiomes in, 629, 629f antelope, 1062

antenna complex, 172 See also light-harvesting complexes antennae, of moths, 866, 867f, 943, 943f Antennapedia gene complex, 422–24, 423f anterior cavity, of eye, 937 anterior ends, 690 anterior pituitary gland: in endocrine system, 1060f and function of hypothalamus, 1063– 64, 1063f, 1064f hormones of, 1064t, 1077 anteroposterior axis, 415 antheridia, 651–52, 652f anthers and anther cells, 674, 841 Anthocerophyta. See hornworts. Anthophyta. See flowering plants (angiosperms). Anthozoa, 704, 704t anthrax, 572 Anthropocene, 1257 anthropogenic, defined, 1257 anthropoidea, 548 antibiotic resistance, acquired, 411 antibiotics: bacterial decomposition of, 574–75 bacterial resistance to, 7, 7f, 462–63, 576 and bacterial translation, 263–64, 264t and digestive system, 976, 980, 987, 988 antibodies: defined, 1116 immunoglobulins as receptors for, 1118–20, 1119f, 1120f monoclonal, 1125 in opsonization, 1120, 1121 from plasma cells, 1120–21, 1121f antibody-mediated responses. See humoral immunity. anticodons, 253, 253f, 254 antidiuresis, 1064 antidiuretic hormone (ADH): and aquaporins, 1054 and posterior pituitary gland, 1064–65 in response to hemorrhage, 1140 and sodium/potassium ion concentrations, 1075–76 and water reabsorption, 1052–53, 1053f antifreeze proteins, 468, 469f antigen-presenting cells (APCs), 1122, 1122f, 1124 antigens: attack against, in adaptive immunity, 1117f, 1118 defined, 1115 presentation of, to cytotoxic T cells, 1123 recognition of, by T cells, 1121–23, 1122f recognition of, in adaptive immunity, 1117, 1117f on red blood cells, 365 antihistamines, 895, 1127–28 anti-inflammatory drugs, 934 antioxidants, 36 antiparallel strands, in DNA, 227–28, 228f antiporters, 119, 120f

INDEX

INDEX I-3

I-4 INDEX

INDEX

antipredator strategies, 1224–26 Antirrhinum majus, 431, 846, 846f antisense RNA: mRNA silencing with, 272–73 and ncRNA as blocker, 267 antiviral drugs, 400 antlers, 754–55, 755f Antp gene, 423 ants: and mutualism, 1229–30, 1230f optimal foraging by, 1189–90, 1189f Anura and anurans, 745, 746f See also frogs anus, in digestive system, 975, 980 aorta, 1016, 1020 APCs. See antigen-presenting cells. aphids, 1230, 1230f apical-basal-patterning genes, 430–31, 430t apical-basal polarity, 764, 765f, 785 apical cells, 429 apical meristems, 643 defined, 761 of plant roots (See root apical meristems) of plant shoots (See shoot apical meristems) apical region, of plants, 430, 764 Apicomplexa phylum, 589, 592t Apis mellifera, 373 Aplysia californica, 917 Aplysina archeri, 703f Apoda, 745, 746f apomixis, 856 apoplasts and apoplastic transport, 823–24, 823f apoptosis, 318 cell communication and, 196–200, 197t, 198f, 199f defined, 183, 196 hormonal control of, 197–99, 198f and positional information, 415f, 416 tissues and, 215 apoptosomes, 200 aposematic coloration, 1225f, 1226 appendages, of arthropods, 717–18 appendicular skeleton, 952 appetite: hormonal regulation of, 1073 and leptin, 999, 1000f apple maggot fly, 506–7 apple scab, 615 apple tree, 676f, 843, 843f AQP2 gene, 1054 aquaporins: in animal bodies, 873 and antidiuretic hormone, 1052, 1065 evolution of, 1053–54, 1054f and membrane transport, 118f, 119 in plants, 819 aquatic animals: external fertilization by, 1090 heat exchange for, 1004 locomotion for, 964 nitrogenous wastes from, 1044 sensory systems of, 942 aquatic biomes, 1171–74

aquatic ecosystems: biomass measurements of, 1252 habitat destruction of, 1269 invasive species in, 1275 primary production in, 1252–53 and species-time hypothesis, 1237 succession in, 1242 aquatic invertebrates, 931–32, 931f aquatic plants, 808 aqueous humor, 947 aqueous solutions, defined, 37 aquifers, 1265 Aquila verreauxii, 752f Arabidopsis genus, 851, 852f Arabidopsis thaliana: development of, 429–31, 430t, 431f FASS gene in, 768 gene regulation in, 282 genome projects with, 458 as model organism, 414–15, 414f, 762 phloem loading in, 819 and plant nutrition, 810–11 root structure of, 777 seed-to-seed life cycle of, 762f stomatal guard cell development in, 774 transport in, 819 arachidonic acid, 972 Arachnida and arachnids, 720, 720f, 721f, 731f, 1034 arachnoid mater, 909 Arber, Werner, 436 arbuscular mycorrhizae (AM) fungi, 633, 634f archaea, 561–80 diversity and evolution of, 562–66 ecological role of, 573–74 in microbiome, 625, 626f nutrition and metabolism of, 572–73 origins of, 540 and origins of eukaryotes, 541–43 protein degradation in, 141–42, 141f reproduction of, 571–72, 571f structure and movement of, 78, 79f, 566–71 summary, 579–80 See also prokaryotes Archaea domain, 9, 10f cellular and molecular features of, 517 and evolutionary relationships of Bacteria, Eukarya, 562–64 and horizontal gene transfer, 532 archaeal genomes: genetic technologies with, 445–46, 446t sequencing of, 446t size of, 445, 446 Archaean eon, 538, 540–43 Archaeopteris, 666, 666f Archaeopteryx, 547 Archaeopteryx lithographica, 750, 750f archegonia, 651, 652f archenteron, 1101–3, 1102f arch of aorta, baroreceptors in, 1133, 1135 Arctium minus, 1231f arginine synthesis, 245, 245f Argopecten irradians, 1217 Aristotle, 496 Armadillium vulgare, 725f

Armillaria ostoyae, 202, 605, 607 armor, 1225f, 1226 armored fishes, 738 army ants, 724f Arnold, William, 172 Arnon, Daniel, 170 arrhythmias, cardiac, 279 ART (assisted reproductive technologies), 1105 arteries: atherosclerotic plaques in, 1038, 1038f in closed circulatory systems, 1012 and energy balance, 1005f function of, 1019, 1020, 1020f arteriolar resistance. See resistance. arterioles: afferent, 1047–49 in digestive system, 979f efferent, 1047 function of, 1019, 1020 and resistance to flow, 1023 in response to hemorrhage, 1138, 1141f Arthrobotrys anchonia, 617f Arthropoda and arthropods, 717–26 audition in, 929 basic characteristics, 695t body plan of, 718–19, 719f characteristics of, 731f Chelicerata subphylum, 720–21 circulatory systems of, 1013 Crustacea subphylum, 724–26, 725f Hexapoda subphylum, 721–24, 722f, 723t, 724f locomotion by, 965 in mangrove islands, 1246–47 muscular-skeletal systems of, 951–52, 952f Myriapoda subphylum, 721, 721f nervous systems of, 905, 906f origins of, 538, 545 segmentation, 693, 693f subphyla of, 719, 719t taxonomic relationships of other Protostomia to, 697–98 Trilobita subphylum, 719, 720f artificial selection, 469–71, 470f, 471f, 638, 638f, 639f See also selective breeding Asarum canadensis, 634f Ascaris lumbricoides, 717 Aschehoug, Erik, 1150–51 asci, 613–15, 614f, 615f ascocarps, 614 Ascomycota and ascomycetes, 606, 606f, 613–16f ascospores, 614 asexual reproduction, 330 in animals, 1085–86, 1085f defined, 1085 in flowering plants, 855–56, 855f of fungi, 609, 609f, 610f, 611, 613f of protists, 596, 596f of sponges, 704 Asgard superphylum, 564 Asian chestnut, 1277 Asian elephants, 516, 1096 Asian gaur, 1292

Asiatic lilies, 846–48, 847f aspens: reproduction in, 855 and species interactions, 1232, 1233f Aspergillus fumigatus, 1113 Aspergillus versicolor, 609f ASPM gene, 916 assimilation, in nitrogen cycle, 1267, 1267f assisted reproductive technologies (ART), 1105 association, statistical, 380 associative learning, 1182 assortative mating, 492 Asteroidea, 727 asters, 794 asthma, 1038–39, 1039f astrocytes, 883 Atelopus zetekl, 1149 AT/GC rule, 228, 230–31, 230f Atheris ceratophora, 748f atherosclerosis, 1038, 1038f athletic exercise, feedforward regulation for, 870, 871f athletic performance, 876–79 atmosphere: reducing-atmosphere hypothesis, 70–71, 70f since origin of Earth, 538 and transpiration, 829 atmospheric circulation, 1160–61 atmospheric pressure, 1024–25 atomic mass, 28–29 atomic mass unit (amu), 29 atomic nucleus, 25, 26 atomic number, 28 atoms, 24–30 and chemical reactions, 36 composition of, 24–25, 25f defined, 2, 3f, 24 electrons in, 27–28, 27f and element composition of living organisms, 29–30, 30t mass of, 28–29, 29t modern model of, 25–26 neutrons in, 29, 30f protons in, 28, 28f summary, 43 ATP (adenosine triphosphate): in Calvin cycle, 175f from catabolic reactions, 137–38, 137f and cell communication, 192, 193f from citric acid cycle, 151, 151–52f, 153 for cross-bridge cycle, 957–58, 958f from cyclic electron flow, 170–71, 171f in endergonic reactions, 130–31, 130f, 131t from fermentation, 160, 161 from glycolysis, 148 hydrolysis of, 129–30, 129f from linear electron flow, 169–70, 170f and membrane transport, 121–22, 122f from mitochondria, 97, 97f nutrients for synthesis of, 971 in oxidative phosphorylation, 153, 155 for phosphorylation of glucose, 131 in photosynthesis, 166, 166f

post-translational sorting of proteins for synthesis of, 101 skeletal muscle classification based on, 961 and spinning of ATP synthase, 156–58f, 156–59 ATPase: energy for Na+/K+-ATPase pump, 886 Na+/K+-ATPase pump membrane transport, 121–22, 122f ATP-binding proteins, 130 ATP-dependent chromatin-remodeling complexes, 296–97, 297f ATP-driven ion pumps, 121–22, 122f ATP hydrolysis: for active transport, 820, 820f in cross-bridge cycle, 957, 958 in muscle contraction, 956 as source of energy for homeostasis, 875 ATP synthase: in cellular respiration, 146f, 154f, 155–59 chemiosmosis by, 153, 155–56, 156f in photosynthesis, 170, 171, 171f spinning by, 156–58f, 156–59 atria: and cardiac cycle, 1018 excitation in, 1017–18, 1017f in single vs. double circulation, 1012 of vertebrate hearts, 1016–17, 1016f atrial natriuretic peptide (ANP), 1076 atrioventricular (AV) node, 1018, 1019 atrioventricular (AV) valves, 1017, 1018 atrophy, muscular, 962, 966 Atta cephalotes, 1189–90, 1189f, 1230f attachment (step in viral reproductive cycle), 395, 396f attack systems, of pathogenic bacteria, 577–78, 577f audition, 929–31 auditory communication, 1191 auditory nuclei, of musicians vs. nonmusicians, 920–21f AUG codon, 260–61 Austin, Thomas, 1211 Australian lungfish, 742f Australopithecus genus, 547, 550–52 Australopithecus afarensis, 550, 551 Australopithecus africanus, 551 autocrine signaling, 185, 185f autoimmune diseases, 1125 autonomic nervous system, 909–11, 911f autophagosomes, 142, 142f autophagy, 142, 142f autosomal inheritance patterns, 358–59 autosomes, 325, 358 autotomy, 727 autotrophs, 572–73 carnivorous plants as, 813–14, 814f defined, 165 in food chains, 1248, 1248f origins of, 540–41 Aux/IAA repressors, 785 auxin-destruction hypothesis, 789 auxin efflux carriers, 785, 787f auxin influx carriers (AUX1), 785, 787f

auxin-responsive genes, 785 auxins, 785–89, 787f, 788f and cell communication, 184, 184f effects of, 785, 795 and ethylene, 791 and leaf development, 770 overview, 786t in phototropism, 786–89, 788f and plant nutrition, 815 and roots, 778 transmembrane transport of, 823 transport of, 785, 787f Averof, Michalis, 694 Avery, Oswald, 222–23 Aves. See birds. avirulence genes (Avr genes), 798, 799f AV node. See atrioventricular (AV) node. Avogadro’s number, 29 Avr genes (avirulence genes), 798, 799f AV valves. See atrioventricular (AV) valves. Axel, Richard, 944–45f, 944–46 axes, body, 419–20, 420f axial skeleton, 952 axillary buds, 770 axillary meristems, 770 axonemes, 86, 88 axon hillocks, 883, 891 axons: action potential propagation along, 891–92, 891f, 892f structure and function of, 882–83, 883f axon terminals: action potential propagation along, 891–92, 891f, 892f defined, 883, 883f in posterior pituitary gland, 1064–65 azaleas, 1159 azidothymidine (AZT), 400

B

Bacillariophyceae. See diatoms. bacilli, 567 Bacillus anthracis, 572 Bacillus subtilis, 260, 403f Bacillus thuringiensis, 579, 1227 See also Bt crops backbone: of DNA, 225 of vertebrates, 734–36, 735f, 736t Bacskai, Brian, 195 bacteria, 561–80 antibiotic decomposition by, 574–75 antibiotic resistance in, 7, 7f, 576 antigens on surface of, 1115 bacteriophages (See bacteriophages) binary fission in, 333 biological nitrogen fixation by, 808–9, 808–9f, 812–14, 813f, 814f cell division in eukaryotes vs., 333–34, 334f complexity of eukaryotic cells vs., 102, 103t diarrhea caused by, 985–86 in digestive system, 978, 980 diversity and evolution of, 562–66

DNA origin of replication in, 231, 231f ecological factors in speciation of, 498 ecological roles and biotechnology applications of, 573–79, 577f, 578f gene expression in, 246f, 247 gene regulation in (See bacterial gene regulation) genome defense for, 275–78, 277f horizontal gene transfer with, 474, 474f inhibition of translation in, 263–64, 264t in microbiome, 623, 623f, 625, 626f mRNA of, 252f in nitrogen cycle, 1267 nutrition and metabolism of, 572–73 origins of, 540 and origins of eukaryotes, 541–43 as pathogens, 1109 and plant behavior, 798 plasmids from, 435 properties of, 403–5f, 403–6 and receptor tyrosine kinases, 190 reproduction of, 571–72, 571f, 572f restriction enzyme function in, 436 ribosomes of, 258, 258t, 259f small subunit rRNA gene sequence of, 260, 260f speciation of, 497 structure and movement of, 78, 79f, 566–71 summary, 579–80 and symbioses of plants, 812–14, 813f, 814f translation in, 262–63, 262f, 263f used in pharmaceutical industry, 1285 See also prokaryotes Bacteria domain, 9, 10f cellular and molecular features of, 517 diversity of, 564–65 and evolutionary relationships of Archaea, Eukarya, 562–64 horizontal gene transfer in, 532 phyla of, 564t bacterial colonies, 405, 405f bacterial gene regulation, 285–94 and environmental changes, 283, 283f overview, 284–85, 285f of transcription, 285–94 bacterial genetics, 403–11 gene transfer in, 406–11, 406t, 407–10f and properties of bacteria, 403–5f, 403–6 summary, 411–12 bacterial genomes: genetic technologies for studying, 445–48, 446t, 447–48f sequencing of, 446–48, 446t, 447–48f size of, 445, 446 bacterial infection, and ulcers, 987–88 bacterial meningitis, 391 bacterial transformation, 221–23f bacteriomes, 543 bacteriophages, 393 genome defense against, 275–78, 277f λ (lambda), 395–98 latency in, 398, 399 P1, 410–11, 411f reproductive cycle of, 398–99, 398f

T4, 394f, 395, 399 in transduction, 410–11, 410f bacteriorhodopsin, 155, 156 Bacteroides genus, 630 Bacteroidetes, 630, 634 bacteroids, 813, 814, 814f baited snap traps, 1202, 1202f baker’s yeast, 330, 448 See also Saccharomyces cerevisiae Balaenoptera acutorostrata, 1272 Balaenoptera borealis, 1272 Balaenoptera musculus, 1272 Balaenoptera physalus, 1272 balance: of energy in animal systems (See energy balance) sense of, 931–33, 931f, 932f balanced polymorphism, 485 balancing selection, 485 bald cypress (Taxodium distichum), 670 baleen whales, sensory systems of, 931 ball-and-socket joints, 953f balloon angioplasty, 1029 banana plants, asexual reproduction in, 855 Bandhavgarh National Park, India, 1166, 1166f Banting, Frederick, 1071–73 bark, of trees, 766f, 776 barnacles, 724–26, 725f, 1222–24 baroreceptor reflex, 1133–35, 1134f baroreceptors: blood pressure sensing by, 1133–35, 1134f determining function of, 1136–37 evolution of, 1135 in rapid phase of response to hemorrhage, 1133–37, 1134f, 1136–37f Barr, Murray, 377 Barr bodies, 378–79, 379t Bartel, David, 74–75 basal bodies, 88 basal cells, 943, 944 basal metabolic rate (BMR), 998 basal nuclei, 914 basal region, of plants, 430, 764 basal transcription, 294 base analogues, 310 base composition, of DNA, 226, 226t basement membrane, 320f, 321 base modification, by chemical mutagen, 310, 310f base pairs, 227–28, 227f, 228f bases: defined, 41 and hydrogen ion concentration, 41 in nucleotides, 224, 224f, 225f base sequence, determining, 440–42, 440f, 441f base substitutions, 305 basic helix-loop-helix (bHLH) proteins, 774 basidia, 615 basidiocarps, 615 Basidiomycota and basidiomycetes, 606, 606f, 613 fruiting bodies of, 615–16, 616f, 617f septal pores of, 613, 614f

INDEX

INDEX I-5

I-6 INDEX

INDEX

basidiospores, 615 basilar membrane, 930 basophils, 1110, 1110f Batesian mimicry, 1225f, 1226 Bateson, William, 366, 384, 386, 422, 431 Batrachochytrium dendrobatidis, 611, 1149 bats, 1004 brain mass for, 907 locomotion by, 965 sensory systems of, 930 wing of, 5, 5f Bayer, Martin, 429 bay scallops, 1217 B-cell receptors, 1118, 1119f B cells: activation of, 1122–23 immunoglobulins from, 1118–20, 1119f, 1120f plasma cells from, 1120–21, 1121f self-molecule recognition by, 1124–25 structure and function of, 1116, 1116f bcr gene, 316 bdellovibrios, 565 Beadle, George, 245–46, 245f Beagle voyage, 460–61, 460f, 461t beaks: and diet of finches, 460–61, 461t diversity of bird, 751, 752f natural selection of size of, 463, 464f and speciation, 504–6 and species interactions, 1222 beans: as annual, 763 as eudicots, 763 seed germination and seedling growth in, 854, 854f structure of mature seeds, 853f beavers: demography for, 1205, 1206, 1206f, 1206t, 1208–9 as keystone species, 1290f, 1291 and species interactions, 1232, 1233f bedrock, 805 beef tapeworms, 707 bee orchid, 1231, 1231f beer production, 854 bees, 724 chromosome number in, 344 haplodiploid system of, 360 inheritance patterns in, 373 innate behaviors, 1181–82 sensory systems of, 925, 937–39 beetles, 724 beets, 794 behavior: animal, and heat exchange rate, 1005–6 defined, 782, 1180 of plants (See plant behavior) behavioral ecology, 1180–1200 altruism, 1193–96, 1194f, 1195f communication, forms of, 1190–92 defined, 1150, 1180 foraging behavior, 1189–90, 1189f and genetics, 1181–87f

group living, 1192–93, 1193f and learning, 1181–87f local movement, 1185–86f, 1185–87 long-range movement, 1187–88, 1188f mating systems, 1196–99 summary, 1199–1200 territory defense, 1190, 1190f See also ecology behavioral isolation, 500 Beijerinck, Martinus, 392 Belding’s ground squirrels, 1195 Bendall, Fay, 174 benefit-cost analysis. See cost-benefit analysis. benign tumor, 314 Benson, Andrew Adam, 175 benzo(a)pyrene, 310 Berg, Paul, 434 Bernal, John, 72 Bernard, Claude, 867 Bertram, Ewart, 377 Best, Charles, 1071–73 beta cells, 1069 β-amyloid, 923 β-galactosidase: gene cloning, 437 and gene regulation, 287f β-globin gene: heterozygote advantage, 485 polymorphisms in, 478 similarity between species, 1097 β-glucose, 50, 50f β-lactamase, 437 β pleated sheets, 59f, 60 β-proteobacteria, 543 β subunit, ATP synthase, 156, 157 Betta splendens, 741 bicarbonate ions, 42 in digestive system, 979 in respiratory system, 1036 bicoid gene, 419–21, 420f bidirectional replication, 231, 231f Bienertia cycloptera, 804f biennial plants, 763–64 Bifidobacterium longum, 635 Big Bang, 535 bilateral symmetry: of animals, 690, 692f flowers with, 845–46 origins of animals with, 543–44 and origins of life, 544 Bilateria, 690f embryonic development of, 691–92, 692f morphological criteria for, 692–94 bilayers, 37, 54f, 55 See also plasma membranes bile, 979 bile ducts, 980f bile salts, 979 binary fission: and bacteria, 404–6, 405f of mitochondria and chloroplasts, 98, 98f and mitotic cell division, 333–34, 334f in prokaryotic cells, 571–72, 571f bindin, 500

binding step, in cross-bridge cycle, 957, 958f binocular vision, 548, 941–42, 942f binomial nomenclature, 11–12, 519 biochemical regulation, of metabolic pathways, 139 biochemistry: defined, 147 genetic material identification in, 220–23 biodiversity, 1280–94 conservation strategies, 1287–93 defined, 1280 and ecosystem functions, 1281–85f levels of, 1280–81, 1281f summary, 1293–94 value of, to human welfare, 1282, 1284–86, 1285f, 1286t biodiversity hot spots, 1287, 1288f biofilms, 568 biogenic amines, 895, 896t biogeochemical cycles, 1262–68 biogeographic regions, 1176–77, 1176f biogeography, 466, 468, 468f, 1175–77, 1176f, 1177f biological communities, 1160–63f, 1160–64 biological complexity, and genome size, 300–301, 300t biological control, 1150 biological diversity (biodiversity): of archaea, 562–65 of bacteria, 562–65 of crustaceans, 725–26, 725f of fungi, 611–16, 612t of mammals, 755–57, 755t, 756f of microbes in microbiomes, 622–28, 623f, 624f, 626–28f of modern plants, 641–48 of protists, 584–92, 592t of ray-finned fishes, 741, 741f of seed plants (See seed plant diversity) See also biodiversity biological evolution, 5–8, 465t See also evolution biological membranes, 106, 107, 107f See also membranes; plasma membranes biological nitrogen fixation, 808–9 biological organization, in plants, 762, 763f biological sources of plant nutrition, 811–16 carnivorous plants, 814–15 mycorrhizal associations, 812 nitrogen-fixing symbioses, 812–14 parasitic plants, 815–16 biological species concept, 499 biological stimuli, 783f biological stresses, 797–99 biologists, investigations by, 13–14, 13f biology, 1–22 cell, 13, 13f classification of living things in, 8–12 core concepts of, 4–5, 4f core skills of, 17–20, 19f defined, 1, 24

energy forms in, 128t evolution in, 5–8 levels of, 2–3, 3f molecular, 13, 13f as scientific discipline, 12–17, 13f, 15f–17f as social discipline, 16–17, 17f summary, 21 bioluminescence: in bacteria, 575, 576f and ctenophores, 702 biomagnification, 1268–69, 1268f, 1269f biomass: defined, 1236 and ecological pyramids, 1251–52, 1251f and species richness, 1240, 1240f biomass production, 1252–54 biomes, 1164–74 cold desert, 1169, 1169f coral reef, 1172, 1172f defined, 1149 hot desert, 1169, 1169f intertidal zone, 1172, 1172f lentic habitats, 1173, 1173f lotic habitats, 1174, 1174f mountain ranges, 1170, 1170f open ocean, 1173, 1173f temperate coniferous forest, 1167, 1167f temperate deciduous forest, 1167, 1167f temperate grassland, 1168, 1168f temperate rain forest, 1166, 1166f tropical deciduous forest, 1166, 1166f tropical grassland, 1168, 1168f tropical rain forests, 1165, 1165f tundra, 1170, 1170f wetlands, 1174, 1174f biophilia, 1286 bioremediation, 579 biosphere, 3f defined, 3, 165 photosynthesis in, 165, 165f biosynthetic reactions, 139 See also anabolic reactions biotechnology: bacterial applications in, 579 fungi’s applications in, 620 See also genetic engineering biotic interactions, 1149 BioTips strategies, 19–20 biparental inheritance, 383 bipedalism, in human evolution, 550 bipolar cells, 941 bird-hipped dinosaurs. See Ornithischia and ornithischians. birds: alimentary canal of, 977, 977f baroreceptors of, 1135 blood pressure for, 1018 and body temperature, 1003 characteristics of, 749–52 circulatory system of, 1012, 1023 cleavage-stage embryos of, 1100, 1100f and deforestation, 1270 digestive system of, 975, 977 dinosaurs and, 750, 751f

double circulation in, 1012, 1013f embryonic development in, 1103 endoskeletons of, 952 energy balance for, 1005, 1005f evolution of, 466 feeding habits of, 971 flightless, phylogenetic trees for, 527–29 genomic imprinting in, 375 and island biogeography, 1245, 1245–46f learning and genetics influencing, 1183–84, 1184f locomotion by, 965 magnetic field sensing by, 934 nitrogenous wastes from, 1044 origins of, 547 pattern of birds’ feet, 510 reproduction in, 1090 and reptiles, 521 resource partitioning by, 1221, 1221f seed dispersal by, 853 sensory systems of, 937, 941 Shannon diversity index for, 1239–40, 1239t species richness of, 1236, 1237f threatened due to overexploitation, 1272–73, 1273f in top-down control model, 1232, 1233f bird songs, 504–6, 1183, 1184f Birks, H. John, 1237 birth, of mammals, 1097–99, 1098f See also animal reproduction Bishop, Michael, 318 bismuth, 987, 988 Bison bison, 1291 1,3-bisphosphoglycerate (1,3-BPG), 149f, 175f, 176 bithorax gene complex, 422, 422f bivalents, 334, 335f Bivalvia and bivalves, 711, 712t blackberries, 852, 853, 853f black-browed albatross, 1204f Blackburn, Elizabeth, 237, 238 black-footed ferrets, 1201, 1211, 1211f black grouse, 1198f black rhinoceros, 755f black truffles, 616f black widow spider, 720, 720f blades, of leaves, 770 Blanton, Laura, 635–36 Blastocladiomycota, 606, 606f, 611 blastocoels, 1100 blastocysts, 1093, 1095, 1101 blastoderm, 1100, 1101 blastomeres, 1100 Blastomyces dermatitidis, 618 blastopores, 691, 1102, 1102f blastula, 690, 690f, 1100, 1101 blebs and blebbing, 196, 197f bleeding heart plant, 648f blindness, 920, 947 Bliss, Timothy, 917 Blobel, Günter, 101 blockers, ncRNAs as, 267

blood: absorption of nutrients into, 979 calcium ion concentration in, 1073–75, 1074f, 1075f carbon dioxide in, 1035, 1036 circulation of, in rapid response to hemorrhage, 1138, 1139f in closed circulatory systems, 1012 composition of, 1014–16 as connective tissue, 863f diffusion of oxygen in, 1025 donating, 1132 gas transport in, 1034–36, 1035f, 1036f glucose concentration in, 867, 868, 868f hormones and energy-yielding molecules in, 1067–70, 1068t loss of (See hemorrhage) partial pressure of oxygen in, 1034–35, 1035f redistribution of, in rapid response to hemorrhage, 1138, 1138f viral diseases of, 393f blood cells, 953 blood clotting: after hemorrhage, 1132 cells involved in, 1015–16, 1016f positive feedback loop for, 870, 871f blood doping, 1081 Blood Falls, 629, 629f blood flow: in closed circulatory system, 1011f, 1012–14 heat exchange rate and skin’s, 1004, 1005f and relationship of blood pressure, resistance, 1022–23 blood flukes, 707 blood glucose concentration: and insulin, 995 and insulin/glucagon, 1069, 1070f range for, 996, 997f blood pressure: and baroreceptor evolution, 1135 and baroreceptor function in mammals, 1136–37 baroreceptor sensing of, 1133–35, 1134f and blood volume, 1132–33, 1132f, 1133f defined, 1018 and hemorrhage, 1132–33, 1132f, 1133f hypertension, 1038 negative feedback loops for, 869, 870f redistribution of blood in response to, 1138, 1138f relationship of blood flow, resistance and, 1022–23 resistance and cardiac output as factors in, 1023–24, 1023t, 1024f blood sugar. See glucose. blood types, 365, 365t blood vessel disease, 1038 blood vessels: and antidiuretic hormone, 1065 in closed circulatory systems, 1011f, 1012–14

comparative features of, 1020f muscle in, 954 treatment for blocked, 1038, 1039f types of, 1019–22 See also capillaries blood volume: and blood pressure, 1132–33, 1132f, 1133f distribution of, 1138, 1138f and hematocrit, 1142, 1143f blooming, of flowers, 846–48, 847f blowflies, 943, 943f, 1229 blubber, 1004 blue jays, 1183f, 1226 blue-light receptors, 793 blue poison dart frogs, 1225f blue-ringed octopus, 711f, 712 blue tits, 1205f, 1229 blue whales, 1023, 1272 BMI (body mass index), 1006 BMP4 protein, 510 BMR (basal metabolic rate), 998 bobcat, 754f body axes: and maternal effect genes, 419–20, 420f in plants vs. animals, 415, 415f body cavities: of bilateria, 692–93, 692f hemolymph in, 1011, 10111f body compartments, for internal fluids, 872–73, 872f body fat. See obesity. body fluids: of animals, pH of, 868t filtration of, 1045–47, 1045f loss of, in endotherms, 1003 in secondary response to hemorrhage, 1140, 1141f secretion of wastes from, 1046–47, 1046f body forms: of animals (See animal bodies) of fungi, 606–7, 607f, 608f bodyguard wasp, 797 body mass: brain mass vs., 906, 907f and metabolic rate, 999, 999f body mass index (BMI), 1006 body organization, in animals, 859–65, 865t body patterns: and Hox genes, 510–12 and spatial expression of development genes, 509–10 body plans: of angiosperms, 761 of animals, 689–90, 689f, 690f of annelids, 714–15, 715f of arthropods, 718–19, 719f of bony fishes, 740, 740f, 741 of cnidarians, 704, 704f, 705 of crustaceans, 725, 725f of echinoderms, 727, 727f of flatworms, 706, 706f of mollusks, 710, 710f of rotifers, 708–9, 708f of sponges, 703, 703f

body surfaces: gas exchange across, 1025 and innate immunity, 1109–10 body temperature: of ectotherms vs. endotherms, 1003, 1003f homeostatic control system for, 868–69, 869f as homeostatic variable, 868t and production efficiency, 1250, 1250f regulation of, 1002–6 body weight, excess, 999, 1006 Boehmeria nivea, 776 Bohr effect, 1040 Bolotin, Alexander, 275 bombardier beetle, 1224–25, 1225f bonds, chemical. See chemical bonds. bone marrow, in immune systems, 1115 bone marrow transplants, 426 bone(s): of birds, 751, 751f components of, 952 as connective tissue, 863f human diseases of, 966 and parathyroid hormone, 1074 skeletal muscle and, 954, 954f bonobos, 1197 bont tick, 720f bony fishes, 740–42 endoskeletons of, 952 See also fishes; osteichthyans bony skeletons, of osteichthyans, 740–42 Bordetella pertussis, 569, 578 boron, 802t Borrelia burgdorferi, 445, 446 Bosch, Carl, 809 Bos gaurus, 1292 Bos javanicus, 1292, 1293f Bothrops jacara, 1284 Botrychium lunaria, 646f bottle cells, 1102, 1102f bottleneck effect, 490 bottom-up control, 1231–32, 1232f botulism, 572 Boveri, Theodor, 355 Bowman, William, 1047 Bowman’s capsule, 1047–49 Boyer, Paul, 156, 157 Boyle’s law, 1027, 1028f, 1030 Boysen-Jensen, Peter, 786–87 1,3-BPG, 175f Brachiopoda and brachiopods characteristics of, 695t, 709, 709f origins of, 545 Brachiosaurus genus, 547 Brachychiton genus, 763f bracts, 775, 775f BRAIN Initiative, 904 brain(s): in central nervous system, 882 defined, 881 digestive-system control by, 985 divisions of, 905–6, 907f energy source for, 997 evolution of myosin and, 956–57, 957f forebrain and complexity of, 906, 907f

INDEX

INDEX I-7

I-8 INDEX

INDEX

brain(s), continued functions of, 910, 912–15f, 912–16, 915t imaging studies of, 919–20, 919f major structures of, 910, 912f mass of, 906, 907f of musicians vs. nonmusicians, 920–21 negative feedback loops involving, 869 in nervous system, 905 nervous tissue in, 861f of primates, 548 prion diseases of, 401–3 respiratory center of, 1036–37, 1037f viral diseases of, 393f brainstem: in nervous system, 912 in response to hemorrhage, 1133, 1135, 1138 branched-stem systems, of plants, 658, 659f branching air tubes, 865–66, 866f Branchiostoma genus, 729 Brassica genus, 792 Brassica oleracea, 470, 470f brassinolide, 786t brassinosteroids, 786t, 792 Brazilian arrowhead viper, 1f BrdU (bromodeoxyuridine), 919 breathing: control of, 1036–37, 1037f by mammals, 1030 See also respiratory systems; ventilation breathing rate, 870, 870f breathing reflex, 1138, 1139f breeding: captive, 1292, 1292f selective, 469–71 See also reproduction Briggs, Winslow, 787–89, 788f Brighamia insignis, 682, 682f Brinegar, Chris, 1214 brittle stars, 727, 728f broccoflower, 470 broccoli, 470 bromodeoxyuridine (BrdU), 919 5-bromouracil, 310 bronchi, in respiratory system, 1028 bronchioles: and asthma, 1038–39, 1039f in respiratory system, 1028, 1029f smooth muscle contraction in, 860, 861 bronchoconstriction, 1039 bronchodilators, 1039 brooding behavior, 1261 Brooker, Robert, 119 Brower, Lincoln, 1226 brown adipose tissue, 1006 brown algae, 591, 1158f brown bear, 633, 634 brown fat cells, 97 Brownian motion, 36 Browning, Adrian, 655–57 Bruneau, Benoit, 1014 brush border: in digestive system, 978 of proximal tubule, 1049, 1051 brush border enzymes, 980–81, 981f

Brussels sprouts, 470 Bryophyta and bryophytes, 791 ecological role of, 648–49 overview, 644 and plant nutrition, 812 reproduction of, 651–53f Bryozoa and bryozoans, 695t, 709, 709f, 731f Bt crops, and host plant resistance, 1227 bubonic plague, 555–56, 577 buccal pumping, 745 Buck, Linda, 944–45f, 944–46 budding, in animal reproduction, 1085, 1085f buds: axillary, 770 of flowering plants, 762 and plant hormones, 790 bud scales, 774, 775f buffalo, 1157, 1158f, 1291 buffalo clover, 1286 buffers, 42, 43 Buffon, George, 459 bulbnose unicorn fish (Naso tonganus), 566 bulk flow, in long-distance plant transport, 825–26, 825f, 826f bundle-sheath cells, 179, 180f, 804 burdock seeds, 1231f Burgess Shale, 544 Burkholderia pseudomallei, 577 Burmese pythons, 1257, 1276–77, 1277f Burton, Harold, 920 burying beetles, 1197 Bush, Guy, 506 butterflies, 724 and island biogeography, 1245, 1245f muscular-skeletal system of, 952 sensory systems of, 946 species interactions, 1225f, 1226 buttress roots, 779, 779f

C

C. See cytosine. cabbage, 470 Cacops genus, 743, 744f cacti: insect herbivores effects on, 1228, 1228f spines of, 775 Cactoblastis cactorum, 1228, 1228f cactus finches, 461t cactus moth, 1228, 1228f cadang-candang, 401 Cade, Robert, 876–79 Cade, Tom, 1292 cadherins, 209, 210f caecilians, 745, 746f Caenorhabditis elegans: gene regulation in, 300 genome projects with, 458 as model organism, 414, 414f, 415 morphological classification of, 698 in mRNA silencing experiments, 272–73 neurons of, 882 reproduction, 717

café marron, 1280–81, 1281f caffeine, 196 Calamospiza melanocorys, 1198 calcitonin, 1074 calcium: as essential nutrient, 972 plant nutrition, 802t calcium-dependent protein kinases (CDPKs), 785 calcium ions, 34 in animal bodies, 874 and cell junctions, 209, 213 at chemical synapses, 893 in cortical reaction, 1090 for cross-bridge cycle, 957–58, 958f electrical excitation and concentration of, 958, 959f hormonal regulation of, 1073–75, 1074f, 1075f muscular-skeletal systems and homeostasis for, 953 in myogenic heart, 1017 and osteoporosis, 966 and plant behavior, 785 regulation of muscle contraction by, 958, 958f and smooth ER, 90 calculation, as BioTIPS strategy, 20 Caldicellulosiruptor bescii, 579 calico cats, 377, 378f California condor, 1292, 1292f California Current, 1164 California sea slugs, 917 Callaway, Ragan, 1150–51 Calliarthron genus, 587f callose, 849, 851 calluses of plants, 789, 790f calmodulin, 785 Calopogon pulchellus, 1231 calories, 998 calorimetry, 998, 998f Calvin, Melvin, 175, 176, 178 Calvin cycle, 174–78 carbohydrate synthesis in, 174–78 and C4 plants, 804 defined, 164 determination of, 176–78 overview, 166, 166f Calypte anna, 752f Cambrian explosion, 544–45 Cambrian period, 538, 544–45 animals in, 687–88, 688f and Hox genes, 512 camellia plant, 805f camels, 1175–76 camouflage, 1225f, 1226 cAMP (cyclic adenosine monophosphate): cell communication and, 192–94, 193f and plant behavior, 785 speed of production of, 194, 195, 195f Campephilus principalis, 1270, 1270f CAM plants, 179, 180f Camponotus ferrugineus, 1230f CAMs (cell adhesion molecules), 208, 209, 210f, 417 Canada, 1167, 1167f Canada lynx, 1226, 1226f

cancer: and cell adhesion molecules, 209 and cell division proteins, 314–16, 315f and cytotoxic T cells, 1123 epigenetic changes associated with, 380–81, 381t glycolysis in cancer cells, 149–50, 150f and growth properties of cells, 320–21, 320f and mutations, 314–21, 316t, 318t, 319f, 320f and non-coding RNAs, 279 progression and effects of, 314, 315f proto-oncogene mutations, 316–17, 317f radioisotopes in treatment of, 29 and tobacco smoke, 1040 and tumor-suppressor genes, 318–20, 318t, 319f viruses as cause of, 317–18, 318t, 1109 See also mutations; specific types of cancer Candida albicans, 609 Canidae and canids, 519, 1096 Canis genus, 519 Canis lupus: classification of, 518 as invasive species, 1275, 1276f selective breeding in, 470, 470f species interactions with, 1232, 1233f Cann, Rebecca, 554 cannabinoids, 679, 681 Cannabis genus, 679–81, 680f Cannabis sativa, 776 Cannon, Walter, 867 cannula, 1132 CAP (catabolite activator protein), 291, 292f Capecchi, Mario, 743 capillaries: in closed circulatory systems, 1012 in digestive system, 979f function of, 1020–21, 1021f of nephrons, 1048 peritubular, 1048 in renal glomerulus, 1049, 1049f Starling forces in, 1140, 1142f vasa recta, 1048 capping, 250 Capra pyrenaica, 1292 capsids, 393 CAP site, defined, 286 capsules, of bacterial cells, 78 captive breeding, 1292, 1292f captured energy, 168 capuchin monkey, 549f carapaces, 725 carbohydrate metabolism: and fat and protein metabolism, 159, 159f smooth ER in, 90 carbohydrates, 48–52 in absorptive state, 992, 992f attachment of proteins to, 112–13, 113f defined, 48 digestion of, 976, 980–82, 981f in membrane structure, 107, 107f

metabolism of (See cellular respiration) organic molecules from, 971 from photosynthesis, 174–78 polysaccharides, 51–52, 52f sugars, 49–50, 50f carbon: antibiotics as bacterial source of, 574–75 archaeal and bacterial sources of, 573–74, 573f atomic mass of, 29 atoms of, 45–48 in covalent bonds, 31f double bonds between, 32 isotopes of, 29 in mass of living organisms, 29 plant nutrition, 802t sporophyte uptake of, 657–58 carbon atoms: α-carbons, 56 in covalent bonds, 46, 46f and functional groups, 46, 47t isomers of molecules containing, 46, 47, 48f carbon cycle: bacteria and archaea in, 573–74 human impact on, 1263, 1263f carbon-14 dating, 536 carbon dioxide: in air, 1024 bryophytes and atmospheric, 648–49 in Calvin cycle, 175–76, 175f, 177f and cellular respiration, 152f in circulatory system, 1010 effects of increased atmospheric, 1264– 64f, 1264–65 forms of, in blood, 1035, 1036 and greenhouse effect, 1260–61, 1260f, 1261t and hemoglobin’s affinity for oxygen, 1035, 1036f modeling molecule of, 32 in photosynthesis, 165, 166f and plant nutrition, 804 plants and atmospheric, 649–50, 650f in respiratory system, 1028 carbon fixation phase (Calvin cycle), 175, 175f, 176 carbon-hydrogen bonds. See hydrocarbons. carbonic acid, 41, 42, 1036 carbonic anhydrase, 1036 carboniferous chondrites, 71 Carboniferous period: and origins of life, 544 plants in, 649, 649f and vertebrates, 744 carbon monoxide, as neurotransmitter, 896 carboxyl groups, 52f, 56, 57, 57f Carcharhinus albimarginatus, 739f Carcharias taurus, 739f Carcharodon carcharias, 739 carcinogens, 314 carcinomas, 320–21 Carcinus maenas, 1189, 1189f cardiac angiography, 1029

cardiac cycle: diastole and systole phases of, 1018, 1018f and electrocardiogram, 1019, 1019f events of, 1017f, 1019 cardiac muscle: in animal bodies, 860, 861f and cell communication, 185 cells of (See myocytes) effects of myocardial infarction on, 1038 force generation by, 953–54 and multicellularity, 211 and myogenic heart, 1017 cardiac output (CO): as factor in blood pressure, 1023–24, 1023t, 1024f in response to hemorrhage, 1134–35, 1138 cardiovascular diseases, 1010, 1037 Carex subspathacea, 1252f Cargill, Susan, 1252 Caribbean Sea, 1172, 1172f caribou, 755f carnations, 794 Carnegiea gigantea, 676f Carnivora and carnivores, 518 and digestive systems, 971 essential nutrients for, 972 carnivores, in food chains, 1248, 1248f carnivorous plants, 801 Carolina parakeet, 1272–73 carotenoids, 98 absorption and action specrtra, 169, 169f and plant nutrition, 804 structure and function of, 168, 168f carotid arteries, 1133, 1135 carpellate flowers, 844, 844f carpels: defined, 672, 841 developmental genetics of, 431 of flowering plants, 674, 674f gametophyte production in, 841 Carpilius maculates, 725f Carpodacus mexicanus, 503 carriers, 119f, 119n* See also transporters Carroll, Sean, 694 carrots, 763, 855 carrying capacity, 1211–12, 1259–60, 1259f cartilage, 863f in endoskeletons, 952 and multicellularity, 215, 215f cartilage-hair hypoplasia (CHH), 266, 278 cartilaginous fishes, 738–40, 739f, 952 cartilaginous skeletons, of chondrichthyans, 739–40, 739f Cas2 gene, 275, 276 Casparian strips, 824 caspase-12 gene, 550 caspases, 199f, 200, 318–19 Cas9 protein, 443 Castanea crenata, 1277 Castor canadensis, 1205, 1206, 1206t catabolic reactions:

defined, 137 requirements and function of, 137–38, 137f catabolism, defined, 84 catabolite activator protein (CAP), 291, 292f catabolite repression, 291 catalase, 95, 131 catalysts: defined, 36, 131 RNA molecules as, 135–36f, 135–37, 137t cataracts, 947, 948f catastrophism, 459 catecholamines, 895 caterpillars: ecological study of, 1152–54, 1153f, 1154f kin selection, 1195, 1195f and plant behavior, 797 catfish, sensory systems of, 925, 946 Catharanthus roseus, 664, 1284 cation exchange, 807 cations, defined, 34 cats, inheritance patterns in, 377, 378f Cattleya genus, 677f Caudipteryx zoui, 750, 750f cauliflower, 470 Cavalli-Sforza, Luca, 408 CCK (cholecystokinin), 985 CDKs (cyclin-dependent kinases), 318, 327–29 cDNA (complementary DNA), 438, 944, 945 cDNA libraries, 438, 439 CDPKs (calcium-dependent protein kinases), 785 CD4 proteins, 1121, 1128 CD8 proteins, 1122 Ceanothus genus, 812 Cech, Thomas, 136 cecums, 980 cell adhesion, 96, 96f, 417, 417f cell adhesion molecules (CAMs), 208, 209, 210f, 417 cell biology, 13, 13f, 69 cell bodies, of neurons, 882, 883f cell communication, 183–201 apoptosis, 196–200, 197t, 198f, 199f cell-to-cell communication (See cell-tocell communication) cellular receptors, 187–90 cellular response, 184, 184f, 190–95 defined, 183 distance between cells in, 185–86, 185f in homeostasis, 870–72 hormonal signaling, 195–96, 195t by neurons, 892–99, 896t, 897f, 899f overview, 183–87 signal transduction, 190–95, 191f, 193–95f three-stage process of, 186–87 cell cycles, 142 defined, 324 of eukaryotes (See eukaryotic cell cycle) and tumor-suppressor genes, 318, 319f cell density, signaling related to, 185

cell differentiation, 215 in animals, 424–29, 425f, 426f, 426t, 428–29f defined, 283, 414 of muscle cells, 427–29 and positional information, 415f, 416 of stem cells, 424–27, 425f, 426f, 426t cell division: bacterial, 404–6, 405f in bacteria vs. eukaryotes, 333–34, 334f and cancer, 314–16, 315f and cell cycle, 325–27, 326f chromosome compaction in, 239, 240f defined, 323 in embryonic development, 1099–1101 and epidermal growth factor, 191f lymphocyte proliferation, 1117, 1118 and mitosis (See mitosis) mitotic, 330–34 and plant hormones, 789–91, 790f and positional information, 415f, 416 and tumor-suppressor genes, 319, 319f, 319t cell elongation, 789–91 cell expansion, 791–92 cell-free translation systems, 254 cell junctions: anchoring junctions, 208, 209f cell adhesion molecules (CAMs), 209, 210f defined, 208 gap junctions, 211–13, 211–13f middle lamella, 213, 213f and multicellularity, 208–14, 208t, 209f–14f plasmodesmata, 213–14, 214f tight junctions, 209–11, 210f, 211f types of, 208t cell-mediated immunity, 1117–18, 1117f, 1121–23, 1122f, 1124f cell membranes. See plasma membranes. cell migration, 415f, 416 cell nucleus, 9, 88–89 of animal cells, 80f in apoptosis, 196, 197f chromosomes in, 88–89, 89f defined, 88 and endomembrane system, 88, 88f of plant cells, 81f post-translational protein sorting to, 101–2, 102f systems biology approach to, 102, 103f cell organization, and proteome, 9f cell plate, 332, 334f cell proliferation, 318–19, 318t, 319f cell receptors. See receptors. cells, 69–105 of animals, 687 in animal tissues, 860–63 ATP for endergonic reactions in, 130– 31, 130f, 131t in blood, 1014–16 and blood pressure, 1132 in body organization, 860, 860f cancer and growth properties of, 320–21, 320f cellular responses to other, 184, 184f

