Biology Today and Tomorrow Without Physiology (MindTap Course List) [6 ed.] 0357127552, 9780357127551

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Chapter

Digging Into Data Features in the Sixth Edition

Page

1

Peacock Butterfly Predator Defenses

18

2

Effects of Dietary Fats on Lipoprotein Levels

46

3

Organelles and Cystic Fibrosis

66

4

One Tough Bug

84

5

Fossil Fuel Emissions

103

6

Dietary Fat Overload Reprograms Mitochondria

119

7

DNA or Protein?

126

8

RIPs as Cancer Drugs

150

9

HeLa Cells Are a Genetic Mess

168

BPA and Abnormal Meiosis

175

10

The Cystic Fibrosis Allele and Typhoid Fever

187

11

Enhanced Spatial Learning Ability in Mice Engineered to Carry an Autism Mutation

213

12

Discovery of Iridium in the K–Pg Boundary

226

13

Resistance to Rodenticides in Wild Rat Populations

246

14

How Plasmodium Summons Mosquitoes

284

15

Removing Fungus-Infected Stumps to Save Trees

310

16

Sustainable Use of Horseshoe Crabs

329

17

Monitoring Iguana Populations

355

18

Changes in Atmospheric Carbon Dioxide

388

19

Plastic Pollution in the Pacific

408

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Biology Today and Tomorrow

Without Physiology

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

Biology Today and Tomorrow

Without Physiology

6e Cecie Starr    Christine A. Evers    Lisa Starr l

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Biology Today & Tomorrow Without Physiology, Sixth Edition Cecie Starr, Christine A. Evers, Lisa Starr

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BRIEF CONTENTS 1 Invitation to Biology  Unit 1  How Cells Work

2 Molecules of Life  3 Cell Structure  4 Energy and Metabolism  5 Photosynthesis  6 Releasing Chemical Energy Unit 2  Genetics

7 DNA Structure and Function 8 Gene Expression and Control

Unit 3 EVOLUTION AND DIVERSITY

12 Evidence of Evolution 13 Processes of Evolution 14 Prokaryotes, Protists, and Viruses 15 Plants and Fungi 16 Animal Evolution Unit 4 ECOLOGY

17 Population Ecology 18 Communities and Ecosystems 19 The Biosphere and Human Effects

9 How Cells Reproduce 10 Patterns of Inheritance 11 Biotechnology

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CONTENTS 1 Invitation to Biology Fernan Federici & Jim Haseloff/Wellcome Images

1.1 The Secret Life of Earth  3 1.2 L ife Is More Than the Sum of Its Parts  4 Life’s Organization  4

1.3 How Living Things Are Alike  6 Organisms Require Nutrients and Energy  6 Organisms Sense and Respond to Change  7 DNA Is Hereditary Material  7

1.4 How Living Things Differ  8

Unit 1 How Cells Work

The Prokaryotes  8 The Eukaryotes  8 Organizing Information about Species  10 Taxonomy 11 Determining Relative Relatedness  11 The Biological Species Concept  12

1.5 The Science of Nature  12 Thinking about Thinking  12 Critical Thinking in Science  13 Experiments 13

2 Molecules of Life 2.1 A Big Fat Problem  27 2.2 Atoms 28 Atomic Structure  28 Elements 28 Isotopes 28 Why Electrons Matter  29

2.3 Chemical Bonds  32 Ionic Bonds  32

The Scientific Method  14

Covalent Bonds  32

Examples of Biology Experiments  15

Bond Polarity  33

1.6 Analyzing Experimental Results 17 Sampling Error  17 Statistical Significance  18 Bias 19 The Importance of Feedback  19

1.7 The Nature of Science  20 What Science Is  20 What Is Not Science  21 What Science Is Not  22 Why Science?  22

2.4 Special Properties of Water  34 Hydrogen Bonds  34 Water as a Solvent  34 Water Stabilizes Temperature  35 Cohesion 35

2.5 Acids and Bases  36 Hydrogen Ions  36 Acids, Bases, and Buffers  37

2.6 The Chemistry of Biology  37 Organic Compounds  37 The Carbon Backbone  38 Modeling Organic Compounds  38 What Cells Do to Organic Compounds  38

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Contents  ix 

2.7 Carbohydrates 39 Simple Sugars  39 Oligosaccharides 40 Polysaccharides 40

2.8 Lipids 41 Fatty Acids  41 WITSALUN/Shutterstock.com

Triglycerides 42 Phospholipids 43 Steroids 43 Waxes 44

2.9 Proteins 44 Protein Structure  44 The Structure–Function Relationship  46

2.10 Nucleic Acids  48

4 Energy and Metabolism

Nucleotides 48

4.1 A Toast to Alcohol Dehydrogenase  75

RNA and DNA  48

4.2 Life Runs on Energy  76 Thermodynamics 76 Chemical Bonds Hold Energy  76

3 Cell Structure

Work 76

3.1 Food for Thought  53

Energy Transfers Are Inefficient  77

3.2 What Is a Cell?  54

4.3 Energy in the Molecules of Life  77

Components of All Cells  54

Chemical Reactions  77

The Surface-to-Volume Ratio  55

Bond Energy  78

Microscopy 55

Storing and Retrieving Energy in Organic Molecules  79

Cell Theory  57

3.3 Cell Membrane Structure  57

4.4 Enzymes and Metabolic Pathways  79

The Lipid Bilayer  57

The Need for Speed  79

Fluid Mosaic Model  57

The Active Site  80

Proteins Add Function  58

Environmental Effects on Enzyme Activity 80

3.4 Prokaryotic Cells  59 Structural Features  60

Molecular Effects on Enzyme Activity 81

Biofilms 61

Metabolic Pathways  82

3.5 Eukaryotic Organelles  62 The Nucleus  62

4.5 Diffusion across Membranes  84 Diffusion of Solutes  84

Mitochondria 63

Tonicity and Osmosis  85

Chloroplasts 63

Turgor Pressure  86

The Endomembrane System  63

3.6 Elements of Connection  66

4.6 Membrane Transport Mechanisms  87 Transport Proteins  87

Cytoskeletal Elements  66

Passive Transport  87

Extracellular Matrix  68

Active Transport  87

Cell Junctions  68

Vesicle-Based Transport  88

3.7 The Nature of Life  70

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x  CONTENTS

5 Photosynthesis

Unit 2 Genetics

5.1 A Burning Concern  93

7 DNA Structure and Function

5.2 Overview of Photosynthesis  95 Storing Energy in Sugars  95

7.1 A Hero Dog’s Golden Clones  123

Stages of Reactions  95

7.2 The Function of DNA  124

Sites of Photosynthesis  95

Killer Bacteria and the Stupid Molecule 124

Stomata 96

5.3 Light Energy  97

Properties of a Hereditary Material  124

Visible Light  97

DNA: The Molecule of Heredity  126

Photosynthetic Pigments  97

7.3 The Structure of DNA  128

Fall Colors  98

Building Blocks of DNA  128

5.4 Light-Dependent Reactions  99

Discovery of DNA Structure  128

Photosystems 99

Anatomy of a DNA Molecule  129

The Noncyclic Pathway  99

7.4 Eukaryotic Chromosomes  130

Photosynthesis in the Dark  101

DNA Packaging  130

5.5 Light-Independent Reactions  102

The Chromosome Number  132

The Calvin–Benson Cycle  102

Autosomes and Sex Chromosomes  132

Efficiency of Sugar Production  102

7.5 DNA Replication  133 The Process of DNA Synthesis  133

6 Releasing Chemical Energy

PCR: DNA Replication in a Tube  134

6.1 Risky Business  107

7.6 Mutations 134

6.2 Carbohydrate Breakdown Pathways  108

Mutations: DNA Sequence Changes  134 Replication Errors  135

Overview of the Pathways  108

UV Light  135

Glycolysis: Sugar Breakdown Begins  109

Ionizing Radiation  136

6.3 Aerobic Respiration  109 Aerobic Respiration Continues  111

Chemicals 136

Electron Transfer Phosphorylation  111

Not All Mutations Are Dangerous  137

Overall ATP Yield of Aerobic Respiration  113

8 Gene Expression

6.4 Fermentation 113 Alcoholic Fermentation  114

and Control

Lactate Fermentation  114

8.1 Ricin, RIP  141

6.5 Food as a Source of Energy  116

8.2 DNA, RNA, and Gene Expression  142

Oxidizing Molecules in Food  116

Genes 142

The Ketogenic Diet   118

Comparing DNA and RNA  143 Information Flow  143

Anthony Pierce/Alamy Stock Photo

8.3 Transcription: DNA to RNA  144 Comparing Transcription and DNA Replication  144 Coding and Noncoding Strands  144 RNA Synthesis  145 A New RNA Is Modified  145

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

Contents  xi 

8.4 RNAs in Translation  146

9.6 Meiosis in Sexual Reproduction  171

The Message in a Messenger RNA  146

Stages of Meiosis  171

The Translators: rRNA and tRNA  147

Crossing Over  174 From Gametes to Offspring  174

8.5 Translation: RNA to Protein  148 Translation in Eukaryotic Cells  148

10 Patterns of Inheritance

How RIPs Interfere with Translation  150

8.6 Products of Mutated Genes  151

10.1 Menacing Mucus  179

Harmful Mutations Are Rare  151

10.2 Tracking Traits  180

Base-Pair Substitutions  151

Early Thoughts about Heredity  180

Deletions and Insertions  152

Mendel’s Pea Plants  180

Mutations in Regulatory Sites  152

Inheritance in Modern Terms  180

8.7 Control of Gene Expression  153

10.3 Mendelian Inheritance Patterns  183

Molecular Switches  153

Segregation of Genes into Gametes  183

Why Cells Control Gene Expression  153 Master Regulators in Embryonic Development  153 DNA Methylations  154

Independent Assortment of Genes into Gametes  184

10.4 Non-Mendelian Inheritance  185

Steve Gschmeissner/Science Photo Library/ Getty Images

Incomplete Dominance in Snapdragons  185 Codominance and Blood Type  186 Pleiotropy and Marfan Syndrome  186 Polygenic Inheritance  186

10.5 Complex Variation in Traits  188 Nature and Nurture  188 Examples of Environmental Effects on Phenotype  188 Continuous Variation  189

9 How Cells Reproduce 9.1 Henrietta’s Immortal Cells  159 9.2 Multiplication by Division  160 The Cell Cycle  160 How Mitosis Maintains the Chromosome Number  161 Why Cells Divide by Mitosis  161

9.3 Mitosis and Cytoplasmic Division  163 Stages of Mitosis  163 Cytoplasmic Division  164

9.4 Cell Cycle Control  165 Checkpoints 165 Losing Control  165 Pathological Mitosis  166 The Role of Telomeres  167

9.5 Sex and Alleles  169 Introducing Alleles  169 On the Advantages of Sex  170

10.6 Human Genetic Analysis  190 Studying Inheritance in Humans  190 Genetic Disorders and Abnormalities 190 Discovering a Breast Cancer Gene  191

10.7 Inheritance Patterns in Humans  192 The Autosomal Dominant Pattern  192 The Autosomal Recessive Pattern  193 The X-Linked Recessive Pattern  194

10.8 Changes in Chromosome Number  196 Polyploidy and Aneuploidy  196 Down Syndrome  196 Sex Chromosome Aneuploidy  196

10.9 Genetic Testing  198 Tests for Newborns  198 Tests for Prospective Parents  198 Prenatal Tests  198 Reproductive Interventions  199

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

xii  CONTENTS

11 Biotechnology

12.3 Natural Selection  223 Darwin and the HMS Beagle 223

11.1 Personal Genetic Testing  203

Great Minds Think Alike  224

11.2 Working with DNA  204

12.4 Fossil Evidence  225

Restriction Enzymes  204

Fossils 225

Recombinant DNA  204

The Fossil Record  226

DNA Cloning  204

Finding a Missing Link  227

PCR 206

Radiometric Dating  227

11.3 Studying DNA  207

12.5 Changes in the History of Earth  229

Sequencing 207

Continents Drift  229

The Human Genome Project  208

Plate Tectonics  229

Genomics 208

The Geologic Time Scale  231

DNA Profiling  209

12.6 Evidence in Form and Function  234

11.4 Genetic Engineering  211

Homologous Structures  234

GMOs 211

Analogous Structures  235

Modified Microorganisms  211

12.7 Molecular Evidence  236

Designer Plants  211

Similarities in DNA and Proteins  236

Biotech Barnyards  212

Similarities in Development  237

11.5 Editing Genomes  214 Gene Therapy  214

13 Processes of Evolution

CRISPR Gene Editing  214

13.1 Farming Superbugs  241 13.2 Alleles in Populations  242 Variation in Shared Traits  242 An Evolutionary View of Mutations  243

Nature Picture Library/Alamy Stock Photo

Allele Frequency  244

13.3 Patterns of Natural Selection  245 Directional Selection  245 Stabilizing Selection in the Sociable Weaver  247 Disruptive Selection in the Black-Bellied Seedcracker 248

13.4 Natural Selection and Diversity  248 Survival of the Sexiest  248 Maintaining Multiple Alleles  249

Unit 3 EVOLUTION AND DIVERSITY

13.5 Nonselective Evolution  250 Genetic Drift  250 Population Bottlenecks  251

12 Evidence of Evolution

The Founder Effect   251

12.1 Reflections of a Distant Past  219

Gene Flow  252

12.2 Old Beliefs, New Discoveries  220

Inbreeding 252

13.6 Speciation 253

The Great Chain of Being  220

Reproductive Isolation  253

New Evidence  221

Allopatric Speciation  255

New Ideas  221

Sympatric Speciation  256

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

Contents  xiii 

13.7 Macroevolution 257

14.7 Viruses 286

Macroevolutionary Patterns  257

Viral Structure  286

Evolutionary Theory  260

Viral Replication  286

13.8 Phylogeny 260 Reconstructing Evolutionary History 260 Applications 261

14 Prokaryotes, Protists, and Viruses 14.1 The Human Microbiota  267 14.2 Origin of Cellular Life  268 Conditions on the Early Earth  268

Viruses and Human Health  288 Viral Mutation and Recombination  289

15 Plants and Fungi 15.1 Fungal Threats to Crops  293 15.2 Plant Traits and Evolution  294 Life Cycles  294 Structural Adaptations  295 Reproduction and Dispersal  295

15.3 Nonvascular Plants  296

The Building Blocks of Life  269

Moss Life Cycle  296

Origin of Metabolism  269

Diversity and Ecology  297

Origin of Genetic Material  270 Origin of Cell Membranes  270 Defining Plausible Pathways  270

14.3 Early Life  271 The Last Common Ancestor of All Life  271

15.4 Seedless Vascular Plants  298 Ferns 298 Horsetails and Lycophytes  299 Coal Forests  300

15.5 Rise of the Seed Plants  301 Seed Formation  301

An Early Divergence  271

Seed Dispersal  301

Fossil Evidence of Prokaryotic Cells  271

Wood Production  301

The Great Oxygenation Event  272

14.4 Modern Bacteria and Archaea  273 Structural Traits  273 Reproduction 274

15.6 Gymnosperms 302 Conifers 302 Cycads and Ginkgos  303

15.7 Angiosperms—Flowering Plants  303

Gene Exchanges  274

Floral Structure and Function  303

Ecology and Diversity of Bacteria  275

Flowering Plant Life Cycle  304

Bacteria and Human Health  275

Angiosperm Success  305

Antibiotics 276

Monocots and Eudicots  305

The Archaea  276

Ecological and Economic Importance 306

14.5 Origin of Eukaryotes  277 Fossil Eukaryotes  277

15.8 Fungal Traits and Diversity  307

A Mixed Heritage  277

Structure of a Fungus  307

The Endosymbiont Hypothesis  278

Lineages and Life Cycles  308

14.6 Protists 279

15.9 Ecological Roles of Fungi  310

Cell Structure  279

Decomposers 310

Free-Living Aquatic Cells  279

Fungal Infections of Plants  310

Algae 281

Fungal Infections of Animals  311

Protists in the Human Body  282

Fungal Infections in Humans  311

Slime Molds  284

Fungal Partnerships  311

Protist Relatives of Animals  284

Human Uses of Fungi  312

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

xiv  CONTENTS

16 Animal Evolution 16.1 Medicines from the Sea  317 16.2 T  raits and Evolutionary Trends 318 Animal Origins  318 Andrey Armyagov/Shutterstock.com

Evolutionary Tree of Animals  318 Early Animals  320 Cambrian Adaptive Radiation  320

16.3 Sponges and Cnidarians  321 Sponges 321 Cnidarians 322

16.4 F latworms, Annelids, and Mollusks 323 Flatworms  323 Annelids 324 Mollusks 324

16.5 Roundworms and Arthropods  326 Roundworms  326 Arthropods Traits  327 Arthropod Lineages  328

16.6 Echinoderms and Chordates  332 Echinoderms 332 Chordates 333 Invertebrate Chordates  333 Vertebrate Traits and Trends  334

16.7 Fishes and Amphibians  335 Jawless Fishes  335 Jawed Fishes  335 Amphibians 336 Declining Amphibian Populations 337

16.8 E  scape from Water— Amniotes 338

Unit 4 ECOLOGY

17 Population Ecology 17.1 Managing Canada Geese  351 17.2 Characteristics of Populations  352 Population Size and Density  352 Population Distribution  352 Age Structure  354 Collecting Population Data  354

17.3 Models of Population Growth  355 Exponential Growth  356 Density-Dependent Limiting Factors  356 Carrying Capacity  356 Logistic Growth  357 Density-Independent Factors  357 Combined Effects of Limiting Factors  357 Human Effects on Carrying Capacity  358

17.4 Life History Patterns  359

Reptiles 339

Biotic Potential  359

Mammals 340

Describing Life Histories  359

16.9 P  rimate and Human Evolution 341

Adaptive Value of Life History Traits  360 Opportunistic Life History  360

Primate Origins and Diversification  343

Equilibrial Life History  361

Early Hominins  343

Effects of Humans as Predators  362

Early Humans  344

Predation and Life History Evolution  361

17.5 Human Populations  362

Homo sapiens 344

Population Size and Growth Rate  362

Neanderthals and Denisovans 345

Fertility Rates and Future Growth  364 Effects of Industrial and Economic Development  365

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Contents  xv 

18.1 Invasion of the Red Imported Fire Ants  369 18.2 Community Structure  370 Nonbiological Factors  370 Biological Factors  371

18.3 Direct Species Interactions  371 Interspecific Competition  371 Predation 372 Herbivory 374 Parasitism 374 Biological Pest Control  375 Commensalism 375 Mutualism 376

18.4 How Communities Change  377 Ecological Succession  377 The Role of Disturbance  378 Species Losses or Additions  378

18.5 The Nature of Ecosystems  379 Food Chains and Webs  380 Energy Capture and Transfers  380 Biological Accumulation and Magnification  382

18.6 T  he Water, Nitrogen, and Phosphorus Cycles 383 The Water Cycle  383 The Phosphorus Cycle  384 The Nitrogen Cycle  385 Nutrient Pollution and Algal Blooms  386

18.7 T  he Carbon Cycle and Climate Change  387 The Carbon Cycle  387 Increasing Atmospheric Carbon Dioxide  388 Ocean Acidification  389 The Greenhouse Effect  389 Global Climate Change  390

19.3 Forest Biomes  399 Tropical Forests  399 Temperate Deciduous Forests  400 Coniferous Forests  400 Deforestation 400

19.4 Grasslands, Chaparral, Deserts, and Tundra  402 Fire-Adapted Biomes  402 Desert 403 Desertification 403 Tundra 404

19.5 Aquatic Ecosystems  405 Streams and Rivers  405 Lakes 405 Nearshore Marine Ecosystems  405 Coral Reefs  406 The Open Ocean and Seafloor  406

19.6 Global Effects of Pollution  407 Talking Trash  407 Acid Rain   408 Destruction of the Ozone Layer  409 Global Climate Change  409

19.7 Conservation Biology  411 The Extinction Crisis  411 The Value of Biodiversity  413 Setting Priorities  413 Protection and Restoration  414 Reducing Human Impacts  414

Appendix I

Answers to Self-Quizzes  418

Appendix II

Periodic Table of the Elements  420

Appendix III

A  Plain English Map of the Human Chromosomes  421

Glossary 422 Index 430

19 The Biosphere and Human Effects 19.1 Decline of the Monarchs  395 19.2 C  limate and the Distribution of Biomes  396 Solar Energy and Latitude  396 Air Circulation and Rainfall  396 Ocean Currents  397 Distribution of Biomes  398

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Buena Vista Images/The Image Bank/Getty Images

18 Communities and Ecosystems

PREFACE The easy, instant availability of information on a global scale is both facilitating and complicating science education. Biology in particular is a huge field, with a wealth of new discoveries being made daily, and biology-related issues such as climate change, gene editing, and the global spread of diseases making headlines all the time. In an age when anyone can post anything, distinguishing fact from opinion is more challenging—and more important—than ever. Biology: Today and Tomorrow Without Physiology presents accurate, up-to-date content in accessible language, with stunning images and beautiful art that bring the narrative to life. This book fosters scientific literacy skills by prioritizing active learning about the process of science, and it engages students with a host of real-world applications that illuminate the relevance of biology in everyday life. Features of This Edition As always, the text has been updated with new discoveries and current research. This edition has been aligned with “Vision and Change” recommendations: Core concepts emphasized and explored in every chapter facilitate learning from every perspective (molecular, cellular, ecological, organismal, and so on), and several new and enhanced features encourage active learning.

in cirrhosis; and an end-of-chapter Critical Thinking question asks students to connect the alcohol flushing reaction with genetically based differences in the alcohol-breakdown pathway. (Discussions related to health and the environment are marked in the index with red and blue squares, respectively.) Section-Based Learning Objectives  learning objectives associated with each section are phrased as activities that students should be able to carry out after reading the text. Chunked Content  To decrease student cognitive load and facilitate chapter review, concepts have been titled in the core narrative of each section. Take-Home Message  At the end of each section, a take-home message box that provides a brief summary of section concepts is useful for study review. Highly Visual Learning  Beautiful art with extended callouts enhances visual learning of complex mechanisms in the new chapter-based closer look feature. The feature includes one or more figure it out questions designed to engage students in an active learning process; an upside-down answer allows a quick check of understanding. On-Page Glossary  An on-page glossary includes boldface key terms introduced in each two-page spread. This spread-based glossary can be used as a quick study aid. All glossary terms also appear in boldface in the Chapter Summary.

Setting the Stage  Each chapter opens with an eye-catching photo and a brief concepts connections feature that links the chapter’s content with concepts in previous and future chapters. The opening application section explores an interesting current event or social issue related to the chapter’s topic. For example, a discussion of binge drinking on college campuses introduces the concept of metabolism in Chapter 4. This Application section links the function of enzymes in the body’s main alcoholbreakdown pathway to hangovers and cirrhosis. Open-ended discussion questions at the end of each Application section are intended to facilitate classroom discussions and critical thinking about the Application’s topic.

Self-Assessment Tools Many figure captions include a figure it out question. At the end of each chapter, self-quiz and critical thinking questions provide additional self-assessment material. Another active-learning feature, the in-text digging into data activity, sharpens analytical skills by asking students to interpret data presented in graphic or tabular form. The data presented are relevant to the chapter and are from published scientific studies.

Emphasis on Relevance  An expanded focus on applications that distinguishes this book allows students to understand the relevance of a topic while learning about it. At every opportunity, opening Application topics are revisited in section content, and in end-of-chapter assessments. For example, Section 4.4 (Enzymes and Metabolic Pathways) includes a paragraph about the role of the coenzyme NADH in the mechanism by which heavy drinking causes fatty liver; in Section 4.5 (Diffusion across Membranes), a discussion about osmotic pressure includes the mechanism by which body tissues swell with fluid

Highlights of Revision Updates 1 Invitation to Biology  Much-expanded material in a new section, “The Nature of Science,” includes detailed coverage of pseudoscience and how it differs from science. New Critical Thinking questions about cherry-picking climate change data and MMR vaccine pseudoscience. 2 Molecules of Life  Application section updated with new FDA ban of PHOs. New content includes current research on pathogenesis of amyloid diseases. New figures: bond polarity;

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 PREFACE  xvii 

patterns of protein secondary structure; prion structure changes. New Critical Thinking question about how using palm oil as a substitute for PHOs is exacerbating deforestation. Closer Look feature: How protein structure arises. 3 Cell Structure  New content includes theory of living systems;

discussion of nuclear pores, tau tangles, and Alzheimer’s disease. New tables: eukaryotic organelles; collective properties of living systems. New photographs: micrographs of gut microbiota, nuclear membrane, and basement membrane. New Critical Thinking question about why some meat contaminated with toxic strains of bacteria is not safe to eat even after cooking. Closer Look features (2): Some interactions among components of the endomembrane system; cell junctions in animal tissues.

4 Energy and Metabolism  New content: how heavy drinking

causes fatty liver; fluid balance in the body. New figures: feed conversion ratio; comparing activation energy in energy-releasing and energy-requiring reactions; enzymes lower activation energy; firefly luciferase. New Critical Thinking question about the alcohol flushing reaction and alcohol metabolism. Closer Look feature: Examples of membrane-crossing mechanisms.

5 Photosynthesis  For this edition, expanded material on

photosynthesis and respiration has been separated into two chapters. New overview section includes discussion of autotrophs, heterotrophs, and stomata function. Other new content: special pairs; bacteria that carry out infrared photosynthesis; increased efficiency of the Calvin–Benson cycle in engineered plants. New Digging Into Data activity about CO2 emissions from fossil fuels. New figures include atmospheric CO2 level over the last 800,000 years; correlation between atmospheric CO2 content and temperature since 1880; how photosynthesis sustains life; correlation between light wavelength and energy; red algae (photosynthetic pigment adaptation). New research correlating wildfire severity with rising global temperatures is included with a stunning photo of the 2018 Mendocino complex wildfire. Closer Look feature: Light-dependent reactions of photosynthesis, noncyclic pathway.

6 Respiration  New content includes Application about mito-

chondrial diseases, cellular respiration, and oxidative stress; introductory section comparing aerobic respiration with fermentation; glycolysis reactions; ketogenic diet mechanism. New figures: glycolysis reactions, alcoholic fermentation reactions; lactate fermentation reactions. New Digging Into Data activity about the reprogramming of brown fat mitochondria by dietary fat overload. Closer Look features (2): Aerobic respiration continues in mitochondria; food to energy.

7 DNA Structure and Function  New content includes introduction

to PCR; expanded material on mutations includes dosedependent DNA damage by ionizing radiation, and cancercausing chemicals in foods and industrial/household products. New figures: components of a nucleotide; micrographs of DNA

packing; mutated flowers from Chernobyl. Closer Look feature: DNA packing in eukaryotic chromosomes. 8 From DNA to Protein  New content includes concepts of coding

and noncoding strands; a beneficial hemoglobin mutation (HbC); and expanded material on epigenetics. New art: how transcription copies a gene into RNA form; comparison of uracil/thymine and ribose/deoxyribose; how transcription produces an RNA copy of a gene; RNA polymerase binding to promoter; alternative splicing; surface renders of ribosome subunits; effect of a mutation in a regulatory site; points of control over gene expression; replication of methylated DNA. New table compares features of DNA and RNA. Closer Look feature: Translation.

9 How Cells Reproduce  New content includes current research and

paradigms on cytoplasmic division and senescence; concept of polygenic inheritance; Mary Claire-King’s discovery of BRCA1. New figures: micrograph showing mitosis in a human embryo; micrograph of mitotic spindle; fluorescence micrographs of checkpoint proteins; different modes of reproduction; meiosis halves the chromosome number, and fertilization restores it. New table comparing asexual and sexual reproduction. New Critical Thinking question about HPV and cancer. Closer Look features (2): Mitosis; meiosis.

10 Patterns of Inheritance  New content includes current paradigms

for CF, Huntington’s, progeria, Tay–Sachs, and DMD; and concept of developmental flexibility in plant phenotype. New photos: cells lining trachea; seasonal changes in plants; albino iris; IVF. Closer Look feature: Breeding experiments with the garden pea.

11 Biotechnology  New content includes forensic genealogy case;

AquAdvantage Salmon; mechanism, applications, and social implications of CRISPR gene editing. New figures: Exponential amplification of DNA by PCR; photo of Golden Rice; example of CRISPR gene editing. New table lists human genome statistics. Closer Look feature: An example of cloning.

12 Evidence of Evolution  Cetacean evolutionary sequence updated

to reflect currently accepted narrative. New art: photo of Dorudon atrox fossil; stem reptile; plate tectonics; paleogeography Mercatur projections. Closer Look feature: Geologic time scale correlated with sedimentary rock in the Grand Canyon.

13 Processes of Evolution  New content includes updated material on

antibiotic resistance and overuse of antibiotics in livestock; forensic phylogenetics case; phylogeny of ST131 superbug. New figures: photos of variation in earlobe attachment; genetic drift, bottleneck, and the founder effect; evolution of ST131. Art updates to reflect current research: HbS allele frequency vs. incidence of malaria; sympatric speciation in wheat. New Critical Thinking question about the EPA’s 2019 approval of medically important antibiotics in the treatment of citrus greening disease. Closer Look feature: How reproductive isolation prevents interbreeding.

14 Prokaryotes, Protists, and Viruses  Updated information about

the role of the human microbiome in health and disease and the

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xviii  PREFACE 

proposed fossil evidence of early life. Increased emphasis on the ecological importance of bacteria. Updated figures illustrating binary fission and bacteriophage replication. New information about antibiotic mechanisms. Discussion of protists now organized around ecology, rather than phylogeny. New Critical Thinking questions about the human virome, and the effects of pesticides on pollinator microbiomes. Closer Look feature: Replication of HIV. 15 Plants and Fungi  Updated figures depicting plant and fungal

life cycles. New table compares plant, fungal, and animal traits. New figure illustrating the hyphae in a mushroom. New photo of peat bog. Updated information about white-nose syndrome in bats. New Critical Thinking question about plant defenses against wheat stem rust. Closer Look features (2): Moss life cycle; fern life cycle.

16 Animal Evolution  New content about and photo of the oldest

known fossil animal. New graphic of sea star anatomy. Updated discussion of early H. sapiens migrations. New Critical Thinking question about medicinal compounds derived from spider venom. Closer Look feature: One model of human evolution.

17 Population Ecology  New content about human overharvesting

of horseshoe crabs lowering the carrying capacity of the environment for migratory red knot sandpipers. Updated nationbased age structure diagrams. New Critical Thinking questions,

estimating size of a Canada goose population, predation on horseshoe crabs, effect of house sparrow introduction on bluebird populations, factors affecting human population growth. Closer Look feature: Logistic growth. 18 Communities and Ecosystems  Revised table better depicts the

variety of interspecific interactions. New content includes biological pest control, biological accumulation and magnification of toxins, nutrient pollution and algal blooms, and ocean acidification. Updated coverage of the rise in atmospheric carbon dioxide and added information about the data that indicate this increase is a result of fossil fuel use. New Critical Thinking questions about studying the history of the atmosphere and pollutant accumulation in marine mammals. Closer Look feature: The nitrogen cycle.

19 The Biosphere and Human Effects  New opening Application

about the decline of monarch butterflies. Content reorganized: Deforestation discussed with forest biomes, desertification with desert biomes. New content includes current threats to Brazilian rainforest. Updated coverage of acid rain, ozone depletion, and biodiversity hot spots. New Digging Into Data activity about marine plastic pollution. New Critical Thinking questions about preserving monarch butterflies, effects of ozone depletion on phytoplankton, and how Brazilian deforestation alters local climate.

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academic advisors We owe a special debt to the following members of our advisory committee for helping us shape the book’s content. We appreciate their guidance. Andrew Baldwin, Mesa Community College Gregory A. Dahlem, Northern Kentucky University Terry Richardson, University of North Alabama Previous Edition advisory members: Charlotte Borgeson, University of Nevada, Reno Gregory Forbes, Grand Rapids Community College Hinrich Kaiser, Victor Valley Community College Lyn Koller, Embry-Riddle Aeronautical University We also wish to thank the following reviewers: Idris Abdi, Lane College Susan L. Bower, Pasadena City College James R. Bray Jr., Blackburn College Randy Brewton, University of Tennessee Steven G. Brumbaugh, Green River Community College Jean DeSaix, University of North Carolina Brian Dingmann, University of Minnesota, Crookston Hartmut Doebel, The George Washington University Johnny El-Rady, University of South Florida Patrick James Enderle, Georgia State University Ruhul H. Kuddus, Utah Valley State College Dr. Kim Lackey, University of Alabama Catarina Mata, Borough of Manhattan Community College Timothy Metz, Campbell University Alexander E. Olvido, University of North Georgia Michael Plotkin, Mt. San Jacinto College Nathan S. Reyna, Oachita Baptist University Laura H. Ritt, Burlington County College Erik P. Scully, Towson University Jennifer J. Skillen, Sierra College Previous Edition Reviewers:

Mimi Bres, Prince George’s Community College Evelyn K. Bruce, University of North Alabama Chantae M. Calhoun, Lawson State Community College Thomas F. Chubb, Villanova University Julie A. Clements, Keiser University, Melbourne Francisco Delgado, Pima Community College Elizabeth A. Desy, Southwest Minnesota State University Josh Dobkins, Keiser University, online Pamela K. Elf, University of Minnesota, Crookston Jean Engohang-Ndong, BYU Hawaii Ted W. Fleming, Bradley University Edison R. Fowlks, Hampton University Martin Jose Garcia Ramos, Los Angeles City College J. Phil Gibson, University of Oklahoma Judith A. Guinan, Radford University Carla Guthridge, Cameron University Laura A. Houston, Northeast Lakeview–Alamo College Robert H. Inan, Inver Hills Community College Dianne Jennings, Virginia Commonwealth University Ross S. Johnson, Chicago State University Susannah B. Johnson Fulton, Shasta College Paul Kaseloo, Virginia State University Ronald R. Keiper, Valencia Community College West Dawn G. Keller, Hawkeye Community College Vic Landrum, Washburn University Lisa Maranto, Prince George’s Community College Kevin C. McGarry, Keiser University, Melbourne Ann J. Murkowski, North Seattle Community College Joshua M. Parke, Community College of Southern Nevada Elena Pravosudova, Sierra College Carol Rhodes, Cañada College Todd A. Rimkus, Marymount University Lynette Rushton, South Puget Sound Community College Marilyn Shopper, Johnson County Community College Jim Stegge, Rochester Community and Technical College Lisa M. Strain, Northeast Lakeview College Jo Ann Wilson, Florida Gulf Coast University

Meghan Andrikanich, Lorain County Community College Lena Ballard, Rock Valley College Barbara D. Boss, Keiser University, Sarasota

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student and instructor resources Cengage Learning Testing Powered by Cognero  This flexible, online system allows you to: ●●

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author, edit, and manage test bank content from multiple Cengage Learning solutions create multiple test versions in an instant deliver tests from your LMS, your classroom, or wherever you want

MindTap  A personalized, fully online digital learning platform of authoritative content, assignments, and services that engages students with interactivity while also offering instructors their choice in the configuration of coursework and enhancement of the curriculum. MindTap is well beyond an eBook, a homework solution or digital supplement, a resource center website, a course delivery platform, or a Learning Management System. It is the first in a new category—the Personal Learning Experience. New for this edition of MindTap: Why Does This Matter to Me?  Immediately capture students’ attention with the new why does this matter to me? activity. This activity connects the upcoming chapter to a realworld scenario to pique engagement and emphasize relevance. Ensure students have read before class and tee up a lively in-class discussion. Chapter-level eBook Learn It  Supplement textbook learning with multimedia instruction. learn its feature chunked instruction that covers the most important concepts in each chapter. learn its serve to reinforce instruction from the textbook. Assign learn its to ensure that your students have read and understand the key concepts before class.

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Instructor Companion Site  Everything you need for your course in one place! This collection of book-specific lecture and class tools is available online via www.cengage.com/login. Access and download PowerPoint presentations, images, instructor’s manual, and more. Acknowledgments Writing, revising, and illustrating a biology textbook is a major undertaking for two full-time authors, but our efforts constitute only a small part of what is required to produce and distribute this one. We are truly fortunate to be part of a huge team of very talented people who are as committed as we are to creating and disseminating an exceptional science education product. Biology is not dogma; paradigm shifts are a common outcome of the fantastic amount of research in the field. Ideas about what material should be taught and how best to present that material to students changes from one year to the next. It is only with the ongoing input of our many academic reviewers and advisors (previous page) that we can continue to tailor this book to the needs of instructors and students while integrating new information and models. We continue to learn from and be inspired by these dedicated educators. On the production side of our team, the indispensable Lori Hazzard orchestrated a continuous flow of files, photos, and illustrations while managing schedules, budgets, and whatever else happened to be on fire at the time. Lori, thank you for your patience and dedication. Thank you also to Ragav Seshadri, Kelli Besse, and Christine Myaskovsky for your help with photoresearch. Copyeditor Heather McElwain and proofreader Heather Mann, your valuable suggestions kept our text clear and concise.

Chapter Homework  Assign chapter homework that encourages students to apply what they have learned.

Thanks to Cengage’s Product Manager Katherine Caudill-Rios, Content Manager Brendan Killion, and In-House Subject Matter Expert Katherine Scheibel.

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Chapter Case Study  Build real-world data analysis and critical thinking skills with short chapter-level cases.

Cengage acknowledges and appreciates Lisa Starr’s contribution of more than 300 pieces of art to this edition.

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Biology Today and Tomorrow

Without Physiology

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1

1.1 The Secret Life of Earth  3

Invitation to Biology

1.2

Life Is More Than the Sum of Its Parts  4

1.3

How Living Things Are Alike  6

1.4

How Living Things Differ  8

1.5

The Science of Nature  12

1.6

Analyzing Experimental Results  17

1.7

The Nature of Science  20

The cloud forest that covers about 2 million acres of New Guinea’s Foja Mountains is extremely remote and difficult to access, even for native people of the region. Explorers are still discovering new species in it.

Concept Connections Tim Laman/National Geographic Image Collection.

Whether or not you have studied biology, you already have an intuitive understanding of life on Earth because you are part of it. Every one of your experiences with the natural world—from the warmth of the sun on your skin to the love of your pet—has contributed to that understanding. The organization of this book parallels nature’s levels of organization, from atoms to the biosphere. Learning about the structure and function of atoms and molecules will prime you to understand how living cells work. Learning about processes that keep a single cell alive can help you understand how multicelled organisms survive. Knowing what it takes for organisms to survive can help you see why and how they interact with one another and their environment.

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Invitation to Biology  Chapter 1  3 

Application 1.1  The Secret Life of Earth

biology  The scientific study of life.

species  A unique type of organism. Could there possibly be any places left on Earth that humans have not yet explored? Actually there are, and many of these places remain unexplored because they are difficult or impossible for us to access. Consider a milehigh cloud forest in the Foja Mountains of western New Guinea. This forest is huge, covering around 2 million acres of the region, but extremely rugged terrain kept it completely isolated from humans. Recently, persistent explorers found an opening in the forest large enough for a helicopter to drop them off. Since then, about forty new species—unique types of organisms— have been found in this forest, including a rhododendron plant with flowers the size of dinner plates, a rat the size of a cat, and a frog with an erectile nose (Figure 1.1A). Today, researchers no longer need to leave their offices to find places that are untouched by humans. In 2012, conservation scientist Julian Bayliss was perusing Google Earth when he spied a curious pimple rising from a jungled A. Paul Oliver discovered this tiny tree frog perched on plain in Mozambique, Africa. The pimple was Mount Lico, a 2,300-foot extinct a sack of rice during the first survey of a cloud forest volcano with a lush rain forest on top of it. Bayliss realized that Lico’s smooth, in the Foja Mountains of New Guinea. It was named the vertical rock face would be extremely difficult to climb, so he suspected that Pinocchio frog because the male’s long nose inflates and points upward during times of excitement. the forest had remained hidden and isolated. Six years later, two professional rock climbers helped Bayliss and his team of experts make the arduous ascent up Mount Lico. Exhaustion quickly gave way to excitement when the mudcaked scientists reached the summit because, as Bayliss had suspected, the forest was pristine. Over the next ten days, the team members discovered a host of new species: snakes, frogs, fish, butterflies, crabs, flowering plants, and so on (Figure 1.1B). New species are discovered all the time, even in unexpected places. In 2018, for example, a new type of tardigrade (a tiny animal) was found in the parking lot of an apartment complex. Each discovery is a reminder that we do not yet know all of the species that share our planet. We don’t even know how many to look for. B. Ana Gledis da Conceição Miranda discovered an as-yet unidentified mouse during the first survey of the rain How do we know what species a particular organism belongs to? What is forest atop Mount Lico, in Mozambique. a species, anyway, and why should discovering a new one matter to anyone other than biologists? You will find the answers to such questions in this book. They are part of the scientific study of life, biology, which is one of many ways Figure 1.1  Discovering new species in unexplored places. (A) Tim Laman/National Geographic Image Collection; (B) Jeffrey Barbee/Allianceearth.org. we humans try to make sense of the world around us. Trying to understand the immense scope of life on Earth gives us some Discussion Questions perspective on where we fit into it. 1. Hundreds of new species are discovered every year, but about 20 species become extinct Ironically, the more we learn about the every minute in rain forests alone—and those are only the ones we know about. Human natural world, the more we realize we activities are responsible for a massive acceleration in the rate of extinctions. Unless this have yet to learn. Whether or not we trend is reversed, we will never know about most of the species that are alive on Earth are aware of it, humans are intimately today. Why does that matter? connected with the world around us. 2. How could the discovery of a new species of plant or animal impact humans beyond Our activities are profoundly changing adding to our knowledge of the world? the entire fabric of life on Earth. 3. Explain the statement “the more we learn about the natural world, the more we realize we These changes are, in turn, affecting have yet to learn.” us in ways we are only beginning to understand.

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4 INTRODUCTION Figure 1.2  The same materials, assembled in different ways, form objects with different properties. The property of “roundness” emerges when these squares are assembled in a certain way.

1.2  Life Is More Than the Sum

of Its Parts Learning Objectives ●● ●●

Describe the successive levels of life’s organization. Use examples to explain how complex properties can emerge from interactions among simpler components.

Biologists study life. What, exactly, is “life”? We may never actually come up with a satisfying definition, because living things are too diverse, and they consist of the same basic components as nonliving things. When we try to define life, we end up with a long list of properties that differentiate living from nonliving things. These properties often emerge from the arrangements or interactions of basic components (Figure 1.2). Consider a complex behavior called swarming that is characteristic of honeybees. When the bees swarm, they fly en masse to establish a hive in a new location. Each bee is autonomous, but the new hive’s location is decided collectively based on an integration of signals from hive mates. A swarm’s collec­­­tive intelligence is a property that does not appear in the swarm’s components (individual bees).

Life’s Organization

atom  The smallest unit of matter.

Biologists view life in increasingly inclusive levels of organization. Interacting components of one level compose larger, more complex structures and systems of the next. The interactions give rise to new properties that emerge at each level. Later chapters detail these systems; here, we give a preview.

biosphere  All regions of Earth where organisms live. cell  Smallest unit of life. community  All populations of all species in a defined area. ecosystem  A community interacting with its environment. molecule  Two or more atoms bonded together. organ  In multicelled organisms, a structure that consists of tissues engaged in a collective task. organ system  In multicelled organisms, a set of interacting organs and tissues that carry out one or more body functions. organism  An individual that consists of one or more cells. population  A group of interbreeding individuals of the same species living in a defined area. tissue  In multicelled organisms, specialized cells organized in a pattern that allows them to perform a collective function.

an atom

– + –

Atoms An atom is the smallest unit of matter. All matter consists of atoms and the fundamental particles that compose them. No atoms are unique to living things.

a molecule

Molecules A molecule consists of atoms that are bonded together. Some molecules are unique to life, and these are more complex than the water molecule depicted here.

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Invitation to Biology  Chapter 1  5 

a cell

Cells The property we call “life” emerges as molecules organize to form cells. The cell is the smallest unit of life. Some, like this plant cell, live and reproduce as part of a multicelled organism; others do so on their own.

a tissue

Tissues A tissue consists of specific types of cells organized in a particular pattern. The arrangement allows the cells to collectively perform a special function. This is dermal tissue on the outer surface of a flower petal.

a community

an ecosystem

Ecosystems An ecosystem is a community interacting with its physical and chemical environment through the transfer of energy and materials. Sunlight and water sustain the community in the Antelope Valley.

an organ

Organs An organ is a structure composed of tissues that collectively carry out a particular task or set of tasks. Flowers are the reproductive organs of some plants.

an organ system

an organism

Organ Systems An organ system is a set of interacting organs and tissues that fulfill one or more body functions. Leaves, stems, flowers, and fruits form the shoot system of this plant. A plant’s body consists of two organ systems: shoots and roots.

Organisms An organism is an individual that consists of one or more cells. Humans consist of many cells, as do other organisms such as this California poppy plant.

the biosphere

The Biosphere The biosphere is the sum of all ecosystems, and it encompasses all regions of Earth’s crust, waters, and atmosphere in which organisms live.

Take-Home Message 1.2 ●●

●●

●●

a population

Populations A population is a group of interbreeding individuals of the same species living in a given area. This population of California poppy plants is in the Antelope Valley California Poppy Reserve.

Communities Populations interact in communities. A community consists of all populations of all species in a given area. This one includes all of the populations of plants, animals, microorganisms, and so on living in the Antelope Valley California Poppy Reserve.

●●

●●

●●

Biologists study life by thinking about it at successive levels of organization. Interactions among the components of each level give rise to complex properties that emerge at the next. All matter consists of atoms and the fundamental particles that compose them. Molecules consist of atoms that are bonded together. The property we call “life” emerges as molecules unique to life become organized into cells. An organism is an individual that consists of one or more cells. Many multicelled organisms have tissues that are organized as organs and organ systems. Interacting individuals compose populations, and interacting populations form communities. A community interacting with its environment constitutes an ecosystem. All ecosystems on Earth form the biosphere.

Top to bottom (left): Umberto Salvagnin; Umberto Salvagnin; California Poppy, © 2009, Christine M. Welter; Lady Bird Johnson Wildflower Center; SPL/Science Source; James Randklev/Exactostock-1672/SuperStock. Top to bottom (right): © Sergei Krupnov, www.flickr.com/photos/7969319@N03; © Mark Koberg Photography; Source: NASA.

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6 INTRODUCTION

1.3  How Living Things Are Alike 1 Producer acquiring energy and nutrients from the environment.

2 Consumer acquiring energy and nutrients by eating a producer.

Learning Objectives ●●

Distinguish producers from consumers.

●●

Describe the movement of nutrients and energy through the world of life.

●●

Explain why homeostasis is important for sustaining life.

All living things share a particular set of key features. You already know one of these features: Because the cell is the smallest unit of life, all organisms consist of at least one cell. For now, we introduce three more: All living things require ongoing inputs of energy and raw materials; all sense and respond to change; and all use DNA as the carrier of genetic information (Table 1.1). Table 1.1  Some Key Features of Life

ENERGY IN SUNLIGHT

Cellular basis

All living things consist of one or more cells.

Requirement for energy and nutrients

Life is sustained by ongoing inputs of energy and nutrients.

Homeostasis

Living things sense and respond to change.

DNA is hereditary material

Genetic information in the form of DNA is passed to offspring.

Organisms Require Nutrients and Energy  

4 Producers harvest energy from the environment. Some of that energy flows from producers to consumers. PRODUCERS

plants and other self-feeding organisms

3 Nutrients that get incorporated into the cells of producers and consumers are eventually released back into the environment (by decomposition, for example). Producers then take up some of the released nutrients. CONSUMERS

animals, most fungi, many protists, bacteria

5 All energy that enters the world of life eventually flows out of it, mainly as heat released back to the environment.

Figure 1.3  The one-way flow of energy and the cycling of materials in the world of life. Top, © Victoria Pinder, http://www.flickr.com/photos/vixstarplus.

Not all living things eat, but all require raw materials—nutrients—and energy on an ongoing basis. A nutrient is a substance that an organism needs for growth and survival but cannot make for itself. Producers and Consumers  Both nutrients and energy are essential to maintain

life, so organisms spend a lot of time acquiring them. However, the source of energy and the type of nutrients required differ among organisms. These differences allow us to classify all living things into two broad categories: producers and consumers (Figure 1.3). A producer makes its own food using energy and simple raw materials it obtains from nonbiological sources 1. Typical plants are producers. By a process called photosynthesis, plants use the energy of sunlight to make sugars from carbon dioxide (a gas in air) and water. Consumers, by contrast, cannot make their own food. A consumer obtains energy and nutrients by feeding on other organisms 2. Animals are consumers. So are decomposers, which feed on the wastes or remains of other organisms. Nutrients released from decomposing consumers return to the environment, where they are taken up by producers. Said another way, nutrients cycle between producers and consumers 3. The One-Way Flow of Energy  Unlike nutrients, energy is not cycled. It flows

through the world of life in one direction: from the environment 4, through organisms, and to the environment 5. This flow maintains the organization of every living cell and body, and it also influences how individuals interact with one another and their environment. The energy flow is one-way, because with each transfer, some energy escapes as heat, and cells cannot use heat as

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Invitation to Biology  Chapter 1  7 

an energy source. Thus, energy that enters the world of life eventually leaves it (Chapter 4 returns to this topic).

Organisms Sense and Respond to Change  An organism cannot survive for very long unless it responds appropriately to specific stimuli inside and outside of itself. Consider how humans and some other animals perspire (sweat) when the body’s internal temperature rises above a certain point (Figure 1.4). The moisture cools the skin, which in turn helps cool the body. All of the internal fluids that bathe the cells in your body are collectively called your internal environment. Temperature and many other conditions in that environment must be kept within certain ranges, or your cells will die (and so will you). By sensing and adjusting to change, all organisms keep conditions in their internal environment within ranges that favor cell survival. Homeostasis is the name for this process, and it is one of the defining features of life.

DNA Is Hereditary Material  Inheritance and Reproduction  With little variation, the same types of molecules

perform the same basic functions in every organism. For example, information in an organism’s DNA (a molecule called deoxyribonucleic acid) guides ongoing cellular activities that sustain the individual through its lifetime. These activities include growth: increases in cell number, size, and volume; reproduction: processes by which individuals produce offspring; and development: in multicelled species, the process by which the first cell of a new individual gives rise to an adult. Inheritance, the transmission of DNA to offspring, occurs during reproduction. All organisms inherit their DNA from one or two parents. DNA Is the Basis of Life’s Unity and Diversity  Individuals of every natural

population are alike in most aspects of body form and behavior because their DNA is very similar: Humans look and act like humans and not like poppy plants because they inherited human DNA, which differs from poppy plant DNA in the information it carries. Individuals of almost every natural population also vary—just a bit—from one another: One human has blue eyes, the next has brown eyes, and so on. Such variation arises from small differences in the details of DNA molecules, and herein lies the source of life’s diversity. As you will see in later chapters, differences among individuals of a species are the raw material of evolutionary processes.

Take-Home Message 1.3 ●●

●●

●●

Energy and nutrients are required to maintain life. Energy flows from the environment, through organisms, and back to the environment. Nutrients cycle between producers and consumers. Organisms sense and respond to conditions inside and outside themselves. They make adjustments that keep conditions in their internal environment within ranges that favor cell survival, a process called homeostasis. All organisms use information in the DNA they inherited from parents to guide activities such as growth, reproduction, and (in multicelled organisms) development. DNA is the basis of similarities and differences among organisms.

Figure 1.4  Living things sense and respond to their environment. Sweating is a physiological response to an internal body temperature that exceeds the normal set point. The response cools the skin, which in turn helps return the internal temperature to the set point. iStock.com/gvillani.

consumer  Organism that acquires energy and nutrients by feeding on the tissues, wastes, or remains of other organisms. development  In multicelled species, the process by which the first cell of a new individual gives rise to an adult. DNA  Deoxyribonucleic acid. Molecule that carries hereditary information. That information guides growth, reproduction, and other cellular activities. growth  Increases in the number, size, and volume of cells. homeostasis  Process in which organisms keep their internal conditions within tolerable ranges by sensing and responding appropriately to change. inheritance  Transmission of DNA to offspring. nutrient  A substance that an organism must acquire from the environment to support growth and survival. photosynthesis  Process by which producers use light energy to make sugars from carbon dioxide and water. producer  An organism that makes its own food using energy and nonbiological raw materials from the environment. reproduction  Processes by which individuals produce offspring.

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8 INTRODUCTION

1.4  How Living Things Differ Learning Objectives

A. Bacteria are the most numerous organisms on Earth. Clockwise from upper left, a bacterium with a row of iron crystals that serves as a tiny compass; a common bacterial resident of mouse stomachs; photosynthetic bacteria; bacteria found in dental plaque.

B. Archaea resemble bacteria, but are more closely related to eukaryotes. Left, an archaeon that grows in sulfur hot springs. Right, two types of archaea from a seafloor hydrothermal vent. Figure 1.5  A few representative prokaryotes. (A) top left, Dr. Richard Frankel; top right, Dr. Kari Lounatmaa/Science Photo Library/Getty Images; bottom left, Source: www.zahnarzt-stuttgart.com; bottom right, © Susan Barnes; (B) left, Dr. Terry Beveridge/Visuals Unlimited/Corbis; right, Source: © Dr. Harald Huber, Dr. Michael Hohn, Prof. Dr. K.O. Stetter, University of Regensburg, Germany.

animal  A multicelled eukaryotic consumer that develops through a series of stages and moves about during part or all of its life. archaea  Singular, archaeon. Group of prokaryotes that are more closely related to eukaryotes than to bacteria. bacteria  Singular, bacterium. Largest and most well-known group of prokaryotes. eukaryotes  Organisms whose cells characteristically have a nucleus. fungus  Plural, fungi. A single-celled or multicelled eukaryotic consumer that breaks down material outside itself, then absorbs nutrients released from the breakdown. plant  A multicelled eukaryotic producer; most are photosynthetic and live on land. prokaryotes  Single-celled organisms with no nucleus. protist  Common term for a eukaryote that is not a fungus, plant, or animal.

●●

Name the prokaryotic groups and how they differ from eukaryotes.

●●

Describe the four main groups of eukaryotes.

●●

Discuss how and why we name species.

●●

Describe the way species are grouped in taxa.

●●

Explain why DNA can be used to determine relative relatedness.

You will see in later chapters how differences in the details of DNA molecules are the basis of a tremendous range of differences among types of organisms. Various classification schemes help us organize what we understand about this variation, which we call Earth’s biodiversity.