INDEX

INDEX I-9

I-10 INDEX

INDEX

cells, continued cytosol, 83–88, 84f, 85t, 86f, 87f death of (See apoptosis) defined, 2, 3f distance between, in cell communication, 185–86, 185f endomembrane system, 90–96 eukaryotic (See eukaryotic cell cycle; eukaryotic cells) and evolution of viruses, 400–401 fluids inside and outside, 37f intracellular fluid volume and shape of, 873, 873f and microscopy, 75–78 of nervous system (See nervous system cells) in organ systems, 884 origin of, on Earth, 69–75, 70f, 71f, 73f, 74f pathogenic bacterial attack on, 577–78, 577f presynaptic and postsynaptic, 892, 893, 893f protein products and characteristics of, 81–82 and protein sorting, 99–102 in retina, 941, 941f semiautonomous organelles, 96–99 sizes and shapes of, 82–83, 82f structure and function of, 78–83 summary, 104–5 systems biology, 102–3, 103f, 103t tissue production by, 214–15 See also specific cell types cell signaling: and multicellularity, 203–4, 203f, 215 by neurons, 888, 888f and plant behavior, 784–85, 785f with plasma membrane, 96, 96f and proteome, 9f stages of, 186–87, 186f See also cell communication; cell-tocell communication cell-signaling proteins, 510 cell surface receptors, 188–89, 188f, 196 cell theory, 69 cell-to-cell communication: defined, 184 distance between cells in, 185–86, 185f multicellularity, 209, 213 process of, 184–85 See also cell communication cell-to-cell contacts, 416–17, 417f cellular membranes. See plasma membrane. cellular regulation, of metabolic pathways, 139 cellular respiration, 145–63 and anaerobic respiration, 159–60, 160f ATP synthase, 155–59 citric acid cycle in, 151–52f, 151–53 defined, 145 fermentation, 160–61, 161f glycolysis in, 147–50 and metabolism, 159, 159f overview, 145–47, 146f oxidative phosphorylation in, 153–55, 154f

and photosynthesis, 165, 165f pyruvate breakdown in, 150–51, 150f summary, 161–62 cellular responses: defined, 184 to hormones, 195–96, 195t overview, 184, 184f in plant cell signaling, 784f to positional information, 415–16, 415f reversal of, 193, 194 signal transduction pathways and, 190–95, 191f, 193–95f stages of, 186–87, 186f cellular water potentials, 821–22, 822f cellulose, 971 in digestive system, 978 and green algae, 594–95f, 594–96 molecular structure of, 51f, 52 plant cell walls, 207, 207f cell walls: cellulose in green algae vs., 595–96 defined, 203 expansion of, in plants, 768, 768f and middle lamella, 213 and multicellularity, 206–8, 207f of plant cells, 81f primary and secondary, 207–8, 207f in prokaryotes, 78 of prokaryotic cells, 568–69, 569f and turgor pressure, 820 Cenozoic era, 544 Centaurea diffusa, 1150–51, 1151f centipedes, 721, 721f central cells, 850, 851 central dogma, of gene expression, 246–47 central nervous system (CNS): embryonic development of, 1103–4, 1103f energy sources for, 993 evolution of, 905 gray and white matter in, 908, 909, 909f and peripheral nervous system, 882, 882f protective structures of, 909, 910f and reflex arcs, 884 sensation processing by, 926–27 viral diseases of, 393f central region, of plants, 430 central vacuoles, 81f, 94, 94f, 768 central zone, of plants, 430 centrioles, 84, 331 centromeres, 330, 342, 342f centrosomes, 331 of animal cell, 80f microtubules in, 84 Centruroides genus, 720, 720f cephalization, 690, 706, 905 Cephalochordata and cephalochordates, 729–30, 730f, 1013 Cephalopoda and cephalopods, 710–14, 711f, 711t, 713f Ceratium hirundinella, 612f cereal plants, 786 cerebellum, function of, 910 cerebral cortex: evolution and development of, 906, 916 folding of, 907f function of human, 913–14, 914f sensory and motor information in, 915f

and sensory systems, 941 cerebral ganglia, 706 cerebrospinal fluid, 909 cerebrum: evolution and development of, 916 evolutionary increases in, 906 function of human, 913–15f, 913–16 nociception in, 934 cervix, 1093, 1098 Cervus canadensis, 1199f Cervus elaphus, 486, 1232 Cervus elaphus nannodes, 1210, 1211f Cestoda and cestodes, 706t, 707 Cetacea and cetaceans, 465–66, 964 CF. See cystic fibrosis. CFTR gene (cystic fibrosis transmembrane regulator gene), 16, 16f cGMP (cyclic guanosine monophosphate), 940, 941 chalk grassland, 1159, 1159f Chambers, Geoffrey, 527 channel proteins, 1053–54, 1054f channels: and membrane transport, 117–19, 117f, 118f and plant transport, 819 transporters vs., 120 chaperone proteins, 101, 102, 102f character displacement, 1221–22, 1222t characters: defined, 350, 350f, 523 inheritance pattern of two, 354–55, 354f shared derived, 523–25 shared primitive, 523, 524f See also inheritance; traits character states, 523 Charadrius vociferus, 1180 Chara zeylanica, 643f Chargaff, Erwin, 226, 226t, 228 charge, of solutes, 114 charged tRNA, 257 See also aminoacyl-tRNA checkpoints (checkpoint proteins), 318, 319f, 327–28, 327f cheetahs, 961, 1190, 1190f Chelicerata and chelicerae, 719t, 720–21 Chelonia mydas, 748f chemical bonds, 30–35 covalent, 31–32, 31f, 32f hydrogen, 33, 33f ionic, 34, 34f, 34t and molecular shapes, 34–35, 35f peptide, 58, 58f polar vs. nonpolar, 32, 32f summary, 43 See also atoms chemical communication, 1191 chemical defenses, 703, 1224–26, 1225f chemical degradation, green algae defense against, 594–95 chemical equilibrium, defined, 36, 130 chemical evolution, 73 chemical gradients, 114–15, 115f chemical mutagens, 310, 310f, 310t chemical potential energy (chemical energy), 128

chemical reactions: and change in free energy, 129–30, 129f condensation, 48 defined, 36, 127 dehydration, 48 endergonic reactions, 130–31, 130f, 131t and energy, 127–31, 128t, 129f, 130f, 131t enzymes and rates of, 131–32, 132f equilibrium for, 130 hydrolysis, 40, 40f, 49, 49f and temperature, 1002 chemicals, epigenetic effects of, 379–80, 380f chemical selection, 73–75, 74f chemical signals, 870–72 See also chemical communication chemical synapses, 892–99 and acetylcholine discovery, 896–98, 897f electrical vs., 892–93 neuron responses to inputs at, 893–95, 895f and neurotransmitter classifications, 895–96, 896t neurotransmitters at, 893, 894f postsynaptic membrane receptors in, 898–99, 899f structure and function of, 894f chemiosmosis, 138, 147, 153, 155–56, 156f chemistry: inorganic, 23 organic, 23, 45 chemoautotrophs, 572–73 chemoreception, 942–47 mammalian olfactory receptors, 943– 45f, 943–46 sensory hairs for, 942–43, 943f taste buds, 946, 946f chemoreceptors: and breathing reflex, 1138, 1139f defined, 927 and respiratory centers, 1037 in sensory hairs, 942–43, 943f Chen, Jun-Yuan, 544 chestnut blight, 615, 1277, 1277f Chetverikov, Sergei, 481 CHH (cartilage-hair hypoplasia), 266, 278 chiasma, 335 Chiba, Yasutane, 98 chickens: as model organisms, 414 pattern formation and foot of, 510 Rous sarcoma virus in, 317–18 skeletal muscle fibers of, 961 chigger mite, 720, 720f Chilopoda, 721, 721f chimpanzees: chromosome structure and number in, 475, 475f cognitive learning by, 1183, 1183f evolutionary studies of, 530–31 genome of humans vs., 550 and human evolution, 548 mating systems of, 1197 molecular clock for, 530 reproductive strategies of, 1205f skulls of humans vs., 512

Chimpanzee Sequencing and Analysis Consortium, 550, 957 Chinese liver fluke, 707, 708f Chinese river dolphin, 1280 CHIP28 protein, 117–19, 118f chitin, 605 in exoskeletons, 951–52 in extracellular matrix, 206 molecular structure of, 52 chitons, 710, 711f, 712t Chlamydomonas genus, 87f, 583f, 597t Chlamydomonas reinhardtii, 94, 543 Chlorarachniophyta, 591, 592t Chlorella pyrenoidosa, 176, 177f chloride ions, 34, 34f, 893, 898 chlorine, 802t chlorofluorocarbons, 1260, 1261t Chlorokybus atmophyticus, 643f chlorophyll, 98 defined, 165 in primary production, 1253, 1253f chlorophyll a: absorption and action spectra of, 169, 169f defined, 168, 168f chlorophyll b: absorption and action spectra of, 169, 169f defined, 168, 168f Chlorophyta, 587, 592t chloroplast genomes, 98 composition of, 449 and evolution of eukaryotes, 542–43 inheritance patterns for, 382–84, 382f, 383f and proteins, 381, 382f chloroplasts, 97–99 cytochrome complexes of mitochondria and, 171–72, 172f in endosymbiosis theory, 98–99, 99f extranuclear inheritance, 381–84, 382f, 383f genetic material and division of, 98, 98f photosynthesis in, 165–66, 166f photosynthetic pigments in, 168 of plant cells, 81f and plant nutrition, 804 post-translational protein sorting to, 101–2, 102f structure and function of, 97–98, 97f chlorosis, 805 choanocytes, 703, 703f Choanomonada and choanoflagellates, 190, 592, 592t, 593f, 689 chocolate, 986 cholecystokinin (CCK), 985 cholera, 445, 985–86, 1143 cholesterol: and fluidity of membranes, 110 as hormone precursor, 1059 and organic molecules, 55, 56f structure and function of, 1061, 1061f choline phosphotransferase, 112f Cholodny, N. O., 787 Chondracanthus canaliculatus, 1242–43, 1243f Chondrichthyes and chondrichthyans, 738–40, 739f

chondrocytes, 215, 215f chondroitin sulfate, 206, 206f Chondrus crispus, 587f Chordata and chordates: basic characteristics, 695t characteristics of vertebrates, 734–36, 735f, 736t common features of, 518 as deuterostomes, 726 embryonic development in, 1103 invertebrate characteristics of, 728–31 nervous systems of, 905, 906f origins of, 545 segmentation, 693, 693f See also Vertebrata and vertebrates chorion, 746, 747f, 1097 chorionic gonadotropin, 1095 chorionic villi, 1097 chromatin: of animal cells, 80f ATP-dependent chromatin-remodeling complexes, 296–97, 297f defined, 238 epigenetic effect of modifications in, 374, 374t of eukaryotic cells, 88 gene regulation and, 296–98 and non-coding RNAs, 270, 271f and nuclear matrix, 239, 239f of plant cells, 81f and tumor-suppressor gene expression, 320 chromatin-remodeling complexes, 298, 299f chromatography, 62, 63, 176, 177–78f chromoplasts, 98 chromosomal compaction, 239, 240f in bacteria, 403–4, 404f in mitotic cell division, 330, 330f and X-chromosome inactivation, 378–79, 379t chromosomal DNA, 435–37, 436f, 436t chromosomal loops, of bacteria, 403–4, 404f chromosomal rearrangements, 342 chromosomal translocation, 316, 316f chromosomes: of bacteria, 403–4, 403f, 404f in bacterial/archaeal genomes, 445, 446 in cell nucleus, 88–89, 89f defined, 221, 238 DNA structure in, 224f of eukaryotes, 448–50, 449f, 449t evolutionary changes in, 474–75, 475f genetic map of, 387–88, 388f and hexaploidy, 1214–15 inheritance and occurrence of, 324–25, 324f linkage/recombination and, 384–88, 385f, 387f, 388f loss of, 320 in meiosis, 334–40, 335f, 336f, 338– 39f, 340t microscopic examination of, 324–25, 325f in mitotic cell division, 330–33 molecular structure of, 238–40

replication of, 330, 330f sets of, 325, 342, 343 structure and number of, 341–46, 345t telomeres of, 237f and transposable elements, 452–54, 453f, 454f vectors vs., 435 chromosome territory, 89, 89f chromosome theory of inheritance, 355–57, 356f, 357f chronic myelogenous leukemia (CML), 316 Chroococcus genus, 565f chrysanthemums, 794 Chthamalus stellatus, 1222–24 Church, George, 574 chylomicrons, 983, 983f, 984, 993 chyme, 978, 984 Chytridiomycota, 606, 606f, 611, 612f chytrids, 611, 612f cigarette smoking. See smoking. cilia: movement by, 86, 87f, 88 of protists, 583, 583f in sensory systems, 943f, 944 structure of, 87f ciliated crowns, 707–9, 708f ciliates, 583, 598, 599, 600f Ciliophora, 589, 592t Cimbex axillaris, 422 Cinchona officinalis, 1284, 1285f cinchona tree, 1284, 1285f circadian rhythms, and plant behavior, 783 circulation: placental and pulmonary, 1096 in vertebrate heart, 1016–17, 1016f circulatory systems, 1011–24 after hemorrhage, 1143 and baroreceptor evolution, 1135 blood composition, 1014–16 blood pressure, flow, and resistance, 1022–24, 1023t, 1024f blood vessels, 1019–22 defined, 1010 and gas transport in blood, 1034–36, 1035f, 1036f organs in, 864 public health issues related to, 1037– 38, 1038f summary, 1040–41 types of, 1011–14, 1011f, 1013f, 1014f valves in, 1022 vertebrate heart, 1016–19 Cirripedia, 725, 725f cis-acting element, 289 cis double bonds, 47 cis-effect, 289 cis Golgi, 91 cis-retinal, 940 cisternae, 90 cisternal maturation model, 91 cis-trans isomers, 47, 48f CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora), 666 citrate, 151, 151–52f citrate synthase, 153

citric acid cycle, 146, 146f, 147, 151–52f, 151–53 citrus fruits, 986 citrus plants, 856 clades, 519 of mammals, 756, 756f of vertebrates, 734, 735f, 736t cladistic approach, 523–25 cladistics, 523–29 cladogram construction in, 523–25 maximum likelihood in, 525 phylogenetic relationships of flightless birds, 527–29 and primitive/derived characters of species, 523 principle of parsimony in, 525 cladogenesis, 502, 519 cladograms: principle of parsimony in selection of, 525 shared derived characters as basis for, 523–25 Cladonia, 632f Cladophora, 583f, 594–95, 623, 623f clams, 709, 711, 711f, 712t, 731f claspers, 740 classes: of echinoderms, 727, 728f, 728t of flatworms, 706–7, 706t, 707f of mollusks, 710–12, 712t in supergroups, 592t in taxonomy, 518 classical conditioning, 1182 claudin, 210 Claviceps purpurea, 611, 611f clay, 72, 806–7 cleavage, 690, 691f, 692 in embryonic development, 1099, 1100 holoblastic, 1100, 1100f, 1101 and implantation in mammals, 1101, 1101f meroblastic, 1100, 1100f cleavage furrow, 332, 334f cleavage phase (glycolysis), 147f, 148 cleavage-stage embryos, 1099–1101 Clements, Frederic, 1241 climate: and biological communities, 1160–63f, 1160–64 conifer adaptations to, 668, 670, 671f origins of life and, 545 climate change: and ecology, 1149 human impact on, 1260–62, 1261t species indicators of, 1290 climax communities, 1241 clitoris, 1093 cloaca: in digestive system, 975, 977f as reproductive organ, 1090 clonal deletion, 1125 clonal inactivation, 1125 clonal selection, in B cells, 1120, 1121f cloning: of endangered species, 1292–93, 1293f of genes (See gene cloning) Clonorchis sinensis, 707, 708f

INDEX

INDEX I-11

I-12 INDEX

INDEX

closed circulatory systems: blood flow in, 1011f, 1012–14 blood pressure and volume in, 1133 of cephalopods, 712 fluid compartments in, 872 closed conformations, 296 Clostridium acetylbutylicum, 473, 474f Clostridium botulinum, 572 Clostridium difficile, 572f Clostridium perfringens, 573 Clostridium symbiosum, 637 Clostridium tetani, 572 clover, 794 clownfish, 11, 11f, 12 clumped dispersion, 1204, 1204f clutch size, 483 CML (chronic myelogenous leukemia), 316 Cnidaria and cnidarians, 690f basic characteristics, 695t budding in, 1085, 1085f characteristics of, 704–5, 704t, 731f digestive systems of, 972, 973 nervous systems of, 905, 906f respiratory systems of, 1025 in succession, 1242 cnidocils, 705 cnidocytes, 705, 705f CNS. See central nervous system. CO. See cardiac output. CO2. See carbon dioxide. coacervates, 72–73, 73f CoA (coenzyme A), 150–51, 150f coactivators, 296, 296f coast redwood tree, 1214–15, 1215f Cobbania corrugata, 650, 650f cocci, 567 Coccidioides immitis, 618 cochlea: deafness caused by hair cells in, 948 structure and function of, 929, 930 cochlear duct, 930 coconuts, 401, 843, 843f cod, 1273, 1273f coding sequences: defined, 253, 253f mutations outside of, 306, 306t point mutations in, 305, 305t translation of, 252f coding strand of DNA, in transcription, 248 codominance, 365, 365t codons, 253, 253f coefficient of relatedness, 1194–95, 1194f coelacanths, 738, 741, 742f coelomates, 692, 692f coeloms, 692, 693, 706 Coen, Enrico, 431 coenzymes, 134 coevolution: defined, 681 of pollination, 681–82, 682f, 682t of seed dispersal, 682–83, 683f in seed plants, 681–83, 682f, 682t, 683f coexistence, 1219–24, 1220f, 1221f, 1222t, 1223–24f cofactors, 134

Coffea arabica, 679 cognitive learning, 1183, 1183f cogongrass, 1291, 1291f cohesin, 330 cohesion: in long-distance plant transport, 828–29, 828f of water, 40f, 41 cohesion-tension theory, 828–29, 828f cohorts, 1204 cold conditions: adaptation to, 1006 biomes and, 1169–70 conifer adaptations to, 668, 670, 671f and distribution of organisms, 1155, 1155f, 1158 See also body temperature; temperature cold desert biomes, 1169, 1169f Coleman, Douglas, 999–1002, 1001f Coleochaete pulvinata, 643f coleoptiles, 786, 852, 853f coleorhiza, 852, 853f colinearity rule, 423 collaboration. See communication and collaboration (core skill). collagen: in bone, 952 defined, 204 in extracellular matrix, 204–6, 204t, 206t nematodes and, 717 collared flycatchers (Ficedula albicollis), 483 collecting ducts, 1050f, 1051–53, 1052f, 1053f collenchyma tissue and cells, 216, 766 colligative properties, defined, 40 Collins, Francis, 16 Collip, James Bertram, 1071–73 colloid, 1065 colon, 980 colonial bentgrass (Agrostis capillaris), 484–85 coloration: flower, 845, 845f and species interactions, 1226 color blindness, 939, 939f colorization, staining vs., 75–76 color vision, 938–39, 939f Columba palumbus, 1193, 1193f columnar epithelial cells, 862 combinatorial control, 294 comb jellies, 731f commensalism, 1217, 1231, 1231f common ancestor: evolution from, 471–73, 471f, 472f, 472t and homologous genes, 473, 473f See also monophyletic groups common ancestors: and allopatric speciation, 502 on phylogenetic trees, 519 vertical evolution from, 531 common bile duct, 979, 980f common collared lizard, 748f common hepatic duct, 980f

common liverwort, 644f communication, 1190–92 cell (See cell communication) plant, 1, 1f by smart plants, 810–11 and social aspect of biology, 17 communication and collaboration (core skill): and HIV infection rate, 1128 social aspects of science, 17 thermal-imaging cameras in studies, 1004f communities and ecosystems, 1236–56 biomass production, 1252–54 food webs, 1248–51f, 1248–52 island biogeography, 1243–48 species richness, 1236–40, 1237f, 1238f, 1239t, 1240f succession, 1240–43 summary, 1254–55 community ecology, 1150f, 1152, 1236 community(-ies), 3, 3f climax, 1241 deep-sea vent, 71f, 72 defined, 1236 community stability, 1240, 1240f compaction, of cleavage-stage embryos, 1100, 1101 companion cells, phloem, 834–35, 834f compare and contrast, as BioTIPS strategy, 20 compartmentalization, of cells, 79 competence factors, 409 competent bacteria, 409 competent cells, 437 competition: in auditory communication, 1191 and coexistence, 1219–24, 1220f, 1221f, 1222t, 1223–24f defined, 1217 with invasive species, 1275, 1276f and life history strategies, 1213–15, 1214f, 1214t, 1215f occurrence rates, 1218–19, 1219f species interactions, 1218–21f, 1218– 24, 1222t, 1223–24f and succession, 1243 types of, 1217t, 1218, 1218f competitive exclusion principle, 1220 competitive inhibitors, 133f, 134 competitors, 1152 complementary base pairing, 227–28, 227f, 228f complementary DNA (cDNA), 438, 944, 945 complement proteins, 1112 complete flowers, 672, 844 complete metamorphosis, 724, 724f complexity: of microbiomes, 623–27, 624f, 626f, 627f of prokaryotic cells, 566–67 complicated processes, sorting out steps in, 20 compost, 806 compound eyes, 935, 936f compound leaves, 770, 770f

compounds, defined, 30–31 compression, and cell walls, 206–7, 207f computerized tomography (CT) scan, 919 concentration, of solutes, 38 osmosis to balance, 115–16, 115f, 116f and simple diffusion, 114 concentration gradients: across neuron membranes, 885–86, 886f, 887t and active transport, 120–21, 121f and electrical gradient, 886–87, 887f and membrane transport, 114–15, 115f and resting membrane potential, 886 condensation reactions, 48 conditioning, 1182–83, 1183f condoms, 1105f, 1106 conduction: of action potential, 891–92, 891f, 892f disorders of, 901–2, 901f heat exchange by, 1003f, 1004 conduction system, in plants, 766, 818 Condylura cristata, 734 cones: structure of, 937, 937f, 938, 938f visual pigments in, 938, 938f confocal fluorescence microscopy, 77f Confuciusornis sanctus, 750, 750f congenital analgesia, 369–70 congenital hypothyroidism, 901 conglomerate, 536 conidia, 609, 609f conifers (Coniferophyta), 644, 668–71f origin of, 546 water loss in, 833 conjugation: bacterial gene transfer in, 406–9, 406t, 407–9f and host plant resistance, 1227 connective tissues: cells in, 862, 863, 863f and multicellularity, 215, 215f Connell, Joseph, 1218, 1219, 1222–24, 1243 connexin, 211 connexon, 211, 211f consciousness, and cognitive learning, 1183 conservation biology, defined, 1280 conservation of energy, law of, 128 conservation strategies, 1287–93 conservative mechanisms, 228, 229f constant regions (C), immunoglobulin, 1118–20 constitutive genes, 282 constitutive mutants, in lac repressor studies, 289–93 contact-dependent signaling, 185, 185f contigs, 626 continental drift: origins of life, 540 and species distribution, 1175, 1176f continuous iteroparity, 1204, 1205f contraception, 1105–6, 1106f contractile pharynx, of nematodes, 1014 contractile tubes. evolution of heart from, 1012–14, 1014f contractile vacuoles, 94–95, 94f, 116, 116f

contraction: of skeletal muscle (See skeletal muscle contraction) of smooth muscle, 860, 861, 954 contrast, in microscopy, 75–76 control groups, 15, 1033 Conuropsis carolinensis, 1272–73 convection, heat exchange by, 1003f, 1004 Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), 666 convergence step (neurulation), 1103f, 1104 convergent evolution, 468–69, 469f Cook, Martha, 594–95 Cooper, Alan, 527–30 Cope’s giant salamander, 746 Coprinus disseminatus, 616f copulation, 1090 coral bleaching, 1290 coral crab, 725f coralloid roots, 667, 667f coral reefs, 705 biomes, 1172, 1172f as indicators of marine processes, 1290 origins of, 545 and temperature, 1155, 1155f, 1156f coral snake, 1225f, 1226 Corchorus capsularis, 776 corepressors, 293, 293f core promoters, 294–95, 294f Coriolis, Gaspard Gustave de, 1162 Coriolis force, 1162, 1162f cork cambium, 777 cork cells, 833–34 cork oak tree, 777 corn: as annual, 763 genetic engineering of, 1285 and host plant resistance, 1227 human domestication of, 683, 683f imperfect flowers of, 844, 844f as monocot, 763 and plant behavior, 787 root pressure refilling in, 828 seed germination and seedling growth in, 854f, 855 selective breeding of, 471, 471f structure of mature seeds, 853f transpiration from, 829 transposable elements in, 453, 453f cornea, 937 corn smut (Ustilago maydis), 617f corona, of rotifers, 707–9, 708f coronary artery disease, 1038 corpus callosum, 913 corpus luteum, 1094 Correns, Carl, 350, 364, 382–83 cortex: of cerebrum (See cerebral cortex) of plants, 766 cortical collecting ducts, 1051–53, 1052f, 1053f cortical reaction, 1089f, 1090 corticoid receptors (CRs), 1076–77 cortisol, 1068, 1069, 1076, 1077, 1127 Corwin, Jeff, 1280

Costanza, Robert, 1286 cost-benefit analysis, 1190 Cotesia rubecula, 797 cotranslational sorting, at endoplasmic reticulum, 99, 100f, 101, 101f cotton, 760, 773, 794 cotyledons: defined, 763 development of, 851 countercurrent exchange, 1005, 1005f, 1026, 1027 countercurrent multiplication systems, 1051 courtship rituals and displays, 1191, 1191f covalent bonds: and atoms (See chemical bonds) carbon atoms in, 46, 46f formation of, 31–32, 31f polar vs. nonpolar, 32, 32f Cowley, Allen, Jr., 1136–37 CpG islands, 298 C3 plants, 178, 179f C4 plants, 804 CAM plants vs., 179, 180f photorespiration in, 179, 180f crabs, 724–26, 725f, 961 cranes, 1199f cranial nerves, 908 cranium, 735 Crassulaceae plant family, 179 crayfish, 932 Crenarchaeota, 564 creosote bushes, 1157 crested porcupine, 754f Cretaceous-Paleogene event, 650, 666, 749, 752 Cretaceous period, 540, 547, 757 Crick, Francis, 226–27, 247 crickets, 499 Crinoidea, 727 crisis ecoregions, 1287 CRISPR-Cas system, 275–78, 277f, 442–44, 444f Crispr gene, 276 cristae, of mitochondria, 97, 147, 584–86, 585f, 586f critical innovations, 642f, 643 critical period, 1184 Crocodilia and crocodiles, 748–49, 749f baroreceptors of, 1135 circulatory system of, 1012 digestive system of, 977 double circulation in, 1012, 1013f origin of, 546 Crocodylus acutus, 749f crop, in digestive system, 975, 977, 977f croplands, soils, 806f crop milk, 977 crop plants: behavior of, 784, 797–98 endosperm of, 851 fruits of, 843 genetically engineered ABA receptor protein for, 831–32 reproduction of, 839 cross-bridge cycle: regulation of, 958, 959f

in skeletal muscle, 957–58, 958f cross-bridges, 955, 957 cross-fertilization, 351, 351f crossing over (chromosomes): and meiosis, 334, 335f recombinant and nonrecombinant offspring of, 386–87, 387f cross-pollination, 841 Crotaphytus collarus, 748f CRs (corticoid receptors), 1076–77 Crustacea and crustaceans: characteristics of, 719t, 724–26, 725f, 731f and multicellularity, 206 muscular-skeletal systems of, 951–52 respiratory systems of, 1034 sensory systems of, 928, 939 Crutzen, Paul, 1257 cryosphere, 628, 629f Cryphonectria parasitica, 615, 1277, 1277f cryptic female choice, 486 Cryptococcus neoformans, 617 Cryptomonads, 588, 589f Cryptomycota microsporidia, 612, 617 Cryptomycota phylum, 605, 606, 606f, 611, 612f Cryptosporidium parvum, 581, 589, 596 CT (computerized tomography) scan, 919 Ctenophora and ctenophores, 695t, 702, 702f, 731f C-terminus, 58, 58f, 254 CTR1 protein kinase, 791 cuboidal epithelial cells, 862, 1049f Cubozoa, 704, 704t cucumbers, 794 cud, 978 cumulus mass, 1089 cup fungi, 615 cupula, 932, 933 Currie, Alastair, 197, 198f Currie, David, 1238 Curvularia protuberata, 618–19, 619f Cuscuta genus, 797 Cuscuta pentagona, 815 cuticles, 647 dermal tissue in, 216 of ecdysozoans, 716 of nematodes, 717 of plants, 766, 773 and transpiration, 829 Cutler, Sean, 831, 832 cutworms, 797 Cuvier, Georges, 459 cyanide, 153 Cyanistes caerules, 1229 cyanobacteria: nitrogen fixation by, 1267 in primary succession, 1241, 1242f Cyanobacteria, 568 blooms of, 561 and chloroplasts, 99 diversity of, 564 fossilized prokaryotes and, 535 in microbiomes in fresh water, 629–30, 629f nitrogen fixation by, 808

and origins of life, 541 oxygen produced by, 1286 plant symbioses with, 812 structure of, 566 Cyanopsitta spixii, 1280 Cycadophyta and cycads, 644, 666–67, 666f, 667f cyclic adenosine monophosphate. See cAMP. cyclic electron flow, ATP from, 170–71, 171f cyclic guanosine monophosphate (cGMP), 940, 941 cyclic photophosphorylation, 170–71, 171f cyclin-dependent kinases (CDKs), 318, 327–29 cyclins, 327–29 CYCLOIDEA gene, 845–46, 846f cyclooxygenase, 108, 127 cyclostomes, 736–37, 737f Cyclotella meneghiniana, 590f Cynognathus genus, 1175 cystic fibrosis (CF): discovery-based science on, 16, 16f inheritance patterns for, 358, 358f phenotypic effects of single gene in, 364 probability of inheriting, 370 cystic fibrosis transmembrane regulator gene (CFTR gene), 16, 16f, 358, 364 cystolic enzymes, 134 cysts, of protists, 596, 596f cytochrome complexes: in cyclic photophosphorylation, 171, 171f in electron transport chain, 169 of mitochondria and chloroplasts, 171–72, 172f cytochrome oxidase, 153, 154f, 155, 160 cytochromes: b, 160, 171 b6, 171 b-c1, 153, 154f, 171, 172f b6-f, 171, 172f c, 153, 154f c1, 171 f, 171 cytogenetics, 324 cytokines, 1111 cytokinesis, 326 in meiosis, 339f in mitotic cell division, 332–33, 333f, 334f cytokinins, 786t, 789, 790f cytoplasm: in bacterial vs. eukaryotic cells, 102 and plasmodesmata, 213–14, 214f cytoplasmic extensions, of protists, 591, 591f cytoplasmic inheritance. See extranuclear inheritance. cytosine (C): in DNA, 224 molecular structure of, 64, 65 and O6-MeG, 227 cytoskeletal filaments, 85–88, 86f, 87f

INDEX

INDEX I-13

I-14 INDEX cytoskeletons: of animal cells, 80f attachment of transmembrane proteins to, 111, 111f of plant cells, 81f and proteome, 9f cytosol, 83–88, 214 of animal cell, 80f cytoskeleton function in, 84–85, 85t molecule synthesis and breakdown in, 83–84 motor proteins and cytoskeletal filaments in, 85–88, 86f, 87f of plant cells, 81f protein sorting in, 99, 100f in synthesis of membrane lipids, 112f systems biology approach to, 102, 103f turgor pressure and, 820 cytosolic leaflets, 107 cytotoxic T cells: antigen presentation to, 1123 attack against antigens by, 1118 in cell-mediated immunity, 1121 functions of, 1117, 1123, 1124f in graft rejection, 1127 in HIV/AIDS, 1128 structure of, 1116f Cyzenis albicans, 1152–53, 1154f

D

INDEX

Dactylorhiza sambucina, 478 Daeschler, Ted, 465 dahlias, 794 Dall mountain sheep, 1207–8 Dalton, John, 29 daltons (Da), 29 D-amino acids, 57 dams, 1265 Danaus plexippus, 1225f, 1226 dance of honeybees, 1192, 1192f dandelions: fruits of, 843 organ fusion in, 845 and plant behavior, 794 reproduction in, 839, 856 as r-selected species, 1213, 1214f seed germination in, 853 Danio rerio, 414, 414f Dantas, Gautam, 574–75 Daphnia pulex, 1086–87 Darimont, Chris, 1271 Dart, Raymond, 551 Darwin, Charles, 184, 458–61, 460f, 469, 477, 496, 513, 670, 715, 782, 786, 815, 1222 Darwin, Erasmus, 458, 459 Darwin, Francis, 184, 782, 786 data analysis, 1153–54, 1154f data interpretation, as BioTIPS strategy, 20 Datana ministra, 1195, 1195f date palms: asexual reproduction in, 855 seed germination in, 853 daughter strands (DNA), 228 Davis, Allen, 743, 744 Davis, Bernard, 408, 408f

Davis, Margaret, 1262, 1262f Davis, Robert, 427–29 dawn redwood, 668f, 670 day length. See photoperiodism. day-neutral plants, 794 ddNTPs (dideoxynucleoside triphosphates), 440–42, 440f DDT (dichlorodiphenyltrichloroethane), 1268–69 dead zones, 808, 1253 deafness, 948 deamination, by chemical mutagen, 310, 310f death-inducing signaling complex, 200 death receptors, 199, 200 Decapoda and decapods, 725f, 726 decibels, 948 deciduous plants, 833 decomposers, 574, 617 decoys, ncRNAs as, 267, 269f, 270 de Duve, Christian, 95 deep-sea vent hypothesis, 71–72, 71f deep-sea vertebrates, 942 deer: hybrid zones for, 503–4 migration and gene flow in, 492 Deevey, Edward, 1207–8 defecation, 980 defenses: in species interactions, 1224–27, 1225f, 1227f of sponges, 703 defensive adaptations, of protists, 593–95f, 593–96 defensive mutualism, 1229, 1230, 1230f deficiency syndromes, plants, 805, 805f deforestation: and carbon cycle, 1263, 1263f species threatened by, 1269–70, 1270f degeneracy of genetic code, 252 degradation, in vacuoles, 94–95, 94f degradative plasmids, 404 dehydration: organ system responses to, 1144 in terrestrial animals, 874 in water-breathing animals, 875 dehydration reactions, 48, 49f, 50f 7-dehydrocholesterol, 1073 deletions of genetic material, 342, 343f DELLA proteins, 790–91, 790f, 791f Delsuc, Frédéric, 731 Demodex brevis, 720 Demodex canis, 720, 721 demography: defined, 1201 in population ecology, 1205–9, 1206t Denali National Park, Alaska, 1170, 1170f denaturation: in PCR, 439f, 440 and temperature, 1002 dendrites, 882, 883f dendritic cells, 1110f, 1111 Dendrobates azureus, 1225f Dendrobates tinctorius, 497f denervation atrophy, 962

Denisovans, 547–48 denitrification, 1267f, 1268 dense connective tissue, 863f density dependence, 1212–13, 1213f density-dependent factors, 1212–13 density-independent factors, 1213 dental plaque, 568 deoxygenated blood, 1012, 1017 deoxynucleoside triphosphates (dNTPs), 232, 440 deoxyribonucleic acid. See DNA. deoxyribonucleotides, 65f deoxyribose, 50, 64 depolarization: defined, 888 in heart, 1017–18 in sensory systems, 926, 940, 944 depolarization phase (action potential), 889, 890f depression, 901 de Queiroz, Kevin, 499 dermal tissue, 216, 216f descent with modification, for seeds and ovules, 660–62, 661f, 662f desert biomes, 1169, 1169f desiccation, and leaf surface, 773–74, 774f desiccation-tolerant plants, 805, 822, 852 Desmidium genus, 583f desmosomes, 208, 209f desmotubule, 214 destruction, of habitats, 1269–71, 1271t detaching step, in cross-bridge cycle, 957, 958f detergents, as amphipathic molecules, 37 determinate cleavage, 691, 691f determinate growth, 762 determined cells, 414 detoxification: in peroxisomes, 84, 95f in smooth ER, 90 detritivores, 1248, 1253, 1254, 1254f detritus, 1248 Deuterostomia and deuterostomes, 691–92, 691f, 726–31 Chordata, 728–31, 729f, 730f Echinodermata, 727–28, 727f, 728f, 728t development: of animals (See animal development) defined, 413 embryonic stage (See embryonic development) and gene regulation, 283–84, 284f genetics of (See developmental genetics) model organisms for study of, 414–15, 414f of neurons, 901–2, 901f phenotype and genes influencing, 509–10 of plants (See plant development) stem cells in, 425–26, 425f, 426f themes in, 413–18 developmental disorders, infertility due to, 1104 developmental genes, and flower structure, 844–46

developmental genetics, 413–33 animal development, 418–29, 426t, 428–29f cell differentiation, 424–29, 425f, 426f, 426t, 428–29f defined, 413 pattern formation, 418–24 plant development, 429–31, 430t summary, 432 themes in development, 413–18 developmental homologies, 472 Devonian period, 465, 512, 540, 544–46, 737, 738, 741, 742 D-glucose, 50f diabetes insipidus, hereditary nephrogenic, 1054 diabetes mellitus: and endocrine system, 1069, 1070, 1073 and energy balance, 1006 type 1, 1125 dialysis, 1055 dialyzer, 1055 Diamond, Jared, 1293 diaphragm, 1029, 1030, 1105–6, 1105f diarrhea, 985–86 diastole, in cardiac cycle, 1018, 1018f diatoms, 334 reproduction, 597–98, 599f supergroup of, 590, 590f Dicamptodon copei, 746 Dicentra genus, 648f Dicerandra frutescens, 1285, 1286 Diceros bicornis, 755f Dichanthelium lanuginosum, 618–19, 619f dichlorodiphenyltrichloroethane (DDT), 1268–69 dichromatic animals, 939 Dictyostelium genus, 592t Dictyostelium discoideum, 591 dideoxy chain-termination method, 440– 42, 440f, 441f dideoxynucleoside triphosphates (ddNTPs), 440–42, 440f diencephalon, 912–13 Diener, Theodor, 401 diet: and beak type of finches, 460–61, 461t epigenetic effects of chemicals in, 379–80, 380f essential nutrients from, 971–72 and human evolution, 552 and obesity, 1007 See also nutrition differential gene regulation: cell communication and, 196 defined, 418 differential interference microscopy, 77f differentiation. See cell differentiation. diffuse knapweed, 1150–51, 1151f diffusion: in animal bodies, 872–73 facilitated, 113, 114f, 117–19, 118f, 819 in plant cells, 819, 820f simple, 113, 114f, 819

DIFP (diisopropyl phosphorofluoridate), 134 digestion: in alimentary canals, 974 of carbohydrates, 976 defined, 970, 971f extracellular, 972–74, 975f by lysosomes, 94 mechanism of, 980–84 and metabolic rate, 998–99 of plants, 815 of proteins, 977–78, 978f regulation of, 984–85, 985f in small intestine, 978–79, 979f digestive cavities: alimentary canals as, 974 gastrovascualar cavities, 973–74, 975f digestive systems, 970–90 absorption of nutrients and, 974–75, 975f, 984 accessory organs, 979–80, 980f alimentary canal, 975–76, 976f and digestion, 972–74, 980–84 esophagus, 977, 977f large intestine, 980 mouth, 976 neural and endocrine control of, 984–85, 985f and nutrition, 970–74t organs in, 864 overview, 975–80 public health issues related to, 985–88 in response to hemorrhage, 1143 small intestine, 978–79, 979f smooth muscle contraction in, 860 stomach, 977–78, 978f summary, 989 of vertebrates, 975–84 viral diseases of, 393f digestive tract, and multicellularity, 211 digger wasps, 1185–86f, 1185–87 dihybrid crosses, 355 dihydroxyaceton phosphate, 148f 1,25-dihydroxyvitamin D, 1061f, 1073– 75, 1074f, 1075f diisopropyl phosphorofluoridate (DIFP), 134 dikaryotic mycelia, 614 dilation, of arterioles, 1020 dimers, 209, 310, 311f dimorphic fungi, 618, 618f Dinobryon genus, 593, 593f dinoflagellates, 333, 589, 590f dinosaurs: birds and, 750, 751f characteristics of, 749, 749f evolution of bird from, 466 and evolution of plants, 650, 650f and origins of life, 546–47 Dinozoa phylum, 589, 592t Diodon hystrix, 1225f dioecious plants, 844 Diomedea melanophris, 1204f Dionaea muscipula, 815, 815f diploblastic organisms, 691 diploid cells, 325 diploid-dominant life cycles, 597–98, 599f

diploid-dominant species, 340f, 341 Diplopoda class, 721, 721f Dipnoi subclass, 741–42, 742f Dipodomys panamintensis, 875 Diptera order, 724 direct intercellular signaling, 185, 185f directionality, of DNA strands, 224–26, 225f directional light, and auxin production, 788–89, 788f directional selection, 483 direct repair, 313 disaccharides, 50, 50f, 206, 206f discovery-based science (discovery science): cystic fibrosis studies, 16 defined, 14 discrete traits, 367 disease(s): and abnormal apoptosis, 196, 197t autoimmune, 1125 and bacterial/archaeal genomes, 445 cardiovascular, 1038 chemistry in diagnosis of, 30 epigenetic changes associated with, 380–81, 381t fungal, 617–18, 617f, 618f infertility due to, 1104 kidney, 1054–56, 1055f mitochondrial, 384, 384t of muscular-skeletal system, 966, 966f and NER system, 313–14, 314f nervous system, 922–23, 922t, 923f non-coding RNAs in, 278–80, 279t pathogens as cause of, 1109 prion, 401–3, 402f, 402t respiratory system, 1038–40 stems cells for treatment of, 425–26, 426t viral, 393, 393f See also specific types disjunct distributions, 1175–76 dispersal of seeds, 1231, 1231f dispersion patterns, 1204, 1204f dispersive mechanism, 228, 229f dispersive mutualism, 1229–31, 1231f displays of intimidation, 1225f, 1226 dissociation constant (Kd), 187 distal tubules, 1049, 1051–53, 1052f, 1053f distant vision, 936f distribution of organisms: altered by climate change, 1262, 1262f environment’s effect on, 1155–60, 1155t, 1156f, 1158f, 1159f disulfide bridges, and protein structure, 60, 61f diurnal animals, 937 diverging fern (Botrychium lunaria), 646f diversifying selection, 484–85, 507 diversity-stability hypothesis, 1240, 1240f, 1281, 1282f division (cell), 214 DNA barcoding, 726 DNA-binding domains, 63 DNA (deoxyribonucleic acid), 220–41

and biochemical identification of genetic material, 220–23 in conjugation, 408–9, 409f copying, via PCR, 439–40, 439f defined, 5, 64, 220 in eukaryotic chromosomes, 238–40 gel electrophoresis of, 438f, 439 for gene cloning, 435–37, 436f, 436t hydrogen bonds in, 33, 33f methylation of (See DNA methylation) molecular structure of, 64–65, 65f mRNA and tRNA vs., 253–54, 253f mutagen effects on, 309–10, 310f, 310t, 311f mutations and sequence of, 305 nucleic acid structure of, 224–28, 226t in nucleotide excision repair, 313, 313f nucleotides in, 64, 65f origin of, on Earth, 75 in plasmids, 404, 404f repair systems of, 312–14, 312t, 313f, 314f repetitive sequences of, 452, 452f replication of, 228–38, 234t, 237t RNA vs., 75 sequences of (See DNA sequences and sequencing) summary, 241 theory of DNA as genetic material, 14 transcription (See transcription) in transformation, 409–10, 410f viral, 393 See also genomes DNA helicase, 232, 232f DNA libraries, for gene cloning, 438–39, 438f DNA ligase, 234–36, 436, 436f DNA methylation: and cancer, 320 and gene regulation, 298–99 and genomic imprinting, 376, 376f DNA methyltransferase, 298 DNA microarrays, 442, 443f, 443t DNA nucleotides, 225f DNA polymerases: in DNA replication, 232, 233f, 235f and spontaneous mutations, 309 structure and function of, 236, 237t DNA primase, 232, 235f, 237f DNA replication, 228–38 chemistry of, 233f in gametogenesis, 1087, 1087f molecular mechanism, 231–35f, 231– 38, 234t, 237f, 237t overview, 228–31, 229f, 230f DNA/RNA/protein world, 75 DNase: in apoptosis, 200 defined, 223 DNA sequences and sequencing, 1238 See also gene sequences DNA supercoiling, 404, 404f DNA synthesis. See DNA replication. DNA topoisomerase, 232, 232f DNA transposons, 453, 453f, 454 dNTPs (deoxynucleoside triphosphates), 232, 440

Dobzhansky, Theodosius, 458, 471, 498 dodders, 797, 815, 816f dodo bird, 1272 dogfish shark, 739f dogs: artificial selection in, 470, 470f baroreceptor function in, 1136–37 chromosome number for, 342 classical conditioning of, 1182 feedforward regulation in, 870 feral, 1275, 1276f and gray wolves, 519 insulin isolation in, 1071–73 respiratory system of, 1030 sensory systems of, 943 Dolly the sheep, 1292 dolphins: brain and body size for, 906 energy balance for, 1005 flipper of, 5, 5f sensory systems of, 931 domains: of proteins, 63, 64f and taxonomy, 9, 10f, 517 domesticated animals, weight gain in, 1006 domestication of flowering plants, 683, 683f dominance (traits): codominance, 365, 365t incomplete, 364–65, 364f and law of segregation, 351 molecular basis for, 363, 363f in pedigree analysis, 358–59, 359f donkeys, and hybrid sterility, 501 donor cells, in conjugation, 408–9, 409f donor DNA, for CRISPR-Cas system, 443 dopamine, 901, 1059 dormancy: for bacterial cells, 572 of seeds, 851–52, 853f Doron, Shany, 1113 dorsal lip, of blastopore, 1102 dorsal side, 690 dorsoventral axis, 415 Dorudon genus, 466 dosage compensation, 378 double bonds, 32, 32f cis vs. trans, 47 in fatty acids, 52–54, 53f in phospholipid tails, 109 double circulation: and baroreceptors, 1135 single circulation vs., 1012, 1013f structure of heart for, 1016–17, 1016f double fertilization, 659 defined, 673 in flowering plants, 842, 850–51, 851f double helix (DNA): and base pairing, 228f deduction of, 226–27, 227f defined, 224 double-stranded DNA, 64–65, 65f double-stranded RNA, 272–73 doves, 977 Down, John Langdon, 345 Down syndrome, 345, 345t

INDEX

INDEX I-15

I-16 INDEX

INDEX

D1 protein, 804 drag, 964 dragonflies: mechanical isolation for, 500 origins of, 546 Drake, Bert, 1264–64 drawing, as BioTIPS strategy, 20 Dreissena polymorpha, 709 drones, 1203 droplet organelles, 79 Drosera intermedia, 801f Drosera rotundifolia, 801f, 815 Drosophila genus, 1013 Drosophila melanogaster: adaptive ratidiation in, 503 alternative splicing and complexity of, 300, 301 chromosomes of, 342, 343, 343f compound eye of, 936f embryonic development of, 414–19, 419f as experimental organism, 358 gene regulation in, 298 genetic map, 388f genome projects with, 458 highly repetitive sequences in, 452 homeotic genes of, 422–24f Hox genes in, 864, 865 inheritance of sex chromosomes in, 360–61 linkage in, 386–87, 386f, 387f as model organism, 414, 414f, 415 morphological classification of, 698 nervous system of, 905 pattern formation in, 418–20, 420f Pax6 genes and eyes of, 513 recombination frequency, 388 segmentation genes of, 420–22 Toll protein in, 1112–15 and X-O system, 359 drought: ABA receptor protein and survival in, 831–32 and leaf abscission, 833, 833f and plant behavior, 797 drugs: and biodiversity, 1284, 1285, 1285f and deforestation, 1270 and neurotransmission, 900t, 901 spiders under influence of, 721f See also antibiotics; specific drugs Dryas drummondii, 142f, 1241 Dubois, Eugene, 552 Duchenne muscular dystrophy, 967 duck-billed platypus, 756, 756f ducks: energy balance for, 1004 pattern formation and foot of, 510 skeletal muscle fibers of, 961 duckweeds, 762, 763, 763f duodenal ulcers, 986, 986f duodenum, 979, 980f, 986, 986f duplication of genetic material, 342, 343f Dutch elm disease, 615 dwarfism, in human evolution, 554 dwarf plants, 792 dyeing poison frog (Dendrobates tinctorius), 497f

dynamic instability, of cells, 84 dynein, 86, 88 dystrophin, 967

E E. coli. See Escherichia coli. E1 and E2 conformations, of Na+/K+ATPase pump, 121–22, 122f eardrum. See tympanic membrane. ear(s): electrical signals in, 930, 930f structure of, 929–30, 929f vestigal muscles for moving, 470 Earth: effects of plants on, 648–50, 649f, 650f origin of cells on, 69–75, 70f, 71f, 73f, 74f origins of life on (See origins of life) tilt and rotation of, 1161–62, 1162f earthworms, 716f characteristics of, 715f sensory systems of, 925 eastern hemlock, 1158 eastern meadowlark, 500 eastern phoebe, 1155 ebola virus, 1108 E-cadherin, 209 ecdysis, 698, 698f, 716, 952 Ecdysozoa, 698, 698f, 716–26 Arthropoda, 717–26, 718f, 719t, 720– 22f, 723t, 724–25f Nematoda, 717, 717f ECG (electrocardiogram), 1019, 1019f echidnas, 468, 469, 469f Echinodermata and echinoderms: characteristics of, 695t, 727–28, 727f, 728f, 728t, 731f as deuterostomes, 726–27 embryonic development in, 1103 muscular-skeletal systems of, 952f nervous system of, 905, 906f origins of, 545 Echinoidea class, 727 Echinops bannaticus, 449–50, 449f Echinops nanus, 449–50, 449f echolocation, 931 Eciton burchelli, 724f ECM. See extracellular matrix. ecological factors, in species identification, 498 ecological footprints, 1259–60, 1259f ecological pyramids, 1251–52, 1251f ecological roles: of bryophytes, 648–49 of fungi, 616–20 of vascular plants, 649–50, 649f, 650f ecological species concept, 499 ecology, 1149–79 archaeal role in, 573–74 bacterial role in, 573–78, 577f, 578f biogeography, 1175–77, 1176f, 1177f biomes, 1164–74 climate and biological communities, 1160–63f, 1160–64 defined, 13, 13f, 14

and environment’s effect on organisms, 1155–60, 1155t, 1156f, 1158f, 1159f hypothesis testing in, 1152–54, 1153f, 1154f protists’ roles in, 582, 582f scale of, 1150–52, 1150f, 1151f summary, 1177–78 See also behavioral ecology; ecosystems; population ecology economics of biodiversity, 1284–86, 1285f EcoRI enzyme, 436 ecosystem diversity, 1280–81, 1281f ecosystem ecology, 1150f, 1152, 1236 ecosystems, 3f defined, 3, 1236 function of, 1281–85f replacement of, 1291, 1291f See also communities and ecosystems Ecotron experiments, 1283–84 ecotypes, 497 ectoderm, 691, 1101, 1102f ectomycorrhizae, 633, 634f ectoparasites, 1229 Ectopistes migratorius, 1272, 1273f ectotherms, 749 body temperature of, 1003, 1003f heat exchange in, 1004f metabolic rate for, 998 thermoreception for, 933 edge effects, 1289–90 edible fungi, 610f Edidin, Michael, 110 effector caspases, 199f, 200 effector cells, 1118 effector molecule, in bacterial gene regulation, 285, 286f effectors, 868 baroreceptor, 1134 plant cell signaling, 784f, 785 efferent arterioles, 1047 efferent nerves, 909 efferent neurons, 884 See also motor neurons E2F protein, 319 EG cells (embryonic germ cells), 426, 427 egestion: defined, 970, 971f of undigested material, 980 EGF (epidermal growth factor), 190–92, 191f EGF receptor (epidermal growth factor receptor), 191 egg cells: defined, 1085 in female reproductive tract, 1093, 1093f in fertilization, 1089–90, 1089f of flowering plants, 841 production of, 1087, 1088f, 1089 egg development, 420, 420f egg-rolling response, 1181, 1181f eggs: amniotic, 746–47, 747f and biomagnification, 1268–69, 1269f Egler, Frank, 1243 Ehlers-Danlos syndrome, 205 Ehrlich, Anne, 1282