The Prokaryotes Organisms can be grouped on the basis of whether they have a nucleus, which is a saclike structure that contains a cell’s DNA. Bacteria (singular, bacterium) and archaea (singular, archaeon) are the organisms whose DNA is not contained within a nucleus (Figure 1.5). All bacteria and archaea are single-celled, which means each individual consists of one cell. Collectively, these organisms are the most diverse representatives of life. Different kinds of bacteria and archaea are producers or consumers in nearly all regions of Earth, some inhabiting such extreme environments as frozen desert rocks, boiling acid hot springs, and nuclear reactor waste. The first cells on Earth may have faced similarly hostile conditions. Traditionally, organisms without a nucleus have been called prokaryotes, but the designation is now used only informally. This is because bacteria and archaea are less related to one another than we once thought, despite their similar appearance. Archaea turned out to be more closely related to eukaryotes, which are organisms whose DNA is contained within a nucleus. Some eukaryotes live as individual cells; others are multicelled.

The Eukaryotes Protists, fungi, plants, and animals are the four groups of eukaryotes (Figure 1.6). Protist is the common term for a eukaryote that is not a fungus, plant, or animal. Collectively, protists vary dramatically, from single-celled consumers to giant multicelled producers. Fungi (singular, fungus) are eukaryotic consumers that secrete substances to break down food externally, then absorb nutrients released by this process. Many are decomposers. Most fungi, including those that form mushrooms, are multicellular. Fungi that live as single cells are called yeasts. Plants are multicelled eukaryotes, and the vast majority of them are photosynthetic producers that live on land. Besides feeding themselves, plants also serve as food for most other land-based organisms. Animals are multicelled eukaryotic consumers that ingest other organisms or components of them. Unlike fungi, animals break down food inside their body. They also develop through a series of stages that lead to the adult form. All animals actively move about during at least part of their lives.

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Invitation to Biology  Chapter 1  9 

Protists are a group of extremely diverse eukaryotes that range from giant multicelled seaweeds to microscopic single cells.

Plants are multicelled eukaryotes. Almost all plants are photosynthetic producers with roots, stems, and leaves.

Fungi are eukaryotic consumers that secrete substances to break down food outside their body. Most are multicelled (left); some are single-celled (above).

Animals are multicelled eukaryotes that ingest other organisms or their parts, and they actively move about during part or all of their life cycle.

Figure 1.6  A few representative eukaryotes. Protists: Top left, worldswildlifewonders/Shutterstock.com; Top center, Courtesy of Allen W. H. Be & David A. Caron; Emiliania huxleyi. Photograph by Vita Pariente. Scanning electron micrograph taken on a Jeol T330A instrument at the Texas A & M University Electron Microscopy Center; Top right, Lebendkulturen.de/Shutterstock.com; Carolina Biological Supply Company; Oliver Meckes/Science Source; Center left, Jag_cz/Shutterstock.com; Center, Martin Ruegner/Radius Images/Getty Images; Edward S. Ross; Center right, London Scientific Films/Exactostock-1598/Superstock; Bottom left, Shironina/Shutterstock.com; Bottom center, Martin Zimmerman, Science, 1961, 133:73–79, © AAAS; Bottom right, Pixtal/Superstock.

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10 INTRODUCTION

domain kingdom phylum class order family genus species

wild carrot

marijuana

apple

prickly rose

dog rose

Eukarya Plantae Magnoliophyta Magnoliopsida Apiales Apiaceae Daucus Daucus carota

Eukarya Plantae Magnoliophyta Magnoliopsida Rosales Cannabaceae Cannabis Cannabis sativa

Eukarya Plantae Magnoliophyta Magnoliopsida Rosales Rosaceae Malus Malus domestica

Eukarya Plantae Magnoliophyta Magnoliopsida Rosales Rosaceae Rosa Rosa acicularis

Eukarya Plantae Magnoliophyta Magnoliopsida Rosales Rosaceae Rosa Rosa canina

Figure 1.7  Taxonomic classification of five species that are related at different levels. Each species has been assigned to ever more inclusive groups, or taxa: in this case, from genus to domain. Note the formal names of the taxa: the dog rose, for example, is a eukaryote (it belongs in the domain called Eukarya) and a plant (kingdom Plantae). From the left, Joaquim Gaspar; Kym Kemp; Sylvie Bouchard/Shutterstock.com; Courtesy of Melissa S. Green, www.flickr.com/photos/henkimaa; Gordana Sarkotic.

Answer: Marijuana, apple, prickly rose, and dog rose

Figure It Out: Which of the plants shown here are in the same order?

Organizing Information about Species  A Rose by Any Other Name . . .  When a new species is discovered, it is given

a unique name. We started naming species thousands of years ago, but naming them in a consistent way did not become a priority until the eighteenth century. At the time, European explorers who were just discovering the scope of life’s diversity started having more and more trouble communicating with one another because species often had multiple names. For example, the dog rose (a plant native to Europe, Africa, and Asia) was alternately known as briar rose, witch’s briar, herb patience, sweet briar, wild briar, dog briar, dog berry, briar hip, eglantine gall, hep tree, hip fruit, hip rose, hip tree, hop fruit, and hogseed—and those are only the English names! Species often had multiple scientific names too, in Latin that was descriptive but often cumbersome. The scientific name of the dog rose was Rosa sylvestris inodora seu canina (odorless woodland dog rose), and also Rosa sylvestris alba cum rubore, folio glabro (pinkish white woodland rose with smooth leaves).

genus  Plural, genera. A group of species that share a unique set of inherited characteristics. taxon  Plural, taxa. A rank in the classification of life; consists of a group of organisms that share a unique set of traits. taxonomy  Practice of naming, describing, and classifying species. trait  An inherited characteristic of an organism or species.

The Linnaean System  Carl Linnaeus was an eighteenth-century naturalist who

standardized a two-part naming system that we still use. By the Linnaean system, every species is given a unique two-part scientific name. The first part is the genus (plural, genera), which is defined as a group of species that share a unique set of inherited characteristics. The second part of a species name is called the specific epithet. Together, the genus name and the specific epithet designate one species. Thus, the dog rose now has one official name, Rosa canina, that is recognized worldwide.

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Invitation to Biology  Chapter 1  11  Archaea

Eukarya

Protists

Plants

Fungi Animals

Bacteria

Figure 1.8  The big picture of life. This diagram summarizes one hypothesis about how all life is connected by shared ancestry. Lines indicate evolutionary connections between the domains.

Taxonomy Traits  The practice of naming, describing, and classifying species is called taxonomy, and it is based on inherited characteristics, or traits. Individuals of

the same species have the same set of traits, and that set of traits is unique to the species. For example, giraffes normally have very long necks, brown spots on white coats, and so on. These are morphological (structural) traits. Individuals of a species also share biochemical traits (they make and use the same molecules) and behavioral traits (they respond the same way to certain stimuli, as when hungry giraffes feed on tree leaves). Taxa  We can rank a species into ever more inclusive categories based on some subset of traits it shares with other species. Each rank, or taxon (plural, taxa), is a group of organisms that share a unique set of traits. Of the major taxa, species is the lowest. Each taxon above species—genus, family, order, class, phylum (plural, phyla), kingdom, and domain—consists of a group of the next lower taxon. For example, the dog rose is among several species in the genus Rosa; Rosa is among several genera in the family Rosaceae; and so on (Figure 1.7). Using this system, we can sort all life into a few categories (Figure 1.8).

Determining Relative Relatedness Comparing Traits  It is easy to tell that humans and dog roses are different species

because they appear very different. Distinguishing between species that are more closely related may be much more challenging (Figure 1.9). In addition, traits shared by members of a species often vary a bit among individuals, as eye color does among people. How do we decide whether similar-looking organisms belong to the same species? The short answer to that question is that we rely on whatever information is available. Early naturalists studied anatomy and distribution—essentially the only methods available at the time—so species were named and classified according to what they looked like and where they lived. Today’s biologists are able to compare traits that the early naturalists did not even know about, including biochemical ones such as details of DNA molecules. Comparing DNA  The information in a molecule of DNA changes a bit each time

it passes from parents to offspring, and it has done so since life began. Over long periods of time, these tiny changes have added up to big differences between species such as humans and dog roses. Thus, differences in DNA are one way to measure relative relatedness: The fewer differences between species, the closer the relationship. For example, we know that the DNA of humans is more similar to chimpanzee DNA than it is to rose DNA, so we can assume that humans are more closely related to chimpanzees than to roses. There are similarities between the DNA of every living species, so all species are related in some way or another. Unraveling these relationships has become a major focus of biology.

Figure 1.9  Four butterflies, two species: Which are which? The top row shows two forms of the species Heliconius melpomene; the bottom row, two forms of H. erato. H. melpomene and H. erato never crossbreed. Their alternate but similar patterns of coloration evolved as a shared warning signal to predatory birds that these butterflies taste terrible. © 2006 Axel Meyer, “Repeating Patterns of Mimicry,” PLoS Biology 4, no. 10 (2006), e341 doi:10.1371/journal.pbio.0040341. Used with permission.

Impact of New Information  The discovery of new information sometimes changes the way we distinguish a particular species or how we group it with others.

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12 INTRODUCTION

For example, Linnaeus grouped plants by the number and arrangement of reproductive parts, a scheme that resulted in odd pairings such as castor-oil plants with pine trees. Having more information today, we place these plants in separate phyla.

The Biological Species Concept Evolutionary biologist Ernst Mayr defined a species as one or more groups of individuals that potentially can interbreed, produce fertile offspring, and do not interbreed with other groups. This “biological species concept” is useful in many cases, but it is not universally applicable. For example, the biological species concept cannot help us classify organisms that have become extinct. It is also not useful for distinguishing species of prokaryotes, which reproduce in a completely different way than eukaryotes. We return to speciation and how it occurs in Chapter 13, but for now it is important to remember that a “species” is a convenient but artificial construct of the human mind.

Take-Home Message 1.4 ●●

●●

●●

●● ●●

●● ●●

●●

Bacteria and archaea are prokaryotes, single-celled organisms whose DNA is not contained in a nucleus. Archaea are more closely related to eukaryotes than to bacteria. Eukaryotes are single-celled or multicelled organisms whose DNA is contained in a nucleus. Fungi are eukaryotic consumers that break down food externally. Some are single-celled. Plants are multicelled eukaryotic producers; most are photosynthetic and live on land. Animals are multicelled eukaryotic consumers that move about for at least part of their lives. Protists are eukaryotes that are not fungi, plants, or animals. We define and classify species based on shared traits. Each species is given a unique two-part name. The more traits that two species have in common, the closer is their relationship.

1.5  The Science of Nature Learning Objectives critical thinking  The act of evaluating information before accepting it. data  Factual information collected from experiments or observations of the natural world. experiment  Procedure designed to evaluate a prediction; typically yields data. hypothesis  A testable explanation for a natural phenomenon. model  Analogous system in an experiment; tested in place of another subject. prediction  Statement, based on a hypothesis, about a condition that should reasonably occur if the hypothesis is correct. science  Systematic study of the observable world. variable  In an experiment, a characteristic or event that differs among individuals or over time.

●●

Detail the process of making and testing a hypothesis.

●●

Explain how a control group is used in an experiment.

●●

Use a suitable example to explain variables.

●●

Give an example, real or hypothetical, of a cause-and-effect relationship.

Thinking about Thinking  Most of us assume that we do our own thinking, but do we, really? You might be surprised to find out how often we let others think for us. Consider how a school’s job (which is to impart as much information as possible to students) meshes perfectly with a student’s job (which is to acquire as much knowledge as possible from the school). In this rapid-fire transfer of information, it can be very easy to forget about the quality of what is being transferred. Any time you accept information without questioning it, you let someone else think for you. Critical thinking is the deliberate process of judging the quality of information before accepting it. When you use critical thinking, you move beyond the content

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Invitation to Biology  Chapter 1  13 

of new information to consider supporting evidence, bias, and alternative interpretations. This may sound complicated, but it just involves a bit of awareness. There are many ways to do it. For example, you might ask yourself some of the following questions while learning something new: ●●

What message am I being asked to accept?

●●

Is the message based on fact or opinion?

●●

Is there a different way to interpret the facts?

●●

What biases might the presenter have?

●●

How do my own biases influence the way I hear this message?

Questions like these are a way of being conscious about learning. They can help you decide whether to allow new information to guide your thoughts and actions.

Critical Thinking in Science  Making Hypotheses  Critical thinking is an integral part of science, the system-

atic study of the observable world and how it works. A line of inquiry in biology typically begins with a researcher’s curiosity about something observable in nature, say, an unusual decrease in the number of birds in a particular area. The researcher reads scientific articles about related observations before making a hypothesis. A hypothesis is a testable explanation for a natural phenomenon. An example of a hypothesis would be: The number of birds is decreasing because the number of bird-eating cats is increasing. Making Predictions  Researchers test hypotheses by evaluating predictions that flow from them. A prediction is a statement of some condition that should reasonably occur if the hypothesis is correct. Making predictions is often called the if–then process, in which the “if ” part is the hypothesis, and the “then” part is the prediction: If the number of birds is decreasing because the number of birdeating cats is increasing, then removing cats from the area should stop the decline in the bird population.

Experiments Researchers evaluate predictions by carrying out systematic observations or experiments. An experiment is a procedure designed to show whether a prediction is true or false, and a typical one yields data—factual information such as measurements or counts. Experimental data that validate a prediction constitute evidence in support of the related hypothesis. In an investigation of our hypothetical bird–cat relationship, the researcher may remove all cats from the area, then count the number of birds over a period of time. If the bird population increases, then the experimental data is evidence in support of the hypothesis. Variables  The bird–cat experiment, like many others, explores a cause-and-effect relationship using variables. A variable is an experimental factor that varies: a characteristic that differs among individuals, for example, or an event that differs over time. In this case, the researcher changes one variable (the number of cats) and monitors another (the number of birds). Models  Some important experiments have ethical or technical restrictions. Such experiments may be performed on a model, or analogous system. For example,

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14 INTRODUCTION

experiments that jeopardize human health are both unethical and illegal, so treatments for human diseases are often tested on animal models. Table 1.2  The Scientific Method

1. Observe some aspect of nature. 2. Make a hypothesis (think of a testable explanation for your observation). 3. Test the hypothesis: a. Make a prediction based on the hypothesis (If . . . then). b. Evaluate the prediction by making systematic observations or performing experiments that yield data. 4. Form a conclusion (determine whether your data validate the prediction and support your hypothesis). 5. Report your work to the scientific community.

Experimental and Control Groups  Biological systems are complex because they typically involve many interdependent variables. It can be difficult or even impossible to study one variable separately from the rest. Thus, biology researchers often perform an experiment on two groups of individuals. An experimental group is a set of individuals that have a certain characteristic or receive a certain treatment. This group is tested side by side with a control group, which is identical to the experimental group except for one variable: the characteristic or treatment being tested. Any differences in experimental results between the two groups is likely to be an effect of changing the variable.

The Scientific Method Forming a hypothesis based on observation, testing the hypothesis by evaluating predictions that flow from it, and making conclusions about the resulting data are collectively called the scientific method (Table 1.2). However, scientific research— particularly in biology—rarely proceeds in a direct, start-to-finish fashion as Table 1.2 might suggest. Researchers often describe their work as a nonlinear process of exploration. Experimental results are often unexpected, and predictions are often wrong. Research usually raises more questions than it answers, so changes in direction are common and there may be no end point. The unpredictability might be frustrating at times, but researchers typically say they enjoy their work because of the surprising twists and turns it takes.

Figure 1.10  Example of scientific research in the field of biology. Tierney Thys travels the world’s oceans to study the giant sunfish (mola). “When it comes to fishes, the mola really pushes the boundary of fish form,” she says. “It seems a somewhat counterintuitive design for plying the waters of the open seas—a rather goofy design—and yet the more I learn about it, the more respect and admiration I have for it.” © Mike Johnson

Table 1.3  A Few Research Specializations in Biology

Field

Focus

Astrobiology

Potential life elsewhere in the universe

Biogeography

Distribution of life on Earth

Bioinformatics

Development of tools to analyze data

Botany

Plant structure and processes

Cell biology

Cell structure and processes

Ecology

Interactions among organisms, and among organisms and their environment

Ethology

Animal behavior

Genetics

Inheritance

Marine biology

Life in saltwater environments

Medicine

Human health

Paleontology

Life in the ancient past

Structural biology

Architecture-dependent function of large biological molecules

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Invitation to Biology  Chapter 1  15 

Hypothesis

Olestra ® causes intestinal cramping. Prediction

If eating Olestra causes cramps, then people who eat it should be more likely to get cramps than people who don’t.

Results

Control Group

Experimental Group

529 people eat regular chips

563 people eat chips made with Olestra

93 people (17.6% ) who ate regular chips got cramps

89 people (15.8%) who ate chips made with Olestra got cramps

People who ate Olestra were about as likely to get cramps as people who didn’t.

Figure 1.11  The steps in a scientific experiment to determine whether Olestra causes intestinal cramps. A report of this study was published in the Journal of the American Medical Association in January 1998. Source: Journal of the American Medical Association in January 1998; background, Superstock.

Figure It Out: What was the variable that the researchers changed?

Answer: The presence of Olestra in potato chips

Experiment

Conclusion

Results of this experiment do not support the hypothesis. Eating Olestra does not cause intestinal cramping.

Examples of Biology Experiments  Biology is the branch of science concerning past and present life, and it includes hundreds of research specializations (Figure 1.10 and Table 1.3). To give you a sense of how biology research works, we summarize two published studies here. Does Olestra® Cause Stomachaches?  In 1996 the U.S. Food and Drug

Administration (FDA) approved Olestra, a fat replacement manufactured from sugar and vegetable oil, as a food additive. Potato chips were the first Olestracontaining food product to be sold in the United States. Controversy about the chip additive soon raged. Many people complained of intestinal problems after eating the chips, and thought that the Olestra was at fault. Two years later, researchers at the Johns Hopkins University School of Medicine designed an experiment to test the hypothesis that Olestra causes cramps (Figure 1.11). The researchers made the following prediction: If Olestra causes cramps, then people who eat Olestra are more likely to get cramps than people who do not eat it. To evaluate their prediction, they used a Chicago theater as a “laboratory.” They asked 1,100 people between the ages of thirteen and thirty-eight to watch a movie and eat their fill of potato chips. Each person received an unmarked bag containing 13 ounces of chips. Some of the bags contained chips made with Olestra. In this experiment, the individuals who received Olestra-containing potato chips constituted the experimental group, and individuals who received regular chips were the control group. A few days after the movie, the researchers contacted everyone and collected any reports of post-movie gastrointestinal problems. Of 563 people making up the experimental group, 89 (15.8 percent) reported having cramps. However, so did 93 of the 529 people (17.6 percent) making up the control group—who had eaten

control group  A group of individuals identical to an experimental group except for the variable under investigation. experimental group  In an experiment, a group of individuals who have a certain characteristic or receive a certain treatment. Typically tested side by side with a control group. scientific method  Making hypotheses, evaluating predictions that flow from them, and forming conclusions based on the resulting data.

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16 INTRODUCTION

A. With wings folded, a resting peacock butterfly resembles a dead leaf, so it is appropriately camouflaged from predatory birds. Experimental Treatment

B. When a predatory bird approaches, a butterfly flicks its wings open and closed, revealing brilliant spots and producing hissing sounds.

C. Researchers tested whether the wing flicking and hissing of peacock butterflies affected predation by blue tits (a type of songbird).

Number of Butterflies Eaten (of total)

Wing spots concealed

5 of 10 (50%)

Wings silenced

0 of 8 (0%)

Wing spots concealed and wings silenced

8 of 10 (80%)

No treatment

0 of 9 (0%)

D. Results of these experiments support only the hypothesis that peacock butterfly spots deter predatory birds. Figure 1.12  Testing the defensive value of two peacock butterfly behaviors: wing-flicking and hissing. Researchers concealed the spots of some butterflies, cut the sound-making part of the wings on others, and did both to a third group; then exposed each butterfly to a hungry blue tit for 30 minutes. (A) Matt Rowlings, www.eurobutterflies.com; (B) Adrian Vallin/Stockholm University; (C) Antje Schulte; (D) Proceedings of the Royal Society of London, Series B (2005) 272: 1203–1207.

Figure It Out: What percentage of butterflies with spots concealed and wings cut survived the test?

the regular chips. People were about as likely to get cramps whether or not they ate chips made with Olestra. The data were not consistent with the prediction, so they did not support the hypothesis that eating Olestra causes cramps. Why Do Butterflies Flick Their Wings and Hiss?  The peacock butterfly is a winged insect named for the large, colorful spots on its wings (Figure 1.12A). In 2005, researchers reported the results of experiments investigating whether certain behaviors of peacock butterflies help the insects defend themselves from insect-eating birds. The study began with the observation that a resting peacock butterfly sits motionless, wings folded. The dark underside of the wings provides appropriate camouflage. However, when a predator approaches, the butterfly exposes its brilliant spots by repeatedly flicking its wings open and closed in a way that produces a hissing sound (Figure 1.12B). A colorful, moving, noisy insect is usually very attractive to insect-eating birds, so the researchers were curious about why the peacock butterfly moves and hisses only in the presence of predators. After they reviewed earlier studies, the scientists made two hypotheses that might explain the wing-flicking behavior: ●●

Answer: 20 percent ●●

Hypothesis 1: Peacock butterflies flick their wings in the presence of a predator because exposing their brilliant wing spots reduces predation. (Peacock butterfly wing spots resemble owl eyes, and anything that looks like owl eyes is known to startle insect-eating birds.) Hypothesis 2: Peacock butterflies hiss in the presence of a predator because the sound reduces predation. (The sound may be an additional defense that startles insect-eating birds.)

The researchers used these hypotheses to make the following predictions: ●●

●●

Prediction 1: If exposing brilliant wing spots by wing-flicking reduces predation, then peacock butterflies without wing spots should be more vulnerable to predation than butterflies with wing spots. Prediction 2: If the hissing sound produced during wing-flicking reduces predation, then silent peacock butterflies should be more vulnerable to predation than hissing butterflies.

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Invitation to Biology  Chapter 1  17 

Next came the experiments. The researchers used a black marker to conceal the wing spots of some butterflies. They cut the wings of other butterflies to disable the sound-making parts. A third group had both treatments: Their spots were concealed and their wings were silenced; and a fourth group had no treatments. Each butterfly was then put into a large cage with a hungry blue tit (a type of butterflyeating bird, Figure 1.12C). Figure 1.12D lists the results. All of the butterflies with unmodified wing spots survived, regardless of whether they could hiss. These results were consistent with the first hypothesis: By exposing brilliant spots, peacock butterfly wing-flicking behavior decreases predation by blue tits. In contrast, a large proportion of butterflies with concealed spots got eaten, whether or not they could hiss. Experimental results were not consistent with the second hypothesis that peacock butterfly hissing reduces predation. Other questions raised by these results offer an example of how research often leads to more research: Do predatory birds other than blue tits respond differently to hissing? If not, does hissing reduce predation by other organisms (such as mice) that eat peacock butterflies? If hissing is unrelated to predation, what is its function? Several additional experiments would be necessary to address these questions.

Take-Home Message 1.5 ●●

●●

●●

●●

●●

Judging the quality of information before accepting it is an active process called critical thinking. Critical thinking is central to science. The field of biology consists of and relies upon the collection and analysis of scientific evidence. A hypothesis is a testable explanation for a natural phenomenon. Researchers test a hypothesis by systematically challenging it in a way that might reveal flaws. A hypothesis is tested by evaluating predictions that flow from it. A prediction is evaluated by experiments (or observations) that yield data. Data that validate a prediction are evidence in support of the related hypothesis; data that invalidate the prediction may be evidence that the hypothesis is flawed. Researchers can unravel cause-and-effect relationships in complex systems by changing one variable at a time.

1.6  Analyzing Experimental Results Learning Objectives ●●

Use an example to explain why generalizing results from a subset can be problematic in research.

●●

Describe statistical significance.

●●

Explain the role of critical thinking in making science a self-correcting process.

Common pitfalls such as sampling error and bias can make research tricky. Standard practices for evaluating results help researchers draw valid, defensible conclusions from them.

Sampling Error In a natural setting, researchers can rarely observe all individuals of a population or all instances of an event. For example, the biologists who explored the cloud forest

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18 INTRODUCTION

Digging Into Data Peacock Butterfly Predator Defenses The photographs below represent the experimental and control groups used in the peacock butterfly experiment discussed in Section 1.5. See if you can identify the experimental groups and match them up with the relevant control group(s). Hint: Identify which variable is being tested in each group (each variable has a control). Adrian Vallin, Sven Jakobsson, Johan Lind and Christer Wiklund, Proc. R. Soc. B (2005: 272, 1203, 1207). Used with permission of The Royal Society and the author.

A. Wing spots concealed

B. Wing spots visible; wings silenced

C. Wing spots concealed; wings silenced

Figure 1.13  In science, discovering an error is not always bad news. Here, Kris Helgen holds a golden-mantled tree kangaroo he found during a 2005 expedition to the Foja Mountain cloud forest. Prior to this expedition, only one tiny population of this critically endangered species was known. Bruce Beehler/Conservation International.

probability  The chance that a particular outcome of an event will occur; depends on the total number of outcomes possible. sampling error  Difference between results obtained from a subset, and results obtained from the whole. statistically significant  Refers to a result that is statistically very unlikely to have occurred by chance alone.

D. Wings painted but spots visible

E. Wings cut but not silenced

F. Wings painted, spots visible; wings cut, not silenced

you read about in Section 1.1 did not—and could not—survey every uninhabited part of the Foja Mountains. The cloud forest itself cloaks more than 2 million acres, so surveying all of it would be unrealistic. When researchers cannot directly observe all individuals of a population or all instances of an event, they may test or survey a subset. Results from the sample are then used to make generalizations about the whole. However, subsets are not necessarily representative of the whole. Consider the golden-mantled tree kangaroo, an animal first discovered in 1993 on a single forested mountaintop in New Guinea. For more than a decade, the species was never seen outside of that area, which is getting smaller every year because of human activities. Then, in 2005, the New Guinea explorers discovered that the golden-mantled tree kangaroo also lives in the Foja Mountains cloud forest (Figure 1.13). Having a second home means this critically endangered animal has a better chance of avoiding extinction. Sampling error is a difference between results obtained from a subset, and results from the whole (Figure 1.14A). Sampling error may be unavoidable, but knowing how it occurs helps scientists minimize it. For example, researchers often try to use large subsets for their studies, because sampling error can be a substantial problem with small ones (Figure 1.14B). To understand why this practice reduces the risk of sampling error, think about flipping a coin. There are two possible outcomes of each flip: The coin lands heads up, or it lands tails up. Thus, the chance that the coin will land heads up is one in two (1/2), or 50 percent. However, when you flip a coin repeatedly, it often lands heads up, or tails up, several times in a row. With just four flips, the proportion of times that the coin actually lands heads up may not even be close to 50 percent (an example of sampling error). With one thousand flips, however, the overall proportion of times the coin lands heads up is much more likely to approach 50 percent.

Statistical Significance Probability is the measure, expressed as a percentage, of the chance that a particular

outcome will occur. That chance depends on the total number of possible outcomes. In our coin-flipping example, there is a 50 percent probability that a flipped coin will land heads up. As another example, imagine 10 million people enter a lottery. Each person has the same chance of winning the lottery: 1 in 10 million, or (an extremely improbable) 0.00001 percent.

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Invitation to Biology  Chapter 1  19 

Analysis of experimental data often includes statistical calculations of probability. Say that you flip a coin four times, and it lands heads up three times. This result—3/4, or 75 percent—is very different from the expected 50 percent, so it is skewed by sampling error. If you flip the coin one hundred times, and it lands heads up 52 times, the result (52 percent) is much closer to the expected result. A result that is highly unlikely to have occurred by chance alone is said to be statistically significant. In this context, the word “significant” does not refer to the result’s importance. Rather, it means that a formal statistical analysis has shown a very low probability (usually 5 percent or less) of the result being inaccurate because of sampling error.

Bias   Like all humans, scientists are subjective by nature, so they risk designing experiments that would produce anticipated results. Consider the Olestra study detailed in Section 1.5. Other scientists criticized the study because it was funded by Procter & Gamble Co., the makers of Olestra. The conflict of interest was a potential source of bias toward a particular conclusion. The critics pointed out that the participants were chosen randomly, which means that the researchers did not pay attention to gender, age, weight, medical history, and so on. These additional variables may well have affected the results of the study.

A. Natalie chooses a random jelly bean from a jar. She is blindfolded, so she does not know that the jar contains 120 green and 280 black jelly beans. The jar is hidden from Natalie’s view before she removes her blindfold. She sees one green jelly bean in her hand and assumes that the jar must hold only green jelly beans (100 percent are green). This assumption is incorrect: 30 percent of the jelly beans in the jar are green, and 70 percent are black. The deviation is sampling error.

The Importance of Feedback Reporting research results in a standard way, such as in a peer-reviewed journal article, gives other scientists an opportunity to check experimental design, data, and conclusions. Why is this important? An open, curated exchange of information allows scientific research to advance by building on a solid foundation of previous discoveries. Let’s go back to our hypothetical bird–cat experiment. Imagine that the researcher’s hypothesis (the bird population is declining because the bird-eating cat population is increasing) was not supported by the experimental results (the bird population continued to decline after cats were removed). The hypothesis may be flawed—but then again, it may not be. A negative result does not necessarily mean that a hypothesis is incorrect. For example, logical flaws in a prediction, or technical flaws in an experiment, can yield results that are unrelated to a hypothesis. Such flaws can be revealed during the peer-review process, or when other scientists read the published article. Consider how the bird–cat researcher may have overlooked variables that were in play during the experiment. Perhaps the bird-eating capacity of cats varies, so that an undomesticated cat eats far more birds than a pet cat. Wild cats are more difficult to catch, so the researcher would likely have relocated mainly cats with the least effect on the bird population. A different experiment, one in which only the wild cats were relocated, may have yielded results in support of the hypothesis. If the bird–cat experiment had been submitted for publication in a scientific journal, other scientists would have probably pointed out this possibility. Conclusions may be the most contentious part of research, because interpreting the meaning of results is a form of judgment. This point gets us back to the role of critical thinking in science. Researchers expect one another to exercise critical thinking, both in their own work and in evaluating the work of others. If a researcher does not test a hypothesis in a way that may reveal flaws, then others will, because exposing errors is just as useful as applauding insights. The scientific

B. Still blindfolded, Natalie randomly picks out 50 jelly beans from the jar. She chooses 10 green and 40 black ones. The larger sample leads Natalie to estimate that one-fifth of the jar’s jelly beans are green (20 percent) and four-fifths are black (80 percent). The larger sample more closely approximates the jar’s actual green-toblack ratio of 30 percent to 70 percent. The more jelly beans that Natalie chooses, the closer her estimates will be to the actual ratio.

Figure 1.14  How sample size affects sampling error. Gary Head.

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20 INTRODUCTION

community consists of critically thinking people trying to poke holes in one another’s ideas. Their collective efforts make science a self-correcting endeavor.

Take-Home Message 1.6 ●●

●●

●●

If a subset under investigation is not representative of the whole, then the resulting data will be skewed by sampling error. The risk of sampling error is greatest with small subsets. Probability calculations can show whether a result is statistically significant (highly unlikely to have occurred by chance alone). Science is inherently a self-correcting process. Hypotheses are tested in ways that may reveal flaws; tests are designed to yield data that can be collected objectively; and results and conclusions are evaluated by a community of skeptics.

1.7  The Nature of Science Learning Objectives Table 1.4  Examples of Scientific Theories

Atomic theory Big bang

All matter consists of atoms and their smaller subatomic parts. In its first moment, our universe began rapidly expanding from an extremely hot, high-density state.

Cell theory

All organisms consist of one or more cells, the cell is the basic unit of life, and all cells arise from preexisting cells.

Evolution by natural selection

Environmental pressures drive change in the inherited traits of a population.

Plate tectonics

Earth’s lithosphere (crust and upper mantle) is cracked into pieces that move in relation to one another.

●●

Name the criteria that qualify a hypothesis for status as a scientific theory.

●●

Explain what happens to a theory when data arise that are inconsistent with it.

●●

Identify some areas of inquiry that science does not address.

●●

Discuss some ways to identify pseudoscience.

What Science Is Theories  You may hear people apply the word “theory” to a speculative idea, as in the phrase, “It’s just a theory.” This everyday usage of the word differs from the specific way it is used in science. Suppose a hypothesis stands after many years of systematic challenges. It is consistent with existing evidence, and researchers use it to make successful predictions about a wide range of other phenomena. A hypothesis that meets these criteria is called a scientific theory (Table 1.4). Theories are our most objective way of describing the natural world. Consider the hypothesis that all matter consists of atoms and their tiny components, which are called subatomic particles. Researchers no longer spend time testing this hypothesis for the compelling reason that, since we started looking 200 years ago, no one has discovered matter that consists of anything else. Thus, the hypothesis—now atomic theory—has been incorporated into our general understanding of matter. This understanding underpins research in many fields, including biology. Even though scientific theories have been thoroughly evaluated and scrutinized, scientists carefully avoid using the word “proven” to describe them. Instead, a theory is “accepted,” along with the possibility—however remote it might be—that new data inconsistent with it might be found. Consider how, like other hypotheses, a theory can never be evaluated under every possible circumstance. For example, testing the validity of atomic theory under all circumstances would require analysis of the composition of all matter in the universe for all time—an impossible task even if someone wanted to try. Theories Can Be Revised  What happens if someone discovers data that is inconsistent with a theory? By definition, a theory has been tested rigorously and repeatedly.

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Invitation to Biology  Chapter 1  21 

New results do not invalidate previous results, but the interpretation of what the results mean can change. Thus, new data inconsistent with a theory may trigger its revision. For example, atomic theory has been modified many times since it was proposed hundreds of years ago. If someone ever discovers matter that does not consist of atoms and subatomic particles, the theory would be revised to include the exception (all matter consists of atoms and subatomic particles except . . .). If many exceptions accumulate, the theory will be rewritten so it better accounts for the discrepancies. The theory of evolution by natural selection, which holds that environmental pressures can drive change in the inherited traits of a population, still stands after more than a century of concerted testing. Natural selection is not the only mechanism by which evolution occurs, but it is by far the most studied. Few other scientific theories have withstood as much scrutiny.

Table 1.5  Using Critical Thinking to Identify Pseudoscience

Science

Pseudoscience

Laws of Nature  A scientific theory differs from a law of nature, which describes a natural phenomenon that always occurs under certain circumstances, but has an incomplete scientific explanation. Laws, unlike scientific theories, do not necessarily include mechanisms. The laws of thermodynamics, which describe energy, are examples. We understand how energy behaves, but not entirely why it behaves the way it does (Chapter 4 returns to energy).

Does the concept concern an observable natural phenomenon?

What Is Not Science

Testable via predictions that flow from a hypothesis. Tests are designed to reveal flaws.

Not everything that uses scientific vocabulary is actually science. Claims, arguments, or methods that are presented as science but do not follow scientific principles are called pseudoscience (pseudo means false). Distinguishing pseudoscience from the real thing can be tricky, but your critical thinking skills will help (Table 1.5). Consider how a scientific hypothesis is a testable explanation for an observable aspect of nature. Pseudoscience, by contrast, can involve mysterious phenomena: “Earth appears older than it is because it came into existence that way,” for example. If this claim were true, then it would be impossible to test because no measurement or observation could reveal Earth’s true age. Claims that cannot be tested are not part of science. In science, making a hypothesis is followed by a systematic challenge that may reveal its flaws. With pseudoscience, making a claim is often followed by a selective search for information that can be used to defend it. The information may be invented, unverified, or anecdotal. Science also progresses: When new data are inconsistent with a hypothesis, the hypothesis is revised. By contrast, pseudoscience tends to be static: Evidence inconsistent with a pseudoscientific claim is typically ignored, dismissed, or denied. Pseudoscience is prevalent, and it is not harmless. Unlike science, it has no requirement for accuracy, truthfulness, or objectivity; communication typically consists of rhetoric intended to persuade the general public. Convincing people that false or misleading information is scientific jeopardizes our individual and collective welfare, for example by undermining public trust in safe and effective vaccines. Widespread vaccination programs all but eradicated dangerous diseases such as measles in the United States and western Europe, but these diseases are now making a comeback because many parents have been persuaded by pseudoscientific rhetoric to refuse vaccinations for their children (Chapter 23 returns to this topic). Measles in particular is extremely contagious, and the consequences of becoming infected can be extremely severe or fatal, especially for children.

Involves only the observable, natural world.

May involve supernatural or mysterious phenomena.

Is the concept testable? Untestable, or untestable in ways that might reveal flaws.

What is the evidence that supports the concept? Data collected from systematic observations or experiments.

Invented or unverified information, anecdotes, rhetoric, or the absence of scientific data.

How is inconsistent evidence addressed? Evidence inconsistent with a hypothesis prompts its revision.

Evidence inconsistent with a claim is ignored, dismissed, or denied.

law of nature  A generalization describing a consistent natural phenomenon that has an incomplete scientific explanation. pseudoscience  Claims, arguments, or methods that are presented as science, but do not follow scientific principles. scientific theory  A hypothesis that stands after many years of systematic testing, is consistent with existing evidence, and is useful for making predictions about a wide range of phenomena.

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22 INTRODUCTION

What Science Is Not

Figure 1.15  Observing an aspect of nature. Near a tent serving as a makeshift laboratory, herpetologist Paul Oliver records the call of a frog on the first expedition to New Guinea’s Foja Mountains cloud forest in 2005. Tim Laman/National Geographic Image Collection.

Science helps us to be objective because it is limited to observable aspects of nature (Figure 1.15). For example, science does not address philosophical questions such as “Why do I exist?” Answers to questions like this one can only come from within, as an integration of all the personal experiences and mental connections that shape our consciousness. This is not to say subjective answers have no value, because no human society can function for long unless its individuals share standards for making judgments, even if they are subjective. Moral, aesthetic, and philosophical standards vary from one society to the next, but all help people decide what is important and good. All give meaning to our lives. Neither does science address the supernatural, or anything that is “beyond nature.” Science does not assume or deny that supernatural phenomena occur, but scientists often cause controversy when they discover a natural explanation for something that was thought to have none. Such controversy arises when a society’s moral standards are interwoven with its understanding of nature. Consider the idea that Earth orbits the sun. This model is generally accepted today, but it was not always so. Nicolaus Copernicus published a mathematical model for this idea in the early 1500s, when the prevailing belief system in Europe had Earth as the immovable center of the universe. In 1610, astronomer Galileo Galilei published evidence for this model, and was quickly convicted of heresy. He was forced to publicly recant his work, prohibited from communicating about it ever again, and spent the rest of his life under house arrest. As Galileo’s story illustrates, exploring a traditional view of the natural world from a scientific perspective may be misinterpreted as a violation of morality. As a group, scientists are no less moral than anyone else, but their work follows a par­ ticular set of principles that other professions do not require.

Why Science?  Science helps us communicate our experiences of the natural world without bias. As such, it may be as close as we can get to a universal language. We are fairly sure, for example, that gravity behaves the same way everywhere in the universe. Intelligent beings on a distant planet would likely understand it the same way we do. Thus, we might well use gravity or another scientific concept to communicate with them, or anyone, anywhere. The point of science, however, is not to communicate with aliens. It is to find common ground here on Earth.

Take-Home Message 1.7 ●● ●●

●●

Science is concerned only with testable ideas about observable aspects of nature. A scientific theory is a hypothesis that has been rigorously tested and is useful for making predictions about other phenomena. Pseudoscience is a claim, argument, or method that is presented as science but does not follow scientific practices.

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Invitation to Biology  Chapter 1  23 

Summary Section 1.1  We do not yet know all the species that live on Earth, in part because we have not yet explored all of its inhabited regions. Identifying new species is part of biology, the scientific study of life. Understanding the scope of life gives us perspective on where we fit into it.

based on traits it shares with other species. The more traits that two species share, the closer is their evolutionary relationship. Shared traits can be used to rank species into ever more inclusive categories called taxa. Species, genus, family, order, class, phylum, kingdom, and domain are taxa.

Section 1.2  Biologists think about life at successive levels of organization. Interactions among components of each level give rise to complex properties that emerge at the next level. All matter, living or not, consists of atoms and their subatomic components. Atoms bond together to form molecules, some of which are unique to life. The property of life emerges as molecules become organized into a cell. Organisms are individuals that consist of one or more cells. In many multicelled organisms, cells are organized as tissues, organs, and organ systems. A population is a group of interbreeding individuals of a species in a given area; a community is all populations of all species in a given area. An ecosystem is a community interacting with its environment. Earth’s largest ecosystem, the biosphere, includes all regions of the planet that hold life.

Section 1.5  Critical thinking, the act of judging the quality of information as one learns, is an important part of science, the systematic study of the observable world. Generally, a researcher observes something in nature, forms a hypothesis (testable explanation) for it, then makes a prediction about what should occur if the hypothesis is correct. Researchers test hypotheses by evaluating predictions that flow from them, and they evaluate predictions by making systematic observations or performing experiments. A typical experiment explores a cause-and-effect relationship between variables, and it yields data. Data that validate a prediction are evidence in support of the related hypothesis. Biological systems in particular are complex and typically influenced by many interacting variables, so researchers often perform an experiment on two groups of individuals. Any differences in results between the experimental group and the control group are presumed to be an effect of changing the variable. An experimental model may be used if working directly with a subject or event is not possible. The scientific method includes making hypotheses, evaluating predictions that flow from them, and forming conclusions based on the resulting data. Research in the real world tends to be a nonlinear process of exploration.

Section 1.3  Life has underlying unity in that all living things have similar characteristics. All organisms must acquire energy and nutrients to sustain themselves. Producers acquire energy and simple raw materials from the environment to make their own food, often by processes such as photosynthesis. Consumers acquire energy and nutrients by feeding on the tissues, wastes, or remains of other organisms. Nutrients cycle between producers and consumers. All organisms sense and respond to change, making adjustments that keep conditions in their internal environment within tolerable ranges—a process called homeostasis. Information in an organism’s DNA guides its development, growth, and reproduction. DNA is the basis of similarities and differences among organisms. The passage of DNA from parents to offspring is called inheritance. Section 1.4  The many types of organisms that currently exist on Earth differ greatly in form and function. Bacteria and archaea, informally called the prokaryotes, are single-celled organisms whose DNA is not contained within a nucleus. Archaea are less related to bacteria than they are to eukaryotes: single-celled or multicelled organisms whose DNA is contained within a nucleus. Protists, plants, fungi, and animals are eukaryotes. The practice of naming and classifying species is called taxonomy. Each species’ name consists of two parts: the genus name and the specific epithet. We define and classify a species

Section 1.6  Standard practices for evaluating results minimize the possibility of error and the effects of bias in research. Researchers try to study large subsets in order to minimize sampling error, which occurs when a subset is not representative of the whole. They also use probability calculations to check whether their results are statistically significant. Results and conclusions are presented for evaluation to the scientific community, which consists of many critically thinking people systematically checking one another’s work. Section 1.7  Opinion and belief have value in human culture, but they are not part of science. Science addresses only testable ideas about observable aspects of the natural world. A scientific theory is a hypothesis that stands after years of systematic tests, and is useful for making predictions about other phenomena. A theory may be revised upon discovery of new data inconsistent with it.

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24 INTRODUCTION

Summary (Continued) A law of nature describes a consistent natural phenomenon but does not include an explanation for it. Claims, arguments, or methods that are not scientific but presented as if they were are pseudoscience. Pseudoscientific rhetoric is prevalent, and unlike science, it has no requirement for accuracy, truthfulness, or objectivity. Convincing people that false or misleading information is scientific jeopardizes our welfare as individuals and as a society.

Answers in Appendix I type of organism. c. multicelled d. undiscovered

2. The smallest unit of matter is the . a. atom c. cell b. molecule d. millimeter 3. The smallest unit of life is the a. atom b. molecule

. c. cell d. organism

4. All organisms must acquire and from the environment to maintain themselves, grow, and reproduce. a. heat; light c. nutrients; energy b. DNA; homeostasis d. producers; consumers 5.

6.

is the transmission of DNA to offspring. c. Homeostasis a. Reproduction b. Development d. Inheritance is a process by which an organism produces offspring. a. Reproduction b. Development

move around for at least part of their life. a. Living organisms c. Species d. Eukaryotes b. Animals

9. A butterfly is a(n) a. organism b. domain c. species d. eukaryote 10. A bacterium is a. an organism b. single-celled

Self-Quiz 1. A species is a(n) a. unique b. new

8.

c. Homeostasis d. Inheritance

7. By sensing and responding to change, organisms keep conditions in their internal environment within ranges that cells can tolerate. This process is called . a. reproduction c. homeostasis b. development d. inheritance

(choose all that apply). e. consumer f. producer g. prokaryote

(choose all that apply). c. an animal d. a eukaryote

11. Bacteria, Archaea, and Eukarya are three a. domains c. genera b. species d. families

.

12. A control group is . a. a set of individuals that have a certain characteristic or receive a certain treatment b. the standard against which an experimental group is compared c. the experiment that gives conclusive results 13. Five randomly selected university students are found to be taller than 6 feet. The researchers concluded that the average height of a university student is greater than 6 feet. This result is likely to be skewed because of . a. experimental error b. sampling error c. a subjective opinion 14. Science addresses only that which is . a. alive c. variable b. observable d. indisputable 15. Match the terms with the most suitable description. a. if–then statement life b. unique type of organism probability c. emerges with cells species d. testable explanation data e. measure of chance hypothesis f. makes its own food prediction g. experimental results producer

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Invitation to Biology  Chapter 1  25 

CRITICAL THinking 1. Where would you look for a new species, and why would you look there? 2. A person is declared dead upon the irreversible ceasing of brain activity, blood circulation, and respiration. Only about 1 percent of a body’s cells have to die for all of these things to happen. How can a person be dead when 99 percent of his or her cells are still alive? 3. We mentioned in Section 1.7 that critics pointed out flaws in the Olestra study. How would you redesign the experiment so these critics would have more confidence in the researchers’ conclusion? 4. Consider the phenomenon called climate change, which refers to an ongoing change in weather patterns driven by an increase in average global temperatures. Temperatures of the atmosphere and ocean have been measured directly for about 200 years, and taken as a whole, these data show a dramatic rising trend (Figure 1.16A). Some skeptics have concluded that Earth’s temperature is not rising because there are short periods of time in which the average global temperatures have not increased (Figure 1.16B). Why do climate scientists find the skeptics’ reasoning problematic?

5. Explain the following statement: “The absence of evidence is not evidence of absence.” 6. The MMR vaccine offers effective protection from three very dangerous diseases (measles, mumps, and rubella). In 1998, the journal Lancet published a scientific paper written by Andrew Wakefield and his colleagues about their study of twelve children with autism. The paper received a lot of media attention because it concluded that vaccination with MMR causes autism. Other groups failed to find such a link, and in 2004, the Lancet published a retraction of the conclusion by ten of the paper’s twelve authors. Eventually, the Lancet retracted the entire paper because it turned out that Wakefield had faked his data. His motive was apparently financial: An attorney suing the MMR vaccine’s manufacturer employed Wakefield specifically to find a link between the vaccine and autism. For decades, other groups have researched the subject intensively, and the (real) science is quite clear: MMR vaccination does not cause autism. The evidence that Wakefield falsified his data is also clear. However, public opinion continues to be swayed by pseudoscience that perpetuates Wakefield’s fraud. Does the incident show that results of scientific studies cannot be trusted? Or does it confirm the usefulness of a scientific approach, because other scientists discovered and exposed the fraud?

0.2 0 20.2 20.4 1880 1885 1890 1895 1900 1905 1910 1915 1920 1925 1930 1935 1940 1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005 2010 2015

20.6

A. The full set of data from 137 years shows an overall trend of rising temperatures.

0.6

0.5

2008

0.4

2007

0.6

2006

0.8

0.7

2005

1

Temperature deviation from average (8C)

Temperature deviation from average (8C)

1.2

B. A selected subset of the data shows a different trend.

Figure 1.16  Cherry-picking climate change data. Formal measurements of global atmospheric and oceanic surface temperatures have been taken every year since the 1800s. Both of these graphs show yearly temperature data as deviations from an average. Temperatures taken between 1951 and 1980 were used to calculate the average. Data for the graphs is from NASA’s Goddard Institute for Space Studies (GISS).

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2

2.1 A Big Fat Problem  27 2.2 Atoms  28 2.3 Chemical Bonds  32

Molecules of Life

2.4 Special Properties of Water  34 2.5 Acids and Bases  36 2.6 The Chemistry of Biology  37 2.7 Carbohydrates  39 2.8 Lipids  41 2.9 Proteins  44 2.10

Nucleic Acids  48

Properties of matter begin with its component atoms. The cubic structure of these tiny crystals is one property that arises from interactions among the two types of atoms that compose salt.

Concept Connections Francois Gohier/Science Source

In this chapter, you will explore the first levels of life’s organization as you encounter examples of how the same building blocks, arranged different ways, form different products (Section 1.2). New properties emerge at each level of organization. Electrons, which are components of atoms, carry energy among molecules in metabolic processes that harvest and store energy, especially photosynthesis (5.3) and respiration (6.2). The structure of lipids gives rise to their function as the foundation of cell membranes (3.3); the structure of proteins, to their function as active participants in metabolism (4.4). Cells use information encoded in the structure of DNA (7.3) to build other molecules (8.2–8.4). Mechanisms of homeostasis (1.3) introduced in this chapter will return again in the context of blood composition (22.9) and body temperature (20.5).

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Molecules of Life  Chapter 2  27 

Application 2.1  A Big Fat Problem The human body requires only about a tablespoon of fat each day to stay healthy, but most people in developed countries eat far more than that. The average American eats about 70 pounds of fat per year, which may be part of the reason why the average American is overweight. Being overweight increases one’s risk for many chronic illnesses. However, the total quantity of fat in the diet may have less of an impact on health than the types of fats eaten. Molecules that make up oils and other fats have three fatty acid tails, each a long chain of carbon atoms that can vary a bit in structure. Fats that have a certain arrangement of hydrogen atoms around those carbon chains are called trans fats. Small amounts of trans fats occur naturally in red meat and dairy products, but the main source of these fats in the American diet has been an artificial food product called partially hydrogenated vegetable oil (PHO). Hydrogenation is a manufacturing process that adds hydrogen atoms to oils in order to change them into solid fats, and it creates abundant trans fats. In 1911, Procter & Gamble Co. introduced partially hydrogenated cottonseed oil as a substitute for the more expensive solid animal fats they had been using to make candles and soaps. The demand for candles then began to wane as more households in the United States became wired for electricity, and P&G looked for another way to sell its proprietary fat. PHO looks a lot like lard, so the company began aggressively marketing it as a revolutionary new food: a solid cooking fat with a long shelf life, mild flavor, and lower cost than lard or butter. By the mid-1950s, PHO had become a major part of the American diet. It was a preferred ingredient for home cooking, and also for preparing a huge variety of manufactured and restaurant foods: French fries, chicken nuggets, and other fried items; as well as margarines, microwave popcorn, cake mixes and frostings, cookies, crackers, peanut butter, pie crusts, pizza dough, and so on. For decades, it was considered to be healthier than animal fats because it was made from plants, but we have known otherwise since 1990. More than any other fat, trans fats negatively affect blood cholesterol levels and the function of arteries and veins. The effects of such changes are quite serious. Eating as little as 2 grams per day (about 0.4 teaspoon) of PHO measurably increases one’s risk of atherosclerosis (hardening of the arteries), heart attack, and diabetes. A small serving of French fries prepared in it contains about 5 grams of trans fats. A ruling by the U.S. Food and Drug Administration (FDA) now prohibits restaurants and food manufacturers from using PHO in their products. However, manufactured foods prepared before June 2018 may contain PHOs, and they can still be sold until 2020. If you want to avoid these foods, check the ingredients list on the package for partially hydrogenated oils (Figure 2.1). Note that PHO-containing products may be marked “0g Trans Fat” even if a single serving contains up to half a gram. All organisms consist of the same kinds of molecules, but small differences in the way those molecules are put together can have big effects. With this concept, we introduce you to the chemistry of life. This is your chemistry, and it makes you far more than the sum of your body’s molecules.

Nutrition Facts Serving Size About 4 (30g) Servings Per Container 12 Amount Per Serving

Calories 160

Calories From Fat 70 % Daily Value

Total Fat 7g Saturated Fat 4.5g Trans Fat 0g Cholesterol 0mg Sodium 100 mg Total Carbohydrate 13g Dietary Fiber 1g Sugars 10g Protein 2g Vitamin A 0% Calcium 0%

10% 20%

4% 4% 4%

Vitamin C 0% Iron 4%

INGREDIENTS: ENRICHED FLOUR, SUGAR, PARTIALLY HYDROGENATED VEGETABLE OIL, COCOA, CORNSTARCH, LEAVENING (BAKING SODA, AMMONIUM PHOSPHATE), SOY LECITHIN, SALT, ARTIFICIAL COLOR, ARTIFICIAL FLAVOR.

Figure 2.1  Partially hydrogenated vegetable oils in packaged foods. Prepared foods manufactured before July 2018 may contain partially hydrogenated vegetable oils, which have a high content of unhealthy trans fats. A food package may be labelled “0g Trans Fat” if a single serving contains less than half a gram. Check the ingredients list for partially hydrogenated oils. Top, Yellow Cat/Shutterstock.com

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28  Unit 1  How Cells Work

Discussion Questions –

+

+

1. Fat is an important nutrient for humans. What roles might it play in the body? 2. Trans fats were banned from foods decades after scientists discovered them to be dangerous for health. Why do you think it took so long? 3. French fries cooked in partially hydrogenated safflower are much crispier and lighter than those cooked in regular safflower oil. If you were at a restaurant that offered a choice, which fries would you order and why?

proton neutron

–

–

electron

Figure 2.2  Atoms. Atoms consist of electrons moving around a nucleus of protons and neutrons. Models such as this one do not show what atoms look like. Electrons move in defined, three-dimensional spaces about 10,000 times bigger than the nucleus. atomic number element symbol mass number

6

C 12

elemental substance element name carbon

Figure 2.3  Example of an element: carbon. Left, Theodore Gray/Visuals Unlimited, Inc.

atomic number  Number of protons in the atomic nucleus; defines the element. electron  Negatively charged subatomic particle; in an atom, moves at high speed around the nucleus. element  A pure substance that consists only of atoms with the same number of protons. isotopes  Forms of an element that differ in the number of neutrons. mass number  Of an isotope, the total number of protons and neutrons in the atomic nucleus. neutron  Uncharged subatomic particle that occurs in the atomic nucleus. nucleus  Of an atom, core that is occupied by protons and (in most atoms) neutrons. proton  Positively charged subatomic particle that occurs in the nucleus of all atoms. radioactive decay  Process in which atoms of a radioisotope emit energy and subatomic particles when their nucleus spontaneously breaks up. radioisotope  An isotope with an unstable nucleus. tracer  A substance that can be traced via its detectable component.

2.2  Atoms Learning Objectives ●●

Use an example to explain why we say that an atom is the smallest unit of a substance.

●●

Explain the difference between an atom and an element.

●●

Describe radioactive decay.

●●

Use the concept of vacancies to explain the chemical activity of atoms.