Ehrlich, Paul, 1282 eight-cell stage, of plant development, 430f Einstein, Albert, 167 Eisner, Tom, 1225 ejaculation, 1090–92, 1091f EKG (electrocardiogram), 1019, 1019f elasmobranch, sensory systems of, 925 elastic fibers, 205, 205f elastin: in blood vessels, 1020 multicellularity and, 204t, 205, 205f elder-flowered orchid, 478 Eldredge, Niles, 508 electrical gradients: across neuron membranes, 885–86, 886f and concentration gradient, 886–87, 887f electrical signals: and contraction of skeletal muscle, 958, 959f electrocardiogram as record of hearts’, 1019, 1019f energy and matter in transmission of, 891 generation and transmission of, in neurons, 888–91f, 888–92 in mammalian ear, 930, 930f of mammalian heart, 1017–18, 1017f in nervous tissue, 861 of skeletal muscle, 960, 960f electrical synapses, 892–93 electric charge: across membranes of neurons, 885–86, 886f of subatomic particles (See atoms) electrocardiogram (ECG, EKG), 1019, 1019f electrochemical equilibrium, 887 electrochemical gradients: with ATP-driven ion pumps, 121–22, 122f defined, 114–15, 115f from electron transport chain, 153, 154f functions of, 122t H+, 153, 170, 170f, 171, 171f for nervous system cells, 886–88, 887f electrogenic pump, 121 electromagnetic radiation, light as, 167, 167f electromagnetic reception, 934, 934f electromagnetic receptors, 927 electromagnetic spectrum, 167, 167f electronegativity, defined, 32 electron flow, in light reactions, 169–71, 170f, 171f electron microscope, 76, 76f electron microscopy. See transmission electron microscopy. electrons: absorption of light energy by, 168, 168f in Calvin cycle, 176 characteristics of, 29, 29t defined, 25 in light reactions, 174, 174f orbitals of, 27–28, 27f in photosystem II, 172–73 potential energy of, 128 in redox reactions, 138–39, 138f valence, 28 See also atoms

electron shells: carbon atom, 46, 46f structure of, 27–28, 27f electron transport chains (ETC): of chloroplasts vs. mitochondria, 171, 172f electrochemical gradient from, 153, 154f free energy and movement along, 155, 155f and photosystems, 169 electrophoresis, 439 electrostatic attraction, 807f elements: defined, 25 ionic forms of, 34, 34t in living organisms, 29–30, 30t, 31f mineral, 30, 30t protons of, 28, 28f trace, 30, 30t elephantiasis, 717, 718f elephants: brain mass for, 907 classification of, 516 cooling by, 1004 disjunct distribution of, 1175 hemoglobin of, 1035 sensory systems of, 925, 931 Elephas maximus, 516 elevation, 1162–64, 1163f elicitors, 798, 799f elk: exponential population growth of, 1210, 1211f as polygynous species, 1199f population genetics, 486 and species interactions, 1232, 1233f Elkinsia polymorpha, 662 Ellis–van Creveld syndrome, 491 elongation, 298, 299f elongation factors, 262 elongation stage: of transcription, 248, 248f, 249 of translation, 261–63, 261f, 262f Elton, Charles, 1226, 1240, 1251, 1281 Embden, Gustav, 147 embolisms, in plant vessels, 827–28 embryogenesis: in flowering plants, 851, 852f somatic, 855, 855f embryonic development, 1099–1104 and adult structures of animals, 418, 419f of animals, 196, 690–91, 691f of brain, 905, 906, 907f cell division in, 1099–1101 defined, 1099 and endocrine systems, 1077–79 gastrulation in, 1101–3, 1102f glycoproteins in, 113 homologies in, 472 neurulation in, 1103–4, 1103f organogenesis in, 1104 pattern formation and positional information in, 416, 416f sites of, 1101f vertebrate hearts during, 1014, 1014f

embryonic germ cells (EG cells), 426, 427 embryonic stem cells (ES cells), 426, 427 embryophytes, 652 embryos: animal (See animal embryos) plant (See plant embryos) emergency contraception pills, 1106 emerging viruses, 399–400, 399f Emerson, Robert, 172 emotional stress, and digestion, 985 emphysema, 1039–40, 1040f empirical thought, 459 EMS (ethyl methanesulfonate), 310 emulsification, of lipids, 983, 983f enantiomers, 47, 48f Encephalartos laurentianus, 666 ENCODE Project, 452 endangered species: cloning of, 1292–93, 1293f defined, 1281 endemic species, 466, 1287, 1288f endergonic reactions: ATP use in, 130–31, 130f, 131t defined, 129 end joining, 443 endocrine disruptors, 1081 endocrine glands, 1058 endocrine signaling, 185f, 186 endocrine systems, 1058–83 after hemorrhage, 1143 defined, 1059 and digestive systems, 985, 985f and growth/development, 1077–79 hormone types and mechanisms of action, 1059–62, 1060f, 1061f, 1061t and immune system, 1127 and metabolism/energy balance, 1065–73, 1068t and mineral balance, 1073–77 and nervous systems, 1062–65, 1063f, 1064t public health issues related to, 1080–81 regulation of absorptive and postabsorptive state by, 994–97, 995f, 997 regulation of organ systems by, 864 and reproduction, 1079–80 in response to illness, 1143 in secondary phase of response to hemorrhage, 1140, 1141f summary, 1081–82 See also hormones endocytosis: membranes in, 123–24, 123t, 124f receptor-mediated, 210 endoderm, 691, 1101, 1102f endodermis: and plant behavior, 795 of plant roots, 778, 779 transport in plant, 824, 824f endomembrane system, 90–96 and cell nucleus, 88, 88f defined, 88 endoplasmic reticulum, 90–91, 90f Golgi apparatus, 91, 91f lysozymes, 94 peroxisomes, 95, 95f

plasma membrane, 95–96, 95f protein movement in, 92–95f systems biology approach to, 102, 103f vacuoles, 94–95, 94f endometrium, 1095, 1101 endomycorrhizae, 633 endomycorrhizal fungi, 633, 634f endoparasites, 1229 endoplasmic reticulum (ER): of animal cells, 80f attachment of carbohydrates and proteins at, 112–13, 113f in cell structure, 90–91, 90f cotranslational protein sorting at, 99, 101, 101f directing polypeptides to, 275, 276f endorphins, 896 endoskeletons: of echinoderms, 727, 727f location of, 952 endosperm: defined, 648 and plant reproduction, 842, 843, 851 endospores, 572 endosporic gametophytes, 661 endosymbiosis, 566, 584–85 and mitochondria/chloroplasts, 98–99, 99f and origin of eukaryotes, 542 primary, 587–88, 587f, 588f secondary, 588–89, 588f, 589f tertiary, 588f, 589 endosymbiosis theory, 99, 99f endothelium, of blood vessels, 1020, 1021 endotherms, 749 altering heat gain/loss rates in, 1004–6 body temperature of, 1003, 1003f evaporation of water from, 876 heat exchange in, 1004f metabolic rate of, 998 energy: in absorptive vs. postabsorptive state, 994t for anabolic reactions, 139 archaeal and bacterial sources of, 572–73 and cell structure/function, 78 and chemical reactions, 127–31, 128t, 129f, 130f, 131t in chemical reactions, 36 defined, 27, 128 and ecological pyramids, 1251–52, 1251f endotherms’ requirements for, 1003 from fats, 54 for flying, 965–66 forms of, 128–29, 129f, 129t for heterotrophs vs. autotrophs, 540–41 hormones and energy-yielding molecules in blood, 1067–70, 1068t light, 167–68, 167f, 168f for locomotion by land animals, 964–65, 965f nutrients for, 971, 972t in photosynthesis, 167 during physical activity, 996, 997 sources and uses of, in animals, 991– 94, 992f, 993f, 994t

See also chemical reactions energy and matter (core concept), 4f, 5 in ATP hydrolysis, 129, 875 in electrical signal transmission, 891 in gene regulation, 283 and genes for proteins that use ATP, 130–31, 131t and glucose, 146 and heat, 1003 in heterotrophic plants, 803 in homeostatic processes, 1021 and ion uptake, 821 and living organisms use of energy, 50 in Na+/K+-ATPase pump, 122, 886 in phagocytosis, 582 in photoreception, 940 of photosynthetic pigments, 173 in production efficiency, 1250 in semiautonomous organelles, 96 for translation, 261 and trophic levels, 1250 energy balance, 991–1009 body temperature regulation, 1002–6 and endocrine system, 1065–73, 1068t energy sources and uses, 991–94, 992f, 993f, 994t metabolic rate and, 997–1002 public health issues related to, 1006–7, 1007f regulation of absorptive/postabsorptive states, 994–97, 995f, 997f summary, 1007–8 energy cycle, 165, 165f energy flow: in food webs, 1248–51f, 1248–52 in Georgia salt marsh, 1253, 1254, 1254f energy intermediates, from catabolic reactions, 137–38, 137f energy investment phase (glycolysis), 147f, 148 energy liberation phase (glycolysis), 147f, 148 energy sources, as homeostatic variable, 868t engineering, of microbiomes, 637–39, 638f, 639f English ivy, 468 enhancers, 295 Entamoeba histolytica, 596 Enterobius vermicularis, 717 Enterococcus faecalis, 411 enterokinase, 982 enteropeptidase, 982 enthalpy (H), 129 entomology, 721 entropy (S), 128, 129f entry (step in viral reproductive cycle), 395, 396f environment: adaptation to, 461–62, 462f cellular responses to, 184, 184f convergent evolution and adaptation to, 468–69, 469f and ecosystem ecology, 1152 effect of, on distribution of organisms, 1155–60, 1155t, 1156f, 1158f, 1159f

INDEX

INDEX I-17

I-18 INDEX

INDEX

environment, continued and exchanges of water and ions between body, 874–76 and heat exchange between animals, 1003–4, 1003f, 1004f internal, homeostatic control of, 868–69, 869f nervous system and adaptations to, 905, 906f in systems with animals, 861 in transformation of bacteria, 409–10, 410f environmental adaptations: and sexual reproduction, 1085–86 since origins of life, 540 environmental factors: continuous phenotypic variation due to, 367–68, 368f in epigenetics, 379–81, 380f, 381t eye adaptations for, 941–42, 942f in gene regulation, 283, 283f and phenotypes, 365, 366 and plants, 764 in seed germination, 853–55, 854f sex differences determined by, 360 See also natural selection environmental science, 1149 environmental sex determination, 360 environmental stimuli: flooding and drought, 797, 797f and flower production, 843–44 gravity, 794–96, 795f, 796f herbivores, 797, 798f light, 793–94 pathogen attacks, 797–99, 799f plant behavior in response to, 783–84, 783f, 792–99 touch, 796–97, 796f types of, 784 environmental stress: and leaf shapes, 770–71, 770f and plant hormones, 792 environments: adaptation to local, 506–8 for mammals, 755–57, 755t, 756f microbiomes in, 628–30, 628f, 629f enzyme-linked receptors, 188, 188f enzymes, 131–37, 136t and chemical reaction rates, 131–32, 132f in coacervates, 72, 73 defined, 33, 47, 83, 84, 131 in digestive system, 978 in DNA synthesis, 233f and enantiomers, 47 factors influencing function of, 133–34, 133f, 134f from genes, 244–45, 245f inhibitors and function of, 133–34, 133f, 134f and metabolism (See metabolism) in proteome, 9f and substrate concentration, 133–34, 133f, 134f substrate recognition and conformational changes by, 132–33, 132f

enzyme-substrate complex, 132–33 eosinophils, 1110, 1110f Ephedra genus, 670 Ephedra californica, 671f epicotyls, 852, 853f epidermal growth factor (EGF), 190–92, 191f epidermal growth factor receptor (EGF receptor), 191 epidermis: and multicellularity, 216–17 of plant stems, 766 Epidermophyton floccosum, 609 epididymis, 1091 epigenetic changes, 320 epigenetic inheritance, 374 epigenetics, 373–90 environmental agents, 379–81, 380f, 381t and extranuclear inheritance, 381–84, 382f, 383f, 384t genomic imprinting, 375–76, 375f, 376f linkage, 384–88, 385f, 387f, 388f overview, 374–75, 374t summary, 388–89 X-chromosome inactivation, 377–79, 377f, 378f, 378t epilimnion, 1171 Epilobium latifolium, 1241 epimutation, 374 epinephrine: cell response to, 192–93, 194f cellular regulation of, 139 differential gene regulation and response to, 196 effects of, in humans, 195–96, 195t in endocrine system, 1059, 1067, 1069 therapeutic uses of, 1080 episomes, 399 epistasis, 366–67, 367f epithalamus, 913 epithelial cells: of digestive systems, 974–76, 979f of nephron, 1049, 1049f as sensory receptors, 926, 926f epithelial tissues: cells in, 862, 862f and multicellularity, 215, 215f epitopes, 1122 EPO (erythropoietin), 1081, 1142–43 epsilon-globin, 451, 1097 EPSP. See excitatory postsynaptic potentials (ESPSs). Epulopiscium genus, 566 equilibrium: chemical, 36 in chemical reactions, 130 electrochemical, 887 Hardy-Weinberg equation under, 480 in population growth, 1209 punctuated, 508–9 and sensory systems, 929, 931–33, 931f, 932f water, 35 equilibrium constant (Keq), 130 equilibrium model of island biogeography, 1244–47f, 1244–48

equilibrium potential, 887 Equisetum telmateia, 646f Equisetum variegatum, 1241 Equus. See horses. Equus asinus, 501 Equus ferus caballas, 501 ER. See endoplasmic reticulum (ER). erection, 1091–92 ergot, 611, 611f Erigeron annuus, 1242 Eriksson, Peter, 919 Erk protein kinas, 191–92 ER lumen, 90 ER membrane: insertion of transmembrane proteins in, 112, 112f synthesis of lipids at, 111–12, 112f erosion, of soil, 805 ER retention signals, 101 ER signal sequence, 101, 112, 112f, 275 erythrocytes: in capillaries, 1021, 1021f defined, 1015 intracellular fluid volume and shape of, 873, 873f and response to hemorrhage, 1142–43, 1143f See also red blood cells erythropoietin (EPO), 1081, 1142–43 ES cells (embryonic stem cells), 426, 427 Escherichia coli, 569f anaerobic respiration by, 160, 160f base pairs in, 403 binary fission in, 405 conjugation in, 408–9 diarrhea due to, 985 DNA polymerases, 236, 237f DNA repair, 313, 313f DNA replication in, 229–30, 229f evolution of, 578 gene expression in, 248–49, 256–58, 260 gene regulation in, 283, 283f gene transfer studies, 406–8, 407f homologous genes of, 473, 474f and horizontal gene transfer, 411, 566 and human disease, 565 lac operon of, 285–93 as model organism, 13 and mutation, 308–9, 308f–9f nucleotide excision repair in, 313, 313f in shotgun DNA sequencing, 448 structure of, 79f esophagus: in digestive system, 975, 977, 977f, 978 epithelial tissue in, 862f An Essay on the Principle of Population (Malthus), 460 essential amino acids, 971–72 essential bodily functions, and hindbrain, 910, 912f essential ecosystem services, 1286, 1286t essential elements, 802, 802f, 802t essential fatty acids, 53, 972 essential nutrients, obtaining, 971–72

ester-bonded phospholipids, 563 ester bonds, 52f estradiol: and birth, 1097, 1098 in endocrine system, 1080 and gametogenesis, 1095 and ovarian cycle, 1095 estrogens, 966 birth and, 1097, 1098 and cell communication, 186–87, 190, 190f molecular structure of, 55, 56f receptors for, 63, 64f, 1062 and reproduction, 1080 synthesis and function of, 1061f ETC. See electron transport chains (ETC). ethanol: and fermentation, 161f nervous system cells and, 899 ethical issues, concerning biodiversity, 1286 ethology, 1180 ethylene: in leaf abscission, 833 and plant behavior, 786t, 791–92, 792f and in plant reproduction, 852 ethyl methanesulfonate (EMS), 310 Euarchontoglires, 757 euchromatin, 239 eudicots: embryogenesis in, 852f evolution and diversity of, 675–76, 676f flowers of, 841, 841f, 844, 844f, 845 leaf form for, 770f structures of, 763, 764t venation in, 771 Euglenida and euglenoids, 585, 585f, 592t Eukarya domain, 688 cellular and molecular features of, 517 and evolutionary relationships of Bacteria, Archaea, 562–64 and horizontal gene transfer, 532 overview, 9, 10f eukaryotes: alternative splicing and complexity of, 300–301, 300t cell division in bacteria vs., 333–34, 334f defined, 9, 10f gene expression in, 246f, 247 gene regulation in (See eukaryotic gene regulation) genomes of, 449 horizontal gene transfer with, 474, 474f and mutualism of bacteria, 576, 577f as parasites, 1109 protein degradation in, 141–42, 141f and receptor tyrosine kinases, 190 ribosomes of, 258, 258t, 259 RNA modification in, 249–51, 250f, 251f transcription in, 249, 249f eukaryotic cell cycle, 323–47 and checkpoint proteins, 327–28, 327f and chromosomes, 324–25, 324f and chromosome structure/number, 341–46, 345t

and cyclins/cylin-dependent kinases, 328–29 meiosis in, 334–40, 335f, 336f, 338– 39f, 340t mitotic cell division in, 330–34 overview, 323–29, 324f, 326–29f phases of, 325–27, 326f sexual reproduction in, 340–41, 341f summary, 346 eukaryotic cells: cell nucleus of, 88–89, 89f cilia and flagella of, 87f complexity of bacterial cells vs., 102, 103t defined, 79 DNA origins of replication in, 231, 231f interacting parts of, 102, 103f lipid synthesis in, 111, 112f membrane component synthesis in, 111–13, 112f, 113f membrane transport (See membrane transport) morphology of, 80 origins of, 541–43 protein sorting in, 99–101, 100f structure and function of, 79, 80f, 81f eukaryotic chromosomes: molecular structure of, 238–40 and telomerase, 236–38, 237f eukaryotic gene regulation, 294–301 and chromatin structure/DNA methylation, 296–99 overview, 283–85, 284f, 285f of RNA modification and translation, 299–301, 300f, 300t, 301f transcription factors and mediator, 294–96 eukaryotic genomes: chromosomes in, 448–50, 449f, 449t evolution of, 450–51, 450f genetic technologies with, 448–51, 449t, 450f, 451f Human Genome Project, 451 Euonymus fortunei, 468, 469f Euphausiacea, 726 euphylls, 658, 659f euploid organisms, 342, 343 Eurasian rosefinch, 503 European rabbits, 1211 Euryarchaeota, 564 eusociality, 1196 eustele, 666 Eutheria and eutherians, 756–57, 756f, 1096–97 eutrophication, 1266, 1267f Evans, Ron, 962–64 evaporation: and global warming, 1262 heat exchange by, 1003f, 1004 heat loss due to, 1005 ion and water exchanges due to, 876 of water, 40f, 41 evapotranspiration rate, 1238, 1238f Everglades National Park, Florida, 1173, 1173f evergreen conifers. See conifers.

evolution, 458–76 and alternative splicing, 300–301, 300t angiosperm, 670–83, 682f, 682t, 683f animal, 650, 650f, 689 aquaporin, 1053–54, 1054f archaeal, 445, 563–66 bacterial, 445, 562f of baroreceptors, 1135 biological, 5–8 of body patterns, 510–12 of cerebral cortex, 916 chemical, 73 collagen, 205–6, 206t color vision, 938–39, 939f common ancestors in, 502 as core concept of biology, 4, 4f cytochrome complex, 171–72, 172f and Darwin, 459–61, 460f defined, 5, 457, 458 diversifying selection, 484 DNA polymerase, 236, 237t and ecology, 1175–76, 1176f eukaryotic cell, 450–51, 450f, 451f, 541–43 evidence for, 465–73, 465t, 466–72f, 472t of eyes, 512–13 flower, 843 of flying animals, 965 of four-chambered heart, 1012–14, 1014f fungal, 605–6, 606f of gene families, 473–74 genetic influences on behavior, 1181–82 and genomics/proteomics, 7–8 gibberellin, 790–91, 790f of globin gene family, 1097, 1097f glucose transporter, 995–96 gymnosperm, 665–70 hexaploidy, 1214–15, 1215f historical precedents for, 459 homeotic gene, 423–24, 424f and horizontal gene transfer, 411, 532–33 hormone and receptor, 1076–77 of horses, 522 host and microbiome, 630–31, 631f of Hox genes, 694, 695f human, 547–58 and human vs. chimpanzee genomes, 550 invertebrate chordates, 729 kin selection, 1195 and lactose intolerance, 981–82 and life cycle stage dominance in plants, 840, 840f of meadowlarks, 501 mitochondrial/chloroplast genomes and proteins, 381, 382f of mitotic cell division, 333–34, 334f and molecular clocks, 529–31 molecular processes underlying, 473–75 and mutations/cancer, 321 myosin, 956–57

and natural selection, 461–64, 461t, 462–64f nervous system, 904–7, 906f, 907f, 908 neurotransmitter receptors, 898–99, 899f neutral theory of, 529 non-Darwinian, 491 and origin of viruses, 400–401 overview, 459–64, 460f, 461t, 462–64f of pathogenic bacteria, 578, 578f and pathogen recognition, 1112–13 plant, 648, 650, 650f of plantlet production, 855–56 polymorphism, 478–79 primate, 548–50 protein domains, 63, 64f of proteins in innate immunity, 1112–13 protist, 584–92, 592t of small subunit rRNAs, 259–60, 260f species’ evolutionary relationships, 584 summary, 475–76 and taxonomy, 518 of Trichomonas vaginalis and Giardia intestinalis, 586 vertebrate jaw, 738, 738f via gradualism and punctuated equilibrium, 508 whole-genome duplications in, 674, 675f evolutionarily conserved species, 260 evolutionary developmental biology (evodevo), 509–14 growth rates and phenotype, 512 Hox genes in, 510–12 Pax6 gene, 512–14 phenotype and genes influencing development, 509–10 evolutionary lineage concept, 499 evolutionary relationships: of animals, 695–98 of Bacteria, Archaea, and Eukarya, 562–64 of fungi, 605, 606f of green algae and modern plants, 642f on phylogenetic trees, 519 of species, 584 species identification based on, 498 in systematics, 519–21 Excavata supergroup, 584–86 excessive light, plant adaptations to, 804 excisionase, 395 excitation-contraction coupling, 958, 959f excitatory postsynaptic potentials (EPSPs), 893–95, 895f excitatory signals, at chemical synapses, 893 excited state, electrons in, 168 excretion, 1045, 1045f excretory systems, 1043–57 defined, 1043 and forms of nitrogenous wastes, 1044, 1044f function of, 1044, 1045, 1045f of insects, 1046–47, 1046f of invertebrates, 1045–46, 1045f and kidneys (See kidneys) kidneys of mammals, 1047–54

overview, 1043–47 public health issues related to, 1054–56, 1055f summary, 1056 of vertebrates, 1047 waste removal processes, 1044–45, 1045f executioner caspases, 199f, 200 exercise: adaptation of skeletal muscle to, 961–62 and energy balance, 996, 997 and immunity, 1127 ion and water imbalance during, 876–79 exergonic reactions: coupling endergonic and, 130 defined, 129 exocrine glands, 1069, 1071 exocytosis, 122–23, 123f, 123t, 210 exons, linkage of, 251, 251f exoskeletons, 698 of arthropods, 718 extracellular matrix, 206 in innate immunity, 1110 location of, 951–52 expansins, 768, 770, 789 expansion, and stretch receptors, 928 experimental groups, 15 experiments: as core of biology, 18 designing, 20 purpose of, 1153 “Experiments on Plant Hybrids” (Mendel), 349 exploitation competition, 1218, 1218f exponential growth, 1210–12f expression phase (CRISPR-Cas system), 277f, 278 extant species, 516 extension sequences, 204, 204f extensors, 954, 954f external gills, gas exchange via, 1025–26, 1025f extinctions: of birds, due to overexploitation, 1272, 1273f caused by habitat destruction, 1269 and distribution of species, 1175, 1176, 1177f due to human overexploitation, 1271–72 in island biogeography model, 1244– 47f, 1244–48 of K-selected species, 1214 origins of life and, 538, 546 extinct species: defined, 516 morphological analysis of, 522 on phylogenetic trees, 519 extracellular concentrations, of ions, 886t extracellular digestion, 972–74, 975f extracellular fluid, 872, 1075–76, 1076f extracellular leaflets, 107 extracellular matrix (ECM): of animal cells, 203–6, 203f–6f, 204t, 206t

INDEX

INDEX I-19

I-20 INDEX extracellular matrix (ECM), continued attachment of transmembrane proteins to, 111, 111f and cell junctions, 208–9, 209f, 210f connective tissue in, 215, 215f, 862 defined, 203 extracellular proteins, in proteome, 9f extranuclear inheritance, 381–84, 382f, 383f, 384t extraterrestrial hypothesis, 71 extremophiles, 563 extrinsic pathway, for apoptosis, 199–200, 199f eye color, spread of, 557f eyecups, 935, 935f eyeless gene, 513 eyes: compound, 935, 936f and Pax6 gene, 512–13 placement of, 941–42, 942f single-lens, 935–37, 936f vertebrate adaptations of, 941–42, 942f

F

INDEX

facilitated diffusion: in animal bodies, 873 defined, 113, 114f and osmosis, 117–19, 118f in plant cells, 819, 820f facilitation, 1241–43f factor VIII, 434 facultative anaerobes, 573 facultative mutualism, 1230 FADH2, 151, 151–52f, 153, 154f Falco peregrinus, 1292 fall field cricket (Gryllus pennsylvanicus), 499 Fallopian tubes, 1093 falsifiable hypotheses, 14 FAMA gene, 774 families, in taxonomy, 518 FAP (fixed action patterns), 1181–82, 1181f, 1182f farming: organic, 808 secondary succession following, 1241 (See also agriculture) Farquhar, Marilyn, 208 far-red-light receptors, 793, 793f fascicles, 954 fasciculata, 1068 FASS gene, 768 fast fibers, 961, 962, 962t fast-glycolytic fibers, 961, 962, 962t fasting, 994, 996, 1067 fast-oxidative fibers, 961, 962t fate (developmental), 422 fat metabolism, 159, 159f fats: absorption of, 983–84, 983f energy storage in, 54 molecular structure, 53, 53f See also triglycerides fat-soluble vitamins, 972, 973t, 984 fatty acids: and energy balance, 993, 994

essential, 53, 972 fat metabolism to, 159 molecular structure of, 52–54, 53f saturated, 53, 53f trans, 54 in triglycerides, 52, 52f unsaturated, 53–54, 53f fatty foods, heartburn and, 986 FDG (fluorodeoxyglucose), 29, 149 feathers, 750, 751f feather stars, 727 Feder, Jeffrey, 506 feedback: in homeostasis (See negative feedback) negative, 869–70, 870f, 985 positive, 870, 871f feedback inhibition, 139, 140f feedforward regulation, and homeostasis, 870, 871f feeding: and hinged jaw, 738, 738f hormonal changes after, 1069–70, 1070f if Bryozoa and Brachiopoda, 709, 709f ion and water exchanges during, 875–76, 876f See also nutrition feeding groove, 584, 585f feet, birds’, 510 Felidae and felines, 517, 972 Felis libyca, 1292 female choice, 487–89 female-enforced monogamy hypothesis, 1197 female gametes, 1087, 1088f, 1089 female gametophytes: development of, 849–50, 850f of flowering plants, 840–41, 840f, 841f, 849–50, 850f production of, 840–41, 840f, 841f female reproductive tract: egg development in, 1093, 1093f gametogenesis in, 1093–94, 1094f ovarian cycle in, 1094–95, 1095f uterine cycle in, 1095 females: external vs. internal fertilization for, 1090 X-chromosome inactivation in, 377–78, 378f feral dogs, 1275, 1276f fermentation, 160–61, 161f ferns: leaves of, 658, 659, 659f life cycle of, 653, 654f origins of, 545 and plant nutrition, 812 sporophytes and gametophytes of, 653, 653f See also pteridophytes ferredoxin (Fd), 169, 171, 171f ferritin protein, 301, 301f fertility: age-specific, 1208–9 data, 1208–9 and nutrition, 1080 rates of, and human population, 1258, 1259, 1259f

of soils, 805–8, 806f fertility plasmids, 404 fertilization: in animal reproduction, 1089–90, 1089f and apomixis, 856 defined, 1085 double, 842, 850–51, 851f in embryonic development, 1099 external vs. internal, 1090 and female reproductive tract, 1093 in flowering plants, 762–63, 841–43, 842f, 843f internal (See internal fertilization) plants and (See plant reproduction, fertilization in) fertilized egg. See zygotes. fertilizers: and nitrogen cycle, 1266–68, 1267f and phosphorus cycle, 1265–66, 1266f, 1267f plant nutrition, 805, 807–9 Festuca idahoensis, 1150–51, 1151f Festuca ovina, 1151, 1151f fetus: hormones for development of, 1077 during pregnancy, 1097 respiratory system of, 1031 fever, 1112, 1143 F factors, 404, 408–9 F1 generation, 351 F2 generation, 351 fiber, dietary, 52 fibers, 766, 863 See also cellulose fibrin, 1016 Fibrobacter genus, 631 fibroblasts, 427, 428–29f fibronectin, 204, 204t, 209 fibrous root system, 767 Ficedula albicollis, 483 Fick’s first law of diffusion, 873 fiddler crab (Uca paradussumieri), 486 fidelity in animal behavior, 1197 field crickets, 499 fight-or-flight response: and cell communication, 192, 193 nervous system and, 910 Fiji, 1165, 1165f filaments, 674 actin, 84–85, 85t bending of, 86, 86f cytoskeletal, 85–88, 86f, 87f flagellar, 570, 570f intermediate, 84, 85t movement of, 86, 86f thick and thin, 955–56, 955f, 956f filtrate: defined, 1045, 1047 in loop of Henle, 1050–51, 1050f production of, 1048–49 in proximal tubules, 1049–50, 1049f filtration: as excretory system function, 1044–45, 1045f of invertebrate wastes, 1045–46, 1045f in kidneys, 1043 of vertebrate wastes, 1047

fimbriae, 1093 finches: competition among, 1221–22, 1222t directional selection in, 482 and evolution, 460–64, 461t, 462–64f natural selection for, 461–62, 462f reproductive isolation in, 504–6 finite rate of increase, 1209 fin whales, 1272 Fiorito, Graziano, 712, 714 fire, 1156, 1156f Fire, Andrew, 272–73 fire ants, 1191 fireflies, 1191, 1191f Firmicutes, 568, 573, 637 first law of diffusion, 873 first law of thermodynamics, 128, 167 first messengers, 192 Fischer, Emil, 132 Fischer, Hans, 168 fishapods, 465, 742 Fisher, Ronald, 477, 1197 fishes: baroreceptors of, 1135 blood pressure for, 1018 and body temperature, 1003 circulatory system of, 1023 cleavage-stage embryos of, 1100, 1100f digestive systems of, 975–78 electromagnetic reception in, 934 and endocrine disrupters, 1081 endocrine system of, 1062, 1065, 1074, 1078, 1078f evolution of terrestrial tetrapods from, 465, 466f Hox genes of, 512 as invasive species, 1275 lateral line system of, 933, 933f locomotion by, 964 molecular homologies for, 473 nitrogenous wastes from, 1044 origins of, 545–47 osmosis processes of, 1158–59 production efficiency of, 1250 reproduction in, 1085 respiratory system of, 1026–27, 1026f, 1030 sensory systems of, 937, 942 single circulation in, 1012, 1013f threatened due to overexploitation, 1273–75, 1273f, 1275f fitness, population genetics and, 482 5′ cap, 250, 250f fixed action patterns (FAP), 1181–82, 1181f, 1182f fixed nitrogen: as plant nutritional requirement, 808–9 symbioses providing, 812–14 flaccidity, 820, 821f flagella: movement by, 86, 87f, 88 of prokaryotic cells, 79, 569–70, 570f of protists, 590–92 of sperm, 1089 structure of, 87f flagellar hairs, of protists, 590–91, 590f flagellates, 583

flagship species, 1290f, 1291 flame cells, 706, 1045 flatus, 980 flatworms: asexual reproduction in, 1085 characteristics of, 705–7, 706t, 707f, 708f, 731f digestive systems of, 973 excretory systems of, 1045–46, 1045f eye cups of, 935, 935f nervous systems of, 905 flavins, 793 flavonoids, 813, 814f flax (Linum usitatissimum), 776 FLC transcription factor, 844 Fleming, Alexander, 1284 Flemming, Walther, 331, 355 flexors, 954, 954f flies, 724, 1189–90, 1189f flightless birds, 527–29 flippases, 112f flooding, and plant behavior, 797, 797f floods, since origin of Earth, 540 floral tubes, and pollinators, 676, 676f Florida Keys, 1246–47 Florida panther, 493, 1290f, 1291 flounder, 1078, 1078f flowering plants (angiosperms), 670–83, 760–81 behavior of (See plant behavior) cells of (See plant cells) defined, 759, 760 diversification of, 675–77 endocrine signaling in, 186 evolution of flowers, 672–74f, 672–75 flowers of (See flowers) fruits of, 677–78, 678f, 682–83, 683f gametic isolation in, 501 growth and development of, 764–69, 765t leaf abscission in, 833 life cycles of, 760–64, 764t, 841, 842f origins of life for, 547 pollination coevolution of, 681–82, 682f, 682t reproduction in (See plant reproduction) root systems of (See roots and root systems) secondary metabolites of, 678–81, 679f, 680f seed production in, 676–77, 676f and seeds (See seeds) shoot systems of (See shoots and shoot systems) stems (See stems and stem systems) summary, 780 tissue types (See vascular tissues of plants) transport in (See plant transport) vascular systems (See vascular systems; vascular tissues) flowers, 843–48 angiosperm, 672, 672f blooming of, 846–48, 847f coevolution of, 681–82, 682f, 682t and cytokinins, 790 defined, 648, 840

development of, 762–63 and dispersive mutualism, 1230–31, 1231f of eudicots vs. monocots, 675–76, 676f evolution of, 672–74f, 672–75 gametophytes from, 840–41, 840f, 841f homeotic genes and development of, 431, 431f of pea plants, 350, 351f production of, 843–44 structure of, 677, 677f, 844–46, 844f–46f flow-through systems, 1027, 1030 fluid compartments, of animal bodies, 872–73, 872f fluidity: defined, 109 of membranes, 109–11, 110f, 111f fluid-mosaic model, 107, 107f fluids, in cells, 37f flukes, 706f, 707 fluorescence, 168 fluorescence microscopy, 77 fluorescent dyes, 212–13, 213f fluorine, 31, 31f fluorodeoxyglucose (FDG), 29, 149 flying, 965–66, 965f flying insects, 1027 fMRI (functional MRI) scans, 919–20, 919f focal adhesions, 208, 209f folding step (neurulation), 1103f, 1104 follicles, 1088f, 1089, 1094, 1094f follicle-stimulating hormone (FSH): and androgens, 1080 in endocrine system, 1080 and oral contraceptives, 1106 in reproduction, 1092, 1094, 1095 follicular cells, 1065 follicular phase, ovarian cycle, 1094–95 food: control over intake of, 999–1000, 1000f, 1073 detection of, 946, 946f processing of, 976–78, 978f food chains, 1248–49, 1248f, 1268–69, 1268f food-conducting cells, phloem, 775–76, 776f food-induced thermogenesis, 998–99 food limitations, and population density, 1232, 1232f food vacuoles, 94f, 95 food webs, 1248–51f, 1248–52 foot, of mollusks, 710 foraging behavior, 1189–90, 1189f Foraminifera, 591, 591f, 592t force, generation of, 955–60 forebrain: development of, 906 folding of, 906, 907f function of, in humans, 912–15f, 912–16, 915t relationship of structures in, 912f forelimbs: of bats vs. birds, 965 as homologous structures, 471, 471f

forestry science, 633 forward primers, 440 fossil fuels: and carbon cycle, 1263, 1263f and climate change, 1260, 1261f nitrogen released by burning, 1268 fossil record: completeness of, 537–38 of cyanobacteria, 541 of distribution of organisms, 1175–76, 1176f as evidence of evolution, 465–67f evidence of evolutionary relationships in, 498 factors affecting, 538t flowers in, 673–75, 674f of invertebrates, 544 moss in, 643–44, 644f and origins of life, 536–38 of prokaryotes, 535 radiometric dating of, 536–37 and speciation, 509 of trilobite, 720f fossils, defined, 536 Fos transcription factor, 192 founder effect, 490–91 Fouquieria splendens, 833, 833f four-chambered heart, 1012–14, 1014f four-o’clock plant: allele and genotype frequencies in, 479–80 incomplete dominance in, 364–65, 364f maternal inheritance in, 382–83, 382f, 383f fovea, 937 FOXP2 gene, 550 fragrance, flower, 845 frameshift mutations, 306 France, 1258, 1258f Frank, Otto, 1138 Frankia genus, 812 Franklin, Rosalind, 226, 226f, 227 Frank-Starling law of the heart, 1138, 1143 free energy (G): change in, 129–30, 129f in oxidative phosphorylation, 155, 155f free neuronal endings, 928f free radicals, 35–36 frequency, of sound waves, 929–31 fresh water, and microbiomes, 629–30, 629f freshwater fishes, 874f, 875, 1158 Friedman, Jeffrey, 1000 Friend, Daniel, 211 Frisch, Karl von, 1180 frogs: acetylcholine activity on heart of, 896–98, 897f bottleneck effect for population of, 490 chemical defenses of, 1226 chromosome number for, 344, 345f distinguishing species of, 497f endocrine system of, 1078, 1078f membrane protein experiments with oocytes of, 119 oocyte maturation in, 328, 328f

as semi-aquatic animals, 465 surface area of skin of, 866, 867f Fromia monilis, 728f frontal lobe, 914, 914f frost, 1155, 1158 fructose-1,6-bisphosphate, 148, 148f fructose-6-phosphate, 148f fruit flies, 342, 448 See also Drosophila melanogaster fruiting bodies, 607 of basidiomycetes, 615–16, 616f, 617f in reproduction, 610–11, 610f, 611f fruits: of angiosperms, 672, 672f, 677–78, 678f, 682–83, 683f coevolution of, 682–83, 683f defined, 648 development of, 763, 852–53, 853f and fertilization, 843, 843f and plant hormones, 785, 790–92 ripening of, 213 for seed dispersal, 843, 843f Frye, Larry, 110 FSH. See follicle-stimulating hormone. FT protein, 844 FtsA protein, 405, 406 FtsZ protein, 405, 406 Fujikawa, Shelly, 73 Fujiwara, Tetsuro, 1031–33 fumarate, in citric acid cycle, 152f Funaria hygrometrica, 656–57, 656f–57f function, relating structure to. See structure and function (core concept). functional complexity, of microbiomes, 625–27, 626f, 627f functional genomics, 440 functional groups, and carbon atoms, 46, 47t functional MRI (fMRI) scans, 919–20, 919f fundamental niche, 1222–24 fungi, 605–21 asexual and sexual reproduction of, 609–11 chestnut blight caused by, 1277 disease-causing, 1149 distinguishing features of, 612t diversity of, 611–16, 612t ecological roles and biotechnology applications of, 616–20 in Eukarya, 9, 10f evolution and distinctive features of, 605–9 gametophyte production in, 340 host-associated microbiomes in, 631–32, 632f and multicellularity, 202 and plant behavior, 798 and plant nutrition, 809, 812, 812f in primary succession, 1242 and resource-based mutualism, 1229–30, 1230f sexual reproduction of, 340, 341f summary, 620–21 used in pharmaceutical industry, 1284, 1285

INDEX

INDEX I-21

I-22 INDEX Fungi kingdom, 517 fungus-like protists, 582, 582f fused joints, 953f fusion step (neurulation), 1103f, 1104

G

INDEX

G. See guanine. GABA. See γ-aminobutyric acid (GABA). GABAA receptor, 898–99, 899f Gage, Fred, 919 GAGs (glycosaminoglycans), 52, 206, 206f galactose, 365 Galápagos finches. See finches. Galápagos Islands, 460, 461t, 462–64, 464f, 504–6 Galeopsis pubescens, 506 Galeopsis speciosa, 506 Galeopsis tetrahit, 506 gallbladder, 979–80, 980f, 985 galls, 565 Gallus gallus, 414 Galvani, Luigi, 884, 885 gametangia, 611, 612, 651, 652f gametes, 325 defined, 1085 formation of, 1087–89, 1088f fungal, 609 in sexual reproduction, 1085 See also female gametes; male gametes; sexual reproduction gametic isolation, 500–501 gametogenesis: in animals, 1087–89, 1088f defined, 1087 in ovaries, 1093–94, 1094f gametophytes, 340, 643 of bryophytes, ferns, and seed plants, 653, 653f defined, 840, 840f development of, 848–51 of flowering plants, 761, 762, 840–41, 840f, 841f, 848–51 placental transfer tissues and, 655–57 production of, 840–41, 840f, 841f gametophytic self-incompatibility (SI), 849, 850f gamma globulin, 1118 γ-aminobutyric acid (GABA), 896, 898–99, 899f γ-globin genes, 451, 1097 γ-proteobacteria, 543 γ subunit, ATP synthase, 156–59 ganglia: of annelids, 905 basal, 914 defined, 908 of retina, 941 gannet, 1190, 1190f gap genes, 421, 421f gap junctions: multicellularity and, 208t, 211–12, 211f–13f and plasmodesmata, 214 size of, 212–13, 213f Garces, Helena, 855

garden peas, Mendel’s studies of, 350–51, 350f, 351f garden plants, flower organ number in, 845 Garrod, Archibald, 244–45, 266 Garstang, Walter, 731 gaseous neurotransmitters, 896, 896t Gaser, Christian, 920–21 gases, 980 in blood, 1034–36, 1035f, 1036f properties of, 1024–25 gas exchange: across body surface, 1025 in air-breathing vertebrates, 1027 in capillaries, 1021, 1021f defined, 1010 in insects, 1027, 1027f in lophophores, 709, 709f in water-breathing animals, 1025–27, 1025f gastric ulcers, 986, 986f gastrin, 985 gastroesophageal reflux, 986 gastrointestinal disorders, 985–86 gastrointestinal (GI) tract, 975 See also alimentary canal Gastropoda and gastropods, 710, 711, 711f, 712t, 964 gastrovascular cavity, 702, 973–74, 975f gastrula, 690f, 691, 1101 gastrulation, 690f, 691, 1099, 1101–3, 1102f gas vesicles, 566 gated channels, 117 gated ion channels, 888, 888f Gatorade, 878 Gause, Georgyi, 1219–20 Gaut, Brandon, 683 G bands, 325, 342 G1 checkpoint, 327, 327f G2 checkpoint, 327–28, 327f geese, 874, 1181, 1181f, 1184, 1184f Gehring, Walter, 513 gel electrophoresis, in gene cloning, 438f, 439 Gemmata obscuriglobus, 567 gene amplification, 316, 317f gene cloning, 434–40 defined, 434 DNA libraries for, 438–39, 438f gel electrophoresis in, 438f, 439 overview, 435f polymerase chain reaction for, 439–40, 439f propagation of host cells in, 437–38, 437f recombinant vectors in, 435–37, 436f, 436t vector and chromosomal DNA for, 435 gene duplications, 450–51, 450f, 451f gene expression, 243–65 and characteristics of organisms, 247 defined, 282 of development-influencing genes, 509–10 epigenetic effects on, 374, 374t eukaryotic RNA modification, 249–51, 250f, 251f

inborn errors of metabolism, 244–45, 244f mutations effecting, 306, 306t one-gene/one-enzyme hypothesis, 245–46, 245f overview, 244–46f, 244–47 and phenotype, 364 summary, 264–65 transcription, 246–49 translation, 246–47, 246f, 252–64, 252f, 252t, 253f, 255–63f, 258t, 263t, 264t gene families, 450–51, 450f, 451f, 473–74, 1096–97, 1097f gene flow, 492 gene interaction, 366 gene mutations. See mutations. gene pools, 478 genera, in taxonomy, 518 general lineage concept, 499 General Sherman tree, 202, 202f general transcription factors (GTFs), 295–96, 295f generational growth rate, 1209 generative cells, 849 gene regulation, 282–303 in bacteria, 285–94, 285f, 286–93f and chromatin structure/DNA methylation, 296–99 of collagen synthesis, 205–6 defined, 282 differential, 196 (See also differential gene regulation) and environmental changes, 283, 283f in eukaryotes, 283–84, 284f, 294–301, 300t of metabolic pathways, 139 overview, 282–85 of RNA modification and translation, 299–301, 300f, 300t, 301f summary, 301–2 timing of, 284–85, 285f transcription factors and mediator, 294–96 genes. See inheritance; specific genes. gene sequences: principle of parsimony for, 526 shared derived character for, 524 See also DNA sequences gene silencing, 845, 845f genetically modified organisms (GMOs), 809 genetic code: and amino acid sequence, 252, 252t deciphering of, 254–56f and translation, 252–56, 252f, 253f, 255–56f genetic disease, 313–14, 314f genetic disorders. See specific disorders. genetic diversity, 1280–81, 1281f genetic drift, 489–91f genetic engineering: and plant nutrition, 810–11 and temperature tolerance, 1157 See also biotechnology genetic expression, 1182 genetic information. See DNA (deoxyribonucleic acid).

genetic mapping, 387–88, 388f genetic maps, defined, 387, 388f genetic material: biochemical identification of, 220–23 changes in total amount of, 342 evolutionary change in, 5–6 in plant vs. animal cells, 382f theory of DNA, 14 in transduction, 410–11, 410f types of changes to, 6–7, 6f, 7f genetic recombination, 1085 genetics: and altruism, 1196 and behavior, 1181–87f defined, 219 of lactose intolerance, 981–82 genetic technologies, 434–56 with bacterial and archaeal genomes, 445–48, 446t, 447–48f with eukaryotic genomes, 448–51, 449t, 450f, 451f gene cloning, 434–40, 436t genomics, 7–8, 440–45, 440f, 441f, 443f, 443t, 444f and repetitive sequences/transposable elements, 452–54 summary, 454–55 See also genomics genetic variation: evolution and, 461 in humans, 557–58 and microevolution, 481 and migration, 492 in populations, 477 and selective breeding, 469 gene transfer: bacterial, 406–11, 406t, 407–10f horizontal, 7, 7f, 8f, 411, 474–75, 474f, 531–33 genome-centric metagenomics, 627 genome defense, non-coding RNAs in, 275–78, 277f genomes: biological complexity and size of, 300–301, 300t of chimpanzees vs. humans, 550 chloroplast, 98 defined, 7, 9f, 78, 224, 283 encoding of ATP-using proteins, 130–31, 131t evolutionary changes in, 474–75, 475f maintenance of integrity of, 318–19, 319f, 319t of mitochondria and chloroplasts, 381, 382f mitochondrial, 98 nuclear, 98 sizes of, 449–50, 450f of Trichomonas vaginalis and Giardia intestinalis, 586 virus, 393, 395 See also DNA (deoxyribonucleic acid) genomes & proteomes connections, 1214–15 genomic imprinting, 375–76, 375f, 376f genomic libraries, 438

genomics, 440–45 CRISPR-Cas technology, 442–44, 444f defined, 7, 434 dideoxy chain-termination method, 440–42, 440f, 441f DNA microarrays, 442, 443f, 443t and evolution, 7–8 genotype frequency: and Hardy-Weinberg equation, 479–80 in population genetics, 479 genotypes: phenotypes vs., 353 testcrosses to determine, 353–54, 354f genotypic variation, in humans, 557–58 geographic isolation, allopatric speciation and, 502–4 geological timescale, 538 geology, and theory of evolution, 459–60 Geomyces destructans, 617 Geospiza fortis, 463–64, 464f, 1221–22 Geospiza fuliginosa, 1221–22 Gerbera hybrida, 846, 846f germination: environmental/internal factors in, 853–55, 854f and fertilization, 843 of flowering plants, 762 and pistils, 849, 850f pollen, 842, 849, 850f seed, 843, 853–55, 854f and succession, 1243 germ layers: and animal diversity, 690–91, 690f in animal embryos, 1101–3, 1102f germ-line cells, mutations in, 307, 307f gestation: internal, 474, 1097, 1097f in mammals, 1096–97, 1096f, 1097t and population ecology, 1211, 1214 GFR (glomerular filtration rate), 1048, 1049 Ghadiri, M. Reza, 72 GH (growth hormone), 1077 giant anteater, 468, 469, 469f giant axons of annelids, 715 giant horsetail (Equisetum telmateia), 646f giant kelps, supergroup of, 590f giant pandas, 1291 giant rhubarb, 812, 813f giant sequoia, 665, 1156, 1156f Giardia intestinalis, 586, 586f, 593 giardiasis, 586 gibberellic acid, 770, 786t, 854 gibberellin-DELLA system, 790, 791f gibberellins, 786t, 789–90, 790f, 791f gibbons, and human evolution, 548 Gibbs, J. Willard, 129 GID1 proteins, 790f, 791, 791f Giemsa stain, 325, 342 GI (gastrointestinal) tract, 975 See also alimentary canal gila monster, 1284 Gilbert, Francis, 1245 Gill, Frank, 1190 gills, 1025–27, 1025f of mollusks, 710 in single circulation, 1012

gill-withdrawal reflex, 917–18, 917f Gilman, Alfred, 189 Gilula, Norton, 211 Ginkgo biloba, 666, 667, 667f Ginkgophyta (gingkos), 644 Giraffa camelopardalis (giraffe), 1, 7, 12, 12f giraffes (Giraffa genus): blood pressure in, 1132 inheritance of acquired characteristics for, 458 species of, 1, 7, 12, 12f gizzards, 975, 977–78, 977f glaciation, since origin of Earth, 540 glaciers: microbiomes of, 628–29, 629f primary succession following retreat of, 1240–42, 1241f, 1242f gladiolus, 794 glands See also specific glands glaucoma, 947, 948f glia (glial cells): myelination of, 892 signals to/from, 883, 883f gliding, 965 global temperature differentials, 1160–61 global warming: human impact on, 1260–62, 1261t species indicators of, 1290 and water cycle, 1265, 1266f See also climate change globin gene family: evolution of, 1097, 1097f and internal gestation in mammals, 1097, 1097f globin genes: evolution of, 450, 451f, 473–74 regulation of, 284, 284f glomerular filtration rate (GFR), 1048, 1049 glomerulosa, 1068 glomerulus, 1047–49, 1049f Glomus genus, 614f Glossopteris genus, 1175 glucagon, 996, 1069, 1070f glucocorticoid receptors (GR), 1076 glucocorticoids: structure and function of, 1061f, 1068 therapeutic uses of, 1080 gluconeogenesis, 993f, 994, 1068 glucose: in absorptive state, 992 blood concentration of, 995, 996, 997f in Calvin cycle, 175 cellular response to, 184, 184f concentration gradient for, 114, 115f concentration of, 38 and endocrine systems, 1066–73, 1070f energy from, 128 in fermentation, 161f free energy change for breakdown of, 155, 155f and gene regulation, 292–93, 292f in GLUT proteins, 995–96 in glycolysis, 146–49, 147f, 148f

human blood concentration of, 867, 868, 868f and metabolism (See cellular respiration; glycolysis) as monosaccharide, 50, 50f phosphorylation of, 131 in photosynthesis, 165 and plant cell walls, 207 in polysaccharides, 51, 51f, 52 in postabsorptive state, 993, 994 glucose-6-phosphate, 148f glucose sparing, 994 glucose transporters (GLUTs): and endocrine system, 1069 evolution of, 995–96 insulin as regulator of, 995, 995f GLUT 1, 996 GLUT 3, 996 GLUT 4, 995–96 glutamate, 139, 896 GLUTs. See glucose transporters (GLUTs). glycans, 207f, 208 glyceraldehyde-3-phosphate (G3P), 175, 175f, 176 and fat metabolism, 159 in glycolysis, 148–49f glycerol: fat metabolism to, 159 in triglycerides, 52, 52f glycine, 57f glycocalyx, 78 glycogen: and cell communication, 193 glucose production from, 993, 993f, 994 molecular structure of, 51, 51f muscular-skeletal systems and, 961 glycogenolysis, 993–94, 993f, 1068, 1069 glycogen phosphorylase, 193, 196 glycogen synthase, 193 glycolate, 178 glycolipids: as membrane components, 112, 113 structure of, 107 glycolysis: in cancer cells, 149–50, 150f in carbohydrate metabolism, 146 as catabolic reaction, 137–38 in cellular respiration, 146–50f, 147–50 defined, 146 glucose and pyruvate in, 147–49, 147f and muscular-skeletal systems, 961 regulation of, 140 glycolytic fibers, 961, 962t glycoproteins, as membrane components, 112, 113 glycosaminoglycans (GAGs), 52, 206, 206f glycosidic bonds, 50, 51f glycosylation: in endoplasmic reticulum, 90 of membrane components, 112–13 glycosyl transferase, 365 glyoxysomes, 95 GMOs. See genetically modified organisms (GMOs). gnathostomes, 737–42

chondrichthyans, 739–40, 739f hinged jaw of, 738, 738f osteichthyans, 740–42 and tetrapods, 742 Gnetales, 670, 671f Gnetum genus, 670, 671f GNOM genes, 764, 765f GnRH (gonadotropin-releasing hormone), 1092, 1106 Gobi Desert, Mongolia, 1169, 1169f Goethe, Johann Wolfgang von, 769 goiters, 1067, 1067f goldenrods, 794 golden silk spiders, 1199f golden-winged sunbird, 1190, 1190f goldfish, sensory systems of, 925 gold foil experiment, 25–26 See also atoms Golgi apparatus: of animal cells, 80f attachment of carbohydrates and proteins at, 112–13, 113f in cell structure, 91, 91f in exocytosis, 122, 123, 123f of plant cells, 81f gonadal steroids, 1077, 1079–80 gonadotropin-releasing hormone (GnRH), 1092, 1106 gonadotropins, 1080 gonads: gametogenesis in, 1087 sex steroids from, 1079–80 gongylidia, 1230 Gonium pectorale, 543 goose barnacle, 725f Gordon, Jeffrey, 635–36 Gorillini and gorillas: chromosome structure and number in, 475, 475f and human evolution, 548 jaw size and muscle attachment in, 957f Gossypium genus, 760 Gould, Elizabeth, 918 Gould, John, 460 Gould, Stephen Jay, 508 G3P. See glyceraldehyde-3-phosphate. G0 phase, 325 G1 phase, 325–27 G2 phase, 325–27 GPP (gross primary production), 1252 GPR56 gene, 916 G-protein-coupled receptors (GPCRs): and cell communication, 188–89, 189f, 192–94, 196 and nervous system cells, 898 in sensory systems, 938, 944, 945 G proteins, 188, 189, 189f, 193 graded potentials, 888–89, 889f gradualism, 508–9 graft rejection, 1127 grains, as fruits, 677 Gram, Hans Christian, 568 Gram-negative bacteria, 568, 569, 569f Gram-positive bacteria, 568, 569, 569f Grant, Peter, 463–64, 464f Grant, Rosemary, 463–64, 464f granum(--a), 97, 166