Atomic Structure You learned in Chapter 1 that an atom is the smallest unit of matter. To understand what that means, you need to know about subatomic particles—the particles that make up atoms: protons, neutrons, and electrons (Figure 2.2). Protons (p+) are positively charged (charge is an electrical property in which opposite charges attract, and like charges repel). One or more protons occupy the central core, or nucleus, of every atom. Most atoms also have uncharged neutrons in their nucleus. Negatively charged electrons (e–) move at high speed around the nucleus. Different atoms can have different numbers of subatomic particles, but most have about the same number of electrons as protons. The negative charge of an electron is the same magnitude as the positive charge of a proton, so the two charges cancel one another. Thus, an atom with exactly the same number of electrons and protons carries no charge.

Elements All atoms have protons. The number of protons in an atom’s nucleus is called the atomic number, and it defines the atom as a particular element. Elements are pure substances, each consisting only of atoms with the same number of protons in their nucleus. For example, the element carbon has an atomic number of 6 (Figure 2.3). All atoms with six protons in their nucleus are carbon atoms, no matter how many electrons or neutrons they have. Elemental carbon (the substance) consists only of carbon atoms, and all of those atoms have six protons. We know of 118 elements, and each is represented by a symbol that is an abbreviation of its name (see Appendix II). Carbon’s symbol, C, is from carbo, the Latin word for coal, which is mostly carbon.

Isotopes All atoms of an element have the same number of protons, but they can differ in the number of other subatomic particles. For example, one carbon atom may have six neutrons, and another may have seven. We call these two carbon atoms

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Molecules of Life  Chapter 2  29 

++++ ++ A. 12C 6 protons 6 neutrons

++++ ++ B. 13C 6 protons 7 neutrons

++++ ++ C. 14C 6 protons 8 neutrons

+– ++++ ++ D. 14N 7 protons 7 neutrons

Figure 2.4  Isotopes of carbon. A–C show protons and neutrons in the nuclei of three naturally occurring isotopes of carbon: carbon 12 (12C), carbon 13 (13C), and carbon 14 (14C). Carbon 14 is a radioisotope, and it decays into nitrogen 14 (14N) when one of its neutrons spontaneously splits into a proton and an electron (D). The electron is emitted as radiation.

isotopes. Isotopes are atoms of the same element that have different numbers of neutrons. The total number of neutrons and protons in the nucleus of an isotope is its mass number. Mass number is written as a superscript to the left of the element’s symbol. The most common isotope of carbon has six protons and six neutrons, so it is 12C, which is pronounced carbon 12 (Figure 2.4). The other naturally occurring carbon isotopes are 13C (six protons, seven neutrons), and 14C (six protons, eight neutrons).

radioactivity

Radioisotopes  Carbon 14 is an example of a radioisotope, or radioactive isotope. Atoms of a radioisotope have an unstable nucleus that breaks up spontaneously. As a nucleus breaks up, it emits radiation (subatomic particles, energy, or both), a process called radioactive decay. The atomic nucleus cannot be altered by heat or any other ordinary means, so radioactive decay is unaffected by external factors such as temperature, pressure, or whether the atoms are part of molecules. Each radioisotope decays at a predictable rate into predictable products. For example, when carbon 14 decays, we know that one of its six neutrons splits into a proton and an electron (Figure 2.4C,D). The proton remains in the nucleus, and the electron is emitted as radiation. The nucleus lost a neutron and gained a proton, so it now has seven of each. All atoms with seven protons are nitrogen atoms. Thus, an atom of 14C (6 protons, 8 neutrons) decays into an atom of 14N (7 protons, 7 neutrons). The rate of this decay has been measured, so we know that about half of the atoms in any sample of 14C will be 14N atoms after 5,730 years. Radioisotope decay is so predictable that researchers can estimate the age of a rock or fossil by measuring its isotope content (Section 12.4 returns to this topic). Tracers  The chemical behavior of an atom arises from the number of protons and

electrons it has. Neutrons have little effect on chemistry, so all isotopes of an element generally have the same chemical properties—and all are interchangeable in a biological system. Researchers take advantage of the interchangeability when they use radioactive tracers to study biological processes. A tracer is any substance with a detectable component such as a radioisotope. When delivered into a biological system such as a cell or a body, a radioactive tracer may be followed by detecting the radiation emitted during decay (Figure 2.5).

Why Electrons Matter  The more we learn about electrons, the weirder they seem. Consider that an electron has mass but no size, and its position in space is described as more of a smudge than a point. It carries energy, but only in incremental amounts: An electron can gain energy only by absorbing the amount needed to boost it to a higher energy level; likewise, it loses energy only by emitting the difference between two energy levels (these concepts will be important to remember when you learn how cells harvest and release energy).

Figure 2.5  A medical application for radioisotopes. A procedure called PET (short for positron-emission tomography) helps us “see” cellular activity inside a living body. A radioactive tracer was injected into this lung cancer patient. Inside the patient’s body, cancer cells took up more of the tracer than normal cells. A PET scanner detected radioactive decay wherever the tracer was, then translated that data into a digital image. A large tumor in the lung and several smaller tumors are visible. Source: © Siemens 1996–2019, https://www.siemens.com/press/en/presspicture/2013 /healthcare/imaging-therapy-systems/him201310002-01.htm?content[]=HIM&content[]=HCIM

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30  Unit 1  How Cells Work The Atomic Apartment Building  Imagine that an atom is a multilevel apartment

building, with the nucleus in the basement. Each “floor” of the building corresponds to a certain energy level, and each has a certain number of “rooms” available for rent. Up to two electrons can occupy each room. Pairs of electrons populate rooms from the ground floor up (lowest to highest energy level). The farther an electron is from the nucleus in the basement, the more energy it has. An electron can move to a room on a higher floor if an energy input gives it a boost, but it quickly emits the extra energy and moves back down. Shell Models  A shell model is a conceptual diagram of how electrons populate an atom, with successive “shells” corresponding to successively higher energy levels (Figure 2.6). Each shell includes all of the rooms on one floor (one energy level) of our atomic apartment building. We draw a shell model of an atom by filling it with electrons (represented as balls or dots) from the innermost shell out, until there are as many electrons as the atom has protons. There is only one room on the first floor—the lowest energy level—and it fills up first. In hydrogen, the simplest element, a single electron occupies that room (Figure 2.6A). Helium, with two protons, has two electrons that fill the room—and the first shell. In larger atoms, more electrons rent the second-floor rooms (Figure 2.6B). When the second floor fills, more electrons rent third-floor rooms (Figure 2.6C), and so on.

Each circle (shell) represents one energy level. To make these models, we fill the shells with electrons from the innermost shell out, until there are as many electrons as the atom has protons. The number of protons in each model is indicated.

first shell

second shell first shell

third shell second shell first shell

Vacancies  When an atom’s outermost shell is filled with electrons, we say that it has no vacancies. Atoms with no vacancies are in their most stable state. When an atom’s outermost shell has room for another electron, it has a vacancy. Atoms with

A. The first shell corresponds to the first energy level, and it can hold up to 2 electrons. Hydrogen has 1 proton, so it has 1 electron and one vacancy. A helium atom has 2 protons, 2 electrons, and no vacancies.

B. The second shell corresponds to the second energy level, and it can hold up to 8 electrons. Carbon has 6 electrons, so its first shell is full. Its second shell has 4 electrons and four vacancies. Oxygen has 8 electrons and two vacancies. Neon has 10 electrons and no vacancies.

C. The third shell corresponds to the third energy level, and it can hold up to 8 electrons. A sodium atom has 11 electrons, so its first two shells are full and the third shell has 1 electron. Thus, sodium has seven vacancies. Chlorine has 17 electrons and one vacancy. Argon has 18 electrons and no vacancies.

1

electron proton

hydrogen (H)

6

carbon (C)

11

sodium (Na)

Figure It Out: Which of these models have unpaired electrons in their outer shell?

2

vacancy helium (He)

8

oxygen (O)

17

chlorine (Cl)

10

neon (Ne)

18

argon (Ar)

Answer: Hydrogen, carbon, oxygen, sodium, and chlorine

Figure 2.6  Shell models.

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vacancy

no vacancy

vacancies tend to get rid of them: In other words, they are chemically active. Consider the element neon (Ne). Neon has 10 protons; with 10 electrons, its outer (third) shell is full—it has no vacancies. Atoms of this element do not interact with other atoms. By contrast, the element sodium has 11 protons; with 11 ele­ ctrons, a sodium atom’s outer (third) shell has one electron and seven vacancies. We can predict that these atoms are chemically active.

Free Radicals  A sodium atom with 11 electrons is not just active, it is extremely

active. Why? This atom has a lone electron in its outer shell, but electrons really like to be in pairs when they populate atoms. Atoms that have unpaired electrons are called free radicals. With a few exceptions, free radicals are very unstable, easily forcing electrons upon other atoms or ripping electrons away from them. Such interactions damage organic molecules such as DNA, which is why free radicals can be dangerous to life. Ions  A sodium atom with 11 electrons will quickly rid itself of its unpaired electron. When that happens, its second shell—which is full of electrons—becomes its outermost, and no vacancies remain. This is the most stable state of a sodium atom, which is why the vast majority of sodium atoms on Earth have 11 protons and 10 electrons. Atoms like this one, with an unequal number of protons and electrons, are ions. Ions are atoms or molecules that carry a net (or overall) charge. Sodium ions have more protons than electrons, so they are positively charged (Figure 2.7A). Note how an ion’s charge is indicated by a superscript to the right of the element symbol: Na+, for example, is the designation for a sodium ion. Atoms of other elements accept electrons and become negatively charged. Chlorine is an example. A chlorine atom has 17 protons; with 17 electrons, its outer shell has seven electrons and one vacancy. This atom has one unpaired electron, so it is a free radical. An uncharged chlorine atom can easily fill its vacancy by pulling an electron off of another atom. When that happens, the chlorine atom has more electrons than protons, so it is negatively charged (Figure 2.7B). This ion is called chloride (Cl–).

Take-Home Message 2.2 ●●

●●

●●

●●

●●

●●

All matter consists of atoms, tiny particles that in turn consist of electrons moving around a nucleus of protons and neutrons. The number of protons in an atom (the atomic number) defines the element. Isotopes are atoms of an element that have different numbers of neutrons. The number of neutrons in an atom is its mass number. Unstable nuclei of radioisotopes emit radiation as they spontaneously break apart (decay). Radioisotopes decay at a predictable rate to form predictable products. When an atom’s outer shell is not full of electrons, it has a vacancy. Atoms with vacancies are chemically active. Atoms with unpaired electrons—free radicals—can destroy biological molecules, so they are dangerous to life. An atom that has a different number of protons and electrons carries a net charge, so it is an ion.

electron loss

11

11

Sodium atom

Sodium ion

11p 11e–

11p+ 10e–

charge: 0

charge: +1

+

A. A sodium atom (Na) becomes a positively charged sodium ion (Na1) when it loses the single electron in its third shell. The atom’s full second shell is now its outermost, so it has no vacancies. electron gain

17

17

Chlorine atom

Chloride ion

17p+ 17e–

17p+ 18e– charge: –1

charge: 0

B. A chlorine atom (Cl) becomes a negatively charged chloride ion (Cl2) when it gains an electron and fills the vacancy in its third, outermost shell. Figure 2.7  Ion formation. Superscripts designate charge. Protons (p+) carry a positive charge; electrons (e–) carry a negative charge. Figure It Out: Does a chloride ion have an unpaired electron?

Answer: No

Top and bottom photos, Kazunori Nagashima/ The Image Bank/Getty Images

Molecules of Life  Chapter 2  31 

free radical  An atom with an unpaired electron. Extreme chemical reactivity makes free radicals dangerous to life. ion  An atom or molecule that carries a net charge. shell model  Conceptual diagram of electron distribution in an atom.

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32  Unit 1  How Cells Work

2.3  Chemical Bonds Learning Objectives oxygen atom chemical bond

O H

H

hydrogen atom

hydrogen atom

Figure 2.8  Chemical bonds make atoms into molecules. Chemical bonds hold atoms together in a particular arrangement that defines the type of molecule. This is a model of a water molecule. Every water molecule consists of two hydrogen atoms bonded to the same oxygen atom.

●●

Describe a chemical bond.

●●

Explain polarity in terms of ionic bonds and covalent bonds.

●●

Write the structural formula for a molecule of water.

A chemical bond is a strong attractive force that arises between two atoms, and the interaction unites the atoms into a molecule. Each molecule consists of atoms held together in a particular number and arrangement by chemical bonds. Consider the molecules that make up water. A water molecule has three atoms: two hydrogen atoms bonded to the same oxygen atom (Figure 2.8). Every water molecule has the identical configuration, whether it is part of an ocean, floating in space, making up vapor in your lungs, and so on. A water molecule is an example of a compound—a molecule that consists of two or more elements. Other molecules have atoms of one element only. The term “bond” applies to a continuous range of atomic interactions. However, we can categorize most bonds into distinct types based on their properties. In this book, we discuss two kinds of chemical bonds: ionic and covalent.

Ionic Bonds  An ionic bond is a strong mutual attraction between ions of opposite charge. For example, a molecule of sodium chloride (NaCl) consists of a sodium ion and a chloride ion held together by an ionic bond (Figure 2.9A). Molecules of sodium chloride make up the substance we know as table salt. Each crystal of salt is a tiny lattice of sodium and chloride ions interacting in ionic bonds (Figure 2.9B).

ionic bond

11

17

Covalent Bonds  Sodium ion

Chloride ion

11p+ 10e–

17p+ 18e–

charge: +1

charge: –1

A. The strong mutual attraction of opposite charges holds a sodium ion and a chloride ion together in an ionic bond.

Na+ Cl –

B. Tiny crystals of sodium chloride (left) compose table salt. Each crystal consists of many sodium and chloride ions locked together in a cubic lattice by ionic bonds (right).

Some atoms can fill their vacancies by sharing electrons with other atoms, an interaction called a covalent bond (left). Covalent bonds can be stronger than ionic bonds, but they are not always so. Table 2.1 shows some of the different ways we represent covalent bonds. In structural formulas, a line between two atoms represents a single covalent bond. For example, a covalent bond links two atoms in molecular hydrogen, so the structural formula of this molecule is HH. Multiple covalent bonds may form between two atoms when they share multiple pairs of electrons. For example, two atoms sharing two pairs of electrons are connected by two covalent bonds, which are represented by a double line between the atoms. A double bond links the two oxygen atoms in molecular oxygen (OO). Three lines indicate a triple bond, in which two atoms share three pairs of electrons. A triple covalent bond links the two nitrogen atoms in molecular nitrogen (NN). A structural formula consists of letters connected by lines. By contrast, a structural model is a three-dimensional representation of atoms and bonds. Double and triple bonds are not distinguished from single bonds in structural models. All covalent bonds are shown as one stick connecting two balls, which represent atoms. We use a common color-coding scheme to distinguish elements in structural models: 1

1

Figure 2.9  Ionic bonds in table salt (NaCl). Bottom left, Francois Gohier/Science Source.

carbon

hydrogen

oxygen

nitrogen

phosphorus

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Molecules of Life  Chapter 2  33 

Table 2.1  Representing Covalent Bonds in Molecules

Representation

Description

Example

Common name

Familiar term

Water

Chemical name

Describes elemental composition.

Chemical formula

Indicates unvarying proportions of elements. Subscripts show number of atoms of an element per molecule. The absence of a subscript means one atom.

Structural formula

Represents each covalent bond as a single line between atoms.

Structural model

Shows relative sizes and positions of atoms in three dimensions.

Shell model

Shows how pairs of electrons are shared in covalent bonds.

A. An ionic bond In an ionic bond, each atom retains its full respective charge, so the bond is completely polar.

Dihydrogen oxide H2O

HOH

B. A polar covalent bond In a polar covalent bond, one atom pulls the shared electrons more than the other, so it has a slight negative charge. The other atom ends up with a slight positive charge. The bond is polar, but less so than an ionic bond. C. A nonpolar covalent bond The atoms participating in a nonpolar covalent bond share electrons equally, so neither has a charge. The bond is completely nonpolar.

1

8

1

Figure 2.10  Comparing bond polarity. Here, polarity is represented in color; red indicates negative charge; blue, positive charge. Uncharged regions are white.

Bond Polarity Consider how, in a molecule of sodium chloride, the sodium and chloride ions retain their respective charges. Thus, one “end” of the molecule has a positive charge, and the other “end” has a negative charge. Any separation of charge into positive and negative regions is called polarity. Ions participating in an ionic bond do not share electrons. Thus, ionic bonds are completely polar (Figure 2.10A). Some covalent bonds are polar, but less so than ionic bonds because atoms participating in them share electrons. In a polar covalent bond, atoms share electrons unequally (Figure 2.10B). A water molecule has two polar covalent bonds. In each bond, the oxygen atom shares electrons with a hydrogen atom. The oxygen pulls the electrons a bit more toward its side of the bond, so it has a slight negative charge, and the hydrogen is left with a slight positive charge. Other covalent bonds are not polar. In a nonpolar covalent bond, atoms share electrons equally (Figure 2.10C). A nonpolar covalent bond links two hydrogen atoms in molecular hydrogen (H2). Neither of the atoms in this molecule carries a charge.

Take-Home Message 2.3 ●●

●●

●●

A molecule consists of atoms held together in a particular number and arrangement by chemical bonds, which can be ionic or covalent. An ionic bond is a strong mutual attraction between ions of opposite charge. An ionic compound is highly polar because the ions do not share electrons, so they retain their full respective charges. Atoms share a pair of electrons in a covalent bond. If the sharing is unequal, the bond is polar. If the sharing is equal, the bond is nonpolar.

chemical bond  A strong attractive force that arises between two atoms; links atoms in molecules. compound  Molecule that has atoms of more than one element. covalent bond  Type of chemical bond in which two atoms share electrons. ionic bond  Type of chemical bond in which a strong mutual attraction links ions of opposite charge. polarity  Separation of charge into positive and negative regions.

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

34  Unit 1  How Cells Work

2.4  Special Properties of Water

slight negative charge –

Learning Objectives ●●

O H

H

+

+

slight positive charge

A. Polarity of the water molecule. Each of the hydrogen atoms in a water molecule bears a slight positive charge (represented by a blue overlay). The oxygen atom carries a slight negative charge (red overlay). a hydrogen bond H

H O

H

O

Using appropriate examples, explain how the polarity of the water molecule gives rise to properties of water that are essential to life.

●●

Draw a hydrogen bond between two water molecules.

●●

Describe the way an ionic substance dissolves in water.

Life evolved in water. All living organisms are mostly water, many of them still live in it, and all of the chemical reactions of life are carried out in water-based fluids. What makes water so fundamentally important for life? Consider the two polar covalent bonds in a water molecule. Overall, the molecule has no charge, but the oxygen atom carries a slight negative charge, and each of the hydrogen atoms carries a slight positive charge. Thus, the molecule itself is polar (Figure 2.11A). This polarity gives rise to the special properties that make water essential to life.

Hydrogen Bonds H

B. A hydrogen bond is an attraction between a hydrogen atom and another atom taking part in a separate polar covalent bond.

The polarity of individual water molecules attracts them to one another: The slight positive charge of a hydrogen atom in one water molecule is drawn to the slight negative charge of an oxygen atom in another. This type of interaction is called a hydrogen bond. A hydrogen bond is an attraction between a covalently bonded hydrogen atom and another atom taking part in a separate polar covalent bond (Figure 2.11B). Like ionic bonds, hydrogen bonds form by the mutual attraction of opposite charges. Unlike ionic bonds, hydrogen bonds do not make molecules out of atoms, so they are not chemical bonds. Hydrogen Bonding in Water  Hydrogen bonds are on the weaker end of the spec-

trum of atomic interactions, which means they form and break much more easily than covalent or ionic bonds. Even so, many of them form, and collectively they can be very strong. Hydrogen bonds form in tremendous numbers among water molecules (Figure 2.11C), and they also stabilize the characteristic structures of biological molecules such as DNA.

C. The many hydrogen bonds that form among water molecules impart special properties to liquid water.

Water as a Solvent The polarity of water molecules makes water an excellent solvent, which means that many other substances can dissolve in it. Substances that dissolve easily in water are hydrophilic (water-loving). Hydrophilic Substances  Ionic solids, which consist of ions held together by ionic

D. Because water molecules are polar, they are attracted to ions that make up ionic solids such as sodium chloride (NaCl). The solid dissolves as water molecules surround the ions and separate them.

bonds, are hydrophilic. Sodium chloride (NaCl) is an example. Remember that ions taking part in an ionic bond retain their respective charges. The polarity of water molecules attracts them to each ion: The oxygens bear a slight negative charge, so they cluster around the positively charged ions (such as Na+). The hydrogens in a water molecule carry a slight positive charge, so they cluster around the negatively charged ions (such as Cl–). The solid dissolves as water molecules surround the ions and separate them (Figure 2.11D). Solute Concentration  When a substance such as NaCl dissolves, its component

ions disperse uniformly among the molecules of the solvent, and it becomes a

Figure 2.11  Hydrogen bonds and water.

solute. Sodium chloride is called a salt because it releases ions other than H+

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Molecules of Life  Chapter 2  35 

and OH– when it dissolves in water (more about these ions in the next section). A uniform mixture such as salt dissolved in water is called a solution. Chemical bonds do not form between molecules of solute and solvent, so the proportions of the two substances in a solution can vary. The amount of a solute that is dissolved in a given volume of fluid is its concentration. Many compounds other than salts are hydrophilic and dissolve easily in water. Sugars are examples. Molecules of these substances have one or more polar covalent bonds, and atoms participating in a polar covalent bond can form hydrogen bonds with water molecules. When one of these solids is added to water, it dissolves because hydrogen bonding with water pulls its individual molecules away from one another and keeps them apart. Unlike ionic solids, molecules of these substances do not dissociate into atoms when they dissolve. Hydrophobic Substances  Water does not interact with hydrophobic (water-

dreading) substances such as oils. Oils consist of nonpolar molecules, and hydrogen bonds do not form between nonpolar molecules and water. Vigorous shaking can disperse water in oil, but hydrogen bonding causes the water to coalesce. As this happens, the water excludes molecules of oil and pushes them together into drops that rise to the surface of the mixture. The same interactions occur at the thin, oily membrane that separates the watery fluid inside cells from the watery fluid outside of them (Chapter 3 returns to this topic).

Water Stabilizes Temperature  All atoms jiggle nonstop, so the molecules they make up jiggle too. We measure the energy of this motion as temperature. Adding energy (in the form of heat, for example) speeds up the jiggling, so the temperature rises. Extensive hydrogen bonding keeps water molecules from moving as much as they would otherwise, so it takes more heat to raise the temperature of water compared with other liquids. Water’s resistance to temperature change is an important part of homeostasis because most of the molecules of life function properly only within a certain range of temperature.

In ice, water molecules are locked in a rigid lattice by hydrogen bonds (top). The molecules in this lattice pack less densely than they do in liquid water, which is why ice floats. A covering of ice can insulate water underneath it, thus keeping aquatic organisms from freezing during long, cold winters (bottom).

Ice  Below 0°C (32°F), water molecules do not jiggle enough to break hydrogen

cohesion  Property in which the molecules of a substance resist separating from one another.

bonds between them, and they become locked in the rigid, lattice-like bonding pattern of ice (Figure 2.12). Individual water molecules pack less densely in ice than they do in water, which is why ice floats. This property is unique—all other known substances become more dense as they solidify—and it is an important reason why life exists on Earth. In subfreezing air temperatures, sheets of ice form on the surface of a body of water such as a lake or sea. This “ice blanket” insulates the underlying water and can keep it from freezing. If ice sank, the entire body of water would freeze quickly, along with the organisms living in it.

Cohesion  © Herbert Schnekenburger

Figure 2.12  Ice.

Molecules of some substances resist separating from one another, a property called cohesion. In water, hydrogen bonds collectively exert a continuous pull on its individual molecules and keep them together. You can see this cohesion as surface tension, which means that the surface of liquid water behaves a bit like a sheet of elastic (left).

Bottom, © Vicki Rosenberg, www.flickr.com/photos/roseofredrock

concentration  Amount of solute per unit volume of solution. hydrogen bond  Attraction between a covalently bonded hydrogen atom and another atom taking part in a separate covalent bond. hydrophilic  Describes a substance that dissolves easily in water. hydrophobic  Describes a substance that resists dissolving in water. salt  Ionic compound that releases ions other than H+ and OH– when it dissolves in water. solute  A dissolved substance. solution  Uniform mixture of solute completely dissolved in a solvent. solvent  Liquid in which other substances dissolve. temperature  Measure of molecular motion.

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36  Unit 1  How Cells Work

— 14

— 13

drain cleaner oven cleaner

more basic

bleach

— 12

— 11

— 10

—9

—8

—7

—6

more acidic

—5

—4

—3

—2

hair remover

household ammonia

milk of magnesia hand soap toothpaste Tums detergents baking soda

Water’s cohesion plays a role in many processes that sustain multicelled bodies. Consider how sweating helps keep your body cool during hot, dry weather. Sweat, which is about 99 percent water, cools the skin as it evaporates. Why? Evaporation is the process in which molecules escape from the surface of a liquid and become vapor. The evaporation of water is resisted by hydrogen bonding among individual water molecules. In other words, overcoming cohesion takes energy. Thus, evaporation sucks energy (in the form of heat) from liquid water, and this lowers the water’s temperature. Cohesion works inside organisms, too. Consider how plants absorb water from soil as they grow. Water molecules evaporate from leaves, and replacements are pulled upward from roots. Cohesion makes it possible for columns of liquid water to rise from roots to leaves inside narrow pipelines of vascular tissue. In some trees, these pipelines extend hundreds of feet above the soil.

Take-Home Message 2.4 ●●

seawater egg white blood, tears

●●

pure water ●●

milk butter corn urine, tea, typical rain black coffee bread beer bananas tomatoes, wine orange juice vinegar cola lemon juice acid rain

—1

gastric fluid

—0

battery acid

A hydrogen bond is an attraction between a covalently bonded hydrogen atom and another atom taking part in a separate covalent bond. Hydrogen bonds are individually weak, but collectively strong. Extensive hydrogen bonding among water molecules arises from the polarity of the individual molecules, and it gives rise to special properties of water that make life possible. Water has cohesion. It can dissolve many substances, and it stabilizes temperature.

2.5  Acids and Bases Learning Objectives ●●

Define pH.

●●

Differentiate between acids and bases.

●●

Describe the way that buffers work.

●●

Explain why pH stability is important in biological systems.

Hydrogen Ions A hydrogen atom, remember, is just an electron and a proton. When a hydrogen atom participates in a polar covalent bond, the electron is pulled away from the proton, just a bit. Hydrogen bonding in water can pull that proton right off of the molecule. The detached proton is called a hydrogen ion (H+). The electron stays with the rest of the molecule and makes it negatively charged (ionic). A water molecule (H2O) that loses a hydrogen ion becomes a hydroxide ion (OH–). The loss is more or less temporary, because the two ions can get back together to form another water molecule.

Figure 2.13  A pH scale. This pH scale ranges from 0 (most acidic) to 14 (most basic). A change of one unit on the scale corresponds to a tenfold change in the hydrogen ion concentration. Red dots signify hydrogen ions (H+) and gray dots signify hydroxide ions (OH–). Also shown are the approximate pH values for some common solutions. Photos, Jupiter Images

Figure It Out: What is the approximate pH of cola?

pH  The relative number of H+ and OH– ions in a water-based solution can vary, and we use a value called pH as a measure of the amount of hydrogen ions. The

higher the concentration of these ions, the lower the pH. If a fluid has an equal number of H+ and OH– ions, its pH is 7 (or neutral). Pure water is like this. If there are more H+ ions than OH– ions, the pH is below 7 (or acidic). Conversely, if there are fewer H+ ions than OH– ions, the pH is above 7 (or basic). A one-unit difference in pH corresponds to a tenfold difference in hydrogen ion concentration (Figure 2.13). One way to get a sense of this pH scale is to taste dissolved baking soda (pH 9), pure water (pH 7), and lemon juice (pH 2).

Answer: 2.5

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Molecules of Life  Chapter 2  37 

Acids, Bases, and Buffers An acid is a substance that gives up hydrogen ions in water. The addition of acid to a solution can lower its pH. By contrast, a base accepts hydrogen ions, so it can raise pH. Metabolic processes continuously release acids and bases into cell and body fluids, but the pH of these fluids typically does not fluctuate much. Why not? Buffers stabilize their pH. A buffer is a set of chemicals that can keep pH stable by alternately donating and accepting ions that affect pH. The Bicarbonate Buffer System  Consider two chemicals, carbonic acid and bicar-

bonate, that occur in the fluid portion of your blood. These chemicals constitute a buffer that normally keeps the blood’s pH between 7.35 and 7.45. When a basic substance enters the blood, it removes hydrogen ions. Carbonic acid molecules immediately release hydrogen ions to replace the ones that were lost. A molecule of carbonic acid that releases a hydrogen ion becomes bicarbonate: H2CO3 carbonic acid

H1 1 HCO32 hydrogen ion bicarbonate

When an acidic substance enters the blood, it releases hydrogen ions. Bicarbonate is a base, and it immediately accepts the excess hydrogen ions. A bicarbonate molecule that accepts a hydrogen ion becomes a molecule of carbonic acid: H1 1 HCO32 hydrogen ion bicarbonate

H2CO3 carbonic acid

By replacing lost hydrogen ions, carbonic acid keeps the pH of blood from rising when a base enters it. By combining with excess hydrogen ions, bicarbonate prevents the pH of blood from falling when an acid enters it. In both cases, the proportion of carbonic acid and bicarbonate molecules shifts, but the pH stays stable. Such stability is a crucial part of homeostasis, because most biological molecules function properly only within a narrow range of pH.

Take-Home Message 2.5 ●● ●● ●●

The concentration of hydrogen ions in a fluid determines its pH. Acids release hydrogen ions in water; bases accept them. Most biological molecules function properly only within a narrow range of pH. Buffers are an important homeostatic mechanism that keeps pH within these ranges.

2.6  The Chemistry of Biology Learning Objectives ●●

Explain the basic structure of an organic molecule.

●●

Describe the different ways of depicting organic molecules.

●●

Explain how the molecules of life are polymers.

●●

Give an example of a metabolic reaction.

Organic Compounds The same elements that make up a living body also occur in nonliving things, but their proportions differ. For example, compared to sand or seawater, a human body

acid  Substance that releases hydrogen ions in water. base  Substance that accepts hydrogen ions in water. buffer  Set of chemicals that can keep the pH of a solution stable by alternately donating and accepting ions that contribute to pH. evaporation  Transition of a liquid to a vapor. pH  Measure of the amount of hydrogen ions in a fluid.

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A. Carbon’s versatile bonding behavior allows it to form a variety of 38  Unit 1  How Cells Work structures, including rings. C C

C

C

C C

A. Carbon’s versatile bonding behavior allows it to form a variety of structures, including rings.

B. Carbon rings form the backbone of many sugars, starches, and fats (including those found in doughnuts).

Figure 2.14  Carbon rings. (B) Getty Images

B. Carbon rings form the Figure 2.15  Modeling a small organic compound. backbone of many sugars, starches, and fats (including All of these models represent the same molecule: those found in doughnuts). glucose, a sugar. O

H

A. A structural formula that shows all of the bonds and atoms can be very complicated, even for a simple molecule. The overall structure is obscured by detail.

H C H HH C O C O HO H

C H

H H

H

C

C

O H

O

OH OH O HO

OH

OH CH2OH

HO

O

HO

OH OH

B. For clarity, some features of structural formulas may be implied but not drawn. In this three-dimensional representation, carbon atoms forming the backbone are not labeled. Neither are the hydrogen atoms bonded to the carbons. C. Using polygons as symbols for rings can O further simplify a structural formula. Some bonds and element labels are omitted.

D. A ball-and-stick model is often used to show the arrangement of atoms and bonds in three dimensions.

has a much larger proportion of carbon atoms. Why? Unlike sand or seawater, a body contains a lot of the molecules of life—complex carbohydrates and lipids, proteins, and nucleic acids—and these molecules consist of a high proportion of carbon atoms. Compounds that consist mainly of carbon and hydrogen atoms are said to be organic. The term is a holdover from a time when such molecules were thought to be made only by living things, as opposed to the “inorganic” molecules that formed by nonliving processes. We now know that organic compounds existed on Earth long before life arose. They even form in deep space.

The Carbon Backbone A carbon atom is unusual among elements because it can make covalent bonds with many other elements. It also has four vacancies, so it can bond with four other atoms—including other carbon atoms. The basic structure of all but the simplest organic compounds is a carbon backbone: a chain of covalently bonded carbon atoms that may be branched or form rings (Figure 2.14). The versatility of carbon atoms means that they can be assembled into a wide variety of organic compounds. A molecule that consists only of carbon and hydrogen atoms is called a hydrocarbon, and it is completely nonpolar. The molecules of life have other elements in addition to carbon and hydrogen, often as part of small molecular groups attached to the carbon backbone. Each of these groups adds a particular chemical property. For example, hydroxyl groups (OH) add polar character to an organic compound, thus increasing its ability to dissolve in water. Sugars have a lot of hydroxyl groups, so they are very soluble. Phosphate groups (PO4) are even more polar than hydroxyl groups, and they are also acidic. Methyl groups (CH3) add nonpolar character, so they can dampen the effect of a polar group.

Modeling Organic Compounds As you will see in the next few sections, the function of an organic molecule arises from and depends on its structure. Researchers make models of organic compounds in order to study different aspects of this relationship. Models can reveal surface properties, changes during synthesis or other biochemical processes, sites of molecular recognition, and so on. Different models allow us to visualize different characteristics. The structure of organic molecules can be quite complex (Figure 2.15A), so representations are typically simplified. For clarity, some of the features may be implied but not represented: element symbols, for example, or hydrogen atoms bonded to a carbon backbone (Figure 2.15B). Carbon rings may be simplified as polygons (Figure 2.15C). Ball-and-stick models depict an organic molecule’s three-dimensional arrangement of atoms (Figure 2.15D). Space-filling models reveal overall shape (Figure 2.15E). Proteins and nucleic acids are often modeled as ribbons, which show how the molecule folds and twists in three dimensions.

What Cells Do to Organic Compounds  E. A space-filling model can be used to show a molecule’s overall shape. Individual atoms are visible in this model.

All biological systems are based on the same organic molecules, a similarity that is one of many legacies of life’s common origin. However, the details of those molecules differ among organisms. Just as atoms bonded in different numbers and arrangements form different molecules, simple organic building blocks bonded in different numbers and arrangements form different versions of the molecules of life. The building blocks—sugars, fatty acids, amino acids, and nucleotides—are called

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Molecules of Life  Chapter 2  39 

monomers when they are used as subunits of larger molecules. A molecule that consists of multiple monomers is a polymer.

Cells link monomers to form polymers, and break apart polymers to release monomers. These and other processes of molecular change are called reactions. Cells constantly run reactions as they acquire and use energy to stay alive, grow, and reproduce. Collectively, these reactions are called metabolism. Metabolism requires enzymes, which are organic molecules (usually proteins) that speed up reactions without being changed by them. Some enzymes remove monomers from polymers in a common metabolic reaction called hydrolysis (Figure 2.16A). The reverse of hydrolysis is a reaction called condensation, in which an enzyme joins one monomer to another (Figure 2.16B).

Take-Home Message 2.6 ●● ●●

●●

●●

The molecules of life are organic (they consist mainly of carbon and hydrogen atoms). The structure of most organic molecules starts with a chain of carbon atoms (the backbone). Small molecular groups attached to the backbone impart chemical character to the molecule. We use different types of models to visualize different structural characteristics of an organic molecule. Considering a molecule’s structural features gives us insight into its function. By processes of metabolism, cells assemble the molecules of life from simpler organic monomers.

H

O + O

H

OH + HO

OH + HO

O + H

O

H

A. Hydrolysis. Cells use this waterrequiring reaction to split polymers into monomers. An enzyme attaches a hydroxyl group and a hydrogen atom (both from water) at the site of the split.

B. Condensation. Cells use this reaction to build polymers from monomers. An enzyme removes a hydroxyl group from one molecule and a hydrogen atom from another. A covalent bond forms between the two molecules, and water also forms.

Figure 2.16  Examples of metabolic reactions. Two common reactions by which cells build and break down organic molecules are shown.

2.7  Carbohydrates Learning Objectives ●●

Describe the structure of carbohydrates and explain their roles in cells.

●●

Using an example, explain how the structure of a polysaccharide gives rise to its function.

●●

Name the function that glycogen serves in the human body.

Carbohydrates are organic compounds that consist of carbon, hydrogen, and oxygen in a ratio of approximately 1:2:1. In cells, carbohydrates are used for fuel, as structural materials, and for storing energy. All carbohydrates are either a sugar or a polymer made from sugar monomers, so they are also called saccharides (saccharide means sugar).

Simple Sugars Monosaccharides (one sugar) are often called simple sugars because they are the simplest carbohydrates, and many of them have a sweet taste. Common monosaccharides have a backbone of five or six carbon atoms. Two or more hydroxyl groups impart solubility, which means that monosaccharides move easily through the water-based internal environments of all organisms. Monosaccharides have extremely important biological roles. Cells break the bonds of glucose, shown in Figure 2.15, to release energy that can be harnessed to power other reactions (Chapter 6 returns to this metabolic process). Ribose and deoxyribose are components of the nucleotide monomers of RNA and DNA, respectively. Cells also use monosaccharides as structural materials to build larger molecules, and as precursors (parent molecules) that are remodeled into other

carbohydrate  Molecule that consists primarily of carbon, hydrogen, and oxygen atoms in a ratio of approximately 1:2:1. enzyme  Organic molecule that speeds up a reaction without being changed by it. metabolism  Collective term for all of the enzyme-mediated reactions in a cell. monomer  Molecule that is a subunit of a polymer. organic  Describes a compound that consists mainly of carbon and hydrogen atoms. polymer  Molecule that consists of multiple monomers. reaction  Process of molecular change.

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

40  Unit 1  How Cells Work OH O

OH O

O O

O

OH O

O O

O

OH O

O O

O

OH O

O

HO

HO

HO

HO

OH

OH

OH

OH

O

O

O

O

O

HO

O

O

O

HO

OH O

O O

O

O

O

HO

OH O

O

O

O

O

HO

OH

O

O

O

O

HO

O

O

O

O

O

O

O

OH O

O O

O

O O

O

A. Cellulose Cellulose is the main structural component of plants. Above, in cellulose, hydrogen bonds stabilize long, straight chains of glucose monomers. The cross-linked chains form long, tough fibers that few organisms can digest. B. Starch Starch is the main energy reserve in plants, which store it in their roots, stems, leaves, seeds, and fruits. Below, starch consists of long, coiled chains of glucose monomers.

OH

OH

OH

O

O

O

O

O

OH O O

O

Figure 2.17  Three of the most common complex carbohydrates and their locations in a few organisms. Each polysaccharide consists only of glucose units (orange polygons), but different bonding patterns that link the subunits result in substances with very different properties. Photo, Blend/Corbis

C. Glycogen Glycogen functions as an energy reservoir in animals, including people. It is especially abundant in the liver and muscles. Above, glycogen consists of highly branched chains of glucose monomers.

molecules. For example, cells of plants and many animals make vitamin C from glucose. Human cells are unable to make this conversion, so we need to get vitamin C from our food.

Oligosaccharides Short chains of covalently bonded monosaccharides are called oligosaccharides (oligo– means a few). Disaccharides consist of two sugar monomers. Lactose, a sugar in milk, is a disaccharide that consists of glucose and galactose monomers. Sucrose, the most plentiful sugar in nature, consists of glucose and fructose monomers. Extracted from sugarcane or sugar beets, sucrose is our table sugar.

Polysaccharides Foods that we call “complex” carbohydrates consist mainly of polysaccharides, which are chains of hundreds or thousands of monosaccharide monomers. The most common polysaccharides—cellulose, starch, and glycogen—all consist only of glucose monomers, but as substances their properties are very different. Why? The answer begins with differences in patterns of covalent bonding that link their monomers. Cellulose  In cellulose, hydrogen bonds cross-link long, straight chains of covalently bonded glucose monomers (Figure 2.17A). Cellulose is the most abundant organic molecule on Earth because it is the major structural material of plants. It forms tough fibers that act like reinforcing rods inside stems and other plant parts, helping these structures resist wind and other forms of mechanical stress.

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Molecules of Life  Chapter 2  41 

Cellulose is insoluble (it does not dissolve) in water, and it is not easily broken down. Some bacteria and fungi make enzymes that can break it apart into its component sugars, but humans and other mammals do not. Dietary fiber, or “roughage,” usually refers to the indigestible cellulose in our vegetable foods. Bacteria that live in the guts of termites and grazers such as cattle and sheep help these animals digest the cellulose in plants. Starch  Plants produce starch, a polysaccharide in which the bonding pattern

between glucose monomers makes a chain that coils up into a spiral (Figure 2.17B). Starch does not dissolve easily in water, but it is easier to break down than cellulose. These properties make the molecule ideal for storing sugars in the watery, enzymefilled interior of plant cells. For example, sugars are moved into developing seeds and then converted to starch for storage. A mature seed may rest for a long time before it sprouts. Then, hydrolysis enzymes break the bonds between the starch’s glucose monomers. The released glucose is used to fuel growth of the young plant until it can make its own food. Humans also have enzymes that break down starch, so this carbohydrate is an important component of our food. Glycogen  Animals and fungi store sugars in the form of glycogen, a polysaccharide

that consists of highly branched chains of glucose monomers (Figure 2.17C). Muscle and liver cells contain most of the glycogen in an animal’s body. When the blood sugar level falls, enzymes in liver cells break down the glycogen, and the released glucose subunits enter the blood.

Take-Home Message 2.7 ●●

●● ●●

Some monosaccharides (simple sugars) are used as monomers or precursors of other organic molecules; others are broken down for energy. Cells assemble monosaccharide monomers into larger carbohydrate molecules. Cellulose, starch, and glycogen all consist of glucose monomers. The different characteristics of these polysaccharides arise from different bonding patterns between the monomers.

2.8  Lipids Learning Objectives ●●

Describe a fat, and identify the difference between saturated and unsaturated fats.

●●

Explain why a phospholipid is both hydrophilic and hydrophobic.

●●

Describe the lipid bilayer.

●●

Give one example of a molecule that is made from cholesterol.

Fatty Acids Lipids are fatty, oily, or waxy organic compounds. One type of lipid, a fatty acid, is

a small organic molecule that consists of a long hydrocarbon “tail” with a carboxyl group “head” (Figure 2.18, next page). The tail is hydrophobic (fatty); the carboxyl group makes the head hydrophilic (and acidic). You are already familiar with the properties of fatty acids because these molecules are the main component of soap: The hydrophobic tails attract oily dirt, and the hydrophilic heads help dissolve the dirt in water.

cellulose  Tough, insoluble polysaccharide that is the major structural material in plants. fatty acid  Lipid that consists of a (hydrophilic) carboxyl group head and a long (hydrophobic) hydrocarbon tail. lipid  Fatty, oily, or waxy organic compound.

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

42  Unit 1  How Cells Work O

head

Figure 2.18  Fatty acids. Each fatty acid molecule has a carboxyl group head that is hydrophilic, and a long hydrocarbon tail that is hydrophobic. Double bonds in the tails are highlighted in red. A. The tail of stearic acid is fully saturated with hydrogen atoms. B. Linoleic acid, with two double bonds, is unsaturated. The first double bond occurs at the sixth carbon from the end of the tail, so linoleic acid is called an omega-6 fatty acid.

tail

C. Linolenic acid is unsaturated. The first double bond occurs at the third carbon from the end, so linolenic acid is called an omega-3 fatty acid. Omega-6 and omega-3 fatty acids are “essential fatty acids,” which means your body does not make them. These fatty acids must come from food. D. The hydrogen atoms around the double bond in oleic acid are on the same side of the tail. Most other naturally occurring unsaturated fatty acids have these cis bonds. E. In trans bonds, the hydrogen atoms are on opposite sides of the tail. Figure It Out: Is elaidic acid saturated or unsaturated?

OH

O

OH

O

OH

O

OH

O

OH

C

C

C

C

C

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

C—H

C—H

C—H

H—C

H—C—H

C—H

C—H

C—H

C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

C—H

C—H

H—C—H

H—C—H

H—C—H

C—H

C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

C—H

H—C—H

H—C—H

H—C—H

H—C—H

C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H—C—H

H

H

H

H

H

D. oleic acid (cis)

E. elaidic acid (trans)

A. stearic acid (saturated)

B. linoleic acid (omega-6)

C. linolenic acid (omega-3)

Answer: Unsaturated

Saturated fatty acids have only single bonds linking the carbons in their tails. In other words, their carbon chains are fully saturated with hydrogen atoms (Figure 2.18A). An unsaturated fatty acid has at least one double bond between carbons making up its tail (Figure 2.18B,C). These double bonds are cis or trans, depending on their geometry (Figure 2.18D,E). fat  A triglyceride. lipid bilayer  Double layer of phospholipids arranged tail-to-tail; structural foundation of all cell membranes. phospholipid  A lipid with two (hydrophobic) fatty acid tails and a (hydrophilic) head that contains a phosphate group. saturated fat  Triglyceride with three saturated fatty acid tails. saturated fatty acid  Fatty acid with only single bonds linking the carbons in its tail. steroid  A type of lipid with four carbon rings and no fatty acid tails. triglyceride  A lipid with three fatty acid tails bonded to a glycerol; a fat. unsaturated fat  Triglyceride molecule with one or more unsaturated fatty acid tails. unsaturated fatty acid  Fatty acid that has at least one double bond between carbons making up its tail.

H2C

CH

O O

C

O

O C

O

C

CH2

Triglycerides 

O

The carboxyl group head of a fatty acid can easily form a covalent bond with another molecule. When the head bonds to a glycerol (a type of alcohol), the fatty acid loses its hydrophilic character. Three fatty acids bonded to the same glycerol form a triglyceride (left), a lipid that is entirely hydrophobic and therefore does not dissolve in water. Triglycerides are the most abundant and richest energy source in vertebrate bodies; gram for gram, they store more energy than carbohydrates.

Saturated Fats  A triglyceride molecule is also called a fat. A saturated fat is a tri-

glyceride with three saturated fatty acid tails. Saturated fatty acid tails are flexible and they wiggle freely, so they can pack together very tightly. This is why substances with a high proportion of saturated fats are firm at room temperature. Foods such as butter and lard that are derived from animals have a high proportion of saturated fats.

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Molecules of Life  Chapter 2  43 

CH2

N+

CH2

O phosphate group

O-—P  O

hydrophilic head

O

one layer of lipids one layer of lipids

CH2

O

CH

CH2

O

O

C

C

O two hydrophobic tails

B. The lipid bilayer. The opposing hydrophilic and hydrophobic properties of phospholipid molecules give rise to this double-layered structure, which is the foundation of all cell membranes.

A. Phospholipid. Two fatty acid tails are attached to a head that contains a phosphate group (yellow). The phosphate group makes the head very hydrophilic; the tails are hydrophobic.

HO

Figure 2.19  Phospholipids make up cell membranes.

cholesterol

OH

Unsaturated Fats  Unsaturated fats are triglycerides with one or more unsaturated

fatty acid tails. Most substances with a high proportion of unsaturated fats are oils— liquid at room temperature. This is because the double bonds in most unsaturated fats are in the cis configuration, and cis bonds kink the fatty acid tails. Kinky tails cannot pack together tightly. By contrast, the partially hydrogenated vegetable oils you read about in Section 2.1 are firm at room temperature because they have a high proportion of trans fats—triglycerides with trans bonds in their tails. Trans bonds do not kink fatty acid tails, so substances with a high proportion of trans fats can pack just as tightly as saturated fats.

O testosterone

♂

OH

HO estradiol (an estrogen)

♀

Phospholipids  A phospholipid is a type of lipid with two long hydrocarbon tails (which, in most organisms, are derived from fatty acids) and a head with a phosphate group in it (Figure 2.19A). The tails are hydrophobic, and the polar phosphate group makes the head hydrophilic. These opposing properties give rise to the lipid bilayer, a two-layered sheet of phospholipids that is the basic structure of all cell membranes (Figure 2.19B). The heads of one layer face the cell’s fluid interior, and the heads of the other layer face the cell’s watery surroundings. Tails of all the phospholipids are sandwiched between the heads, so the interior of a lipid bilayer is highly hydrophobic.

Steroids  Steroids are lipids with no fatty acid tails; they have a rigid backbone with a characteristic pattern of four carbon rings. Small molecular groups attached to the rings define the type of steroid. These molecules have varied and important physiological functions in plants and animals. Cholesterol, the most common steroid in animal tissue, is remodeled into other molecules such as vitamin D (required to keep teeth and bones strong) and steroid hormones (Figure 2.20).

Figure 2.20  Steroids. Top, cells remodel cholesterol into many other compounds, including estradiol and testosterone: two steroid hormones that govern reproduction and secondary sexual traits. Despite the small differences in structure, the two hormones have very different effects in the body. They are the source of sex-specific traits in many species, including wood ducks (bottom). Bottom, Jack Nevitt/Shutterstock.com

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44  Unit 1  How Cells Work

CLOSER LOOK Figure 2.22  How protein structure arises.

H H O

H N C C OH

+

H N C C OH

CH2

HC CH3

CH2

valine

S

CH3

H H O

Figure It Out: What do the red lines between the boxes represent?

Answer: Peptide bonds

H H O

H H O

H N C C

N C C OH

CH2

valine

histidine

leucine

threonine

CH3

S

CH3 methionine

methionine

HC CH3

CH2

CH3 methionine

2 Primary structure. As the chain lengthens, it becomes a valine

1 The peptide bond. A condensation reaction joins the carboxyl group of one

amino acid and the amine group of another to form a peptide bond. In this example, a peptide bond forms between the amino acids methionine and valine.

polypeptide. The linear sequence of amino acids making up the polypeptide is primary structure. It gives rise to higher orders of structure that form the protein’s shape—and ultimately, its function. This is part of the amino acid sequence of a polypeptide called globin.

Waxes  A wax is a water-repellent substance that consists of a complex, varying mixture of lipids. These lipids pack very tightly, so waxes are firm at room temperature. Plants secrete waxes onto their exposed surfaces to restrict water loss and to repel pests. Other types of waxes protect, lubricate, and soften skin and hair. Bees store honey and raise new generations of bees inside a honeycomb of secreted beeswax.

Take-Home Message 2.8 ●●

amine group

H H O H N C C OH

carboxyl group

R group

●●

●● ●●

Figure 2.21  Generalized structure of an amino acid.

●●

Each amino acid consists of an amine group, a carboxyl group, and an “R group” bonded to the same carbon atom. The R group determines the type of amino acid.

Fatty acids are lipids with dual chemical character: a hydrophilic head, and hydrophobic tails. A triglyceride is a fat. Saturated fats have three saturated fatty acid tails; unsaturated fats have one or more unsaturated tails. Phospholipids are the main component of lipid bilayers. Steroids are lipids with a characteristic four-ring structure. They serve varied and important physiological roles. Waxes are firm, water-repellent substances composed of varying mixtures of lipids.

2.9  Proteins Learning Objectives amino acid  Small organic compound that is a monomer of proteins. Consists of a carboxyl group, an amine group, and one of twenty R groups, all bonded to the same carbon atom. The R group determines the amino acid. peptide bond  A covalent bond between the amine group of one amino acid and the carboxyl group of another. Joins amino acids in proteins. protein  Organic molecule that consists of one or more amino acid chains folded into a specific shape. wax  Firm, water-repellent substance that is a complex mixture of lipids.

●●

Draw the generalized structure of an amino acid.

●●

Describe and give general examples of the four levels of protein structure.

●●

Using an appropriate example, explain why changes in protein structure can be dangerous.

Protein Structure Amino Acid Monomers  A protein is an organic molecule that consists of one or more chains of amino acids folded up into a specific shape. An amino acid is a small organic compound with an amine group (NH2), a carboxyl group (COOH, the acid), and an “R group” that defines the type of amino acid. All three groups are attached to the same carbon atom (Figure 2.21). Cells make the thousands of different proteins they need from only 20 kinds of amino acids.

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proline

Molecules of Life  Chapter 2  45 

pocket proline tamic ca ac cid gluta tamic ca ac cid gluta helix

heme helix

3 Secondary structure. Secondary 3 Secondary structure. Secondary

refers to characteristic structure refersstructure to characteristic patterns helices and sheets. patterns such as helicessuch and as sheets. patterns arise when hydrogen These patternsThese arise when hydrogen bonds that amino form between bonds that form between acids amino acids make the polypeptide make the polypeptide twist and turn. twist and turn.

4 Tertiary structure. Interactions between

different parts of the polypeptide make helices and sheets fold up together into functional domains. These domains are tertiary structure. In this example, the helices of the globin chain form a pocket for a small molecule called a heme (in red).

The Peptide Bond  The covalent bond that links amino acids in a chain is called a peptide bond. During protein synthesis, a peptide bond forms between the carboxyl group of the first amino acid and the amine group of the second (Figure 2.22 1). Another peptide bond links a third amino acid to the second, and so on. A short chain of amino acids is called a peptide; as the chain lengthens, it becomes a polypeptide.

5 Quaternary structure. Many proteins

have quaternary structure, which is an association of multiple polypeptides. A working molecule of hemoglobin, shown here, consists of four globin chains (green and blue), each holding its heme. Figure Summary A protein’s primary structure consists of a linear sequence of amino acids (a polypeptide). Each type of protein has a unique primary structure. Tertiary structure arises when loops, helices, and sheets fold up into a domain. Proteins with quaternary structure consist of multiple polypeptide chains. Data source: PDB ID:1BBB. Silva, M.M., Rogers, P.H., Arnone, A. (1992) “A third quaternary structure of human hemoglobin A at 1.7-A resolution.” J.Biol.Chem. 267: 17248–17256

Primary and Secondary Structure  Protein structure begins with a series of amino acids that become joined into a polypeptide during protein synthesis 2. The order of the amino acids in the series is called primary structure, and it defines the type of protein. Primary structure determines the higher orders of structure that make up the protein’s final shape. This shape begins to arise even before protein synthesis has finished, as hydrogen bonds that form between amino acids cause the lengthening polypeptide to twist and turn in three dimensions. The hydrogen bonds pull sections of the polypeptide into characteristic patterns such as helices (coils) and sheets connected by flexible loops and tight turns (Figure 2.23). These are patterns of secondary structure 3. Each type of protein has a unique primary structure, but almost all proteins have helices, sheets, or both. Tertiary and Quaternary Structure  Hydrogen bonding and

other interactions between different parts of the polypeptide can fold helices and sheets into compact, functional domains 4. These domains are the protein’s tertiary structure. Domains often have a complex three-dimensional architecture; some resemble tiny barrels (left), propellers, sandwiches, and so on. Each has a particular role in the proData source: PDB ID:2W5J. Vollmar, tein. For example, some barrel domains rotate like motors; M., Shlieper, D., Winn, M., Buechner, C., Groth, G. “Structure of the C14 others form tunnels through cell membranes that allow ions rotor ring of the proton translocating chloroplast ATP synthase.” (2009) to cross. A large protein may have several domains, each J. Biol. Chem. 284:18228. contributing a particular function to the molecule. Many proteins have quaternary structure, which means they consist of two or more polypeptide chains that are closely associated or covalently bonded together 5. Many enzymes are like this. So are fibrous proteins, which aggregate by the

a helix

a sheet

protein with a helix and a sheet

Figure 2.23  Secondary structure in proteins. The structure of almost all proteins includes helices, sheets, or both. The small protein on the right has one helix and one sheet. Tight turns reverse the direction of the polypeptide to form the sheet; flexible loops connect the sheet to the helix. Right, data source: PDB ID:1PGX. Achari, A., Hale, S.P., Howard, A.J., Clore, G.M., Gronenborn, A.M., Hardman, K.D., Whitlow, M. “1.67-A X-ray structure of the B2 immunoglobulin-binding domain of streptococcal protein G and comparison to the NMR structure of the B1 domain.” (1992) Biochemistry 31: 10449–10457.