INDEX

INDEX I-23

I-24 INDEX

INDEX

grasping hands, of primates, 548 grasses: competition among, 1150–51, 1151f rhizomes of, 777 seed germination of, 853, 854, 854f grasshoppers, 718f, 1232, 1232f grassland biomes, 805 grasslands, 1282, 1285f grass-pink orchid, 1231 grassquit finch, 460 gravitropism, 794, 795, 795f, 796f gravity, 794–96, 795f, 796f and baroreceptors, 1135 and bulk flow, 825–26, 825f, 826f and plant size, 825–26 and venous blood flow, 1022 gray fox (Urocyon cinereoargenteus), 466, 468f gray matter, 908, 909, 909f gray wolf (Canis lupus), 518 Grb protein, 191 Great Barrier Reef, 705 greater apes, 548 great white sharks, 739 green algae: and cellulose, 594–95f, 594–96 characteristics of, 587 and domains, 517 and evolutionary relationships of modern plants, 642f, 643 in intertidal zone, 1242–43, 1243f and light, 1158, 1159f greenhouse effect, 1260–61, 1260f, 1261t Greenland sharks, 740 green plants: light as resource for, 802–4, 803f nutrients required by, 801–2 and parasitic plants, 815–16, 816f green stomach, 815 green turtle, 748f Greider, Carol, 237, 238 Gremlin gene, 510 GR (glucocorticoid receptors), 1076 Griffith, Frederick, 221–23f, 409 Griffith, John Stanley, 402 gross primary production (GPP), 1252 See also primary production Groudine, Mark, 316 ground finches, 461t, 463–64, 464f ground squirrels, 1195 ground tissue, 216, 216f group living, 1192–93, 1193f group selection, 1194 grouse, 1198f growth: and blooming of flowers, 848 determinate vs. indeterminate, 762 of flowering plants, 761, 764–69, 765t hormonal control of, 1077–79 and plant behavior, 791–92 plant nutrition for, 802–4, 802t, 803f population, 1210–15 population, rate of, 1208–9 primary, 765–66, 765t in root systems, 777–79, 778f, 779f secondary, 765t, 766 of stem cells, 425f

tissues and cell, 215 vegetative, 762 growth factors: defined, 190 mutations effecting, 314, 315f growth hormone (GH), 1077 growth processes, of fungi, 607–9, 608f, 609f growth rates, and phenotype, 512 Grus japonensis, 1199f Gryllus pennsylavanicus, 499 Gryllus veletis, 499 GTFs (general transcription factors), 295–96, 295f GTP (guanosine triphosphate), 151, 152f, 188, 189f, 260 guanine (G): in DNA, 224 molecular structure of, 64, 65 guanosine diphosphate (GDP), 188, 189f guanosine triphosphate (GTP), 151, 152f, 188, 189f, 260 guard cells: stomatal, 774, 774f tissues, 216 transpiration regulation by, 829–31, 830f Guerrier-Takada, Cecilia, 135 guides, ncRNAs as, 267, 269f Gulf Stream, 1163–64 Gunnera species, 812, 813f Gunning, Brian, 655–57 guppies, 486f GUS gene, 810, 811 Gustafsson, Lars, 483 gustation, 942, 946–47 gut microbiomes, 635–36 guttation, 828, 828f Guyton, Arthur, 1136 Gymnogyps californicus, 1292, 1292f gymnosperms: defined, 665 evolution and diversity of, 665–70 origins of, 546–47 overview, 647, 647f and plant nutrition, 812 Gymnothorax meleagris, 741f

H

HAART (highly active antiretroviral therapy), 1129 Haber, Fritz, 809 habitat isolation: and allopatric speciation, 502–4 as prezygotic isolating mechanism, 499 habitats: destruction, 1269–71, 1271t of fungi, 611 and plant nutrition, 803 of protists, 582–83, 583f representative, 1287, 1288f restoration of, 1287, 1291, 1291f habituation, 1182 Hadean eon, 538 Hadley, George, 1160 Haemophilus influenzae:

base pairs in, 403 sequencing genome of, 446–48 Haemophilus influenzae type b (Hib), 922 hagfish, 737, 737f hair cells: deafness caused by, 948 mechanoreception by, 928–29, 928f in vestibular system, 932 hair follicles, 928f hairs: of mammals, 753, 754f of plant roots (See root hairs) Haldane, J. B. S., 70, 477 half-life, 141, 536 halophytes, 1159 Hamilton, W. D., 1193–95 Hamilton’s rule, 1195 Hammock, Elizabeth, 1197 Hammond, John, 810–11, 810–11f hamsters, 1096 hamstrings, 954 Hanczyc, Martin, 73 hands, of primates, 548 Hanuman langurs, 1194, 1194f Hapalochlaena lunulata, 711f, 712 haplodiploid systems, 360, 360f, 1196 haploid cells, 325 haploid-dominant life cycles, protists with, 596–97, 596f haploid-dominant species, 340f, 341 haplorrhini, 548 haptophytes, 588, 589f Harberd, Nicholas, 791 Hardy, Godfrey Harold, 479 Hardy-Weinberg equation, 479–80, 492 Harrison, Susan, 1289 Hatch, Marshall, 179 Hatch-Slack pathway, 179 H+-ATPase proton pump, 820, 829 haustoria, 617, 617f, 798, 815, 1229 hawkweeds, 856 Hayes, Marianne, 329 Hayes, William, 408 hazardous waste. See pollution. head region (motor protein), 85 hearing, 929–31 hearing loss, 948 heart attacks, 1010, 1038 heart beat, 1017 heartburn, 986 heart disease, 1038, 1039 heart rate (HR): feedforward regulation of, 870 in response to hemorrhage, 1134 heart(s): and blood pressure, 1132 cardiac muscle in, 860, 953, 954 comparative features of mammalian, 1023t effects of heart attack on, 1010 four-chambered, 1012–14, 1014f Frank-Starling law of, 1138, 1143 muscle (See cardiac muscle) myogenic, 1017 neurotransmitter activity on, 896–98, 897f

and response to hemorrhage, 1138 venules/veins and blood flow to, 1021–22, 1021f of vertebrates, 1016–19 heart stage, of plant development, 429, 430f heart valves, 1018, 1018f heat: biomes and, 1165–66, 1168–69 and body temperature, 1002 production of, 1006 See also body temperature; temperature heat capacity, defined, 39–40 heat exchange: altering endotherms’ rates of, 1004–6 between animals and environment, 1003–4, 1003f, 1004f heat of fusion, defined, 39 heat of vaporization, defined, 39, 40 heat shock proteins (HSPs), 1157 heat stress, in plants, 618–19, 619f heavy metals, tolerance of, 484 Hebblewhite, Mark, 1232 Hebert, Paul, 726 Hedera helix, 468, 469f hedgerows, 1289, 1289f Heitz, Emil, 239 Helianthus genus, 677f Helicobacter pylori, 565, 578, 987–88 helium, 25f Heloderma suspectum, 1284 helper T cells: antigen presentation to, 1122, 1122f and B-cell activation, 1122–23 in graft rejection, 1127 and HIV/AIDS, 399–400, 399f 1128, 1129 structure and function of, 1116f, 1117 hematocrit, 1015, 1140, 1142–43, 1143f hematopoietic stem cells, 426, 426f hemicellulose, 207f, 208 hemidesmosomes, 208, 209f hemiparasites, 1228 hemispheres, of cerebrum, 913, 913f Hemitripterus americanus, 468, 469f hemizygous individuals, 360 hemlocks, 1241–42, 1242f hemochromatosis, 106 hemocoel, 1011 hemocyanin, 1034 hemodialysis, 1055–56, 1055f hemoglobin: affinity of, for oxygen, 1034–35, 1035f, 1036f composition of, 246 and erythrocytes, 1015 and erythropoietin, 1142 evolution of, 1097 gene family of, 450, 451 and gene regulation, 284 molecular structure of, 60 as respiratory pigment, 1034, 1034f hemolymph, 1011, 1011f hemophilia A, 360–61, 361f, 377, 378, 434

hemorrhage, 1131–47 and blood pressure/organ function, 1132–33, 1132f, 1133f defined, 1131 as public health issue, 1144–45 rapid phase of response to, 1133–39, 1134f, 1136–39f secondary phase of response to, 1140– 44, 1144t summary of, 1145–46 hemp (Cannabis sativa), 776 Hennig, Willi, 516 Hepatophyta. See liverworts. herbaceous plants: phloem loading in, 836 vascular systems of, 775 See also plants herbivores: digestive systems of, 971 effects of increased carbon dioxide on, 1264–65 essential nutrients for, 972 and evolution of plants, 650, 650f in food chains, 1248, 1248f and plant behavior, 784, 797, 798f plant communication in response to, 1, 1f species interaction with plants, 1226–28 herbivory: effects of carbon dioxide on, 1264–65 species interactions, 1217, 1226–28, 1227f, 1228f hercules beetles, 1191, 1191f herds, 1193 hereditary nephrogenic diabetes insipidus, 1054 heritability, 5 See also inheritance hermaphrodites, 702, 1085 herpes simplex viruses, 399 Hertz, Heinrich, 929 Heterocentrotus trigonarius, 728f Heterocephalus glaber, 686 heterochromatin, 239, 240f heterochrony, 512, 512f heterocytes, 573 heterospory, 658, 660, 661 heterotherms, 1003 heterotrophs, 573, 606 animals as, 687 defined, 165 in food chains, 1248, 1248f origins of, 540–41 plants as, 803, 803f, 812 protists as, 582, 582f heterozygote advantage, 485 heterozygous individuals, 353, 492–93 heterozygous individuals, nonrandom mating effects on, 492–93 Hevea brasiliensis, 679 hexaploidy, 1214–15, 1215f Hexapoda and hexapods, 719t, 721–24, 722f, 723t, 724f See also Insecta and insects hexenols, 797, 798f hexokinase, 132, 132f

hexoses, 50 Hfr strains, of E. coli, 408 Hib (Haemophilus influenzae type b), 922 hibiscus, 676f, 845 Hibiscus cannabinus, 776 hierarchical models, 18 high-blood pressure, medication for, 1 highly active antiretroviral therapy (HAART), 1129 highly repetitive sequences, 452 high molecular-mass hyaluronan (HMMHA), 686 Hill, Robin, 174 Hillig, Karl, 679–80, 680f hindbrain: development of, 906 function of, in humans, 910, 912f, 915t hinged jaw, of gnathostomes, 738, 738f hinge joints, 953f hinge region, immunoglobulin, 1118 hippocampus, 914–15, 918–19 Hippocampus bargibanti, 1225f hippopotamuses, 465 Hirudo medicinalis, 716f histamine, 1111 in allergies, 1127–28, 1128f as neurotransmitter, 895 histidine synthesis, 410–11, 410f histone acetyltransferase, 297 histone code hypothesis, 297 histones (histone proteins): in chromosomal compaction, 240f and gene transcription, 297, 297f, 298, 299f in nucleosomes, 238, 238f histone variants, 297, 298f Histoplasma capsulatum, 618 HIV (human immunodeficiency virus): as emerging virus, 399–400, 399f and probiotic treatments, 637 reproductive cycle of, 395–98 HMM-HA (high molecular-mass hyaluronan), 686 H1N1 influenza, 399 Hoffman, Jules, 1113, 1115 Holland, Scott, 920, 921 Holley, Robert, 257 holobiont, 630 holoblastic cleavage, 1100, 1100f, 1101 hologenome, 630 holoparasites, 1228, 1228f Holothuria argus, 728f Holothuroidea, 727 homeobox, 423, 423f homeodomain, 423, 423f homeostasis: in animal bodies, 867–79, 868t and autonomic nervous system, 911 for blood glucose concentration, 996, 997f control of internal environment for, 868–69, 869f defined, 859 and excretory systems, 1043 and feedforward regulation, 870 hemorrhage as challenge to (See hemorrhage)

and hindbrain, 910, 912f insulin and glucagon in, 1069, 1070f for internal fluids, 872–78 and kidney disease, 1054–56, 1055f in living organisms, 1021 local and long-distance chemical signals in, 870–72 and muscular-skeletal systems, 953 negative feedback in, 869–70, 870f and parathyroid hormone, 1074–75, 1074f and plants, 784 and positive feedback, 870 in vertebrates, 867–68, 868f, 868t homeostatic control systems, 868–69, 869f, 870f, 1133 homeostatic response to hemorrhage: rapid phase of, 1133–39, 1134f, 1136–39f secondary phase of, 1140–44, 1144t homeotherms, 1003 homeotic genes: defined, 422 evolution of, 423–24, 424f and flower development, 431, 431f and segment characteristics, 422–24 homing pigeons, 934 Hominidae and hominids, 548, 552f Homininae family, 548 Hominini and hominins, 547, 550 hominoids, 547 Homo genus, 550–54, 957 Homo erectus, 552 Homo ergaster, 552 Homo florensiensis, 554 homogentisic acid, 245 Homo habilis, 547 Homo heidelbergensis, 552–53 homologies (anatomical homologies): and evolution, 471–73, 471f, 472f, 472t in systematics, 521–23 of vertebrates, 471, 471f homologous chromosomes (homologs): defined, 325 and eukaryotic cell cycle, 325 and law of segregation, 356, 356f in meiosis I, 335–39f, 340t homologous genes: from common ancestral genes, 473, 473f for eye evolution, 513 and gene duplication, 450, 450f homeotic genes as, 423–24, 424f and photosynthesis, 171, 172f homology, defined, 325 Homo neanderthalensis, 552–55 homophilic binding, 209 Homo sapiens: evolution of, 547, 549f migration of, 554 homozygous individuals, 353, 492–93 honeybees, 373 innate behaviors, 1181–82 and Nosema ceranae, 611, 612f sensory systems of, 925, 937–39 tactile communication among, 1192, 1192f

See also bees honeycreepers, 503 hoof-and-mouth disease, 1108 hook, flagellar, 570, 570f Hooke, Robert, 75 hooks of plant stems, 791 hookworms, 717 hop plant, 854 horizontal cells, 941 horizontal gene transfer, 411 in archaea, 565–66 in bacteria, 565–66 and evolution, 7, 7f, 8f, 474–75, 474f and systematics, 531–33 hormonal signaling, 195–96, 195t hormones: apoptosis control by, 197–99, 198f during birth, 1097–99, 1098f and blood glucose concentration, 996, 997f and circulatory system, 1022 classes of, 1059, 1060f, 1060t defined, 186, 770, 1058 and food intake, 999–1000, 1000f in growth and development, 1077–79 and immune system, 1127 localized signals in, 871–72 and male reproductive tract, 1092–93, 1093f mechanisms of action of, 1059–62, 1061f, 1061t metabolism/energy balance control by, 1065–73, 1068t and mineral balance, 1073–77 misuse of, 1080–81 negative feedback loops involving, 869 and osteoporosis, 966 and ovarian cycle, 1094–95, 1095f plant (See plant hormones) and rate of digestion, 985, 985f in reproduction, 1079–80 therapeutic use of, 1080 and uterine cycle, 1095 horned bush viper, 748f horns, of mammals, 754–55, 755f hornworts, 644, 645f See also Bryophyta and bryophytes Horowitz-Scherer, Rachel, 238 horsehair worm (Paragordius varius), 2t horses: evolution of, 6–7, 6f, 522 feedforward regulation in, 870, 871f and hybrid sterility, 501 respiratory system of, 1030 vertical evolution of, 6f horsetails, 545, 1241 Horvath, Philippe, 275 host-associated microbiomes, 630–37 acquisition of, 630 in animals, 633–37 and evolution of hosts, 630–31, 631f in fungi, 631–32, 632f lichens, 631–32, 632f in plants, 632–33, 633f

INDEX

INDEX I-25

I-26 INDEX

INDEX

host cells: in gene cloning, 437–38, 437f for protists, 599–602, 601f host plant resistance, 1227 host plants, 1152, 1227 host range, of viruses, 393, 393f hosts: and evolution of microbiomes, 630–31, 631f of parasites, 1228–29 and virus characteristics, 392, 392t HOTAIR, 270, 271f, 279 hot desert, 1169, 1169f house cricket (Acheta domesticus), 2t HoxA-3 gene, 864, 865 HoxC genes, 270 Hox genes: and animal evolution, 688 and body segment specialization, 694, 695f in developmental genetics, 424, 424f in embryonic development, 1104 in evolutionary developmental biology, 510–12 evolutionary relationships among animals from, 695–98 and limb formation, 742–44 and organ development, 864–65 HR. See heart rate (HR); hypersensitive response (HR). HSF1, 192 HSPs (heat shock proteins), 1157 H+/sucrose symporter, 121, 121f human body: waste removal in, 40–41 water in, 36 Human Connectome Project, 904 human evolution, 547–58 Australopithecus and Paranthropus genera, 550 bipedalism in, 550 as continuous process, 555–57 and genotypic vs. phenotypic variation in humans, 557–58 Homo genus, 551–54 interbreeding in, 554 migration of Homo sapiens, 554 primate evolution and, 548–50 human genome: cancer and mutations in, 321 composition of, 448 genome of chimpanzees vs., 550 receptor tyrosine kinases encoding in, 190 repetitive sequences in, 452, 452f transmembrane protein-encoding genes, 109 Human Genome Project, 451 human immunodeficiency virus. See HIV. human impact, 1257–79 on biogeochemical cycles, 1262–68 on climate change, 1260–62, 1261t habitat destruction, 1269–71, 1271t human population growth, 1257–60, 1258f, 1259f and invasive species, 1275–77, 1276f, 1277f

overexploitation, 1271–75 pollution and biomagnification, 1268– 69, 1268f, 1269f preserving areas without, 1287–88 summary, 1277–78 Human Microbiome Project, 634 human population growth, 1257–60, 1258f, 1259f humans: absorptive state for, 992 aneuploidy in, 345, 345t audible pitch range for, 930 baroreceptor evolution in, 1135 baroreceptor location in, 1134f biodiversity preservation as goal of, 1293 bipedalism as characteristic of, 550 blood glucose concentration, 867, 868, 868f blood pressure for, 1018, 1132 brain and body size for, 906 brain of, 906, 907f, 910, 912f breathing reflex in, 1138, 1139f cell types in, 283, 284f chromosome number for, 342, 344–45 chromosome structure and number in, 475, 475f and coevolution of flowers, 843 collagen types in, 205–6, 206t developmental homologies in, 472 digestive systems of, 976, 976f, 978, 981–82 disorders impacting public health for (See public health issues) DNA polymerases, 236, 237f ear of, 929f, 930f embryonic development (See embryonic development) endocrine systems of, 1077, 1080 epigenetic changes associated with disease in, 380–81, 381t epigenetics of muscle cells in, 374 epinephrine’s effects in, 195–96, 195t evolutionary studies of, 530–31 evolution of (See Human evolution) and flower fragrance, 845 forebrain function in, 912–15f, 912–16, 915t genotypic vs. phenotypic variation in, 557–58 germ-line vs. somatic cell mutations in, 307, 307f gestation period of, 1096 globin gene family in, 450, 451f globin genes of, 284, 284f gut microbiomes in, 630, 631f hindbrain function in, 910, 912f as hunters, 1271, 1272f hypothalamus and pituitary gland in, 1062–63, 1063f immunoglobulin genes of, 1119 inbreeding by, 492–93 inheritance of mitochondrial genomes in, 384, 384t intestinal surface area of, 866, 867f latency in viruses for, 399 limb development in, 416, 416f

lymphatic system in, 1116f melanin production in, 183–84 microbiome of, 623, 623f midbrain function in, 910, 912 missing NER system components in, 313–14, 314f mitochondrial inheritance in, 384 molecular clock for, 530 molecular homologies in, 472–73 muscular-skeletal system of, 951 myosin and brain of, 956–57, 957f nervous system structure and function in, 907–16, 915t neurons in, 882 non-coding RNAs and disease in, 278–79, 279t olfaction by, 943, 944 oxygen-hemoglobin dissociation curve for, 1034–35, 1035f parasites of, 1109 pattern formation in, 417–18, 418f pedigree analysis of traits in, 358–59, 358f, 359f photoreception by, 937–39 pituitary gland of, 1062 recessive X-linked traits in, 360–61 reproduction (See animal reproduction) reproductive systems of, 1090–95 respiratory system of, 1029f, 1030, 1039f and seed plant diversity, 683, 683f selective breeding by, 469–71 skeletal muscle fibers of, 961 skeleton of adult, 953f skulls of chimpanzees vs., 512 urinary system of, 1048f vestigal structures in, 471, 472 viral diseases in, 393f X chromosome inactivation in, 377, 378 human welfare: conservation as benefit to, 1270 value of biodiversity to, 1282, 1284–86, 1285f, 1286t Humboldt Current, 1164 humidity, 825 hummingbirds, 874 humoral immunity, 1117–21 immunoglobulins and antibodies in, 1118–20, 1119f, 1120f plasma cells and antibodies in, 1120– 21, 1121f stages in, 1117–18, 1117f humpback whales, 1197 Humulus genus, 854 humus, 805–6, 806f hunchback gene, 420 Hundred Heartbeat Club, 1280 hunger, 946 hunting, by humans, 1271–72, 1272f Huntington disease, 358, 359f Hurtrez-Bousses, Sylvie, 1229 Hutchinson, G. Evelyn, 1221 Hutton, James, 460 Hyacinth macaw, 752f hyaluronic acid, 206 hybrid breakdown, 500f

hybrid inviability, 500f hybridization, of inheritance patterns, 350 hybrid sterility, 500f hybrid zones, 503–4 hydra, 731f hydrocarbons, 46 hydrochloric acid, 41, 977 hydrogen: atomic mass, 28, 29 atomic structure, 25f in covalent bonds, 31, 31f in mass of living organisms, 29 plant nutrition, 802t hydrogen bonds: in molecules, 33, 33f and protein structure, 60, 61f hydrogen cyanide, 797 hydrogen fluoride, 31, 31f hydrogen gas, 70–71 H+ electrochemical gradient, 153, 170, 170f, 171, 171f hydrogen ions (H+): acids/bases and concentration of, 41 H+/sucrose symporter, 121, 121f and pH, 41–42, 42f and respiratory systems, 1035 hydrogen peroxide: and chemical reactions, 131 and free radicals, 36 from peroxisomes, 95 and plant behavior, 798, 799f hydrogen phosphate ion, 809 hydrogen sulfide, 71, 71f, 72 hydrological cycle. See water cycle. hydrolysis reactions: of ATP (See ATP hydrolysis) defined, 40, 49f in lysosomes, 94 with organic molecules, 49, 49f hydrophilic molecules, 37 hydrophilic solutes, 114, 114f hydrophobic effect, and protein structure, 60, 61f hydrophobic molecules, 37 See also lipids; phospholipid bilayer; plasma membranes hydroponic studies, 805, 810 hydroskeletons, 951 hydrostatic pressure, 805, 1048–49 See also turgor pressure hydrostatic skeletons, 692, 693f hydroxide free radicals, 95 hydroxide ions (OH-), 41 20-hydroxyecdysone, 1061f, 1079 hydroxyl groups, 52f Hydrozoa, 704, 704t hyenas, 882, 882f Hylobatidae, 548 Hymenoepimecis argyraphaga (wasps), 2t Hymenoptera, 724 hyoid bone, 553 hyperosmotic solutions, 1047, 1050–52, 1158 hyperpolarization, 888, 890, 940 hypersensitive response (HR), 798, 799f hypersensitivities, 1127–28, 1128f hypertension, 1038

hyperthermia, 1112 hyperthermophiles, 563 hyperthyroidism, 1066 hypertonic solutions, 115, 115f hyphae (hypha): in body forms, 606–7, 608f growth of, 607–8, 608f hypocotyls, 852, 853f hypoglycemia, 996 hypolimnion, 1171 hypo-osmotic, 1158 hypothalamic-releasing hormones, 1064 hypothalamus: in endocrine system, 1060f and energy balance, 996, 999 function of, 912, 913 function of anterior pituitary gland and, 1063–64, 1064f hormones of vertebrates, 1064t, 1077 and oxytocin/antidiuretic hormone, 1064–65 relationship of pituitary gland and, 1062–63, 1063f hypotheses: defined, 14 proposing, 20 testing of, 14–16, 15f, 1152–54, 1153f, 1154f theories vs., 14 hypothyroidism, 1066 hypotonic solutions, 115, 115f Hyracotherium genus, 6 Hystrix africaeaustralis, 754f H zone, 955

I

IAA–, 785, 787f IAAH, 785, 787f I band, 955 IBOL (International Barcoding of Life) project, 726 ICBN (International Code of Botanical Nomenclature), 519 ice, 39 microbiomes in, 628–29, 628f sea levels and global warming, 1261–62 Ice Ages, 547 ICSP (International Commission on Systematics of Prokaryotes), 516 ICZN (International Commission on Zoological Nomenclature), 519 idiosyncratic hypothesis, 1281, 1282f Ig. See immunoglobulins. IgA, 1118 IgD, 1119 IgE, 1118, 1119, 1127 Igf2 gene, 375–76 IgG, 1118 IgM, 1118 igneous rock, 536 ileum, 980 illicit drugs, and neurotransmission, 900t, 901 illness, homeostatic response to, 1143

See also disease(s) image, in retina, 941, 941f imaging studies, of brain region function, 919–20, 919f immigration: and group selection, 1194 in island biogeography model, 1244– 47f, 1244–48 immune systems, 1108–30 adaptive immunity, 1115–26, 1116f, 1117f, 1119–22f, 1124–26f defined, 1108 innate immunity, 1109–15, 1111f, 1113–14f and pathogen types, 1109 public health issues related to, 1126– 29, 1129f in response to hemorrhage, 1143 in response to illness, 1143 summary, 1129–30 viral diseases of, 393f immune tolerance, 1124–25 immunity: active, 1126 adaptive, 1108, 1115–26, 1116f, 1117f, 1119–22f, 1124–26f cell-mediated, 1117–18, 1117f, 1121– 23, 1122f, 1124f defined, 1108 humoral, 1117–21, 1117f, 1119–21f innate, 1108–15, 1111f, 1113–14f lifestyle’s influence on, 1126–27 passive, 1126 immunoglobulins (Ig): from B cells, 1118–20, 1119f, 1120f classes and structure of, 1118–19, 1119f and recombination, 1119–11120, 1120f immunological memory, 1125–26, 1126f Imperata cylindrica, 1291, 1291f imperfect flowers, 672, 844, 844f implantation, in mammals, 1097, 1101, 1101f imprinted genes, 375–76, 375f, 376f imprinting, behavioral, 1184 inactivation gate, 889 inborn errors of metabolism, 244–45, 244f inbreeding, population genetics of, 492–93 inbreeding depression, 493 inclusive fitness, 1195–96 incomplete dominance, and phenotype, 364–65, 364f incomplete flowers, 672, 844 incomplete metamorphosis, 724, 724f incompressibility, 40 incus, 929, 930 independent assortment: law of, 354–57, 354f, 357f in sweet peas, 384–86, 385f independent events, product rule for, 369–70 indeterminate cleavage, 691f, 692 indeterminate growth, 762, 763f Indian peafowl (Pavo cristatus), 486 Indian pipe, 802, 803, 803f indicator species, 1290, 1290f indirect calorimetry, 998, 998f

individual selfish behavior, 1194, 1194f indoleacetic acid, 785, 786t induced fit, 133 induced mutations, 309, 310t inducers, 287 inducible operons, 287 induction, 417, 417f industrial applications, of bacteria, 579 industrial nitrogen fixation, 808, 809 infanticide, 1194, 1194f infections: cytotoxic T cells in, 1123, 1124f and inflammation, 1110–12, 1111f prevention of, after hemorrhage, 1143 infectious diseases. See specific diseases. infertility, causes of, 1104–5 inflammation, 1110–12, 1111f with allergies, 1127 in response to hemorrhage, 1143 and shock, 1145 inflorescences (flowers), 677, 677f, 846, 846f influenza virus, 394f information (core skill): alternative splicing and complexity, 300–301, 300t ATP-using proteins, 130–31, 131t bacterial cell division, 405 biology, 4f, 5 cancer cell glycolysis, 149–50, 150f cell structure and function, 78 cellular response to hormones, 196 cerebral cortex development, 916 continuous genotypic variation, 368 DNA, 225, 247, 253–54, 253f DNA barcoding, 726 DNA base sequence, 225 flower symmetry mutations, 846 garden pea studies by Mendel, 350 gene regulation, 284 genetic engineering and temperature tolerance, 1157 genetic material, 220 germ-line vs. somatic cell mutations, 307 hexaploidy, 1215 Hox genes and organ development, 864–65 human genome, 452 legume-rhizobia symbioses, 813–14, 814f microbiome diversity, 624 mitochondrial/chloroplast genomes and proteins, 381, 382f mitosis, 330 nervous system, 908–9, 909f neurotransmitter receptor subunits, 898–99, 899f pattern formation control, 418 plant genomes as indicator of evolutionary changes, 648 protein products and characteristics of cells, 81–82 reproductive cloning, 1293 RNA vs. DNA, 75 stomatal guard-cell development, 774, 774f transmembrane proteins, 108–9, 109t

infrared light, 934, 934f infundibular stalk, 1063 Ingenhousz, Jan, 164 ingestion, of food, 970, 971f ingroups, on cladograms, 524 inheritance, 348–72 of chromosomes, 324–25, 324f chromosome theory of, 355–57, 356f, 357f defined, 219 extranuclear, 381–84, 382f, 383f, 384t gene interactions in, 366–68, 367f, 368f Mendel’s laws, 349–52f, 349–55, 354f (See also Mendelian inheritance patterns) molecular basis for variations, 363–66, 363f, 364f, 365t, 366f pedigree analysis of human traits, 358–59, 358f, 359f polygenic, 367–68, 368f and probability, 368–70 and sex chromosomes, 359–62 summary, 370–71 See also gene expression inheritance of acquired characteristics, 459 inherited disorders. See specific disorders. inhibition: feedback, 139, 140f and gene regulation (See repressors) in succession, 1242–43, 1243f inhibitors, of enzymes, 133–34, 133f, 134f inhibitory postsynaptic potentials (IPSPs), 893–95, 895f inhibitory signals, at chemical synapses, 893 initiation factors, 260 initiation stage: of transcription, 248, 248f of translation, 260–61, 261f, 262f initiator caspases, 199f, 200 initiator procaspases, 199f, 200 injectisomes, 577, 577f injuries, and inflammation, 1110–12, 1111f innate behaviors, 1181, 1181f, 1184 innate immunity, 1109–15 and body surfaces, 1109–10 defined, 1108 evolution of proteins in, 1112–13 inflammation, 1110–12, 1111f interferons and complement, 1112 phagocytes, 1110–11, 1110f Toll proteins, 1113–14f, 1113–15 inner bark, 666, 776 inner ear, 929, 930 inner segment of photoreceptors, 937 innexin, 211 inorganic chemistry, 23 inorganic compounds: plant nutrition, 806–7 in soil, 806–7, 806f, 807f inorganic fertilizers, 808 inorganic nutrients, for animals, 970 inorganic phosphate (Pi): from ATP hydrolysis, 129–30, 129f in cross-bridge cycle, 957 inorganic soil constituents, 806–7

INDEX

INDEX I-27

I-28 INDEX

INDEX

inositol triphosphate (IP3): and animal development, 1090 and plant behavior, 785 inputs, at chemical synapses, 893–95, 895f Insecta and insects, 721–25, 731f compound eyes of, 935, 936f excretory systems of, 1046–47, 1046f hormonal control of development in, 1078–79, 1079f Hox genes in, 510 key features of, 722, 722f and multicellularity, 206 nitrogenous wastes from, 1044 orders of, 722, 723t, 724 origin of, 545 and plant nutrition, 801 pollination via, 841 reproduction and development of, 724, 724f and respiratory system of mammals, 865–66, 866f sensory hairs of, 942–43, 943f species richness of, 1237, 1237f, 1238 tracheal systems of, 1027, 1027f insecticide, 960 insulin: and blood glucose concentration, 1069, 1070f blood levels of, 38–39 and cell communication, 188 cell signaling by, 96 in Golgi apparatus, 91 isolation of, 1071–73 regulation of, 996 as regulator of metabolism, 995, 995f therapeutic uses of, 1080 insulin-dependent diabetes. See type 1 diabetes mellitus. insulin-like growth factor 1 (IGF-1), 1077 integral membrane proteins, 108, 108f, 210 integrase, 395 integration (step in viral reproductive cycle), 395, 396f integrators, 868, 869, 1133 integrins, 209, 210f integumentary system, 1143 integuments, 658, 841 interbreeding, in human evolution, 554 intercalated discs, 1017 intercellular receptors, 189–90, 190f intercellular transport, 211, 211f interference competition, 1218, 1218f interference phase (CRISPR-Cas system), 277f, 278 interferons, 1112 interleukin-1 (IL-1), 1113, 1123 interleukin-2 (IL-2), 1123, 1124 intermediate filaments, 84, 85t, 209 intermediate lobe, of pituitary gland, 1063 internal clock, 1188 internal environment, homeostatic control of, 868–69, 869f internal fertilization, of vertebrates, 747 internal fluids: adaptation to osmotic challenges, 879 of animals, 872–78

and athletic performance with temperature, 876–79 body compartments for, 872–73, 872f exchanges of water and ions with environment, 874–76 water and ion balance in, 873–74 internal gestation, 474, 1097, 1097f internal gills, gas exchange via, 1026–27, 1026f internal organs. See organs. internal stimuli, plant behavior as response to, 783–84, 783f International Barcoding of Life (IBOL) project, 726 International Code of Botanical Nomenclature (ICBN), 519 International Commission on Systematics of Prokaryotes (ICSP), 516 International Commission on Zoological Nomenclature (ICZN), 519 interneurons, 884, 884f internodes, 770 interphase, 325, 331, 332f intersexual selection, 486 interspecies hybrids, 499 interspecific competition, 1218, 1218f interstitial fluid, 872 and capillaries, 1020 and secondary response to hemorrhage, 1140, 1142f intertidal zone, 1157, 1158f, 1171, 1172, 1172f, 1222–24, 1242–43, 1243f intertropical convergence zone (ITCZ), 1161 intestines: and cell junctions, 208, 209f–11f, 210 in digestive system, 977f epithelial tissue in, 862f surface area of, 866, 867f intimidation displays, 1225f, 1226 intracellular concentrations, of ions, 886t intracellular digestion, 972, 973 intracellular fluid, 872, 873, 873f intracellular fluid volume, and cell shape, 873, 873f intracellular receptors: hormone action through, 1059, 1061, 1062 of lipid-soluble hormones, 1062 intrasexual selection, 486 intraspecific competition, 1218, 1218f intrauterine device (IUD), 1105f, 1106 intrinsic pathway, apoptosis, 200 intrinsic rate of increase, 1210 introduced species: as invasive, 1274–75 population ecology, 1150–51, 1151f species interactions with, 1228, 1228f and species richness, 1240 introns: and cDNA libraries, 438, 439 removal of, 251, 251f invagination, 862, 1101–3, 1102f invasive species, 1150–51, 1151f, 1275– 77, 1276f, 1277f inverse density-dependent factors, 1213 inversions, 342, 343f

invertebrates, 701–33 asexual reproduction in, 1085 characteristics of animal phyla, 731, 731t cnidarians, 704–5, 704t ctenophores, 702, 702f deuterostomes, 726–31, 728t digestive system of, 977 ecdysozoans, 716–26, 717f, 718f, 719t, 720–22f, 723t, 724–25f effects of, on plant populations, 1227– 28, 1228f electrical synapses of, 893 excretory systems of, 1045–46, 1045f extracellular matrix, 206 fossil record of, 544 gap junctions, 211 hormonal control of growth/ development in, 1078–79, 1079f Lophotrochozoa, 705–16, 706t, 712t nitrogenous wastes from, 1044 origins of, 543–46 photoreception in, 935, 935f, 936f, 937 phyla of, 731, 731t Porifera, 702–4, 703f production efficiency of, 1250 respiratory systems of, 1025 sense of balance for, 931–32, 931f skeletons of, 951 summary, 732–33 water loss from body surface of, 876 inverted pyramid of numbers, 1252 inverted repeats (IRs), 453 in vitro fertilization, 1105 in vitro translation systems, 254 See also cell-free translation systems involution, 1101–3, 1102f iodine, 901 iodine deficiency, 1066–67, 1067f iodine-deficient goiter, 1067, 1067f ion channels: gated, 888, 888f ligand-gated, 189, 189f ion electrochemical gradients: and ATP-driven ion pumps, 121–22, 122f functions of, 122t ionic bonds, 34, 34f, 34t, 60, 61f ionizing radiation, 310 ionotropic receptors, 898, 899f ion pumps, 121–22, 122f ions: balance of ions and water in internal fluids, 873–74 concentration gradients for, 885–86, 886f, 886t defined, 34 electrochemical gradients and movement of, 885–86, 886f, 886t exercise and homeostatic balance of, 876–79 hydroxide, 41 in ionic bonds, 34, 34f, 34t in kidney filtrate, 1050–53, 1050f, 1052f, 1053f obligatory exchanges between body and environment of, 874–76

and resting membrane potential, 885 at root-hair membranes, 820, 821f transport of, in roots, 823–24, 823f, 824f in water, 37, 37f IP3, 785 IPSP. See inhibitory postsynaptic potentials (IPSPs). iris (of eye), 937 iron: gene regulation and toxicity of, 301, 301f and plant nutrition, 802t, 805f iron regulatory element (IRE), 301 iron regulatory protein (IRP), 301, 301f irregular flowers, 845 irreversible inhibitors, 134 IRs (inverted repeats), 453 island biogeography, 1243–48, 1288–89, 1289f island dwarfing, 468 island fox, 466, 468, 468f islands, evolutionary evidence from, 466, 468, 468f islets of Langerhans, 1069, 1071 isocitrate, 152f isocitrate dehydrogenase, 153 isoforms, 1062 isolated continents, evolutionary evidence from, 468 isomers, 46, 47 cis-trans, 47, 48f of glucose, 50, 50f of organic molecules, 46, 47, 48f stereo-, 47, 48f structural, 47, 48f iso-osmotic solutions, 1047 Isopoda and isopods, 725f, 726 isotonic solutions, 115, 115f isotope-labeling methods, 176–78 isotopes, 29, 30f Isurus oxyrinchus, 739 ITCZ (intertropical convergence zone), 1161 iteroparity, 1204, 1205f IUD (intrauterine device), 1105f, 1106 Ivanovski, Dmitri, 392 ivory-billed woodpecker, 1270, 1270f

J

jack pine, 1156 Jackson, David, 434 Jacob, François, 286, 287, 289–91 Janke, Axel, 12 Jansen, Zacharias, 75 jasmonic acid, 784 Javan banteng, 1292, 1293f jawed fish, 737–42 jawless fishes, 737–38, 737f jaws: of gnathostomes, 738, 738f muscle attachment and size of, 957, 957f Jefferies, Robert, 1252

jejunum, 980 jellyfish, 704–5, 704t, 731f, 905 Jenkins, Farish, 465 JH (juvenile hormone), 1079 Jirtle, Randy, 379 Johannsen, Wilhelm, 352 Johanson, Donald, 550 joining (J) segments, 1119 joints, 952–53, 953f jumping, 965 junctional folds, 960 juniper (Juniperus scopularum), 669f junk DNA, 452 Jurassic period, 547 jute (Corchorus capsularis), 776 juvenile hormone (JH), 1079

K

Kakadu National Park, Australia, 1174, 1174f Kalanchoë species, 855–56, 855f Kandel, Eric, 917, 918 kangaroo, 1275 kangaroo rats, 875 kangaroos, pregnancy in, 1096 Kaposi sarcoma, 1129 karyogamy, 614 karyotypes, 324f, 325 kenaf, 776 keratins: in human evolution studies, 554 in intermediate filaments, 84 ketone bodies. See ketones. ketones, 994 keystone hypothesis, 1281, 1282f keystone species, 1290f, 1291 kidney disease, 1054–56, 1055f kidneys, 1047–54 and antidiuretic hormone, 1064 Bowman’s capsule, 1048, 1049 development of, 1104 distal tubule and cortical collecting ducts, 1051–53, 1052f, 1053f in endocrine system, 1060f and evolution of aquaporins, 1053–54, 1054f filtration in, 1043, 1045 internal structure of, 1048f loop of Henle, 1050–51, 1050f in mammalian urinary system, 1048f nephrons, 1047–48, 1049f proximal tubules, 1049–50, 1049f response to hemorrhage by, 1140, 1141f kidney stones, 1054 kidney tubules, epithelial tissue in, 862f killdeer, 1180 kilocalories (kcal), 998 Kimura, Motoo, 491 kinesis, 1185 kinetic energy, 128, 128f kinetic skull, 747, 748, 748f kinetochore, 330, 331 Kinetoplastea phylum, 592t kinetoplastids, 585–86, 585f kingdoms, 517, 592t

Kinosita, Kazuhiko, 157–59 kin selection, 1194–96, 1194f, 1195f Kirschvink, Joseph, 540 kiwis (birds), 528–29 Klinefelter syndrome, 378 KM (substrate concentration), 133–34, 133f Knoll, Max, 76 knowledge, theories as, 14 KNOX protein, 771 Koch, Robert, 577 Koch’s postulates, 577 Koeleria cristata, 1150–51, 1151f Koeleria laerssenii, 1151, 1151f Koella, Jacob, 1228 koff (ligand•receptor complex dissociation rate), 187 Köhler, Wolfgang, 1183 Kolbe, Hermann, 45 Kolreuter, Joseph, 348 kon (ligand•receptor complex formation rate), 187 Korarchaeota, 564 Kortschak, Hugo, 179 Koshland, Daniel, 133 Kozak, Marilyn, 261 K-Pg extinction event. See CretaceousPaleogene event. Kraatz, Ernest G., 422 Krebs, Hans, 151 Krebs cycle, 151 See also citric acid cycle K-selected species, 1213–15, 1214f, 1214t K/T event. See Cretaceous-Paleogene event. kudu, 755f Kühne, Wilhelm, 131, 956 Kusky, Timothy, 72

L

labia majora, 1093 labia minora, 1093 labor, 724, 724f, 1098–99, 1098f laboratory mouse. See mouse. lac activators, 291–93, 292f lacA gene, 286, 287 Laccaria bicolor, 634f lacI gene, 286, 289, 289f lacI- mutants, 289–91 Lack, David, 483, 1221 lac operons: activators of, 291–93, 292f function of, 285–86, 287f mutations of, 306 repressors of, 286–91 lac repressor, 286–91 lactase, 981 lactate, 160 lactation, 1064 lacteals, in digestive system, 979, 979f, 984 lactic acid, 119, 160, 161f, 1138 Lactobacillus genus, 637 Lactobacillus plantarum, 567f Lactococcus lactis, 567f lactose, 50, 556, 981 gene regulation of utilization, 283, 283f

and lac operon, 288f, 292–93, 292f lactose intolerance, 556, 981–82 lactose metabolism, 285–86, 287f See also lac operon lactose permease, 119, 287f lacunae, 215 lacY gene, 286, 287 lacZ gene, 286, 287, 436, 437 Laetiporus sulphureus, 617f lagging strands, replication of, 232–36, 234f, 235f Lake, James, 697 Lake Erie, 1266, 1267f Lake Placid mint, 1285, 1286 lakes: annual cycle of temperate, 1171, 1171f eutrophication in, 1266, 1267f lake trout, 1276, 1276f Lamarck, Jean Baptiste, 308, 348, 459 λ phage, 395–99 lamellae, 1026, 1027 Laminaria genus, 598f Laminaria digitata, 1158f laminin, 204, 204t L-amino acids, 57 lampreys, 737–38, 737f Lampropeltis elapsoides, 1225f, 1226 lancelets, 729–30, 730f land animals: amniotes as, 746–47, 747f locomotion for, 964–65, 965f landmarks, used by animals, 1185–86f, 1185–87 landmass features, 1162–64, 1163f landmass formation, since origin of Earth, 540 land plants: alternation of generations in, 840 features of, 643–44, 644f, 662t green algae as ancestors of, 643 origin of, 545 phyla of, 644 reproductive features of, 651–54 supergroup containing, 586–89 Land Plants and Relatives supergroup, 517 landscape ecology, 1289–90, 1289f Langerhans, Paul, 1071 language skill, and Alzheimer disease, 922–23, 923f langur monkeys, 756f, 1194, 1194f lanthanum, 211, 211f Lap-Chee Tsui, 16 large intestine, 975, 980 Larix laricina, 670 lark bunting, 1198 larvae: of crustaceans, 725, 725f and developmental genetics, 418, 419f hormones for development of, 1078, 1079f larynx, 1028 Lassar, Andrew, 427–29 “last of the wild” areas, 1287, 1288 Late Devonian extinction, 738 latency: in bacteriophages, 398, 399 in human viruses, 399

lateral line systems, 740, 933, 933f lateral meristems, 766f, 776–77 lateral movement, by transmembrane proteins, 110–11, 111f Latham, Robert, 1238 Lathyrus odoratus, 366–67, 367f Latimeria chalumnae, 742f Latrodectus mactans, 720, 720f Laurasiatheria, 757 Lauterbur, Paul, 919 law of conservation of energy, 128 law of independent assortment: and chromosome theory of inheritance, 356–57, 357f and inheritance pattern for two characters, 354–55, 354f law of segregation: and chromosome theory of inheritance, 355f, 356 and inheritance pattern of single trait, 351–53, 352f laws of inheritance, Mendel’s, 349–52f, 349–55, 354f laws of thermodynamics, 167 leaching, 806, 825 lead-207, 536 leading strands, replication of, 232–36, 234f, 235f leaf abscission, 833–34, 833f, 834f leafcutter ants, 1189–90, 1189f, 1229–30, 1230f leaf cuttings, 855 leaf folding, 796, 796f leaflets, 107, 770–71 leaf miners, 1264–65 leaf primordia, 766, 770–71 leaf veins: development of, 767 pattern of and breakage tolerance for, 771–72f, 771–73 leafy sea dragon, 741f leak channels, 886 Leakey, Louis, 551–52 learning: and behavior, 1181–87f model-based, 18–19, 19f by mollusks, 712–14, 713f nervous system cells in, 917–21 leaves. See plant leaves. Leber’s hereditary optic neuropathy (LHON), 384 LEC1 gene, 856 Leder, Philip, 254–56 Lederberg, Esther, 308–9, 408 Lederberg, Joshua, 308–9, 406–8, 407f leeches, 715–16, 716f left-right axis, 415 leghemoglobin, 814, 814f Legionella pneumophila, 578 legumes, 677, 812–14, 813f, 814f Leishmania, 586, 586f leks, 1198, 1198f Lemaitre, Bruno, 1113–14f, 1113–15 Leman, Luke, 72 Lemna genus, 762, 763f Lemna gibba, 845 lenses, of single-lens eyes, 935, 937