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46  Unit 1  How Cells Work

Digging Into Data Effects of Dietary Fats on Lipoprotein Levels Cholesterol that is made by the liver or that enters the body from food does not dissolve in blood, so it is carried through the bloodstream in lipoproteins, which are aggregate structures of variable amounts and types of lipids and proteins. High-density lipoproteins (HDL) carry cholesterol away from tissues for elimination from the body. Low-density lipoproteins (LDL) carry cholesterol to cells throughout the body. A “cholesterol test” measures the levels of both types of lipoproteins in blood. As the LDL-to-HDL ratio increases, so does the risk of cardiovascular disease. In 1990, Ronald Mensink and Martijn Katan published a study that tested the effects of different dietary fats on blood lipoprotein levels. Their results are shown in Figure 2.25. 1. 2. 3. 4.

In which group was the level of LDL highest? In which group was the level of HDL lowest? Which group had the lowest LDL-to-HDL ratio? Rank the three diets according to their predicted effect on cardiovascular health.

Main Dietary Fats cis fatty acids

trans fatty acids

saturated fats

optimal level

LDL

103

117

121

40

ratio

1.87

2.44

2.2

electrons  hydrophilic b. number of protons in nucleus   atomic number c. polar; dissolves easily in water   hydrogen bonds d. collectively strong   positive charge e. protons < electrons   negative charge f. measure of molecular motion  temperature g. decays  pH h. electron sharing   covalent bond i. reflects H+ concentration  radioisotope 14. Match the molecules with the best description. a. protein primary structure wax b. an energy carrier starch c. water-repellent secretions triglyceride d. richest energy source DNA e. sugar storage in plants polypeptide f. sugar storage in animals and fungi ATP g. carries heritable information glycogen 15. Match each molecule with its component monomers. protein a. phosphate, fatty acids b. amino acids, sugar(s) phospholipid c. glycerol, fatty acids glycoprotein d. nucleotides fat e. glucose only nucleic acid f. sugar, phosphate, base cellulose g. amino acids nucleotide h. glucose, fructose sucrose

CRITICAL THinking 1. Palm oil extracted from tropical palm trees has become the preferred substitute for partially hydrogenated oils in manufactured foods. Like PHO, palm oil has a longer shelf life and is less expensive than animal fats, and it is similarly firm at room temperature because about half of its component fats are saturated. Unlike PHO, however, palm oil contains no trans fats, so it has no appreciable effect on blood cholesterol and it has not been banned from manufactured foods. Accordingly, the use of palm oil in packaged food products is accelerating rapidly. Currently, half of the $375 billion worth of packaged food products that U.S. consumers buy every year are made with it. In response to the dramatic increase in the demand for palm oil, more oil palms are being planted—mainly in countries where tropical rain forests are being cut down at an astonishing rate for this purpose. By decimating the forests, the palm oil industry is wiping out the last remaining populations of critically endangered species such as Sumatran tigers and orangutans. Local and global attempts to regulate deforestation have failed dismally. Is it a problem that endangered species in tropical regions are going extinct because of the demand for palm oil? If so, how would you address it? 2. Alchemists were the forerunners of modern-day chemists. Many of these medieval scholars and philosophers spent their lives trying to transform lead (atomic number 82) into gold (atomic number 79). Explain why they never succeeded. 3. Draw a shell model of a lithium atom (Li), which has 3 protons, then predict whether lithium ions are positively charged or negatively charged. 4. Why are all salts compounds? 5. Solutes dissolve more quickly in warm water than in cold water. Why? 6. Polonium is a rare element with 33 radioisotopes. The most common one, 210Po, has 84 protons and 128 neutrons. When 210Po decays, it emits an alpha particle, which is a helium nucleus (2 protons and 2 neutrons). The decay of 210 Po is tricky to detect because alpha particles do not carry very much energy compared to other forms of radiation. For example, they can be stopped by a single sheet of paper or a few inches of air. That is one reason that authorities failed to discover toxic amounts of 210Po in the body of former KGB agent Alexander Litvinenko until after he died suddenly and mysteriously in 2006. What element does an atom of 210Po become after it emits an alpha particle?

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3

3.1

Food for Thought  53

3.2 What Is a Cell?  54 3.3 Cell Membrane Structure  57

Cell Structure

3.4 Prokaryotic Cells  59 3.5 Eukaryotic Organelles  62 3.6 Elements of Connection  66 3.7 The Nature of Life  70

Each cell making up this plant seedling contains a nucleus (orange spots), which is the defining characteristic of eukaryotes. A plasma membrane (blue-green) surrounds each cell.

Concept Connections Fernan Federici and Jim Haseloff/Wellcome Images

Reflect on life’s levels of organization (Section 1.2). You will use your understanding of lipid and protein structure (2.8 and 2.9) as you learn about how these molecules assemble in cell membranes. The composition of cell membranes allows cells to maintain special internal environments, a function that is critical for life (4.5–4.6). This chapter introduces structures required for processes that occur in all cells, including protein synthesis (8.2, 8.4) and cell division (9.2, 9.3); and additional structures that allow different types of cells (1.4) to carry out special processes such as photosynthesis (5.1) or aerobic respiration (6.3). The chapter also revisits the nature of science (1.8) and the use of tracers in research (2.2).

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Cell Structure  Chapter 3  53 

Application 3.1  Food for Thought There are about as many single-celled organisms living in and on a human body as there are human cells. Most are bacteria in the digestive tract, where they have a critical role in health: They help with digestion, make essential vitamins, prevent the growth of dangerous germs, and shape the immune system. One of the most common intestinal bacteria is Escherichia coli. Most of the hundreds of types, or strains, of E. coli are beneficial, but a few make a toxic protein that can severely damage the lining of the intestine. After ingesting as few as 10 cells of a toxic strain, a person may become ill with severe cramps and bloody diarrhea that lasts up to 10 days. In some people, complications of infection result in kidney failure, blindness, paralysis, and death. Each year, about 265,000 people in the United States become infected with toxinproducing E. coli. Strains of E. coli that are toxic to people live in the intestines of cows and other animals without sickening them. Humans are exposed to the bacteria when they come into contact with feces of animals that harbor them, for example by eating contaminated ground meat. An animal’s feces can contact its meat during slaughter. Bacteria in the feces stick to the meat, then get thoroughly mixed into it during the grinding process. People also become infected with toxic E. coli by eating fresh fruits and vegetables that have contacted animal feces. Bacteria are sticky, so washing produce with water does not remove them all (Figure 3.1). In 2018, people in 36 states across the United States became ill after eating lettuce grown in one region of Arizona, where the crop had been irrigated with contaminated water that contained toxic E. coli. The bacteria likely entered the water via runoff from upstream livestock farms. Of those infected, 96 people were hospitalized, 27 developed kidney failure, and 5 died. Food growers and processors have been taking steps intended to reduce outbreaks of food-borne illnesses. Meat and produce are being tested for some bacteria before sale, and improved documentation should allow a source of contamination to be pinpointed more quickly. Still, in a typical year, around 700,000 pounds of food contaminated with toxic bacteria are recalled from Figure 3.1  Escherichia coli cells sticking to the surface grocery shelves and food processing facilities. of a lettuce leaf. Raw meat contaminated with bacteria is not necessarily discarded by Custom Medical Stock Photo/Getty Images food processors; it may be cooked and resold as ready-to-eat products such as canned chili and frozen dinners. Cooking kills bacteria, and it is one way to ensure food safety. Raw beef trimmings, which have a high risk of contact with fecal matter during the butchering process, are effectively sterilized when sprayed with ammonia. Ground to a Discussion Questions paste, the resulting product is termed “lean finely textured beef” 1. Do you think our food is becoming more or less safe? or “boneless lean beef trimmings.” This product is routinely 2. Lean finely textured beef is much less expensive than reguused as a filler in prepared food products such as hamburger lar ground meat, and it has no living bacteria in it. Would you patties, fresh ground beef, hot dogs, lunch meats, sausages, choose foods prepared with it? Why or why not? frozen entrees, and canned foods. Meat industry organizations 3. Why do you think E. coli strains that are toxic to humans do not and the U.S. Department of Agriculture (USDA) agree that lean harm cows? finely textured beef, appetizing or not, is perfectly safe to eat because any live bacteria in it have been killed.

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3.2  What Is a Cell?

cytoplasm  In a eukaryotic cell, collective term for everything between the cell’s plasma membrane and its nucleus. In a prokaryotic cell, everything enclosed by the plasma membrane.

Learning Objectives

cytosol  Jellylike mixture of water and solutes enclosed by a cell’s plasma membrane. nucleus  Plural, nuclei. Of a eukaryotic cell, organelle that holds the cell’s DNA. organelle  Structure that carries out a specialized function inside a cell.

●●

Describe the three components that all cells have.

●●

Explain why the surface-to-volume ratio limits cell size.

●●

Describe the way a light microscope works.

●●

List four generalizations of cell theory.

You learned in Section 1.2 that the property we call life emerges as molecules become organized into cells. All living things—even the largest, most complex organisms—are composed of these microscopic units of life. How does a free-living cell like a bacterium differ from a body cell? And how do trillions of individual cells function as a collective to form a body? To understand the answers to these questions, you have to learn a bit about what cells consist of and how they function. In this chapter, we focus on cellular components: structures that are common to all cells, and some that differentiate one cell type from another.

plasma membrane  Membrane that encloses a cell and separates it from the external environment. ribosome  Organelle of protein synthesis. surface-to-volume ratio  Relationship in which the volume of an object increases with the cube of the diameter, and the surface area increases with the square.

Components of All Cells Cells vary in shape and in what they do, but all share certain organizational and functional features. For example, each cell starts out life with a plasma membrane, DNA, and cytosol (Figure 3.2). The Plasma Membrane  A cell’s plasma membrane separates its contents from the external environment. With little variation, the basic structure of a plasma membrane (and any other cell membrane) is the lipid bilayer (Section 2.8). As you will see shortly, many different proteins embedded in a lipid bilayer or attached to one of its surfaces carry out particular membrane functions. Only certain materials can cross cell membranes, so a plasma membrane controls the exchange of materials between the cell’s internal and external environments.

cytosol DNA in nucleus

plasma membrane

Cytosol  The plasma membrane encloses a jellylike mixture of water, sugars, ions, and proteins called cytosol. A major part of a cell’s metabolism occurs in cytosol, and the cell’s other internal components, including organelles, are suspended in it. Organelles are structures that carry out special functions inside a cell. Ribosomes, for example, are the organelles that carry out protein synthesis, and all cells have them.

Figure 3.2  General organization of a cell. Cells vary in size and shape, but all start out life with a plasma membrane, cytosol, and DNA. This one is a cell from a plant.

electron microscopes small molecules

molecules of life lipids

0.1 nm

light microscopes

carbohydrates

1 nm

viruses proteins

DNA

10 nm

100 nm

mitochondria, chloroplasts

1 µm

most bacteria

most eukaryotic cells

10 µm

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Cell Structure  Chapter 3  55 

DNA  Every cell starts out life with DNA. A eukaryotic cell’s DNA is contained in an organelle called the nucleus (plural, nuclei). In eukaryotic cells, the cytosol

and all other cellular components between the nucleus and plasma membrane are collectively called cytoplasm. In prokaryotes (bacteria and archaea), DNA is suspended directly in cytosol, so the definition of cytoplasm differs from eukaryotes. In prokaryotes, cytoplasm includes everything enclosed by the plasma membrane, including DNA.

Diameter (cm)

2

3

6

12.6

28.2

113

Volume (cm3)

4.2

14.1

113

Surface-to-volume ratio

3:1

2:1

1:1

Surface area (cm2)

The Surface-to-Volume Ratio A living cell must exchange substances with its environment. Nutrients must enter the cell fast enough to sustain its metabolism, and wastes must leave the cell before reaching toxic levels. These exchanges occur across the plasma membrane, which can handle only so many exchanges at a time. The rate of exchange across a plasma membrane depends on its surface area: The greater the area, the more substances can cross it during a given interval. Thus, cell size is limited by a physical relationship called the surface-to-volume ratio. By this ratio, an object’s volume increases with the cube of its diameter, but its surface area increases only with the square.

Figure 3.3  Surface-to-volume ratio. This physical relationship between surface area and volume constrains cell size and shape. Surface area and volume of three round cells are compared here. Table 3.1  Equivalent Units of Length

Equivalent

Limits on Cell Size  Let’s apply the surface-to-volume ratio to a round cell. As

Figure 3.3 shows, when a cell expands in diameter, its volume increases faster than

its surface area does. Imagine that the cell expands until it is four times its original diameter. The volume of the cell has increased 64 times (43), but its surface area has increased only 16 times (42). Each unit of plasma membrane must now handle exchanges for four times as much cytoplasm (64 ÷ 16 = 4). If the cell gets too big, the inward flow of nutrients and the outward flow of wastes across that membrane will not be fast enough to keep the cell alive. Thus, even the largest cells are tiny (Figure 3.4 and Table 3.1). Constraints on Cell Form  The surface-to-volume ratio also constrains cell form in multicelled organisms. Consider the muscle cells that run the length of your thigh. Although surprisingly long, each of these cells is very thin, so it exchanges substances efficiently with fluids in the surrounding tissue.

Unit

Meter(s)

Inch(es)

kilometer

1,000

39,370

meter (m)

1

39.37

centimeter (cm)

1/100

0.4

millimeter (mm)

1/1,000

0.04

micrometer (µm)

1/1,000,000

0.00004

nanometer (nm)

1/1,000,000,000

0.00000004

Figure 3.4  Relative sizes. Below, the diameter of most cells is between 1 and 100 micrometers. Table 3.1 shows conversions among units of length.

Microscopy

CDC; Edward S. Ross; Vladimir Davydov/iStock/Getty Images; A Cotton Photo/Shutterstock. com; Akugasahagy/Shutterstock.com; photomaster/Shutterstock.com; PhotoMediaGroup/ Shutterstock.com; DaddyBit/iStock/Getty Images; Dorling Kindersley/Getty Images; © Cengage 2019

Before microscopes were invented, no one knew that cells existed because nearly all are invisible to the naked eye. Today, we have a variety of microscopes and techniques that allow us to see different aspects of cell structure.

Figure It Out: Which is smaller, a protein, a water molecule, or a lipid?

Answer: A water molecule

human eye (no microscope) human eye (no microscope) frog eggs

100 µm

100 µm

1 mm

giant sequoia giant sequoia

small animals small animals

frog eggs

1 mm

1 cm

1 cm 10 cm

10 cm

1m

1m

10 m

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10 m

100 m

100 m

56  Unit 1  How Cells Work

50 µm

A. The green blobs visible in this light micrograph (LM) of a living cell are ingested algae. Hairlike structures on the cell’s surface are waving cilia that propel this motile organism through fluids.

B. A light micrograph taken with polarized light shows edges in relief. This technique reveals ingested algae and some internal structures that are not visible in A.

Figure 3.5  Different microscopes reveal different characteristics. All of these micrographs show the same organism, a protist called Paramecium, that is about 250 µm long. (A) iStock.com/Nancy Nehring; (B) Michael Abbey/Science Source; (C) SPL/Science Source; (D) Microworks/PhototakeUSA.com; (E) SPL/Science Source

Figure It Out: What is the approximate width of a Paremecium ?

C. In this fluorescence micrograph, yellow pinpoints the location of a particular protein in the membrane of organelles called contractile vacuoles. These organelles are visible in B, but less so.

D. A transmission electron micrograph (TEM) reveals several types of internal structures in a plane (slice). Ingested algae are being broken down inside food vacuoles.

E. A scanning electron micrograph (SEM) shows details of the cell’s surface, including its thick coat of cilia. The cell ingests its food via the indentation (also visible in A).

Light Microscopy  Visible light illuminates a sample in a light microscope. Inside the instrument, curved lenses focus light that passes through a specimen, or bounces off of one, into a magnified image (Figure 3.5A). Microscopes that use polarized light can yield images in which the edges of some structures appear in three-dimensional relief (Figure 3.5B). A photograph of an image enlarged with a microscope is called a micrograph; one taken with visible light is called a light micrograph (abbreviated LM). Most cells are nearly transparent, so their internal details may not be visible unless they are first stained. Staining a cell means exposing it to dyes or other substances that only some of its parts soak up. Parts that absorb the most dye appear darkest. Staining increases contrast (the difference between light and dark), thus allowing us to see a greater range of detail.

Answer: 50 µm

Fluorescence Microscopy  Fluorescent dyes consist of molecules that absorb light

of a particular color, then emit light of a different color. These dyes are often used as tracers in microscopy to pinpoint the location of a molecule or structure of interest in a cell (Figure 3.5C). For example, a common fluorescent dye binds preferentially to DNA. This dye emits blue light after absorbing ultraviolet (UV) light. When cells are stained with the dye and then illuminated with UV light, their DNA glows blue. A micrograph of the emitted light reveals the location of the DNA in the cell.

Electron Microscopy  Structures smaller than about 200 nanometers in diameter

appear blurry under light microscopes. To observe objects of this size range clearly, we use an electron microscope. Two types of electron microscope use magnetic fields as lenses to focus a beam of electrons onto a sample. A transmission electron microscope directs electrons through a thin specimen, and the specimen’s internal details appear as shadows in the resulting image, which is called a transmission

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Cell Structure  Chapter 3  57 

electron micrograph, or TEM (Figure 3.5D). A scanning electron microscope directs a beam of electrons across the surface of a specimen that has been coated with a thin layer of metal. The metal then emits radiation that can be converted into an image (a scanning electron micrograph, or SEM) of the surface (Figure 3.5E). SEMs and TEMs are always black and white; colored versions have been digitally altered to highlight specific details.

Cell Theory Hundreds of years of observations led to the way we now answer the question, What is a cell? Today we know that cells carry out metabolism and homeostasis, and reproduce either on their own or as part of a larger organism. By this definition, each cell is alive even if it is part of a multicelled body, and all living organisms consist of one or more cells. Cells reproduce by dividing, so it follows that all existing cells must have arisen by division of other cells. Taken together, these principles constitute the cell theory, which is a foundation of modern biology (Table 3.2).

Table 3.2  Cell Theory

1. Every living organism consists of one or more cells. 2. The cell is the basic structural and functional unit of life. Cells are individually alive even as part of a multicelled organism. 3. All living cells arise by division of preexisting cells.

Take-Home Message 3.2 ●●

●● ●●

●●

All cells start life with a plasma membrane, cytosol, and DNA. In eukaryotic cells only, the DNA is contained within a nucleus. The surface-to-volume ratio limits cell size and influences cell shape. Typical cells are visible only with the help of microscopes. Different microscopy techniques reveal different aspects of cell structure. All organisms consist of one or more cells; the cell is the basic structural and functional unit of life; and each new cell arises from another cell.

3.3  Cell Membrane Structure Learning Objectives ●●

Describe the structure of a lipid bilayer.

●●

Explain the fluid mosaic model of cell membranes.

●●

List the functions of four common types of membrane proteins.

The Lipid Bilayer The basic structure of almost all cell membranes is a lipid bilayer that consists mainly of phospholipids (Figure 3.6A, next page). Remember from Section 2.8 that the head of a phospholipid is polar and hydrophilic, so it interacts with water molecules. The two long hydrocarbon tails are nonpolar and hydrophobic, so they do not interact with water molecules. As a result of these opposing properties, phospholipids swirled into water spontaneously organize themselves into lipid bilayer sheets or bubbles (right), with tails together, and heads facing the watery surroundings. This bilayer organization of lipids means that a membrane’s two surfaces are hydrophilic, and its core is hydrophobic.

Fluid Mosaic Model Many molecules—cholesterol, proteins, and so on—are embedded in or attached to the lipid bilayer of a cell membrane, and most of them move around the membrane more or less freely. The fluid mosaic model describes a cell membrane as a

cell theory  Theory that all organisms consist of one or more cells; the cell is the basic unit of life; all cells come from division of preexisting cells; and all cells pass hereditary material (DNA) to offspring. fluid mosaic  Model of a cell membrane as a twodimensional fluid of mixed composition.

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58  Unit 1  How Cells Work

extracellular fluid hydrophilic heads bilayer hydrophobic tails

hydrophilic heads cytoplasm

A. The lipid bilayer forms the framework of typical cell membranes. In a watery fluid, phospholipids spontaneously organize into two layers: hydrophobic tails together, and hydrophilic heads facing outward.

B. Adhesion proteins fasten cells together or to external proteins. This one connects filaments inside animal cells to proteins outside the cells.

Figure 3.6  Cell membrane structure. A Organization of phospholipids in cell membranes. B–E Examples of common membrane proteins. Each type adds a specific function to a membrane. Many have an extremely complex structure; for clarity, they are often modeled as abstract blobs or geometric shapes.

two-dimensional fluid of mixed composition. The “mosaic” part of the name comes from the many different types of molecules that make up the membrane. Membrane fluidity occurs because phospholipids in the bilayer are not chemically bonded to one another; they stay organized in a watery environment as a result of hydrophobic and hydrophilic interactions. Thus, individual phospholipids in the bilayer drift sideways and spin around their long axis, and their tails wiggle. Variations on the Model  The types and proportions of molecules composing a cell

membrane determine its properties. For example, membrane flexibility decreases with increasing cholesterol content. A membrane’s fluidity depends on the length and saturation of its phospholipids’ fatty acid tails (Section 2.8). Fluidity is also affected by temperature, pH, and pressure; cells can counter shifts in these environmental conditions by dynamically altering the composition of their membranes. Archaea don’t even build their phospholipids with fatty acids. Archaeal phospholipid tails are branched and saturated, and their connection to the glycerol head has a structure rarely found in phospholipids of other groups. The structure of archaeal phospholipids gives rise to a dense, durable membrane that is stable even at extreme temperatures. Unique membrane composition was one of the clues that led scientists to place these organisms in their own kingdom.

Proteins Add Function A cell membrane physically separates an external environment from an internal one, but that is not its only task. Many types of proteins are embedded in a cell membrane, and each kind of protein imparts a specific function to it. Thus, different cell membranes can have different tasks depending on which proteins they include. A plasma membrane incorporates certain proteins that no internal cell membrane has, so it has functions that no other membrane does. For example, cells stay organized in animal tissues because adhesion proteins in their plasma membranes fasten them together and hold them in place (Figure 3.6B). This arrangement strengthens a tissue, and can constrain certain membrane proteins to an upper, lower, or side surface of the cell. Plasma membranes and some internal membranes incorporate receptor proteins, which trigger a change in the cell’s activities in response to a stimulus

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Cell Structure  Chapter 3  59 

C. Receptor proteins trigger a change in cellular activity in response to a stimulus such as binding to a particular substance. This one occurs on cells of the immune system.

D. Enzymes speed reactions that occur near membranes.This one is part of a set of molecules that collectively break down drugs and other toxins.

E. Transport proteins bind to molecules on one side of the membrane, and release them on the other side. This one transports glucose.

(Figure 3.6C). Each type of receptor protein responds in a particular way to a particular stimulus. The stimulus is often a molecule such as a hormone that binds to the receptor, and the cell’s response may involve metabolism, movement, division, or even cell death. All cell membranes have enzymes (Figure 3.6D). Some of these enzymes act on other proteins or lipids that are part of the membrane; others use the membrane as a scaffold. All membranes also have transport proteins, which move specific substances across the bilayer (Figure 3.6E). Transport proteins are important because the hydrophobic core of a lipid bilayer is impermeable to most hydrophilic substances, including the ions and polar molecules that cells must take in and expel on a regular basis (we return to this topic in Section 4.5).

Take-Home Message 3.3 ●● ●●

●●

●●

A cell membrane can be modeled as a two-dimensional fluid of mixed composition. The basic structure of almost all cell membranes is the lipid bilayer: two layers of phospholipids, tails sandwiched between heads. Other molecules mingle among the phospholipids. The properties of a cell membrane depend on the types and proportions of molecules composing it. Each type of protein in a cell membrane imparts a specific function to it.

3.4  Prokaryotic Cells Learning Objectives ●●

Identify the two characteristics that originally defined prokaryotes.

●●

Describe some of the structures shared by bacteria and archaea.

●●

Describe a biofilm, and explain how it benefits its inhabitants.

Bacteria and archaea are the smallest and most metabolically diverse forms of life that we know about. All are single-celled, but individual cells of many species cluster

adhesion protein  Plasma membrane protein that helps cells stick together in animal tissues. receptor protein  Membrane protein that triggers a change in cell activity in response to a stimulus such as a hormone binding to it. transport protein  Protein that moves specific ions or molecules across a membrane.

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60  Unit 1  How Cells Work

0.5 µm

0.5 µm

0.5 µm

A. Escherichia coli is a common bacterial inhabitant of human intestines. Short, hairlike structures are pili; longer ones are flagella.

B. Pseudanabaena are a type of cyanobacteria, an ancient lineage of photosynthetic bacteria. Photosynthesis occurs at internal membranes that look like stripes in this photo. Dark structures are carboxysomes, organelles that assist photosynthesis.

C. Helicobacter pylori, a bacterium that can cause stomach ulcers when it infects the lining of the stomach, takes on a ball-shaped form (shown) that offers protection from environmental challenges such as antibiotic treatment.

Figure 3.7  Some representative prokaryotes. (A) Biophoto Assoc./Science Source; (B) SPL/Science Source; (C) Science Photo Library/ Science Source; (D) Cryo-EM image of Haloquadratum walsbyi, isolated from Australia. Courtesy of Zhuo Li (City of Hope, Duarte, California, USA), Mike L. Dyall-Smith (Charles Sturt University, Australia), and Grant J. Jensen (California Institute of Technology, Pasadena, California, USA); (E) © K. O. Stetter and R. Rachel, Univ. Regensburg; (F) Archivo Angels Tapias y Fabrice Confalonieri

Figure It Out: Panels A–D and F show transmission electron micrographs (TEM). What kind of micrograph is shown in E?

in filaments or colonies (Figure 3.7). Outwardly, cells of the two groups appear so similar that archaea were once presumed to be an unusual group of bacteria. Both groups lack a nucleus, so they were named prokaryotes: a word that means “before the nucleus.” By 1977, it had become clear that archaea are more closely related to eukaryotes than to bacteria, so they were given their own separate domain. The term “prokaryote” is now an informal designation only. Chapter 14 revisits them in more detail; here we present an overview of structures shared by both groups (Figure 3.8).

Structural Features

Answer: Scanning electron micrograph (SEM)

Cytoplasm  The cytoplasm of a prokaryote 1 contains many ribosomes, and in

1 cytoplasm 2 plasmid 3 DNA in nucleoid 4 plasma membrane 5 cell wall 6 capsule 7 pilus 8 flagellum Figure 3.8  General body plan of bacteria. Archaea do not have capsules, but otherwise they appear very similar to bacteria—at least outwardly. Their molecular architecture differs.

some species, additional organelles. Membrane-enclosed organelles are uncommon among prokaryotes, but some bacterial groups have them. Cytoplasm may also include plasmids 2, which are small circles of DNA that carry a few genes (units of inheritance). Plasmid genes can provide advantages such as resistance to antibiotics. However, the essential genetic information of a typical prokaryotic cell occurs on a large, circular molecule of DNA located in an irregularly shaped region of cytoplasm called the nucleoid 3.

Cell Wall  Like all cells, bacteria and archaea have a plasma membrane 4. Almost all have a rigid cell wall 5 surrounding the plasma membrane. A wall

protects the cell and supports its shape. Cell walls are not membranes and they do not consist of lipids. The composition of archaeal cell walls and bacterial cell walls differs, but water and solutes can easily move through both types. A second membrane surrounds the cell wall of many bacteria (and a few archaea). Like the plasma membrane, this outer membrane consists of a lipid bilayer with embedded proteins.

External Structures  In many bacteria, a thick, sticky capsule 6 encloses

the cell wall (or the second membrane in species that have one). The capsule helps the cells adhere to many types of surfaces, and it offers protection against some predators and toxins. Some archaea have a coating that is similar to the bacterial capsule.

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Cell Structure  Chapter 3  61 

1 µm

0.5 µm

D. The square archaeon Haloquadratum walsbyi prefers brine pools saltier than soy sauce. Gas-filled organelles (white structures) buoy these highly motile cells, which can aggregate into flat sheets a bit like floor tiles.

E. Ferroglobus placidus is an archaeon that thrives in superheated water spewing from the ocean floor. The durable composition of archaeal membranes (note gridlike texture) keeps them intact at extreme heat and pH.

0.5 µm

F. The archaeon Thermococcus gammatolerans lives under extreme conditions of salt, temperature, and pressure. It is by far the most radiation-resistant organism ever discovered, capable of withstanding thousands of times more radiation than humans can.

Protein filaments called pili (singular, pilus) 7 project from the surface of some bacteria and archaea. Pili help these cells move along or cling to surfaces. One type of pilus attaches to another cell and then shortens, reeling in the attached cell. When the two cells make contact, DNA is transferred from one to the other. Many prokaryotes also have one or more flagella projecting from their sur­ face. Flagella (singular, flagellum) are long, slender cellular structures used for motion 8. A prokaryotic flagellum rotates like a propeller that drives the cell through fluid habitats.

Biofilms Bacteria often live so close together that an entire community shares a loose capsule called a slime layer. A communal living arrangement in which single-celled organisms occupy a shared mass of slime is called a biofilm. A biofilm is often attached to a solid surface, and may include bacteria, algae, fungi, protists, and/or archaea. Participating in a biofilm allows the cells to linger in a favorable spot rather than be swept away by fluid currents, and to reap the benefits of living communally. For example, rigid or netlike secretions of some species serve as permanent scaffolding for others; species that break down toxic chemicals allow more sensitive ones to thrive in habitats that they could not withstand on their own; and waste products of some serve as raw materials for others. The human gastrointestinal tract hosts a large and beneficial biofilm (Figure 3.9). Other biofilms, including the dental plaque that forms on our teeth, can be harmful to human health.

Take-Home Message 3.4 ●●

●●

●●

Prokaryotic cells (bacteria and archaea) do not have a nucleus. Most or all of their DNA occurs in a nucleoid. Almost all prokaryotes have a cell wall that surrounds, reinforces, and protects the plasma membrane. A community of single-celled organisms living within a shared mass of slime is called a biofilm.

Figure 3.9  A beneficial biofilm. This SEM of human fecal matter reveals a few of the more than 30,000 species of bacteria that normally inhabit our large intestine. These organisms form a biofilm that protects intestinal surfaces from colonization by harmful species, while producing needed vitamins and helping us digest our food. Eye of Science/Science Source

biofilm  Community of microorganisms living within a shared mass of secreted slime. cell wall  Rigid, permeable structure that surrounds the plasma membrane of some cells. flagellum  Plural, flagella. Long, slender cellular structure used for motion. pilus  Plural, pili. Protein filament that projects from the surface of some prokaryotic cells.

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62  Unit 1  How Cells Work Table 3.3  Some Components of Eukaryotic Cells

Learning Objectives

Organelles with membranes Nucleus

Protects and controls access to DNA

Endoplasmic reticulum (ER)

Makes and modifies new lipids and polypeptides, among other tasks

Golgi body

Modifies and sorts polypeptides and lipids

Vesicle

Transports, stores, or breaks down substances

Mitochondrion

Aerobic respiration

Chloroplast

Photosynthesis

Lysosome

Intracellular digestion

Peroxisome

Breaks down organic molecules, toxins

Vacuole

Stores, breaks down substances

Organelles without membranes Ribosome

Assembles polypeptides Contributes to cell shape, internal organization, and movement

nuclear envelope

nuclear pore DNA

A. Nucleus of a pancreas cell from a mouse. The nuclear envelope, DNA, and nuclear pores are visible in this TEM.

1 µm

●●

Explain the function of membranes that enclose organelles.

●●

List the functions of the cell nucleus and explain how these functions arise from its structure.

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Summarize the path of a new protein as it moves through the endomembrane system.

●●

Describe the similarities and differences between mitochondria and chloroplasts.

A typical eukaryotic cell is larger than a typical prokaryote, and has many more components (Table 3.3). Both types of cells have ribosomes in their cytoplasm; other organelles are enclosed by lipid bilayer membranes. An enclosing membrane allows an organelle to regulate the types and amounts of substances that enter and exit. Through this control, the organelle maintains a special internal environment that allows it to carry out a particular function—for example, isolating toxic or sensitive substances from the rest of the cell, transporting substances through cytoplasm, or providing a favorable environment for a special process. Compartmentalizing such processes maximizes the cell’s metabolic efficiency. Membrane-enclosed organelles are generally characteristic of eukaryotes, but a few bacterial lineages have them. The nucleus, endoplasmic reticulum, Golgi bodies, chloroplasts, and mitochondria occur only in eukaryotic cells.

The Nucleus

Other components Cytoskeleton

3.5  Eukaryotic Organelles

1 µm

B. This micrograph shows the edge of a nucleus from a mouse cell. Green fluorescence shows the nuclear lamina underlying the nuclear envelope (not shown). Red pinpoints nuclear pores; blue, DNA.

Figure 3.10  Structure of the cell nucleus. © Kenneth Bart; U.S. National Library of Medicine

A cell nucleus serves two important functions. First, it keeps the cell’s DNA—its one and only copy of hereditary material—away from metabolic processes that might damage it. Isolated in its own compartment, the DNA stays separated from the bustling activity of the cytoplasm. Second, a nucleus controls the passage of certain molecules across its membrane. The nucleus has a special membrane, the nuclear envelope, that carries out this function (Figure 3.10A). Nuclear Envelope  A nuclear envelope consists of two lipid bilayers folded

together like a sandwich that encloses a narrow intermembrane space. The outer bilayer is studded with ribosomes, and the inner bilayer is supported by a dense mesh of fibrous proteins called the nuclear lamina (Figure 3.10B). Thousands of nuclear pores span both bilayers, each a complex assembly of hundreds of proteins. RNA and proteins can enter or exit the nucleus only by passing through a nuclear pore, but the pore selects which of these molecules move through it. Consider protein synthesis, a process that occurs in cytoplasm and requires the participation of many molecules of RNA. RNA is produced where the DNA resides—in the nucleus. Thus, RNA molecules must move from nucleus to cytoplasm. Proteins that participate in RNA synthesis must move in the opposite direction, because this process occurs in the nucleus. In both cases, nuclear pores transport the molecules in the appropriate direction. Bacteria in one unusual lineage have double membranes surrounding their DNA, and the recent discovery that pores in these membranes are structurally similar to the complex nuclear pores of eukaryotic cells may challenge the simplistic way we differentiate prokaryotes from eukaryotes. Nuclear Pores, Tau, and Alzheimer’s Disease  A nuclear pore can move about

1,000 selected molecules per second across the nuclear envelope, and disruption of this function is linked to neurodegenerative disorders such as Alzheimer’s disease. The brain of a patient with Alzheimer’s has two characteristics: amyloid

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Cell Structure  Chapter 3  63 

plaques (Section 2.9) between brain cells, and tau tangles inside the cells. Tau tangles are fibrous clumps of misfolded proteins; they consist of a protein (called tau) that is produced incorrectly when amyloid fibrils are present. Defective tau proteins inter­ ­act abnormally with nuclear pore proteins. This interaction causes the tau proteins to aggregate into tangles, and it also alters nuclear pores in a way that makes them leaky. Among other effects, proteins that should stay in cytoplasm accumulate in the nucleus, and RNA molecules that should stay in the nucleus accumulate in cytoplasm. These outcomes disrupt the function of the cell, eventually leading to its death.

outer membrane inner membrane outer compartment (intermembrane space) inner compartment (matrix)

0.5 µm

Figure 3.11  The mitochondrion. Two membranes, one folded inside the other, form the ATP-making machinery of this eukaryotic organelle. The TEM shows a mitochondrion in a cell from bat pancreas. Keith R. Porter

Mitochondria  As you will see in Chapter 4, biologists think of the nucleotide ATP as a type of cellular currency because it carries energy between reactions. Cells require a lot of ATP. The most efficient way they can produce it is by aerobic respiration, an oxygen-requiring series of reactions that harvests energy from sugars by breaking their bonds. In eukaryotes, aerobic respiration occurs inside organelles called mitochondria (singular, mitochondrion). Each has two membranes, one highly folded inside the other, that form its ATP-making machinery (Figure 3.11). Almost all eukaryotic cells (including plant cells) contain mitochondria. Cells with a very high demand for energy typically have a lot of them. In many ways, mitochondria resemble bacteria. Mitochondria have their own DNA, which is circular and otherwise similar to bacterial DNA. They also divide independently of the cell, and they have their own ribosomes. These features led to the theory that mitochondria evolved from bacteria that took up permanent residence inside a host cell (we return to this topic in Section 14.6).

1 µm

two outer membranes stroma inner (thylakoid) membrane

Chloroplasts  Photosynthetic cells of plants and many protists have chloroplasts, which are organelles specialized for photosynthesis. Plant chloroplasts are oval or disk-shaped (Figure 3.12). Each has two outer membranes enclosing a semifluid interior called stroma, which contains enzymes and the chloroplast’s own DNA. In stroma, a third, highly folded membrane forms a single, continuous compartment. Photosynthesis occurs at this inner membrane, which is called the thylakoid membrane. In many ways, chloroplasts resemble the photosynthetic bacteria from which they evolved.

The Endomembrane System  The endomembrane system is a multifunctional network of membrane-enclosed organelles that occur throughout a cell’s cytoplasm. Its main function is to make, modify, and transport lipids and proteins for the cell’s membranes, and proteins for secretion to the external environment. The endomembrane system also destroys toxins, recycles wastes, and has other special functions. Components of the system

Figure 3.12  The chloroplast. Plant chloroplasts have two outer membranes. Photosynthesis occurs at a third, much-folded inner membrane that is called the thylakoid membrane. TEM shows a chloroplast from a cell in a corn leaf. Omikron/Science Source

chloroplast  Organelle of photosynthesis in the cells of plants and photosynthetic protists. mitochondrion  Eukaryotic organelle that produces ATP by aerobic respiration. nuclear envelope  A double membrane that constitutes the outer boundary of the nucleus. Nuclear pores in it control the entry and exit of large molecules.

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64  Unit 1  How Cells Work

CLOSER LOOK Figure 3.13  Some interactions among components of the endomembrane system.

plasma membrane

Some vesicles that bud from Golgi bodies fuse with the plasma membrane, so their contents are expelled from the cell. Figure It Out: Do Golgi bodies make proteins?

Vesicles that form at the plasma membrane bring substances into the cell.

enzymes

Answer: No

4 Golgi Body Proteins and lipids that vesicles deliver to a Golgi body are modified and sorted into new vesicles. These vesicles carry the finished molecules to the plasma membrane for secretion or insertion into the lipid bilayer.

Vesicles that bud from rough ER transport proteins to Golgi bodies.

2 Rough ER Ribosomes attached to rough endoplasmic reticulum (ER) give it a “rough” appearance. Polypeptides assembled on the ribosomes thread into the ER’s interior, where they take on tertiary structure. Figure Summary The endomembrane system is a series of organelles (rough and smooth ER, Golgi bodies, and vesicles) that interact to make, modify, and transport lipids and proteins. Some components have additional functions. An animal cell is illustrated here.

1 Lysosomes Some vesicles that bud from Golgi bodies become lysosomes, which contain powerful enzymes. Lysosomes fuse with other vesicles, releasing the enzymes into them. Some vesicles that bud from smooth ER transport proteins and lipids to Golgi bodies.

3 Smooth ER Some proteins made in rough ER migrate through the ER compartment to smooth ER. These proteins are packaged in vesicles, or stay as enzymes that assemble phospholipids. Smooth ER also stores calcium ions, and in some cells it has additional functions.

vary among different types of cells, but here we introduce its main components: vesicles, endoplasmic reticulum, and Golgi bodies (Figure 3.13). Vesicles  Vesicles are sacs that form by budding from other organelles of the endo-

membrane system, or when a patch of plasma membrane sinks into the cytoplasm. Many types carry substances from one organelle to another, or to and from the plasma membrane. Some are a bit like trash cans that collect or dispose of waste, debris, or toxins. Enzymes in vesicles called lysosomes break down particles such as cellular debris and bits of waste. Bacteria, cell parts, and other particles taken in by a cell are delivered to lysosomes for disassembly 1. Vesicles called peroxisomes contain enzymes that break down organic molecules as well as toxic hydrogen peroxide and ammonia produced by these reactions. Large, fluid-filled vacuoles store or break down waste, debris, toxins, or food. Some cells have contractile vacuoles that expel excess water (contractile vacuoles

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Cell Structure  Chapter 3  65 

are visible in Figure 3.5C). In plants, lysosome-like vesicles fuse to form a very large central vacuole that makes up most of the volume of the cell (a central vacuole is illustrated to the left of the nucleus in Figure 3.2). Fluid pressure in a central vacuole keeps plant cells plump, so stems, leaves, and other plant parts stay firm. Endoplasmic Reticulum  The nuclear envelope is often considered to be part of the

endomembrane system. This is because endoplasmic reticulum is an extension of the outer lipid bilayer of the nuclear envelope. Endoplasmic reticulum (ER) is an extensive system of sacs and tubes that enclose a single, continuous compartment. ER makes lipids and proteins for the cell’s membranes, and proteins for secretion. Two kinds of ER, rough and smooth, are named after their appearance in electron micrographs. The membrane of rough ER is typically folded into flattened sacs, and has thousands of attached ribosomes that give it a “rough” appearance 2. These ribosomes make polypeptides that thread into the ER’s interior as they are assembled. Enzymes in the interior of rough ER fold and modify the polypeptides, for example by cutting them or attaching oligosaccharides. New membrane proteins become inserted into the ER membrane or attached to it. Proteins that will be secreted from the cell are released into the ER compartment, as are proteins that will stay in the endomembrane system as enzymes. Some of the proteins made by rough ER migrate through the ER compartment to the smooth ER 3. Smooth ER has no ribosomes, so it does not make its own proteins. Its major function is to make phospholipids, and in some cells it has other functions such as steroid hormone production. Abundant smooth ER in liver cells releases glucose from glycogen. Smooth ER also stores calcium ions in its interior, and new peroxisomes form as vesicles that bud from it.

Golgi Body  The folded membrane of the Golgi body (or Golgi apparatus) looks

a bit like a stack of pancakes 4. Vesicles that bud from ER fuse with a Golgi body, thus delivering new proteins and lipids to it. Enzymes in the Golgi’s interior make final modifications to these molecules, and the finished products are then sorted and packaged into new vesicles. Some of these vesicles deliver membrane proteins, secreted proteins, and lipids to the plasma membrane. Other vesicles that bud from the Golgi become lysosomes. In plant cells, the Golgi body has an additional, major function: It makes complex polysaccharides for the cell wall.

Take-Home Message 3.5 ●●

●●

●●

●●

●●

A nucleus and other membrane-enclosed organelles are characteristic of eukaryotic cells. Organelle membranes maximize metabolic efficiency by compartmentalizing cellular processes. A nucleus protects and controls access to a eukaryotic cell’s DNA. Nuclear pores allow certain proteins and RNA molecules to enter and exit the nucleus. Mitochondria specialize in producing ATP by aerobic respiration. Each has two membranes, one highly folded inside the other. Chloroplasts carry out photosynthesis in plants and some protists. Plant chloroplasts have two outer membranes and a highly folded inner (thylakoid) membrane. The endomembrane system is a set of membrane-enclosed organelles—endoplasmic reticulum (ER), Golgi bodies, and vesicles—that collectively make, modify, and transport lipids and proteins for the cell’s membranes, and secreted proteins. Some components function in storage, transport, or breakdown of substances or particles.

endoplasmic reticulum (ER)  System of sacs and tubes that is an extension of the nuclear envelope. Smooth ER makes phospholipids, stores calcium, and has additional functions in some cells; ribosomes on the surface of rough ER make proteins. Golgi body  Also called Golgi apparatus. Organelle that modifies new proteins and lipids, then sorts and packages the finished products into vesicles. lysosome  Enzyme-filled vesicle that breaks down cellular wastes and debris. vesicle  Saclike, membrane-enclosed organelle; different kinds store, transport, or break down their contents.

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66  Unit 1  How Cells Work

Digging Into Data Organelles and Cystic Fibrosis

1. Which organelle contains the least amount of CFTR protein in normal cells? In cells from a patient with CF? 2. In which organelle is the amount of CFTR protein most similar in both types of cells? 3. Where is the CFTR protein getting held up in cells of people who have CF?

ER vesicles

Amount of CFTR protein

A plasma membrane transport protein called CFTR moves chloride ions out of cells lining cavities and ducts of the lungs, liver, pancreas, intestines, and reproductive system. Water that follows the ions creates a thin film that allows mucus to slide easily through these structures. People with cystic fibrosis (CF) have too few copies of the CFTR protein in the plasma membranes of their cells. Not enough chloride ions leave the cells, so not enough water leaves them either. The result is thick, dry mucus that clogs the airways to the lungs and other passages. Symptoms include difficulty breathing and chronic lung infections. Researchers tracked the location of the CFTR protein as it was being produced in cells from people with CF (Figure 3.14).

Golgi

normal cells

CF cells

Figure 3.14  Cellular location of the CFTR protein. Graph compares the amounts of CFTR protein in organelles of normal and cells from patients with cystic fibrosis. Endoplasmic reticulum, vesicles traveling from ER to Golgi, and Golgi bodies were tested.

3.6  Elements of Connection Learning Objectives ●●

Describe the function of three types of cytoskeletal elements in eukaryotes.

●●

Explain how motor proteins move cell parts.

●●

Use examples to explain different functions of extracellular matrix (ECM).

●●

Describe the three major types of cell junctions in animals.

Cytoskeletal Elements cilia  Singular, cilium. Short, hairlike, motile structures that project from the plasma membrane of some eukaryotic cells. cytoskeleton  Network of protein filaments that support, organize, and move cells and their internal structures. intermediate filament  Stable cytoskeletal element of animals and some protists; structurally supports cells and tissues. Different types are assembled from different fibrous proteins. microfilament  Cytoskeletal element of eukaryotes; reinforces cell membranes and functions in cell movement. Fiber of actin subunits. microtubule  Cytoskeletal element of eukaryotes; forms a dynamic scaffolding for many cellular processes involving movement. Hollow filament of tubulin subunits. motor protein  Type of energy-using protein that interacts with cytoskeletal elements to move the cell’s parts or the whole cell.

The cytoplasm of all cells includes a system of protein filaments collectively called the cytoskeleton. Elements of the cytoskeleton reinforce, organize, and move cell structures, and often the whole cell. Some are permanent; others form only at certain times. Both prokaryotes and eukaryotes have cytoskeletal elements. Here, we discuss three types that occur in eukaryotic cells: microtubules, microfilaments, and intermediate filaments. Microtubules  Long, hollow cylinders called microtubules are cytoskeletal elements

that function in movement (Figure 3.15A). They consist of subunits of the protein tubulin and can rapidly assemble when they are needed, and disassemble when they are not. For example, during the process of cell division, microtubules assemble, separate the cell’s chromosomes, then disassemble. Microfilaments  Fine fibers called microfilaments consist primarily of subunits of

the protein actin (Figure 3.15B). In many cells, a mesh of microfilaments is part of the cell cortex, a region of cytoplasm just inside the plasma membrane. The mesh, which connects to and supports the plasma membrane, forms a scaffolding for proteins that function in cellular movement, contraction, shape changes, and migration (Figure 3.16).

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Cell Structure  Chapter 3  67  tubulin subunit

actin subunit

dimer tetramer

sheet of tetramers

coiled sheet

10 µm 25 nm

A. Microtubule Involved in moving cell parts or the whole cell.

6–7 nm

B. Microfilament Reinforces cell membranes; role in muscle contraction.

8–12 nm

C. Intermediate filament Structurally supports cell membranes and tissues. Most stable element.

Figure 3.16  Cytoskeletal elements in a nerve cell. This fluorescence micrograph shows microtubules (yellow) and microfilaments (blue) in the growing end of a nerve cell. These cytoskeletal elements support and guide the cell’s lengthening in a particular direction. Dylan T. Burnette and Paul Forscher

Figure 3.15  Cytoskeletal elements. Intermediate Filaments  Animal cells and some protists have a third type of cytoskeletal element: the intermediate filament (Figure 3.15C). Intermediate filaments

form a stable framework that lends structure and resilience to cells and tissues. Several types of intermediate filaments are assembled from different fibrous proteins. For example, intermediate filaments that consist of lamins form the nuclear lamina of animal cells, and also help regulate processes inside the nucleus such as DNA replication. Cells in your hair follicles assemble keratin into intermediate filaments that make up your hair. Motor Proteins  Motor proteins that associate with cytoskeletal elements move cell parts when energized by a phosphate-group transfer from ATP. A cell is like a bustling train station, with molecules and structures being moved continuously throughout its interior. Motor proteins are a bit like freight trains, dragging cellular cargo along tracks of microtubules and microfilaments (Figure 3.17). Eukaryotic flagella move because microtubules that run lengthwise through them interact with a motor protein called dynein. These flagella propel sperm and other motile cells through fluid by whipping back and forth. (The propellerlike rotation of prokaryotic flagella arises from a different mechanism that does not involve microtubules). The interaction of dynein with microtubules also gives rise to the rhythmic waving motion of short, hairlike cilia (singular, cilium) that project from the plasma membrane of some eukaryotic cells. Cilia often occur in clumps that beat in unison. Their coordinated movement can propel a cell through fluid, and stir fluid around a stationary cell. Cilia on thousands of cells lining your airways sweep inhaled particles away from your lungs.

Figure 3.17  Motor proteins. Here, kinesin (tan) drags a vesicle (pink) as it inches along a microtubule.

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68  Unit 1  How Cells Work

SPL/Science Source

Some eukaryotic cells, including the amoeba at left, form pseudopods, or “false feet.” As these temporary, irregular lobes bulge outward, they can move the entire cell or engulf a target such as prey. Elongating microfilaments in the cell cortex force the lobe to advance in a steady direction. Motor proteins attached to the microfilaments drag the plasma membrane along with them.

Extracellular Matrix  cornea surface

basement membrane

Figure 3.18  Basement membrane. In this section of human cornea (a part of the eye), basement membrane is visible as a dark line under the cells. Ralph C. Eagle/Science Source

Many cells secrete extracellular matrix onto their surfaces. Extracellular matrix (ECM) is a complex mixture of molecules that structurally supports and physically protects the cells that secrete it. A cell wall is an example of ECM. You already learned that prokaryotes have cell walls; plants have them too, as do fungi and some protists. The composition of the wall differs among these groups. Like a prokaryotic cell wall, a eukaryotic cell wall is porous: Water and solutes easily cross it on the way to and from the plasma membrane. Animal cells have no walls, but some types secrete an extracellular matrix called basement membrane (Figure 3.18). Despite the name, basement membrane is not a cell membrane; it does not consist of a lipid bilayer. Rather, it is a sheet of fibrous material that structurally supports and organizes tissues. Bone cells secrete an ECM of collagen, a fibrous protein, hardened into a mineral by bonding with calcium, magnesium, and phosphate ions. A covering called cuticle is a type of ECM secreted by cells at a body surface. In plants, a cuticle of waxes and proteins helps stems and leaves retain water and fend off insects (Figure 3.19). Crabs, spiders, and other arthropods have a cuticle that consists of a polysaccharide called chitin.

Cell Junctions cuticle outer cell of leaf photosynthetic cell inside leaf

Figure 3.19  A plant ECM. This section through a plant leaf shows the cuticle, a protective covering of deposits secreted by living cells. George S. Ellmore, Ph.D.

cell junction  Molecular assembly that connects a cell to another cell or to extracellular matrix. cuticle  Secreted covering at a body surface. extracellular matrix (ECM)  Complex mixture of substances secreted by a cell onto its surface; composition and function vary by cell type. pseudopod  A temporary protrusion from a eukaryotic cell that helps it move or engulf prey.

In multicelled eukaryotes, cells can interact with one another and their surroundings by way of cell junctions. Cell junctions are molecular assemblies that connect a cell directly to other cells or to ECM. Cells send and receive substances and signals through some junctions. Other junctions help cells recognize and stick to each other in tissues. Three types of cell junctions are common in animal tissues: tight junctions, adhering junctions, and gap junctions. Plants have cell junctions called plasmodesmata. Tight Junctions  In tissues that line body surfaces and internal cavities, rows of adhesion proteins in the plasma membrane of adjacent cells connect to form zipperlike tight junctions (Figure 3.20A). By fastening the plasma membranes together, tight junctions prevent body fluids from seeping between the cells. For example, the lining of the stomach is leakproof because tight junctions seal its cells together. These junctions keep gastric fluid, which contains acid and destructive enzymes, safely inside the stomach. Some bacteria that infect the stomach lining cause painful peptic ulcers by damaging tight junctions, so gastric fluid leaks into and injures the underlying layers of tissue. Adhering Junctions  Adhesion proteins also assemble into various types of adher-

ing junctions, which are a bit like snaps that fasten cells to one another and to basement membrane (Figure 3.20B–D). These junctions strengthen a tissue because they connect to cytoskeletal elements inside each cell. Contractile tissues (such as heart muscle) have a lot of adhering junctions, as do tissues subject to abrasion or

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Cell Structure  Chapter 3  69 

CLOSER LOOK Figure 3.20  Cell junctions in animal tissues.

Figure Summary Cell junctions connect cells to other cells and to extracellular matrix in animal tissues. Different types are assembled from different proteins. Tight junctions (A), three types of adhering junc­ tions (B, C, and D), and gap junctions (E) are shown.

Figure It Out: Which of these cell junctions connects to ECM?

A B

A. Tight junctions form a waterproof seal between plasma membranes of adjacent cells.

C E

D

basement membrane

B. These adhering junctions connect the plasma membranes of adjacent cells to microfilaments inside the cells.

Answer: D

stretching (such as skin). Because adhering junctions connect a cell’s interior with its exterior, the cell can use these connections to sense its position in a tissue. Gap Junctions  Gap junctions are closable channels that connect the cytoplasm of

adjoining animal cells (Figure 3.20E). When open, they permit water, ions, and small molecules to pass directly from the cytoplasm of one cell to another. These channels allow entire regions of cells to respond to a single stimulus. Heart muscle and other tissues in which the cells perform a coordinated action have many gap junctions. Plasmodesmata  Plasmodesmata are open channels that connect the cytoplasm of

C. These adhering junctions connect the plasma membranes of adjacent cells to intermediate filaments inside the cells.

adjoining plant cells. These cell junctions extend across the cell walls, and, like gap junctions, they allow substances to flow quickly from cell to cell.