INDEX

INDEX I-29

I-30 INDEX

INDEX

lenticels, 777 lentic habitats, 1171, 1173, 1173f leopard frog (Rana pipiens), 328 Leopold, Aldo, 1291 Lepas anatifera, 725f Lepidoptera, 724 leptin: and animal reproduction, 1105 effects of high doses of, 1002 endocrine function of, 1073 and energy balance, 991 and food intake, 999–1000, 1000f and reproductive hormones, 1080 Leptospira genus, 567f Lepus americanus, 1226, 1226f lesser apes, 548 lesser bush baby, 549f lettuce, 794, 853 lettuce seeds, 793, 794f leucoplasts, 98 leukemia, 197, 316, 317f leukocytes, 1015, 1110 lever arm, 85 Levine, Arnold, 318 Lewis, Edward, 422 Leydig cells, 1090, 1092 L-glucose, 50, 50f LH. See luteinizing hormone. LHON (Leber’s hereditary optic neuropathy), 384 Liang, Haiyi, 846–48, 847f Liard, Jean, 1136 lichens, 631–32, 632f nitrogen fixation by, 808f in primary succession, 1241, 1242f Liebig, Justus von, 1252 Liebig’s law of the minimum, 1252 life cycles, 340, 760–64, 764t life history strategies, 1213–15, 1214f, 1214t, 1215f life origins. See origins of life. lifestyle, and immunity, 1126–27 life tables, 1206, 1206t, 1207–8f ligand-binding domain, 64 ligand-gated ion channels: and cell communication, 189, 189f at chemical synapses, 893 in muscular-skeletal systems, 960 and neurons, 888 ligand•receptor complex, 187 ligands, 117, 187 light: as electromagnetic radiation, 167, 167f excessive, 804 as limiting resource, 1158, 1159f, 1252–53 in photosystem II, 172–74, 173f and phototaxis, 1185 and pigments, 167–68, 168f and plant nutrition, 802–4, 803f plants’ detection of, 793–94, 793f, 794f in sensory systems, 937, 940–41 light-absorbing pigments, 938, 938f light focusing, in single-lens eye, 936f, 937 light-harvesting complexes, 169, 172–74 light microscope and light microscopy, 76, 76f, 77f

light reactions, 166–72 cytochrome complexes, 171–72, 172f defined, 164 electron flow in, 169–71, 170f, 171f and light energy, 167–68, 168f overview, 166, 166f pigments in, 167–69, 168f, 169f lignins, 646 plant cell walls, 208 and plant tissue, 216 and plant transport, 826, 827 structure and function of, 775, 776 Liguus fasciatus, 711f lilies, 676f blooming in, 846–48, 847f flowers of, 844, 845 Lilium casablanca, 846–48, 847f Lillum genus, 676f Limax maximus, 896 limbic system, 914–15, 934 limbs: of amphibians, 744–46 of bats vs. birds, 965 development of, in humans, 416, 416f length of, in tetrapods, 743–44 of tetrapods, 742–44 Limenitis archippus, 1225f, 1226 limiting factors: plant nutrition, 802 in primary production, 1252–53, 1252f lineage, defined, 499 lineages, 6, 6f See also evolution linear chromosomes, of eukaryotes, 448– 50, 449f, 449t linear electron flow, 169–70, 170f linear movement, detection of, 932f line transect, 1202 linkage, 384–88, 385f, 387f, 388f linkage groups, 384 linker proteins, 209 Linnaeus, Carolus, 459, 516 linoleic acid, 53, 53f, 972 Linum usitatissimum, 776 lionfish, 741f lipases, digestion of lipids by, 983–84, 983f lipid-anchored proteins, 108 lipid droplets, 54 lipid exchange proteins, 111 lipid metabolism, 994 lipid rafts, 109 lipids, 52–56 in absorptive state, 992 digestion of, 983–84, 983f fatty acids, 52–54, 53f and membrane fluidity, 109, 110, 110f in membrane structure, 107, 107f organic molecules from, 971 phospholipids, 54–55, 54f and smooth ER, 91 steroids, 55, 56f synthesis of, for membranes, 111–12, 112f triglycerides, 52, 52f waxes, 55 lipid-soluble hormones, 1062

lipolysis, 994 lipopolysaccharides, 568, 569, 1112–13 lipoprotein lipase, 993 liposomes, 73, 73f Lipotes vexillifer, 1280 liquid-liquid phase separation, 79 literature search, as BioTIPS strategy, 20 litterfall, 1241, 1242 liver: in digestive system, 979, 980f in endocrine system, 1060f in postabsorptive state, 993, 994 liverworts, 644, 644f, 655f See also Bryophyta and bryophytes living organisms: amino acids found in, 57f biological investigations of, 13–14, 13f biological organization of, 3f buffers and pH in, 42 classification of, 8–12 classification system for, 517f CRISPR-Cas technology for, 442–44, 444f element composition of, 29–30, 30t, 31f energy use by, 50 evolutionary history of, 5, 5f functions of water in, 40–41, 40f homeostasis in, 1021 organic molecules found in, 48, 49t lizard-hipped dinosaurs. See Saurischia and saurischians. lizards, 747–48, 748f, 1014 loam, 806, 807 lobe-finned fishes: characteristics of, 741–42, 742f and shared derived characters of reptiles, amphibians, 736 lobes, of cerebral cortex, 913–14, 914f lobsters: characteristics of, 724–26, 725f muscular-skeletal system of, 952 sensory systems of, 946 local chemical signals, in homeostasis, 870–72 local environments, adaptation to, 506–8 local movement, 1185–86f, 1185–87 local nutrient cycles, 1265–66 loci, gene, 356, 356f locomotion: in animals, 964–66, 965f defined, 951 and sensory system, 933 and types of skeletal muscle fibers, 961 Loewenstein, Werner, 212–13 Loewi, Otto, 896–98, 897f logistic equation, 1211 logistic growth, 1211–12, 1212f, 1220, 1220f logistic growth pattern, 1220, 1220f Lohka, Manfred, 329 Lokiarchaeota, 542, 564 Lømo, Terje, 917 long-day plants, 794 long-distance chemical signals, in homeostasis, 870–72 long-distance plant transport, 819, 824–36 ABA receptor protein, 831–32f, 831–33 bulk flow, 825–26, 825f, 826f

leaf abscission, 833–34, 833f, 834f overview, 818, 819f in phloem, 834–36 and stomata in transpiration regulation, 829–31, 830f transpiration in, 828–29, 828f, 829f in xylem, 826–28, 827f long-distance regulation, of digestive system, 985 longhorn sculpin (Trematomus nicolai), 468, 469f longitudinal growth, and blooming of flowers, 848 long-leaf pine, 1291 long-range movement, 1187–88, 1188f longstamen rice, 1285f long-term memory, 918, 918f long-term potentiation (LTP), 917 Lonicera japonica, 783f loop domain formation, 403–4 loop domains, 403–4, 404f loop of Henle, 1047, 1048, 1050–51, 1050f loose connective tissue, 863f lophophores, 698, 699f, 709, 709f Lophotrochozoa, 698, 699f, 705–16 Annelida, 714–16, 715f, 716f Bryozoa and Brachipoda, 709, 709f Mollusca, 709–14, 712t Platyhelminthes, 705–7, 706t, 707f, 708f Rotifera, 707–9, 708f See also Annelida; Brachiopoda; Bryozoa; Mollusca; Platyhelminthes; Rotifera Lorenz, Konrad, 1180, 1184, 1184f lorises, 933 lotic habitats, 1171, 1174, 1174f lotus plant, 853 Lovette, Irby, 1245 Loxodonta africana, 516 Loxodonta cyclotis, 516 Loxosceles reclusa (brown recluse spider), 720 LTP (long-term potentiation), 917 lubricant, water as, 40f, 41 Lucy, 550 lumbar puncture, 910 lumen, of endoplasmic reticulum, 90 lung cancer: and cellular respiration, 149, 150f and mutations, 320–21, 320f and respiratory systems, 1040 lung disease, 1040 lungfishes, 738, 741–42, 742f lungs: of air-breathing vertebrates, 1027, 1028f of amphibians, 744–46 development of, 1104 emphysema and damage to, 1039–40, 1040f endocrine systems and, 1077 epithelial tissue in, 862f expansion of, 1029–30, 1030f and pleural sacs, 1028, 1029 surfactant in, 1030–31 tidal volume and size of, 1030

Lupinus alba, 809 LURES proteins, 849, 850 luteal phase, 1095 luteinizing hormone (LH), 1080 and androgen, 1080 and oral contraceptives, 1106 and reproduction, 1092, 1094, 1095 Lycoperdon perlatum, 610f lycophylls, 658, 659f Lycopodiophyta and lycophytes: life cycle of, 653 overview, 645–47, 645f and plant hormones, 791 Lycopodium obscurum, 645f Lyell, Charles, 460 Lyme disease, 455 lymph, 979, 1115 lymphatic systems, 1115, 1116f, 1143 lymphatic vessels, 979f lymph nodes, 1115, 1116f lymphocyte receptors, 1117, 1124–25 lymphocytes: activation and proliferation of, 1117, 1117f, 1118 defined, 1115 recirculation of, 1115–16, 1116f types of, 1116–17, 1116f lymphoid organs, 1115, 1116f lymphoid tissues, 1115, 1116f lymph vessels, 1115 Lynch, Michael, 1086, 1086–87f lynx, 1226, 1226f Lynx canadensis, 1226, 1226f Lynx rufus, 754f Lyon, Mary, 377 lysogenic cycle, 395, 398, 398f lysogeny, 398, 399 lysosomes: of animal cells, 80f autophagy in, 142 lysozymes, 94, 398 Lystrosaurus genus, 1175 lytic cycle, 398, 398f

M

MacAlister, Cora, 774 macaques, 957f MacArthur, Robert, 1221, 1244, 1244f, 1245 MacLeod, Colin, 222–23 MacLeod, John, 1071–73 MAC (membrane attack complex), 1112 macroalgae, 583 macroevolution, 458, 496 macromolecules, 2 defined, 45 formation of, 48, 49f gel electrophoresis of, 438f, 439 lysosome digestion of, 94 macronutrients, 802, 802f, 802t macroparasites, 1228 macrophages, 95 and cytotoxic T cells, 1123 and inflammation, 1112 phagocytosis by, 124 structure and function of, 1110, 1110f

macula, 947 macular degeneration, 947, 948f Madagascar periwinkle (Catharanthus roseus), 664 madreporite, 727, 727f MADS box genes, 431 magnesium, 213, 802t magnesium ions, in animal bodies, 874 magnetic fields, sensing of, 934 magnetic resonance imaging (MRI), 901, 919–20, 919f magnetosomes, 567 Magnetospirillum magnetotacticum, 567 magnification, in microscopy, 76 Magnolia genus, 675 Magnoliids, 675 Mahadevan, Lakshminarayanan, 846–48, 847f Mahlberg, Paul, 679–80, 680f maize, human domestication of, 683, 683f See also corn major depressive disorder, 901 major grooves, in DNA, 228 major histocompatibility complex (MHC) proteins, 1121–24, 1127 Mako sharks, 739 Malacostraca, 726 malaria: parasite causing, 1109 and protists, 599, 601f, 602 and sickle cell disease, 485 species interactions with, 1228 malate, in citric acid cycle, 152f male-assistance hypothesis, 1197 male gametes, 1087–89, 1088f male gametophytes: in flowering plants, 840–41, 840f, 841f, 848–49, 849f pollen grains as, 848–49, 849f production of, 840–41, 840f, 841f male reproductive tract (human): hormone action on, 1092–93, 1093f structure of, 1090–92, 1091f males: coloration of African cichlid, 487–89 X-linked traits in, 360–61 malignant tumors, 314 Maller, James, 329 malleus, 929, 930 malnourishment, and gut microbiome, 635–36 Malpighian tubules, 719, 1046–47, 1046f Malthus, Thomas, 460 malting, 854 maltose, 50 Malus genus, 676f Mammalia class, 518–19 mammals, 752–57 aquaporins in, 1053 baroreceptor evolution in, 1135 baroreceptor function in, 1136–37 blood pressure in, 1018, 1132, 1133 body organization of, 860, 860f body temperature of, 1003 brain mass vs. body mass in, 906, 907f cell differentiation in, 424–29 cerebral cortex folding in, 906, 907f

characteristics of, 752–57, 753t, 754–56f, 755t circulatory system of, 1012, 1015, 1023 citric acid cycle regulation in, 153 cleavage-stage embryos of, 1100, 1100f, 1101 color vision of, 939 connective tissue in, 863f diversity of, 755–57, 755t, 756f DNA methylation in, 298 double circulation in, 1012, 1013f ear of, 929–30, 929f, 930f electrical excitation of heart in, 1017– 18, 1017f embryonic development in, 1103 endocrine signaling in, 186 endocrine systems of, 1062, 1064, 1077, 1080 endoskeletons of, 952 energy balance in, 1005–6 erythrocytes in spleen of, 1143 estrogen receptor in, 190, 190f evolution of whales from, 465, 467f extrinsic pathway in, 199–200, 199f gene regulation in, 283–84 GLUTs in, 995 heart of, 1016, 1016f, 1023t hemorrhage in, 1132 Hox genes in, 510 immune system of, 1123–25, 1125f immunoglobulins of, 1118 implantation in, 1101, 1101f ion concentrations across neurons of, 886t iron toxicity prevention, 301, 301f kidneys of, 1047–54 lactose intolerance for, 981–82 memory in, 918 molecular homologies for, 473 nitrogenous wastes from, 1044 olfactory receptors of, 943–45f, 943–46 oogenesis in, 1089 origins of life for, 547 plasma and interstitial fluid in, 1140 pregnancy and birth in, 1096–99, 1096f, 1097t, 1098f respiratory activity of, 1037, 1037t respiratory center in, 1036–37, 1037f respiratory system of insects and, 865–66, 866f respiratory systems of, 1028–33, 1029f, 1032–33f response to hemorrhage in, 1138 satiety factor in, 1000–1002, 1001f sensory receptors in skin of, 927–28, 928f sensory systems of, 937 small subunit rRNA gene sequence of, 260, 260f stem cells of, 424–25, 425f threatened due to overexploitation, 1271–72 tight junctions, 210, 211 urinary system of, 1047, 1048f ventilation control for, 1036 X-chromosome inactivation in, 377–78, 378f

mammary glands, 752–53, 1064 Manchurian cranes, 1199f Mancuso, Katherine, 939 manganese, and plant nutrition, 802t mangroves, 779–80, 779f, 1159 Mansfield, Peter, 919 mantles and mantle cavities, of mollusks, 710 manure, 808 many-eyes hypothesis, 1193, 1193f map distance between genes, 388 maple syrup, 826, 826f maple trees, scientific method and, 15–16, 15f map units (mu), 388 Marchantia polymorpha, 644f Margulis, Lynn, 98 marijuana, 901 See also Cannabis genus marine animals, salt glands of, 876, 876f marine fishes: calcitonin in, 1074 excretory systems of, 1047 marine invertebrates, respiratory systems of, 1026 marker genes, 627 Markert, Clement, 328–29 mark-recapture technique, 1202–3, 1203f marmosets, neurogenesis in, 918 Márquez, Luis, 618–19, 619f Marrella genus, 544f Marsden, Stuart, 1239 Marshall, Barry, 987–88 marsupials, 756 and biogeography, 468 disjunct distribution of, 1175 pregnancy for, 1096 Masai Mara Game Reserve, Kenya, 1168, 1168f mass: atomic, 28–29 of living organisms, 29–30, 30t molecular, 38 weight vs., 29 mass extinctions, and origins of life, 540 mass flow. See bulk flow. mass-specific BMR, 999, 999f mastax, 708, 708f mast cells: in allergies, 1127–28, 1127f structure and function, 1110f, 1111 Masui, Yoshio, 328–29 mate choice, 508 mate-guarding hypothesis, 1197 maternal effect genes, 419–20, 420f, 421f maternal hormones, 1095 maternal inheritance, 382–84, 382f, 383f, 384t maternal plant body, embryos in, 655, 655f mathematical models, 18, 846–48, 847f mating: communication in, 1191, 1191f fungal, 609 mating systems, 1196–99 matrix-targeting sequence, 101, 102, 102f matrotrophy, 652

INDEX

INDEX I-31

I-32 INDEX

INDEX

matter: and cell structure/function, 78 defined, 24 states of, 39–40, 39f See also energy and matter (core concept) maturation-promoting factor (MPF), 329 mature mRNA, 250, 250f Maximow, Alexander, 767 maximum likelihood analysis, 525 maximum sustainable yield (MSY), 1274–75, 1275f Mayer, Adolf, 392 Mayr, Ernst, 498, 513 McCarty, Maclyn, 222–23 McClintock, Barbara, 453, 453f McClung, C. E., 359 McEwen, Bruce, 918 McKusick, Victor, 266, 491 MCPH1 gene, 916 meadowlarks, 500 mealybugs, 542 mean fitness of the population, 482 meat, essential amino acids in, 971 mechanical defenses, 703, 1227, 1227f mechanical forces, and leaf development, 770 mechanical isolation, 500 mechanical vibrations, in hearing, 930, 931f mechanistic models, 18 mechanoreception, 927–33 audition (hearing), 929–31 by hair cells, 928–29, 928f by lateral line system of fishes, 933, 933f sense of balance, 931–33, 931f, 932f by skin receptors, 927–28, 928f by stretch receptors, 928 mechanoreceptors: defined, 926 hair cells as, 928–29, 928f in lateral line system, 933, 933f in skin, 927–28, 927f stretch receptors, 928 medial Golgi, 91 mediator, and homeotic gene, 423 mediator protein complex, 295, 296, 296f Medicago sativa, 507 medications. See drugs. medicine: personalized, 479 stem cells in, 426–27, 427t medium ground finch, 463–64, 464f medulla oblongata, function of, 910 medusa form, of cnidarians, 704, 704f, 705 meetings, scientific, 17 megabase pair, 445 megadiversity countries, 1287 megapascals (MPa), 821 Megaptera novaeangliae, 1197 megasporangia, 658 megaspores, 658, 841 Megazostrodon genus, 546 meiosis, 334–40, 335f, 336f, 338–39f, 340t bivalent formation and crossing over, 335, 336f

and chromosome theory of inheritance, 356–57, 356f, 357f defined, 335 in gametogenesis, 1087, 1087f, 1089, 1094 identifying phase of cell in, 337 mitosis vs., 337, 340t nondisjunction in, 344, 344f phase I, 335–37, 336f, 338–39f, 340t, 344, 344f, 1087, 1087f, 1094 phase II, 337, 338–39f, 339, 340t, 1087, 1087f, 1089, 1094 Meissner corpuscles, 927, 928f Mek protein kinase, 191 melanin, 183–84, 556 melanocytes, 1104 melatonin, 1059 melioidosis, 577 Mello, Craig, 272–73 melting points. See temperature. membrane attack complex (MAC), 1112 membrane permeability, 886 membrane potentials: action, 889–92, 890f, 891f defined, 885 graded, 888–89, 889f neuron signaling via, 888, 888f in photoreception, 940, 940f and plant transport, 820 threshold, 889 membrane proteins, 107–8, 108f See also transmembrane proteins membrane receptors, of water-soluble hormones, 1061–62 membranes, 106–26 component synthesis in eukaryotic cells, 111–13, 112f, 113f electrochemical gradients and ion movement across, 885–86, 886f, 886t of eukaryotic cells, 79, 80f, 81f in exocytosis and endocytosis, 122–24, 123f, 123t, 124f fluidity of, 109–11, 110f, 111f gradients across neuron, 885–86, 886f phospholipids in, 55 structure of, 107–9, 107f, 108f, 109t summary, 124–25 temperature and structure of, 1002 transport proteins in, 117–22, 122t transport through, 113–16, 114f, 116f See also plasma membranes membrane sacs, of protists, 589, 589f, 590f membrane transport, 113–16 and concentration gradients, 114–15, 115f defined, 113 osmosis, 115–16, 115f, 116f phospholipid bilayer in, 114, 114f and plasma membrane, 96, 96f proteins (See membrane proteins) types of, 113, 114f membrane vesicles, 90 memory: and Alzheimer disease, 922–23, 923f immunological, 1125–26, 1126f nervous system cells in, 917–21

memory cells, 1118 Mendel, Gregor, 348–55, 349f, 363, 366, 477, 790 Mendelian inheritance patterns, 349t, 363f, 373 See also inheritance Mendel’s laws of inheritance, 349–52f, 349–55, 354f and garden pea studies of Mendel, 350–51, 350f, 351f and genotype vs. phenotype, 353 law of independent assortment, 354–55, 354f law of segregation, 351–53, 352f Punnett square for predicting outcomes under, 353 and testcrosses, 353–54, 354f meninges: of central nervous system, 909, 910f and meningitis, 922 meningitis, 922 menisci, 828 menopause, 1094 menstrual cycle and menstruation, 1084, 1095 Menten, Maud, 133 Mercenaria mercenaria, 711f Merismopedia genus, 565f meristemoids, 774 meristems: and cytokinins, 790 defined, 761 development in, 429–31, 430f, 430t primary, 765–67, 765t, 766f, 767f stem cells in, 767–68 meroblastic cleavage, 1100, 1100f Merostomata, 720 merozygotes, 289 Meselson, Matthew, 228–30, 229f mesoderm, 691, 1101, 1102f mesoglea, 704, 704f mesohyl, 703 Mesonychoteuthis hamiltoni, 712 mesophyll: of C4 and CAM plants, 179, 180f and multicellularity, 216 photosynthesis in, 165, 166f and plant cells, 766 and plant nutrition, 804, 804f structure and function, 803 Mesostigma viridae, 643f Mesozoic era, 544, 650, 650f messenger RNA. See mRNA. metabolic cycles, 151, 152 metabolic pathways: aerobic respiration (See glycolysis) defined, 137, 137f glycolysis, 147–49, 147f, 148f regulation of, 139–40, 140f metabolic rate, 997–1002 and activity, digestion, and body mass, 998–99, 999f and control of food intake, 999–1000, 1000f defined, 991 measuring, 998, 998f and thyroid hormone, 1066

metabolic water, 875 metabolism: anabolic reactions in, 139 of archaea, 573 of bacteria, 573 in brown adipose tissue, 1006 catabolic reactions in, 137–38, 137f and cellular respiration, 159, 159f in cytosol, 83 defined, 83, 127, 991 and endocrine system, 1065–73, 1068t endoplasmic reticulum in, 90–91, 90f inborn errors of, 244–45, 244f insulin as regulator of, 995, 995f lactose, 285–86, 287f overview of, 137–40, 137f, 138f, 140f redox reactions in, 138–39, 138f regulation of, 139–40, 140f and RNA vs. DNA, 75 See also energy metabolites: from microbiome, 627 and microbiome function, 627, 628 metabotropic receptors, 898, 899f metacentric chromosomes, 342, 342f metagenome, 625 meta-metabolome, of microbiomes, 628 Metamonada and metamonads, 586, 586f, 592t metamorphosis, 418 of amphibians, 745 of insects, 724, 724f metanephridia, 710, 1046, 1046f metaphase checkpoint, 327f, 328 metaphase chromosomes, 239, 240f metaphase I (meiosis), 336, 338f metaphase II (meiosis), 338f metaphase (mitosis), 330f, 331, 333f, 342f metaphase plate, 331 metaproteome, of microbiomes, 628 Metasequoia glyptostroboides, 668f, 670 metastasis, 209, 314 Metatheria and metatherians, 756, 756f, 1096 metatranscriptome, of microbiomes, 628 meteorites, 71, 540, 547 methane: in chemical reaction, 36 as greenhouse gas, 1260, 1261t in Miller and Urey experiments, 70–71 molecular shape of, 35f methane oxidation, by microbiome, 627, 627f, 628f Methanobrevibacter genus, 630–31 methanogens, 573–74 Methanopyrus genus, 563 methanotrophs, 574 methicillin-resistant Staphylococcus aureus (MRSA), 411, 462–63, 569 methylation. See DNA methylation. methyl-CpG-binding proteins, 298 mex-3 RNA, 271 Meyerhof, Otto, 147 Meyerowitz, Elliot, 431 Meyers, Ronald, 913 MFOs (mixed-function oxidases), 1227 MHC (major histocompatibility complex) proteins, 1121–24, 1127

mice. See mouse (Mus musculus). micelles, 37, 38f, 983, 983f Michaelis, Leonor, 133 Michaelis constant, 133 microbes, 1238, 1250 counting, 571–72, 571f and lichens, 631–32, 632f and probiotic treatments, 637–38 and tight junctions, 210, 211 microbial science, 633 microbiomes, 622–40 diversity and functions of microbes in, 622–28, 623f, 624f, 626–28f engineering of, 637–39, 638f, 639f host-associated, 630–37 manipulation of, 637 of physical systems, 628–30, 629f summary, 639–40 microbiota, 627 microcephalin, 916 microcystin, 629–30 Microcystis genus, 629, 629f microevolution, 458, 481, 496 microfibrils, 207, 207f and guard cells, 830f and plant cell expansion, 768, 769f microfilaments (actin filaments), 84–85, 85t micrographs, 75 micronutrients, 802, 802f, 802t microorganisms: anaerobic respiration by, 160, 160f cell function and structure (See prokaryotes) and soils, 805 See also algae; archaea; bacteria; fungi; protozoa; viruses microparasites, 1228 micropyle, 842 microRNA (miRNA): and leaf development, 770 and ncRNAs as decoys, 267, 270 and RNA interference, 271, 273, 274f, 275 microscope, defined, 75 microscopy: chromosomal examination via, 324–25, 324f types of, 75–78 microsporangia, 658 microspores, 658, 841, 848–49 microsporidia, 611, 612, 612f microtubule organizing centers (MTOCs), 331 microtubules: in cytoskeleton, 84, 85t in mitotic spindle, 331 and plant cell expansion, 768, 769f microvilli: in digestive system, 978, 979f of sensory structures, 935, 946 Micrurus fulvius, 1225f, 1226 midbrain: development of, 906 function of, in humans, 910, 912, 915t middle ear, 929 middle lamellae, 208t, 213, 213f Miescher, Friedrich, 224

migration (animal), 492 in behavioral ecology, 1187–88, 1188f of cells, 215 and distribution of species, 1175, 1176, 1177f of Homo erectus, 552 of Homo sapiens, 554 and magnetic field sensing, 934 migration (cell), 215 migratory birds, locomotion by, 965 milk: in digestive system, 981 mammalian production of, 753t, 754– 56f, 755–57, 755t Miller, Stanley, 70–71 millipedes, 721, 721f mimicry, 1225f, 1226 Mimosa pudica, 782, 783f, 796, 796f MI (myocardial infarction), 1038 mineralcorticoids, 1061f, 1076 mineral elements, 30, 30t mineralization, 809 mineralocorticoid receptors (MRs), 1076–77 minerals: absorption of, 978, 984 in bone, 952 for carnivorous plants, 814–15 from diet, 972, 974t and endocrine systems, 1073–77 as homeostatic variable, 868t and mycorrhizal associations, 812, 812f symplastic and apoplastic transport of, 823–24, 823f in xylem, 826–28, 827f, 828f minke whales, 1272 Minnesota, 1167, 1167f minor grooves, in DNA, 228 Mirabilis jalapa, 364–65, 364f allele and genotype frequencies in, 479–80 maternal inheritance in, 382–83, 382f, 383f miR-200 family, 279 miRNA. See microRNA. Mirounga angustirostris, 490 missense mutations, 305, 306f, 316, 317f mistletoe, 1228, 1229 mist nets, 1202, 1202f Mitchell, Peter, 153 mites, 720–21 mitochondria, 97–99 of animal cell, 80f ATP use by, 155 and cytochrome complexes of chloroplasts, 171–72, 172f in endosymbiosis theory, 98–99, 99f and extranuclear inheritance, 381, 382f, 384, 384t genetic material and division of, 98, 98f of plant cells, 81f post-translational protein sorting to, 101–2, 102f structure and function of, 97, 97f mitochondrial genomes, 98 composition of, 449 and evolution of eukaryotes, 542–43

extranuclear inheritance and, 381, 382f, 384, 384t human migration studies with, 554 and proteins, 381, 382f mitochondrial matrix, 97, 102f mitochondrial pathway (apoptosis), 200 mitosis: identifying phase of cell in, 337 meiosis vs., 337, 340t in M phase, 326 phases of, 331–33 mitotic cell division, 330–34 and binary fission, 333–34, 334f chromosomal compaction and replication for, 330, 330f mitotic spindle formation for, 330, 331, 331f phases of mitosis in, 331–33 mitotic spindles, 330, 331, 331f Mittermeier, Russell, 1287 mixed-function oxidases (MFOs), 1227 mixotrophs, 593, 593f M line, 955 Mnemiopsis leidyi, 702 Mnium genus, 645f moas, 528–29 modalities. See stimulus(--i). model-based learning, 18–19, 19f modeling (core skill): abnormal separation in meiosis II, 339 action potential, 890–91 adenovirus, 394 alimentary canal, 978 amino acid substitution, 188 angiosperm lineages, 764 aquaporins, 1053 ATP synthase, 157 body size, 1199 brain region activation, 919 calcium homeostasis, 1075 carbon cycle, 1263 carbon dioxide molecule, 32 color blindness transmission, 939 crRNA, 277 dental plaque, 568 DNA, 226 double circulation, 1013 energy cycle, 165 fern leaves, 659 fluid flow in response to hemorrhage, 1142 food web, 1249 germination, 854 glucose homeostasis, 997 glycosyl transferase, 365 graded potentials, 889 gravity and plant size, 825–26 with Hardy-Weinberg equation, 480 homeostatic control systems, 869 homeotic genes, 423 immunoglobulin binding, 1119 insect species, 723 interbreeding, 555 LH and FSH blood concentration, 1095 lichens, 632 lipid droplets, 54 logistic growth, 1212

microsporidian fungi, 612 neuromuscular junction after insecticide, 960 O6-MeG and cytosine, 227 parasitism percentage, 1154 phylogenetic trees, 260, 692 plant responses in space, 783 pollination, 682 protist life cycles, 601 reptilian phylogenetic tree, 748 rivet hypothesis, 1282 root nodule development, 814 SAS-6 proteins, 87f smooth muscle contraction, 860, 861 top-down control, 1233 transitional forms, 466 transmembrane proteins, 108 transposition outcome, 453 vision-related brain structures, 916 X-chromosome inactivation, 378 model organisms: defined, 12–13 in development genetics, 414–15, 414f for nervous system, 917 See also Arabidopsis thaliana; Caenorhabditis elegans; Drosophila melanogaster; Escherichia coli; mouse (Mus musculus); Saccharomyces cerevisiae moderately repetitive sequences, 452 modern plants: diversity of, 641–48 features of, 662t gymnosperms and angiosperms as, 647–48, 647f, 648f phyla of, 644 See also specific types modified leaves, 774–75, 775f Mojica, Francisco, 275 molarity, 38 molar solution, 38 molecular biology, 13, 13f molecular clocks, 529–31 molecular evolution, 459 molecular formulas, 30 molecular homologies, 472–73, 472f molecular mass, 38 molecular paleontology, 527 molecular systematics, 522–23 molecules, 30–36 amphipathic, 37, 38f, 54–55, 107 and chemical reactions, 36 covalent bonds in, 31–32, 31f, 32f defined, 2, 3f, 24 free radicals, 35–36 in Golgi apparatus, 91, 91f hydrogen bonds and van der Waals forces in, 33, 33f hydrophilic, 37 hydrophobic, 37 ionic bonds in, 34, 34f, 34t organic (See organic molecules) shapes of, 34–35, 35f summary, 43 synthesis and breakdown of, in cytosol, 83–84

INDEX

INDEX I-33

I-34 INDEX

INDEX

molecules, continued in water, 37, 37f See also organic molecules moles (mol), 29 Molina, Mario, 1257 Mollusca and mollusks, 709–14 body plan of, 710, 710f characteristics of, 695t, 731f classes of, 710–12, 712t and endocrine disrupters, 1081 eyes of, 513 learning behavior of, 712–14, 713f nervous systems of, 905, 906f origins of, 545 reproduction in, 710, 712f reproduction strategies of, 1197 respiratory systems of, 1034 shells of, 710, 711f molting, 698, 952, 1078–79, 1079f molybdenum, in plant nutrition, 802t Monactinus genus, 583f monarch butterflies and caterpillars, 1183f, 1187–88, 1188f, 1225f, 1226 monkeys, 1182 color blindness in, 939 hominoids vs., 548 molecular homologies for, 473 Monoclea genus, 655f monoclonal antibodies, 1125 monocots: evolution and diversity of, 675–76, 676f flowers of, 841, 844, 845 leaf form for, 770f structures of, 763, 764t monocular vision, 942, 942f monocytes, 1110, 1110f Monod, Jacques, 286, 287, 289–91 monoecious plants, flowers of, 844, 844f monogamous mating systems, 1197, 1197f, 1199f Monogenea and monogeneans, 706t, 707 monomers, 48, 49f, 972 monomorphic genes, 478 monophagous parasites, 1228 monophyletic groups, 519, 521 monosaccharides, 49–50, 50f, 980 monosomic organisms, 344, 345 monosymmetric flowers, 845 Monotremata and monotremes, 756, 1096, 1175 Monotropa uniflora, 802, 803, 803f Monstera deliciosa, 803f mood: effect of drugs on, 900t and neurological disorders, 900, 901 Moore, Peter, 262 moraines, 1241 moray eel, 741f Morelia veridis, 748f Morgan, Thomas Hunt, 360–61, 384, 386–88 morphine, 901 morphogens, in developmental genetics, 416–17, 417f morphology: of bilateria, 692–94 defined, 413

of Ecdysozoa and Lophotrochozoa, 698–99, 698f, 699f of fungi, 606, 607f of mammals, 755–57, 755t, 756f of Protostomia, 696, 696f of species, 497–98 and systematics, 521–22 mortality factors, 1212–13, 1213f morula, 1101 Morus bassanus, 1190, 1190f mosaics, 377 Mosquito Barcoding Initiative, 726 mosquitoes, 726, 1228 mosses: alternation of generations in, 840, 840f in fossil record, 643–44, 644f gametophyte and sporophyte size in, 340 phyla of, 644, 645f and placental transfer tissues, 655–57 plant tissue in, 216 in primary succession, 1241, 1242f See also Bryophyta and bryophytes moths: antennae of, 943, 943f antennae surface area, 866, 867f sensory systems of, 931 motility, 569–70, 570f, 583–84, 583f, 584f motion, hair cells in detection of, 928–29, 928f motor, flagellar, 570, 570f motor end plates, 960 motor function, in cerebral cortex, 915f motor neurons, 884, 884f motor problems, and nerve cell disorders, 901–2, 901f motor proteins: and cytoskeletal filaments, 85–88, 86f, 87f movement of, 86, 86f mountain avens, 142f, 1241 mountain hemlocks, 1241–42 mountain ranges, 1170, 1170f mountains, 1162 mountain sheep, 1207–8, 1208f Mount St. Helens, 1236, 1242 Mourer-Chauviré, Cécile, 527 mouse (Mus musculus): Alzheimer disease research with, 923 bacterial transformation experiments in, 221–22, 221f circulatory systems of, 1014 dietary effects of coat color in, 379–80, 380f directional selection in, 483 genetic drift in populations, 489–90 genome projects with, 458 genomic imprinting, 375–76, 375f gestation period of, 1096 hemoglobin of, 1035 homeostatic control system of, 869 homeotic genes of, 424, 424f Hox genes of, 864 “marathon mice”, 962–64 as model organism, 414, 414f satiety factor studies in, 1000–1002, 1001f

seed dispersal by, 1231f stem cell studies in, 427 surface area of neurons in, 866, 867f Toll-like receptors of, 1112–13 mouth: in digestive system, 975, 976, 977f in respiratory system, 1028 mouthparts, of insects, 722, 722f movement corridors, 1289, 1289f movement(s): adaptation of skeletal muscle fibers for, 961, 962t of animals, 687 of archaea, 569–71, 570f, 571f of bacteria, 569–71, 570f, 571f detection of, in water, 933, 933f of lipids in membranes, 109 and motor proteins, 85–88, 86f, 87f of plants, 782, 783f skeletal muscle for, 954, 954f of transmembrane proteins, 110–11, 111f vestibular systems’ detection of, 932f MPF (maturation-promoting factor), 329 M phase, 325–27 MRI (magnetic resonance imaging), 901, 919–20, 919f mRNA (messenger RNA), 246 DNA and tRNA vs., 253–54, 253f in initiation stage of translation, 260–61, 260f mature, 250, 250f and microbiome function, 627, 628 non-coding RNAs and degradation of, 270–75 and one-gene/one-enzyme hypothesis, 246 silencing of, 272–73 in termination stage of translation, 263, 263f in translation, 252–53, 252f MRSA (methicillin-resistant Staphylococcus aureus), 411, 462–63, 569 MRs (mineralocorticoid receptors), 1076–77 MS (multiple sclerosis), 901–2, 901f, 1125 MSY (maximum sustainable yield), 1274–75, 1275f MTOCs (microtubule organizing centers), 331 mucilage: and bacteria, 568, 568f of carnivorous plants, 815 microbiomes in, 628, 628f Mucoromycota, 606f, 611–13, 613f, 614f mucosa, alimentary canal, 975, 976 mucus, proteoglycans in, 113 mud salamanders, 746f Muir, John, 1286 mules, 501 Müller, Paul, 1268 Müllerian mimicry, 1225f, 1226 Mullis, Kary, 439 multicellular eukaryotes. See multicellular organisms.

multicellularity, 202–18 cell junctions, 208–14, 208t, 209f–14f cell walls, 206–8, 207f defined, 202 and eukaryotic gene regulation, 283, 284f extracellular matrix, 203–6, 203f–6f, 204t, 206t summary, 217 tissues, 214–16, 215f, 216f of volvocine algae, 543 multicellular organisms, 81 animals as, 687 development of, 414 gene regulation and developmental stages of, 283–84, 284f hormonal signaling in, 195–96, 195t origins of life for, 543–44 multiple alleles, 365, 365t multiple sclerosis (MS), 901–2, 901f, 1125 multipotent stem cells, 425f, 426 Murie, Adolph, 1207–8 muscle attachment, and jaw size of primates, 957, 957f muscle cells: differentiation of, 414, 427–29 epigenetics in, 374 fermentation in, 160–61 heat production from, 1006 mitochondria in, 97 muscle contraction. See contraction. muscle cramps, 966 muscle fibers. See skeletal muscle fibers. muscle tissue (muscles): cardiac (See cardiac muscle) cells in, 860–61, 861f and digestive system, 979f multicellularity of, 215f, 216 nervous system control of digestive, 984–85 skeletal muscle (See skeletal muscle) smooth (See smooth muscle) muscular dystrophy, 966, 967 muscular-skeletal systems, 951–69 and animal locomotion, 964–66, 965f animal skeleton types, 951–53, 952f, 953f public health issues related to, 966–67, 966f, 967f response to hemorrhage by, 1138, 1143 skeletal muscle fibers, 960–64, 962t, 963–64f skeletal muscle structure and force generation, 953–60 summary, 967–68 musicians, brain structures of, 920–21 Mus musculus. See mouse (Mus musculus). mussels, 1158f Mustela nigripes, 1201 mutagens: calculating mutation rate for, 312 testing for, 311–12, 311f types of, 309–10, 310f, 310t, 311f mutant alleles, 363 mutation rate, calculating, 312

mutations, 304–22 in cancer, 314–21, 316t, 318t, 319f, 320f and cancer (See cancer) causes of, 308–11f, 308–12, 310t and chemical selection, 74f and chromosome structure, 342, 343f consequences of, 304–7, 305t, 306f, 306t, 307f with CRISPR-Cas technology, 442–44, 444f defined, 5, 244, 304 diversifying selection, 485 and DNA repair, 312–14, 312t, 313f, 314f elimination of, in populations, 1086–87 and energy balance, 1000–1001 and genetic drift, 491 and group selection, 1194 infertility caused by, 1104 and microevolution, 481 in myosin, 956–57, 957f in myostatin-endcoding genes, 967, 967f in plants, 774 as random events, 308–9 in scientific process, 445 studying development via, 419 summary, 321–22 in vertical evolution, 6–7, 6f MUTE gene, 774 mutualism: of bacteria and eukaryotes, 576, 577f species interactions, 1217, 1229–31, 1230f, 1231f myasthenia gravis, 1125 mycelia (mycelium), 606–9, 607f, 609f myc gene, 316 mycoheterotrophy, 812 Mycoplasma pneumoniae, 578, 578f mycorrhizae, 613, 633, 633f, 812, 812f mycorrhizal fungi, microbiomes of, 633, 633f Myc transcription factor, 192 myelin and myelin sheath, 882, 883f, 892, 892f Myers, Norman, 1287 Myers, Ransom, 1217 MYH16 gene, 957 MyoA gene, 427 myocardial infarction (MI), 1038 myocytes, 1017, 1019 MyoD gene, 427, 428–29f myofibrils: and sarcoplasmic reticulum/T-tubules, 958, 959f structure of, 955, 955f myogenic hearts, 1017 myoglobin: gene family of, 451 in muscular-skeletal systems, 961 MyoH gene, 427 myosin: in cross-bridge cycle, 957 cross-bridges (See cross-bridges) defined, 955 evolution of, 956–57

myostatin, 967, 967f Myriapoda and myriapods, 719t, 721, 721f Myrica genus, 812 Myrmecophaga tridactyla, 468, 469f myrtle, 812 Mysticeti suborder, 466 Mytilus edulis, 1158f myxobacteria, 565 Myxococcus xanthus, 570

N

N-Acetylgalactosamine, 365 NADH: in cellular respiration, 146f, 147 from citric acid cycle and, 151, 151– 52f, 153 and fermentation, 160 in glycolysis, 148 in oxidative phosphorylation, 153, 154f, 155 in pyruvate oxidation, 150, 150f from reduction of NAD+, 138–39, 138f NADH dehydrogenase, 154f, 160 NAD+ (nicotinamide adenine dinucleotide): and citric acid cycle, 153 and fermentation, 160 in oxidative phosphorylation, 154f in pyruvate oxidation, 150 reduction of, 138–39, 138f NADP+: and cyclic photophosphorylation, 171 energy of electrons bound to, 174, 174f NADPH (nicotinamide adenine dinucleotide phosphate): in Calvin cycle, 175f, 176 defined, 167 from linear electron flow, 169–70, 170f in photosynthesis, 166, 166f, 167 Naeem, Shahid, 1281, 1283–84 Nägeli, Karl, 221, 355 nails, of primates, 548 Na+/K+-ATPase pump, 121–22, 122f and endocrine system, 1065, 1066 energy for, 886 and repolarization, 889 naked mole rat, 686 Namib Desert, Namibia, 1169, 1169f nasal passage, epithelial tissue in, 862f Naso tonganus (bulbnose unicorn fish), 566 Nathans, Daniel, 436 National Institutes of Health, 451 natriuresis, 1076 natural enemies, 1152, 1232–33, 1233f natural killer (NK) cells: structure and function of, 1110–11, 1110f, 1116f and virus-infected/cancerous cells, 1123 natural products industry, 1285f, 1286 natural selection: for antibiotic resistance, 462–63 defined, 6, 461 (See also evolution) and evolution, 461–64, 461t, 462–64f finch studies of, 463–64, 464f

fitness in, 482 in human evolution, 555 patterns of, 482–85 in population genetics, 482–85 and reproductive success, 482 sexual selection as type of, 485–87 nature preserves, design of, 1288–89, 1289f navigation, spatial, 1187–88, 1188f N-cadherin, 209 ncRNAs. See non-coding RNAs. NDVI (normalized difference vegetation index), 1253f Neanderthals. See Homo neanderthalensis. near vision, 936f Necator americanus, 717 neck length, of animals, 694, 694f necrotic spots in plants, 798, 799f Nectarinia jugularis, 1239–40 Nectarinia reichenowi, 1190, 1190f negative control, 285 of lac operon, 286–91 of trp operon, 293–94, 293f negative feedback, 985 in homeostasis, 869–70, 870f in systems, 1092 negative frequency-dependent selection, 485 negative gravitropism, 794, 795f negative pressure filling, in lungs, 1027, 1029–30, 1030f negative regulation, of cell division, 319, 319f, 319t negative reinforcement, 1182–83 Neisseria gonorrhoeae, 565 Neljubov, Dimitry, 791 Nelumbo nucifera, 853 Nematoda and nematodes: characteristics of, 695t, 717, 717f, 731f circulatory systems of, 1013–14 genome projects with, 448 neurons of, 882 Neoceratodus forsteri, 742f Neodohrniphora curvinervis, 1189–90, 1189f Neotestudina rosatii, 609f Nepenthes genus, 815, 815f Nephila clavipes, 1199f nephrons, 1047–50f, 1055, 1140, 1141f nephrostomes, 1046 NER. See nucleotide excision repair. Nernst, Walther, 887 Nernst equation, 887 nerve cells. See nervous system cells; neurons. nerve cords, of flatworms, 905 nerve impulses. See action potentials. nerve nets, 905 nerves: defined, 881, 883 information conveyance by, 908–9, 909f nerve signals, 215–16 nervous system cells, 881–903 electrical and chemical communication by, 892–99, 896t, 897f, 899f electrical properties of, 884–88, 886t generation and transmission of electrical signals by, 888–91f, 888–92

in learning and memory, 917–21 overview, 882–84 public health issues related to, 900– 902, 900t, 901f signals to and from, 882–83, 882f, 883f summary, 902 types of neurons, 882–84, 884f nervous system(s), 904–42 and blood glucose concentration, 996, 997f cells of (See nervous system cells) cellular basis of learning and memory in, 917–21 and circulatory system, 1022 defined, 881 and digestive systems, 984–85 and endocrine system, 1062–65, 1063f, 1064t evolution and development of, 904–7, 906f, 907f and food intake, 999–1000, 1000f and heart beat, 1017 and immune system, 1127 model organisms for, 917 public health issues related to, 922–23, 922t, 923f in rapid phase of response to hemorrhage, 1133, 1138, 1138f regulation of absorptive and postabsorptive state by, 994–97, 995f, 997 regulation of organ systems by, 864 structure and function of vertebrate, 907–16, 915t summary, 923–24 and ventilation, 1036–37, 1036f nervous tissue: cells in, 861–62, 861f multicellularity, 215–16, 215f nesting gannet, 1190, 1190f net primary production (NPP), 1252 See also primary production net reproductive rate, 1209 neural crest, 1103, 1103f, 1104 neural tube, 1103, 1104 neurodegenerative diseases, 401–3, 402f, 402t neurofibrillary tangles, in Alzheimer’s disease, 922 neurogenesis, and learning/memory, 918–19 neurogenic hearts, 1017 neurohormones, 1064 neurological disorders, and non-coding RNAs, 279 neuromodulators, 896 See also neuropeptides neuromuscular junction: acetylcholine in, 895 electrical stimulation of muscle fibers in, 960, 960f and insecticide, 960 neurons: abnormal development of, 901–2, 901f and cell communication, 185 communication by, 892–99, 896t, 897f, 899f

INDEX

INDEX I-35

I-36 INDEX

INDEX

neurons, continued defined, 881 in digestive system, 976, 979f, 984 electrical properties of, 884–88, 886t electric signal generation/transmission by, 888–91f, 888–92 hormones synthesized by, 1064 in human nervous system, 908 from hypothalamus, 1064–65 ion concentration gradients across, 885–86, 886f, 886t in learning and memory, 917–21 localized signaling in, 871 in nerve nets, 904 in nervous tissue, 861 proteins produced by, 82 regulation of, 898–99, 899f responses to synaptic inputs by, 893–95 as sensory receptors, 926, 926f signals to/from, 882–83, 883f structure of, 79, 80f surface area of, 866, 867f types of, 882–84, 884f neuroparasitology, 2 neuropeptides, 896, 896t neuroscience, 881, 904 Neurospora crassa, 245 neurotransmitters: and cell communication, 185 at chemical synapses, 893, 894f and circulatory system, 1022 classifications of, 895–96, 896t defined, 888 and digestive system, 984 disorders impacting, 900, 901 gaseous, 896, 896t and illicit drugs, 900t, 901 localized signaling by, 871 and postsynaptic membrane receptors, 898, 899f in sensory systems, 929, 941 neurulation, in embryonic development, 1099, 1103–4, 1103f neutral mutations: and maximum likelihood, 525 in molecular clock, 530 neutral theory of evolution, 529 neutral variation, 491 neutrons: characteristics of, 28, 29, 29t defined, 25 in isotopes, 29, 30f neutrophils: and inflammation, 1112 structure and function of, 1110, 1110f newborns, with RDS, 1031–33 NFR (nucleosome-free regions), 298 niches, 1219–24, 1220f, 1221f, 1222t, 1223–24f nickel, in plant nutrition, 802t Nicolson, Garth, 107 nicotinamide adenine dinucleotide. See NAD+. nicotinamide adenine dinucleotide phosphate. See NADPH. Nicrophorus defodiens, 1197 Nierhaus, Knud, 259

Nigeria, 1258, 1258f El Niño, 1156 Nirenberg, Marshall, 254–56 nitrate, 160 nitrate reductase, 160 nitric oxide: and erection, 1092 as neurotransmitter, 896 and plant hormones, 784 nitrification, 1267, 1267f nitrite, 160 nitrogen: in covalent bonds, 31f electron shells and orbitals of, 27–28, 27f in living organisms, 29 and plant nutrition, 802t, 808–9 and primary production, 1252, 1252f, 1253 nitrogenase, 808, 809, 809f nitrogen cycle, 1266–68, 1267f nitrogen fixation: by microbiome, 627 in nitrogen cycle, 1267, 1267f plant–bacteria symbioses for, 812–14, 813f and plant nutritional requirements, 808–9, 808f–9f in primary succession, 1241 by prokaryotes, 573 nitrogen-limitation hypothesis, 1232, 1232f nitrogen mustards, 310 nitrogenous wastes: exchanges of ions and water to eliminate, 874 forms of, 1044, 1044f removal processes for, 1044–45, 1045f Nitrosomonas genus, 565 nitrous acid, 310 nitrous oxide, 798, 799f, 1260, 1261t NK cells. See natural killer cells. N-linked glycosylation, 113, 113f nociception, 933–34 nociceptors, 927, 933–34 nocturnal animals, sensory systems of, 937, 944 nodes: of phylogenetic trees, 519 of shoots, 769–70 nodes of Ranvier, 883, 892 Nod factors, 813 nodules, legume root, 813–14, 813f, 814f nodulins, 813, 814f noise-induced hearing loss, 948 Nomarski microscopy, 77f nonassociative learning, 1182 nonchordates, SSU rRNA of, 729, 729f non-coding RNAs (ncRNAs), 266–81 binding by, 267, 268f and chromatin structure/transcription, 270, 271f defined, 244 examples of, 270t functions of, 267, 269f, 270, 270t and genome defense, 275–78, 277f

in human disease and plant health, 278–80, 279t, 280t and one-gene/one-enzyme hypothesis, 246 overview, 259f, 267–70, 268f, 270t and protein sorting, 275, 276f summary, 280 and translation, 270–75 noncompetitive inhibitors, 133f, 134, 139 non-Darwinian evolution, 491 nondisjunction, 344, 344f nonionizing radiation, 310 nonmigratory birds, feeding habits of, 971 nonmusicians, brain structures of, 920–21 nonpolar covalent bonds: and amino acids, 57, 57f and carbon atoms, 46, 46f defined, 32 nonrandom mating, 491–93 nonrecombinant offspring, 386–87, 387f nonsense mutations, 305 nonshivering thermogenesis, 1006 norepinephrine: and asthma, 1039 in endocrine system, 1059, 1067 and nervous system cells, 901 in response to hemorrhage, 1135, 1138 normalized difference vegetation index (NDVI), 1253f norm of reaction, 366, 366f North American beaver, 1205, 1206, 1206f, 1206t Northern elephant seal (Mirounga angustirostris), 490 northern leopard frog (Rana pipiens), 498 Northern spotted owl, 1290–91, 1291f Nosema ceranae, 611, 612f nose(s): olfactory structures of, 943–44, 943f in respiratory system, 1028 notochords, 518, 729, 729f, 1102f, 1103 Nottebohm, Fernando, 918 Nowell, Peter, 316 NPP (net primary production), 1252 N-terminus, 58, 58f, 254 nuclear envelopes: of animal cells, 80f of eukaryotic cells, 88, 89f of plant cells, 81f nuclear genomes: of eukaryotes, 448–50, 449f, 449t and evolution of eukaryotes, 542 mitochondrial and chloroplast vs., 98 repetitive sequences in, 452, 452f size of, 449 Nuclearia genus, 591, 592f nuclear lamina, 239 nuclear localization domain, 63 nuclear matrix: chromatin in, 239, 239f, 240f of eukaryotic cells, 88, 89 nuclear pores: of animal cells, 80f of eukaryotic cells, 88 of plant cells, 81f nuclear receptors, 63, 64f nucleic acids, 64–65

defined, 224 DNA and, 224–28, 226t DNA structure, 64–65, 65f nucleotides in, 64, 65f organic molecules from, 971 RNA structure, 65 nucleoids, 78, 98, 403, 403f nucleolus: of animal cells, 80f function of, 89 of plant cells, 81f nucleosome-free regions (NFR), 298 nucleosomes, 238, 238f, 239f and ATP-dependent chromatin remodeling, 297f and eukaryotic genes, 298, 299f nucleotide excision repair (NER): function of, 313, 313f genetic disease related to, 313–14, 314f nucleotides: base pairing of, 227–28, 227f, 228f components of, 224, 224f, 225f defined, 224 in DNA strands, 224–26, 225f in structure of RNA and DNA, 64, 65, 65f nucleus: atomic, 25, 26 cell (See cell nucleus) nervous system, 908, 1063 nudibranchs, 711, 711f, 712t, 1025, 1025f nurse cells, 420 Nüsslein-Volhard, Christiane, 421, 1112, 1113 nutation, 782, 783f nutrients: absorption of, 974–75, 975f, 984 in absorptive state, 992–93, 992f in capillaries, 1021, 1021f defined, 801, 970 for energy and molecular synthesis, 971, 972t essential, 971–72 organic, 971, 972t plant, 801–2, 802f, 802t in postabsorptive state, 993–94, 993f in primary production, 1252–53, 1252f nutrition: and animal diversity, 687, 688f for animals, 970–74t for archaea, 572–73 for bacteria, 572–73 defined, 970 and immunity, 1126–27 infertility due to, 1104–5 of plants (See plant nutrition) for protists, 593, 593f and reproduction, 1080

O

O2. See oxygen. oak trees, 1269–70 alternation of generations in, 840, 840f as K-selected species, 1213, 1214f photosynthesis in leaves of, 179, 180f

oak winter moth, 1152–54, 1153f, 1154f oats, 786–87 Obama, Barack, 904 obesity: genetic influences, 243 as global public health issue, 1006–7, 1007f and leptin, 991 and satiety factor in mammals, 1000, 1001, 1001f obligate aerobes, 573 obligatory ion and water exchanges, 874–76 obligatory mutualism, 1230 observational learning behavior, of mollusks, 712–14, 713f observations, 18, 1152–53, 1154f OCA2 gene, 325, 556 occipital lobes, 920 occludin, 210 oceans: currents in, 1163–64, 1163f microbiomes in, 628–29, 628f ocellaris clownfish, 11, 11f ocelli, 705 Ochoa, Severo, 254 ocotillo (Fouquieria splendens), 833, 833f octapeptide, 58f octet rule, 31, 31f octopuses: characteristics of, 709, 711–12, 711f, 712t learning behavior of, 712–14, 713f nervous system of, 905 neurons in, 882 Octopus vulgaris, 713f, 714 Odobenus rosmarus, 754f Odontoceti suborder, 466 odor molecules, olfactory receptor binding to, 943–45f, 943–46 Odum, Howard, 1252 Office of Human Genome Research, 451 offspring, from vegetative reproduction, 855, 855f Ohno, Susumu, 377 oils: defined, 53 as hydrophobic molecules, 37 Okazaki, Reiji, 232 Okazaki, Tsuneko, 232 Okazaki fragments, 232–36, 234f olfaction: defined, 942 sensory hairs for, 942–43, 943f olfactory bulbs, 914, 944 olfactory receptors, mammalian, 943–45f, 943–46 oligodendrocytes, 883 oligosaccharide transferase, 113, 113f O-linked glycosylation, 113 Olympic Coast National Marine Sanctuary, Washington, 1172, 1172f Olympic National Park, Washington, 1166, 1166f omasum, 978 O6-MeG, cytosine and, 227 ommatidia, 719, 935, 936f

omnivores, 971 oncogenes, 314 and cell division proteins, 314–16, 315f, 316t environmental activation of, 381 and immunity, 1123 from proto-oncogenes, 316–17, 317f one-gene/one-enzyme hypothesis, 245–46, 245f 100 Heartbeats: The Race to Save the Earth’s Most Endangered Species (Corwin), 1280 1000 Genomes Project, 557 one-way valves, in veins, 1022, 1022f onions, seed germination and seedling growth in, 854, 854f On the Origin of Species (Darwin), 461, 513 oocytes: cyclins and cdks in maturation of, 328–29 in embryonic development, 418, 419f formation of, 1088f, 1094, 1094f positional patterns in, 417, 417f oogenesis, in animals, 1087, 1088f, 1089 oogonia, 1087, 1088f Oparin, Alexander, 70 open circulatory systems: fluid compartments in, 872 hemolymph in, 1011, 10111f of mollusks, 710 and respiratory systems, 1027 open conformations, 296 open ocean, 1173, 1173f operant conditioning, 1182–83, 1183f operator, defined, 286 opercular cavity, 1026 operculum, 740, 740f, 1026, 1027 operons, defined, 285 See also lac operon; trp operon Operophtera brumata, 1152–54, 1153f, 1154f Ophiarachna genus, 728f Ophiostoma genus, 615 Ophiuroidea subclass, 727 Ophrys apifera, 1231, 1231f opiate peptides, 896 See also neuropeptides Opisthokonta supergroup, 517, 584, 591–92, 591f, 592f, 605, 688 opsins, 938–40 opsonization, 1120, 1121 optic disc, 937 optic nerves, 937 optimal foraging, 1189–90, 1189f optimality theory, 1189–90 Opuntia stricta, 1228, 1228f oral contraceptives, 1105f, 1106 orangutans: chromosome structure and number in, 475, 475f and human evolution, 548 orbitals, 27–28, 27f and absorption of light, 168 of carbon, 46, 46f orchids, 1231, 1231f orders:

of amphibians, 745–46, 746f of birds, 751, 752f, 753t of insects, 722, 723t, 724 of mammals, 755–56, 755t in taxonomy, 518 Ordovician period, 540, 544, 738 Oreamnos americanus, 1203f organelles: defined, 79 droplet, 79 of eukaryotic cells, 79, 80f, 81f genomes of, 381–84, 382f, 383f, 384t protein movement through, 92–95f protein sorting to, 99–102 recycling of, 142, 142f semiautonomous, 96–99, 102, 103f organ fusion, and flower shape, 845 organic chemistry, 23, 45 organic compounds, in phloem, 834–36, 834f, 835f organic farming, 808 organic fertilizers, 807–8 organic molecules, 45–67 from anabolic reactions, 139 in bone, 952 carbohydrates, 48–52, 50f, 51f carbon atoms in, 45–48, 46f, 47t, 48f for catabolic reactions, 137–38, 137f classes of, 48, 49t defined, 45 energy from breakdown of, 997 fermentation of, 160–61, 161f formation of, 48, 49f lipids, 52–54f, 52–56, 56f nucleic acids, 64–65, 65f nutrients for synthesizing, 971, 972t origin of, on Earth, 70–72, 70f, 71f in placental transfer tissues, 655–57 proteins, 56–64, 56t, 57–59f, 61–64f in proximal tubule, 1049 recycling of, 137, 141–42, 141f, 142f summary, 66 organic nutrients, in animals, 970, 971, 972t organismal ecology, 1150, 1150f organisms: defined, 2, 3, 3f effects of abiotic factors on, 1155t environment’s effect on distribution of, 1155–60, 1155t, 1156f, 1158f, 1159f gene expression and characteristics of, 247 model, 12–13 organization: and cell structure/function, 78 of living organisms, 3f and multicellularity, 203 organizing center, of plant, 430 organ of Corti, 930, 931f organogenesis, in embryonic development, 1099, 1104 organs and organ systems: in animal bodies, 863–65, 864f, 865t arteries and blood flow to, 1020, 1020f of birds, 751, 751f in body organization, 860, 860f

compensation for hemorrhage by, 1143–44, 1144t components of, 976 defined, 2, 3f, 214 effects of hemorrhage on, 1132–33, 1132f, 1133f embryonic development of, 1104 of flowers, 844–45, 844f genetic basis of, 844 Hox genes and development of, 864–65 lymphoid, 1115 from primary meristems, 765–67, 765t, 766f, 767f production of, 214–15 redistribution of blood to, 1138, 1138f in secondary phase of response to hemorrhage, 1143–44, 1143t skeletal muscle as, 954, 954f stretch receptors in, 928f structure and function of cells in, 884 thermoreceptors in, 933 tissues in, 863–65, 864f, 865t variety of, in flowering plants, 762, 763, 764t organ transplants, 1127 Orgel, Leslie, 72 orientation, 1188, 1188f Origin of Eukaryotic Cells (Margulis), 99 origins of life, 535–59 for animals, 687–88, 688f dinosaurs, 546–47 environmental changes since, 540 eukaryotic cells, 541–43 and fossil record, 536–38 heterotrophs and autotrophs, 540–41 and human evolution, 547–58 invertebrates and land plants/animals, 544–46 mammals and flowering plants, 547 multicellular organisms and animals, 543–44 overview, 538–47 prokaryotic cells, 540 summary, 558 viruses, 400–401 origins of replication, for DNA, 231–32, 231f, 234f Ornithischia and ornithischians, 749, 749f Ornithomimus genus, 650, 650f Ornithorhynchus anatinus, 756f Orr, Matthew, 1189–90 orthologs, 473, 473f See also homologous genes Oryza longistaminata, 1285, 1285f Oryza nivara, 683 Oryza rifipogon, 683 Oryza sativa, 683, 1285, 1285f Oscillatoria genus, 565f osmoconformers, 879 osmolarity, 874, 875, 875f osmolarity, of filtrate in kidney, 1050–52, 1050f osmoregulators, 879 osmosis: animal adaptations to osmotic challenges, 879 in animal bodies, 873, 879

INDEX

INDEX I-37

I-38 INDEX

INDEX

osmosis, continued by fish, 1158–59 and fungal growth, 607–8, 608f as membrane transport, 115–16, 115f, 116f in plant cells, 819, 822 and plant hormones, 791 osmotic stress, plant adaptations to, 822 osmotrophs, 593 ossicles, 929 osteichthyans, 740–42 osteoblasts, 952 osteoclasts, 952 osteocytes, 952 osteomalacia, 966 osteoporosis, 966, 966f ostriches, 529 otoliths, 932 outer bark, 776 outer ear, 929 outer segment, of photoreceptors, 937 outgroups, on cladograms, 524 out-of-Africa hypothesis, 554 ova. See egg cells. oval window, 929, 930 ovarian cycle: follicle and oocyte development in, 1094, 1094f and hormone secretion, 1094–95, 1095f ovaries: in endocrine system, 1060f, 1080 of flowering plants, 843, 852–53 of flowers, 673 gametogenesis in, 1087, 1093–94, 1094f overeating, and heartburn, 986 overexploitation, 1271–75 overheating, by endotherms, 1003 overweight, 1006 oviducts, 1093 oviparous species, 740 Ovis dalli, 1207–8 ovulation, and oogenesis, 1089 ovules: descent with modification for, 660–62, 661f, 662f development of, 762 in evolution of seeds, 658–60, 660f female gametophyte development in, 849–50, 850f of flowering plants, 841, 849–50, 850f, 851f sperm cell delivery to, 850–51, 851f Owen, Richard, 749 owls, sensory systems of, 931 oxaloacetate: and in citric acid cycle, 151, 151–52f and photosynthesis, 179 oxidation, 138 and fermentation, 160–61, 161f of NADH, 155 of pyruvate, 150–51, 150f oxidation-reduction (redox) reactions: defined, 70 electron transfer in, 138–39, 138f oxidative fibers, 961, 962, 962t oxidative phosphorylation, 146f, 147, 153–55, 154f

ATP synthase in, 153, 155 electron transport chain, 153, 154f free energy changes in, 155 NADH oxidation, 155 oxygen: affinity of hemoglobin for, 1034–35, 1035f, 1036f in air, 1024 in atmosphere, 538 atmospheric, and life origins, 649 and blood pressure, 1132 in circulatory system, 1010, 1014 in covalent bonds, 31f delivery of, in rapid response to hemorrhage, 1138, 1139f diffusion in blood of, 1025 in double bonds, 32, 32f in mass of living organisms, 29 partial pressure of, 1034–35, 1035f in photosynthesis, 165, 166, 166f from photosystem II, 172–74, 173f plant nutrition, 802t prokaryotic response to, 572–73 and respiratory pigments, 1034, 1034f in respiratory system, 1028 See also circulatory systems; respiratory systems oxygenated blood, 1012, 1017 oxygen-hemoglobin dissociation curve, 1034–35, 1035f, 1036f oxytocin: at birth, 1098 and posterior pituitary gland, 1064–65 oysters, 709, 711, 711f, 712t ozone layer, 167, 545

P

P680, 169, 170f, 172–74, 173f P680*, 172–73, 173f P680+, 173, 173f P700, 169 Pääbo, Svante, 527, 550 pacemaker, 1017–18 See also sinoatrial (SA) node Pacific Northwest, 1174, 1174f Pacific yew (Taxus brevifolia), 664 Pacinian corpuscles, 927, 928f pain, detection of, 933–34 pair-rule genes, 421, 421f, 422 Pakicetus genus, 465, 466 Palade, George, 92–94, 208 Paland, Susanne, 1086, 1086–87f paleontologists, 536 Paleotapirus genus, 1175 Paleozoic era, 544–46 palindromic sequences, 436 palisade parenchyma, 766, 767 palmate venation, 770–72f, 771–73 Palumbi, Steve, 1272 Pampas, Argentina, 1287, 1288f PAMPs (pathogen-associated molecular patterns), 1112, 1115 Panamanian golden frog, 1149 Panamic porkfish (Anisotremus taeniatus), 502 Panax quinquefolicus, 1274

pancreas: and cell functions, 92 in digestive system, 979, 980f endocrine function of, 1060f, 1069–72f, 1069–73 pancreatic duct, 980f Pangaea, 546 Panini tribe, 548 panther, 1290f, 1291 panting, 1005 Pan troglodytes, 549f, 1205f paper chromatography, 176, 177–78f Paphiopedilum rothschildianum, 1274, 1274f Papilio xuthus, 939 parabiosis, 1000, 1001f paracrine signaling, 185, 185f, 871 Paragordius varius, 2t parallel evolution, 401 paralogs, 450, 473 Paramecium and paramecia, 583f central vacuole of, 94f cilia of, 583f contractile vesicle of, 116 horizontal gene transfer to, 474, 474f movement of, 86, 87f Paramecium aurelia, 1219–20, 1220f Paramecium bursaria, 1219–20, 1220f Paramecium caudatum, 116f, 599, 600f, 1219–20, 1220f Paranthropus genus, 550–52, 551f paraphyletic groups, 521 parapodia, 715 parasites: defined, 1228 as density-dependent factor, 1212 eukaryotic, 1109 and leafcutter ants, 1189–90, 1189f nematodes as, 717, 718f of oak winter moths, 1152–54, 1153f, 1154f plants as, 797, 815–16, 816f protists as, 586, 586f, 599–602, 601f parasitism, 1217, 1228–29, 1228f, 1229f parasitoids, 1224 parasympathetic division, of autonomic nervous system, 910, 911f parathyroid glands, 1060f, 1074, 1074f parathyroid hormone (PTH), 953, 966, 1074–75, 1075f Parazoa, 690f Pardee, Arthur, 289–91 parenchyma tissues and cells, 216, 766, 767 parental care, by primates, 548 parental strands (DNA), 228 parietal lobe, 914, 914f Park, Sang-Youl, 831–32 Parkinson’s disease, 914 Parnas, Jacob, 147 parsimony principle, 525 parsnips, as biennial plants, 763 Parthenium argentartum, 1286 Parthenocissus quinquefolia, 682–83 parthenogenesis, 709, 1085 partial pressure of oxygen (PO2): in blood, 1034–35, 1035f

defined, 1024–25 particulate inheritance, 348 partly apoplastic phloem loading, 835, 835f, 836 parturition, of mammals, 1097–99, 1098f Parus caeruleus, 1205f passenger pigeon, 1272, 1273f passerines, 1221, 1221f passive immunity, 1126 passive transport: defined, 113 in digestive systems, 974–75, 975f between fluid compartments in animals, 872 in plant cells, 819, 820f and transmembrane gradient, 115 passive trapping mechanisms, 815 Patau, Klaus, 378–79 patch testing, 1119 patellar tendon reflex, 884 paternal inheritance, 383 pathogen-associated molecular patterns (PAMPs), 1112, 1115 pathogens: bacteria as, 576–78, 577f, 578f defined, 391, 1109 fungi as, 617–18, 617f, 618f and interferon/complement proteins, 1112 invasive species as, 1277, 1277f opsonization of, 1120, 1121 and phagocytes, 1110–11, 1110f and plant behavior, 784, 791, 797–99, 799f recognition of, 1112–13 types of, 1109 See also disease(s) pattern formation: and adult structures, 418, 419f in animals, 415, 418–24 body axes, 419–20, 420f defined, 415 in plants, 415 positional information for, 415–16, 415f segment characteristics, 422–24 segment development, 420–22, 421f, 422f and speciation, 509–12 and transcription factors, 417–18, 418f Pauling, Linus, 226, 523 Pavlov, Ivan, 870, 917, 1182 Pavo cristatus, 486 Pax6 gene, 413, 512–14 Payen, Anselme, 207 PCR (polymerase chain reaction), for gene cloning, 439–40 pea aphid, 507 peafowl (Pavo cristatus), 486 pea plants, 790, 791 epistasis in, 367, 367f Mendel’s studies of, 350–51, 350f, 351f protein function and dominance in, 363, 363f seed germination and seedling growth in, 854f, 855 sex determination in, 360

peat mosses, 649 peat mosses, methane oxidation in, 627, 627f, 628f pectinases, 213 pectins, 207f, 208, 213 pedal glands, 708, 708f pedicels, 672 pedigree analysis: of human traits, 358–59, 358f, 359f of inbreeding, 492–93 peer-review process, 16 Pelecanus onocrotalus, 752f Pelomyxa genus, 584f Peltigera ponojensis, 632f penicillins. See antibiotics. penis, 1090 pentadactyl limbs, 743 pentoses, 49, 50 PEP carboxylase, 179 PEP (phosphoenolpyruvate), 137, 149f, 179 pepsin, 134, 977 pepsinogen, 977 peptide bonds, 58, 58f, 254 peptidoglycan, 568, 569 peptidyltransferase, 267 peptidyl transfer reaction, in elongation stage of translation, 262, 262f per capita growth rates, 1210 perception, 925–26 peregrine falcon, 1292 perennials, 764 perfect flowers, 672, 844 perforin, 1123 perianth, 844 defined, 672 pollinators and diversification of, 676, 676f pericarp, 843, 852 pericycle, 778 periderm, 777 Peridinium limbatum, 596f perilymph, 930 periodic table, 28, 28f peripheral chemoreceptors, and breathing reflex, 1138, 1139f peripheral membrane proteins, 108 peripheral nervous system (PNS): central nervous system and, 882, 882f, 908 evolution of, 905 somatic and autonomic systems in, 909–10, 911f peripheral zone, of plants, 430 periphyton, 583 peristalsis, 977, 980 peritubular capillaries, 1048 periwinkle plants, 383–84 permanent forms of contraception, 1105 permeability: of filtrate in kidney, 1050, 1050f of phospholipid bilayer, 114, 114f selective, 113 Permian period, 540, 546, 649, 650, 745 Peromyscus leucopus, 1231f peroxisomes, 95, 95f of animal cell, 80f

of plant cells, 81f post-translational protein sorting to, 101–2, 102f personalized medicine, 479 perspiration: and athletic performance, 877, 878 and homeostasis, 859 ion and water loss through, 876 pesticides, 1268–69 petals: defined, 672, 841 and developmental genetics, 431 petioles, 770, 833, 834f PET (positron-emission tomography) scans, 29, 30f, 149, 150f Petromyzon marinus, 737f, 1275–76, 1276f petunia (Petunia hybrida), 845f P generation, 351 p53 genes and proteins, 318, 472–73, 472f pH, 41–43 and buffers, 42 defined, 41–42, 42f and distribution of organisms, 1159–60, 1159f and enzyme function, 134 and hemoglobin’s affinity for oxygen, 1035 as homeostatic variable, 868t summary, 43 Phaeophyceae, 591 phages. See bacteriophages. phagocytes and phagocytosis: and inflammation, 1112 in innate immunity, 1110–11, 1110f phagocytosis, 95, 584 energy and matter in, 582 as intracellular digestion, 972 membranes in, 124 by protists, 584, 585f phagosome (phagocytic vacuole), 124 phagotrophs, 593 Phallus impudicus, 610f Phanerozoic eon, 538, 544–47 pharmaceutical industry: biodiversity benefits to, 1284, 1285 and deforestation, 1270 pharmaceuticals. See drugs. pharyngeal slits, 729, 729f pharynx: in digestive system, 975, 977 in respiratory system, 1028 phase contrast microscopy, 77f phase separation, and droplet organelles, 79 phenolic compounds, 1227, 1227f phenotypes: continuous variation in, 367–68, 368f and dietary chemicals, 379–80, 380f environmental influence on, 365, 366 and epistasis, 366–67, 367f and gene expression, 364 and genes influencing development, 509–10 genotypes vs., 353 and growth rates, 512 and incomplete dominance, 364–65, 364f

and speciation rate, 509–10 variation of, in humans, 557–58 phenylalanine, 244, 244f phenylthiocarbamide (PTC), 481 pheophytins (Pp), 169, 173, 173f pheromones, 943, 1191, 1197 Philanthus triangulum, 1185–86f, 1185–87 Philippine eagle, 1280 Philodina genus, 708f phloem, 645 bulk flow in, 826 food-conducting cells of, 775–76, 776f long-distance plant transport in, 834–36 as plant tissue, 216 and primary stem structure development, 766, 767 secondary, 776 phloem loading, 835–36, 836f phloem sap, 825, 826, 835, 836 phoresy, 1231 phosphatase, 112f phosphate ions, in animal bodies, 874 phosphates: in nucleotides, 224, 224f, 225f smart plants’ communication about, 810–11, 810–11f phosphodiesterase: and cell communication, 194 and sensory systems, 940, 941 phosphodiester linkage, 225 phosphoenolpyruvate (PEP), 137, 149f, 179 phosphoenolpyruvate (PEP) carboxylase, 179, 804 phosphofructokinase, 148 2-phosphoglycerate, 149f 3-phosphoglycerate dehydrogenase, 140 3-phosphoglycerate (3PG), 149f, 175f, 176, 178 phospholipid bilayer: in membrane structure, 107 in membrane transport, 114, 114f See also plasma membranes phospholipids, 54–55, 54f in membranes, 107 synthesis of, at ER membrane, 111, 112f phospholipid tails, and membrane fluidity, 109 phosphorus: plant adaptations for acquiring, 809 plant nutrition, 802t, 808 and primary production, 1252, 1252f phosphorus cycle, 1265–66, 1266f, 1267f phosphorylase kinase, 193 phosphorylation: defined, 130 enzymes for, 131 oxidative (See oxidative phosphorylation) photo-, 170–71, 171f substrate-level, 138, 146 photic zone, 1158 photoautotrophs, 165, 572, 593 photoheterotrophs, 573 photons, 167, 940–41, 940f photon theory of light, 167

photoperiodism: and plant behavior, 794, 795f and plant reproduction, 844 photophosphorylation, 170–71, 171f photopsins, 938 photoreception, 934–42 color vision, 938–39, 939f eyecups and compound eyes, 935, 935f, 936f light-absorbing pigments, 938, 938f photons in, 940–41, 940f photoreceptor cells, 937–40f, 937–41 retina, 941, 941f single-lens eyes for, 935–37, 936f vertebrate eye adaptations, 941–42, 942f photoreceptor cells, 937–40f, 937–41 and photons, 940–41, 940f structure and function of, 935, 936f types of, 937–38, 937f, 938f visual pigments in, 938, 938f photoreceptors, 935 defined, 927 plant, 793–94 photorespiration: in C4 plants, 179, 180f and photosynthetic efficiency, 178–79, 179f, 180f photosynthesis, 164–82 in biosphere, 165, 165f Calvin cycle in, 166, 166f, 174–78, 175f, 177–78f in CAM plants, 179, 180f in chloroplasts, 97–98, 97f, 165–66, 166f in C4 plants, 179, 180f defined, 164 and leaf shapes, 770–71, 770f and leaf surface, 773–74, 774f and leaf veins, 767 light reactions in, 166–72 overview, 164–67, 165f, 166f and photorespiration, 178–79, 179f photosystem features, 172–74, 173f, 174f products of, 170 stages of, 166–67, 167f summary, 181 variations in, 178–80, 179f, 180f photosynthetic algae, 582f photosynthetic organisms, 625, 626f photosynthetic pigments, of plants, 168–69, 169f photosystem II (PSI II): and coordination of photosystem I, 169–70, 170f electrons in, 174, 174f events in, 169 function of, 172–74, 173f photosystem I (PSI I): and coordination of photosystem II, 169–70, 170f electrons in, 174, 174f photosystems, 172–74, 173f, 174f phototaxis, 1185 phototropin, 793 phototropism: and auxin, 786–89, 788f

INDEX

INDEX I-39

I-40 INDEX

INDEX

phototropism, continued and cell communication, 184, 184f defined, 784 Photuris versicolor, 1191, 1191f Phycodurus eques, 741f phyla, 517 of animals, 689–92, 694–95, 695t, 731, 731t of invertebrates, 731, 731t of land plants, 644 in microbiome, 625 in supergroups, 592t Phyllidia ocellata, 711f phylogenetic tree: for Alveolata, Stramenopila, and Rhizaria, 589, 589f for angiosperms, 675, 675f of animals, 689, 689f, 692, 695–99 and cladograms, 523 for eukaryotic supergroups, 584, 584f for flightless birds, 527–29 of land plants and protists, 586, 587f for mammals, 756, 756f maximum likelihood analysis for, 525 of microbiome bacteria and archaea of, 625, 626f modeling, 260 and molecular clocks, 530–31 for Opisthokonta supergroup, 591, 591f for Protostomia, 696, 696f for seedless vascular plants and seed plants, 664, 665f in systematics, 519–23 phylogeny: animal, 689–92, 690f, 701, 701f defined, 519 Physalia physalis, 705f Physcomitrella genus, 648 Physcomitrella patens, 643 physical activity: and circulatory systems, 1011 energy during, 996, 997 and metabolic rate, 998 in treatment of obesity, 1007 The Physical Basis of Life (Bernal), 72 physical environment, plants’ influence on, 648–50, 649f, 650f physical mutagens, 310, 310t, 311f physical stimuli, plant responses to, 783f physical stresses, plant responses to, 797 physical systems, microbiomes of, 628–30, 629f physiological ecology, 1150 physiological variables, range for, 867–68, 868f, 868t physiology, defined, 13, 13f phytochromes, 793–94, 793f Phytophthora infestans, 582, 582f, 590, 593 phytoplankton, 582 pia mater, 909 Picoides borealis, 1291 pigeon milk, 977 pigeons, 934 digestive system of, 977 navigation by, 1188 selective breeding of, 469

pigments: light-absorbing, 938, 938f and light, 167–69, 168f 169f, 938, 938f in light reactions, 167–69, 168f, 169f photosynthetic (See coloration) respiratory, 1034, 1034f visual, 938, 938f, 940–41, 940f pili, 79, 570, 571f pill bug, 725f, 726 Pillitteri, Lynn, 774 piloting, 1188 pineal gland, 1060f pine trees, 647, 647f, 668, 669f pinnate venation, 770–72f, 771–73 pinocytosis, 123, 124 PIN proteins, 785, 787f Pinus genus, 647, 647f, 668, 669f Pinus banksiana, 1156 Pinus palustris, 1291 Pinus ponderosa, 668f Pinus resinosa, 634f pinworms, 717 pioneer stage, 1241 pipefish, 1198 pistils: defined, 672–73, 841 organ fusion in, 845 and pollen germination, 849, 850f structure of, 674f, 762 Pisum sativum, 350–51, 350f, 351f pitcher plant, 815, 815f pitfall traps, 1202, 1202f pith, 776 Pithecopahga jefferyi, 1280 pits, of tracheary elements, 668, 826 pituitary giants and gigantism, 1077, 1077f pituitary gland, 913 anterior, 1060f, 1063–64, 1064f posterior, 1060f, 1064–65 and relationship of hypothalamus, 1062–63, 1063f pit vipers, 934, 934f, 1284 pivot joints, 953f PKA. See protein kinase A (PKA). placenta: of mammals, 756 during pregnancy, 1096–97, 1096f placental animals, 468 placental transfer tissues, of plants, 655–57 Placodermi, 738 Planaria, photoreception in, 935, 935f Planctomycetes phylum, 567 planetesimals, 535 Plantae kingdom, 517, 586, 592t plant behavior, 782–800 cell signaling, 784–85, 784f defined, 782 environmental stimuli responses, 783–84, 783f, 792–99 and hormones (See plant hormones) overview, 782–85, 783f, 784f summary, 799–800 plant cells: bacterial and animal cells vs., 102, 103t and cell communication, 184 cell junctions, 208, 208t, 213–14, 213f, 214f

cell walls, 206–8, 207f central vacuole of, 94f compartments in, 84f cytokinesis in, 332, 334f genetic material in, 382f meiosis in, 335 mitosis in, 331 nucleus and endomembrane system of, 88f osmosis in, 116, 116f semiautonomous organelles of, 96f structure of, 81f and transport (See plant transport) viroids in, 401, 401f water absorption by, 768, 769f See also eukaryotic cells plant development, 429–31, 430t development in animals vs., 429 of flowering plants, 761, 762, 764–69, 765t of organs and organ systems, 864–65 plant embryos: defined, 414 development of, 851–52, 852f evolutionary importance of, 655–57f, 655–58 and fertilization, 842–43 of flowering plants, 761, 761f, 762f, 790 in maternal plant body, 655, 655f meristems from, 429–31, 430f, 430t in seeds, 851–52, 852f, 853f plant evolution, 641–63 diversity of modern plants, 641–48 effects on Earth of, 648–50, 649f, 650f embryos, 655–57f, 655–58 leaves and seeds, 658–62 and plant features, 662, 662t reproductive features of land plants, 651–54 summary, 662–63 plant hormones, 785–92, 786t auxins, 785–89, 787f, 788f cytokinins, 789, 790f defined, 784 and environmental stresses, 792 ethylene, 791–92, 792f gibberellins, 789–90, 790f, 791f and plant leaf development, 770 plant leaves: of C4 and CAM plants, 179, 180f cell walls, 208 defined, 646, 761 evolution of, 658, 659f of ferns, 659 and flower organs, 672–75 and hormones, 790 host-associated microbiomes in, 632–33, 633f of lycophytes and pteridophytes, 645, 646 modifications of, 774–75, 775f nematode within, 717f and nutrition, 805, 805f photosynthesis in, 165, 166f photosynthetic pigments in, 168, 169 shade adaptations of, 803, 803f

shapes of, 770–71, 771f structure and development of, 766–67, 767f surfaces of, 773–74, 774f vein patterns in, 771–72f, 771–73 plantlets, of Kalanchoë daigremontiana, 855–56 plant nutrition, 801–17 biological sources of nutrients, 811–16, 812–16f requirements of plants, 801–5, 802f–5f, 802t soil in, 805–11, 806–11f summary, 816 plant pathogens, 791, 797–99, 799f plant reproduction, 839–57 alternation of generations, 840, 840f asexual, 855–56, 855f in conifers, 668, 669f embryo, seed, fruit, and seedling development, 851–55 fertilization in, 841–43, 842f, 843f flower parts in, 672–73, 672f, 673f flowers in, 840–41, 840f, 841f, 843–48 gametophytes and double fertilization in, 848–51 in land plants, 651–54 overview, 839–43 seeds for, 660 summary, 856–57 plant roots. See roots and root systems. plants: and acidic soils, 42 as autotrophs, 541 body plan axes in, 415, 415f cells of (See plant cells) chloroplasts of, 165–66, 166f chromosome number changes for, 345–46, 345f and conservation strategies, 1287 consumption of, 971 developmental genetics for, 429–31, 430t and dispersive mutualism, 1230–31, 1231f effects of carbon dioxide on, 1264–65 in Eukarya, 9, 10f evolutionary change in, 648 features of, 662, 662t flowering (See flowering plants [angiosperms]) flowers (See flowers) fungal disease in, 617, 617f, 618f gametophyte production in, 340 genetic engineering of, 1157 gravity and size of, 825–26 growth of, 791–92 gymnosperms (See gymnosperms) heat stress in, 618–19, 619f host-associated microbiomes in, 632–33, 633f as invasive species, 1275 light as limiting resource for, 1158, 1159f mammalian digestion of, 754 microbiomes of, 638, 638f non-coding RNAs and health of, 279–80, 280t

origins of, 544–46 pattern formation for, 415 photosynthetic pigments of, 168–69, 169f phototropism in, 184, 184f population density of, 1202 roots of (See roots and root systems) seeds of (See seeds) sex determination in, 360 sexual reproduction in, 340, 341f shoots (See shoots and shoot systems) species interactions with herbivores, 1226–28, 1227f, 1228f stems of (See stems and stem systems) symbioses of bacteria and, 812–14, 813f, 814f threatened due to overexploitation, 1274, 1274f tissues of, 216, 216f, 822–24, 823f, 824f used in pharmaceutical industry, 1284 vernalization in, 374 See also specific plants plant tissue culture, 789, 790f plant transport, 818–38 at cell level, 819–22 long-distance, 824–36 overview, 818–19, 819f summary, 836–37 at tissue level, 822–24, 823f, 824f plaques: in Alzheimer disease, 922 athersclerotic, 1038 plasma: blood, 1015 fluid compartments for, 872 and secondary response to hemorrhage, 1140, 1142f plasma cells: in attack on antigen, 1118 from B cells, 1120–21, 1121f structure and function of, 1116, 1116f plasma membranes: of animal cells, 80f in apoptosis, 196, 197f as biological membranes, 106 cell communication through, 189–90, 190f function of, 95–96, 95f hormones acting through, 1059, 1061, 1062 of plant cells, 81f in plant roots, 777 in prokaryotic cells, 78 See also receptors plasmids: defined, 435 described, 404, 404f plasmodesmata: and cell junctions, 208t, 214, 214f and plant transport, 823, 835, 836 Plasmodium genus, 581, 584, 589, 1109 Plasmodium falciparum: life cycle of, 599, 601f, 602 and sickle cell disease, 485 species interactions with, 1228

plasmogamy, 614 plasmolysis, 116, 820, 821f plasticity, of brain, 920 plastids, 97 primary, 587–88, 587f secondary, 588–89, 589f plastocyanin (Pc), 169, 171, 171f Platalea ajaja, 752f platelets, 870, 1015–16, 1016f Platyhelminthes and platyhelminths: characteristics of, 695t, 705–7, 706t, 707f, 708f, 731f nervous systems of, 905, 906f respiratory systems of, 1025 platypus, 934, 1096 pleiotropy, 364 Pleodorina californica, 543 Plesiometa argyra, 2t pleural sacs, 1028–30 pluripotent stem cells, 425f, 426 pneumatophores, 779, 779f Pneumocystis jiroveci, 400, 617 PNS. See peripheral nervous system. podocytes, 1047, 1049f Podos, Jeffrey, 504–6 Poecilia reticulata, 486f Pogonia ophioglossoides, 1231 poinsettias, 775, 794 point mutations, 305, 305f, 443, 444f Poiseuille, Jean Marie Louis, 1022 Poiseuille’s law, 1022 poison ivy, 1127 poisons. See toxins. polar bears, 1290, 1290f polar covalent bonds: and amino acids, 57, 57f and carbon atoms, 46, 46f defined, 32, 32f See also chemical bonds polarity: and protein structure, 50 of solutes, 114 polar molecules, in water, 37, 37f polar transport, 785 poles of mitotic spindle, 331 pollen: defined, 658 development of, 762 in evolution of seeds, 658–60, 660f pollen coat, 849 pollen germination, 842, 849, 850f pollen grains, 841, 848–49, 849f pollen tubes, 842, 850–51, 851f pollination: and angiosperm diversification, 676, 676f coevolution of, 681–82, 682f, 682t defined, 658, 841 and gametic isolation, 501 and germination of pollen, 849 and petals, 672 pollination syndromes, 681–82, 682t pollinators, 676, 676f, 681–82, 682f, 1230–31 and coevolution of flowers, 843 and flower fragrance, 845

pollution: and biogeochemical cycles, 1262–68 and biomagnification, 1268–69, 1268f, 1269f polyandrous mating systems, 1197f, 1198, 1199f polyandry, 1198 poly A tail, 250, 250f polycistronic mRNA, 285 polygenic inheritance, 367–68, 368f Polygonum genus, 673f polygynous mating systems, 1197–99f polygyny, 1197 polymerase chain reaction (PCR), for gene cloning, 439–40, 439f polymers: formation and breakdown of, 48, 49f origin of organic, 72 polysaccharides as, 51–52, 52f and protobionts, 72–73, 73f polymicrogyria, 916 polymorphism, 478–79 balanced, 485 defined, 478 for lactose intolerance, 982 polypeptides, 246 and coding sequences, anticodons, codons, 252, 252t defined, 5 in elongation stage of translation, 261–63, 262f and gene mutations, 305–6, 306f and genetic code, 252, 252t as hormones, 1059, 1061–62 in proteins, 58, 58f and signal recognition particle, 275, 276f in translation, 252–54, 252f, 253f polyphagous parasites, 1228 polyphyletic groups, 521 Polyplacophora, 710, 711f, 712t polyploid organisms, 343, 343f, 345–46, 345f polyploidy, and sympatric speciation, 506 polyps, cnidarian, 704, 704f, 705 polysaccharides: and carbohydrates, 51–52, 52f digestion of, 980–81 in extracellular matrix, 203f, 206, 206f Polysiphonia genus, 598f polysymmetric flowers, 845 Ponginac family, 548 pons, function of, 910 population density, 1202–3 and food limitations, 1232, 1232f and natural enemies, 1232–33, 1233f and parasites, 1229 and predators, 1226, 1226f population ecology, 1201–16 defined, 1150, 1150f, 1201 demography, 1205–9, 1206t dispersion, 1204, 1204f introduced species, 1150–51, 1151f overview, 1201–2 population density, 1202–3 population growth, 1209–15 population size, 1202–3 reproductive strategies, 1204–5, 1205f

summary, 1216 population genetics, 477–95 defined, 477 and genes in populations, 478–81 genetic drift, 489–91f migration and nonrandom mating, 491–93 natural selection, 482–85 sexual selection, 485–89 summary, 493–94 population growth: and fertility data, 1208–9 human, 1257–60, 1258f, 1259f and population ecology, 1209–15 and theory of evolution, 460 population(s): defined, 3, 3f, 458, 477, 1201 as dynamic units, 478 elimination of harmful mutations in, 1086–87 genes in, 478–81 genetic drift and size of, 489–91 mean fitness of, 477 and natural selection, 461–64 population size, 1202–3, 1212–13, 1213f Populus tremuloides, 1232 p orbitals, 27 porcupine fish, 1225f, 1226 Porifera: basic characteristics, 695t 702–4, 703f, 731f porkfish (Anisotremus virginicus), 502 Porphyra genus, 587 portal veins, 1063 Portuguese man-of-war, 705f Posidonia oceanica, 202 positional information: and morphogens/cell-to-cell contacts, 416–17, 417f for pattern formation, 415–16, 415f positive control, of lac operon, 291–93, 292f positive feedback: during birth, 1097–99, 1098f and homeostasis, 870, 871f for shock, 1145, 1145f positive gravitropism, 794, 796f positive pressure filling, 1029 positive reinforcement, 1182–83 positron-emission tomography (PET) scans, 29, 30f, 149, 150f postabsorptive state: blood glucose concentration in, 996 defined, 992 energy sources in, 994t nutrients in, 993–94, 993f regulation of, 994–97, 995f, 997f postanal tail, 729, 729f posterior cavity, of eye, 937 posterior end, 690 posterior pituitary: axon terminals in, 1064–65 in endocrine system, 1060f structure and location of, 1063f postsynaptic cells, 892, 893, 893f postsynaptic membrane receptors: neuronal regulation via, 898–99, 899f

INDEX

INDEX I-41

I-42 INDEX

INDEX

postsynaptic membrane receptors, continued and neurotransmitters, 898, 899f post-translational sorting, to organelles, 100f, 101–2, 102f postzygotic isolating mechanisms, 499, 500f potassium: as essential nutrient, 972 plant nutrition, 802t, 808 potassium channels, 886, 888–90, 892 potassium ions: in animal bodies, 874 hormonal regulation of, 1075–76 and kidney disease, 1055 in kidney filtrate, 1051–52, 1052f Na+/K+-ATPase pump, 121–22, 122f, 886, 889 and neurons, 885–87, 887f, 890 potatoes, 777, 794, 855 potential energy, 128, 128f Pounds, J. Alan, 1149 powdery mildews, 614 Powell, Mike, 951 The Power of Movement in Plants (Darwin & Darwin), 782 power stroke, in cross-bridge cycle, 957, 958f PPAR-δ gene, 962–64 P1 phage, 410–11, 410f P protein, 835 prairie dogs, 1195, 1195f prairies: biomes, 1168, 1168f habitat restoration of, 1291, 1291f prebiotic soup, 70 prebiotic synthesis, 70 Precambrian era, 538 precipitation, patterns of, 1262 predation: defined, 1217 and density dependence, 1212, 1213 by fungi, 617, 617f and group living, 1193, 1193f by invasive species, 1275–77, 1276f, 1277f and negative frequency-dependent selection, 485 of oak winter moths, 1152–54, 1154f and plants, 814–15 sensory systems for, 931, 934, 942 species interactions, 1224–26 sponge defenses against, 703 predators, humans as, 1271–72, 1272f predictions: as BioTIPS strategy, 20 from hypotheses, 14 modeling to make, 19, 19f prednisolone, 197 prednisone, 197 pregnancy: and contraceptive methods, 1105–6, 1106f heartburn during, 986 in mammals, 1096–97, 1096f, 1097t oxytocin during, 1064 preinitiation complex, 249, 249f, 295, 295f, 298, 299f premature infants, with RDS, 1031–33

pre-mRNA, 247 alternative splicing of, 299–300, 300f modification of, 250, 250f splicing of, 251, 251f Presbytis entellus, 756f pressure: and bulk flow, 825–26, 825f, 826f of gases, 1024–25 root, 828, 828f skin receptors for, 927–28, 927f and solubility of gases, 1025 turgor, 820, 821f, 822 pressure-flow hypothesis, 836, 836f pressure potential, 822 pressure waves, in ear, 930, 930f presynaptic cell, 892, 893f prey densities. See predation. prezygotic isolating mechanisms, 499–501 prickly pear cactus, 1228, 1228f prickly rhubarb, 812, 813f primary active transport, 121 primary cell walls, 207–8, 207f primary consumers, 1248, 1248f primary electron acceptor, 172–74, 173f primary endosymbiosis, 587–88, 587f, 588f primary growth, of flowering plants, 765–66, 765t primary immune response, 1125, 1126f primary lymphoid organs, 1115, 1116f primary meristems, 765–67, 765t, 766f, 767f primary oocytes, 1087, 1093–94 primary plastids, 587–88, 587f primary producers, 1248, 1248f primary production, 1252–54 primary shoot meristems, 766, 766f primary spermatocytes, 1087 primary stems, 766, 766f primary structure, of proteins: described, 58–59, 59f and three-dimensional structure, 61–63 primary succession, 1240–41, 1241f primary vascular tissues: characteristics of, 775–76, 775f, 776f development of, 766 primates: Alu sequence in, 452 chromosome structure and number in, 475, 475f digestive systems of, 976 DNA sequence changes in, 530 evolution of, 548–50 jaw size and muscle attachment in, 957, 957f reflexes of, 884 sensory systems of, 933, 941 primer annealing, in PCR, 439f, 440 primer extension, in PCR, 439f, 440 primers: DNA polymerases and, 233f, 234f in PCR, 439, 440 principle of parsimony, 525 prions, 401–3, 402f, 402t probability, in genetics, 368–70 probiotic treatments, 637–38 problem-solving skills, 19–20

proboscis of insects, 722 processivity, 233 process of science (core skill): acetylcholine discovery, 896–98, 897f animal models in physiological studies, 998 animal models of nervous system for, 917 antibiotic decomposition by bacteria, 574–75 Arabidopsis thaliana as model organism in, 762 athletic performance and temperature, 876–79 auxin in phototropism, 788–89, 788f bacterial infection and ulcers, 987–88 blooming of flowers, 846–48, 847f brain structures of musicians vs. nonmusicians, 920–21 Calvin cycle determination, 176–78 cellulose and green algae, 594–95 DNA experiments, 222–23 ecosystem function and species richness, 1283–84 effects of increased carbon dioxide, 1264–64f, 1264–65 equilibrium model of island biogeography, 1246–47 fundamental and realized niches, 1222–24 gene cloning, 435 genetically engineered ABA receptor protein, 831–32 genetic traits and inheritance of sex chromosomes, 361–62 gene transfer studies, 406–8, 407f genome sequencing, 446–48 gut microbiomes, 635–36 hormonal control of apoptosis, 197–99, 198f hypothesis testing in, 15f immune function of Toll protein, 1113– 14f, 1113–15 invasive species, 1150–51, 1151f isolation of insulin, 1071–73 and lateral movement of lipids, 110 leaf breakage and venation, 771–72f, 771–73 limb length in tetrapods, 743–44 “marathon mice”, 962–64 memory and local movement of animals, 1185–86f, 1185–87 model organisms in, 414 modern model of atom, 25–26 multicellularity, 212–13 muscle cell differentiation genes, 427–29 mutagenesis in, 445 mutation experiments, 308–9 natural selection, 463–64, 464f observational learning behavior in invertebrates, 712–14, 713f observation and experimentation in, 18 phylogenetic tree of flightless birds, 527–29 and plant nutrition, 810–11 protein movement in endomembrane system, 92–95f

reproductive isolation in finches, 504–6 ribozyme discovery, 135–36f, 135–37, 136t rotary model of ATP synthase, 157–59 satiety factor in mammals, 1000–1002, 1001f sexual reproduction and harmful mutations, 1086–87 sexual selection in cichlids, 487–89 surfactant for newborns with RDS, 1031–33 survivorship curve, 1207–8 symbiosis and heat stress in plants, 618–19, 619f taxonomic relationships among Protostomia, 697–98 tRNA–ribosomal binding, 254–56 X-ray diffraction, 226 procollagen, 204, 204f producers of organic compounds, 574 production efficiency, 1250–51, 1250f product rule, 369–70 products: defined, 36 of photosynthesis, 170 progesterone: and eukaryotic cell cycle, 328 and reproduction, 1094 synthesis and function of, 1061f, 1080 programmed cell death. See apoptosis. progressive evolution, 400–401 progymnosperms, 666, 666f Proisocrinus ruberrimus, 728f prokaryotes: defined, 9, 10f fossilized, 535 functions and structures of, 78–79, 79f nitrogen fixation by, 573 and oxygen, 572–73 as pathogens, 1109 See also archaea; bacteria prokaryotic cells: binary fission in, 333–34, 334f, 571–72, 571f cell-wall structures of, 568–69, 569f complexity of, 566–67 origins of, 540 shapes of, 567–68 proliferative phase, 1095 prometaphase I (meiosis), 336, 338f prometaphase II (meiosis), 338f prometaphase (mitosis), 331, 332f promiscuous mating systems, 1197, 1197f promoters, 294–95, 294f promoter sequence of transcription, 247, 247f proofreading, 236 prophage, 395 prophase I (meiosis), 336, 338f prophase II (meiosis), 338f prophase (mitosis), 331, 332f proplastids, 97, 98, 383, 383f proprioception, 931 prostaglandins, 934, 1098 prosthetic groups, 134, 153 Protapirus genus, 1175 protease inhibitors, 400