Take-Home Message 3.6 ●● ●●

●●

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Dynamically assembled microtubules help move cell parts and the whole cell. Networks of microfilaments reinforce cell shape, and function as scaffolding for other proteins. Motor proteins associate with microtubules and microfilaments to bring about movement. Intermediate filaments form a stable framework that lends structure and resilience to cells and tissues. Many cells secrete material that forms an extracellular matrix (ECM) on their surfaces. ECM varies in composition and function depending on cell type. A cell wall is a type of ECM made by plant cells, fungi, and some protists. Animal cells have no wall. Cell junctions structurally and functionally connect cells in tissues. In animal tissues, some cell junctions connect cells with basement membrane.

D. These adhering junctions attach the plasma membrane of a cell to basement membrane and to intermediate filaments inside the cell.

E. Gap junctions are closable channels that connect the cytoplasm of adjacent cells.

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70  Unit 1  How Cells Work

3.7  The Nature of Life Learning Objectives

table 3.4  Collective Properties of a Living System

●●

Explain why it is difficult to define “life.”

●●

List some properties common to living things.

In this chapter, you learned about the structure of cells, which have at minimum a plasma membrane, cytosol, and DNA. Differences in other cellular components— the presence or absence of a particular organelle, for example—are often used to categorize life’s diversity. What about life’s commonality? The cell is the basic unit of life, but a cell does not spring to life from cellular components mixed in the proper amounts and proportions. What is it, exactly, that makes a cell, or an organism that consists of them, alive? Many brilliant people have thought about that question, but it still doesn’t have a concise answer. When we try to define life, we end up with a very long list of properties that set the living apart from the nonliving (Section 1.3). However, even that list can be tricky. For example, living things have a high proportion of the organic molecules of life, but so do the remains of dead organisms in seams of coal. Organisms use energy to reproduce themselves, but computer viruses, which are arguably not alive, can do that too. Living things can pass hereditary material to offspring, but a single living rabbit (for example) cannot. No list of properties reliably and unambiguously unites all things that we would consider alive, and excludes all things we would consider not alive. So how do biologists, who study life as a profession, define it? According to evolutionary biologist Gerald Joyce, the simplest definition of life might well be “that which is squishy.” He says, “Life, after all, is protoplasmic and cellular. It is made up of cells and organic stuff and is undeniably squishy.” The point is that defining life may be impossible—and also irrelevant from a scientific perspective. The property that we call “life” is not the same as properties (such as homeostasis, reproduction, and metabolism) associated with the state of being alive; a description of an organism that is alive is not a description of the life of the organism. However, that very long list of properties is far from useless: It constitutes a working theory of living systems, a way of looking at a biological system as part of a network of relationships rather than an assembly of individual components. You have already been introduced to many of the properties associated with life (Table 3.4). The remaining units of this book explore biologists’ current understanding of these properties.

Consists of one or more cells Harvests matter and energy from the environment Requires water Makes and uses complex carbon-containing molecules Engages in self-sustaining biological processes such as homeostasis and metabolism Has the capacity to respond to internal and external stimuli Has the capacity for growth Changes during a lifetime, for example by maturing and aging Passes hereditary material (DNA) to offspring Has the capacity to adapt to environmental pressures over successive generations

Take-Home Message 3.7 SeaSandSun/Shutterstock.com

●● ●●

●●

●●

Our best definition of “life” consists of a list of properties common to living things. Organisms make and use the organic molecules of life. DNA is their hereditary material. In living things, the molecules of life are organized as one or more cells that engage in self-sustaining biological processes. Living things change over lifetimes, and also over successive generations.

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Cell Structure  Chapter 3  71 

Summary Section 3.1  A huge number of bacteria live in and on the human body. Most of them are beneficial; only a few types can cause disease. Contamination of food with disease-causing bacteria can result in illness that is sometimes fatal.

By the cell theory, every organism consists of one or more cells; the cell is the basic unit of life; all living cells arise by division of preexisting cells; and all cells pass hereditary material (DNA) to offspring when they divide.

Section 3.2  Cells share certain structural and functional features; all start out life with a plasma membrane, DNA, and cytosol. The plasma membrane separates a cell from its environment, and controls which materials enter and exit it. The plasma membrane encloses jellylike cytosol, in which the cell’s other components (including ribosomes) are suspended (Figure 3.21). In prokaryotic cells, DNA is suspended in cytosol. A eukaryotic cell’s DNA is contained within a nucleus, which is a membraneenclosed organelle. The definition of cytoplasm differs between prokaryotes and eukaryotes. In prokaryotes, cytoplasm comprises everything enclosed by the plasma membrane. In eukaryotes, cytoplasm comprises everything between the plasma membrane and the nucleus. The surface-to-volume ratio limits cell size and influences cell shape. Almost all cells are too small to see with the naked eye, so we use microscopes to observe them. Different microscopes and techniques reveal different internal and external details of cells.

Section 3.3  The basic structure of almost all cell membranes is a phospholipid bilayer with many other molecules attached or embedded in it. A cell membrane can be described as a fluid mosaic of lipids, proteins, and other molecules. The properties of a cell membrane depend on the molecules that compose it. Each type of protein in a cell membrane adds a specific function to it. All cell membranes have enzymes, and all have transport proteins that help substances move across the membrane. Plasma membranes and some internal membranes have receptor proteins that trigger a change in cell activities in response to a specific stimulus. In animals, plasma membranes also incorporate adhesion proteins that lock cells together in tissues. Section 3.4  Bacteria and archaea (the prokaryotes) are singlecelled organisms with no nucleus. Typically, a large, circular molecule of DNA carries the cell’s essential genetic information, and it occurs in a region of cytoplasm called the nucleoid. Many

nuclear envelope DNA Cytoskeleton Structural support, movement

microtubules microfilaments intermediate filaments

Mitochondrion Production of ATP by aerobic respiration

Plasma Membrane Selectively controls the kinds and amounts of substances moving into and out of cell

Nucleus Protects, controls access to DNA

Ribosomes (attached to rough ER and free in cytoplasm) Protein synthesis Rough ER Protein production Smooth ER Makes phospholipids, stores calcium Golgi Body Finishes, sorts proteins and lipids Lysosome Breaks down particles, debris

Figure 3.21  Some cellular components typical of eukaryotes, illustrated in an animal cell.

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72  Unit 1  How Cells Work

Summary Summary (Continued) prokaryotes also have plasmids that carry some additional genetic information, and some have motile structures (flagella) and other projections (pili). Almost all prokaryotes have a protective, rigid cell wall that surrounds the plasma membrane. Some have a second cell membrane around the wall, and/or a sticky capsule. Bacteria and other single-celled organisms may live together in a shared mass of slime as a biofilm. Section 3.5  Membrane-enclosed organelles maximize cellular efficiency by compartmentalizing tasks and substances that may affect or be affected by other processes in the cell. All eukaryotic cells start out life with a nucleus, which protects and controls access to the cell’s DNA. The outer boundary of the nucleus is a nuclear envelope, a double lipid bilayer studded with special pores that allow selected RNA and protein molecules to pass into and out of the nucleus. Structural specializations of mitochondria allow them to produce ATP by aerobic respiration. In eukaryotes, photosynthesis takes place at the inner (thylakoid) membrane of chloroplasts. The endomembrane system is a series of interacting, membrane-enclosed organelles (endoplasmic reticulum (ER), Golgi bodies, and vesicles) that produce lipids and proteins for the cell’s membranes, and proteins for secretion. Endoplasmic reticulum (ER) is a continuous system of sacs and tubes extending from the nuclear envelope. Polypeptides made by ribosomes on rough ER are folded and modified in its interior. Smooth ER makes phospholipids, stores calcium ions, and has additional functions in some cells. Vesicles that bud from ER deliver proteins and lipids to Golgi bodies, where they are given final modifications and sorted into new vesicles. Some vesicles that bud from the Golgi deliver proteins and lipids to the plasma membrane; others become enzyme-containing lysosomes, which break down cellular debris and other particles. Peroxisomes are vesicles that break down organic molecules and toxins. Section 3.6  A cytoskeleton of protein filaments is the basis of cell shape, internal structure, and movement. In eukaryotes, ATP-driven motor proteins interact with microfilaments and microtubules to bring about movement, for example of pseudopods, cilia, and eukaryotic flagella. Microfilaments form a cell cortex that supports the plasma membrane. Stable intermediate filaments reinforce animal cell membranes and tissues. Several types of intermediate filaments are composed of different fibrous proteins.

Many cells secrete an extracellular matrix, or ECM, onto their surfaces. The composition and function of ECM varies depending on cell type. In animals, an ECM called basement membrane supports and organizes cells in tissues. A cell wall is another example of ECM. Cells of plants, fungi, and some protists have walls, but animal cells do not. Many eukaryotic cell types also secrete protective cuticle. Cell junctions structurally and functionally connect cells in tissues. Plasmodesmata connect the cytoplasm of adjacent plant cells. In animals, gap junctions are closable channels that connect adjacent cells. Adhering junctions that connect to cytoskeletal elements fasten animal cells to one another and to basement membrane. Tight junctions form a waterproof seal between cells. Section 3.7  Differences among cell components allow us to categorize life. Our best definition of “life” consists of a set of properties that collectively describe living things: They consist of cells that harvest energy and matter from the environment. They also make and use complex carbon-based molecules; require water; grow; engage in self-sustaining biological processes; respond to stimuli; change over their lifetime, and over generations; and pass hereditary material (DNA) to offspring.

Self-Quiz Answers in Appendix I 1. All cells have these three things in common: a. cytoplasm, DNA, and organelles with membranes b. a plasma membrane, DNA, and a nucleus c. cytosol, DNA, and a plasma membrane d. a cell wall, cytoplasm, and DNA 2. Which of the following is not a principle of the cell theory? a. Every cell arises from division of another cell. b. A cell is alive even as part of a multicelled body. c. Eukaryotic cells have a nucleus, and prokaryotic cells do not. d. The cell is the basic unit of life. 3. Unlike eukaryotic cells, prokaryotic cells __________ . a. have no plasma membrane b. have RNA but not DNA c. have no nucleus

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Cell Structure  Chapter 3  73 

4. The surface-to-volume ratio __________ . a. does not apply to prokaryotic cells b. is part of the cell theory c. constrains cell size

13. __________ fasten animal cells to one another and to basement membrane. a. Plasmodesmata c. Tight junctions b. Adhering junctions d. Gap junctions

5. True or false? Ribosomes are only found in eukaryotes.

14. Which of the following organelles contains no DNA? a. nucleus c. mitochondrion b. Golgi body d. chloroplast

6. Cell membranes consist mainly of __________ and __________ . a. lipids; carbohydrates b. phospholipids; proteins c. lipids; ECM d. phospholipids; ECM 7. Which of the following statements is correct? a. Some animal cells are prokaryotic. b. Only eukaryotic cells have mitochondria. c. The plasma membrane is the outermost boundary of all cells. 8. In a lipid bilayer, the __________ of all the lipid molecules are sandwiched between all of the __________ . a. hydrophilic tails; hydrophobic heads b. hydrophilic heads; hydrophilic tails c. hydrophobic tails; hydrophilic heads d. hydrophobic heads; hydrophilic tails 9. The main function of the endomembrane system is __________ . a. building and modifying proteins and lipids b. isolating DNA from toxic substances c. secreting extracellular matrix onto the cell surface d. producing ATP by aerobic respiration 10. What controls the passage of molecules into and out of the nucleus? a. endoplasmic reticulum, an extension of the nucleus b. nuclear pores, which consist of many proteins c. dynamically assembled microtubules d. tight junctions 11. Put the following structures in order according to the pathway of a secreted protein: a. plasma membrane b. Golgi body c. endoplasmic reticulum d. post-Golgi vesicles 12. No animal cell has a __________ . a. plasma membrane b. flagellum c. lysosome d. cell wall

15. Match each cell component with its main function. mitochondrion a. connection chloroplast b. protects surfaces ribosome c. ATP production nucleus d. protects DNA cell junction e. protein synthesis f. photosynthesis flagellum cuticle g. movement

CRITICAL THinking 1. Like toxic strains of E. coli, a type of bacteria called Staphylococcus aureus produces a toxic protein that can cause serious illness if ingested. Both types of bacteria die at a temperature of 71°C (160°F). Meat contaminated with toxic E. coli becomes safe to eat after it has been heated to this temperature, but meat contaminated with S. aureus is not safe to eat even after it has been heated to 95°C (203°F). Why the difference? 2. A person is declared to be dead upon the irreversible ceasing of spontaneous body functions: brain activity, or blood circulation and respiration. However, only about 1 percent of a person’s cells have to die for all of these things to happen. How can someone be dead when 99 percent of his or her cells are still alive? 3. In a classic episode of Star Trek, a gigantic amoeba floating in space engulfs an entire starship. Spock blows the cell to bits before it has a chance to reproduce. Think of at least one inaccuracy that a biologist would identify in this scenario. 4. In plants, the cell wall forms as a young plant cell secretes polysaccharides onto the outer surface of its plasma membrane. Being thin and pliable, this primary wall allows the cell to enlarge and change shape. In mature woody plants, cells in some tissues deposit material onto the primary wall’s inner surface. Why doesn’t this secondary wall form on the outer surface of the primary wall? 5. Is the organism pictured in Figure 3.5 prokaryotic or eukaryotic? How can you tell?

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4

4.1 A Toast to Alcohol Dehydrogenase  75 4.2 Life Runs on Energy  76 4.3 Energy in the Molecules of Life  77

Energy and Metabolism

4.4 Enzymes and Metabolic Pathways  79 4.5 Diffusion across Membranes  84 4.6 Membrane Transport Mechanisms  87

Fireflies emit light at night to attract mates. The emission of visible light by a living organism is called bioluminescence, and it is an effect of reactions that release energy stored in chemical bonds. In fireflies, the reactions are powered by ATP.

Concept Connections Witsalun/Shutterstock.com

In this chapter, you will gain insight into the one-way flow of energy through the world of life (Sections 1.2, 1.3) as you learn about energy and the laws of nature (1.7) that describe it. Cells store energy in chemical bonds of carbohydrates (2.7) by metabolic pathways such as photosynthesis (5.2), and retrieve energy in those bonds by pathways of respiration (6.2). Electrons (2.2) carry energy from one molecule to another in these pathways. You will revisit the relationship between the structure and function of organic molecules (2.8, 2.9) as you learn about enzymes that make up metabolic pathways (2.6), and about ways in which substances cross cell membranes (3.3). Later chapters discuss enzymes in context of DNA replication (7.5), gene expression (8.3 to 8.5), genetic engineering (11.2, 11.5), and digestion (24.3); membrane transport in context of muscle contraction (21.4) and nervous system signaling (25.3); and metabolism in context of genetic disorders (10.7).

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Energy and Metabolism  Chapter 4  75 

Application 4.1 A Toast to Alcohol Dehydrogenase Most college students are under the legal drinking age, but alcohol abuse continues to be the most serious drug problem on college campuses throughout the United States (Figure 4.1). Almost half of university students regularly consume five or more alcoholic beverages within a two-hour period—a selfdestructive behavior called binge drinking—and one in eight have consumed 10 or more drinks in a row. Drinking large amounts of alcohol in a brief period of time is an extremely risky behavior, both for the drinkers and people around them. Every year, thousands of students end up in the emergency room for alcohol poisoning. Around 600,000 students injure themselves while under the influence of alcohol, and 1,800 die from alcohol-related injuries. Intoxicated students physically assault 690,000 people and sexually assault 97,000 others. Before you drink, consider what you are consuming. All alcoholic beverages—beer, wine, hard liquor, alcoholic energy drinks, and so on— contain the same ingredient: ethanol. Ethanol is a toxin that interferes with the function of cells throughout the body; psychoactive effects arise as it scrambles signals between brain cells. Bingeing too much alcohol disrupts enough Figure 4.1  A tailgate party at a Notre Dame–Alabama of these signals that the brain can no longer control essential body functions, football game. with potentially lethal effects. Streeter Lecka/Getty Images Sport/Getty Images ALCOHOL POISONING Liver cells make an enzyme, alcohol dehydrogenase (ADH), which is part of a metabolic pathway that detoxifies ethanol. ADH converts ethanol to acetAlcohol poisoning occurs when high levels of alcohol ALCOHOL POISONING suppress the nervous and respiratory systems and aldehyde. Acetaldehyde is even more toxic than ethanol, with physiological the body struggles to rid itself of toxins produced Alcohol poisoning occurs when high levels of alcohol effects that include increased heart rate and respiration rate, decreased blood from the breakdown of alcohol. Signs of this suppress the nervous and respiratory systems and pressure, nausea, vomiting, headache, and constriction of the airways to the dangerous condition can include: the body struggles to rid itself of toxins produced lungs. A second enzyme, ALDH, converts the acetaldehyde into a nontoxic salt from the breakdown of alcohol. Signs of this • Mental confusion, stupor, coma, dangerous condition can include: called acetate. This pathway can detoxify between 7 and 14 grams of ethanol or the person cannot be roused an hour in the average healthy adult. The average alcoholic beverage contains Mental confusion, stupor, coma, • Vomiting between 10 and 20 grams of ethanol, which is why having more than one drink or the person cannot be roused • Slow or irregular breathing in any two-hour interval may result in a hangover. An acetaldehyde overdose is • Vomiting • Hypothermia or low body the most likely source of various hangover symptoms. • Slow or irregular temperature, bluishbreathing or pale skin If you regularly drink more alcohol than your enzymes can detoxify, then • Hypothermia or low body Alcoholtemperature, poisoning can bluish lead toor permanent the damage it does to your body will be permanent. Ethanol breakdown harms pale skinbrain damage or death, so a person showing any of these liver cells, so the more a person drinks, the fewer liver cells are left to do the signs requires immediate medical attention. Don’t Alcohol poisoning can lead to permanent brain breaking down. In the United States, alcohol abuse is the leading cause of wait. Call 911 if you suspect alcohol poisoning. damage or death, so a person showing any of these cirrhosis, a condition in which the liver becomes so scarred and hardened signs requires immediate medical attention. Don’t wait. Call 911 if you suspect alcohol poisoning. that it loses its function. (The term cirrhosis is from the Greek kirros, meaning “orange-colored,” after the abnormal skin color of people with the disease.) A cirrhotic liver can no longer remove drugs and other toxins from the blood, so they accumulate in Discussion Questions the brain, impairing mental function and altering 1. There are many reported “cures” for hangovers, including eating a greasy personality. Restricted blood flow through the liver breakfast, drinking sports drinks, and taking aspirin. Understanding the biolcauses veins to enlarge and rupture, so internal ogy behind hangovers, what would you recommend as a way to treat them? bleeding is a risk. These and other outcomes of 2. Why do you think so many university students binge-drink? liver malfunction damage the body and increase 3. Given the serious risks associated with underage drinking, do you think alcosusceptibility to diabetes and liver cancer. Once hol should be banned from all college campuses? Why or why not? cirrhosis has been diagnosed, a person has about a 50 percent chance of dying within 10 years.

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76  Unit 1  How Cells Work

4.2  Life Runs on Energy

heat energy

Learning Objectives time

●●

Describe the concept that energy tends to disperse.

●●

Explain why a chemical bond holds energy.

●●

Use the first and second laws of thermodynamics to explain why the total amount of energy available for doing work in the universe always decreases.

Energy is formally defined as the capacity to do work, but this definition is not very Figure 4.2  Energy disperses spontaneously. Heat spontaneously flows from a hot pan into cool air of a kitchen, until the temperature of both is the same. The total amount of heat energy in the system stays the same.

satisfying. We know from observations that energy can take different forms such as light, heat, electricity, motion (which is called kinetic energy), and that one form of energy can be converted to another. Think about how a lightbulb changes electricity into light, and an electric oven changes it into heat. A fan changes electricity into the kinetic energy of its blades.

Thermodynamics The formal study of heat and other forms of energy is called thermodynamics (thermo– means “heat”; dynam means “power”). By making careful measurements, thermodynamics researchers discovered that the total amount of energy in a system before and after every conversion is always the same. In other words, energy cannot be created or destroyed—a phenomenon that is the first law of thermodynamics. Energy also tends to spread out, or disperse, until no part of a system holds more than another part. In a kitchen, for example, heat always flows from a hot pan to cool air until the temperature of both is the same. The total amount of heat in our kitchen system doesn’t change, but the heat concentrated in the pan will always spread to the air (Figure 4.2). We never see cool air raising the temperature of a hot pan. The tendency of energy to spread out spontaneously is the second law of thermodynamics.

Chemical Bonds Hold Energy

Figure 4.3  Illustration of potential energy. By opposing gravity’s downward pull, the rope attached to the rock keeps this man from falling. Similarly, a chemical bond that joins two atoms keeps them from flying apart. Greg Epperson/Shutterstock.com

energy  The capacity to do work. first law of thermodynamics  Energy cannot be created or destroyed. potential energy  Energy stored in the arrangement of objects in a system. product  A molecule that is produced by a chemical reaction. reactant  A molecule that enters a chemical reaction and is changed by participating in it. second law of thermodynamics  Energy tends to disperse spontaneously.

Biologists use the concept of energy dispersal as it applies to chemical bonding, because energy flow in living things occurs mainly by the making and breaking of chemical bonds. Consider how two unbound atoms can vibrate, spin, and rotate in every direction. A covalent bond between the atoms restricts their movement, so they are able to move in fewer ways than they did before bonding. In other words, the kinetic energy of the two atoms decreases when they bond. Energy cannot be destroyed, so the excess kinetic energy doesn’t just disappear. In this case, it becomes stored in the bond as potential energy, which is energy stored in the arrangement of objects in a system (Figure 4.3). If we break the bond to free the two atoms, the potential energy is converted back to kinetic energy.

Work Doing work involves energy transfers. Consider what happens when you push a heavy box across a floor. In this case, a body (you) transfers energy to another body (the box) to make it move (the work). Similarly, a plant cell works to make sugars. Inside the cell, one set of molecules harvests the energy of light, then transfers it to another set of molecules. The second set of molecules uses the energy to build sugars from carbon dioxide and water. This particular energy transfer involves the conversion of light energy to chemical energy. Most other types of cellular work occur by the transfer of chemical energy from one molecule to another.

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Energy and Metabolism  Chapter 4  77 

Energy Transfers Are Inefficient As you learn about how energy drives cellular processes, remember that no energy transfer is 100 percent efficient. At least some energy escapes each transfer—typically, by dispersing in the form of heat. As a simple example, an incandescent lightbulb converts only about 5 percent of the energy of electricity into light. The remaining 95 percent of the energy ends up as heat that disperses from the bulb. Dispersed heat is not useful for doing work. Because some energy in every transfer disperses as heat, and dispersed heat is not useful for doing work, we can say that the total amount of energy in the universe available for doing work is always decreasing. Is life an exception to this inevitable decrease? Energy becomes concentrated in each new organism as the molecules of life assemble and organize into cells. Even so, living things constantly use energy to grow, to move, to acquire nutrients, to reproduce, and so on. Energy transfers occur in all of these processes, and some energy disperses with each transfer (Figure 4.4). Unless the losses are replenished with energy from another source, life’s complex organization will end. The energy that fuels most life on Earth comes from the sun. That energy flows through producers, then consumers (Figure 4.5). During its journey, the energy is transferred many times. With each transfer, some energy escapes as heat until, eventually, all of it is permanently dispersed. However, the second law of thermodynamics does not say how quickly the dispersal has to happen. Energy’s spontaneous dispersal is resisted by chemical bonds. Think of the bonds in the countless molecules that make up your skin, heart, liver, fluids, and other body parts. Those bonds hold the molecules, and you, together—at least for the time being.

Take-Home Message 4.2 ●● ●● ●●

●●

Energy, which is the capacity to do work, cannot be created or destroyed. Energy disperses spontaneously. Energy can be transferred between systems or converted from one form to another, but some disperses (usually as heat) during each exchange. Sustaining life’s organization requires ongoing energy inputs to counter energy dispersal. Organisms stay alive by replenishing themselves with energy they harvest from someplace else.

4.3  Energy in the Molecules of Life Learning Objectives ●●

Explain chemical bond energy.

●●

Describe activation energy.

●●

Explain how cells store and retrieve energy in organic molecules.

Chemical Reactions Remember from Section 2.6 that chemical reactions change molecules into other molecules. All cells store and retrieve energy in chemical bonds of the molecules of life, and these activities occur by way of reactions. During a reaction, one or more reactants (molecules that enter the reaction and become changed by it) become one or more products (molecules that are produced by the reaction). Intermediate molecules may form between reactants and products.

Figure 4.4  Feed conversion ratio. It takes more than 10,000 pounds of feed to raise a 1,000-pound steer. Where do the other 9,000 pounds go? About half of the steer’s food is indigestible and passes right through it. The animal’s body breaks down molecules in the remaining half to access energy stored in chemical bonds. Only about 15 percent of that energy goes toward building body mass. The rest disperses as heat. Martin Metsemakers/Shutterstock.com

A. Energy In Sunlight reaches environments on Earth. Producers in those environments capture some of its energy and convert it to other forms that can drive cellular work. PRODUCERS

B. Some of the energy captured by producers ends up in the tissues of consumers. CONSUMERS

C. Energy Out With each energy transfer, some energy escapes into the environment, mainly as heat. Living things do not use heat to drive cellular work, so energy flows through the world of life in one direction overall.

Figure 4.5  The flow of energy through the world of life. Energy (yellow arrows) flows from the environment into living organisms, then to the environment.

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78  Unit 1  How Cells Work Reactants

Products

+ 2H2 (hydrogen)

O2 (oxygen)

4 hydrogen atoms

2 oxygen atoms

2H2O (water)

4 hydrogen atoms 2 oxygen atoms

6

Energy

glucose C6H12O2

+

oxygen O2

Figure 4.6  Chemical bookkeeping. In equations that represent chemical reactions, reactants are written to the left of an arrow that points to the products. A number before a chemical formula indicates the number of molecules. Atoms may shuffle around, but the same number of atoms that enter a reaction remain at its end.

energy in +

6

6

carbon dioxide CO2

water H2O

A. Some reactions convert molecules with lower energy to molecules with higher energy, so they require a net energy input in order to proceed.

We show a chemical reaction as an equation in which an arrow points from reactants to products: + 2H2 (hydrogen)

O2 (oxygen)

2H2O (water)

A number before a chemical formula in such equations indicates the number of molecules; a subscript indicates the number of atoms of that element per molecule. Notice that atoms shuffle around in a reaction, but they never disappear: The same number of atoms that enter a reaction remain at the reaction’s end (Figure 4.6).

Bond Energy 6 +

oxygen O2

Energy

glucose C6H12O2

energy out 6

+

carbon dioxide CO2

6 water H2O

B. Other reactions convert molecules with higher energy to molecules with lower energy, so they end with an energy release. Figure 4.7  The ins and outs of energy in chemical reactions. Figure It Out: Which law of thermodynamics explains energy inputs and outputs in chemical reactions?

Answer: The first law

activation energy  Minimum amount of energy required to start a chemical reaction.

Every chemical bond holds a certain amount of energy. That is the amount of energy required to break the bond, and it is also the amount of energy released when the bond forms. The particular amount of energy held by a bond depends on the elements involved. Consider two covalent bonds, one between a hydrogen and an oxygen atom (HO), the other between two hydrogen atoms (HH). Both of these bonds hold energy, but different amounts of it. Now consider bond energy in a reaction. We can calculate the total amount of energy held in reactants by adding up the energy of all their bonds, and we can do the same for the products. If the reactants have less bond energy than the products, the reaction will not proceed without a net energy input (Figure 4.7). If the reactants have more bond energy than the products, the reaction will end with a net release of energy. Why Earth Does Not Go Up in Flames  The molecules of life release energy when

they combine with oxygen (a gas in air). Think of how a spark ignites wood in a campfire. Wood is mostly cellulose, which consists of long chains of glucose monomers (Section 2.7). When organic molecules such as cellulose burn (combust), they react with oxygen in a way that breaks their bonds, and the bond energy is released all at once. This burst of energy can spark the same reaction with other molecules, which is why wood keeps burning after it has been lit. Earth is rich in oxygen and organic molecules. Why doesn’t it burst into flames? Luckily for us, most, reactions will not start without at least a small input of energy. We call this input activation energy. Activation energy is the minimum amount of energy required to get a chemical reaction started, and it is a bit like an energy hill that reactants must climb before they can coast down the other side to become products (Figure 4.8). Both energy-requiring and energy-releasing reactions have activation energy.

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Energy and Metabolism  Chapter 4  79 

Activation energy

Activation energy

Reactants

Products

Energy

In graphs that show energy changes during a reaction, activation energy is an energy hill. Activation energy prevents a reaction from starting spontaneously.

Energy

Figure 4.8  Activation energy.

Net energy output

Net energy input

Products Reaction progress

Tero Hakala/Shutterstock.com

A. Activation energy in an energy-releasing reaction.

Reactants

Reaction progress

B. Activation energy in an energy-requiring reaction.

Storing and Retrieving Energy in Organic Molecules Cells store energy by running reactions that assemble organic molecules (Figure 4.9A). These reactions require energy, and some of it ends up in the bonds that hold the molecules together. For example, light energy drives the reactions of photosynthesis, which collectively build sugars such as glucose. Unlike light, glucose (and the energy in its bonds) can be stored in a cell. Cells retrieve energy stored in organic molecules by running reactions that disassemble them (Figure 4.9B). For example, the reactions of aerobic respiration collectively release the energy of glucose by breaking the bonds between its carbon atoms. Breaking these bonds releases energy that cells use for other purposes. You will see shortly how energy released from some reactions drives others. (We return to the reactions of photosynthesis and aerobic respiration in Chapters 5 and 6.)

C. Wood continues to burn (combust) after it has been lit. This is because combustion releases a burst of energy that sparks the same reaction with other molecules. Activation energy prevents wood from spontaneously combusting.

Take-Home Message 4.3 ●●

●● ●●

Some reactions will not run without a net input of energy. Others end with a net release of energy. Activation energy prevents a reaction from proceeding spontaneously. Cells store energy in chemical bonds by assembling organic molecules. They retrieve the stored energy by breaking the bonds of these molecules.

4.4  Enzymes and Metabolic Pathways Learning Objectives ●●

Explain enzyme specificity and how it arises.

●●

Describe metabolic pathways and mechanisms that regulate them.

●●

Explain how cells use electron transfer chains.

●●

Describe the role of ATP in a cell’s energy economy.

The Need for Speed A living cell teems with reactions. Its ongoing functions, as well as special processes such as cell division, require a continuous supply of organic molecules that must be assembled and disassembled as needed. Enzymes that mediate these reactions allow them to occur at an astonishing rate. Consider the bicarbonate buffer that keeps the pH of your blood stable (Section 2.4). Bicarbonate is the product of a

Figure 4.9  Cells store and retrieve energy in the chemical bonds of organic molecules. energy in

small molecules (e.g., carbon dioxide, water)

energy-requiring reactions

organic compounds (carbohydrates, fats, proteins)

A. Cells run energy-requiring reactions to assemble organic compounds. Building these compounds stores energy in their bonds. organic compounds (carbohydrates, fats, proteins)

energy-releasing reactions

small molecules (e.g., carbon dioxide, water)

energy out

B. Cells break the bonds of organic molecules to retrieve energy stored in them.

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80  Unit 1  How Cells Work

A. Hexokinase is an enzyme that adds a phosphate group to glucose and other six-carbon sugars. The box indicates its active site.

B. A phosphate group and a glucose molecule meet in the enzyme’s active site. After the two molecules react, the product (glucose-6-phosphate) will leave the active site. Figure 4.10  An active site in an enzyme. Data source: PDB ID 3B8A: Kuser, P., Cupri, F., Bleicher, L., Polikarpov, I. Crystal structure of yeast hexokinase PI in complex with glucose: A classical “induced fit” example revised. (2008) Proteins, 72: 731–740.

enzyme

substrates

A. An enzyme can act only on molecules that “fit” its active site. Such molecules are called the enzyme’s substrates. B. An active site squeezes substrates together, stretches their bonds, or causes some change that lowers activation energy, so the reaction proceeds. product

C. The product leaves the active site after the reaction is finished. The enzyme is unchanged, so it can work again.

Figure 4.11  The active site. An active site is a pocket in an enzyme where substrates bind and the reaction occurs. For simplicity, enzymes and their active sites are often depicted as blobs or geometric shapes.

reaction that combines water and carbon dioxide, and the enzyme that mediates this reaction in your body makes it run 10 million times faster than it would on its own.

The Active Site Most enzymes are proteins, and each speeds up a particular reaction without being changed by it (Section 2.6). An enzyme acts only on specific reactants, which are called its substrates. The enzyme’s component polypeptides fold to form an active site, which is a pocket where substrates bind and the reaction occurs (Figure 4.10). After the reaction, the active site releases the product(s), so more substrates can bind. Substrates are complementary in shape, size, polarity, and charge to an active site (Figure 4.11). That fit is the reason why each enzyme acts on specific reactants. An enzyme can speed a reaction by reducing activation energy—lowering the barrier that prevents the reaction from proceeding (Figure 4.12). When we talk about activation energy, we are really talking about the energy required to bring the bonds of reactants to their breaking point. Binding at an active site may bring reactants to this state by (for example) squeezing them together, stretching their bonds, or forcing them into a particular shape. As the reactant bonds break, product bonds begin to form.

Environmental Effects on Enzyme Activity  Each enzyme works best in a particular range of conditions. Thus, factors such as temperature, pH, and salt concentration can influence the rate of the reaction it mediates. Temperature  The greater the energy of reactants, the less activation energy is

required to start the reaction. Adding heat to a system increases its energy, so the rate of an enzyme-mediated reaction increases with temperature—but only up to a point. Like other proteins, an enzyme denatures (unfolds) above a characteristic temperature, and as it loses shape, it also loses function (Section 2.9). The reaction rate falls sharply as the enzyme stops working (Figure 4.13A).

pH  Most enzymes function within a specific range of pH, and that range depends on the enzyme. Consider two enzymes that play a role in human digestion (Figure 4.13B). The enzyme pepsin, which works best at low pH, begins the process of protein breakdown in the very acidic environment of the stomach (pH 2). During digestion, the stomach’s contents pass into the small intestine, where the pH rises to about 7.5. Pepsin denatures above pH 5.5, so this enzyme stops working in the small intestine. Protein breakdown continues with the assistance of trypsin, an enzyme that functions well at the higher pH. Salts  Salts release ions other than H+ when they dissolve in water (Section 2.4),

and the types and amounts of these ions in a fluid influence the activity of many enzymes. Too little salt, and polar parts of the enzyme attract one another so strongly that the molecule’s shape changes. Enzymes also lose function when the salt concentration is too high. This is because too much salt disrupts hydrogen bonds: those that hold the enzyme in its characteristic shape, and those that keep the enzyme dissolved in water. Optimal salt concentration varies by the enzyme. Consider the enzymes of bacteria that inhabit the Dead Sea and other places where the water is very salty. These

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Energy and Metabolism  Chapter 4  81 

Activation energy with enzyme

Reactants

Enzyme activity

Products

20

Reaction progress

Figure 4.12  Enzymes lower activation energy. An enzyme increases the rate of a reaction by lowering its activation energy.

trypsin

pepsin

Enzyme activity

Activation energy without enzyme

T. aquaticus polymerase

40 60 80 Temperature (°C)

2

100

Answer: An energy-requiring reaction

enzymes function best in a salt concentration that is extremely high—up to 10 times the optimal salt concentration for enzymes of other bacteria.

6 pH

8

10

B. The pH-dependent activity of two digestive enzymes. Pepsin acts in the stomach, where the normal pH is 2. Trypsin acts in the small intestine, where the pH is normally around 7.5.

A. The temperature-dependent activity of a DNA synthesis enzyme from two species of bacteria: E. coli, which inhabits the human gut (normally 37°C); and Thermus aquaticus, which lives in hot springs around 70°C.

Figure It Out: Does this graph illustrate an energyrequiring reaction or an energy-releasing reaction?

4

Figure 4.13  Enzymes, temperature, and pH. Each enzyme works best within a characteristic range of conditions. Figure It Out: What is the optimum temperature for the E. coli polymerase?

Answer: About 40°C

Energy

E. coli polymerase

Molecular Effects on Enzyme Activity A cell conserves energy and resources by making only what it needs at any given moment—no more, no less. Several mechanisms allow it to maintain, raise, or lower the production of thousands of different substances. Consider that chemical reactions do not only run from reactants to products. Many also run in reverse at the same time, with some products being converted back to reactants:

reactant

enzyme

product

The rates of the forward and reverse reactions often depend on the relative concentrations of reactants and products. A high concentration of reactants favors the forward reaction, and a high concentration of products favors the reverse reaction:

reactant

substrate

product

product

Other mechanisms actively influence enzyme function. For example, the activity of many enzymes changes when specific ions or molecules bind to them. These substances can act as regulators that activate or deactivate an enzyme (Figure 4.14). Consider how some enzymes are active only when they have an attached phosphate group; such enzymes can be “switched on” by adding a phosphate group, and “switched off ” by removing it. Cofactors and Coenzymes  Most enzymes cannot function properly without

assistance from metal ions or small organic molecules. These assistants are called cofactors. Cofactors for many human enzymes are (or are derived from) essential dietary vitamins and minerals. Organic cofactors are called coenzymes. Unlike enzymes, coenzymes are modified by taking part in a reaction. They are regenerated in separate reactions. Coenzymes that temporarily associate with enzymes are a bit like a common currency in cells, because different enzymes use the same ones. These coenzymes carry

regulatory molecules

Figure 4.14  Regulatory molecule binding to enzymes. Specific ions or molecules that bind to an enzyme change its shape in a way that enhances or inhibits its activity. Figure It Out: Is this enzyme activated or deactivated when the regulatory molecules bind to it? Answer: Activated

reactant

active site

active site  Pocket in an enzyme where substrates bind and a reaction occurs. coenzyme  An organic cofactor. cofactor  A metal ion or small non-protein organic molecule that associates with an enzyme and is necessary for its function. substrate  Of an enzyme, specific molecule that can bind to the enzyme’s active site and be converted to a product. A reactant in an enzyme-mediated reaction.

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82  Unit 1  How Cells Work

adenine three phosphate groups

ribose

A. Bonds between phosphate groups hold a lot of energy. ATP has two of these bonds.

chemical groups, atoms, or electrons from one reaction to another, and often into or out of organelles. Consider one coenzyme, NAD+ (nicotinamide adenine dinucleotide), that is used by hundreds of different enzymes. During some reactions, electrons and hydrogen atoms are transferred to NAD+, so the coenzyme becomes NADH. During other reactions, electrons and hydrogen atoms are removed from NADH, so NAD+ forms again: NAD+ 1 electrons 1 H+

NADH

NAD+ 1 electrons 1 H+

ATP: A Special Coenzyme  Some coenzymes are multifunctional molecules. The

B. Like many other animals, the firefly (left) emits light to attract mates (right). Light-producing reactions in these beetles run on energy provided by ATP. energy out

ADP + Pi

energy in

ATP C. ADP forms in a reaction that removes a phosphate group from ATP (Pi is an abbreviation for phosphate group). Energy released in this reaction drives other reactions that are the stuff of cellular work. ATP forms again in energy-requiring reactions that phosphorylate ADP. Figure 4.15  The nucleotide ATP, an important energy currency in a cell’s metabolism. (B) left, Cathy Keifer/Shutterstock.com; right, Witsalun/Shutterstock.com

electron transfer chain  Series of enzymes and other molecules in a cell membrane that accept and give up electrons in turn, thus releasing the energy of the electrons in steps. feedback inhibition  Of a metabolic pathway, regulatory mechanism in which a reaction product slows or stops a pathway that produces it. metabolic pathway  A series of enzyme-mediated reactions by which cells build, remodel, or break down an organic molecule. phosphorylation  Chemical reaction in which an enzyme attaches a phosphate group to an organic molecule.

nucleotide ATP (adenosine triphosphate, Section 2.10) is a component of RNA, and it also functions as a coenzyme in many reactions by donating and accepting phosphate groups. Bonds between phosphate groups hold a lot of energy compared to other bonds, and ATP has two of them holding its three phosphate groups together (Figure 4.15A). When a phosphate group is transferred to or from a nucleotide, this bond energy is transferred along with it. Thus, the nucleotide can receive energy from an energy-releasing reaction, and it can donate energy to an energy-requiring one. A reaction in which an enzyme attaches a phosphate to an organic molecule is called a phosphorylation. ADP (adenosine diphosphate) forms when an enzyme transfers a phosphate group from ATP to another molecule during a phosphorylation. Cells constantly run this reaction to drive energy-requiring reactions (Figure 4.15B). Thus, they must constantly replenish their stockpile of ATP—by running energy-releasing reactions that phosphorylate ADP (Figure 4.15C). This cycle of using and replenishing ATP couples energy-requiring reactions with energy-releasing ones. ATP participates in so many reactions that it is a major part of a cell’s energy economy, and we use a cartoon coin to symbolize it.

Metabolic Pathways Building, rearranging, or breaking down an organic molecule often occurs stepwise, in a series of enzymatic reactions called a metabolic pathway. Some metabolic pathways are linear, meaning that the reactions run straight from reactant to product (Figure 4.16A). Others are cyclic. In a cyclic pathway, the last step regenerates a reactant of the first step (Figure 4.16B). Changes in the activity of a single enzyme can affect an entire metabolic pathway. In some cases, the product of a series of enzymatic reactions inhibits the activity of one of the enzymes in the series (Figure 4.17). This type of regulatory mechanism, in which a change that results from an activity decreases or stops the activity, is called feedback inhibition. A cell’s metabolism consists of many interconnected metabolic pathways, with products of some pathways affecting the operation of others. The overlap provides a fine level of regulatory control over the cell’s activities. Heavy Drinking Causes Fatty Liver  One of the many damaging effects of

consuming excessive amounts of alcohol involves feedback inhibition in liver cells. ALDH, the second enzyme in the metabolic pathway you learned about in Section 4.1, requires the coenzyme NAD+. As ALDH converts acetaldehyde to acetate, the NAD+ is converted to NADH. Drinking too much alcohol causes too much NADH to form; other reactions that convert it back to NAD+ cannot keep up with the excess. The accumulation of NADH affects many other reactions that use

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Energy and Metabolism  Chapter 4  83  reactant

reactant enzyme 1

enzyme 3 reactant

intermediate enzyme 2

enzyme 2

product

Figure 4.17  Feedback inhibition.

enzyme 3

A. A linear pathway runs straight from reactant to product.

intermediate

intermediate

intermediate

intermediate

product

X

enzyme 1

product enzyme 2

B. The last step of a cyclic pathway regenerates a reactant for the first step.

Figure 4.16  Linear and cyclic metabolic pathways.

this coenzyme. For example, excess NADH inhibits enzymes in pathways that break down fatty acids, so fat collects in globules in the liver. This condition persists even after drinking stops and the excess NADH is cleared. Electron Transfers  Capturing and harvesting energy can be dangerous for cells.

For example, the bonds of organic molecules such as glucose hold enough energy to harm a cell if released all at once, as occurs during combustion (burning) reactions with oxygen (Figure 4.18A). Most cells use oxygen to break the bonds of organic molecules, but they have no way to harvest the uncontrolled burst of energy released by combustion. Instead, they break the bonds of an organic molecule one by one, in steps that release energy in small, usable amounts. Most of these steps are electron transfers, in which one molecule accepts electrons from another. An electron transfer chain is a series of membrane-bound enzymes and other molecules that give up and accept electrons in turn. Electrons lose energy during these transfers, so they are at a higher energy level when they enter a chain than when they leave. Energy given off by an electron as it drops to a lower energy level is harvested by molecules of the electron transfer chain to do cellular work (Figure 4.18B). In Chapters 5 and 6, you will learn about electron transfer chains in energy-harvesting steps of photosynthesis and aerobic respiration.

In this example, two enzymes act in sequence to convert a substrate to a product. The product inhibits the activity of the first enzyme. Figure It Out: Is this pathway cyclic or linear? Answer: Linear

enzyme 1

Figure 4.18  Comparing uncontrolled (A) and controlled (B) energy release. The overall reaction is the same in both cases: C6H12O6 + O2 glucose oxygen

CO2 + H2O + carbon water energ energy dioxide

(A) SPL/Science Source

A. Below, glucose reacts with oxygen in combustion. The direct transfer of electrons from glucose to oxygen breaks the bonds of both molecules. Energy is released all at once, in the form of light and heat.

energy

carbon dioxide + water glucose + oxygen

Take-Home Message 4.4 ●●

●●

●●

●●

●●

Binding at an enzyme’s active site causes a substrate’s bonds to reach their breaking point, and the reaction can run spontaneously to completion. Each enzyme works best within a characteristic range of environmental conditions. Many enzymes require the assistance of cofactors. When a phosphate group is transferred from a nucleotide to another molecule, energy is transferred along with it. ATP in particular couples reactions that release energy with reactions that require energy. A metabolic pathway is a series of enzyme-mediated reactions. Some pathways involve electron transfer chains. Cells conserve energy and resources by producing only what they need at a given time. This control can arise from mechanisms such as feedback inhibition that affect individual steps in a metabolic pathway.

glucose + oxygen

H+

e–

carbon dioxide + water e–

B. Above, glucose reacts with oxygen in a series of electron transfers. Electrons are transferred from glucose to oxygen in steps (represented here as a staircase). With each transfer, the electrons lose a little energy ( ) that can be harnessed for cellular work.

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84  Unit 1  How Cells Work

Digging Into Data One Tough Bug

1. What do the dashed lines in the graphs signify? 2. Of the four enzymes profiled in the graphs, how many function optimally at a pH lower than 5? How many retain significant function at pH 5? 3. What is the optimal pH for the carboxylesterase?

A. Deep inside one of the most toxic sites in the United States: Iron Mountain Mine, in California. The water in this stream, which is about 1 meter (3 feet) wide in the photo, is hot (around 40°C, or 104°F), heavily laden with arsenic and other toxic metals, and has a pH of zero. Slime streamers growing in it are a biofilm dominated by a species of archaea, Ferroplasma acidarmanus.

carboxylesterase

α-glucosidase

GlyFa1

GlyFa2

1 2 3 4 5 6 pH

1 2 3 4 5 6 7 pH

1 2 3 4 5 6 pH

1 2 3 4 5 6 pH

Enzyme activity

The genus Ferroplasma consists of a few species of acid-loving archaea. One species, F. acidarmanus, was discovered in water draining from one of the most contaminated sites in the United States: the Iron Mountain Mine, in California (Figure 4.19A). F. acidarmanus cells live in groundwater that seeps into the mine. They have an ancient energy-harvesting pathway, an electron transfer chain that pulls electrons from pyrite (an iron–sulfur mineral that is particularly abundant in the area). The pathway gives off a lot of heat, which raises the water temperature to as much as 50°C, or 122°F. It also produces so much sulfuric acid that the water has a negative pH. The hot, acidic water dissolves other minerals as it flows through the mine, so it ends up with extremely high concentrations of metal ions such as copper, zinc, cadmium, and arsenic. Despite living in an environment with a compos­i­ tion similar to hot battery acid, F. acidarmanus cells keep their internal pH at a cozy 5.0. However, most of the enzymes in the cells’ cytoplasm function best at very low pH (Figure 4.19B). Thus, researchers think Ferroplasma may have an unknown type of internal compartment that keeps their enzymes in a highly acidic environment.

B. The pH profiles of four enzymes that occur in cytoplasm of F. acidarmanus. Researchers had expected these enzymes to function best at the cells’ cytoplasmic pH (5.0). Figure 4.19  pH anomaly of Ferroplasma acidarmanus enzymes. (A) Courtesy of Dr. Katrina J. Edwards; (B) Adapted from Golyshina et al., Environmental Microbiology, 8(3): 416–425. 2006 John Wiley and Sons.

4.5  Diffusion across Membranes Learning Objectives ●●

Name three factors that influence the rate and direction of diffusion.

●●

Explain selective permeability in terms of lipid bilayers.

●●

Describe the relationship between osmosis and turgor pressure in cells.

Diffusion of Solutes Metabolic pathways require the participation of molecules and ions that must move across membranes and through cells. Diffusion, the spontaneous spreading of atoms or molecules through a fluid or gas, is an essential way in which this movement occurs. An atom or molecule is always jiggling, and this internal movement causes it

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gresei/Shutterstock.com

Energy and Metabolism  Chapter 4  85 

to randomly bounce off of nearby objects, including other atoms or molecules. Rebounds from such collisions propel solutes through a liquid, with the result being a gradual and complete mixing (you can see this mixing when tea diffuses through hot water, left).

Gases

Water

Ions

Hydrophobic molecules

Small polar molecules

Large polar molecules

Direction and Rate of Diffusion  Temperature, concentration, and charge affect the

direction and rate of diffusion.

Temperature. Atoms and molecules jiggle faster at higher temperature, so they collide more often. Thus, diffusion occurs more quickly at higher temperatures. Concentration. A difference in solute concentration between adjacent regions of solution is called a concentration gradient. Solutes tend to diffuse “down” their concentration gradient, from a region of higher concentration to one of lower concentration. Why? Consider that moving objects (such as molecules) collide more often when they are more crowded. Thus, during a given interval, more molecules are bumped out of a region of higher concentration than are bumped into it.

Figure 4.20  Selective permeability of lipid bilayers. Water and other small polar molecules can diffuse through a lipid bilayer, but less freely than hydrophobic molecules and gases. A lipid bilayer is completely impermeable to ions and large polar molecules.

Charge. Each ion or charged molecule in a fluid contributes to the fluid’s overall electric charge. A difference in charge between two regions of fluid (a charge gradient) can affect a solute’s diffusion between them. For example, positively charged substances such as sodium ions will tend to diffuse toward a region with an overall negative charge, and vice versa. Selective Permeability of Lipid Bilayers  Lipid bilayers are selectively permeable,

which means that only some substances can diffuse through them (Figure 4.20). The long, nonpolar tails of phospholipids make the core of a lipid bilayer quite hydrophobic. Gases and hydrophobic molecules (such as fats and steroids) diffuse freely through this core, but ions and large polar molecules (such as sugars and proteins) cannot. Water and other small polar molecules diffuse slowly through a lipid bilayer by seeping between the lipid tails.

Tonicity and Osmosis When a lipid bilayer separates two fluids with differing solute concentrations, water will diffuse through it. The direction and rate of this diffusion depend on the relative solute concentration of the two fluids, which we describe in terms of tonicity. If the overall solute concentrations of the two fluids differ, the fluid with the lower concentration of solutes is said to be hypotonic (hypo–, under). The other one, with the higher solute concentration, is hypertonic (hyper–, over). Water diffuses from a hypotonic fluid into a hypertonic one. The diffusion will continue until the two fluids are isotonic, which means they have the same overall solute concentration. The diffusion of water through a membrane is so important in biology that it is given a special name: osmosis (Figure 4.21). Cells and Osmosis  If a cell’s cytoplasm becomes hypertonic with respect to the

fluid outside of its plasma membrane, water will diffuse into the cell. If the cytoplasm becomes hypotonic, water will diffuse out. In either case, the solute concentration of the cytoplasm may change. If it changes enough, the cell’s enzymes will stop working, with lethal results. Most cells have homeostatic mechanisms that compensate for osmosis. In cells with no such mechanism, the volume—and solute

selectively permeable membrane

Figure 4.21  Osmosis. A membrane separates two fluids of differing solute concentration. The membrane is selectively permeable: Water can cross it, but the solute (red dots) cannot. The fluid volume changes in the two compartments as water diffuses through the membrane from the hypotonic solution to the hypertonic one.

diffusion  The spontaneous spreading of molecules or atoms through a fluid or gas. hypertonic  Describes a fluid that has a high overall solute concentration relative to another fluid. hypotonic  Describes a fluid that has a low overall solute concentration relative to another fluid. isotonic  Describes two fluids with identical solute concentrations. osmosis  Diffusion of water through a selectively permeable membrane.

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86  Unit 1  How Cells Work A. Turgor pressure is high in these cells of an iris petal. They are plump with cytoplasm.

2% sucrose

2% sucrose

10% sucrose

water

B. Turgor pressure is low in these cells of a wilted iris petal. The cytoplasm shrank, and the plasma membrane is pulled away from the cell wall.

Figure 4.23  Osmotic pressure keeps plant parts erect. Perennou Nuridsany/Science Source

A. What happens when a selectively permeable bag containing a solution of sucrose is immersed in solutions of different tonicities.

concentration—of cytoplasm changes when water diffuses into or out of the cell (Figure 4.22).

Turgor Pressure B. Red blood cells in an isotonic solution (such as the fluid portion of blood) have an indented disk shape.

C. Red blood cells immersed in a hypertonic solution shrivel up because water diffuses out of them.

Even in a hypotonic environment, a cell wall can resist an increase in the volume of cytoplasm due to osmosis. In the case of plant cells, cytoplasm usually contains more solutes than soil water does. Thus, water usually diffuses from soil into a plant—but only up to a point. Stiff walls keep plant cells from expanding very much, so an inflow of water causes pressure to build up inside them. Pressure that a fluid exerts against a structure that contains it is called turgor pressure. When enough pressure builds up inside a plant cell, water stops diffusing into it. The amount of turgor pressure that is enough to stop osmosis is called osmotic pressure. Osmotic pressure keeps walled cells plump, just as high air pressure inside a tire keeps it inflated. A young land plant can resist gravity to stay erect because turgor pressure inside its cells is high (Figure 4.23A). If the plant does not get enough water to replace what it uses, the cytoplasm of its cells shrinks (Figure 4.23B). As turgor pressure inside the cells decreases, the plant wilts. Fluid Balance in the Body  Osmotic pressure is also part of homeostatic mecha-

D. Red blood cells immersed in a hypotonic solution swell up because water diffuses into them. 15 µm

Figure 4.22  Effects of tonicity. Like a selectively permeable bag filled with a solution of sucrose and water (A), red blood cells have no mechanism to compensate for osmosis (B–D).

nisms inside our bodies. Consider a protein called albumin that is made by the liver. Under normal circumstances, blood contains a high level of albumin that makes it hypertonic with respect to tissue fluids. Blood vessel walls are permeable to water, but not to proteins, so water diffuses from tissues into blood until osmotic pressure is reached inside the vessels. Thus, the albumin content of the blood determines the balance of fluid between blood and body tissues. Cirrhosis caused by alcohol abuse disrupts this balance because the liver can no longer make albumin. When the blood does not contain enough albumin, not enough water leaves tissue fluids, so body tissues swell with fluid, especially in the legs and feet.