INDEX I-43 in innate immunity, 1112–13 for lactose metabolism, 285–86, 287f in membrane structure, 107, 107f and microbiome function, 627, 628 of mitochondria and chloroplasts, 381, 382f and ncRNAs, 267 olfactory receptor, 944–45f, 944–46 organic molecules from, 971 origin of, on Earth, 75 polypeptides in, 58, 58f primary and three-dimensional structure of, 61–63 and prions, 401–3, 402f, 402t in proteosome, 141–42, 141f in ribosomes, 257–59, 258t, 259 sorting of, in cells, 99–102 sorting of, to organelles, 99–102 structural determinants for, 60–62, 61f structural hierarchy of, 58–60, 59f temperature and structure/function of, 1002 transmembrane (See transmembrane proteins) See also membrane proteins; proteomes protein secretion pathways, 92–95f protein sorting, and non-coding RNAs, 275, 276f protein subunits, 60 Proteobacteria, 565, 568, 575 proteoglycans, 113, 206, 206f proteolysis, 91 proteomes, 283 ATP-binding proteins and, 130–31 defined, 8, 9f, 81 See also proteins proteomics: defined, 8 and evolution, 7–8 proteosomes, 141–42, 141f Proterozoic eon, 538, 541, 543–44 prothoracic glands, 1078–79 prothoracicotropic hormone (PTTH), 1078–79 Protista kingdom, 517 protists, 581–604 competition among, 1228 ecological roles of, 582, 582f in Eukarya, 9, 10f evolution and supergroups of, 584–92, 592t habitats of, 582–83, 583f in microbiome, 623, 623f motility of, 583–84, 583f, 584f nutritional and defensive adaptations of, 593–95f, 593–96 overview, 581–84 reproductive adaptations of, 596–601f, 596–602 SSU rRNA of, 695, 695f summary, 602–3 protobionts, 72–74, 73f, 74f protonephridia, 706, 1045–46, 1045f proton pumps, in plant cells, 820, 829 protons: characteristics of, 28, 29, 29t

defined, 25 of elements, 28, 28f See also atoms proto-oncogenes, mutations in, 316–17, 317f protostomes, 691–92, 691f Protostomia: phylogenetic tree for, 696, 696f taxonomic relationships among, 697–98 Prototheria and protherians, 756, 756f, 1096 protozoans, 2t, 582 proventriculus, in digestive system, 977, 977f proviruses, 395 proximal tubules, 1047, 1049–51, 1049f proximate causes of behavior, 1180 Prusiner, Stanley, 402 Psaronius genus, 546 Pseudoceros bifurcus, 707f pseudocoelomates, 692, 692f pseudocoeloms, 692, 692f of nematodes, 717 of rotifers, 707–9, 708f pseudogenes, 450 Pseudomonas aeruginosa, 578 Pseudomonas syringae, 1157 Pseudomyrmex ferruginea, 1230f pseudopodia, 583–84, 584f, 591 Pseudotriton montanus, 746f PSI and PSII. See photosystems (I and II). Psilocybe genus, 611 Psilotum nudum, 646f, 647f psychoneuroimmunology, 1127 PTC (phenylthiocarbamide), 481 pteridophytes: life cycle of, 653, 654f overview, 645–47, 646f, 647f Pterois volitans, 741f pterosaurs, 965 PTH (parathyroid hormone), 953, 966, 1074–75, 1075f PTTH (prothoracicotropic hormone), 1078–79 puberty: and endocrine systems, 1062, 1077, 1080 and nutrition, 1080, 1104 and reproduction, 1092 public health issues: animal reproduction and, 1104–6, 1105f and circulatory system, 1037–38, 1038f and digestive systems, 985–88 and endocrine systems, 1080–81 and energy balance, 1006–7, 1007f and excretory systems, 1054–56, 1055f hemorrhage, 1144–45 and immune systems, 1126–29, 1129f and muscular-skeletal systems, 966–67, 966f, 967f and nervous system, 922–23, 922t, 923f and nervous system cells, 900–902, 900t, 901f and respiratory systems, 1038–40, 1039f, 1040f and sensory systems, 947–48, 948f pulmonary arteries, 1017

pulmonary circulation, 1012, 1096 pulse-chase experiments, 92, 92–93f pulvini, 796, 796f, 797 Puma concolor, 493, 1290f, 1291 pumps: active transport, 121 thoraco-abdominal, 1138, 1139f punctuated equilibrium, 508–9 Pundamilia nyererei, 487f Pundamilia pundamilia, 487f Punnett, Reginald, 353, 366, 384, 386 Punnett square, 353, 480 pupae, 418, 419f pupation, hormones for, 1079, 1079f pupil, of eye, 935, 937 purification, of DNA, 222–23 purified proteins, chemiosmotic research using, 155–56, 156f purines, 64, 224, 225f purple bacteria, 99 purple loosestrife, 1275, 1276f P wave, 1019 Pycnogonida, 720 pygmy sea horse, 1225f pyramid of biomass, 1251f, 1252 pyramid of energy, 1251f, 1252 pyramid of numbers, 1251–52, 1251f Pyrenean ibex, 1292 pyrimidines, 64, 224, 225f pyruvate: in catabolic reaction, 137 in cellular respiration, 146f, 147, 150–51, 150f in fermentation, 160, 161f in glycolysis, 146–49 pyruvate dehydrogenase, 150, 150f

Q

QRS wave, 1019 quadrats, 1202, 1202f quadriceps, 954 quahog clams, 711f quantitative analysis, of overexploitation, 1274–75, 1275f quantitative reasoning (core skill): carbon uptake by sporophytes, 657–58 cardiac output, resistance, and blood pressure, 1024 developmental mutants, 419 dominance, 363 energy expenditure for flying, 965–66 genetic drift, 489 insulin concentration, 38–39 mark-recapture technique, 1203 mutagenesis, 445 phyla in microbiome, 625 predatory behavior, 1187 surface area/volume of cells, 83 quantitative traits, 367 Quaternary period, 547 quaternary structure, of proteins, 59f, 60 Quercus suber, 777 quiescent center, 778 quinine, 1284 Quinn, Jim, 1289 quorum sensing, 568

INDEX

proteases: in catabolic reactions, 137 and cell functions, 91 defined, 200, 223 digestion of proteins by, 982, 982f HIV drugs targeting, 400 organic molecule recycling in, 141 protected areas, 1287–88, 1288f protection: for central nervous system, 909, 910f and leaf surface, 773–74, 774f for lungs, 1028, 1029 secondary metabolites for, 678–81, 679f, 680f protective attributes. See defenses. protective roles, of fungi, 618 protein coat, in exocytosis and endocytosis, 123, 123f, 124f protein-encoding genes: characteristics of organisms and products of, 247 defined, 244 and microbiome functions, 627, 627f, 628f and mRNA, 246 point mutations in, 305, 305t promotors and regulatory elements in, 294–95, 294f regulation of, 284–85, 285f transcriptional activation of, 298, 299f transcription of, 247–48, 247f, 295, 295f protein kinase A (PKA): and cell communication, 192–94, 193f and learning/memory, 918 protein kinases: cascades of, 190–92, 191f enzyme-linked receptors, 188, 188f protein metabolism, 159, 159f protein phosphatases, 194 protein-protein interactions, 60, 61f, 78 proteins, 56–64, 246 in absorptive state, 992 and alternative splicing, 299–300, 300f amino acids in, 56–58, 57f and association of membranes, 107–9, 108f ATP-using, 130–31, 131t attachment of carbohydrates to, 112–13, 113f of bacterial pathogens, 578, 578f categories and functions of, 56t and cell characteristics, 81–82 complement, 1112 complexity of DNA vs., 221 defined, 5, 56, 58 digestion of, 977–78, 978f, 982, 982f DNA replication, 232, 232f, 233f dominance and function of, 363, 363f in endomembrane system, 92–95f in endoplasmic reticulum, 90–91, 90f eukaryotic transcription, 249, 249f extracellular matrix, 203f, 204t functional domains of, 63, 64f and glycogenolysis and gluconeogenesis, 994 and homeotic genes, 423, 423f

I-44 INDEX

R

INDEX

rabbits, 1211, 1217, 1218f learning and memory in, 917 sensory systems of, 943 racing stripe flatworm, 707f Racker, Efraim, 155–56 radial cleavage, 691f, 692 radial loop domains, 239, 239f, 240f radial patterns, 415 radial symmetry: of flowers, 845–46 of plants, 764–65, 765f radiation, heat exchange by, 1003f, 1004 radicles, 852, 853f radio collars, 1203 radioisotopes: defined, 29, 30f fossil dating with, 536–37 and photosynthesis, 176 Radiolaria, 591, 591f, 592t radiometric dating, 536–37 radishes, 794 radula, of mollusks, 710 Rafflesia arnoldii, 1228, 1228f Raf protein kinase, 191 RAG-1 and RAG-2 enzymes, 1120 ragweed (genus Ambrosia), 849 rain, acid, 1160 rainfall, and buffalo density, 1158f rain forests: as biomes, 1165, 1165f, 1166, 1166f mycorrhizal associations in, 812, 812f soils, 805, 806f transpiration in, 829, 829f rain shadows, 1162, 1163f ramie, 776 Ramosmania rodriguesii, 1280–81 RAMs. See root apical meristems. Rana pipiens, 328, 497f Rana sylvatica, 745, 745f Rana utricularia, 497f random coiled regions, 60 random dispersion, 1204, 1204f randomized control trial (RCT), 1033 random mating, 492 random sampling error, 369 Rangifer tarandus, 755f Ranunculus adoneus, 782, 782f Raphus cucullatus, 1272 rapid phase (response to hemorrhage), 1133–39, 1144t baroreceptors in, 1133–37, 1134f, 1136–37f nervous system in, 1138, 1138f respiratory system in, 1138, 1139f raptors, sensory systems of, 941 Ras protein, 191 Ras protein, and cancer, 316, 316f rate-limiting steps, 139–40 rats: hippocampus of, 915 nephron of, 1049f operant conditioning of, 1182 rattlesnakes, skeletal muscle fibers of, 961 Ray, John, 459, 516 ray-finned fishes, 738, 741, 741f

rays, 739 sensory systems of, 934 species interaction with, 1217 Rb protein, 319, 319f, 848 RBR protein, 774 RCT (randomized control trial), 1033 RDS (respiratory distress syndrome), 1031–33 reabsorption: in distal tubule and cortical collecting duct, 1051–53, 1053f as excretory system function, 1045, 1045f in loop of Henle, 1050–51, 1050f in proximal tubules, 1049–50, 1049f reactants, defined, 36 reaction centers, 169 reading frames, 253 realized niche, 1222–24 receptacles of flowers, 672 receptor activation, in plant cell signaling, 784f receptor-mediated endocytosis, 123, 124f, 210 receptor potential, 926 receptors: activation of, 35, 186–91f, 784f, 785 binding of signal molecules to, 187 and cell communication, 187–90 conformational changes in, 187 defined, 183 and differential gene regulation, 196 and evolution of hormones, 1076–77 immunoglobulins as, 1118–20, 1119f, 1120f nuclear, 63, 64f plant cell signaling, 784–85, 785f See also sensory systems receptor tyrosine kinases, 190–92, 191f recessive alleles, and inbreeding, 493 recessive traits: family pedigree for, 358, 358f and law of segregation, 351 X-linked, 360–61 recipient cells, in conjugation, 408–9, 409f reciprocal altruism, 1196 reciprocal cross, 383 reciprocal translocations, 342, 343f recirculation, of lymphocytes, 1115–16 recombinant bacteria. See bacteria. recombinant DNA technology, 434 See also cloning recombinant human growth hormone, 1080 recombinant offspring, 386–87, 387f recombinant vectors: defined, 437 in gene cloning, 435–38, 436f, 436t, 437f recombination, and immunoglobulin structure, 1119–11120, 1120f recombination-activating genes, 1120 recombination frequency, 387–88, 388f recreational drugs, and neurotransmission, 900t rectum, 980 Recurvirostra Americana, 752f

recycling: of ATP, 130, 130f of organelles, 142, 142f of organic molecules, 137, 141–42, 141f, 142f red algae: characteristics of, 587, 587f in intertidal zone, 1242–43, 1243f and light, 1158, 1159f origins of, 543 and plant behavior, 787 red blood cells, 1015 and inheritance patterns, 365, 365t intracellular fluid volume and shape of, 873, 873f in sickle cell disease, 305, 306f red carpenter ant, 1230f red clover, pea aphids on, 507 red-cockaded woodpecker, 1291 red-eyed tree frog, 746f red-green color blindness, 939 red kangaroos, 951 red-light receptors, 793, 793f red mangrove (Rhizophora mangle), 1246–47 red muscle fibers, 961 See also oxidative fibers redox reactions. See oxidation-reduction (redox) reactions. reducing-atmosphere hypothesis, 70–71, 70f reduction, in redox reactions, 138 reduction and carbohydrate production phase (Calvin cycle), 175, 175f, 176 reductionism, 13 redundancy hypothesis, 1281, 1282, 1282f reflex: baroreceptor, 1133–35, 1134f breathing, 1138, 1139f gill-withdrawal, 917–18, 917f patellar tendon, 884 reflex arcs, 884, 885f refractory periods, action potential, 890 Regan, Tom, 1286 regeneration, 1085, 1085f regeneration of RuBP phase (Calvin cycle), 175, 175f, 176 regressive evolution, 401 regular flowers, 845 regulation: of absorptive/postabsorptive states, 994–97, 995f, 997f of appetite, 1073 of body temperature, 1002–6 of collagen synthesis, 205–6 of digestion, 984–85, 985f feedforward, 870, 871f of glycolysis, 148 of metabolic pathways, 139–40, 140f of muscle contraction, 958, 959f of neurons, 898–99, 899f of organ systems, 864 of oxidative phosphorylation, 153, 155 of potassium ions, 1075–76 of sodium ions, 1075–76, 1076f of transpiration, 829–31, 830f See also gene regulation

regulatory elements, 294–95, 295f regulatory sequences, 247f, 248, 285 regulatory T cells, 1117 regulatory transcription factors, 285, 286f rehabilitation of habitats, 1291, 1291f Reich, David, 550 reindeer, 755f reintroduction, of species, 1292, 1292f rejection, of transplanted kidney, 1056 relative abundance, of species, 1238–39 relative refractory period, 890 relative water content (RWC), 822, 822f relay proteins, 191 release factors, 263 release (step in viral reproductive cycle), 397f, 398 Remingtonocetus genus, 466 renal corpuscles, 1047, 1049f renal cortex, 1047, 1050, 1051 renal failure, 1054–55 renal medulla, 1047, 1050–51 renal pelvis, 1047 renal tubule, 1047, 1048 renin, 1140 repeatability, of experiments, 16 Repenomamus genus, 752 repetitive sequences: characteristics of, 452, 452f and genome sizes, 449–50, 449f replica plating, 308, 309 replication, 1153 DNA (See DNA replication) of genetic material, 221 replication forks, in DNA replication, 231, 232, 232f repolarization phase (action potential), 889–90, 890f representative habitats, 1287, 1288f repressible operons, 294 repressors: eukaryotic, of transcription, 294–95, 296f of lac operon, 286–91 and plants, 785 and small effector molecules, 285, 286f reproduction: of animals (See animal reproduction) of archaea, 571–72, 571f asexual (See asexual reproduction) of bacteria, 404–6, 405f, 571–72, 571f, 572f defined, 1084 of fungi, 609–11 and nutrition, 1080 of plants (See plant reproduction) of protists, 596–601f, 596–602 secondary metabolites for, 678–81, 679f, 680f sexual (See sexual reproduction) sexual selection, 485–87 in sponges, 704 of viruses, 395–401 reproductive isolation: as characteristic of species, 498 in finches, 504–6 mechanisms of, 499–502 reproductive strategies, 1204, 1205f

reproductive success, 482 See also natural selection reproductive systems: after hemorrhage, 1143 of flowering plants, 762 of humans, 1090–95 viral diseases of, 393f reptiles: body temperature of, 1003 characteristics of, 747–49 circulatory system of, 1012, 1023 cleavage-stage embryos of, 1100, 1100f digestive system of, 975, 977 endoskeletons of, 952 energy balance for, 999 locomotion by, 964 nitrogenous wastes from, 1044 origins of, 546 as paraphyletic group, 521 reproduction in, 1085 sensory systems of, 941 shared derived characters of amphibians, lobe-finned fish and, 736 resetting step, in cross-bridge cycle, 957, 958f resistance exercise, 961, 962 resistance genes (R genes), 798 resistance plasmids, 404 resistance (R): and arteriole radius, 1023 as factor in blood pressure, 1023–24, 1023t, 1024f relationship of blood pressure, blood flow and, 1022–23 resolution, in microscopy, 75, 76, 76f resonance energy transfer, 168, 172 resource-based mutualism, 1229–30, 1230f resource partitioning, 1221, 1221f resource prediction, 1194 resources: communication about, 1192, 1192f and competition, 1218–19, 1219f and population growth, 1210–12 respiration: aerobic respiration, 146 cellular (See cellular respiration) defined, 146, 1010 ion and water exchanges in, 874–75, 875f See also glycolysis respiratory center, 1036–37, 1037f respiratory chain, 153 See also electron transport chains (ETC) respiratory diseases, 1038 respiratory distress syndrome (RDS), 1031–33 respiratory pigments, and oxygen, 1034, 1034f respiratory pump, 1138, 1138f respiratory systems, 1024–42 defined, 1010 and gas properties, 1024–25 and gas transport in blood, 1034–36, 1035f, 1036f

of insects and mammals, 865–66, 866f of mammals, 1028–33, 1029f, 1032–33f public health issues related to, 1038– 40, 1039f, 1040f in rapid phase of response to hemorrhage, 1138, 1139f in response to altitude change, 1143 structure and function of, 865–66, 866f, 1028–33, 1029f, 1032–33f summary, 1041–42 types of, 1025–27f, 1025–28 ventilation control, 1036–37, 1037f, 1037t respiratory tract, viral diseases of, 393f resting membrane potential, 885–86, 886f, 890f restoration of habitat, 1287, 1291, 1291f rest-or-digest response, 910 restriction enzymes (endonucleases), in gene cloning, 435–36, 436f, 436t restriction point, 327 reticular formation, 912 reticularis, 1068 reticulum, 978 retina: cellular organization of, 941, 941f and glaucoma, 947 of single-lens eye, 935, 937 retinal, 47, 938, 940 retrotransposons, 454, 454f retroviral insertion, 316–17, 317f retroviruses, 395 reuptake, 893 reverse primers, 440 reverse transcriptase, 395 in HIV infection, 1128 and transposition, 454 reverse transcription, 75 reversible inhibitors, 133f, 134 reversible reactions, 128 revised models, 19, 19f R factors, 404 R genes (resistance genes), 798 rhabdoms, 935 Rhagoletis pomenella, 506–7 Rheinberger, Hans-Jörg, 259 rheotaxis, 1185 rhesus monkeys, neurogenesis in, 918, 919 rheumatoid arthritis, 1125 Rhizaria supergroup, 589, 589f, 591, 591f Rhizobium genus and rhizobia, 565, 573, 812–14, 813f, 814f, 1267 Rhizoctonia solani, 609f rhizomes, 777 Rhizophora mangle, 1246–47 Rhizopus stolonifer, 611–13, 613f rhizosphere, 633 rhododendrons, 1159 Rhodophyta, 587, 587f, 592t rhythm method, 1106 ribonuclease: primary structure of, 59, 59f three-dimensional structure of, 61–63, 62f–63f ribonuclease P (RNase P), 135–36f, 135–37 ribonucleic acid. See RNA. ribonucleotides, 65f

ribose, 50, 65 ribosomal-binding site, 252f ribosomal RNA. See rRNA. ribosomal subunits, 89 evolutionary conservation of, 259–60, 260f and gene expression, 259, 259f in initiation stage of translation, 260–61, 260f ribosomes: anabolism by, 84 of animal cells, 80f composition of, 257–59, 258t, 259 in elongation stage of translation, 262–63, 262f function of, 89 of plant cells, 81f of prokaryotic cells, 78 tRNA binding to, 254–56 ribozymes, 251 discovery of, 135–36f, 135–37, 136t ncRNAs as, 267 RNA as, 73 ribulose bisphosphate (RuBP): in Calvin cycle, 175, 175f, 176 in photorespiration, 178 rice (Oryza sativa), 683, 790, 1285, 1285f Richmond, Barry, 1182 rickets, 966, 966f Ricklefs, Robert, 1238, 1245 ring canal, 727 ring worms. See Annelida and annelids. Riordan, John, 16 RISC (RNA-induced silencing complex), 271, 273, 274f, 275 river beauty, 1241 rivet hypothesis, 1282 RNAi. See RNA interference. RNA-induced silencing complex (RISC), 271, 273, 274f, 275 RNA interference (RNAi): and flower fragrance, 845 and non-coding RNAs, 271–75 RNA modification, 247 in eukaryotes, 249–51, 250f, 251f eukaryotic gene regulation for, 299– 301, 300f, 300t, 301f in ncRNAs, 270–75 RNA polymerases: and gene regulation, 295 in transcription, 248–49, 248f, 249f RNA primers, 237f RNA (ribonucleic acid), 225f as catalyst, 135–36f, 135–37, 137t defined, 5, 64 and gene expression (See gene expression) molecular structure of, 65 (See also ribonuclease) non-coding (See non-coding RNAs [ncRNAs]) nucleotides in, 64, 65f origin of, on Earth, 72, 73 ribonuclease in, 59 in RNA world, 73–75 synthetic, 254–55 from transcription, 248–49, 248f, 249f

viral, 393 and viroids, 401, 401f RNase, 223 RNase P (ribonuclease P), 135–36f, 135–37 RNA splicing, 251 See also splicing RNA transcription. See transcription. RNA triplets, and tRNA–ribosomal binding, 254–56 RNA world, 73–75, 74f Rocha, Roberta, 1272 rocks, weathering of, 806 Rocky Mountain goat, 1203f Rocky Mountains, Colorado, 1170, 1170f Rodbell, Martin, 188, 189 Rodhocetus genus, 466 rods: structure of, 937, 937f, 938, 938f visual pigments in, 938, 938f Roland, Jen, 1154 root apical meristems (RAMs): defined, 765 in embryonic development, 430 growth and tissue specialization from, 777–78, 777f stem cells in, 767–68 root caps, 777, 778, 778f root cortex, 778 root-hair membranes, 820, 821f root hairs: and plant nutrition, 813, 814f and root growth, 778, 779f root pressure, 828, 828f roots and root systems: adaptations of, 777–80, 778f, 779f of cycads, 667, 667f defined, 646, 761 host-associated microbiomes in, 632–33, 633f internal growth and specialization in, 777–79, 778f, 779f of lycophytes and pteridophytes, 645, 646 modified roots, 779–80, 779f and plant behavior, 794, 795, 796f and plant hormones, 785, 791 and plant nutrition, 809, 814f and soil (See soils) structure and development of, 767 and succession, 1243 symplastic and apoplastic transport in, 823–24, 823f vascular system (See vascular systems of plants; vascular tissues of plants) root-shoot axis, 415 root sprouts, 855 Roseate spoonbill, 752f rose pogonia, 1231 roses, 794 rosy periwinkle, 1284 rotary machine model, for ATP synthase, 156–59 rotation: of Earth, 1161–62, 1162f by transmembrane proteins, 110–11, 111f vestibular systems’ detection of, 932f

INDEX

INDEX I-45

I-46 INDEX Rothenbuhler, W. C., 1181–82 Rothschild’s orchid, 1274, 1274f Rotifera and rotifers, 695t, 707–9, 708f, 731f roughage. See cellulose. rough endoplasmic reticulum (rough ER), 80f, 81f, 90 round dance, 1192, 1192f round window, 929, 930 roundworms, 717, 731f See also Nematoda and nematodes Rous, Peyton, 317 Rous sarcoma virus (RSV), 317–18 Rowland, Frank, 1257 rRNA (ribosomal RNA), 247 evolution of, 259–60, 260f in ribosomes, 257–59, 258t, 259 r-selected species, 1213–14, 1214f, 1214t RSV (Rous sarcoma virus), 317–18 rubisco: in Calvin cycle, 175f, 176 in photorespiration, 178 RuBP. See ribulose bisphosphate. Ruffini corpuscles, 927, 928f rumen, 978 ruminants, stomach specialization for, 978, 978f Ruminococcus gnavus, 637 Runcaria heinzelinii, 661–62, 661f Ruska, Ernst, 76 rusts, 616, 617f Rutherford, Ernest, 25–26 Rwanda, 1293 RWC (relative water content), 822, 822f

S

INDEX

sable antelope, 1225f Saccharomyces cerevisiae, 620 alternative splicing and complexity of, 301 asexual reproduction by, 610f genome projects with, 458 mitotic cell division in, 330 Saccharum officinarum, 1158 saccule, 932 Sack, Lawren, 771–72f, 771–73 saguaro cactus, 676f Sahelanthropus tchadensis, 547 salamanders, 745–46, 746f, 882 salicylic acid, 127 saliva, in digestive system, 976 salivation: classical conditioning of, 1182 feedforward regulation of, 870 salmon, 1285f, 1286 Salmonella genus, 985 Salmonella enterica, 565, 570f, 577 Salmonella typhimurium, 311–12, 311f, 411 salmonellosis, 577 saltatory conduction, 891f, 892 salt concentrations, 1158–59, 1159f salt glands, 876, 876f salt marshes, 1253–54, 1254f salt marsh sedge, 1252f salts. See sodium chloride.

saltwater consumption. See seawater, drinking of. saltwater fishes: and ecology, 1158–59 water and ion homeostasis for, 874f, 875 See also fishes Salvelinus namaycush, 1276, 1276f Salvini-Plawen, Luitfried von, 513 SAM. See shoot apical meristems (SAM). sand dollars, 727 sand dunes, 1242 sandpiper, 1198 sandstone, 536 sand tiger sharks, 739f sandy soil, 806–7, 806f, 807f Sanger, Frederick, 440 SA node. See sinoatrial node. sarcomas, 317 sarcomeres, 955 sarcoplasmic reticulum, 958, 959f Sarcopterygii, 738, 741–42, 742f SAR (systemic acquired response), 798, 799f SAS-6 proteins, 87f satiety, 999 satiety factor, in mammals, 1000–1002, 1001f saturated fatty acids, 53, 53f Saurischia and saurischians, 749, 749f savanna, 1168, 1168f SA/V (surface area/volume ratio), 866 sawfly (Cimbex axillaris), 422 Sayornis phoebe, 1155 scaffolds, ncRNAs as, 267 scale of ecology, 1150–52, 1150f, 1151f scanning electron microscopy (SEM), 70, 78f scarlet king snake, 1225f, 1226 scent trails, 1191 Schimper, Andreas, 98 Schistosoma genus, 707 schistosomiasis, 707 Schlaug, Gottfried, 920–21 Schleiden, Matthias, 69 Schmithorst, Vincent, 920, 921 Schwann, Theodor, 69 Schwann cells, 883 science, defined, 12 science and society (core skill): beef tapeworms, 707 chemistry for disease diagnosis, 30 climate change and precipitation patterns, 1262 corn domestication, 683 cyanobacterial blooms, 561 ergots, 611 habitat restoration, 1291 heart and blood vessel diseases, 1038 heart disease treatments, 1039 and HIV infection rate, 1128 human impact on species populations, 1272 insulin and hormonal treatments for disease, 1071 lung disease, 1040 microbiomes, 629

MRI imaging in disease treatment/ prevention, 901 mutagenicity testing, 311 obesity, 1007 species interaction, 1228 spiders as indicators of contamination, 721 sugar-maple tapping, 826, 826f threatened species and human impact, 1269 total fertility rates, 1259 viral illness transmission, 1124 viruses, 393 visual disorder treatments, 948 scientific method, 13, 15f See also process of science (core skill) scientific models (models), 18–19 sclera, 937 sclereids, 766 sclerenchyma tissues and cells, 216, 766, 776 Scolopax minor, 942, 942f Scolopendra heros, 721, 721f Scorpionida and scorpions, 720–21 Scotto, Pietro, 712, 714 SC (self-compatible) plants, 849 Scyliorhinus canicula, 739f Scyphozoa, 704, 704t sea cucumbers, 727, 728f sea hare, 917 sea horses, 1226 sea lampreys, 737f, 1275–76, 1276f sea levels, and global warming, 1261–62 sea lilies, 727, 728f seals, energy balance for, 1004 sea raven (Hemitripterus americanus), 468, 469f sea slugs: cellular changes with memory in, 918, 918f gill-withdrawal reflex of, 917, 917f seasonal iteroparity, 1204, 1205f seasonality, 1161–62, 1162f sea stars, 727, 728f characteristics of, 727–28, 727f, 728f, 728t, 731f nervous systems of, 905 regeneration in, 1085, 1085f sea turtles, 1185, 1188 sea urchins, 727, 728f characteristics of, 727–28, 727f, 728f, 728t, 731f gametic isolation in, 500 reproduction in, 1089, 1090 seawater, drinking of, 876 seaweeds, 583 See also algae secondary active transport, 121 secondary amenorrhea, 1084, 1105 secondary carnivores, 1248, 1248f secondary cell walls, 207f, 208 secondary consumers, 1248, 1248f secondary endosymbiosis, 588–89, 588f, 589f secondary growth, of flowering plants, 765t, 766

secondary immune response, 1125, 1126f secondary lymphoid organs, 1115, 1116f secondary meristems, 776–77, 776f secondary metabolites: of angiosperms, 678–81, 679f, 680f as plant defense, 1227, 1227f as plant response to herbivores, 797 secondary oocytes, 1089, 1093 secondary phase (response to hemorrhage), 1140–44, 1144t endocrine and urinary systems in, 1140, 1141f hematocrit changes in, 1142–43, 1143f organ systems in, 1143–44, 1143t water movement in, 1140, 1142, 1142f secondary phloem, 776 secondary plastids, 588–89, 589f secondary sex characteristics: and endocrine system, 1080 sexual selection of, 487 secondary spermatocytes, 1087 secondary structure, of proteins, 59–60, 59f secondary succession, 1241 secondary vascular tissues, 776–77, 776f, 777f secondary xylem, 776–77, 779 See also wood second law of thermodynamics, 128 second messengers: and cell communication, 192–95 of plant cell signaling, 784f, 785 signal amplification and speed with, 194–95, 195f secretin, 985 secretion: as excretory system function, 1045, 1045f of insect wastes, 1046–47, 1046f of potassium ions, 1051–52 of vertebrate wastes, 1047 secretory activity, digestive, 984–85 secretory pathway, 91, 91f secretory phase, ovarian cycle, 1095 secretory vesicles, 91, 1059 Sedentaria, 715, 716f sedimentary rocks, 536 seed coats, 659, 660f, 852 seed dispersal: by angiosperms, 677–78, 678f, 682–83, 683f coevolution of, 682–83, 683f and dispersive mutualism, 1231, 1231f fruit for, 843, 843f systems for, 853 seedless vascular plants, 664, 665f See also Lycopodiophyta and lycophytes; pteridophytes seedlings: apical-basal polarity in, 765f in embryo development, 430f and ethylene, 791–92, 792f and fertilization, 843 of flowering plants, 761–63 growth patterns of, 854–55, 854f

seed plant diversity, 664–85 angiosperm evolution and diversity, 670–83, 682f, 682t, 683f coevolution in, 681–83, 682f, 682t, 683f gymnosperm evolution and diversity, 665–70 human influences on, 683, 683f overview, 664–65, 665f, 665t summary, 684 seed plants: body plan of, 415, 415f gametophyte and sporophyte size in, 340 innovations of, 665f maternal inheritance in, 383 origin of, 545 overview, 647–48, 647f, 648f and phylogenetic tree for seedless vascular plants, 664, 665f sporophytes and gametophytes of, 653, 653f See also flowering plants; gymnosperms seeds: of angiosperms, 676–77, 676f from apomixis, 856 coats of (See seed coats) and commensalism, 1231, 1231f of conifers, 668, 669f and cytokinins, 790 defined, 647, 761 descent with modification for, 660–62, 661f, 662f dispersal of (See seed dispersal) embryos in, 851–52, 852f, 853f embryos of (See plant embryos) evolution of, 658–62, 660f, 661f factors in germination of, 853–55, 854f fertilization and development of, 842–43, 843f in flowering plant life cycle, 760–64, 764t germination of, 843, 853–55, 854f and life history strategies, 1213, 1214f phytochrome effects on, 793–94, 794f seed coats (See seed coats) seed-to-seed lifetime, 762t, 763, 764 Seehausen, Ole, 487–89, 508 segmentation: of bilateria, 693–94, 693f, 694f and homeotic genes, 422–24 and Hox gene, 694, 695f in invertebrates, 714, 715f in neurulation, 1103–4, 1103f in pattern formation, 417 segmentation genes, 420–22, 421f, 422f segmented worms, 714–16, 715f, 716f, 731f, 905 See also Annelida and annelids segment-polarity genes, 421, 421f, 422 segregation, law of, 351–53, 352f, 356, 356f sei whales, 1272 Selaginella moellendorffii, 648 selectable markers, 437 selection, forms of. See natural selection; selective breeding.

selective breeding, 469–71 selective permeability, 113 selective serotonin reuptake inhibitors (SSRIs), 901 self-compatible plants (SC), 849 self-fertilization, 350, 351, 351f self-incompatible plants (SI), 849, 850f selfish herd, 1193 selfishness, 1193–94, 1194f self molecules: and adaptive immunity, 1124–25 antigens complexed with, 1121–23, 1122f self-pollination, 841 self-replication, and protobionts, 72 self-splicing, 251 semelparity, 1204, 1205f semen, 1091 semiautonomous organelles, 96–99 chloroplasts, 97–99 mitochondria, 97–99 systems biology approach to, 102, 103f Semibalanus balanoides, 1222–24 semicircular canals, 932 semiconservative mechanism, 228, 229f semifluid membranes, 109, 110f semilunar valves, 1017, 1018, 1018f seminiferous tubules, 1090, 1091 semiterrestrial lifestyle, of amphibians, 744–46 Semnopithecus entellus, 1194, 1194f SEM (scanning electron microscopy), 70, 78f Senebier, Jean, 164–65 sensation, 925–27, 926f, 927f senses, defined, 925 sensitive plant (Mimosa pudica), 782, 783f, 796, 796f sensitization, to allergens, 1127 sensors, 868, 869, 1133 See also receptors sensory hairs, 942–43, 943f sensory inputs: in cerebral cortex, 915f and midbrain, 910, 912 sensory neurons, 883–84, 884f sensory receptors: defined, 926, 926f structural similarities in, 947 types of, 926–27 See also specific types of receptors sensory systems, 925–50 chemoreception, 942–47 of chondrichthyans, 740 CNS processes of, 926–27 electromagnetic reception, 934, 934f and endocrine system, 1062 mechanoreception, 927–33 and nervous system, 905, 906f overview, 925–26, 926f, 927f photoreception, 934–42 public health issues related to, 947–48, 948f stimulus strength, 926, 927f summary, 948–49 thermoception and nociception, 933–34

sensory transduction, 925, 926 sepals: defined, 672, 841 developmental genetics of, 431 septal pores, of ascomycetes and basidiomycetes, 613, 614f septum(--a), 607 Sequoiadendron giganteum, 202, 665, 1214 Sequoia sempervirens, 1214–15, 1215f sequoia trees, 202 serine, 140 serine/threonine kinases, 188 serotonin, 194, 195, 195f, 895, 901 Serratia marcescens, 260 Sertoli cells, 1091, 1092 setae, of annelids, 715 Setaria faberi, 1242 Setophaga ruticilla, 1232 set point, 868 sex chromosomes, 325 inheritance related to, 359–62 Morgan’s experiments on, 361–62 sex characteristics and, 359–60, 360f sex determination, 359–60, 360f sex-linked genes, 360 sex pili, 408–9, 409f sex steroids, 1077, 1079–80 sexual dimorphism, 485, 1198, 1198–99f sexual life cycles. See sexual reproduction. sexually transmitted diseases (STDs), 1104 sexual reproduction: in animals, 1085–87 (See also animal reproduction) defined, 1084 elimination of harmful mutations with, 1086–87 in eukaryotic cell cycle, 340–41, 341f in flowering plants, 839–40 (See also specific processes) in fungi, 609–15, 610f, 611f, 613f, 615f, 616f in plants, 761, 761f in protists, 596–600f speciation and, 497 in sponges, 704 sexual selection: in population genetics, 485–89 and sympatric speciation, 508 sgRNA (single guide RNA), 442, 443, 444f shade, 803, 803f shade leaves, 803, 803f shading responses, 794 Shakespeare, William, 840 shale, 536 Shannon diversity index, 1238–40, 1239t shared derived characters: on cladograms, 523–25 defined, 523 of reptiles, amphibians, and lobe-finned fish, 736 shared primitive characters, 523, 524f sharks, 739 as osmoconformers, 879 sensory systems of, 934

species interactions with, 1217 shattering of wheat, 683 sheep, survivorship curve for, 1207–8 shells: of amniotic eggs, 746, 747f of mollusks, 710, 711f Shigella genus, 985 shingles, 399 shivering thermogenesis, 1006 shock: defined, 1131 positive feedback cycle for, 1145, 1145f shoot apical meristems (SAMs): defined, 765 in embryonic development, 430 flower development from, 841 and plant behavior, 791 and plant growth, 765–67 radial symmetry in, 765f and shoot structure, 770 shoots and shoot systems, 769–77 defined, 761 and developmental genetics, 429, 429f of flowering plants, 769–72f, 769–77 growth of, 762 and hormones, 770 and leaf modifications, 774–75, 775f leaf shapes, 770–71, 771f leaf surfaces, 773–74, 774f leaf venation, 771–72f, 771–73 negative gravitropism in, 794, 795f stem modifications, 777 stem vascular systems, 775–77 structure of, 769–70, 769f vascular systems (See vascular systems of plants; vascular tissues of plants) shore crabs, 1189, 1189f short-day plants, 794 short-interfering RNAs (siRNAs), 845 SHORT ROOT, 779 short stature, 1077, 1080 short-term memory, 918, 918f shotgun DNA sequencing, 446–48, 625 “Should Trees Have Standing?” (Stone), 1286 shrews: cardiac output of, 1023 sensory systems of, 931 shrimp, 724–26, 725f Shubin, Neil, 465 Siamese fighting fish, 741 sickle cell disease: heterozygote advantage for carriers of, 485 mutations causing, 305, 306f population genetics for, 477 side chains, amino acid, 57–58, 57f, 60 sieve plates and sieve plate pores, 835 sieve-tube elements, 776, 834–36, 834f sigma factor, 248 signal amplification, 194–95, 195f signaling molecules. See cell communication. signal recognition particles (SRPs), 101, 101f, 275, 276f signals: at chemical synapses, 893

INDEX

INDEX I-47

I-48 INDEX

INDEX

signals, continued defined, 183 in mammalian ear, 930, 930f for nervous system cells, 882–83, 882f, 883f signal transduction pathways: in apoptosis, 199–200, 199f and cancer, 314–16, 315f, 316t in cell signaling, 186, 186f and cellular responses, 190–95, 191f, 193–95f defined, 96 and differential gene regulation, 196 hormones in, 1062 and multicellularity, 209 in photoreceptors, 940–41, 940f and plant behavior, 784f signal transmission, of electrical signals, 891 sign stimuli, 1181, 1182f silencers, 295 silent mutations, 305 silt, 806–7, 806f Silurian period, 544, 738 silvertip shark, 739f Simberloff, Daniel, 1245–47 simple diffusion: in animal bodies, 872 and membranes, 113, 114f phospholipid bilayer as barrier to, 114, 114f in plant cells, 819 simple epithelial tissue, 862 simple leaves, 770, 770f See also plant leaves simple Mendelian inheritance, 363f See also Mendelian inheritance simple translocations, 342, 343f Simpson, George Gaylord, 499 Singer, S. Jonathan, 107 single circulation, 1012, 1013f single-factor crosses, 351–52, 352f single guide RNA (sgRNA), 442, 443, 444f single-lens eye, 935–37, 936f single-nucleotide polymorphisms (SNPs), 478–79, 557–58 single-species approach, 1290–91, 1290f single-strand binding proteins, 232, 232f Sinha, Neelima, 855 sinoatrial (SA) node, 1017–19, 1134 Siphonops annulatus, 746f siRNAs (short-interfering RNAs), 845 siRNAs (small-interfering RNAs), 271, 273, 274f, 275 SI (self-incompatible) plants, 849, 850f sister chromatids, 325 in meiosis II, 337 production of, 330, 330f Sitka spruce trees (Picea sitchensis), 1241, 1242f 16S rRNA: in amplicon analysis of microbiome, 625, 626f molecular features of gene for, 498 size, of solutes, 114 size-exclusion chromatography, 62, 63 skates, 739, 1217

skeletal muscle, 953–60 adaptation of, 961–62 in animal bodies, 860, 861f cell response to epinephrine in, 192–93, 194f and circulatory system, 1022 cross-bridge cycling in, 957–58, 958f electrical stimulation of, 960, 960f evolution of myosin, 956–57 excitation-contraction coupling, 958, 959f fibers, 960–64, 962t, 963–64f force generation in, 955–60 functions of, 954, 954f glucose consumption by, 992 heat production and activity of, 1006 and metabolic rate, 998 and muscular dystrophy, 967 myofibril structure in, 955, 955f overdevelopment of, 967, 967f regulation of contraction, 958, 959f stretch receptors in, 928f structure of, 953–57 thick and thin filaments in, 955–56, 956f See also muscular-skeletal systems skeletal muscle contraction, 216 and electrical excitation, 958, 959f excitation-contraction coupling, 958, 959f movement of bone by, 954 regulation of, 958, 959f thin and thick filaments in, 955–56, 956f skeletal muscle fibers: adaptation of, 961, 962t defined, 954 electrical excitation and contraction of, 958, 959f electrical stimulation of, 960, 960f myofibrils in, 955, 955f types of, 960–64, 962t, 963–64f skeletons: of birds, 751, 751f defined, 951 endoskeletons (See endoskeletons) exoskeletons (See exoskeletons) functions of vertebrate, 952–53, 953f and muscles (See skeletal muscle) types of, 951–52, 952f skin: epithelial tissue in, 215 heat exchange rate and blood flow in, 1004, 1005f in innate immunity, 1109–10 mechanoreceptors in, 927–28, 928f and multicellularity, 204, 206, 210–11 and response to hemorrhage, 1143 thermoreceptors in, 933 viral diseases of, 393f skin cells: proteins produced by, 82 structure of, 79, 80f skin damage, 870, 871 Skinner, B. F., 1182 Skinner box, 1182 Skou, Jens, 121

skulls: heterochrony of, 512 kinetic, 747, 748, 748f of mammals, 754 survivorship curve created from, 1207–8 Slack, Roger, 179 Slatyer, Ralph, 1243 sleep movements of plants, 797 sliding filament mechanism, 956 slime molds, 543 SLOSS debate, 1289 sloths, skeletal muscle fibers of, 961 slow fibers, 961, 962t slow-oxidative fibers, 961, 962t slugs, 709, 711, 712t small effector molecules, 285 small-interfering RNAs (siRNAs), 271, 273, 274f, 275 small intestine: absorption of amino acids in, 982, 982f absorption of carbohydrates in, 980–81, 981f absorption of lipids in, 983–84, 983f cell junctions in, 208, 209f digestion of proteins in, 982, 982f in digestive system, 975, 978–79, 979f in endocrine system, 1060f hormonal regulation of digestion in, 985, 985f vitamin, mineral, and water absorption in, 984 vitamin D in, 1074, 1075 small ribosomal subunit (SSU) rRNA: of chordates vs. nonchordates, 729, 729f evolutionary relationships among animals from, 695–98 evolution of, 259–60, 260f taxonomic relationships among Protostomia from, 697–98 smart plants, 810–11, 810–11f smell senses. See olfaction. Smith, Hamilton, 436, 446, 448 smoking: and heartburn, 986 and respiratory system, 1040 smooth endoplasmic reticulum (smooth ER), 90–91 of animal cell, 80f and digestive system, 983 of plant cells, 81f smooth muscle: in animal bodies, 860, 861f force generation by, 954 modeling contraction of, 860, 861 SMR (standard metabolic rate), 998 snails, 709, 711f, 712f, 712t, 731f snakes: antipredator strategies of, 1225f, 1226 characteristics of, 747–48, 748f locomotion by, 964 species identification with, 498–99 snake venom, medication developed from, 1 snapdragons, 431, 794, 846, 846f snowball Earth hypothesis, 540

snow buttercup, 782, 782f snowshoe hares, 1226, 1226f snowy owl, 942, 942f SNPs (single-nucleotide polymorphisms), 478–79, 557–58 snRNP, 251 social aspects, of biology, 16–17, 17f social behavior, 548, 1197 social bonds, 1192, 1192f societal applications of science. See science and society (core skill). societal benefits. of biodiversity, 1284–86, 1285f, 1293 sodium: as essential nutrient, 972 plant nutrition, 802t properties of sodium chloride vs., 31 sodium channels, 886, 888–90 in photoreception, 940 in propagation of action potential, 891–92 sodium chloride: ionic bonding in, 34, 34t properties of sodium vs., 31 in water, 37, 37f sodium hydroxide, in water, 41 sodium ions, 34, 34f in animal bodies, 873 electrochemical gradient for, 115, 115f hormonal regulation of, 1075–76, 1076f in kidney filtrate, 1051–52, 1052f Na+/K+-ATPase pump, 121–22, 122f, 886, 889 and neurons, 885, 886, 890 in response to hemorrhage, 1140, 1141f soil bacteria, 574–75 soil base, 805 soil erosion, 805 soil horizons, 805, 806f soil organic matter, 805–6, 806f soils: in different ecosystems, 1253 and distribution of organisms, 1158–60, 1159f microbiomes in, 630 nitrogen fixation, 808–9, 808f, 809f phosphorus acquisition from, 809 physical structure, 805–8, 806f, 807f in plant nutrition, 805–11, 806f–11f and smart plants, 810–11, 810–11f soil science, 633 solar radiation: and climate, 1160, 1160f and greenhouse effect, 1260, 1260f See also ultraviolet radiation solar system, origin of, 535 solubility, of gases, 1025 soluble wastes: of invertebrates, 1045–46, 1045f removal processes for, 1044–45, 1045f solute concentration, 820, 821f solute potential, 821 solutes: in active transport, 120–21, 121f binding of, by transporters, 119–20, 120f in capillaries, 1020, 1021, 1021f

in channels, 117–19, 117f, 118f in concentration, 38 defined, 37, 114 movement between fluid compartments by, 872–73 osmosis and concentration of, 115–16, 115f, 116f osmotic adjustment of, 822 in plant tissues, 823, 823f in proximal tubule, 1049, 1050 reabsorption of, 1049–50, 1049f and solubility of gases, 1025 solutions: acidic, 42, 42f alkaline, 42, 42f aqueous, 37 defined, 37 molar, 38 solvents, 37, 114 somatic cells: mutations in, 307, 307f and X-chromosome inactivation, 377–78, 378f somatic embryogenesis, 855, 855f somatic nervous system, 909 somatostatin, 1077 Somniosus microcephalus, 740 songbirds, skeletal muscle fibers of, 961 songs of birds. See bird songs. s orbitals, 27 sorting signals, 99, 101 SoS signal transduction pathway, 191 sound, detection of, 928–29, 928f sound waves, detection of, 929–30, 929f source pools, 1244 Sousa, Wayne, 1242–43 southern leopard frog (Rana utricularia), 497f soybeans, 794 spacecraft, plant responses in, 783 spacer acquisition, 275–76, 278 Spartina grasses, 1159, 1159f, 1253–54, 1254f spatial navigation, 1187–88, 1188f spatial patterning. See body patterns. spatial summation, 894, 895f speciation, 496–515 defined, 496 and evolutionary developmental biology, 509–14 and identification of species, 497–502 mechanisms of, 502–8 pace of, 508–9 summary, 514 species: binomial nomenclature for, 519 biogeographical evidence of evolution of, 466, 468, 468f of Cannabis, 679–80, 680f characteristics and histories of, 497–99 classification (See taxonomy) in Darwin’s theory of evolution, 459–61, 460f defined, 3, 458, 459, 496 DNA barcoding to identify, 726 and domains, 517

evolutionary relationships of, 584 and fertilization location, 1090 homologies between, 471–73, 471f, 472f, 472t horizontal gene transfer between, 411, 474, 474f identification of, 497–502 interspecies interactions (See parasites; predation) nuclear genomes of, 448–50, 449f, 449t oxygen-hemoglobin dissociation curve differences based on, 1035, 1036f reproductive isolation to maintain, 499–502 shared primitive and derived characters of, 523 small subunit rRNAs of, 259–60, 260f in supergroups, 592t taxonomic hierarchy for, 517–19 species-area effect, 1238 species-area hypothesis, 1237f, 1238 species-area relationships, 1244, 1245, 1245f species concepts, 499 species-distance relationships, 1244, 1245, 1246f species diversity: as level of biodiversity, 1280–81, 1281f and species richness patterns, 1236–40, 1237f, 1238f, 1239t See also biodiversity species interactions, 1150, 1217–35 bottom-up versus top-down control in, 1231–33, 1232f, 1233f commensalism, 1231, 1231f competition, 1218–21f, 1218–24, 1222t, 1223–24f herbivory, 1226–28, 1227f, 1228f mutualism, 1229–31, 1230f, 1231f parasitism, 1228–29, 1228f, 1229f predation, 1224–26 summary, 1234 types of, 1217, 1217t species-productivity hypothesis, 1238, 1238f species richness, 1236–40, 1237f, 1238f, 1239t, 1240f, 1281–85f species-time hypothesis, 1237, 1237f species turnover, 1245–47 specific heat, defined, 39–40 SPEECHLESS gene, 774 speed, of signals sent with second messengers, 194–95, 195f spermatids, 1087 spermatogenesis: in animals, 1087–89, 1088f testosterone supplements and, 1092–93 spermatogonia, 1087, 1088f spermatozoa. See sperm cells. sperm cells: cryptic female choice, 486 defined, 1085 in fertilization, 1089–90, 1089f of flowering plants, 841, 850–51, 851f gametogenesis in, 1087–89, 1088f meiosis in, 335 movement of, 86, 87f

and structure of male reproductive tract, 1090–92, 1091f Spermophilus beldingi, 1195 Sperry, Roger, 913 Sphagnum mosses, 649, 652f S phase, 325–27 sphincter, 980f, 986 spicules of sponges, 703 spiders, 1199f, 1232, 1232f characteristics of, 720–21 zombie parasites, 2t spinach, 794 spinal cord, 882, 905 spinal nerves, 908 spinal tap, 910 spines, of plants, 775, 775f spiny fishes, 738 spiracles: in arthropods, 719 and respiratory systems, 1027 spiral cleavage, 691f, 692 spirilli, 567 spirochaetes, 567 Spix’s macaw, 1280 spleen, 1115, 1143 spliceosomes, 251, 251f splicing: alternative, 299–301, 300f, 301t and gene expression, 251, 251f split-brain surgery, 913, 913f sponges: characteristics of, 702–4, 703f, 731f digestive systems of, 972 Hox genes of, 424 muscular-skeletal systems of, 952 nervous system of, 905 pattern formation in, 417 reproduction in, 1085, 1087 spongin, 703 spongocoel, 703 spongy parenchyma, 766, 767 spontaneous generation, 496 spontaneous mutations, 309, 310t spontaneous reactions, 129, 131 sporangia, 652, 848 spores, 607, 643 of Ascomycota, 613–15, 614f, 615f of Mucoromycota, 611–13, 613f, 614f sporophytes, 340, 643 carbon uptake by, 657–58 defined, 840, 840f fertilization and development of, 841– 43, 842f, 843f of flowering plants, 761–63, 763f and placental transfer tissues, 655–57 of vascular plants, 653–54 sporophytic self-incompatibility (SI), 849, 850f sporopollenin, 652, 849 spotted sandpiper, 1198 spring field cricket (Gryllus veletis), 499 spring overturn, 1171 spruce trees, 142f, 1241 sqamous epithelial cells, 862 SQD1 gene, 810–11 Squamata, 747–48, 748f

squids: characteristics of, 709, 711–12, 711f, 712t, 731f nervous system of, 905 src gene, 318 SRPs. See signal recognition particles. SRY gene, 359 SSRIs (selective serotonin reuptake inhibitors), 901 SSU rRNA. See small ribosomal subunit (SSU) rRNA. stability of communities, 1240, 1240f stabilizing selection, 483–84 Stahl, Franklin, 228–30, 229f staining, for microscopy, 75–76 stamens: defined, 672, 841 developmental genetics, 431 gametophyte production in, 841 organ fusion in, 845 of seed-producing plants, 673–74, 674f staminate flowers, 844, 844f standard fluorescence microscopy, 77f standard light microscopy, 77f standard metabolic rate (SMR), 998 stanozolol, 1058 stapes, 929, 930 Staphylococcus aureus, 411, 462–63 starch, molecular structure of, 51, 51f starfish. See sea star. Starling, Ernest, 1138, 1140 Starling forces, 1140, 1142, 1142f starlings, 1188, 1188f star-nosed mole (Condylura cristata), 734 start codon, 252, 252f states of matter, 39–40, 39f statistical analysis: as BioTIPS strategy, 20 of parasitism, 1152–53, 1154f statocysts, and sense of balance, 931–32, 931f statocytes, 795 statoliths, 795, 931, 932 STDs (sexually transmitted diseases), 1104 stearic acid, 53, 53f Stedman, Hansell, 957 Stegosaurus, 749, 749f Stein, Gertrude, 840 Steitz, Thomas, 262 stem cells, 424–27 defined, 425 development of, 425–26, 425f medical use of, 426–27, 426t in meristems, 767–68 in nervous system, 918 properties of, 425 stem parenchyma. See parenchyma tissues and cells. stems and stem systems: defined, 761 host-associated microbiomes in, 632–33, 633f of lycophytes and pteridophytes, 645, 646 modifications of, 777 vascular systems (See vascular systems of plants; vascular tissues of plants)