Take-Home Message 4.5 ●●

ISM/Hervé CONGE/Medical Images.com ●●

●●

The rate and direction of diffusion depends on temperature and regional differences in charge and solute concentration. Lipid bilayers are selectively permeable. Gases and nonpolar molecules diffuse freely through them; ions and large polar molecules cannot. Water and some other small polar molecules can diffuse slowly through. Water diffuses through a selectively permeable membrane, from a hypotonic to a hypertonic fluid. This movement, osmosis, is opposed by turgor pressure.

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Energy and Metabolism  Chapter 4  87 

4.6  Membrane Transport Mechanisms Learning Objectives ●● ●●

Explain why a cell requires transport proteins in its plasma membrane. Use appropriate examples to describe the way transport proteins selectively move molecules across membranes.

●●

Explain why active transport requires energy and passive transport does not.

●●

Describe the mechanisms by which cells take in and expel materials in bulk.

Transport Proteins  Even though ions and large polar molecules cannot diffuse directly through lipid bilayers, they can cross a cell membrane through transport proteins embedded in it (Section 3.3). In most cases, a transport protein binds a solute and changes shape in a way that releases the solute to the opposite side of the membrane. Each type of transport protein allows a specific substance to cross: Calcium pumps pump only calcium ions; glucose transporters transport only glucose; and so on. This specificity is an important part of homeostasis. Consider how the composition of cytoplasm depends on movement of particular solutes across the plasma membrane, which in turn depends on the transporters in it. Glucose is an important source of energy for most cells, so they normally take up as much as they can from extracellular fluid. This uptake occurs via glucose transporters in the plasma membrane. As soon as a molecule of glucose enters cytoplasm, an enzyme called hexokinase (shown in Figure 4.10) phosphorylates it. Phosphorylation traps the molecule in the cell because the transporters are specific for glucose, not phosphorylated glucose. Thus, phosphorylation prevents the molecule from moving back through the transport protein and leaving the cell.

Passive Transport Osmosis is one example of passive transport, a membrane-crossing mechanism that requires no energy input. Another example is facilitated diffusion, in which a solute crosses a membrane by diffusing through a transport protein. Facilitated diffusion requires no energy input because the movement of the solute is driven by its concentration gradient, or by a difference in charge across the membrane. For most transport proteins that work in facilitated diffusion, binding of a solute is sufficient to trigger the change in shape that delivers the solute to the other side of the membrane. A glucose transporter works this way (Figure 4.24 1, next page). Other passive transport proteins are gated, which means they open and close in response to a stimulus such as a shift in electric charge or binding to a signaling molecule. Still others form pores (permanently open channels through a membrane) with an internal configuration that allows particular molecules to squeeze through.

Active Transport  Solutes required for many cellular processes must be moved across a membrane against their concentration gradient, and this requires energy. With active transport, a transport protein uses energy to pump a solute across a cell membrane. The function of many active transport proteins involves a shape change triggered by a phosphate-group transfer from ATP.

active transport  Energy-requiring mechanism in which a transport protein pumps a solute across a cell membrane against the solute’s concentration gradient. facilitated diffusion  Passive transport mechanism in which a solute follows its concentration gradient across a membrane by moving through a transport protein. passive transport  Membrane-crossing mechanism that requires no energy input. turgor pressure  Pressure that a fluid exerts against a structure that contains it.

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88  Unit 1  How Cells Work

CLOSER LOOK Figure 4.24  Examples of membrane-crossing mechanisms.

3 Active Transport: Sodium–Potassium Pump

Figure It Out: Which is hypotonic with respect to glucose: extracellular fluid or cytoplasm?

Answer: Cytoplasm

1 Facilitated Diffusion:

2 Active Transport: Calcium Pump

This protein binds to a molecule of glucose in extracellular fluid. Binding triggers a shape change that releases the glucose into cytoplasm.

calcium pump

Glucose Transporter

Na+

Ca+

glucose transporter

Calcium ions (Ca+) in cytoplasm enter a calcium pump.

Figure Summary A plasma membrane is a hub of activity. Molecules, ions, and particles are constantly entering and exiting the cell via transport proteins and vesicles.

Na+

K+

P

ADP + Pi glucose

sodium–potassium pump

ATP

A phosphategroup transfer from ATP causes a shape change that releases the Ca+ into extracellular fluid.

ATP

ADP

Sodium ions (Na+) in cytoplasm enter the pump. A phosphate group transfer from ATP triggers a shape change.

P

The shape change causes the pump to release the Na+ to extracellular fluid. Potassium ions (K+) in extracellular fluid enter the pump.

P

K+

The pump releases the phosphate group and the K+ into cytoplasm.

This protein pumps sodium ions from cytoplasm to extracellular fluid, and potassium ions in the other direction. ATP provides energy required for transporting both ions against their concentration gradient.

The Calcium Pump  Calcium ions act as potent messengers that trigger various processes inside cells. Thus, the concentration of these ions in cytoplasm must be kept thousands of times lower than in extracellular fluid. This gradient is maintained by calcium pumps, which export calcium ions from a cell by active transport 2. The Sodium-Potassium Pump  Another example of active transport involves sodium–potassium pumps. Nearly all cells in your body have these transport proteins, which pump two substances in opposite directions across the membrane: sodium ions from cytoplasm to extracellular fluid, and potassium ions from extracellular fluid to cytoplasm 3.

Vesicle-Based Transport  Vesicles are constantly carrying materials to and from a cell’s plasma membrane. Cells use them to take in or expel materials in bulk (as opposed to one molecule or ion at a time via transport proteins). A vesicle forms when an external or internal stimulus causes a patch of membrane to balloon into the cytoplasm. When a cell membrane is stretched or otherwise disturbed, the phospholipids will spontaneously rearrange themselves to maintain a bilayer configuration. This property helps round off the balloon as a vesicle, and also seals the rupture in the membrane. endocytosis  Process by which a cell takes in a small amount of extracellular fluid (and its contents) by the ballooning inward of the plasma membrane. exocytosis  Process by which a cell expels a vesicle’s contents to extracellular fluid. phagocytosis  “Cell eating”; an endocytic pathway by which a cell engulfs a large particle such as another cell.

Endocytosis  There are several pathways of endocytosis, but all bring materials into the cell. In one endocytic pathway, a small patch of plasma membrane balloons into the cytoplasm 4. When the balloon pinches off in the cytoplasm, it becomes a vesicle that encloses a droplet of extracellular fluid (along with whatever solutes and particles are suspended in it). This type of endocytosis is nonspecific about what it brings into the cell, so it is used for sampling the composition of extracellular fluid. Other pathways of endocytosis target specific extracellular substances.

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Energy and Metabolism  Chapter 4  89 

Figure It Out: Does the activity of the sodium–potassium pump affect charge of the fluid near the plasma membrane?

4 Endocytosis

Answer: Yes. It increases the charge of extracellular fluid to relative to cytoplasm.

5 Exocytosis

6 Phagocytosis The cell extends pseudopods (lobes of cytoplasm) around an extracellular target.

A pit forms in the plasma membrane, trapping molecules, fluid, and particles near the cell’s surface in a vesicle as it deepens and sinks into the cytoplasm.

Figure It Out: What do these colored balls represent?

A vesicle in cytoplasm fuses with the plasma membrane. Lipids and proteins of the vesicle’s membrane become part of the plasma membrane as its contents are expelled to the environment.

The bulging lobes fuse around the target, forming a vesicle that sinks into cytoplasm.

Answer: Different solutes

Exocytosis  Cells expel materials in bulk by exocytosis. In this process, a vesicle in

the cytoplasm moves to the cell’s surface and its membrane fuses with the plasma membrane. As the fusion occurs, the contents of the vesicle are released to the surrounding fluid 5.

Phagocytosis  With phagocytosis, a cell engulfs a particle such as a microorganism or cellular debris. Phagocytosis means “cell eating,” and many single-celled protists such as amoebas feed by this special endocytic pathway. Some of your white blood cells use phagocytosis to engulf viruses and bacteria, cancerous body cells, and other threats to health (Figure 4.25). Phagocytosis begins when a cell comes into contact with a particle, and receptors in its plasma membrane bind to molecules on the particle’s surface. The binding triggers pseudopods (Section 3.6) to extend from the plasma membrane and surround the particle. As the pseudopods merge around the particle, it becomes trapped inside a vesicle that sinks into cytoplasm 6.

Take-Home Message 4.6 ●● ●● ●●

●●

●●

Figure 4.25  Phagocytosis. This phagocytic white blood cell is engulfing tuberculosis bacteria (red). SPL/Science Source

Ions and large polar molecules cross cell membranes through transport proteins. Each type of transport protein moves a specific solute across a cell membrane. In facilitated diffusion (a type of passive transport), a solute follows its concentration gradient through a transport protein. The movement requires no energy input. In active transport, a transport protein pumps a solute across a membrane against its concentration gradient. The movement requires an energy input, as from ATP. By endocytosis and exocytosis, cells use vesicles to take in and expel substances in bulk. Phagocytosis is a special form of endocytosis in which cells engulf particles.

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90  Unit 1  How Cells Work

Summary Section 4.1  Alcohol abuse continues to be the most serious drug problem on college campuses. Drinking more alcohol than the body’s enzymes can detoxify damages the body, and it can be lethal in the short term and the long term. Section 4.2  Energy cannot be created or destroyed (first law of thermodynamics), and it tends to disperse spontaneously (second law of thermodynamics). Energy can be transferred between systems or converted from one form to another (for example, potential energy can be converted to kinetic energy), but some disperses, often as heat, during every such exchange. Work occurs as a result of energy transfers. Sustaining life’s organization requires ongoing energy inputs. Energy flows in one direction through the biosphere, starting mainly from the sun, then into and out of ecosystems. Producers and then consumers use the energy to drive cellular work. Section 4.3  In chemical reactions, reactants are converted to products. Some reactions require a net energy input to proceed, and others end with a net energy release. Both types of reactions have activation energy. Cells store energy in chemical bonds by building organic compounds (in energy-requiring reactions), and they retrieve the stored energy by breaking the compounds apart (in energy-releasing reactions). Section 4.4  Enzymes greatly enhance the rate of reactions without being changed by them. Each enzyme has an active site that is complementary in shape, size, polarity, and charge to its substrate, and each works best within a characteristic range of conditions, including temperature, salt concentration, and pH. Cellular mechanisms that influence enzyme function allow cells to conserve energy and resources by producing only what they need at a given time. Many enzymes can be activated or inactivated when specific ions or molecules bind to them. Cofactors associate with enzymes and assist their function. Some cofactors are metal ions; organic cofactors are called coenzymes. Many coenzymes carry chemical groups, atoms, or electrons from one reaction to another. The nucleotide ATP functions as a coenzyme in many different reactions. Phosphategroup transfers (phosphorylations) to and from ATP couple energy-releasing reactions with energy-requiring reactions. A metabolic pathway is a stepwise series of enzymemediated reactions that collectively build, remodel, or break down an organic molecule. Mechanisms that start, stop, or alter the rate of a single reaction in the series can affect the entire pathway. The products of some metabolic pathways inhibit their own production, a regulatory mechanism called feedback inhibition.

Some pathways include electron transfer chains that allow cells to harvest energy in small, usable amounts. Section 4.5  The rate and direction of diffusion are influenced by temperature and regional differences in concentration and charge. A lipid bilayer is selectively permeable. Gases and nonpolar molecules move freely through it; water and some other small polar molecules can slowly diffuse through. Lipid bilayers are impermeable to ions and large polar molecules. When a lipid bilayer separates two fluids of different solute concentrations, water diffuses across it, from the hypotonic to the hypertonic fluid. There is no net movement of water between isotonic solutions. Osmosis, the movement of water across a membrane, is opposed by turgor pressure. Section 4.6  Transport proteins move particular ions or molecules across membranes. In facilitated diffusion, a solute binds to a transport protein that releases it to the opposite side of the membrane. The movement is a type of passive transport (no energy input is required). With active transport, a transport protein uses energy (often in the form of a phosphate-group transfer from ATP) to pump a solute across a membrane against its concentration gradient. Exocytosis and endocytosis are vesicle-based transport mechanisms that move substances in bulk across plasma membranes. Cells expel substances with exocytosis, and they bring substances into cytoplasm with endocytosis. Some cells use phagocytosis to engulf large particles such as other cells.

Self-Quiz Answers in Appendix I 1.

is the main source of energy for the world of life. a. Food           c. Sunlight b. Water          d. ATP

2. Which of the following statements is not correct? a. Energy cannot be created or destroyed. b. Energy cannot change from one form to another. c. Energy tends to disperse spontaneously. 3. If we liken a reaction to an energy hill, then a reaction that is an uphill run. a. requires energy      c. runs backward b. releases energy       d. uses an enzyme and a cofactor

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Energy and Metabolism  Chapter 4  91 

4. In an energy-requiring reaction, activation energy is a bit like . a. a burst of speed at the top of a reaction b. products coasting downhill c. a hill that reactants must climb 5.

are always changed by participating in a reaction. a. Enzymes   b. Phosphate groups   c. Reactants

6. Name an environmental factor that influences enzyme function. 7. A metabolic pathway . a. may build or break down molecules b. generates heat c. can include an electron transfer chain d. all of the above 8. Which of the following statements is not correct? a. Some metabolic pathways are cyclic. b. Glucose can diffuse directly through a lipid bilayer. c. All coenzymes are cofactors. d. Osmosis is an example of diffusion. 9. A solute tends to diffuse from a region where it is concentrated to another where it is concentrated. a. more, less b. less, more 10.

cannot diffuse directly through a lipid bilayer. a. Water c. Ions b. Gases d. Nonpolar molecules

11. Immerse a human red blood cell in a hypotonic solution, and water . a. diffuses into the cell c. shows no net movement b. diffuses out of the cell d. moves in by endocytosis 12. Internal fluid pressure against a cell wall or membrane is called . a. osmosis c. diffusion b. turgor pressure d. osmotic pressure 13. A transport protein requires ATP to pump sodium ions across a membrane. This is a case of . a. passive transport c. facilitated diffusion b. active transport d. osmosis 14. Vesicles form in a. endocytosis b. exocytosis

. c. phagocytosis d. all of the above

15. Match each term with its most suitable description. reactant a. assists enzymes b. forms at reaction’s end phagocytosis c. enters a reaction first law of d. currency in a cell’s thermodynamics energy economy product e. one cell “eats” another cofactor f. energy cannot be concentration gradient created or destroyed passive transport g. motivates diffusion cyclic pathway h. no energy input required ATP i. goes in circles

CRITICAL THinking Figure 4.26  Alcohol flushing reaction. For some people, drinking even a small amount of alcohol causes the face to redden. Left, before drinking. Right, after drinking. Source: Brooks P. J., Enoch M.-A., Goldman D., Li T-K., Yokoyama A. (2009). “The Alcohol Flushing Response: An Unrecognized Risk Factor for Esophageal Cancer from Alcohol Consumption,” PLoS Med 6(3): e1000050. https://doi.org/10.1371 /journal.pmed.1000050

1. For some people, drinking even a small amount of alcohol causes the face to redden (Figure 4.26). This effect is informally called “Asian flush” because it occurs in a very high percentage of people with East Asian descent. The flushing reaction is a physiological response to an overdose of acetaldehyde. What might cause acetaldehyde to accumulate to toxic levels after drinking a small amount of alcohol? 2. Beginning physics students are often taught to remember the basic concepts of thermodynamics with two phrases: First, you can never win. Second, you can never break even. Explain. 3. Jessica wanted to make gelatin shots for her next party, but felt guilty about encouraging her guests to consume alcohol. She tried to compensate for the toxicity of the alcohol by adding pieces of healthy fresh pineapple to the shots, but when she did, the gelatin never solidified. What happened? Hint: Gelatin is a mixture of proteins. 4. The enzyme catalase combines two hydrogen peroxide molecules (H2O2 + H2O2) to make two molecules of water (2H2O). A gas also forms. What is the gas?

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

5 Photosynthesis

5.1

A Burning Concern  93

5.2

Overview of Photosynthesis  95

5.3

Light Energy  97

5.4

Light-Dependent Reactions  99

5.5

Light-Independent Reactions  102

Energy flow through nearly all ecosystems begins when producers harvest the energy of sunlight to make sugars by way of photosynthesis. Plants are the main producers on land.

Concept Connections biletskiy/Shutterstock.com

Photosynthesis is a pathway (Section 4.4) by which producers (1.3) capture the energy of light (4.2) and store it in the bonds (4.3) of sugars (2.7). Energy stored in sugars can be released to power other pathways (6.2) that sustain entire ecosystems (18.5). The chapter revisits experimental design (1.6), electron energy (2.2), membrane proteins (3.3), chloroplasts (3.5), extracellular matrix (3.6), enzymes (4.4), concentration gradients (4.5), and active transport (4.6).

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

Photosynthesis  Chapter 5  93  

Application 5.1  A Burning Concern

Atmospheric CO2 content (ppm)

Your body is about 9.5 percent carbon by weight, which means that you contain an enormous number of carbon atoms. Where did they all come from? Those atoms may have passed through other consumers before you ate them, but originally they were components of producers. The vast majority of produc­ ers get their carbon from carbon dioxide (CO2), a gas in air. Thus, your carbon atoms—and those of most other organisms on land—were recently part of Earth’s atmosphere, in molecules of CO2. Most of the producers that humans eat are plants. Plants make their own food by photosynthesis, a metabolic pathway that uses light energy to drive the assembly of carbohydrates—sugars—from carbon dioxide and water. Photosynthesis removes carbon dioxide from the atmosphere, and locks its carbon atoms in organic compounds that make up living things. When plants and other organisms break down organic compounds for energy, carbon atoms are released in the form of CO2, which then reenters the atmosphere. For billions of years, these two processes have constituted a more or less balanced cycle of the biosphere: The amount of carbon dioxide that photo­ synthesis removes from the atmosphere is roughly the same amount that A. Antarctic ice core sample. The bubbles are pockets of organisms release back into it. At least it was, until humans came along. air that became trapped in the ice when it formed—tiny samples of Earth’s atmosphere. The deeper the ice, the As early as 8,000 years ago, humans began older the air in the bubbles. burning forests to clear land for agriculture. When trees and other plants burn, most of the carbon in their tissues is released into the atmosphere 400 as CO2. Fires that occur naturally release carbon dioxide the same way. However, we burn a lot more 350 today than our ancestors ever did. In addition to 300 wood, we are burning fossil fuels—coal, petroleum, and natural gas—to satisfy our growing population’s 250 increasing demand for energy. Fossil fuels are the organic remains of ancient organisms. When they 200 burn, carbon that has been locked in organic mol­ ecules for hundreds of millions of years is released 150 0 800,000 600,000 400,000 200,000 into the atmosphere as CO2. Years before present Fossil fuel use began in earnest in the mid1800s, and has increased every year since then. B. The CO2 level has fluctuated over the last 800,000 years, but never rose above 300 ppm (parts per million) until the early 1900s. In the last 150 years, we have released enough carbon In 2017 alone, we burned enough of these fuels to dioxide to raise the atmospheric level above 400 ppm. Our use of fossil fuels is by far the release almost 40 billion tons of CO2. largest source of these emissions. Measurements that are less direct than ice core data indicate We have been adding far more carbon dioxide that the last time the atmosphere held 400 ppm of CO2 was almost 3 million years ago. to the atmosphere than photosynthetic organisms have been removing from it, so the atmosphere’s Figure 5.1  Ice core data reveal the carbon dioxide content of the atmosphere for the last CO2 content has been rising dramatically. Today, 800,000 years. the carbon dioxide level is higher than it has been (A) www.photo.antarctica.ac.uk; (B) Data source: Bereiter, B., Eggleston, S., Schmitt, J., Nehrbass-Ahles, C., Stocker, T. F., Fischer, H., Kipfstuhl, for at least 800,000 years (Figure 5.1). How do we S., and Chappellaz, J., 2015. Revision of the EPICA Dome C CO record from 800 to 600 kyr before present. Geophysical Research Letters. doi: 10.1002/2014GL061957. know? Tiny pockets of Earth’s ancient atmosphere remain in Antarctica, preserved in ice that has Figure It Out: How much did the carbon dioxide content of the atmosphere been accumulating in layers, year after year. increase between 25,000 years ago and today? Air and dust trapped in each layer reveal the 2

Answer: It has doubled.

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94  Unit 1 How Cells Work

1.0 1.0

425 425 400 400

0.5 0.5

Atmospheric CO2 content (ppm)

Temperature anomaly (°C)

Temperature anomaly (°C)

lowerlower thanthan average average temperature temperature atmospheric atmospheric CO2 CO content 2 content

375 375 350 350

0.0 0.0

325 325 300 300

2018

2010 2018

2000 2010

1990 2000

1980 1990

1970 1980

1960 1970

1950 1960

1940 1950

1930 1940

1920 1930

1910 1920

1900 1910

1890 1900

275 275 1880 1890

1880

-0.5 -0.5

Atmospheric CO2 content (ppm)

higher higher thanthan average average temperature temperature

composition of the atmosphere during the time the layer formed. To access the layers for analysis, researchers drill vertically through the ice and remove long cylinders called ice cores. The deeper the ice, the older the layers. The deepest layer they have found is 800,000 years old. Carbon dioxide is one of the gases that traps heat in the atmosphere, so the increasing carbon dioxide level is causing a parallel increase in global temperatures (Figure 5.2). This, in turn, is reshaping climates all over the world, with increasingly dire effects for us and other life on Earth. Chapter 19 returns to the topic of climate change.

Year Year

A. Direct A. Direct measurements measurements sincesince 18801880 reveal reveal the correlation the correlation between between rising rising CO2 CO content of the of the 2 content atmosphere atmosphere and and increasing increasing global global temperatures. temperatures. Temperature Temperature anomaly anomaly means means a deviation a deviation in in temperature temperature fromfrom a 100-year a 100-year average. average.

B. Seemingly small changes in global temperature have major effects in the environment. For example, rising temperatures are causing the western United States to become hotter and drier, so wildfires are increasing in severity. Between 1984 and 2015, the annual amount of forest burned by wildfire in this region doubled—an effect of a 0.64°C (1.15°F) increase in global temperature during the same period. This photo shows part of the 2018 Mendocino complex wildfire that burned more than 450,000 acres in California.

Figure 5.2  Cause and effect: Rising carbon dioxide content of the atmosphere is fueling climate change. (A) Data source, CO2: Dr. Pieter Tans, NOAA/ESRL (www.esrl.noaa.gov/gmd/ccgg/trends/) and Dr. Ralph Keeling, Scripps Institution of Oceanography (scrippsco2.ucsd.edu/); and Etheridge, D. M., Steele, L. P., Langenfelds, R. L., Francey, R. J., Barnola J. M., and Morgan, V. I., 1996. Natural and anthropogenic changes in atmospheric CO2 over the last 1000 years from air in Antarctic ice and firn. Journal of Geophysical Research, 101:4115–4128. Data source, temperature: NOAA National Centers for Environmental information, Climate at a Glance: Global Time Series, published October 2018, retrieved on October 18, 2018 from https://www.ncdc.noaa.gov/cag/; (B) Mark McKenna/Zuma Press/TNS

Discussion Questions 1. Not all of the carbon dioxide in the atmosphere was released from burning fossil fuels. A lot of it was released by natural processes such as breakdown of organic molecules by living organisms. How do you think researchers determine the origin of CO2 molecules in a sample of air? 2. Biological materials harvested from agricultural products are processed into biofuels—oils, gases, and alcohols that we use as fuel. Biofuels made from photosynthetic organisms such as plants are carbon-neutral, which means the amount of CO2 released when we burn them is the same amount of CO2 they removed from the atmosphere by photosynthesis. Most biofuels are produced from food crops, and growing food crops for our expanding population is using up one of Earth’s limited resources: physical space suitable for agriculture. Do you think biofuels are a good alternative to fossil fuels? 3. Researchers are attempting to develop technologies that can remove carbon dioxide from the atmosphere. Would implementing these negative emissions technologies have a negative effect on individual or global efforts to reduce carbon emissions? 4. The CO2 content of the atmosphere has fluctuated with some regularity over the last 800,000 years. Why do you think this fluctuation has occurred?

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Photosynthesis  Chapter 5  95  

5.2  Overview of Photosynthesis Learning Objectives ●●

Explain why we say that photosynthesis feeds most life on Earth.

●●

Describe the basic structure of the thylakoid membrane in a plant cell.

●●

Write an equation that summarizes the overall pathway of photosynthesis.

●●

Explain the function of stomata.

Storing Energy in Sugars  All life is sustained by inputs of energy, but not all forms of energy can sustain life. Sunlight, for example, is abundant here on Earth, but it cannot directly power energy-requiring reactions that all organisms must run to stay alive. For this purpose, the energy of light must first be converted to the energy of chemical bonds (Section 4.3). Unlike light, chemical energy can power the reactions of life, and it can be stored for later use. Autotrophs and Heterotrophs  Energy flow through ecosystems on Earth begins with autotrophs, which are producers (Section 1.3). All organisms need carbon to

build the molecules of life, and autotrophs obtain it from an inorganic molecule: carbon dioxide (CO2). All organisms also need energy; plants and almost all other autotrophs obtain their energy by photosynthesis. Photosynthesis harnesses the energy of sunlight to drive the assembly of sugars from CO2 and water. The sugars can be stored as polysaccharides for later use, remodeled into other organic compounds, or broken down to release energy held in their bonds (a topic of Chapter 7). Heterotrophs (consumers) cannot use CO2 as a carbon source; they get their carbon from organic molecules. Almost all heterotrophs get their energy from these molecules too. Thus, directly or indirectly, photosynthesis feeds most life on Earth (Figure 5.3).

carbon dioxide

sunlight

oxygen organic molecules

water

Stages of Reactions The main pathway of photosynthesis is often summarized by this equation: CO2  H2O

light energy

sugars



O2

(CO2 is carbon dioxide, H2O is water, and O2 is oxygen gas). Photosynthesis is not a single reaction, however; it is a metabolic pathway with many reactions that occur in two stages. The reactions of the first stage require light, so they are collectively called the light-dependent reactions. The “photo” in photosynthesis means light, and it refers to the conversion of light energy to chemical energy during this stage. The main light-dependent pathway produces O2 and the coenzymes ATP and NADPH. The “synthesis” part of photosynthesis refers to the sugar-building reactions of the second stage. These are collectively called the light-independent reactions because light energy does not power them. Instead, they run on energy delivered by the coenzymes that formed during the first stage. At the end of the second stage, the coenzymes are recycled to work again in the light-dependent reactions.

Sites of Photosynthesis In plants and photosynthetic protists, and cyanobacteria, the light-dependent reactions are carried out by molecules embedded in a thylakoid membrane. In eukaryotes, the membrane occurs in chloroplasts, and it encloses a continuous

Figure 5.3  Photosynthesis sustains life. Most autotrophs sustain themselves by carrying out photosynthesis, a pathway that uses the energy of light, and carbon from carbon dioxide, to build organic molecules. Most heterotrophs get their energy and carbon from organic molecules assembled by other organisms.

autotroph  Producer. Organism that makes its own food using energy from the environment and carbon from CO2. heterotroph  Consumer. Organism that obtains carbon from organic molecules. photosynthesis  Metabolic pathway by which most autotrophs use the energy of light to make sugars from carbon dioxide and water. thylakoid membrane  Inner membrane system of chloroplasts and cyanobacteria; site of lightdependent reactions of photosynthesis.

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

96  Unit 1 How Cells Work

outer membranes thylakoid membrane thylakoid compartment stroma

A. Chloroplasts in leaf cells of a moss.

stroma

B. A plant chloroplast has three membranes.

C. Part of the thylakoid membrane, cutaway view.

Figure 5.4  Zooming in on chloroplast structure. In plants and other eukaryotes, photosynthesis occurs in chloroplasts. The light-dependent reactions take place at the thylakoid membrane. The light-independent reactions run in stroma. Michael Eichelberger/Visuals Unlimited.

internal compartment. Plant chloroplasts have two outer membranes enclosing a single thylakoid membrane that is folded into stacks of interconnected disks (Figure 5.4). The thylakoid membrane is suspended in a cytosol-like fluid called stroma, as are the chloroplast’s own DNA and ribosomes. The light-independent reactions take place in stroma. Chloroplasts are descendants of ancient cyanobacteria, which is why photosynthesis in eukaryotes is similar to cyanobacterial photosynthesis. Modern cyanobacteria have multiple thylakoid membranes suspended in their cytoplasm.

Stomata Most land plants have a thin, waterproof cuticle that limits evaporative water loss from their aboveground parts (Section 3.6). Gases cannot diffuse across the cuticle, but CO2 needed for the light-independent reactions must enter the plant, and O2 produced by the light-dependent reactions must escape it. Thus, the surfaces of leaves and stems are studded with tiny, closable pores called stomata (singular, stoma; Figure 5.5). Stomata close to conserve water on hot, dry days. They open to allow CO2 from the air to diffuse into the plant’s tissues, and O2 to diffuse in the other direction. Thus, stomata balance a plant’s need for gas exchange with its requirement for water.

Take-Home Message 5.2 ●●

●●

●● ●●

Figure 5.5  Stomata on the surface of a leaf. When these tiny pores close, they conserve water. When they open, they allow gas exchange between the plant’s internal tissues and air. The exchange is required for photosynthesis.

●●

●●

Autotrophs (producers) obtain carbon from CO2. Almost all use photosynthesis to obtain energy from sunlight. Heterotrophs (consumers) obtain carbon from organic molecules. Almost all get energy from these molecules too. Photosynthesis harnesses the energy of light to produce sugars from CO2 and water. Photosynthesis reactions occur in two stages. The light-dependent reactions use light energy to produce coenzymes (the main pathway also produces O2). These coenzymes power the light-independent reactions, which produce sugars. The light-dependent reactions occur at a thylakoid membrane, which, in eukaryotes, is inside chloroplasts. In chloroplasts, the light-independent reactions occur in stroma. Stomata on plant surfaces close to conserve water. They open to allow gas exchange required for photosynthesis.

Top, canstockphoto.com; bottom, D. Kucharski K. Kucharska/Shutterstock.com

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5.3  Light Energy

pigment  Organic molecule that can absorb light of certain wavelengths. Wavelengths that are not absorbed impart a characteristic color.

Learning Objectives ●●

Explain the relationship between light wavelength and energy.

●●

Describe pigments.

●●

Explain why organisms use different pigments for photosynthesis.

stomata  Singular, stoma. Closable pores on the surface of aboveground plant parts. When open, they allow the plant to exchange gases with air. When closed, they limit water loss.

To understand how photosynthesis works, you need to understand a little about light. Light is electromagnetic radiation, a type of energy that moves through space in waves, like waves move across an ocean. The distance between the crests of two successive waves is called wavelength, and it is measured in nanometers (nm). Light travels in different wavelengths. Wavelength and energy are related: The shorter the wavelength, the higher the energy. All light of the same wavelength has the same amount of energy.

stroma  Cytosol-like fluid between the thylakoid membrane and the two outer membranes of a chloroplast. wavelength  Distance between the crests of two successive waves.

Visible Light Light that is visible to the human eye is a small part of the spectrum of electromagnetic radiation emitted by the sun (Figure 5.6). Visible light travels in wavelengths between 380 and 750 nm, and it is the main form of energy that drives photosynthesis. Our eyes perceive particular wavelengths in this range as different colors; a combination of all of these wavelengths appears white. White light separates into its component colors when it passes through a prism, or raindrops that act as tiny prisms. A prism bends longer wavelengths more than it bends shorter ones, so a rainbow of colors forms.

Photosynthetic Pigments Photosynthesis requires the use of pigments to trap the energy of visible light. Pigments are organic molecules that selectively absorb light of specific wavelengths, a bit like antennas specialized for receiving light. The light-trapping region of a pigment molecule has a special structure that allows electrons to move freely between its atoms. Only light with exactly enough energy to boost one of these electrons to a higher energy level (shell) is absorbed, which is why a pigment absorbs light of only certain wavelengths.

Figure 5.6  Properties of light.

visible light gamma rays

X-rays

ultraviolet (UV) radiation

near-infrared radiation

infrared radiation

microwaves

longest wavelengths (lowest energy)

shortest wavelengths (highest energy)

400 nm

radio waves

500 nm

600 nm

700 nm

B. Light’s wavelength and energy are related. The shorter the wavelength, the greater the energy. Thus, violet light has more energy than blue light, and so on.

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energy

A. Electromagnetic radiation moves through space in waves that we measure in nanometers (nm). Visible light makes up a very small part of this energy. Raindrops or a prism can separate visible light’s different wavelengths, which we see as different colors. About 25 million nanometers are equal to 1 inch.

Amount of light absorbed

98  Unit 1 How Cells Work

chlorophyll a chlorophyll b

nm: 400

chlorophyll f

phycoerythrin phycocyanin

β-carotene

500

600

700

Figure 5.7  Photosynthetic pigments. The curves in this graph show the efficiency with which a few photosynthetic pigments absorb different wave­ lengths of visible light. Using a combination of pigments maximizes the range of wavelengths that an organism can capture for photosynthesis.

Wavelengths of light that are not absorbed give each pigment its characteristic color. The main photosynthetic pigment in eukaryotes and cyanobacteria is chlorophyll a. Chlorophyll a absorbs all wavelengths of visible light except green, so this pigment appears green to us. Accessory Pigments  In addition to chlorophyll a, most photosynthetic organisms use accessory pigments, including other chlorophylls. Using accessory pigments expands the range of wavelengths they can capture for photosynthesis (Figure 5.7). Different species use different combinations of pigments for photosynthesis. Like all organisms, photosynthesizers are adapted to the particular environments in which they live, and light that reaches different environments varies in its proportions of wavelengths. Consider that seawater absorbs green and blue-green light less efficiently than other colors. Thus, more green and blue-green light penetrates deeper ocean water. Algae that live in deep water tend to be rich in accessory pigments that absorb green and blue-green light, so they appear red to us (Figure 5.8). Additional Roles  In plants, accessory pigments have roles in addition to photo-

synthesis. Appealing colors, for example, attract pollinators to flowers and animals to ripening fruits. You are already familiar with accessory pigments because their color is visible in many everyday plant products. Oranges, for example, are orange because they contain beta-carotene (β-carotene), which neutralizes free radicals and also has roles in signaling pathways between chloroplast and nucleus. Roses are red and violets are blue because their cells make anthocyanin, a natural sunscreen.

Fall Colors

Figure 5.8  An organism’s photosynthetic pigments adapt it to life in a particular environment. Algae such as this Polysiphonia that can live far below the surface of the ocean tend to be rich in phycoerythrin, phycocyanin, and other pigments that absorb green and blue-green light. These are the wavelengths of visible light that penetrate water most efficiently. F. Neidl/Shutterstock.com

In most plants, chlorophylls are usually so abundant that their green color masks the colors of the other pigments. Plants that change color during autumn are preparing for a period of dormancy; they conserve resources by moving nutrients from tender parts that would be damaged by winter cold (such as leaves) to protected parts (such as roots). Chlorophylls are not needed during dormancy, so they are disassembled and their components recycled. Yellow and orange accessory pigments are also recycled, but not as quickly as chlorophylls. Their colors begin to show as the chlorophyll content declines in leaves (Figure 5.9). In some plants, anthocyanin synthesis Figure 5.9  Accessory pigments become visible in fall. Chlorophyll a, the main photosynthetic pigment in most organisms, is green. Accessory pigments become visible in many plants as they prepare for dormancy in fall. Photobac/Shutterstock.com

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Photosynthesis  Chapter 5  99  

also increases just before dormancy, and this pigment adds red and purple tones to turning leaf colors.

Take-Home Message 5.3 ●●

●●

●●

●●

Light travels in waves, with wavelength related to energy. We see different wavelengths of visible light as different colors. Visible light is the main form of energy that drives photosynthesis. Pigments capture light energy for photosynthesis. Each pigment selectively absorbs light of specific wavelengths. The main photosynthetic pigment in eukaryotes and cyanobacteria is chlorophyll a. Accessory pigments have additional roles. Using a combination of pigments allows a photosynthetic species to efficiently capture the wavelengths of light available in its typical environment.

5.4  Light-Dependent Reactions Learning Objectives ●●

Describe the conversion of light energy to chemical energy during photosynthesis.

●●

Explain why oxygen forms during light-dependent reactions.

●●

Describe electron transfer phosphorylation.

When a pigment absorbs light, one of its electrons jumps to a higher energy level. The electron quickly drops back down to a lower shell by emitting its extra energy. In the thylakoid membrane, energy emitted by a pigment’s electron is not lost to the environment. In this special membrane, photosynthetic pigments occur in clusters held together by proteins. These clusters can hold on to the emitted energy by passing it back and forth, a bit like volleyball players pass a ball among team members.

Photosystems In addition to pigment clusters, a thylakoid membrane includes thousands of photosystems, each a very large complex of pigments, proteins, and cofactors. Two chlorophyll a molecules in the center of a photosystem are held closely together in a particular arrangement that gives the pair special properties. This “special pair” acts as a unit, and it can capture energy being passed around the thylakoid membrane. When a special pair absorbs this energy, one of its electrons jumps to a higher energy level, but does not emit the extra energy. Instead, the excited electron pops off of the special pair and enters a nearby electron transfer chain, taking its extra energy and its negative charge with it. The special pair is left with an unpaired electron and a positive charge. Electrons are the basis of chemical bonds, so this separation of charge marks the conversion of light energy to chemical energy.

The Noncyclic Pathway Photosystems operate in two versions of light-dependent reactions, a cyclic pathway and a noncyclic pathway. Both produce ATP. In addition to ATP, the noncyclic pathway also produces oxygen (O2) and NADPH. Many bacterial species use only the cyclic pathway, so these organisms release no oxygen during photosynthesis. Plants, photosynthetic protists (such as algae), and cyanobacteria use both. Here, we focus on the noncyclic pathway.

chlorophyll a  Main photosynthetic pigment in eukaryotes and cyanobacteria.

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100  Unit 1 How Cells Work

The noncyclic pathway involves two types of photosystems, type I and type II (named in order of their discovery). During the reactions (Figure 5.10), a photosystem II absorbs light energy, then releases electrons that travel through an electron transfer chain to photosystem I. Photosystem I absorbs light energy, then releases electrons that travel through a second electron transfer chain. The electrons end up in NADPH. Photosystem II Releases Electrons  The reactions of the noncyclic pathway begin

when the special pair in a photosystem II absorbs energy 1 and releases an excited electron. The electron immediately enters a nearby electron transfer chain in the thylakoid membrane.

Oxygen Forms  A special pair that has lost an electron must be supplied with a

replacement electron from another molecule. Photosystem II pulls replacement electrons from water molecules in the thylakoid compartment. Losing electrons causes water molecules to break apart into hydrogen ions and oxygen atoms 2. The hydrogen ions remain in the thylakoid compartment; the oxygen atoms combine as oxygen gas (O2), which diffuses out of the cell.

A Hydrogen Ion Gradient Forms  Meanwhile, the excited electron released by

photosystem II moves through the electron transfer chain 3. As the electron passes from one molecule in the chain to the next, it emits its extra energy. Molecules of the chain use this energy to actively transport hydrogen ions (H+) across the membrane, from the stroma to the thylakoid compartment 4. Thus, the movement of electrons through the electron transfer chain sets up and maintains a hydrogen ion gradient across the thylakoid membrane.

NADPH Forms  Photosystem I accepts electrons at the end of the electron transfer

chain, and these electrons replenish electrons lost by this photosystem’s special pair. Thus, while water provides replacement electrons for photosystem II, photosystem II provides replacement electrons for photosystem I. The noncyclic pathway continues as the special pair of a photosystem I absorbs light energy and releases an excited electron 5. The electron immediately enters a second electron transfer chain. At the end of this chain, the coenzyme NADP+ accepts electrons along with H+, thereby becoming NADPH 6: NADP+ + electrons + H+

NADPH

ATP Forms  The hydrogen ion gradient that forms across the thylakoid membrane

electron transfer phosphorylation  Process by which electron flow through electron transfer chains sets up a hydrogen ion gradient that drives ATP formation.

is a type of potential energy that can be tapped to make ATP. The H+ ions want to follow their concentration gradient by moving back into the stroma, but ions cannot diffuse through the lipid bilayer (Section 4.5). H+ leaves the thylakoid compartment only by flowing through ATP synthases embedded in the thylakoid membrane 7. An ATP synthase functions as both a transport protein and an enzyme: The flow of hydrogen ions through an ATP synthase causes it to phosphorylate ADP, so ATP forms in the stroma 8. Any process in which the flow of electrons through electron transfer chains drives the formation of ATP is called electron transfer phosphorylation. At this point in photosynthesis, light energy has been converted to the chemical bond energy of ATP. That energy is now available to drive sugar synthesis and other processes in the cell.

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Photosynthesis  Chapter 5  101  

CLOSER LOOK Figure 5.10  Light-dependent reactions of photosynthesis, noncyclic pathway.

Figure It Out: What is the immediate source of replacement electrons for PSI?

Answer: An electron transfer chain.

1 A photosystem II (PSII) absorbs light energy and releases an electron.

1 energy thylakoid

stroma

5 A photosystem I

from PSII enter an electron transfer chain in the thylakoid membrane.

3 electron

5 energy

H+

transfer chain

6

e–

electron transfer chain

causes ATP synthases to phosphorylate ADP, so ATP forms in the stroma.

NADPH NADP1 1 H+

H+

ATP synthase

ATP

8

ADP 1 Pi

4

e–

PSI

e–

e–

e–

H+ H+ H+ H+ H+

H 2O

8 Hydrogen ion flow

through an electron transfer chain, then combine with NADP1 and H1, so NADPH forms.

e–

ee––

2

6 Electrons from PSI move

(PSI) absorbs light energy and releases an electron.

e–

PSII thylakoid compartment

3 Electrons released

O2

2 PSII pulls replacement electrons from water

molecules, which then break apart into oxygen atoms and hydrogen ions. The oxygen atoms combine as O2, which diffuses out of the cell.

7

H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+

4 Energy emitted by electrons moving through

the electron transfer chain is used to actively transport hydrogen ions (H1) from the stroma to the thylakoid compartment. A hydrogen ion gradient forms across the thylakoid membrane.

7 Hydrogen ions in the

thylakoid compartment follow their gradient across the thylakoid membrane by flowing through ATP synthases.

Figure Summary ATP and oxygen gas are produced in this pathway.

Photosynthesis in the Dark Some photosynthetic organisms can adapt themselves to different environments by swapping out their special pairs. Researchers recently discovered that one species of bacteria can carry out light-dependent reactions in the dark. In sunlight, the bacteria make special pairs for their photosystems using the standard chlorophyll a. When moved to an environment where there is no visible light (such as the interior of a warm laboratory cabinet), they start making special pairs with another pigment, chlorophyll f. These “special” special pairs absorb near-infrared light, which we feel as heat but can’t see. It had long been thought that only visible light could power the light-dependent reactions, so this discovery is changing the way we understand photosynthesis here on Earth—and also the way we evaluate other planets for the potential to sustain life.

Electrons e– that travel through two different electron transfer chains end up in NADPH. Pi is an abbreviation for phosphate group.

Take-Home Message 5.4 ●●

●●

●●

The light-dependent reactions convert light energy to chemical energy. The main (noncyclic) pathway produces ATP, NADPH, and oxygen (O2). Photosynthetic pigments in the thylakoid membrane capture light and transfer its energy to photosystems. When a photosystem absorbs light energy, it releases excited electrons that enter electron transfer chains in the membrane. The flow of electrons through electron transfer chains sets up a hydrogen ion gradient that drives ATP formation, a process called electron transfer phosphorylation.

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102  Unit 1 How Cells Work

5.5  Light-Independent Reactions Learning Objectives

g water light energy

lightdependent reactions

CO2 water

NADPH, ATP NADP+, ADP

lightindependent reactions

●●

State the role of carbon fixation in photosynthesis.

●●

Explain how coenzymes connect the light-dependent reactions with the Calvin–Benson cycle.

●●

Describe photorespiration.

You learned in Section 5.2 that the reactions of the second stage of photosynthesis are light-independent because light energy does not power them: They can run night and day. Energy that drives these reactions is provided by phosphate-group transfers from ATP, and electrons from NADPH. Both molecules are products of the light-dependent reactions (Figure 5.11).

The Calvin–Benson Cycle

chloroplast O2

sugars

Figure 5.11  Coenzymes connect the first- and secondstage reactions of photosynthesis. Light energy drives the production of ATP in the lightdependent reactions. Coenzymes that form in this stage drive sugar production in the light-independent reactions.

CO2

The light-independent reactions are collectively called the Calvin–Benson cycle (Figure 5.12). This cyclic pathway uses carbon atoms from CO2 to build the carbon backbones of sugar molecules. Extracting carbon atoms from an inorganic source (such as CO2) and incorporating them into an organic molecule is called carbon fixation. The Reactions  In chloroplasts, the Calvin–Benson cycle runs in stroma. The reactions begin when the enzyme rubisco attaches CO2 to a five-carbon organic compound called RuBP. This carbon-fixation reaction produces an unstable six-carbon molecule that immediately splits into two three-carbon molecules called PGA. NADPH and ATP are used to convert the PGA molecules to PGAL, a threecarbon sugar. Most of the PGAL is used to regenerate RuBP, the starting compound of the Calvin–Benson cycle. The remaining PGAL is exported from the chloroplast into the cell’s cytoplasm. Products  PGAL is the official product of the Calvin–Benson cycle, and it can be

PGA

RuBP

ATP Calvin–Benson Cycle

ADP + Pi NADPH

ADP + Pi ATP

NADP+

assembled into a variety of other carbohydrates, including glucose. Plant cells make sucrose, their main sugar, from PGAL. Cells in photosynthetic parts of a plant (such as leaves) export sucrose for transport to nonphotosynthetic parts (such as roots). When sucrose production exceeds demand—for example, during a sunny day when the light-dependent reactions are running at top speed—some PGAL molecules are not exported from chloroplasts, and these are assembled into starch. Starch is disassembled at night, and its monosaccharide monomers are used to produce sucrose. An uninterrupted supply of sucrose can sustain the plant’s metabolism even in the dark.

Efficiency of Sugar Production

PGAL

sucrose

Figure 5.12  The Calvin–Benson cycle. This sketch shows a cross section of a chloroplast with Calvin–Benson reactions cycling in the stroma. The reactions run three times to produce one three-carbon sugar (PGAL). Black balls signify carbon atoms. Water is a substrate in several reactions, but not shown for clarity.

When a plant’s stomata are open, its photosynthetic tissues can exchange gases with air: CO2 required for the Calvin–Benson cycle can diffuse into photosynthetic tissues, and O2 produced by the light-dependent reactions can diffuse out of the plant. When stomata close to conserve water on hot, dry days, this gas exchange comes to a halt. Both stages of photosynthesis run during the day. With stomata closed, the O2 level in the plant’s tissues rises, and the CO2 level declines. This outcome can reduce the efficiency of sugar production because both gases are substrates of rubisco, and they compete for its active site (Section 4.4). Rubisco starts the Calvin–Benson cycle by attaching CO2 to RuBP. It also starts a pathway called photorespiration by attaching O2 to RuBP. The rest of the photorespiration pathway converts the product of this reaction, a molecule called PG, to a substrate of the Calvin–Benson cycle.

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Photosynthesis  Chapter 5  103  

Digging Into Data Fossil Fuel Emissions

1. Approximately how much did CO2 emissions from natural gas increase between 1930 and 1990? 2. About how much CO2 was released from coal in 1970? 3. In 2015, how much CO2 was released from fossil fuel use?

40,000

coal oil

35,000

CO2 Emissions (megatons)

Early photosynthesizers, like their modern descen­­ d­ ants, used rubisco to fix carbon from carbon dioxide. Some of the organic molecules originally assembled in their light-independent reactions remain today, in the form of coal, oil, and natural gas. Burn­ ing these fossil fuels essentially reverses the process of carbon fixation: Organic molecules are broken apart, and their carbon atoms are released into the atmosphere in CO2. Since the industrial revolution, we have been burning an increasing amount of fossil fuels, so we have been releasing an increasing amount of CO2 into the atmosphere (Figure 5.13).

natural gas 30,000 25,000 20,000 15,000 10,000 5,000 0 1870

1890

1910

1930

1950

1970

1990

2010

Figure 5.13.  Global CO2 emissions from burning coal, oil, and natural gas, 1860 to 2015. The graph shows stacked emission data. One megaton = 1 million tons (2 billion pounds). Data sources: Carbon Dioxide Information Center Numeric Data Collection: Production of CO2 from Fossil Fuel Burning by Fuel Type, 1860–1982. DOI: 10.3334/CDIAC/ffe.ndp006; Boden, T. A., Marland, G., and Andres, R.J., 2016. Global, Regional, and National Fossil-Fuel CO2 Emissions. Carbon Dioxide Information Analysis Center, Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tenn., U.S.A. doi 10.3334/CDIAC/00001_V2016

ATP is required, and intermediates must be transported among three organelles. Photorespiration produces CO2 (so carbon is lost instead of being fixed), and also ammonia that must be detoxified (requiring additional ATP). These extra steps and energy requirements make photorespiration an extremely inefficient way to produce sugars. Plants compensate for the inefficiency by making a lot of rubisco: It is the most abundant protein on Earth. Synthetic Shortcuts  Researchers trying to increase productivity of food crops have introduced shortcuts into the photorespiration pathway of some plants. Like photorespiration, the altered pathways convert PG into substrates of the Calvin– Benson cycle, but they are shorter, require no ATP, and occur entirely in the chloroplast. The engineered plants produce sugars more efficiently than unmodified plants, so they grow more quickly. This research also has applications in carbon sequestration, which involves efforts to reduce climate change by removing CO2 from the atmosphere.

Take-Home Message 5.5 ●●

●● ●●

●●

NADPH and ATP produced by the light-dependent reactions power the lightindependent reactions of the Calvin–Benson cycle. The Calvin–Benson reactions collectively use carbon atoms from CO2 to build sugars. Incorporating carbon from an inorganic source into an organic molecule is called carbon fixation. When a plant’s stomata close, gas exchange required for photosynthesis ends, and photorespiration can reduce the efficiency of sugar production.

Calvin–Benson cycle  Cyclic carbon-fixing pathway that builds sugars from CO2; light-independent reactions (second stage) of photosynthesis. carbon fixation  Process in which carbon from an inorganic source such as CO2 becomes incorporated (fixed) into an organic molecule. rubisco  Carbon-fixing enzyme of the Calvin–Benson cycle.

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104  Unit 1 How Cells Work

Summary Section 5.1  By the pathway of photosynthesis, plants use the energy of light to build sugars from water and carbon dioxide (CO2). Photosynthesis removes CO2 from the atmosphere, and the metabolic activity of most organisms puts it back. Humans have been disrupting this cycle by burning fossil fuels, an activity that has been adding far more CO2 to the atmosphere than photosynthesis can remove. The resulting imbalance is the major cause of climate change. Section 5.2  Plants and other autotrophs make their own food using energy from the environment and carbon from carbon dioxide. Most autotrophs use photosynthesis to obtain energy in the form of light. Humans and almost all other heterotrophs obtain energy and carbon from organic molecules. Photosynthesis occurs in two stages. The light-dependent reactions collectively capture the energy of light, and use it to produce ATP; the main pathway also produces NADPH and O2. Coenzymes that form in the light-dependent reactions deliver energy to the light-independent reactions, which collectively build sugars from CO2 and water: g water light energy

lightdependent reactions

CO2 water

NADPH, ATP NADP+, ADP

lightindependent reactions

chloroplast O2

sugars

The light-dependent reactions are carried out by molecules in the thylakoid membrane, which, in photosynthetic eukaryotes, occurs in chloroplasts. The thylakoid membrane of chloroplasts is suspended in stroma, the site of the light-independent reactions. In land plants, gas exchange required for photosynthesis occurs through open stomata. Stomata close to conserve water. Section 5.3  Light energy travels in waves; the shorter the wavelength, the higher the energy. Wavelengths of light that we can see—visible light—drive photosynthesis. A pigment absorbs light of particular wavelengths only; wavelengths that are not absorbed give the pigment its characteristic color. The main photosynthetic pigment, chlorophyll a, absorbs violet and red light, so it appears green. Accessory pigments absorb additional wavelengths and often have other purposes. Different species use different combinations of pigments to maximize photosynthetic efficiency in particular environments.

Section 5.4  Clusters of photosynthetic pigments in the thylakoid membrane absorb light energy and pass it to photosystems. Absorbing light energy causes a photosystem’s special pair to release electrons. In the noncyclic pathway, electrons released from a photosystem II flow through an electron transfer chain. Photosystem II replaces lost electrons by pulling them from water, which then splits into H+ and O2. Electron flow through the electron transfer chain sets up a hydrogen ion gradient that drives ATP formation, a process called electron transfer phosphorylation. Energy emitted by electrons as they move through the chain drives active transport of hydrogen ions into the thylakoid compartment. The ions follow their gradient back across the membrane through ATP synthases, so ATP forms. Photosystem I accepts electrons at the end of the electron transfer chain. Electrons released from photosystem I move through a second electron transfer chain. NADP+ accepts the electrons at the end of this chain, so NADPH forms. Section 5.5  NADPH and ATP produced by the light-dependent reactions power the light-independent reactions of the Calvin– Benson cycle, which builds sugars from water and CO2. The reactions begin when the enzyme rubisco carries out carbon fixation by attaching CO2 to an organic molecule. The product of the Calvin–Benson cycle is PGAL, a three-carbon sugar that plant cells can convert to other carbohydrates. When stomata close, CO2 for the light-independent reactions cannot enter the plant’s tissues, and O2 produced by the light-dependent reactions cannot leave. When this occurs, photorespiration can make sugar production inefficient.

Self-Quiz Answers in Appendix I 1. A cat eats a bird, which ate a caterpillar that chewed on a weed. Which organisms are autotrophs? Which are heterotrophs? 2. Plants use photosynthesis. a. sunlight b. sugars

as an energy source to drive c. O2 d. CO2

3. The carbon that land plants use for photosynthesis comes from . a. glucose c. water b. the atmosphere d. soil

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Photosynthesis  Chapter 5  105  

4. In cyanobacteria and photosynthetic eukaryotes, the lightdependent reactions proceed in/at the . a. thylakoid membrane c. stroma d. cytoplasm b. plasma membrane

14. In many plants, photorespiration caused by the day can make sugar production inefficient. c. stomata closing a. photosynthesis running b. water availability d. carbon fixation

5. Closed stomata a. limit gas exchange b. permit water loss

15. Match the term with the best description. PGAL a. self-feeder autotroph b. site of photosystems heterotroph c. Calvin–Benson cycle product pigment d. consumer carbon dioxide e. carbon-fixing enzyme rubisco f. like an antenna thylakoid membrane g. big in the atmosphere wavelength h. part of a photosystem special pair i. related to energy

. c. prevent photosynthesis d. minimize photorespiration

6. Using multiple pigments allows autotrophs to a. be multicolored in fall b. live where there is no water c. fix carbon more efficiently d. use more wavelengths of light for photosynthesis 7. Which of the following statements is incorrect? a. Pigments absorb light of certain wavelengths only. b. Many accessory pigments are multipurpose molecules. c. Chlorophyll a is green because it absorbs green light. 8. In the light-dependent reactions, . a. carbon dioxide is fixed b. electrons flow through electron transfer chains c. CO2 accepts electrons

1. Plants and other photosynthesizers require carbon dioxide to produce sugars in the Calvin–Benson cycle. How do you think the current rise in the atmospheric content of CO2 will affect the light-dependent reactions in photosynthetic organisms? .