INDEX

INDEX I-49

I-50 INDEX

INDEX

Stenaptinus insignis, 1224–25, 1225f stereocilia: in audition, 930 in lateral line system, 933 olfactory cilia vs., 944 sound and motion detection by, 928–29 in vestibular system, 932 stereoisomers, 47, 48f stereoscopic vision, 941 sternum, 751 steroids: and cellular communication, 190 evolution of and hormone receptors and, 1076–77 gonadal/sex, 1077, 1079–80 molecular structure of, 55, 56f receptors for, 1062 structure of, 1059 synthesis and function of, 1061f sterols, 55 Steward, F. C., 855 stickleback fishes, 1181, 1182f stigmas, 673, 841 Stigonema, 565f Stiling, Peter, 1264–64 stimulus(--i): defined, 925 endocrine response to, 1062 external (See environmental stimuli) graded potential and strength of, 888–89, 889f hair cells’ reaction to, 928–29, 928f internal, 783–84, 783f strength of, in sensory systems, 926, 927f stinging cells, cnidarian, 705, 705f stinging nettles, 773 stingrays, 739f STM gene, 856 Stoeckenius, Walther, 155–56 Stoemer, Eugene, 1257 stomach: digestion of proteins in, 982, 982f in digestive system, 975, 977–78, 978f disorders of, 986, 986f in endocrine system, 1060f general features of, 977 hormonal regulation of digestion in, 985, 985f muscle in, 954 specialized, 977–78, 978f stretch receptors in, 928 tissue types in, 863–64, 864f stomach acid, 986 stomata, 647 defined, 818 development of, 766 guard-cell development in, 774, 774f opening and closing of, 830f, 831 and photorespiration, 178 and photosynthesis, 165, 166f plant nutrition, 804 regulation of transpiration by, 829–31, 830f and tissues, 216 Stone, Christopher, 1286 stop codons, 252f, 253, 263, 263f

storage, in vacuoles, 94–95, 94f Stork, Nigel, 721 stovepipe sponge, 703f Strahl, Brian, 297 Stramenopila supergroup, 589–91, 589f, 590f strands, DNA, 224–26, 225f antiparallel, 227–28, 228f defined, 224 leading and lagging, 232–36, 234f, 235f synthesis of, 232, 234f Strasburger, Eduard, 355 stratified epithelial tissue, 862 strawberries, 794 strength: and cell walls, 206–7, 207f multicellularity and, 203 strepsirrhini, 548 Streptococcus pneumoniae, 221–23, 409, 568, 569f Streptophyta and streptophytes, 587, 641 streptophyte algae: features of, 662t as relatives of land plants, 643, 643f reproduction of, 651, 651f stress(es): environmental, 792 and immunity, 1127 infertility due to, 1104–5 stretch receptors, 928 striated muscles. See skeletal muscle. Strix occidentalis, 1290–91, 1291f stroke volume (SV), 1023–24, 1134 stroma, 97, 166 stromatolites, 541 Strong, Donald, 1238 strong acids, 41 Struck, Torsten, 715 structural formula, defined, 31 structural isomers, 47, 48f structural models, 18 structural proteins, in extracellular matrix, 204–5, 204t structural support, and multicellularity, 203 structure and function (core concept): animal body, 865–67, 866f, 867f in biological evolution, 5 as BioTIPS strategy, 20 bird beak, 752 cerebral cortex, 907 cholesterol, 1061 circulatory system valve, 1022 collagen, 205–6, 206t as core concept of biology, 4, 4f cytochrome complex, 171–72, 172f development of cell types, 1102 DNA, 228, 230 DNA polymerase, 236, 237t endomycorrhizal fungus, 634 enzyme, 132 epithelial tissue, 862 estrogen and testosterone, 56 estrogen receptor, 190 exoskeleton, 698 external gill, 1025 GABAA receptor, 899

guide ncRNA, 269 hemoglobin, 1034 homologies, 471 in horse evolution, 522 hypha, 608 jaw, 738 lignin, 775 mesophyll, 803 in molecular interactions, 35 organ system cells, 884 over conifer life cycle, 669 photoreceptor cell, 936, 938 prion, 402 protein, 61 protein product, 81–82 renal glomerulus capillaries, 1049 ribosome, 259 skeletal muscle, 955 small intestine, 979 sperm cell, 1088 thick and thin filament, 956, 956f thylakoid, 566 torus, 670 transporter, 119 tRNA, 257 vascular plant, 647 whale, 467 strychnine tree, 213 Sturnella magna, 500 Sturnella neglecta, 500 styles, of flowers, 673, 841 stylets of nematodes, 717 subatomic particles: in atoms, 24–25, 25f characteristics of, 29t submetacentric chromosomes, 342, 342f subphyla, of arthropods, 719, 719t subsidence zones, 1161 subsoil, 805 subspecies, 497 substrate, of fungi, 606 substrate-level phosphorylation, 138, 146 substrates, enzyme recognition of, 132–33, 132f subterranean root microbiomes, 633 subtypes, receptor, 1062 subunits, receptor, 898–99, 899f succession, 1240–43 succinate, in citric acid cycle, 152f succinate reductase, 153 succinyl-CoA, 152f sucker shoots, 855 sucrose: as disaccharide, 50, 50f H+/sucrose symporter, 121, 121f in phloem, 835 suction traps, 1202 sugar beets, as biennial plants, 763 sugarcane, 1158 sugar maples, 826, 828, 833, 1262, 1262f sugars: molecular structure of, 49–50, 50f in nucleotides, 224, 224f, 225f See also glucose sugar sinks, 836 sugar sources, 836 sulfate ions, in animal bodies, 874

Sulfolobus genus, 564, 573 sulfur, plant nutrition, 802t sulfur shell fungus, 617f sunbird, 1190, 1190f sundews, 801, 801f, 815, 815f sunflowers, 677f, 794, 846 sun leaves, 803, 803f sunlight. See light; ultraviolet radiation. sun tracking, 784, 797 supergroups, 584–92, 592t Alveolata, 589–90, 589f, 590f Amoebozoa, 591 defined, 517 Excavata, 584–86, 585f, 586f of land plants and algae, 586–89 Opisthokonta, 591–92, 591f, 592f Rhizaria, 591, 591f Stramenopila, 590–91, 590f supernovas, 535 support: from endoskeletons, 952 as function of water, 40, 40f from skeletal muscle, 954 supporting cells, 943, 944 surface area: animal structures requiring extensive, 866–67, 867f and cell size/shape, 82–83, 82f and mass-specific BMR, 999 of small intestine, 978–79, 979f surface area/volume ratio (SA/V), 866 surface tension, 40f, 41, 828, 1030–31 surfactant: in lungs, 1030–31 for newborns with RDS, 1031–33 survival: hearing as advantage for, 930–31 and life history strategies, 1213–15, 1214f, 1214t, 1215f survival patterns, 1205–8 survivorship curves, 1205–8 suspensors, of plants, 851 Sutherland, Earl, 194 Sutter, Nathan, 470 Sutton, Walter, 355 Svedberg, Theodor, 258 Svedberg units, 258 SV (stroke volume), 1023–24, 1134 swamp wallaby, 756, 756f sweat glands: epithelial tissue in, 862 and evaporative heat loss, 1005 sweep nets, 1202 sweet pea: epistasis in, 366–67, 367f independent assortment in, 384–86, 385f swim bladder, 741 swimming, 964, 1036, 1037 swine flu, 399 sycamore trees, 774 symbiosis: defined, 576 and heat stress in plants, 618–19, 619f and mitochondria/chloroplasts, 98–99 and plant nutrition, 812–14, 813f, 814f symbiotic relationships, bacteria in, 576–78, 577f, 578f

symmetry: of animals, 690, 690f of flowers, 845, 846, 846f Symons, Robert, 434 sympathetic division, of autonomic nervous system, 910, 911f sympathetic nervous system, 1140, 1143 sympatric speciation, 506–8, 1221–22, 1222t symplastic phloem loading, 835, 835f, 836 symplasts and symplastic transport, 823–24, 823f symplesiomorphy, 523 symporters, 119, 120f, 121, 121f, 820 synapomorphy, 523 synapses: defined, 892 electrical vs. chemical, 892–93 neuron responses to inputs at, 893–95, 895f neurotransmitters at, 893 synapsis of bivalents, 335 synaptic cleft, 892 synaptic plasticity, 918 Syncerus caffer, 1157, 1158f Synechococcus, 628 synergids, 849 Syngnathus typhle, 1198 synthesis of viral components (step in viral reproductive cycle), 395, 397f, 398 synthetic microbiomes, 637 synthetic RNA, 254–55 systematics, 516–34 and cladistics, 523–29 defined, 516, 519–21 and horizontal gene transfer, 531–33 molecular clocks in, 529–31 morphological and genetic homology in, 521–23 phylogenetic trees in, 519–23 summary, 533 and taxonomy, 517f systemic acquired response (SAR), 798, 799f systemic circulation, 1012 systemic lupus erythematosus, 1125 systems biology: cells in, 102–3 defined, 13–14, 13f systems (core concept), 4f, 5 after hemorrhage, 1143 animals and environments as, 861 autonomic nervous system and homeostasis, 911 gene expression and phenotype, 364 homeostasis in, 1021 internal and environmental stimuli in, 784 legume-rhizobia symbioses as, 813–14, 814f lymphatic, 1116 metabolic cycles in, 152 microbiomes as, 623–25 multicellularity in, 543 mutualism, 1230 mycorrhizal fungi in, 812 negative feedback in, 1092

of organs, 976 of seed dispersal, 853 segmentation in, 421 of tissues and organs, 860 of unicellular bacteria and archaea, 567 systole, in cardiac cycle, 1018, 1018f Szostak, Jack, 73, 74–75, 238

T

T. See thymine. T3. See thyroid hormone. table salt. See sodium chloride. table sugar. See sucrose. Tachyglossus aculeatus, 468, 469f tactile communication, 1192, 1192f tadpoles, 1078, 1078f Taenia pisiformis, 707f tagmata, 718 taiga, 1167, 1167f tail region (motor protein), 85 tamarack (Larix laricina), 670 Tangl, Eduard, 213 tannins, 777 tapeworms, 706f, 707, 707f tapirs, 1176, 1177f taproot systems, 767 Taq polymerase, 440 tarsiers, 933 taste: sensory hairs for, 942–43, 943f vertebrate structures in, 946, 946f taste senses. See gustation. TATA box, 294, 294f Tatum, Edward, 245–46, 245f, 406–8, 407f taxis, 1185 Taxodium distichum, 670 taxonomic complexity, of microbiomes, 624f, 625–27, 626f, 627f taxonomic relationships, among Protostomia, 697–98 taxonomy: changes in, 12 of clownfish, 11f defined, 8, 516 and phylogenetic trees, 519–21 in systematics, 517f and unity/diversity of life, 9–12, 10f Taxus brevifolia, 664, 669f T4 bacteriophages, 394f, 395, 399 Tbx5 gene, 1014 T-cell receptors, 1121, 1122f T cells: antigen recognition by, 1121–23, 1122f HIV and, 399–400, 399f self-molecule recognition by, 1124–25 structure and function of, 1116–17, 1116f T1DM (type 1 diabetes mellitus), 1069, 1070, 1073 T2DM (type 2 diabetes mellitus), 1070 Teal, John, 1253 teeth, of mammals, 753–54, 754f teleost fishes, digestive systems of, 977 telocentric chromosomes, 342, 342f telomerase, 236–38, 237f telomeres, 236–38, 237f

telophase I (meiosis), 336–37, 339f telophase II (meiosis), 339f telophase (mitosis), 332, 333f temperate coniferous forest, 1167, 1167f temperate deciduous forest, 1167, 1167f temperate forests, primary production in, 1253 temperate grassland, 1168, 1168f temperate phages, 398–99, 398f temperate rain forest, 1166, 1166f temperature: and athletic performance, 876–79 atmospheric circulation driven by, 1160–61 body temperature regulation, 1002–6 carbon’s molecular stability at, 46 detection of, 933 and distribution of organisms, 1155–58f and enzyme function, 134, 134f and fats, 53, 53f and hemoglobin’s affinity for oxygen, 1035 as homeostatic variable, 868t and membrane fluidity, 110 since origin of Earth, 538 and solubility of gases, 1025 template strand, of DNA, 230, 248–49, 248f, 249f temporal isolation, 499 temporal lobe, 914, 914f temporal models, 18 temporal summation, 894, 895f temporary forms of contraception, 1105–6 TEM (transmission electron microscopy), 76, 78f tendons, 954 tendrils, 774, 775f tensile strength, of collagen, 204 tension, in long-distance plant transport, 828–29, 828f teosinte, 683, 683f tepals, 672, 841, 846–48, 847f Terborgh, John, 1291 terminal repeats, 454 termination codons, 253 termination stage: of transcription, 248f, 249 of translation, 261f, 263, 263f terminators, 247, 247f terpenoids: and plant behavior, 797 and species interactions, 1227, 1227f terrapins. See turtles. terrestrial animals, 545 baroreceptors of, 1135 dehydration in, 874 eggs cell and embryos of, 474 energy balance in, 1006 internal fertilization in, 1090 obligatory ion and water exchanges in, 874, 874f oxygen diffusion in blood for, 1025 water loss from body surface of, 876 terrestrial biomes, 1164–70 terrestrial ecosystems, 1252, 1252f terrestrial vertebrates, digestive systems of, 976, 977

territories: communication about, 1191 defense of, 1190, 1190f tertiary consumers, 1248, 1248f tertiary endosymbiosis, 588f, 589 Tertiary period, 547 tertiary plastids, 589 tertiary structure, of proteins, 59f, 60 testable hypotheses, 14 testcrosses, 353–54, 354f, 386 testes: and androgen, 1080 in endocrine system, 1060f, 1080 gametogenesis in, 1087 testosterone: in endocrine system, 1058, 1080 molecular structure of, 55, 56f in reproduction, 1092 and spermatogenesis, 1092–93 TEs (transposable elements), 452–54 test-tube babies, 1105 Testudines, 747, 748f tetracycline, 409–10, 411f tetrahydrocannabinol (THC), 679, 680f Tetrahymena thermophila: cilia of, 87f ribozyme in, 136 Tetrao tetrix, 1198f tetraploid organisms, 343, 343f tetrapods, 742–46 and amniotes, 746 amphibians, 744–46 endocrine system of, 1065, 1074 evolution of, 465, 466f Hox genes of, 512 limbs of, 742–44 locomotion by, 965 origin of, 545–46 TFIID (transcription factor II D), 295–96, 295f TFM (trifluoromethyhl nitrophenol), 1276 TFRs (total fertility rates), 1258, 1259, 1259f TG (thyroglobulin), 1065 thalamus, function of, 912 thale cress (Arabidopsis thaliana), 414–15, 448 Thaumarchaeota, 564 THC (tetrahydrocannabinol), 679, 680f theca, 1089 themoreceptors, 927 theories, hypotheses vs., 14 theory of evolution. See evolution. therapeutic drugs, and neurotransmission, 900t thermal-imaging cameras, studies using, 1004 Therman, Eeva, 378–79 thermoception, 933 thermoceptors, 933 thermoclone, 1171 thermocyclers, 440 thermodynamics: defined, 128 laws of, 128, 129, 167 Thermus aquaticus, 579 theropods, 547

INDEX

INDEX I-51

I-52 INDEX

INDEX

thickening and elongation step (neurulation), 1103f, 1104 thick filaments: in muscle contraction, 955–56, 956f and myofibrils, 955, 955f structure and function of, 956, 956f thigmotropism, 795–96 thin filaments: in cross-bridge cycle, 957 in muscle contraction, 955–56, 956f and myofibrils, 955, 955f structure and function of, 956, 956f Thiomargarita amibiensis, 566, 573 thirst, and homeostasis, 859 30-nm fiber, 238, 239f thoracic breathing, 746 thoraco-abdominal pump, 1138, 1139f thorns, 1227, 1227f Thornton, Joseph, 1076 thought (cognitive function), 922–23, 923f threatened species, 1269, 1269f, 1271–75f, 1281 three-cell model, of global circulation, 1161, 1161f three-dimensional structure, of proteins, 61–63 threshold concentration, for morphogens, 417 threshold potential, 889 thrifty genes, 243, 1007 throat. See pharynx. thrombocytes, 1015 thylacine, 1275 Thylacine cynocephalus, 1275 thylakoid lumen, 166 thylakoid membrane, 97, 166 thylakoids: and photosynthesis, 166 structure and function of, 566 thymine dimer, formation of, 310, 311f thymine (T): and DNA, 224 molecular structure of, 64, 65 thymus gland, 1115 thyroglobulin (TG), 1065, 1066 thyroid gland, endocrine function of, 1060f, 1065, 1066f thyroid hormone: and animal growth/development, 1078, 1078f classification of, 1059 and metabolism, 1065–67, 1066f, 1067f receptors for, 1062 therapeutic uses of, 1080 thyroid-stimulating hormone (TSH), 1064, 1065, 1067 thyrotropin-releasing hormone (TRH), 1064, 1065, 1067 thyroxine (T4), 1065, 1066f Tiaris obscura, 460 ticks, 720–21 tidal ventilation, in mammals, 1030 tidal volume, 1030 tight junctions, 208t, 209–11, 210f, 211f Tiktaalik roseae, 465, 742 Tilman, David, 1240, 1282

tilt, of Earth, 1161–62, 1162f time-lapse video, of blooming flowers, 846–48, 847f Tinbergen, Niko, 1180, 1181, 1185–86f, 1185–87 TIR1 complex, 785 tissue culture, plant, 789, 790f tissues: in animal bodies, 860–64f, 860–65, 865t arteries and blood flow to, 1020, 1020f in body organization, 860, 860f defined, 2, 3f of flowering plants, 765–66, 765f lipid metabolism by, 994 lymphoid, 1115, 1116f multicellularity of, 214–16, 215f, 216f in organs and organ systems, 863–65, 864f, 865t of plants (See plants) in small intestine, 979f specialization of, in root systems, 777–79, 778f, 779f specialized cells in, 860–63 TLRs (Toll-like receptors), 1112, 1115 TMV (tobacco mosaic virus), 392, 392f, 394f, 395 TNF (tumor necrosis factor), 1124 tobacco mosaic virus (TMV), 392, 392f, 394f, 395 tobacco plants, stomata of, 829 tobacco smoke, 1040 tobacco smoking. See smoking. tolerance, 1243, 1243f Toll-like receptors (TLRs), 1112, 1115 Toll proteins, 1112–15 tomatoes and tomato plants: ABA receptor proteins in, 831–32f, 831–33 chromosome number for, 342 and plant behavior, 794, 797, 798f Tonegawa, Susumu, 295, 1119 tongue, taste cells on, 946 Tonicella lineata, 711f tonsils, 1115 top-down control, 1231–33, 1232f, 1233f TOPLESS protein, 851 topsoil, 805, 806f torus(--i), of conifers, 668, 670f total fertility rates (TFRs), 1258, 1259, 1259f total peripheral resistance (TPR), 1023– 24, 1134, 1135 totipotent stem cells, 425f, 426 touch: plant responses to, 796–97, 796f, 815 skin receptors for, 927–28, 927f toxic fungi, 610–11, 611f toxins: defined, 593 infertility due to, 1105 Toxoplasma gondii, 2t, 1228 TPR (total peripheral resistance), 1023–24, 1134, 1135

trace elements, 30, 30t tracheae and tracheal systems: in arthropods, 719 of insects, 1027, 1027f in respiratory system, 1027, 1028 tracheary elements, 826 tracheids, 645 in primary vascular tissues, 775–76 in xylem, 826, 827f, 828 tracheophytes, 645, 647f tracking device, 1203 tracts, nervous system, 908–9, 909f traffic signals (sorting signals), 99, 101 Tragelaphus strepsiceros, 755f traits, 350 See also inheritance transcribed region, of DNA, 247f transcription, 246–49 bacterial regulation of, 284–94 and cell communication, 190–92, 190f and DNA microarrays, 442, 443f, 443t eukaryotic regulation of, 294–99 of imprinted genes, 376, 376f and non-coding RNAs, 270, 271f transcriptional start site, 294, 294f transcription factor II D (TFIID), 295–96, 295f transcription factors: in bacterial gene regulation, 285, 286f cell communication and, 186, 190–92, 192f defined, 249 in eukaryotic gene regulation, 294–96 and flowering time, 844 and gibberellins, 790–91, 790f in pattern formation, 417–18, 418f See also specific transcription factors transcriptome, 628 trans double bonds, 47 transducin, 940 transduction: by bacteria, 410–11, 410f and gene transfer, 406, 406t in hearing, 930, 931f and stimuli strength, 926, 927f See also signal transduction pathways trans-effects, 289 transepithelial transport, 210 trans fatty acids, 54 transfer RNA. See tRNA. transformation, 221–23 by bacteria, 409–10, 410f and gene transfer, 406, 406t trans Golgi, 91 transitional forms: of birds, 750, 750f as evidence of evolution, 465, 466f of tetrapods, 742 transition state, 131 translation, 252–64 and antibiotics, 263–64, 264t eukaryotic gene regulation, 299–301, 300f, 300t, 301f functional sites for, 259, 259f and genetic code, 252–56, 252f, 253f, 255–56f

machinery of, 256–60, 256t, 257–59f, 258t and non-coding RNAs, 270–75 overview, 246–47, 246f stages of, 260–64, 263t, 264t translocation, 342, 343f chromosomal, 316, 317f and plant transport, 836 of ribosome, 262–63, 262f transmembrane gradient, 114–15, 115f See also concentration gradient transmembrane proteins: and associations of membranes, 108 genes encoding for, 108–9, 109t insertion in ER membrane, 112, 112f movements of, 110–11, 111f See also membrane proteins transmembrane transport, 823–24, 823f transmissible spongiform encephalopathies (TSEs), 402–3 transmission, of genetic material, 221 transmission electron micrographs, of viruses, 394f transmission electron microscopy (TEM), 76, 78f transpiration: and bulk flow, 825 defined, 818 in long-distance plant transport, 828– 29, 828f, 829f stomata in regulation of, 829–31, 830f transplantation, 1056, 1127 transport: of auxin, 785, 787f in flowering plants (See plant transport) through membranes, 113–16, 114f, 116f transport across membranes. See membrane transport. transporters: channels vs., 120 in plant cells, 819 solute-binding by, 119–20, 120f transport proteins, 117–22 active transport by, 120–21, 121f ATP-driven ion pumps, 121–22, 122f channels, 117–19, 117f, 118f and osmosis, 117–19, 118f in proteome, 9f solute-binding by transporters, 119–20, 120f See also membrane proteins transposable elements (TEs), 452–54 transposase, 454 transposition, 453, 453f, 454, 454f trans-retinal, 940 transverse tubules (T-tubules), 958, 959f, 960 traps, 1202, 1202f traumatic injury, hemorrhage and death due to, 1145 tree and warbler finches, 461t tree ferns, 546 tree finches, 461t tree frogs, muscular-skeletal system of, 951 tree of life, 532–33 tree python, 748f

INDEX I-53 tropism, defined, 784 tropomyosin, 958, 958f troponin, 958, 958f trp operon, 293–94, 293f trp repressor, 293–94, 293f true-breeding lines, 351 truffles, 614, 616f Trypanosoma brucei, 586f, 587 trypsin, 982 trypsinogen, 982 tryptophan: as corepressor, 293, 293f hormones derived from, 1059 Tschermak, Erich von, 350 TSEs (transmissible spongiform encephalopathies), 402–3 tsetse flies, 726 TSH (thyroid-stimulating hormone), 1064, 1065, 1067 Tsuga candensis, 1158 Tsuga heterophylla, 1241–42, 1242f Tsuga mertensiana, 1241–42 T-tubules (transverse tubules), 958, 959f, 960 tubal ligation, 1105, 1105f tube cells, 849 tube feet, 727, 727f Tuber melanosporum, 616f tubers, 777, 855 tube worms, 715, 716f tule elk, 1210, 1211f tulips, flowers of, 845 tumor necrosis factor (TNF), 1124 tumors, 314 See also cancer tumor-suppressor genes, 314, 318–20, 318t, 319f environmental inhibition of, 381 function of, 318–19, 318t, 319f inhibition by mutations, 319–20, 319f tundra, 1170, 1170f tunic, 731 tunicates, 729, 730–31, 730f Turbellaria and turbellarians, 706, 706t, 707f turgidity, 40, 820, 821f turgor pressure, 94, 820, 821f, 822 Turkana boy, 552 Turner syndrome, 344, 378 turtles, 546, 747, 748f T waves, 1019 two-cell stage, of plant development, 430f two-dimensional paper chromatography, 176, 177–78f two-factor cross, 354, 354f, 384–86, 385f tympanic membrane, 929, 930 type 1 diabetes mellitus (T1DM), 1069, 1070, 1073, 1125 type 2 diabetes mellitus (T2DM), 555, 1070 type I alveolar cells, 1028 type II alveolar cells, 1028, 1030 Tyrannosaurus rex, 547, 749, 749f tyrosine, hormones derived from, 1059 tyrosine kinases, 188

U

U. See uracil. UAS (unmanned aircraft systems), 1203 ubiquinone (QB), 153, 154f, 160, 169, 171, 171f ubiquitins, 141, 141f, 142 Uca paradussumieri, 486 ulcers, 986–88 ultimate causes of behavior, 1180 ultraviolet radiation (UV light): and melanin, 183–84 mutations by, 310 and plant nutrition, 804 vitamin D from, 1073 Ulva, 1242–43, 1243f umami, 946 Umbilicaria, 632f umbrella species, 1290–91, 1290f umbrella thorn acacia (Vachellia tortillis), 1 undigested material, egestion of, 980 unicellular organisms: development of, 414 digestive systems of, 972 fossils of, 538 horizontal gene transfer in, 532 uniform dispersion, 1204, 1204f uniformitarianism, 460 uniporters, 119, 120f unipotent stem cells, 425f, 426 United States, obesity as public health issue in, 1006–7, 1007f University of Florida, 876–78 unmanned aircraft systems (UAS), 1203 unsaturated fatty acids, 53–54, 53f unsaturated lipids, 109 unusable energy, 129 upwellings, 1253 uracil, 65 uracil (U), 224 uranium-235, 536 urbanization, 1269 urea: in excretory system, 1044, 1051 Wöhler’s studies of, 45, 46 uremia, 1055 urethra: in females, 1093 in males, 1091 Urey, Harold, 70–71 uric acid, 1044 urinary bladder, 1047 urinary system: epithelial tissue in, 862f of mammals, 1047, 1048f urinary systems: in response to altitude change, 1144 in response to illness, 1143 secondary phase of response to hemorrhage, 1140, 1141f urine, 1045, 1047, 1140, 1141f Urochordata and urochordates, 729–31, 730f urochordates, 1013 Urocyon cinereoargenteus, 466, 468f Urocyon littoralis, 466, 468f Urodela, 745–46, 746f

Ursus arctos, 633, 634 Ursus maritimus, 1290, 1290f usable energy, 129 Ustilago maydis, 617f uterine cycle, 1095, 1095f uterus: during birth, 1098 and oxytocin, 1064 during pregnancy, 1096–97, 1096f preparation of, for embryo, 1095 structure of, 1093 utricle, 932 U-tubes, 408, 408f UV light. See ultraviolet radiation (UV light). UV radiation. See ultraviolet radiation. UvrA protein, 313 UvrB protein, 313 UvrC protein, 313 UvrD protein, 313

V

vaccinations, 1126 Vachellia tortillis (umbrella thorn acacia), 1 vacuoles, 94–95, 94f in intracellular digestion, 972 phagocytic, 124 water in plant cell, 768, 768f vagina, 1090, 1093 vaginal diaphragms, 1105–6, 1105f vagus nerve, 898 valence electrons, 28 valves: in circulatory system, 1022 of heart, 1018, 1018f in veins, 1022, 1022f vampire bats, 1196 van Alphen, Jacques, 487–89, 508 van der Waals dispersion forces, 33, 60, 61f Van Helmont, Jan Baptista, 164 van Niel, Cornelis, 165 Van Valen, Leigh, 499 vaporization, of water, 39 variable regions (V), immunoglobulin, 1118, 1119 variation, of genetic material, 221 varicella-zoster, 399 Varmus, Harold, 318 vasa recta capillaries, 1048 vascular bundles, 766 vascular cambium, 666, 776 vascular plants, 644 apoptosis in, 416 ecological roles of, 649–50, 649f, 650f lycophytes and pteridophytes, 645–47 origin of, 545 phylogenetic tree for seed plants and seedless, 664, 665f reproduction by, 653–54 See also flowering plants (angiosperms); gymnosperms; Lycopodiophyta and lycophytes; pteridophytes

INDEX

trees: effects of climate change on, 1262, 1262f origin of, 545 species richness of, 1237–38, 1237f, 1238f Trematoda and trematodes, 706t, 707, 708f Trematomus nicolai, 468, 469f TRH (thyrotropin-releasing hormone), 1064, 1065, 1067 trial-and-error learning, 1182–83, 1183f Triassic period, 540, 546–47 trichomes, 216, 773 Trichomonas vaginalis, 586, 586f, 593 trichromatic color vision, 939 trifluoromethyhl nitrophenol (TFM), 1276 Trifolium pratenae, 507 Trifolium repens, 1155, 1156f Trifolium stoloniferum, 1286 triglycerides: absorption of, 983f in absorptive state, 992–93, 992f molecular structure of, 52, 52f See also fats triiodothyronine (T3), 1065, 1066f, 1067 See also thyroid hormone Trilobita and trilobites, 545, 719, 720f trimeric proteins, 199 triple response in plants, 791, 792f triplets, 253–56 triple X syndrome, 344, 378 triploblastic organisms, 691, 1099 triploid organisms, 343, 343f trisomic organisms, 344–45 Triticum aestivum, 345–46, 345f tRNA (transfer RNA), 247 aminoacyl-tRNA synthetase charging of, 257, 258f DNA and mRNA vs., 253–54, 253f in elongation stage of translation, 261–63, 262f in initiation stage of translation, 260–61, 260f ribosomal binding of, 254–56 structure of, 257, 257f trochophore larvae, 698, 699f Trombicula alfreddugesi, 720, 720f trophectoderm, 1101 trophic levels: and biomagnification, 1268–69 defined, 1248–49, 1249f and ecological pyramids, 1251–52, 1251f species richness in, 1283–84, 1283f trophic-level transfer efficiency, 1251 tropical deciduous forest, 1166, 1166f tropical forests, primary production in, 1253 tropical grassland, 1168, 1168f tropical pitcher plant, 815, 815f tropical rain forests: mycorrhizal associations in, 812, 812f soils, 805, 806f as terrestrial biome, 1165, 1165f transpiration in, 829, 829f

I-54 INDEX

INDEX

vascular systems of plants: characteristics of, 775–77 primary, 775–76, 775f, 776f secondary, 776–77, 776f, 777f See also plant transport vascular tissues of plants: and auxin, 785 multicellularity of, 216, 216f vas deferens, 1091 vasectomy, 1105, 1105f vasoconstriction, 1023 in response to hemorrhage, 1138 in shock, 1145 vasodilation, 1023 vasopressin, 1052, 1065 See also antidiuretic hormone (ADH) vasotocin, 1065 vector DNA, for gene cloning, 435–37, 436f, 436t vectors: defined, 435 in DNA libraries, 438, 438f vegetal pole, of embryo, 1110, 1110f vegetarian finch, 461t vegetarians, 972 vegetative growth, in flowering plants, 762 vegetative reproduction, in flowering plants, 855, 855f vein patterns, in leaves, 771–72f, 771–73 veins: after hemorrhage, 1132 in closed circulatory systems, 1012 and energy balance, 1005f function of, 1021–22, 1022f portal, 1063 veligers, 710, 712f velocity, of chemical reactions, 133–34, 133f venation, plant leaf, 770–72f, 771–73 venom, drugs derived from, 1, 1f Venter, Craig, 446, 448 ventilation: air flow in, 1028, 1029f control of, 1036–37, 1037f, 1037t defined, 1025 in gills, 1027 negative pressure filling in, 1030, 1030f tidal, 1030 ventral side, 690 ventricles: and cardiac cycle, 1018 of central nervous system, 909, 910f excitation in, 1018 and response to hemorrhage, 1138 in single vs. double circulation, 1012 of vertebrate hearts, 1016–17, 1016f Venturia inaequalis, 615 venules: in digestive system, 979f function of, 1021–22, 1022f Venus flytrap, 815, 815f Vergnaud, Giles, 275 vernalization, 374 Vernanimalcula guizhouena, 544 Verreaux’s eagle, 752f

vertebrae, 734 Vertebrata and vertebrates, 734–58 adaptive immunity cells for, 1116f amniotes, 746–52 anatomical homologies of, 471, 471f anterior pituitary gland and hypothalamic hormones, 1064t audition in, 929 blood calcium ion concentration in, 1073–75, 1074f, 1075f brains of, 905–6, 907f characteristics of, 734–36, 735f, 736t Chordata and, 729 circulatory systems of, 1012, 1013f, 1020 cyclostomes, 736–37, 737f defined, 734 digestive systems of, 975–84 endocrine system of, 1059, 1060f, 1065, 1067, 1080 endoskeletons of, 952 epidermal growth factor in, 191 excretory systems of, 1047 extracellular matrix, 206 eye adaptations of, 941–42, 942f fluid compartments in, 872, 872f gap junctions, 211 gnathostomes, 737–42 heart of, 1016–19 homeostasis in, 867–68, 868f, 868t hormonal control of growth in, 1077– 78, 1077f, 1078f immunoglobulins of, 1118 as invasive species, 1275 locomotion by, 964, 965 lungs of, 1027, 1028f mammals, 752–57, 753t, 754–56f, 755t nervous system structure and function in, 907–16, 915t nervous tissue of, 861f neurlation in, 1103, 1103f, 1104 neurons and glial cells of, 882–83, 883f origins of, 538, 545 in phylum Chordata, 728–29 pituitary gland of, 1062, 1063 production efficiency of, 1250, 1250f reflexes of, 884 respiratory systems of, 1025 sense of balance for, 932, 932f, 933 shared derived characters of, 523 single-lens eye of, 935–37, 936f skeleton functions for, 952–53, 953f skeletons (See endoskeletons; exoskeletons) sodium and potassium ion contrations for, 1075–76, 1076f steroid hormones, 190 stomach of, 863–64, 864f, 977–78 stomach specialization among, 977–78 summary, 757 tetrapods, 742–46 Toll proteins in, 1112 vertical evolution, 6–7, 6f, 8f, 474, 531, 566 vesicles: in chemical synapses, 893

chemiosmotic research using, 155–56, 156f in exocytosis and endocytosis, 122–23, 123f, 124f structure of, 566 vesicular transport model, 91 vessel elements: of vascular tissues, 775 in xylem, 826–28, 827f vessels: in angiosperms, 672 in xylem, 826–28, 827f vestibular system, and sense of balance, 932, 932f, 933 vestigial structures, 471–72, 472t Via, Sara, 507 Vibrio cholerae, 445, 565, 567f, 985–86, 1143 Vibrio fischeri, 577f Vibrio parahaemoliticus, 570f vibrios, 567 viceroy butterfly, 1225f, 1226 vigilance in groups, 1193, 1193f villi: chorionic, 1097 in digestive system, 978, 979f vincristine, 1284 viral assembly (step in viral reproductive cycle), 397f, 398 viral envelope, 393 viral genetics, 391–403 and properties of viruses, 392–95, 392t, 393f, 394f and reproductive cycles, 395–401 summary, 411 viroids and prions vs. viruses, 401–3, 401f, 402f, 402t viral genomes, variability in, 393, 395 viral reproductive cycles, 395–401 of emerging viruses, 399–400, 399f and HIV antiviral drugs, 400 and origin of viruses, 400–401 steps in, 395–99 viral vectors, 435 Virchow, Rudolf, 69, 204, 323 Virginia creeper (Parthenocissus quinquefolia), 682–83 viroids, 401, 401f virulence, 798 virulence plasmids, 404 virulent phages, 399 viruses: cancer related to, 317–18, 318t cytotoxic T cells and, 1123 and humoral immunity, 1118 as pathogens, 1109 properties of, 392–95, 392t, 393f, 394f structure and variability of, 392–95, 392t, 393f, 394f viroids and prions vs., 401–3, 401f, 402f, 402t visceral mass, of mollusks, 710 Viscum album, 1228 visible light, 167 vision: brain structures related to, 916

CNS processing in, 926 color, 938–39, 939f for deep-sea vertebrates, 942 of primates, 548 See also photoreception “Vision and Change in Undergraduate Biology Education” conference, 4, 4f, 17 visual communication, 1191, 1191f visual disorders, 947–48, 948f visual field, effects of visual disorders on, 947, 948f visual image, in retina, 941, 941f visual loss, 947 visual nuclei, of musicians vs. nonmusicians, 920–21f visual pigments: photons and conformation of, 940–41, 940f in rods and cones, 938, 938f visual system. See photoreception. vitalism, 45 vitamin A, 938 vitamin C, 972 vitamin D: and calcium ion concentration, 1073– 74, 1073f and eye color, 556 vitamins: absorption of, 978, 980, 984 from diet, 972, 973t as nutrients, 971 viviparous species, 740 Vmax (maximum reaction velocity), 133–34, 133f Vogt, Peter, 318 volcanic eruptions: primary succession following, 1240–41 since origin of Earth, 540 voles, 1197 Volta, Alessandro, 884, 885 voltage-gated ion channels, 888, 889, 891 volts, 885 volume: blood, distribution of, 1138, 1138f and blood pressure, 1132–33, 1132f, 1133f intracellular fluid, 873, 873f and surface area, 866 volume, cell: and cell size/shape, 82–83, 82f and vacuoles, 94–95, 94f volvocine algae, 543 Volvox aureus, 543 von Haeseler, Arndt, 527 von Mayer, Julius, 165 Vries, Hugo de, 350

W

Wächtershäuser, Günter, 71 Wackernagel, Mathis, 1259 Waddington, Conrad, 374 waggle dance, 1192, 1192f Walcott, Charles, 544 Wald, George, 938

INDEX I-55 stomata and loss of, 829–31, 830f summary, 43 in tracheophytes, 647f and waxes, 55 in xylem, 826–28, 827f, 828f water availability, 1157, 1158f water-breathing animals: ion and water balance for, 874–75, 875f respiratory systems of, 1025–27, 1025f water-conducting cells, of xylem, 775, 775f water cycles, 1265, 1266f water deficit, 829 water-holding capacity, of soil, 805–7, 806f, 807f Waterland, Robert, 379 water potential, 820–22, 822f Waters, Colin, 1257 water-soluble hormones, 1059, 1061–62 water-soluble vitamins, 972, 973t, 984 water stress, 829–32 water vapor, 39 as greenhouse gas, 1260, 1261t from transpiration, 818, 829, 829f See also transpiration water vascular systems, 727–28, 727f, 728f, 728t Watson, James, 226–27, 451 wavelength, 167, 929 waxes, 55 waxy cuticles of plants, 215, 216 weak acids, 41 weaponry, as predation defense, 1225f, 1226 weathering, 806 web of life, 7, 8f, 532–33 web spinning, 720–21, 721f weight, mass vs., 29 weight, and relative water content, 822 Weinberg, Wilhelm, 479 Weintraub, Harold, 427–29 Weismann, August, 221, 355 Welwitschia mirabilis, 670, 671f Went, Frits, 787 western hemlocks, 1241–42, 1242f western meadowlark, 500 wetlands, 1174, 1174f whales: evolution of, 465, 467f sensory systems of, 925, 930 threatened due to overexploitation, 1272, 1272f wheat, 179, 180f, 365–66, 366f, 790 wheat rust, 616, 617f whisk fern (Psilotum nudum), 646f White, Philip, 810 white blood cells, 1015 See also leukocytes white clover, 1155, 1156f white-crowned sparrows, 1183, 1184f white-handed gibbon, 549f white-handed gibbons. See gibbons. white matter, 908, 909f whitemouth moray eel, 741f white muscle fibers, 961

See also glycolytic fibers white-nose syndrome, 1108 white of eyes. See sclera. White pelican, 752f Whittaker, Robert, 517, 1164 whole-genome duplications, in flowering plant evolution, 674, 675f whole metagenomic sequencing (WMS), of microbiome, 624f, 625–26, 627f whooping cough, 569 whorls, flower, 844, 844f Wieschaus, Eric, 421, 1112, 1113 wild mustard plant, 470, 470f wild-type alleles, 363 Wilkins, Maurice, 226, 227 Wilkinson, Gerald, 1196 Williams, George C., 1194 willow trees, 127, 1232, 1233f Wilmut, Ian, 1292 Wilson, Allan, 527, 554 Wilson, E. O., 497, 1244, 1244f, 1246–47, 1280–82, 1286 Wilson, Henry V., 417 wind: and anemotaxis, 1185 and Coriolis force, 1162 and effects temperature, 1157, 1158f plant responses to, 795–96 wings, 751f, 965 wintercreeper, 468, 469f winter wheat, flowering of, 844 witchweeds, 815 WMS (whole metagenomic sequencing), of microbiome, 624f, 625–26, 627f Woese, Carl, 517 Wöhler, Friedrich, 45, 46 Wolf, Larry, 1190 wolves, 1232, 1233f wood: defined, 665 in gynmosperm evolution, 665–66, 666f and roots, 777 and secondary xylem, 776 structure of, 776, 776f, 777 Woodcock, Christopher, 238 wood frog, 745, 745f wood lice, 725f, 726 woodpeckers, 1270, 1270f wood pigeon, 1193, 1193f woody plants: as eudicots, 763 phloem loading in, 835, 836 plant-bacterial symbioses, 812 secondary growth in, 766 vascular systems of, 775 See also flowering plants (angiosperms); gymnosperms woody progymnosperms. See progymnosperms. woody roots, 778 work ethic, 1182 World Health Organization, 985 worms, 1085 See also Annelida and annelids; flatworms; Nematoda and nematodes wounds, plant responses to, 835, 835f

wound sealing, after hemorrhage, 1132 Wright, Sewall, 477 Wright, Stephen, 683 Wuchereria bancrofti, 717 Wyllie, Andrew, 197, 198f Wynne-Edwards, V. C., 1193–94 Wyoming, 1168, 1168f

X

Xanax, 899 X-chromosome inactivation, 377–79, 377f, 378f, 378t X chromosomes: of chimpanzees vs. humans, 550 inactivation of, 377–79, 377f, 378f, 378t and muscular-skeletal systems, 967 number of, 378, 378t Xenartha, 757 Xenopus laevis, 414 xeroderma pigmentosum (XP), 304, 313–14, 314f X-Gal, 437 X inactivation center (Xic), 378, 378t Xist gene, 379 X-linked genes, 360–61 X-O system, 359, 360f X-ray diffraction pattern: of DNA, 226, 226f of ribosomes, 259, 259f xylem, 645, 646 bulk flow in, 825, 825f and Casparian strips, 824 and cytokinins, 792 long-distance plant transport in, 818, 825f, 826–28, 827f as plant tissue, 216 and primary stem structure development, 766, 767 secondary, 776–77, 779 (See also wood) and transpiration, 828–29 water-conducting cells of, 775, 775f X-Y system, 359, 360f

Y

Yamanaka, Shinya, 427 Yasumura, Yuki, 791 yeast: fermentation in, 161 genome size of, 449 yeasts, 609, 620 asexual reproduction by, 609, 610f cell division in, 334 cellular response by, 184, 184f Yersinia pestis, 577 yew tree, 669f yolk, 1100 yolk plug, 1103 yolk sac, 746, 747f Yoshida, Masasuke, 157–59 Young, Larry, 1197 Yucca constricta, 498 Yucca pallida, 498 yucca species, 498

INDEX

Walker, Brian, 1281 Walker, John, 157 Wallabia bicolor, 756f Wallace, Alfred Russel, 461, 482, 1176 Wallin, Ivan, 98 wall pores, of peat moss, 627, 627f walruses, 754f, 1004 warblers, 1221, 1221f Warburg, Otto, 149 Warburg effect, 149 Warren, J. Robin, 987–88 wasps, 2t, 724, 882 waste removal: exchanges of ions and water in, 874 processes for, 1044–45, 1045f wastes, water in elimination of, 40–41, 40f water, 36–41 absorption of, 768, 769f, 975, 978, 984 absorption of, in plant cells, 768, 769f and aldosterone, 1051, 1052 and amphipathic molecules, 37, 37f balance of ions and water in internal fluids, 873–74 bulk flow of, 825–26, 825f, 826f cell-based transport of, in plants, 820–22, 821f, 822f in chemical reactions, 36 circulation of, through sponges, 703, 703f cohesion-tension theory and transport of, 828–29, 828f, 829f concentration of solute in, 38–39 defined, 36 dissolution of gases in, 1025 and distribution of organisms, 1158–60, 1159f exercise and homeostatic balance of, 876–79 functions of, 40–41, 40f hydrogen and hydroxide ions in, 41 hydrogen bonds in, 33f ions and polar molecules in, 37, 37f leaf abscission and loss, 833–34 leaf vein damage and flow of, 773 in lycophytes and pteridophytes, 646–47, 647f in mass of living organisms, 29 molecular shape of, 35f movement between fluid compartments by, 873 movement detection in, 933, 933f movement of, in osmosis, 115–16, 116f obligatory exchanges between body and environment of, 874–76 in photosynthesis, 165, 173f and plant nutrition, 802f, 804–5 polar covalent bonds, 32, 32f in proximal tubule, 1049, 1050 proximity to, and climate, 1162–63, 1163f reabsorption of, 1050–51, 1050f, 1052–53, 1053f resistance of, for aquatic animals, 964 in sandy soil, 806, 807, 807f and secondary response to hemorrhage, 1140, 1142, 1142f states of, 39–40, 39f

I-56 INDEX

Z

Zea mays, 683, 828, 829, 844, 844f zeatin, 786t zebra, 1132f zebrafish, 414 zebra mussel, 709

zero population growth, 1210 zeta-globin, 1097 zeta-globin genes, 451 Zika virus, 399 zinc, in plant nutrition, 802t zinnia, 676f Z line, 955

zombie parasites, 1, 2, 2t zona pellucida, 1089, 1090 zone of elongation, 778, 778f zone of maturation, 778–79, 778f, 779f Z scheme, 174, 174f Zuckerkandl, Emile, 523

Z-W system, 359, 360f zygomorphic flowers, 845 zygosporangia, 614f zygospores, 611, 613, 614f zygotes: defined, 414, 1085 of flowering plants, 842, 851, 851f

INDEX