10. The atoms in the oxygen molecules released during photosynthesis come from . a. sugars c. water b. CO2 d. O2 11. In the light-dependent reactions, what accumulates in the thylakoid compartment of chloroplasts? a. sugars c. O2 b. hydrogen ions d. CO2 12. In the light-independent reactions, . a. carbon is fixed b. electrons flow through electron transfer chains c. ATP forms 13. The Calvin–Benson cycle starts with a. the absorption of light energy b. carbon fixation c. the release of electrons from photosystem II d. NADP+ formation

CRITICAL THinking

.

2. About 200 years ago, Jan Baptista van Helmont wanted to know where growing plants get the materials necessary for increases in size. He planted a tree seedling weighing 2.2 kilograms (5 pounds) in a barrel filled with 90 kilograms (200 pounds) of soil and then watered the tree regularly. After five years, the tree had gained almost 75 kilograms (164 pounds), and the soil’s weight was unchanged. He incorrectly concluded that the tree had gained all of its additional weight by absorbing water. How did the tree really gain most of its weight? 3. While looking into an aquarium, you see bubbles coming from an aquatic plant (right). What are the bubbles?

Martin Shields/Alamy Stock Photo

9. When a photosystem absorbs light, a. water forms and exits the cell b. electrons are transferred to ATP c. its special pair releases electrons d. rubisco fixes carbon

.

during

4. Under intense illumination, photosystem II stops releasing electrons to electron transfer chains; instead, it emits absorbed energy as heat. This minimizes the damage that excess light causes to photosystems. Why would too much light damage photosynthetic machinery?

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6

6.1

Risky Business  107

6.2

Carbohydrate Breakdown Pathways  108

6.3 Aerobic Respiration  109

Releasing Chemical Energy

6.4

Fermentation  113

6.5

Food as a Source of Energy  116

Like you, a dolphin breathes air to provide its cells with a fresh supply of oxygen for aerobic respiration. Carbon dioxide released from aerobically respiring cells leaves the body in each exhalation.

Concept Connections Anthony Pierce/Alamy Stock Photo

Strategies for acquiring energy and carbon differ (Sections 5.2 and 14.5), but all organisms have metabolic pathways (4.4) that harvest energy (4.2) stored in the chemical bonds of organic molecules. Some reactions (2.6, 4.3) of aerobic respiration occur in mitochondria (3.5). Carbohydrate (2.7), lipid (2.8), and protein (2.9) components of food (23.3) can be broken down for energy in aerobic respiration. The chapter also revisits free radicals (2.2), membrane transport (4.5, 4.6), photosynthesis, (5.2), and electron transfer phosphorylation (5.4).

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Releasing Chemical Energy  Chapter 6  107  

Application 6.1  Risky Business Mitochondrial diseases are genetic (heritable) disorders caused by mitochondrial defects, with symptoms that range from mild to major progressive loss of neurological and muscular function, blindness, deafness, diabetes, strokes, seizures, gastrointestinal malfunction, and disabling weakness (Figure 6.1). How can such tiny organelles have such a major impact on the body? Human cells—particularly nerve cells and muscle cells—require a lot of ATP, and mitochondria can make it very efficiently for them. Mitochondria, remember, have their own DNA and divide independently of the cell. Errors in the DNA of some mitochondria affect their ability to make ATP, but not their ability to divide. Mitochondria are passed to a cell’s descendants, and a cell that inherits a lot of defective mitochondria may not have enough ATP to function properly. A body that has a lot of malfunctioning cells doesn’t function properly either. In mitochondria, electron transfer chains in an internal membrane system set up hydrogen ion gradients that power ATP synthesis. Cellular respiration refers to pathways that use an electron transfer chain to harvest energy from organic molecules—mainly glucose—and make ATP. Oxygen molecules (O2) accept electrons at the end of mitochondrial electron transfer chains. Anything that involves or requires oxygen is said to be aerobic, so oxygen-requiring cellular respiration is called aerobic respiration. Aerobic respiration is an efficient way to make ATP, but it is also risky. Electrons occasionally escape mitochondrial electron transfer chains and combine with O2, forming reactive free radicals. Normally, the cell uses some of the free radicals for various processes, and it detoxifies the rest. This cellular balance goes awry if any components of the electron transfer chains are faulty or missing, for example as a result of errors in mitochondrial DNA. Free radicals form faster than cells can use them, an imbalance called oxidative stress. The excess of free radicals damages cells, and thus disrupts tissues they compose. Oxidative stress caused by mitochondrial malfunction is associated with mitochondrial diseases and many other conditions, includ­ing diabetes, cancer, cardiovascular disease, Alzheimer’s and Parkinson’s diseases, muscular dystrophies, and autism.

Discussion Questions 1. What normal cellular processes might require free radicals? 2. Antioxidants are molecules that prevent cellular damage caused by free radicals. Several kinds can neutralize free radicals that form during aerobic respiration. How do you think they work? 3. A child inherits mitochondria from the mother only. Some women’s eggs contain a lot of defective mitochondria, so their children have a high risk of mitochondrial disorders. A reproductive technology called mitochondrial donation can help these women have healthy babies. Children born using the technology have nuclear DNA inherited from the mother and father, and mitochondria from a donor. When they reproduce, the donated mitochondria are passed to future generations. What genetic or social implications might this technology have?

Figure 6.1  Mitochondrial disorders. Top, Carter, one of thousands of children born every year with a devastating mitochondrial disorder, died when he was 7 years old. Bottom, a cross section of a nerve cell shows how these cells are packed with mitochondria (gold). Nerve and muscle cells require a lot of ATP, so they are particularly affected by mitochondrial malfunction. Top, AP Images/Jackson Citizen Patriot, J. Scott Park; Bottom, Dr. David Furness/Wellcome Images

aerobic  Involving or requiring the presence of oxygen. aerobic respiration  Oxygen-requiring cellular respiration; breaks down glucose and produces ATP, carbon dioxide, and water. cellular respiration  Any of several pathways that break down organic molecules (typically glucose) to form ATP and include an electron transfer chain.

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108  Unit 1 How Cells Work

6.2  Carbohydrate Breakdown

GLYCOLYSIS

Pathways ACETYL–CoA FORMATION

Learning Objectives

CITRIC ACID CYCLE

●●

Write an equation that summarizes aerobic respiration.

●●

Describe the way substrates and products link photosynthesis and aerobic respiration.

●●

●●

Explain why the breakdown of glucose in fermentation yields less ATP than aerobic respiration. Describe glycolysis in terms of energy.

Overview of the Pathways

ELECTRON TRANSFER PHOSPHORYLATION

Figure 6.2  Overview of aerobic respiration. Aerobic respiration has four steps: glycolysis, acetyl–CoA formation, the citric acid cycle, and electron transfer phosphorylation. In eukaryotes only, the last three steps occur in mitochondria.

E N ERG Y OSYNTHESIS OT PH

Plants, algae, and other autotrophs harvest energy directly from the environment, and convert it to chemical bond energy of sugars (Section 5.2). They and all other organisms use energy in the bonds of sugars to power the various energy-requiring reactions that sustain life (Section 4.3). However, in order to use the energy stored in sugars, cells must first transfer it to molecules—especially ATP—that can participate directly in these reactions. Cells harvest energy from glucose by breaking its carbon backbone, one bond at a time. This releases the energy of the molecule stepwise, in small increments that can be captured for cellular work. A number of different pathways drive ATP synthesis by breaking the bonds of glucose this way. Some of these pathways involve electron transfer chains, and others do not, but all are ancient. Aerobic Respiration  Cellular respiration uses electron transfer chains to make

CO2

O2

H2O

sugars

ATP, and in many modern organisms the process is aerobic. Aerobic respiration completely breaks apart the backbone of a glucose molecule; all six carbon atoms are released from the cell in the form of carbon dioxide: C6H12O6

CO2

oxygen

carbon dioxide

1

H2O

1

ATP

water

A

N

glucose

ER

O2

1

OB

TI IC R E S PIR A

O

E NER N ERG GY Y

Figure 6.3  Substrates and products link photosynthesis with aerobic respiration. Background photo, Subbotina Anna/Shutterstock.com

anaerobic  Occurring in (or requiring) the absence of oxygen. fermentation  Any of several anaerobic pathways that break down organic molecules (typically glucose) to produce ATP without the use of an electron transfer chain. glycolysis  Set of reactions that collectively convert one molecule of glucose to two molecules of pyruvate, for a net yield of two ATP and two NADH.

The equation means that glucose and oxygen are converted to carbon dioxide and water, for a yield of ATP. Aerobic respiration is not a single reaction, however. It is a pathway with many reactions that occur in four stages: glycolysis, acetyl–CoA formation, the citric acid cycle, and electron transfer phosphorylation (Figure 6.2). These individual pathways are linked by products and substrates, and all involve electron transfers (Section 4.4). Note that carbon dioxide and water are the raw materials of photosynthesis, which produces sugars and, in most organisms, releases oxygen (Section 5.2). Aerobic respiration uses sugars and oxygen, and it produces carbon dioxide and water. Thus, raw materials and products connect the two pathways in most of the biosphere (Figure 6.3). Fermentation  Anything that occurs in (or requires) the absence of oxygen is said to be anaerobic. Fermentation refers to anaerobic pathways that break down

organic molecules—mainly glucose—to make ATP without the use of electron transfer chains. Many organisms supplement aerobic respiration with fermentation, and a few species of bacteria use it exclusively. Fermentation pathways do not break all of the carbon–carbon bonds in a glucose molecule, so they do not produce as much ATP

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

Releasing Chemical Energy  Chapter 6  109  

as aerobic respiration. Aerobic respiration is much more efficient; you and other large, multicelled organisms could not live without its higher ATP yield.

Glycolysis: Sugar Breakdown Begins Aerobic respiration and fermentation begin in cytoplasm, with glycolysis. Glycolysis is a series of reactions that produce ATP by converting one molecule of glucose to two molecules of pyruvate, an organic compound with a three-carbon backbone (Figure 6.4). Energy-Requiring Steps  A cell invests two ATP in the energy-requiring reactions

that begin glycolysis. These reactions convert one (six-carbon) glucose to two molecules of the three-carbon sugar PGAL. First, a phosphate group is transferred from ATP to the glucose, so glucose-6-phosphate forms 1. A phosphate-group transfer from a second ATP 2 produces an intermediate that splits to form two molecules of PGAL 3. Both PGAL molecules continue in the next reactions.

GLYCOLYSIS

1 A phosphate group is transferred from ATP to glucose. Glucose-6-phosphate is the product of this reaction.

Yield  Glycolysis breaks one carbon–carbon bond of a glucose molecule. The energy released by breaking that bond is captured in electrons carried by NADH, and in the high-energy bonds of ATP. The reactions use two ATP and produce four, so glycolysis yields two ATP. The two NADH and two pyruvates produced by glycolysis are required for the later stages of aerobic respiration and fermentation.

Take-Home Message 6.2 ●●

●●

●●

Cellular respiration uses electron transfer chains to harvest energy from glucose and make ATP. Aerobic respiration is a type of cellular respiration that requires oxygen. Fermentation pathways harvest energy from glucose to make ATP without the use of an electron transfer chain. These pathways are anaerobic, and they yield less ATP than aerobic respiration. Glycolysis is the first stage of aerobic respiration and fermentation. The reactions of glycolysis, which occur in cytoplasm, convert one glucose molecule to two ATP, two NADH, and two pyruvates.

ADP P

glucose-6-phosphate

2 A phosphate group is transferred from a second ATP, forming a six-carbon molecule with two phosphate groups.

ADP

P

P

3 The six-carbon molecule is split into two three-carbon PGAL.

Energy-Harvesting Steps  The remaining reactions of glycolysis harvest energy

from the two PGAL molecules. A second phosphate group is attached to each PGAL, and during this reaction electrons and hydrogen ions end up in NADH 4. Four ATP form when four phosphate groups are transferred from intermediates to ADP 5. Pyruvate is the product of the final reaction 6. Two PGAL enter these steps, so two pyruvates form.

glucose

Energy-Requiring Steps

P P 2 PGAL

Energy-Harvesting Steps

e–

4 A phosphate group is

added to each PGAL. Electrons and hydrogen ions end up in NADH during this reaction.

NADH NADH P

P

P

P 4 ADP

5 Two phosphate groups are transferred from each intermediate to two ADP, so four ATP form.

6 The product of the final reaction is pyruvate.

2 pyruvate

Figure 6.4  Glycolysis. The first stage of sugar breakdown occurs in the cytoplasm of all cells. Figure It Out: What is the net yield of ATP in glycolysis?

Answer: Two ATP per glucose

6.3  Aerobic Respiration   Learning Objectives ●●

Explain why aerobic respiration requires O2 and releases CO2.

●●

Describe the movement of energy during acetyl–CoA formation and the citric acid cycle.

●●

Describe ATP formation in the last stage of aerobic respiration.

For every molecule of glucose that enters glycolysis, two pyruvate molecules form in cytoplasm. Pyruvate can be further broken down in aerobic respiration, which

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2 Pyruvate produced by glycolysis is transported

pyruvate

into a mitochondrion.

CLOSER LOOK Figure 6.5  Aerobic respiration continues in mitochondria.

cytoplasm

outer membrane intermembrane space inner membrane matrix

ACETYL–COA FORMATION

A coenzyme A

3 A reaction splits a carbon–carbon

NADH

e– e–

bond of pyruvate, producing a molecule of CO2 and another product, acetyl–CoA, that enters the citric acid cycle. Electrons and a hydrogen ion end up in NADH.

CO2

1 An inner

acetyl–CoA

A

membrane divides the interior of a mitochondrion into two compartments. The outer compartment is called the intermembrane space. The inner compartment is called the mitochondrial matrix.

A coenzyme A

oxaloacetate citrate e– e–

NADH

Figure It Out: How many lipid bilayers does a mitochondrion have?

CITRIC ACID CYCLE

e– e–

FADH FADH22

CO2 CO2

NADH

Answer: Four

e– e–

ADP + Pi

Figure It Out: How many NADH and FADH2 form from the breakdown of two pyruvates?

4 Further reactions release

NADH

e– e–

two CO2, and electrons and hydrogen ions end up in two more NADH. Three carbons entered the reactions (in pyruvate), and three have now exited the cell (in CO2).

5 An inorganic phosphate group (Pi ) is added to ADP, so ATP forms. Electrons and hydrogen ions end up in NADH and FADH2.

Figure It Out: How many ATP form in the last three stages of aerobic respiration? Answer: About 36

Answer: 8 NADH and 2 FADH2

ELECTRON TRANSFER PHOSPHORYLATION 6 The NADH and FADH2 that

formed in previous stages deliver electrons and hydrogen ions to an electron transfer chain in the inner mitochondrial membrane. 10 NADH 2 FADH FADH22

7 Energy released by electrons moving through

the electron transfer chain fuels the active transport of hydrogen ions (H+) from the matrix to the intermembrane space. A hydrogen ion gradient forms across the inner membrane.

H+ e– e–

the end of the electron transfer chain and combines with hydrogen ions, so water forms. H2O

H+

electron transfer chain

8 O2 accepts electrons at

9 Hydrogen ion flow back to the

matrix through an ATP synthase drives the synthesis of about 34 ATP.

H+

ADP + Pi

H+

matrix e–

inner membrane

e–

e–

e– H+ H+ + H + H H+

intermembrane space

ATP synthase

O2

H+ H+ + + + H+ H+ H+ H H H

H

+ +H

H+ H+

Figure Summary After glycolysis, aerobic respiration continues with acetyl–CoA formation, the citric acid cycle, and electron transfer phosphorylation. Follow the carbons

to understand the movement of matter.

Follow the electrons

e–

to see the movement of energy.

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Releasing Chemical Energy  Chapter 6  111  

continues with acetyl–CoA formation, the citric acid cycle, and electron transfer phosphorylation. In prokaryotes, these steps occur in cytoplasm; in eukaryotes, they occur in mitochondria (Figure 6.5). Mitochondria have two membranes. The folded inner membrane divides the interior of the organelle into two compartments. The compartment between the two membranes is called the intermembrane space, and the inner compartment is the mitochondrial matrix 1.

Aerobic Respiration Continues A pyruvate molecule has two carbon–carbon bonds. The next two steps of aerobic respiration, acetyl–CoA formation and the citric acid cycle, break both of these bonds. Energy released when the bonds break is captured in ATP, and in electrons carried by NADH and another coenzyme, FADH2. All of the carbon atoms that were once part of glucose end up in CO2, which diffuses out of the cell. Acetyl–CoA Formation  In eukaryotes, aerobic respiration continues when the two pyruvate molecules that formed during glycolysis enter a mitochondrion. Pyruvate is transported across the mitochondrion’s two membranes and into the matrix 2. There, a reaction breaks one carbon–carbon bond of pyruvate, releasing a molecule of CO2 3. The remaining two-carbon fragment of pyruvate becomes attached to a coenzyme (coenzyme A, abbreviated CoA), forming a molecule of acetyl–CoA. Electrons and a hydrogen ion end up in an NADH. Both pyruvates from glycolysis undergo this reaction, so two acetyl–CoA molecules form. Each now carries two carbon atoms into the citric acid cycle. The Citric Acid Cycle  The citric acid cycle, also called the Krebs cycle, is a cyclic

pathway that releases energy by breaking apart acetyl–CoA. The energy is captured in the form of electrons carried by coenzymes, and in ATP. The cycle is named after its first intermediate: citrate, the ionic form of citric acid. It is cyclic because a substrate of the first reaction, a molecule called oxaloacetate, is a product of the last. The citric acid cycle begins when acetyl–CoA reacts with oxaloacetate to form citrate. Further reactions split CO2 from two intermediates, and electrons and hydrogen ions end up in two NADH 4. ATP, FADH2 and another NADH form in the remaining reactions 5, which also regenerate oxaloacetate. Tallying Up  Two acetyl–CoA molecules formed from the breakdown of two pyruvates, and both were dismantled in the citric acid cycle. At this point in aerobic respiration, six carbons entered the reactions as part of a glucose molecule, and six carbons have exited the cell, in six molecules of CO2. The two ATP that formed during the citric acid cycle add to the small net yield of two ATP from glycolysis. However, many coenzymes have accepted electrons: two NADH in acetyl–CoA formation, and six NADH and two FADH2 in the citric acid cycle. Add in the two NADH from glycolysis, and the full breakdown of each glucose molecule has a big potential payoff. Twelve coenzymes will deliver electrons— and the energy they carry—to the final stage of aerobic respiration, electron transfer phosphorylation.

Electron Transfer Phosphorylation The last stage of aerobic respiration is electron transfer phosphorylation (Section 5.4). In eukaryotes, this pathway occurs at the inner membrane of mitochondria.

citric acid cycle  Also called the Krebs cycle. Cyclic pathway that dismantles acetyl–CoA to produce CO2, NADH, FADH2, and ATP.

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112  Unit 1 How Cells Work A Hydrogen Ion Gradient Forms  The reactions of electron transfer phosphoryla-

tion begin with the NADH and FADH2 that formed in the earlier stages of aerobic respiration. These coenzymes now deliver their cargo of electrons and hydrogen ions to an electron transfer chain in the inner mitochondrial membrane 6. As the electrons pass through the electron transfer chain, they emit energy. Molecules in the chain harness that energy to actively transport hydrogen ions (H+) across the mitochondrion’s inner membrane, from the matrix to the intermembrane space 7. Thus, the movement of electrons through the electron transfer chain sets up and maintains a hydrogen ion gradient across the inner membrane.

Figure 6.6  Summary of aerobic respiration in eukaryotes.

GLYCOLYSIS

Glycolysis (in cytoplasm) splits a glucose molecule into 2 pyruvates. Two ATP form, and 2 NAD+ accept electrons and hydrogen ions, so 2 NADH form.

glucose (C6H12O6 ) GLYCOLYSIS

2 NADH

2

2 pyruvate

6 CO2

ACETYL–CoA FORMATION

In the mitochondrial matrix, enzymes break a carbon–carbon bond in each pyruvate, producing 2 CO2 (which leave the cell), 2 acetyl–CoA, and 2 NADH.

ACETYL–CoA FORMATION

2 NADH 2 NADH

2 acetyl–CoA

2 CO2

CITRIC ACID CYCLE

In the mitochondrial matrix, the 2 acetyl–CoA are broken down to 4 CO2 (which leave the cell). Two ATP form. The reactions also produce 6 NADH and 2 FADH2.

CITRIC ACID CYCLE

6 NADH 2 FADH2

ELECTRON TRANSFER PHOSPHORYLATION ELECTRON TRANSFER PHOSPHORYLATION

At the inner membrane, electrons from the 12 coenzymes power the synthesis of approximately 34 ATP. Water forms when oxygen accepts electrons at the end of electron transfer chains.

O2

oxygen

4 CO2 2

34

H2O

water

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Releasing Chemical Energy  Chapter 6  113  

Water Forms  Oxygen (O2) accepts electrons at the end of mitochondrial electron

transfer chains. When O2 accepts electrons, it combines with hydrogen ions to form water 8. ATP Forms  The H+ gradient that forms in electron transfer phosphorylation is a

type of potential energy that can be tapped to make ATP. The gradient motivates the movement of hydrogen ions back into the matrix, but ions cannot diffuse through a lipid bilayer (Section 4.5). The ions return to the matrix only by flowing through ATP synthases in the inner mitochondrial membrane. The flow causes these proteins to attach phosphate groups to ADP, so ATP forms 9.

Overall ATP Yield of Aerobic Respiration Glycolysis, acetyl–CoA formation, and the citric acid cycle produce four ATP for each molecule of glucose that enters aerobic respiration. The reactions also load 12 coenzymes with electrons, and these carry enough energy to fuel the synthesis of about 34 additional ATP in electron transfer phosphorylation (Figure 6.6). Thus, the breakdown of one glucose molecule by aerobic respiration yields about 38 ATP, but that number is just a theoretical maximum. The actual yield is lower because there are indirect metabolic costs associated with this pathway. For example, pyruvate and NADH must be actively transported across mitochondrial membranes, and the many enzymes that carry out the process must be assembled. Efficiency  Compared with fermentation, aerobic respiration is a much more efficient way of harvesting energy from glucose. However, energy is transferred many times during this pathway, and some disperses with every transfer (Section 4.2). Of the energy released from glucose in aerobic respiration, about 60 percent disperses as metabolic heat.

Take-Home Message 6.3 ●● ●●

●●

●●

In eukaryotes, aerobic respiration concludes in mitochondria. Acetyl–CoA formation and the citric acid cycle convert the two pyruvate that formed in glycolysis to six CO2. Two ATP, eight NADH, and two FADH2 also form. In the final stage of aerobic respiration, electrons carried by NADH and FADH2 power ATP synthesis in electron transfer phosphorylation. Oxygen is the final electron acceptor in the reactions. The maximum theoretical yield of aerobic respiration is about 38 ATP per glucose.

6.4  Fermentation LEARNING OBJECTIVES ●●

Describe ATP formation in fermentation pathways.

●●

Explain why fermentation, unlike aerobic respiration, requires no oxygen.

●●

List some commercial uses of alcoholic and lactate fermentation.

●●

Describe the way muscle cells use both aerobic respiration and fermentation.

Almost all cells can carry out fermentation. Fermentation is anaerobic, but aerobically respiring cells use it even when oxygen is present. Why would a cell carry out

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114  Unit 1 How Cells Work GLYCOLYSIS

glucose

2 2 NAD+

4

e– e–

NADH

e– e–

NADH

2 pyruvate

REGENERATING NAD+

2 CO2

e– e–

NADH

e– e–

NADH

2 NAD+ 2 ethanol

A. Alcoholic fermentation begins with glycolysis, and the final steps produce two CO2, two NAD+, and two ethanol molecules. The net yield is two ATP (from glycolysis).

fermentation when aerobic respiration yields so much more ATP? Aerobic respiration is complicated. More than 60 different types of proteins are required to carry out its many reactions, so the pathway tends to monopolize a cell’s protein-building machinery. Fermentation is much simpler. It requires relatively few proteins, so it is faster and uses fewer cellular resources. Fermentation’s fast, low-budget ATP production is advantageous in some circumstances. For example, by prioritizing fermentation over aerobic respiration, fast-growing cells can devote more of their resources to building proteins that support growth. An organic molecule (not oxygen) is the final acceptor of electrons in fermentation pathways. These pathways occur entirely in cytoplasm, and they are named after their end product. Here, we discuss two: alcoholic fermentation, which produces ethanol; and lactate fermentation, which produces lactate. Both begin with glycolysis; the remaining reactions simply serve to remove electrons and hydrogen ions from NADH, so NAD+ forms. Regenerating NAD+ allows glycolysis—and the ATP it produces—to continue. Thus, the net yield of fermentation consists of the two ATP from glycolysis.

Alcoholic Fermentation Glycolysis, the first step of alcoholic fermentation, produces 2 ATP, 2 NADH, and 2 pyruvates (Figure 6.7A). The second stage of the pathway begins with a reaction that breaks one carbon–carbon bond of pyruvate. This reaction produces a molecule of CO2 (which diffuses out of the cell) and a two-carbon intermediate. In the final reaction, electrons and hydrogen ions are transferred from NADH to the intermediate, regenerating NAD+ and producing (two-carbon) ethanol. Both pyruvates from glycolysis enter the second stage of alcoholic fermentation, so this stage produces 2 CO2, 2 NAD+, and 2 ethanol molecules. The pathway’s yield of 2 ATP comes from glycolysis. Beer and Wine Production  Fermentation by a yeast called Saccharomyces cerevisiae

(Figure 6.7B) helps us produce some foods. Beer brewers often use barley that has been germinated and dried (a process called malting) as a source of glucose for fermentation by this yeast. As the yeast cells make ATP for themselves, they also produce ethanol (which makes the beer alcoholic) and CO2 (which makes it bubbly). Flowers of the hop plant add flavor and help preserve the finished product. Winemakers use crushed grapes as a source of sugars for fermentation by Saccharomyces yeasts. The ethanol produced by the cells makes the wine alcoholic, and the CO2 is allowed to escape to the air.

B. Saccharomyces cerevisiae cells (top). One product of alcoholic fermentation by this yeast (ethanol) makes beer alcoholic; another (CO2) makes it bubbly. Holes in bread are pockets where CO2 released by fermenting yeast cells accumulated in the dough. Figure 6.7  Alcoholic fermentation. (B) Top, London Scientific Films/Oxford Scientific/Getty Images; bottom left, Elena Boshkovska/ Shutterstock.com; bottom right, optimarc/Shutterstock.com

alcoholic fermentation  Fermentation pathway that produces ATP, ethanol, and carbon dioxide. lactate fermentation  Fermentation pathway that produces ATP and lactate.

Bread  To make bread, flour is kneaded with water, yeast, and sometimes other

ingredients. Flour contains starch and a protein called gluten. Kneading causes the gluten to form polymers in long, interconnected strands that make the resulting dough stretchy and resilient. The yeast cells in the dough first break down the starch into its glucose subunits, then use the sugars for alcoholic fermentation. The CO2 they produce accumulates in bubbles that are trapped by the mesh of gluten strands. As the bubbles expand, they cause the dough to rise. The ethanol product of fermentation evaporates during baking.

Lactate Fermentation Glycolysis, the first stage of lactate fermentation, produces 2 ATP, 2 NADH, and 2 pyruvates (Figure 6.8A). The second stage of the pathway consists of

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Releasing Chemical Energy  Chapter 6  115  

a single reaction that transfers electrons and hydrogen ions from NADH to pyruvate. This reaction regenerates NAD+ and also converts pyruvate to (threecarbon) lactate. No carbon–carbon bonds are broken, so lactate fermentation produces no CO2. Both pyruvates from glycolysis enter the second stage of lactate fermentation, so this stage produces 2 NAD+ and 2 lactate molecules. The pathway’s yield of 2 ATP comes from glycolysis.

GLYCOLYSIS

glucose

2 2 NAD+

4

e– e–

NADH

e– e–

NADH

e– e–

NADH

e– e–

NADH

Yogurt  We use lactate fermentation by beneficial bacteria to prepare many foods.

Yogurt, for example, is made by allowing bacteria such as Lactobacillus bulgaricus and Streptococcus thermophilus to grow in milk (Figure 6.8B). Milk contains a disaccharide (lactose) and a protein (casein). The cells first break down the lactose into its monosaccharide subunits, then use the sugars for lactate fermentation. The lactate they produce reduces the pH of the milk, which imparts tartness and causes the casein to form a gel.

2 pyruvate

REGENERATING NAD+

2 NAD+

Fermentation in Muscle Cells  Cells in animal skeletal muscles can carry out both

aerobic respiration and lactate fermentation. In these cells, aerobic respiration, with its greater efficiency, predominates under most circumstances. However, there are times when fermentation is required, for example when intense exercise depletes oxygen in muscles faster than it can be replenished. Under the resulting anaerobic conditions, muscle cells produce ATP mainly by lactate fermentation. This pathway makes ATP quickly, so it is useful for strenuous bursts of activity, but the low ATP yield does not support prolonged exertion (Figure 6.8C). Contrary to popular opinion, the buildup of lactate in muscles after exercise does not cause muscle soreness the following day. Lactate very quickly leaves muscles and enters the bloodstream, where cells that are not oxygendepleted take it up. These cells convert the lactate back to pyruvate for use in aerobic respiration. Hibernation  Lactate fermentation sustains a few animals that hibernate without oxygen for long periods of time. Consider how some freshwater turtles spend winter months unable to breathe because they are buried in mud or trapped under ice. The normal metabolic rate of a turtle is much lower than a warm-blooded animal in the first place, but during these times it drops even lower, to about 1/10,000 the rate of a resting mammal. Very little ATP is required to maintain such a low metabolism, so the individual can meet its energy requirements by using only lactate fermentation. Excess lactate produced by the pathway is taken up by the animal’s bones and shell.

2 lactate

A. Lactate fermentation begins with glycolysis, and the final steps produce two NAD+ and two lactate molecules. The net yield is two ATP (from glycolysis).

B. Yogurt is a product of lactate fermentation by bacteria in milk. The micrograph shows Lactobacillus bulgaricus (red) and Streptococcus thermophilus (purple) in yogurt.

Take-Home Message 6.4 ●● ●●

●● ●●

Almost all cells can carry out fermentation, which occurs entirely in cytoplasm. Compared with aerobic respiration, fermentation is faster, requires fewer cellular resources, and can operate when oxygen is scarce. It also produces much less ATP. Fermentation’s small ATP yield (two per molecule of glucose) occurs by glycolysis. The final step in fermentation pathways is a transfer of electrons from NADH to an organic molecule, thus regenerating NAD+ necessary for glycolysis to continue.

C. Intense activity such as sprinting quickly depletes oxygen in muscles. Under anaerobic conditions, ATP is produced mainly by lactate fermentation. Fermentation does not make enough ATP to sustain strenuous activity for long.

Figure 6.8  Lactate fermentation. (B) left, iStock.com/Kaycco; right, SCIMAT/Science Source; (C) Maxisport/Shutterstock.com

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116  Unit 1 How Cells Work

6.5  Food as a Source of Energy LEARNING OBJECTIVES ●●

Explain how oxidizing an organic compound can fuel ATP production.

●●

Describe how organic molecules other than glucose are broken down in aerobic respiration.

During the first stages of aerobic respiration, electrons from glucose are transferred to coenzymes. In other words, glucose becomes oxidized (which means it gives up electrons) and coenzymes become reduced (they accept electrons). Oxidizing an organic compound breaks the covalent bonds of its carbon backbone. Aerobic respiration generates a lot of ATP by fully oxidizing glucose, completely dismantling it carbon by carbon. Coenzymes that are reduced during the process deliver electrons to electron transfer chains, and the energy of these electrons powers ATP synthesis.

Oxidizing Molecules in Food In addition to glucose, cells harvest energy from other organic compounds by oxidizing them. Fats, complex carbohydrates, and proteins in food can be converted to molecules that enter aerobic respiration at various stages (Figure 6.9). As in glucose breakdown, oxidizing these compounds breaks their carbon–carbon bonds. Coenzymes are reduced in the process, and the energy of the electrons they carry ultimately drives the synthesis of ATP in electron transfer phosphorylation. Fats  A triglyceride molecule has three fatty acid tails attached to a glycerol head

New Africa/Shutterstock.com

(Section 2.8). Cells dismantle triglycerides by first breaking the bonds that connect the tails to the head 1. Nearly all cells in the body can oxidize the released fatty acids by splitting their long backbones into two-carbon fragments. These fragments are converted to acetyl–CoA, which can enter the citric acid cycle 2. Enzymes in liver cells convert the glycerol to PGAL, which is an intermediate of glycolysis 3. On a per-carbon basis, fats are a richer source of energy than carbohydrates because more reactions are required to fully break them down. Coenzymes accept electrons in these oxidation reactions. The more coenzymes that become reduced, the more electrons can be delivered to the ATP-forming machinery of electron transfer phosphorylation.

Carbohydrates  The digestive system of humans and other mammals breaks down many oligosaccharides and polysaccharides to their monosaccharide monomers 4. Glucose can be broken down in aerobic respiration, but so can other 6-carbon sugars such as fructose 5. Sucrose, our common table sugar, is a disaccharide that consists of glucose and fructose monomers. A digestive enzyme breaks the bond between the two monomers, releasing the monosaccharides. The first reaction of glycolysis is carried out by an enzyme called hexokinase (pictured in Figure 4.10). Hexokinase phosphorylates glucose, producing glucose-6-phosphate that continues in the reactions. Hexokinase also phosphorylates fructose, producing fructose6-phosphate. Fructose-6-phosphate is the substrate of the third reaction of glycolysis, so it can continue in the reactions too. Eating carbohydrates raises the level of monosaccharides in blood. When cells take up more monosaccharides than they need for energy, glucose and fructose are diverted away from glycolysis and into a pathway that builds glycogen. Between meals, the blood glucose level falls. Then, stored glycogen is broken down to glu­ cose, which maintains a basal level of blood glucose. Eating too many carbohydrates causes glucose and fructose to enter a pathway that builds triglycerides, and

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Releasing Chemical Energy  Chapter 6  117  

CLOSER LOOK Figure 6.9  Food to energy.

OH

H2C O O

C

O

C

CH

CH2

O

O

O

O

The three fatty acid tails of a triglyceride (fat) are separated from the glycerol head.

O

HO

HO

OH

OH

OH

O

fatty acids

glycerol H

OH C

H—C—H

H

C

H C

H—C—H H—C—H

C

H

OH OH OH

O

H—C—H H—C—H H

OH O

O

O

O

Monosaccharide monomers are released from a polysaccharide.

6 A protein is broken apart into its amino acid monomers.

O

O

O

HO

5

6-carbon sugars such as glucose are substrates of glycolysis.

PGAL

HO

amino acids

CH2OH O

H H O

H H N

H N C C OH

H

7

The amino group is split from an amino acid and becomes waste.

GLYCOLYSIS

to PGAL, which is an intermediate of glycolysis. acetyl-CoA

2 The hydrocarbon tails of a fatty acid are broken apart into 2-carbon fragments. These fragments are attached to coenzyme A, forming acetyl–CoA that enters the citric acid cycle.

NADH

pyruvate

R O O

C C OH R

3 Glycerol is converted

H—C—H H—C—H

HO OH O

H

H—C—H

H—C—H

O

monosaccharides

H—C—H

H—C—H

4

O

O

HO

O

O

O

O

OH O

O

O

HO

O

HO

O

O

O

O

O

OH O

O

O

O

1

C

OH O

O

HO

O

Proteins

Polysaccharides

8

Depending on the R group, the organic fragment of the amino acid is converted to pyruvate, acetyl-CoA, or an intermediate of the citric acid cycle.

pyruvate

acetyl−CoA

Figure It Out: Does the breakdown of amino acids release CO2? Answer: Yes

Fats

acetyl-CoA

Krebs CITRIC Cycle ACID CYCLE

Figure It Out: Do the breakdown products of proteins enter glycolysis? Answer: No

Figure It Out: Which generates more ATP, a fatty acid or a glycerol?

NADH, FADH2

ATP

ATP

ATP

ELECTRON TRANSFER Electron Transfer PHOSPHORYLATION Phosphorylation

Answer: A fatty acid

acetyl–CoA is diverted away from the citric acid cycle and into a pathway that builds fatty acids. This is why excess dietary carbohydrates end up as fat. Proteins  Enzymes in the digestive system split dietary proteins into their amino acid

Figure Summary The body converts fats, complex carbohydrates, and proteins to molecules that can enter aerobic respiration at various stages. Photo, shabaneiro/Shutterstock.com; Data for protein render from PDB ID 2TRK: Katti, S., LeMaster, D., Eklund, H. Crystal structure of thioredoxin from Escherichia coli at 1.68 A resolution. (1990) J.Mol.Biol. 212: 167–184.

subunits 6, which are absorbed into the bloodstream. Cells use these free amino acids to build proteins or other molecules. When you eat more protein than your body needs for this purpose, the amino acids are broken down. The amino (NH2) group is removed 7, and the carbon backbone is split into fragments. The removed

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118  Unit 1 How Cells Work

amino group is converted to urea, a waste product that is eliminated in urine. The carbon-containing fragments are converted to pyruvate, acetyl–CoA, or an intermediate of the citric acid cycle 8. These molecules enter aerobic respiration at the acetyl–CoA formation stage or the citric acid cycle.

The Ketogenic Diet The currently popular ketogenic diet is extremely low in carbohydrates, moderate in proteins, and high in fats. This regimen triggers a metabolic shift in the way the body harvests energy from foods. The brain requires a lot of glucose, which is usually provided by the breakdown of polysaccharides. If the concentration of glucose in blood falls below a critical level, brain function declines rapidly, and permanent brain damage is possible. As you might expect, the body has several mechanisms that keep the brain supplied with glucose. The primary mechanism involves the liver. When blood glucose begins to fall, glycogen stored in liver cells is broken down, and its glucose monomers are released into the bloodstream (Section 2.6). The bloodstream carries the glucose to the brain and other parts of the body. The liver stores only enough glycogen to stabilize blood glucose in the short term (such as between meals). After 24 hours of fasting, the liver runs out of glycogen and a pathway called gluconeogenesis takes over. Gluconeogenesis means “glucose regeneration,” and this pathway produces glucose from two pyruvates—essentially the reverse of glycolysis. It can keep the blood glucose stable during a few days of fasting. Most of the pyruvate that enters the gluconeogenesis pathway is derived from three molecules: glycerol, lactate, and oxaloacetate. When carbohydrate intake remains extremely low, almost all of the oxaloacetate in a liver cell becomes diverted to gluconeogenesis. Oxaloacetate is the first substrate of the citric acid cycle, so when its availability declines, the cycle slows. Then, acetyl–CoA produced by fatty acid and amino acid breakdown starts to accumulate. The accumulation of acetyl–CoA in liver cells triggers a pathway called ketogenesis. Ketogenesis converts acetyl–CoA to molecules called ketone bodies. The liver releases these molecules into the bloodstream, and other cells (including brain cells) convert them back to acetyl–CoA for use in the citric acid cycle. By forcing the body to use lipids and proteins rather than carbohydrates for energy, the ketogenic diet induces a metabolic state called dietary ketosis that mimics starvation without depriving the body of required nutrients. It has been used since the 1920s to reduce seizures in people with epilepsy, and it has recently gained popularity for weight loss. The diet is also being investigated as a therapy for conditions related to metabolic syndrome and neurological disorders such as Alzheimer’s disease. However, the reason why dietary ketosis has beneficial effects is controversial, and it is very unsafe for people with type 1 diabetes and some other health conditions. Check with your health practitioner before trying it.

Take-Home Message 6.5 ●●

●●

Oxidizing organic molecules breaks their carbon backbones, releasing electrons. The energy of the released electrons can be harnessed to drive ATP formation in aerobic respiration. First the digestive system and then individual cells convert molecules in food (fats, complex carbohydrates, and proteins) into substrates of glycolysis or later steps of aerobic respiration.

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Releasing Chemical Energy  Chapter 6  119  

Dietary Fat Overload Reprograms Mitochondria

0.25 Weight of brown fat per mouse (grams)

The bodies of humans and other mammals store triglycerides in two kinds of tissue: white fat and brown fat. The main function of white fat is to store triglycerides for future energy needs. Brown fat has more mitochondria than white fat, and these are used to generate body heat. Mitochondria in brown fat make thermogenin, a transport protein that allows hydrogen ions to move across the inner mitochondrial membrane. Hydrogen ions that move through this protein (instead of ATP synthase) power no ATP formation. Thus, thermogenin un­­couples the operation of mitochondrial electron transfer chains from ATP synthesis. In cells of brown fat, organic compounds are rapidly broken down by aerobic respiration. Electrons pass through mitochondrial electron transfer chains, which actively transport hydrogen ions from the matrix to the intermembrane space. However, hydrogen ion gradient formation is inefficient because thermogenin makes the inner membrane “leaky,” so not much ATP forms. Thus, the major product of aerobic respiration in these cells is heat lost from the ongoing electron transfers. In 2015, Daniele Barbato and his colleagues investigated the effect of a high-fat diet on brown fat in mice. They maintained an experi­ mental group of mice on a high-fat diet (60 percent fat), and a control group of mice on a normal diet (12 percent fat). Results are shown in Figure 6.10.

Mitochondrial oxygen consumption (mmol O2/min/mg protein)

Digging Into Data 0.20 0.15 0.10 0.05 0.00 ND

HFD

8 6 4 2 0 ND

HFD

Figure 6.10  Effects of a high-fat diet on brown fat. ND, normal diet group. HFD, high-fat diet group. Oxygen consumption was normalized for protein concentration. 1. The number of mitochondria per gram of brown fat tissue was found to be identical in both groups. Which group had the highest total number of brown fat mitochondria per mouse? 2. In which group was the oxygen consumption per mitochondrion greatest? 3. How did a high-fat diet affect brown fat?

Summary Section 6.1  Cellular respiration pathways use electron transfer chains to harvest energy from organic molecules and make ATP. Aerobic respiration is oxygen-requiring (aerobic) cellular respiration. Mitochondria make ATP by aerobic respiration. Some mitochondria have errors in their DNA that alter components of their electron transfer chain. These errors can reduce the cell’s production of ATP, and increase its production of dangerous free radicals. Devastating mitochondrial diseases are a heritable outcome of defective mitochondria that can still divide. Oxidative stress due to mitochondrial malfunction plays a role in these and many other health conditions. Section 6.2  Autotrophs harvest energy from the environment and convert it to chemical bond energy of sugars. All organisms harvest energy stored in sugars. Aerobic respiration makes ATP by converting glucose and oxygen to carbon dioxide in water. The reactions proceed in four stages: glycolysis, acetyl–CoA formation, the citric acid cycle, and electron transfer phosphorylation.

Pathways of fermentation are anaerobic (they do not require oxygen), and yield fewer ATP than aerobic respiration. Glycolysis, the first stage of aerobic respiration and fermentation pathways, occurs in cytoplasm. The reactions convert one (six-carbon) molecule of glucose to two (three-carbon) molecules of pyruvate, for a yield of two ATP. Electrons and hydrogen ions released by the reactions end up in two NADH. Section 6.3  In eukaryotes, aerobic respiration continues when pyruvate that formed in glycolysis is transported into mitochondria. In the mitochondrial matrix, each pyruvate is converted to acetyl– CoA in a reaction that produces CO2 and NADH. Both acetyl–CoA molecules then enter the citric acid cycle, which produces CO2, NADH, and FADH2, and ATP. At this point in aerobic respiration, the two pyruvates from glycolysis have been dismantled to CO2. Four ATP have formed, and electrons and hydrogen ions released during the reactions are carried by 12 coenzymes.

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120  Unit 1 How Cells Work

Summary (Continued) The coenzymes deliver electrons and hydrogen ions to an electron transfer chain in the inner mitochondrial membrane. In electron transfer phosphorylation, molecules of the electron transfer chain harness electron energy to actively transport hydrogen ions into the mitochondrion’s intermembrane space. The resulting hydrogen ion gradient across the inner membrane drives the ions through ATP synthases, so ATP forms. At the end of the

Figure 6.11  Reviewing ATP production in aerobic respiration.

glucose G LYC O LYSIS 2 pyruvate 2 ATP 2 NADH ACETYL–CoA FORMATION 2 acetyl–CoA 2 CO2 2 NADH

CITRIC ACID CYCLE

4 2 6 2

Section 6.4  Fermentation yields less ATP than aerobic respiration, but it is faster and requires fewer cellular resources. No oxygen is required; an organic molecule is the final electron acceptor. There are several fermentation pathways, and all occur entirely in cytoplasm. Alcoholic fermentation produces CO2 and ethanol. The end product of lactate fermentation is lactate. Both of these pathways begin with glycolysis. The final reactions regenerate the NAD+ required for glycolysis to continue, but they produce no ATP. Thus, fermentation’s overall yield of 2 ATP per glucose comes entirely from glycolysis. We use fermentation in microorganisms to produce some foods. Fermentation also supplements metabolic activities in multicelled eukaryotes. Section 6.5  Oxidizing an organic molecule breaks its carbon backbone. The first three stages of aerobic respiration fully oxidize glucose, and electrons released by this process drive ATP formation in the final stage. Organic molecules other than glucose can also be oxidized in aerobic respiration. In humans and other mammals, first the digestive system and then individual cells convert fats, proteins, and complex carbohydrates in food to molecules that are intermediates in glycolysis or other pathways of aerobic respiration.

Self-Quiz

CO2 ATP NADH FADH2

Answers in Appendix I O2

ELECTRON TRANSFER PHOSPHORYLATION

34 ATP H2O

electron transfer chains, oxygen accepts electrons and combines with hydrogen ions, so water forms. The theoretical maximum yield of aerobic respiration is 38 ATP per molecule of glucose (Figure 6.11).

1. Mitochondrial defects can be inherited because ___________ . a. mitochondria produce ATP in all eukaryotic cells b. mitochondria contain their own DNA and divide independently of the cell c. the balance of free radicals tips toward oxidative stress d. errors in DNA can affect mitochondrial electron transfer chains 2. Is the following statement true or false? Unlike animals, which make many ATP by aerobic respiration, plants make all of their ATP by photosynthesis.

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Releasing Chemical Energy  Chapter 6  121  

3. Glycolysis occurs in the ___________ of all cells. a. nucleus c. plasma membrane d. cytoplasm b. mitochondrion

12. Carbon dioxide is produced during ___________ fermentation. a. lactate c. aerobic b. alcoholic d. eukaryotic

4. Which molecule does not form during glycolysis? c. FADH2 a. NADH b. Pyruvate d. ATP

13. One of the main differences between aerobic respiration and fermentation is ___________ . a. fermentation occurs only in prokaryotic cells b. ATP forms only in aerobic respiration c. fermentation uses no electron transfer chains d. aerobic respiration requires no oxygen

5. In eukaryotes, the citric acid cycle takes place in the ___________ of mitochondria. a. outer membrane b. intermembrane space c. inner membrane d. matrix 6. After __________ molecules of pyruvate have been dismantled, six carbons have exited the cell in CO2. a. one c. three b. two d. six 7. __________ accepts electrons at the end of electron transfer chains in aerobic respiration. a. Water c. O2 b. H+ d. NADH 8. Most of the energy that aerobic respiration releases from glucose ends up in ________ . c. heat a. NADH b. ATP d. electrons 9. Put the following pathways in the order they occur during aerobic respiration. a. electron transfer phosphorylation b. acetyl–CoA formation c. citric acid cycle d. glycolysis 10. In eukaryotes, the final reactions of fermentation are completed in __________ . a. the nucleus b. mitochondria c. the plasma membrane d. cytoplasm 11. Which of the following is not produced by an animal muscle cell operating under anaerobic conditions? a. heat d. ATP b. pyruvate e. lactate c. PGAL f. oxygen

14. Which of the following molecules cannot be oxidized to produce ATP? a. glucose c. pyruvate b. a fatty acid d. oxygen 15. Match the term with the best description. mitochondrial matrix a. needed for glycolysis b. inner space product of glycolysis c. produces CO2 NAD+ d. pyruvate alcoholic fermentation e. no oxygen required anaerobic f. reduced coenzyme NADH g. oxygen required oxidative stress h. intermediate in fatty mitochondrial electron acid breakdown transfer phosphorylation i. outcome of defective acetyl–CoA mitochondria

CRITICAL THinking 1. Carter, pictured in Figure 6.1, had genetic defects that impaired the function of two components of mitochondrial electron transfer chains: an enzyme that removes electrons from NADH, and a protein complex that moves hydrogen ions from the mitochondrial matrix to the intermembrane space. How would these impairments have affected aerobic respiration in Carter’s cells? 2. Explain how the escape of electrons from electron transfer chains reduces the ATP yield of aerobic respiration. 3. How is the function of the thylakoid membrane similar to that of the inner mitochondrial membrane? 4. Why does CO2 form in alcoholic fermentation, but not in lactate fermentation? 5. The way ATP forms in glycolysis differs from the way ATP forms in electron transfer phosphorylation. Explain the difference.

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7

7.1

A Hero Dog’s Golden Clones  123

7.2 The Function of DNA  124 7.3 The Structure of DNA  128

DNA Structure and Function

7.4 Eukaryotic Chromosomes  130 7.5 DNA Replication  133 7.6 Mutations  134

Information encoded in DNA is the basis of visible traits that define species and distinguish individuals. Identical twins appear identical because they inherited identical DNA.

Concept Connections zagorodnaya/Shutterstock.com

In this chapter, you will learn how information encoded in the structure of DNA (Section 2.10) gives rise to its function as the hereditary material of all organisms (1.3). Changes in an organism’s DNA, whether inherited (8.6, 9.4) or as a result of environmental influences (8.7), may affect its form and function. Genetic disorders arise this way (10.6), but so do innovations that are the foundation of evolutionary change (13.7). This chapter also revisits experiments (1.6, 1.7), free radicals and tracers (2.2), proteins (2.9), the cell nucleus (3.5), and enzymes and metabolic pathways (4.4).

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DNA Structure and Function  Chapter 7  123 

Application 7.1  A Hero Dog’s Golden Clones On September 11, 2001, a terrorist attack caused the collapse of the World Trade Center in New York. When the news reached Canadian police officer James Symington, he immediately drove his police dog Trakr from Nova Scotia to the disaster site, in order to help with search and rescue efforts. Within hours of arriving, the dog led rescuers to the area where the final survivor of the attacks was trapped. The woman had been clinging to life, buried under rubble from the building where she had worked. Symington and Trakr worked for three days nonstop, until Trakr collapsed from smoke and chemical inhalation, burns, and exhaustion (Figure 7.1). Trakr survived the ordeal, but later lost the use of his limbs from a degenerative neurological disease probably linked to toxic smoke exposure at the World Trade Center site. The hero dog died in April 2009, but his DNA lives on in his genetic copies—his clones. Symington’s essay about Trakr’s superior nature and abilities as a search and rescue dog won the Golden Clone Giveaway, a contest to find the world’s most clone-worthy dog. Before Trakr died, researchers harvested DNA from a few of his cells, and then shipped it to Sooam Biotech Research Foundation in Korea. The company’s founder, Hwang Woo-suk, inserted the DNA into donor dog eggs, which were then implanted into surrogate mother dogs. Five puppies, all clones of Trakr, were delivered to Symington in July 2009. Symington began training them to be search and rescue dogs for his humanitarian organization, Team Trakr Foundation. Training a dog for K-9 duty (as a law enforcement or military dog) requires a substantial investment of time. Each K-9 recruit must undergo months of intensive training just to determine its suitability, and many end up as pets because Figure 7.1  A hero dog and his clones. they don’t make the cut. Of the dogs who do pass their training, a rare few Top, James Symington and his dog Trakr assisted in become elite, which means they have exceptional performance in search and the search for victims at Ground Zero, September 2001. rescue, bomb detection, narcotics investigations, and so on. Symington’s essay about Trakr’s superior abilities in search and rescue operations won an opportunity to have the dog Soon after Trakr was cloned, Sooam began cloning elite K-9s for police and cloned. Bottom, Symington with Trakr’s clones in 2009. military forces in Korea and other countries. The clones have the genetic underTop, Splash News/Newscom; Bottom, Ben Glass, courtesy of BioArts International pinnings for their donors’ exceptional abilities, so they are presumed to have the potential to become elite too. In 2015, Hwang resurrected Trakr’s frozen DNA to produce more of his clones, and donated three of them (Trakr 588, Trakr 589, and clone  Genetically identical copy of an organism. Trakr 592) to a university to begin K-9 training. Cloning works because each cell inherits DNA from a Discussion Questions parent cell. That DNA is like a 1. Cloning an animal produces genetically identical individuals. What professional sectors other than master blueprint: It contains all law enforcement and the armed forces might benefit from using cloned animals? of the information necessary 2. Would there be advantages (or disadvantages) of populating a K-9 force entirely with clones of a to rebuild the cell and, in the single dog? case of animals and other mul3. Woolly mammoths were huge elephant-like mammals that became extinct about 10,000 years ticelled organisms, the entire ago. In 2013, fossil hunters found perfectly preserved remains of a woolly mammoth—complete individual. With this unit, we with blood and other tissues—in Siberian permafrost. Sooam is part of an international alliance turn to genetics: the informastudying whether DNA recovered from this animal can be used to clone it, using elephants as tion that DNA holds, how cells surrogate mothers. What are some of the pros and cons of resurrecting an extinct animal? use it, and how it passes from one generation to the next.

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124  Unit 2 GENETICS

7.2  The Function of DNA Learning Objectives ●●

Discuss the role of DNA in the continuity of life.

●●

Explain why animal clones can be produced from a single body cell.

●●

Describe differentiation.

It took decades of research to come to the understanding that deoxyribonucleic acid—DNA—is the hereditary material common to all life. As a substance (Figure 7.2), DNA was first described in 1869 by Johannes Miescher, a chemist who extracted it from cell nuclei. Miescher determined that DNA is not a protein, and that it is rich in nitrogen and phosphorus, but he never learned its function.

Killer Bacteria and the Stupid Molecule

Figure 7.2  Purified DNA in a test tube. DNA’s role as the carrier of hereditary information was uncovered over decades, as researchers built upon one another’s discoveries. Science Photo Library/Science Source

About 60 years after Miescher discovered DNA, Frederick Griffith found an unexpected clue about its function. Griffith was studying pneumonia-causing bacteria in the hope of making a vaccine. He discovered that these deadly bacteria contained a substance that could transform harmless bacteria into lethal ones. The transformation was permanent and heritable: Even after hundreds of generations, descendants of the transformed cells retained the ability to kill. What was the substance that transformed harmless bacteria into killers? In 1940, Oswald Avery, Colin MacLeod, and Maclyn McCarty decided to identify the substance, which they called the “transforming principle.” The team killed pneumonia-causing bacteria with heat, made a sterile extract of the killed cells, and checked the extract for its ability to transform bacteria. Treating the extract with enzymes that degrade lipids and proteins did not prevent transformation, so the transforming principle could not be lipid or protein. The researchers realized that the substance they were seeking must be a nucleic acid—DNA or RNA. DNA-degrading enzymes destroyed the extract’s ability to transform cells, but RNA-degrading enzymes did not. These results indicated that DNA had to be the transforming principle. Like most other scientists, Avery, MacLeod, and McCarty had assumed that proteins were the material of heredity. After all, traits are diverse, and proteins are the most diverse biological molecules. DNA was widely assumed to be too simple to encode genetic information, because it has only four nucleotide components (Section 2.10); experts of the era even described DNA as “a stupid molecule.” Avery and his team gathered clear evidence that DNA is the material of inheritance, but they were still skeptical. Convincing themselves took years of further research, and only then did they publish their results. The team were also careful to point out that they had not proven DNA was the only hereditary material.

Properties of a Hereditary Material Avery, MacLeod, and McCarty’s surprising result prompted a stampede of other scientists into the field of DNA research, and the resulting explosion

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DNA Structure and Function  Chapter 7  125 

of discovery confirmed DNA’s role as the molecule of heredity. Key in this advance was the realization that any molecule, DNA or otherwise, had to have the following four properties in order to function as the sole hereditary (genetic) material: 1. Complete genetic information must be transmitted along with the molecule from one generation to the next. 2. Body cells of any individual of a species should contain the same amount of it. 3. It must be exempt from major metabolic change—the quantity of the material should not fluctuate over time in cells of a given type. 4. It must be capable of storing the huge amount of information that would be required to build a new individual. Hershey and Chase  In the early 1950s, Alfred Hershey and Martha Chase proved

that DNA, and not protein, satisfies the first property of a hereditary molecule: It transmits a full complement of genetic information from one generation to the next. Hershey and Chase worked with bacteriophage, a type of virus that infects bacteria (Figure 7.3A). Like all viruses, these infectious particles carry hereditary material that specifies how to make new viruses. After a virus injects a cell with this material, the cell starts making new virus particles. Hershey and Chase carried out a series of experiments proving that a bacteriophage injects DNA, not protein, into bacteria (Figure 7.3B,C).

Figure 7.3  Hershey–Chase experiments. Alfred Hershey and Martha Chase carried out experiments to determine the composition of the hereditary material that bacteriophage inject into bacteria. The experiments were based on the knowledge that proteins contain more sulfur (S) than phosphorus (P), and DNA contains more phosphorus than sulfur. Bottom left, Eye of Science/Science Source

A. Top left, model of a bacteriophage. Bottom left, micrograph of bacteriophage injecting DNA into a bacterium. DNA inside protein coat hollow sheath tail fiber

35S remains outside cells

Virus particle coat proteins labeled with 35S DNA being injected into bacterium

B. In one experiment, bacteriophage were labeled with a radioisotope of sulfur (35S), a process that makes their protein components radioactive. The labeled viruses were mixed with bacteria long enough for infection to occur, and then the mixture was whirled in a kitchen blender. Blending dislodged viral parts that remained on the outside of the bacteria. Afterward, most of the radioactive sulfur was detected outside the bacterial cells. The viruses had not injected protein into the bacteria. Virus DNA labeled with 32 P

32P remains

inside cells

Labeled DNA being injected into bacterium

C. In another experiment, bacteriophage were labeled with a radioisotope of phosphorus (32P), a process that makes their DNA radioactive. The labeled viruses were allowed to infect bacteria. After the external viral parts were dislodged from the bacteria, the radioactive phosphorus was detected mainly inside the bacterial cells. The viruses had injected DNA into the cells—evidence that DNA is the genetic material of this virus.

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126  Unit 2 GENETICS

Digging Into Data DNA or Protein? The graph shown in Figure 7.4 is reproduced from the original 1952 publication by Hershey and Chase. Bacteriophage were labeled with radioactive tracers and allowed to infect bacteria. The virus–bacteria mixtures were then whirled in a blender to dislodge any viral components attached to the exterior of the bacteria. Afterward, radioactivity from the tracers was measured. 1. Before blending, what percentage of each isotope, 35S and 32P, was extracellular (outside the bacteria)? 2. After 4 minutes in the blender, what percentage of each isotope was extracellular? 3. How did the researchers know that the radioisotopes in the fluid came from outside of the bacterial cells and not from bacteria that had been broken apart by whirling in the blender? 4. The extracellular concentration of which isotope increased the most with blending?

Figure 7.4  Detail from Alfred Hershey and Martha Chase’s publication describing their experiments with bacteriophage. “Infected bacteria” refers to the percentage of bacteria that survived the blender. Credit: (5) © From A. D. Hershey & M. Chase, “Independent Functions of Protein and Nucleic Acid in Growth of Bacteriophage,” Journal of General Physiology 36(1952): 39–56.

Final Clues  In 1948, the second property expected of a hereditary molecule was

pinned on DNA. By meticulously measuring the amount of DNA in cell nuclei from a number of species, André Boivin and Roger Vendrely proved that body cells of any individual of a species contain precisely the same amount of DNA. Proof that DNA has the third property expected of a hereditary molecule came from a demonstration that DNA does not undergo metabolic change: Daniel Mazia’s laboratory discovered that the protein and RNA content of cells varies over time, but the DNA content does not. The fourth property—that a hereditary molecule must somehow encode a huge amount of information—would be proven along with the discovery of DNA’s structure, a topic we continue in the next section.

DNA: The Molecule of Heredity The continuity of life is based on DNA. When a cell reproduces, it passes a copy of its DNA to each of its descendant cells. Information in that DNA is the basis of cellular form and function, and, in the case of multicelled animals, it also directs the development and functioning of the entire body. Thus, the inheritance of DNA is the reason why offspring are similar to their parent(s) in both form and function, generation after generation. Identical Twins Have Identical DNA  Consider how identical twins have identical

DNA, so their bodies develop the same way (which is why they appear identical, as in the chapter opening photo). Identical twins are the product of a natural process called embryo splitting. The first few divisions of a fertilized egg form a tiny ball of cells that sometimes splits spontaneously. If both halves develop independently, identical twins result. Animal breeders have long exploited this process with a technique called artificial embryo splitting. A ball of cells grown from a fertilized egg is teased apart into two halves that develop as separate embryos. The embryos are implanted in surrogate mothers, who give birth to identical twins.

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DNA Structure and Function  Chapter 7  127 

Clones Have Identical DNA  Twins produced by embryo splitting are genetically

identical to one another, but they are genetically different from their parents. This is because, in humans and most other animals, offspring have two parents whose DNA differs slightly in sequence (Chapter 9 returns to this topic). An exact genetic copy of an existing individual can be produced by somatic cell nuclear transfer (SCNT), a laboratory procedure in which the nucleus of an unfertilized egg is replaced with the nucleus of a donor’s somatic cell (Figure 7.5A). A somatic cell is a body cell, as opposed to a reproductive cell such as an egg or sperm. If all goes well, the transplanted DNA directs the development of an embryo, which is then implanted into a surrogate mother. The animal born to the surrogate is a clone of the donor. Trakr’s clones were produced this way. “Cloning” means making an identical copy of something, and it can refer to deliberate interventions intended to produce a genetic copy of an organism. SCNT is a form of reproductive cloning, which is any technology that produces clones of an animal from a single cell. Animal breeders use these technologies because cloned animals have the same desirable features as their DNA donors (Figure 7.5B). Among other benefits, offspring can be produced from a donor animal that is castrated or even dead. SCNT is also used to produce human embryos for research purposes. For example, cells of cloned embryos help researchers unravel the molecular mechanisms of human genetic disorders. Soon, replacement tissues and organs for people with incurable diseases may be generated from their own cloned cells.

A micropipette punctures the egg and sucks out the nucleus. All that remains inside the egg’s plasma membrane is cytoplasm. Another micropipette inserts a skin cell from a donor animal. An electric current will cause the cell to release its nucleus into the egg’s cytoplasm. If the egg begins to divide, an embryo forms. A. SCNT with cells from cattle. These micrographs were taken by scientists at Cyagra, a company that specializes in cloning livestock.

Cells with Identical DNA Can Differ  Cells making up a multicelled body have

different forms and functions: Skin cells differ from brain cells, which differ from heart cells, and so on. All of these cells have the same DNA. If DNA is the basis of form and function, how can cells with identical DNA be different? During early development, an embryo’s cells start using different subsets of their DNA. As they do, the cells become different in form and function. This process is called differentiation. Differentiation in animals is usually a one-way path: Once a cell specializes, all of its descendant cells will be specialized too. By the time a liver cell, muscle cell, or other differentiated cell forms, most of its DNA has been turned off, and is no longer used (Chapter 8 returns to this topic). In order to produce a clone from a somatic cell, the cell’s DNA must be reprogrammed so the parts that trigger embryonic development are turned back on, and the parts that make the cell specialized are turned off. Egg cell cytoplasm can reprogram the DNA in a donor cell nucleus during SCNT, but the process is inefficient. Few SCNT-generated embryos survive implantation in surrogates.

B. Champion dairy cow Nelson’s Estimate Liz (right) and her clone, Nelson’s Estimate Liz II (left), who was produced by SCNT. Liz II started winning championships before she was one year old.

Figure 7.5  Cloning cattle by SCNT (somatic cell nuclear transfer). (A–B) Courtesy of Cyagra, Inc., www.cyagra.com

Take-Home Message 7.2 ●●

●●

●●

●●

DNA is the basis of the continuity of life, the genetic bridge between generations. Information in DNA, the source of form and function, passes from parent to offspring. A cell’s DNA has all the information necessary to build a new cell, and in the case of multicelled organisms, a new body. Clones appear identical because they have identical DNA. Reproductive cloning technologies such as SCNT can be used to produce animal clones from a single cell. During development of a multicelled organism, cells differentiate as they start using different subsets of their DNA.

differentiation  Process in which cells become specialized during development; occurs as different cells in an embryo begin to use different subsets of their DNA. somatic cell nuclear transfer (SCNT)  Reproductive cloning method in which the nucleus of an unfertilized egg is replaced with the nucleus of a donor’s body cell.

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128  Unit 2 GENETICS OH

O

Figure 7.6  Components of a nucleotide.

N

Each nucleotide has three components: a nitrogen-containing base, a sugar, and one, two, or three phosphate groups. The base and the phosphate group(s) are attached to the sugar’s carbon backbone.

N

N

SUGAR

P

OH

P P

O N N

N

NH2

O

deoxyguanosine triphosphate

SUGAR

P

OH

P P

NH2 N

BASE

deoxycytosine triphosphate

O OH

P P

O N N

deoxythymidine triphosphate

O

O P P

OH

SUGAR

phosphate group(s)

Learning Objectives ●●

Identify the subunits of DNA and how they differ.

●●

Give an overview of the structure of a DNA molecule.

●●

Describe base pairing.

●●

Explain how DNA holds information.

Section 2.10 introduced nucleotides as monomers of nucleic acids (DNA and RNA). Each nucleotide has three components: a nitrogen-containing base, a five-carbon sugar, and phosphate groups (Figure 7.6). DNA takes its name from deoxyribose, the sugar component of its nucleotides. Only four types of nucleotides make up DNA (Figure 7.7). The four types differ in their component base: adenine (abbreviated A), guanine (G), thymine (T), or cytosine (C). Nucleotide structure had been worked out in the early 1900s, but just how the four kinds are arranged in a DNA molecule was a puzzle that took 50 years to solve.

1950, when Erwin Chargaff (one of many researchers investigating DNA’s function) made two important discoveries about the molecule. First, the amounts of adenine and thymine are identical in any DNA molecule, as are the amounts of cytosine and guanine (A = T and G = C). We call this discovery Chargaff ’s first rule. Chargaff ’s second discovery, or rule, is that the adenine/thymine content of a DNA molecule differs from the cytosine/thymine content (A = T ≠ G = C), and that the magnitude of this difference varies among species.

The Theoreticians: Watson and Crick  Around the same time that Chargaff

BASE thymine (T)

P

Chargaff’s Rules  Clues about DNA’s structure started coming together around SUGAR

P

P

Discovery of DNA Structure O

N

cytosine (C)

P

Building Blocks of DNA

N

BASE guanine (G)

NH2

7.3  The Structure of DNA

N

O

deoxyadenosine triphosphate

+

HO

N

BASE adenine (A)

N

+

BASE

NH2 N

O

N

SUGAR OH

P

Figure 7.7  The four nucleotides that make up DNA. Nucleotides that become assembled into a DNA molecule have a deoxyribose sugar and three phosphate groups. They differ in their component bases (blue): adenine (A), guanine (G), cytosine (C), and thymine (T).

discovered his rules, James Watson and Francis Crick were sharing ideas about the structure of DNA. The helical (coiled) pattern of secondary structure that occurs in many proteins (Section 2.9) had just been discovered, and Watson and Crick suspected that the DNA molecule was also a helix. The two spent many hours arguing about the size, shape, and bonding requirements of the four DNA nucleotides. They pestered chemists to help them identify bonds they might have overlooked, fiddled with cardboard cutouts, and made models from scraps of metal connected by suitably angled “bonds” of wire.

The Experimentalist: Rosalind Franklin  Rosalind Franklin had also been investigating the structure of DNA. Like Crick, Franklin was expert in X-ray crystallography, a technique in which X-rays are directed through a purified and crystallized

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National Library of Medicine

DNA Structure and Function  Chapter 7  129 

substance. Atoms in the substance’s molecules scatter the X-rays in a pattern that can be captured as an image. Researchers use the pattern to calculate the size, shape, and spacing between any repeating elements of the molecules— all of which are details of molecular structure. Franklin (left) had been told she would be the only one in her department working on the structure of DNA, so she did not know that Maurice Wilkins was already doing Rosalind Franklin the same thing just down the hall. No one had told Wilkins about Franklin’s assignment; he assumed she was a technician hired to do his X-ray crystallography work. And so a clash began. Wilkins thought Franklin displayed an appalling lack of deference that technicians of the era usually accorded researchers. To Franklin, Wilkins seemed prickly and oddly overinterested in her work.

A. C. Barrington Brown © 1968 J. D. Watson

National Library of Medicine

Theory Meets Experiment  Wilkins and Franklin had been given identical samples

of DNA for crystallography. As molecules go, DNA is gigantic, and it was difficult to crystallize given the techniques of the time. Franklin’s meticulous work with her sample yielded the first clear X-ray diffraction image of DNA as it occurs in cells (left). She gave a presentation on this work in 1952. She had used the image to calculate that a DNA molecule is very long compared to its diameter of 2 nanometers. She had also identified a repeating pattern every 0.34 nanometer along its length, and another every 3.4 nanometers. Franklin concluded that DNA had two nucleotide chains twisted into a double helix, with a backbone of phosphate groups on the outside, and bases arranged in an unknown way on the inside. She had calculated the distance between its chains and between its bases, the pitch (angle) of the helix, and the number of bases in each coil. Crick, with his crystallography expertise, would have recognized the significance of the work—if he had been there. Watson was in the audience but he was not a crystallographer, and he did not understand the implications of Franklin’s X-ray diffraction image or her calculations. Franklin started to write a research paper on her findings. Meanwhile, and perhaps without her knowledge, Watson and Wilkins reviewed Franklin’s X-ray diffraction image, and Watson and Crick read a report detailing Franklin’s unpublished data. Crick, who had more experience with molecular modeling than Franklin, immediately understood what the image and the data meant. Watson and Crick now had all the information they needed to build the first accurate model of DNA (left). Dozens of scientists contributed to the discovery of DNA’s structure, but only three received recognition from the general public for their work. Rosalind Franklin died in 1958. Because the Nobel Prize is not given posthumously, she did not share in the 1962 honor that went Watson and Crick with to Watson, Crick, and Wilkins for the discovery of the their model of DNA structure of DNA.

Anatomy of a DNA Molecule Each DNA molecule has two chains (strands) of nucleotides coiled into a double helix. Covalent bonds link the deoxyribose of one nucleotide and a phosphate group

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130  Unit 2 GENETICS

of the next, forming a sugar–phosphate backbone (Figure 7.8). The backbone of the two strands runs in opposite directions, with the nucleotide bases positioned internally. Most scientists had assumed that the bases had to be positioned on the outside of the helix, so they would be accessible to DNA-copying enzymes (you will see shortly how these enzymes access internally positioned bases). Hydrogen bonds between paired bases hold the strands together:

The two sugar–phosphate backbones run in parallel but opposite directions. Think of one strand as upside down compared with the other.

A phosphate group joins one sugar to the next. These links form the sugar–phosphate backbone of each strand.

T

C

C

C

G

T

A

G

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A P

phosphate

P

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sugar

A P

P

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one base pair

DNA Sequence  Even though DNA is composed of only four nucleotides, the order in which one base follows the next along a strand—the DNA sequence—varies

P

T

G

Notice how the strands “fit.” They are complementary, which means the base of each nucleotide on one strand pairs with a suitable partner base on the other. Only two types of base pairings form: adenine pairs with thymine; guanine, with cytosine. This pattern (A–T, G–C) is the same in all molecules of DNA (which explains Chargaff ’s first rule).

A

G

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C

tremendously among species (which explains Chargaff ’s second rule). As you will see in later chapters, DNA sequence is a code that cells can read, and the encoded information is the basis of form and function in cells, individuals, species, and all life. DNA molecules can be hundreds of millions of nucleotides long, so they can encode a massive amount of this information. DNA sequences that are common among organisms are the basis of shared traits; sequences that differ are the basis of traits that distinguish individuals and define species. Thus DNA, the molecule of inheritance in every cell, is the basis of life’s unity. Variations in its sequence are the foundation of life’s diversity.

P

P

T

Take-Home Message 7.3

A

Hydrogen bonds link internally positioned nucleotide bases

P

Figure 7.8  The DNA double helix.

centromere  Of a duplicated eukaryotic chromosome, constricted region where sister chromatids attach to each other. chromosome  A structure that consists of DNA together with associated proteins; carries part or all of a cell’s genetic information. DNA sequence  Order of nucleotide bases in a strand of DNA. histone  Type of protein that associates with the DNA double helix; one of many proteins that structurally organize eukaryotic chromosomes. sister chromatids  Of a duplicated chromosome, the two identical DNA molecules, attached to one another at the centromere.

●●

●●

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A DNA molecule consists of two chains (strands) of nucleotides coiled into a double helix. Hydrogen bonds form between pairs of internally positioned bases: A pairs with T, and G pairs with C. The order of nucleotide bases along a DNA strand (the DNA sequence) encodes information that is the basis of traits.

7.4  Eukaryotic Chromosomes Learning Objectives ●●

Describe the way DNA is organized in a chromosome.

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Explain the meaning of diploid.

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Distinguish between autosomes and sex chromosomes.

DNA Packaging The DNA molecules in a human cell collectively have about 6 billion base pairs, and would be about 6.5 feet (2 meters) long if stretched out. How can that much DNA cram into a nucleus less than 10 micrometers in diameter? Proteins associate

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DNA Structure and Function  Chapter 7  131 

CLOSER LOOK Figure 7.9  DNA packing in eukaryotic chromosomes.

4 The DNA-wrapped histones assemble into a 30-nm fiber. histone

3 The resulting spool-like structure is 11 nm in diameter.

2 At regular intervals, the DNA wraps around a core of histone proteins.

1 The two strands

of a DNA molecule form a double helix that is 2 nm in diameter.

9 The 250-nm fiber packs into the chromosome’s most condensed form.

0 A condensed, duplicated chromosome has an “X” shape that is formed by sister chromatids joined at the centromere. Each chromatid is 500 to 750 nm in diameter.

5 Proteins lasso the 30-nm fiber into loops.

Figure It Out: How many DNA molecules compose this chromosome? Answer: Two

6 The loops draw together tightly, forming a pleated structure.

8 The coils

twist into a 250-nm fiber.

7 The pleated structure coils up.

with DNA molecules to form structures called chromosomes. These proteins pack the DNA very tightly by organizing it into a series of coiled fibers (Figure 7.9). In each eukaryotic chromosome, the DNA molecule’s double helix wraps at regular intervals around proteins called histones, forming spool-like structures that look like beads on a string in micrographs. Interactions among the DNA-wrapped histones coil the DNA into a 30-nanometer (nm) fiber that proteins lasso into loops. Unless the cell is dividing, its chromosomes usually exist in various combinations of these spools, coils, and loops, which allow access to the DNA for tasks such as RNA synthesis (Chapter 8 returns to this topic).

Figure Summary Above, many proteins associate with a DNA molecule and organize it into successively higher orders of packing, but only the histone proteins are featured here. nm, nanometers. Below, micrographs of chromosomes.

Sister Chromatids  Most of the time, a eukaryotic chromosome consists of one DNA molecule (and its associated proteins). A cell preparing to divide will duplicate its DNA. After duplication, a eukaryotic chromosome consists of two identical DNA molecules attached to one another at a region called the centromere. The two identical halves of a duplicated eukaryotic chromosome are called sister chromatids: 2 µm

centromere sister chromatid sister chromatid a chromosome (unduplicated)

a chromosome (duplicated)

“Beads on a string”

The 30-nm fiber

A fully condensed, duplicated human chromosome.

Oscar Miller, Jr; B. Hamkalo; Andrew Syred/Science Source

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132  Unit 2 GENETICS Packing for Cell Division  Just before the cell divides, its DNA packs into an even 1

2

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8

4

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10

more highly condensed form that is less likely to become damaged during the division process. The loops of the 30-nm fiber draw together tightly, a bit like pleats. The pleated structure coils, and then coils again to produce a 250-nm fiber. This fiber packs into the chromosome’s most condensed form, which looks like an “X” under a microscope.

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The Chromosome Number Most prokaryotes have a single circular chromosome. By contrast, the DNA of a eukaryotic cell is divided among some number of linear chromosomes that differ in length and centromere location. The number of chromosomes in a cell of a given species is called the chromosome number, and it is a characteristic of the species. For example, the chromosome number of humans is 46, so our body cells have 46 chromosomes. Actually, human body cells have two sets of 23 chromosomes: two of each type. Cells with two sets of chromosomes are diploid, or 2n (n stands for “number”).

A. Karyotype of a female human, with 22 pairs of autosomes and identical sex chromosomes (XX).

1

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9

Karyotypes  Chromosome number is revealed in a karyotype, an image of an W

B. Karyotype of a female Australian brush turkey. Like other birds, females of this species have nonidentical sex chromosomes (ZW).

individual cell’s chromosomes. To create a karyotype, cells are treated to make the chromosomes condense, and then stained so the chromosomes can be distinguished under a microscope. A micrograph of a single cell is digitally rearranged so the chromosomes are lined up by centromere location, and arranged according to size, shape, and length.

Autosomes and Sex Chromosomes Figure 7.10  Autosomes and sex chromosomes. (A) © University of Washington Department of Pathology; (B) © 2017 Ortega et al. Karyotype analysis and sex determination in Australian Brush-turkeys (Alectura lathami). PLoS ONE 12(9): e0185014. https://doi.org/10.1371/journal.pone.0185014

Figure It Out: What is the diploid chromosome number of an Australian brush turkey?

Answer: 20

autosome  A chromosome of a pair that is the same in males and females; a chromosome that is not a sex chromosome. chromosome number  The total number of chromosomes in a cell of a given species. diploid  Having two of each type of chromosome characteristic of the species (2n). DNA polymerase  Enzyme that carries out DNA synthesis during DNA replication; uses a DNA template to assemble a complementary strand of DNA. DNA replication  Process by which a cell makes copies of its DNA. karyotype  Image of an individual cell's complement of chromosomes arranged by size, length, shape, and centromere location. primer  Short, single strand of DNA or RNA that serves as an attachment point for DNA polymerase. sex chromosome  Chromosome involved in determining anatomical sex; member of chromosome pair that differs between males and females.

In a human body cell, 22 of the 23 pairs of chromosomes are autosomes. The two autosomes of each pair are the same in both females and males, and they have the same length, shape, and centromere location. They also hold information about the same traits. Think of them as two sets of books on how to build a house. Your father gave you one set. Your mother had her own ideas about wiring, plumbing, and so on. She gave you an alternate set that says slightly different things about many of those tasks. Members of a pair of sex chromosomes differ between females and males, and the differences determine an individual’s sex. The sex chromosomes of humans are called X and Y. The body cells of a typical human female have two X chromosomes (XX, Figure 7.10A); those of a typical human male have one X and one Y chromosome (XY). This pattern—XX females and XY males—occurs in most mammals, but there are other patterns. Female butterflies, moths, birds (Figure 7.10B), and certain fishes have two nonidentical sex chromosomes, and the two sex chromosomes of males are identical. Environmental factors influence or determine sex in some species of invertebrates, turtles, and frogs. As an example, the temperature of the sand in which sea turtle eggs are buried determines the sex of the hatchlings.

Take-Home Message 7.4 ●● ●●

●● ●●

Proteins organize and pack DNA in chromosomes. A eukaryotic cell’s DNA is divided among a characteristic number of linear chromosomes that differ in length and shape. Diploid cells have two copies of each chromosome. Members of a pair of sex chromosomes differ between males and females. Chromosomes that are the same in both sexes are called autosomes.

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DNA Structure and Function  Chapter 7  133 

7.5  DNA Replication Learning Objectives ●●

State the purpose of DNA replication, and describe the process.

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Describe nucleic acid hybridization.

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Explain why DNA replication is said to be semiconservative.

When any cell reproduces, it divides. Both descendant cells must inherit a complete copy of the parent cell’s genetic information, or they will not be like the parent cell. Thus, in preparation for division, a cell copies its chromosomes so that it contains two sets: one for each of its future offspring. The process in which a cell copies its chromosomes is called DNA replication. Each molecule of DNA is copied in its entirety, and two molecules of DNA that are identical to the parent molecule are produced. The enzyme that carries out DNA synthesis during replication is DNA polymerase.

The Process of DNA Synthesis DNA Strands Separate  Before DNA replication, a chromosome consists of one

molecule of DNA—one double helix (Figure 7.11). As replication begins, enzymes pry apart the two DNA strands: One untwists the double helix, and another breaks the hydrogen bonds that hold the strands together 1. The two DNA strands then begin to separate from one another. Primers Hybridize  As the DNA strands separate, their interDNA 1 primer

hybridization

nally positioned bases become exposed, and another enzyme starts making primers. A primer is a short, single strand of DNA or RNA that serves as an attachment point for DNA polymerase. Exposed nucleotide bases on a DNA strand can form hydrogen bonds with complementary bases of a primer. In other words, a primer base-pairs with a complementary strand of DNA. The establishment of base pairing between single-stranded nucleic acids is called hybridization (left). Hybridization is spontaneous and is driven entirely by hydrogen bonding.

DNA Polymerase Assembles Nucleotides  DNA synthesis begins when a DNA

polymerase attaches to a primer that has hybridized with a DNA strand 2. The polymerase then moves along the strand, using the sequence of exposed nucleotide bases as a template (guide) to assemble a new strand of DNA from free nucleotides 3. A DNA polymerase follows base-pairing rules: When it reaches an A in the template strand, it adds a T to the new DNA strand; when it reaches a G, it adds a C; and so on. Thus, the DNA sequence of each new strand is complementary to the parental strand. An enzyme called DNA ligase seals any gaps in the sugar–phosphate backbones of the new strands 4.

CLOSER LOOK Figure 7.11  DNA replication.

1 As replication enzymes begins, enzymes begin to unwind and separate the two strands of DNA. 2 Primers base-pair with the single DNA strands. primer

3 Starting at

primers, DNA polymerases (green boxes) assemble new strands of DNA from nucleotides, using the parent strands as templates.

DNA polymerase nucleotide

DNA ligase

4 The enzyme DNA ligase seals any gaps in the sugar–phosphate backbone of each strand. 5 Each parental DNA strand (blue) serves as a template for assembly of a new strand of DNA (magenta). The new DNA strand winds up with its template, so two doublestranded DNA molecules result. One strand of each is parental (conserved), and the other is new, so DNA replication is said to be semiconservative. Figure It Out: Do DNA polymerases copying different strands of the parent molecule move in the same direction or opposite directions? Answer: Opposite

Two DNA Molecules Are Produced  Both strands of the parent molecule are copied

at the same time. As each new DNA strand lengthens, it winds up with its parental strand into a double helix. So, after replication, two double-stranded molecules of DNA have formed 5. One strand of each molecule is parental (conserved), and the other is new, so replication is said to be semiconservative. Both molecules are replicas of the parent molecule. In a eukaryotic cell, these molecules are sister chromatids that remain attached at the centromere until cell division occurs.

Figure Summary The two strands of a DNA molecule are separated, and DNA polymerases use each as a template to synthesize a new, complementary strand of DNA. The process produces two double-stranded DNA molecules, each a replica of the parent molecule.

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134  Unit 2 GENETICS

PCR: DNA Replication in a Tube The polymerase chain reaction (PCR) is probably best known as a technique used by forensic labs to help “catch the bad guys,” but it is actually DNA replication in a test tube. Forensic scientists can identify a particular person from unique sequences in his or her DNA. However, in forensic situations, there may not be enough DNA available to analyze. This is where PCR comes in. With PCR, DNA polymerase is added to a tube that contains primers, free nucleotides, and a sample of DNA that serves as a template. As in DNA replication, the polymerase uses the primers as attachment points for synthesis of a new strand of DNA. Unlike DNA replication, which makes one copy of the template, PCR produces millions of copies: plenty for a forensic analysis. PCR is particularly useful in forensics because it allows investigators to identify an individual from only a tiny amount of DNA—even the DNA from a single cell left at a crime scene will do. (You will learn more about PCR and its role in DNA fingerprinting in Chapter 10.)

Take-Home Message 7.5 ●● ●●

●●

A cell copies its chromosomes by replicating its DNA. In DNA replication, each strand of the double helix serves as a template for synthesis of a new, complementary strand of DNA from free nucleotides. DNA replication produces two DNA molecules that are replicas of the parent molecule.

7.6  Mutations Learning Objectives G C

G C

A T

C G

T A

C G

C G

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C G

T A

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C G

A T

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Using examples, explain how mutations can arise.

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Describe some cellular mechanisms that can prevent mutations from occurring.

G C

Mutations: DNA Sequence Changes

base change G

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A. Repair enzymes can recognize a mismatched base (magenta), but they sometimes fail to correct it before DNA replication. DNA replication G

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B. After replication, both strands base-pair properly. Repair enzymes can no longer recognize the error, which has now become a mutation that will be passed on to the cell’s descendants. Figure 7.12  How a replication error becomes a mutation.

DNA is the basis of form and function in all cells, and all life. If the sequence of a cell’s DNA changes, the information it encodes can change too. A very extensive system for monitoring and repairing DNA molecules helps cells protect the integrity of their vital genetic information. Even so, the system is not perfect, and the sequence of a cell’s DNA sometimes becomes altered. Major alterations typically cause the cell to die; minor ones may not. Any that do not disrupt function enough to prevent the cell from dividing can be passed to its descendants. A permanent change in the DNA sequence of a chromosome is called a mutation. Mutations that alter DNA’s instructions may have harmful or lethal outcomes (Sections 8.6 and 9.4 return to this topic). Cancer, for example, begins with mutations, as do many genetic disorders. Sources of Mutation  Mutations can be introduced into DNA in several ways. Some

are the outcome of errors during DNA replication, but most are a consequence of DNA damage—breaks in the sugar–phosphate backbone, for example, or alterations in the structure of nucleotide bases. Mutations occur when the cell’s repair mechanisms fail to fix the damage.

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DNA Structure and Function  Chapter 7  135 

Replication Errors Sometimes, a newly replicated DNA strand is not exactly complementary to its parent strand. A nucleotide may get deleted during DNA replication, for example, or an extra one inserted. Occasionally, the wrong nucleotide is added. Most of these replication errors occur simply because DNA polymerases work very quickly. A eukaryotic polymerase can add about 50 nucleotides per second to a strand of DNA; a prokaryotic polymerase can add up to 1,000 per second. Mistakes are inevitable, and some DNA polymerases make a lot of them. Proofreading and Mismatch Repair  Most polymerases can proofread their work, reversing the synthesis reaction to remove an error, then resuming synthesis in the forward direction. Errors missed during this proofreading process can be corrected later, because bases that are not properly paired distort the double helix. The distortion is recognized by molecules that can repair the mismatch. The nonparental (new) strand is cut, and the section containing the mismatch is removed. A DNA polymerase then uses the parental strand as a template to replace the missing nucleotides, and DNA ligase seals any gaps in the new strand. How Replication Errors Become Mutations  Sometimes, proofreading and

mismatch repair fail to correct an error. The error cannot be detected after a second round of DNA replication, because both strands will then base-pair properly (Figure 7.12). When the cell divides, its descendants will inherit the error as a mutation.

thymine dimer

UV Light Nucleotide Dimers  DNA easily absorbs wavelengths of ultraviolet (UV) light radiating from the sun (Section 5.3). When it does, covalent bonds form between adjacent thymine or cytosine bases. The resulting dimer makes a kink in the DNA double helix (Figure 7.13). Dimers cause mutations because polymerases tend to copy kinked DNA incorrectly. Dimers can also block the progress of a polymerase, so DNA replication stalls or collapses. This outcome often causes the chromosome to break up. Usually, chromosomal breaks cause cell death, but cells that do survive often have mutations at the sites of breakage. This is because repairing double-strand DNA breaks is a highly inaccurate process of bringing the appropriate pieces together, and replacing nucleotides that were lost or damaged at the breaks. It requires the use of a sister chromatid (or another chromosome) as a template for DNA synthesis. Nucleotide Repair  Cells can repair a dimer by excising a short section of the DNA

strand that contains it. DNA polymerase then uses the other strand as a template to replace the missing nucleotides, and DNA ligase seals the gaps. This mechanism is critical for repairing a variety of types of damage to nucleotides. A tremendous number of enzymes and other proteins participate in nucleotide repair mechanisms, and DNA damage may accumulate if any of them are faulty or missing. Many types of cancer and several genetic disorders arise this way.

Figure 7.13  A thymine dimer. Exposure to UV light causes covalent bonds to form between adjacent bases on a DNA strand. The resulting dimer distorts the double helix. Dimers caused by UV rays in sunlight are a major source of mutations that lead to skin cancer. Data source: PDB ID: 1TTD. McAteer, K., Jing, Y., Kao, J., Taylor, J. S., Kennedy, M. A. Solutionstate structure of a DNA dodecamer duplex containing a Cis-syn thymine cyclobutane dimer, the major UV photoproduct of DNA. (1998) Journal of Molecular Biology 282: 1013–1032.

Skin Cancer  UV light does not penetrate very far into tissues, but the damage it

causes at body surfaces is significant. For every second a skin cell spends in the sun, 50 to 100 dimers form in its DNA. This is why exposing unprotected skin to sunlight or other sources of UV light can cause skin cancer.

mutation  Permanent change in the DNA sequence of a chromosome.

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136  Unit 2 GENETICS

Ionizing Radiation Rosalind Franklin died at the age of 37, of ovarian cancer that may have been caused by extensive exposure to X-rays during her work. At the time, the link between X-rays, mutations, and cancer was not understood. Today, we know that high-energy forms of electromagnetic radiation (gamma rays, X-rays, and the shorter wavelengths of UV light) have enough energy to slam electrons out of atoms. The atoms become ions with unpaired electrons—very reactive free radicals that damage biological molecules (Section 2.2). Breakage and Cross-Links  Exposure to ionizing radiation can severely damage DNA, for example by directly breaking chromosomes (Figure 7.14). It also breaks chromosomes indirectly by causing covalent bonds to form between bases on opposite strands of the DNA double helix. These cross-links prevent DNA strands from separating during replication, an outcome that results in chromosome breakage. Cells can repair cross-links, but the process is complicated and has a high risk of introducing mutations. Figure 7.14  DNA damaged by ionizing radiation. These are the chromosomes of a human white blood cell that has been exposed to ionizing radiation. Few have the normal “X” shape; most are fragmented or have taken on an abnormal structure. Any cell that survives such damage would have an extremely high risk of mutation. Courtesy of M. Hirai and Y. Suto at the National Institutes for Quantum and Radiological Science and Technology

Dose-Dependent Damage  The extent to which DNA is damaged by ionizing radia-

tion increases with the level of exposure, and so does the mutation rate (Figure 7.15). A small, natural background level of ionizing radiation occurs at the surface of the Earth, but humans can be exposed to much higher levels. For example, devices such as televisions, smoke detectors, and gas lanterns emit radiation; and medical procedures such as X-rays, CT scans, and radiation therapy provide substantial doses.

Chemicals Many mutations are caused by chemicals that bind to nucleotide bases. DNA polymerases tend to skip bases that have been altered in this way, or copy them incorrectly during replication. An altered base may also cause chromosome breakage by blocking DNA replication. Small amounts of mutation-causing chemicals are produced in the body during normal metabolic processes, but by far the greatest source of exposure to these chemicals is the environment. Following are a few examples. Some of these compounds bind directly to nucleotide bases; others are broken down after they enter the body, and the breakdown products bind to bases. Smoking  Tobacco smoke in particular contains thousands of chemicals, at least 70 of which have been proven to cause mutations that can lead to cancer. Smoking causes about 30 percent of all cancer deaths in the United States, but using other tobacco products such as smokeless tobacco, snuff, and chewing tobacco is also dangerous. These products contain the same mutation-causing chemicals as tobacco smoke. Simply painting some of these chemicals on the skin of animals causes tumors to form. Foods  Some foods contain mutation-causing chemicals. Nitrites, for example,

are added to cured foods such as sausages and bacon, and they form when meat is smoked or cooked at high temperature. Aflatoxins are produced by fungi that contaminate peanuts and other nuts. Acetaldehyde (the chemical that is produced by the body during alcohol consumption, Section 4.1) has several mutation-causing effects: It binds to bases directly, cross-links the two strands, and causes covalent bonds to form between nucleotide bases and other organic molecules in the cell.

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DNA Structure and Function  Chapter 7  137 

Figure 7.15  Mutated flowers from Chernobyl.

normal flower

In 1986, a catastrophic accident at the Chernobyl nuclear power plant in Ukraine released a massive amount of radiation. These Ranunculus flowers were collected in the Exclusion Zone, an area of about 1,000 square miles that is still dangerously contaminated. All but one are abnormal—an effect of mutations caused by radiation exposure. Taavi Tuulik

Industrial and Household Products  A host of industrial products cause mutations. Chemicals in petroleum (crude oil) and its derivative products are particularly dangerous. Vinyl chloride, a chemical used to produce the common plastic PVC, is found in landfills and hazardous waste sites. It also leaches out of products such as water pipes that are made from PVC. Formaldehyde is a chemical ingredient in many soaps, personal care products, cleaning supplies, animal feed, house paint, and so on. It is also used to manufacture building supplies such as particleboard and insulation, and it is one of the many cancer-causing chemicals in cigarette smoke and automobile exhaust.

Not All Mutations Are Dangerous Mutations can occur in any type of cell, and in any part of the cell’s DNA. Those that arise during formation of gametes can be passed to​offspring, and in fact each human child is born with an average of 64 new mutations. It is important to remember that not all mutations are dangerous—some are even beneficial. As you will see in Chapter 13, mutations are the raw material of evolution.

Take-Home Message 7.6 ●●

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Mutations are permanent changes in DNA sequence, and they can be passed to a cell’s descendants. Proofreading and mismatch repair mechanisms correct most replication errors. Uncorrected errors may become mutations. Environmental factors that damage DNA can cause mutations. UV light, ionizing radiation, and chemicals that bind to nucleotide bases are examples. Mutations can have harmful consequences such as cancer or genetic disorders, but many do not. Some mutations are beneficial.

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138  Unit 2 GENETICS

Summary Section 7.1  The now-common practice of making clones (exact genetic copies) of adult animals works because the DNA in each body cell contains instructions for building the organism. Section 7.2  Identifying deoxyribonucleic acid (DNA) as the hereditary material of life took decades of research involving many scientists. Experiments with bacteria were key to the discovery. Somatic cell nuclear transfer (SCNT) and other types of reproductive cloning technologies can produce genetically identical individuals (clones) from a body cell of an adult animal. Cells in multicelled bodies differ because they use different subsets of their DNA. Differentiation is the process by which cells become specialized during embryonic development.

Section 7.5  Before a cell divides, it copies all of its DNA (by DNA replication) so both of its cellular offspring inherit a complete set of chromosomes. For each molecule of DNA that is copied, two DNA molecules are produced; each is a duplicate of the parent. One strand of each molecule is new, and the other is parental. During DNA replication, enzymes unwind and separate the two strands of the double helix, and assemble primers that base-pair (hybridize) with the single DNA strands. Starting at the primers, DNA polymerase enzymes use the sequence of bases on each strand as a template to assemble new, complementary strands of DNA from free nucleotides. DNA ligase seals any gaps.

Section 7.3  A nucleotide has three components: a five-carbon sugar, a nitrogen-containing base, and phosphate groups. Bonds between the sugar of one nucleotide and a phosphate group of the next form the sugar–phosphate backbone of nucleic acid chains (strands). DNA strands are assembled from four types of nucleotides. Each has a deoxyribose sugar, a chain of three phosphate groups, and one of four bases: adenine (A), guanine (G), cytosine (C), or thymine (T). A molecule of DNA consists of two nucleotide strands coiled into a double helix, with the sugar–phosphate backbones running in parallel but opposite directions. Hydrogen bonds between internally positioned bases of the nucleotides hold the two strands together. The bases pair in a consistent way: A with T, and G with C. The order of bases along a strand of DNA—the DNA sequence—varies among species, and this variation is the basis of life’s diversity.

Section 7.6  DNA replication is not a perfect process, so errors such as incorrect, missing, or extra nucleotides are inevitable. Proofreading by DNA polymerases corrects most replication errors as they occur. Uncorrected errors become mutations, which are permanent changes in the DNA sequence of a chromosome. Mutations can be passed to descendant cells. Those that alter information encoded in DNA can affect cell functioning. Environmental agents such as UV light, ionizing radiation, and some chemicals that bind to nucleotides damage DNA. Cells have repair mechanisms that can fix most DNA damage. Unrepaired damage causes replication errors and other events that result in mutations. Some mutations are dangerous. Cancer and genetic disorders begin with mutations, but not all mutations are harmful.

Section 7.4  Proteins such as histones associate with a eukaryotic DNA molecule to form a chromosome. These proteins twist and pack the DNA very tightly into the nucleus. The DNA of a eukaryotic cell is divided among a number of chromosomes that differ in length and centromere location. When duplicated, a eukaryotic chromosome has an X shape and consists of two sister chromatids attached at the centromere. Each sister chromatid has one DNA molecule. Diploid (2n) cells have two sets of chromosomes (two of each type of chromosome). Chromosome number is the total number of chromosomes in a cell, and it is a characteristic of the species. For example, in humans, a normal body cell has 23 pairs of chromosomes, so the chromosome number of humans is 46. An image showing all of the chromosomes in a cell is called a karyotype. Members of a pair of sex chromosomes differ among males and females. Chromosomes of pairs that are the same in males and females are autosomes.

Self-Quiz Answers in Appendix I 1.

 is an example of reproductive cloning. a. Somatic cell nuclear transfer (SCNT) b. Multiple offspring from the same pregnancy c. Artificial embryo splitting

2. Which property would any molecule have to have in order to function as the sole hereditary material of life? a. Adenine must pair with thymidine, and guanine with cytosine. b. Cells of different species must contain different amounts of it. c. Offspring must inherit a full complement of genetic information.

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DNA Structure and Function  Chapter 7  139 

3. Which is not a nucleotide base in DNA? a. adenine c. glutamine   e. cytosine b. guanine d. thymine

13. Which of the following is incorrect? a. Smoking can lead to mutations because chemicals in tobacco bind to nucleotide bases. b. Differences in nucleotide bases are the basis of variation in traits. c. Chromosomes in a eukaryotic cell are packed most tightly when the cell is dividing.

4. What are the base-pairing rules for DNA? a. A–G, T–C c. A–T, G–C b. A–C, T–G d. A–A, G–G, C–C, T–T 5. Similarities in in traits. a. karyotype b. DNA sequence

14. All mutations . a. arise from DNA damage b. lead to evolution

 are the basis of similarities c. the double helix d. chromosome number

6. One species’ DNA differs from others in its . a. nucleotides c. double helix d. sugar–phosphate backbone b. sequence 7. In eukaryotic chromosomes, DNA wraps around a. histone proteins c. centromeres b. sister chromatids d. nucleotides

.

8. Chromosome number . a. refers to a particular chromosome in a cell b. is a characteristic of a species c. is the number of autosomes in cells of a given type d. is the same in all species 9. Human body cells are diploid, which means they a. contain two chromosomes b. have two full sets of chromosomes c. contain both autosomes and sex chromosomes d. divide to form two cells

15. Match the terms appropriately. nucleotide      a. replication enzyme clone        b. does not determine sex copy of an organism autosome      c. DNA polymerase    d. nitrogen-containing base, mutation        sugar, phosphate bacteriophage    e. injects DNA semiconservative    f. can cause cancer replication      g. something old, something new

CRITICAL THinking .

10. When DNA replication begins, . a. the two DNA strands separate b. the two DNA strands condense for base transfers c. old strands move to find new strands d. mutations occur 11. Which of the following is (are) not required for DNA replication to occur? a. DNA polymerase c. primers b. nucleotides d. all are required 12. A duplicated eukaryotic chromosome takes on an “X” shape when . a. sister chromatids condense b. the DNA breaks c. DNA replication is occurring

c. are caused by radiation d. change the DNA sequence

1. During fertilization, two reproductive cells (egg and sperm) combine their DNA to create a new individual. Why, during SCNT, is it necessary to use a somatic cell from the donor rather than a reproductive cell such as a sperm? 2. Determine the sequence of the complementary strand of DNA that forms on this template DNA fragment during replication: G G T T T C T T C A A G A G A | | | | | | | | | | | | | | | _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 3. Why is it important for DNA proofreading and mismatch repair that DNA molecules are double-stranded (not single-stranded)? 4. PCR has become an essential tool in forensic analysis, but it does have limitations. What are some potential problems with the technique that would impact its utility in a forensic case? 5. Xeroderma pigmentosum is an inherited disorder character­ized by rapid formation of many skin sores that develop into cancers. All forms of radiation trigger these symptoms, includ­­­­­ing fluorescent light, which contains UV light in the range of 320 to 400 nm. In most affected individuals, at least one of nine particular proteins is missing or defective. What is the collective function of these proteins?

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8 Gene Expression and Control

8.1

Ricin, RIP  141

8.2

DNA, RNA, and Gene Expression  142

8.3

Transcription: DNA to RNA  144

8.4

RNAs in Translation  146

8.5

Translation: RNA to Protein  148

8.6

Products of Mutated Genes  151

8.7

Control of Gene Expression  153

A single nucleotide change gives rise to the hairless appearance of a sphynx cat. The change alters instructions in DNA for making keratin, a fibrous protein that is a component of hair. Sphynx cats make hair, but it falls out before it can lengthen.

Concept Connections Glennis Siverson

Cells use information in the sequence of nucleotides in DNA (Section 7.4) to make RNA and proteins (2.9, 2.10). That information is the basis of inherited traits (7.2), so mutations that alter it (7.6) can affect form and function. Such mutations are the raw material of evolution (13.2–13.4), and some give rise to genetic disorders (10.6 to 10.8). This chapter also revisits cell components (3.3, 3.5), membrane-crossing mechanisms (4.5, 4.6), enzymes and metabolic pathways (4.4), chromosome structure (7.4), and DNA replication (7.5).

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Gene Expression and Control  Chapter 8  141  

Application 8.1  Ricin, RIP Castor-oil plants grow wild in tropical regions, and they are widely cultivated for their seeds (Figure 8.1A). The seeds of the plant—castor beans—are rich in castor oil, which is used as an ingredient in plastics, cosmetics, paints, soaps, and many other items. The seeds are also rich in ricin, a toxic protein that effectively deters insects, birds, and mammals from eating them. Ricin is extremely toxic to humans when inhaled, ingested, or injected. Most cases of ricin poisoning occur as a result of eating castor-oil seeds, and just a few of these are enough to kill an adult. Purified, a dose of ricin as small as a few grains of salt is lethal, and there is no known antidote. Ricin’s toxicity was known as long ago as 1888. Several countries tried (unsuccessfully) to weaponize it during the First and Second World Wars, but the production, possession, and use of toxic chemicals as weapons has since been outlawed in most parts of the world. No special skills or equipment are required to extract ricin from castor beans, however, so controlling its production is impossible. Thus, ricin appears periodically in the news, mostly in reports of amateur criminals getting caught extracting it or trying to poison someone with the purified material. Perhaps the most famous ricin poisoning occurred in 1978, at the height of the Cold War, when defectors from countries under Russian control were targets for assassination. Bulgarian journalist Georgi Markov had defected to England and was working for the BBC. As he made his way to a bus stop on a London street, an assassin used a modified umbrella (Figure 8.1B) to fire a tiny pellet of ricin into Markov’s leg. Markov died in agony three days later. Ricin inactivates ribosomes, the organelles that assemble amino acids into proteins, so it is called a ribosome-inactivating protein (RIP). Other RIPs are made by some bacteria, fungi, algae, and many plants (including food crops such as tomatoes, barley, and spinach). Most of these proteins are not particularly toxic in humans because they do not cross intact cell membranes very well. By contrast, ricin and other toxic RIPs can enter cells. These proteins have a structural domain that binds to carbohydrates attached to the surface of plasma membranes. Binding of an RIP to these molecules triggers endocytosis (Section 4.6), so the cell takes in the RIP. Once inside the cell, a second domain of the RIP—an enzyme—begins to inactivate ribosomes. One molecule of ricin can inactivate more than 1,000 ribosomes per minute. If enough ribosomes are affected, protein synthesis grinds to a halt. Proteins are critical to all life processes, so cells that cannot make them die quickly. Fortunately, few people actually encounter ricin. Contact with other toxic RIPs is much more common. Bracelets made from beautiful seeds were recalled from stores in 2011 after a botanist recognized the seeds as jequirity beans. These beans contain abrin, an RIP even more toxic than ricin. Shiga toxin, an RIP made by Shigella dysenteriae bacteria, causes a severe bloody diarrhea (dysentery) that can be lethal. Some strains of E. coli bacteria make Shiga-like toxin, an RIP that causes intestinal illness (Section 3.1). RIPs have antiviral, antifungal, and anticancer properties, and plants that make them have been used as traditional medicines for many centuries. Now, Western scientists are investigating RIPs for use as drugs. For example,

A. Seeds of the castor-oil plant are the source of ribosome-busting ricin.

B. Bulgarian spy’s weapon: an umbrella modified to fire a tiny pellet of ricin into a victim. An umbrella like this one was used to assassinate Georgi Markov on the streets of London in 1978. Figure 8.1  Ricin. (A) Amawasri Pakdara/Shutterstock.com; Eugene Sergeev/Shutterstock.com; (B) Cary Wolinsky/ National Geographic Image Collection

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142  Unit 2 GENETICS

DNA promoter

gene 1 transcription begins here

gene 2 transcription ends here

RNA copy of gene 1

Figure 8.2  Transcription copies a gene into RNA form. Information encoded in a DNA molecule occurs in units called genes. During transcription, a gene is copied into RNA form. Transcription begins at a regulatory site called a promoter.

gene 3

researchers have modified ricin’s cell-binding domain to recognize plasma membrane proteins that are especially abundant in cancer cells. The modified ricin preferentially enters—and kills—cancer cells. Ricin’s toxic enzyme domain has also been attached to an antibody that can find cancer cells in a person’s body. The intent of such strategies: to assassinate the cancer cells without harming normal ones.

Discussion Questions 1. Plants produce RIPs to defend themselves from attack by insects and other animals, bacteria, fungi, and viruses. Why might an organism like E. coli (a bacterium) produce an RIP? 2. Eukaryotic organisms that produce toxic RIPs have their own ribosomes. Why do you think that protein synthesis in these organisms is unaffected by the RIPs they produce? 3. If RIPs from plants can benefit human health, why don’t humans and other animals produce their own?

8.2  DNA, RNA, and Gene Expression Learning Objectives gene  Unit of information encoded in the sequence of nucleotide bases in DNA; encodes an RNA or protein product. gene expression  Multistep process of converting information encoded in the DNA sequence of a gene into an RNA or protein product. messenger RNA (mRNA)  RNA that carries a protein-building message. ribosomal RNA (rRNA)  RNA component of ribosomes. transcription  Process in which a gene is copied into RNA form (transcribed); RNA synthesis. transfer RNA (tRNA)  RNA that delivers amino acids to a ribosome during translation. translation  Process by which a polypeptide is assembled according to the protein-building information in an mRNA.

●●

Compare the structure and function of DNA and RNA.

●●

Describe a gene.

●●

Explain the flow of information during gene expression.

Genes You learned in Chapter 7 that chromosomes are like a set of books that provide instructions for building and operating an individual. You already know the alphabet used to write those books: the four letters A, T, G, and C, for the four nucleotides in DNA: adenine, thymine, guanine, and cytosine. The “instructions” in a chromosome are encoded in the sequence of nucleotides making up its DNA, and they occur in units called genes. Cells can use the sequence of nucleotides in a gene—its coding sequence—to make an RNA or protein product. Converting information in a gene to the gene’s product is a multistep process called gene expression. Gene expression begins with transcription, the process in which a gene is copied into RNA form (Figure 8.2). The RNA is a copy of the gene, just as a paper transcript of a conversation carries the same information in a different format.

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Gene Expression and Control  Chapter 8  143  

A.A.Above, Above,a atypical typicalRNA RNAmolecule moleculeisissingle-stranded. single-stranded. A ADNA DNAmolecule molecule(opposite) (opposite)isisdouble-stranded. double-stranded.

Comparing DNA and RNA Structure  Most DNA is double-stranded and most RNA is single-stranded

(Figure 8.3A), but otherwise the two molecules are very similar in structure. Like a strand of DNA, a strand of RNA is a chain of nucleotides, each with phosphate groups, a sugar, and one of four bases. Three bases—adenine, cytosine, and guanine—occur in both RNA and DNA nucleotides, but the fourth base differs slightly (Figure 8.3B). In DNA, the fourth base is thymine (T); in RNA, it is uracil (U). Ribose, the sugar in an RNA nucleotide, differs slightly from deoxyribose, the sugar in a DNA nucleotide (Figure 8.3C). These small differences in nucleotide structure give rise to the very different functions of DNA and RNA (Table 8.1).

O

uracil (U)

thymine (T)

O

N N

N O

N

O

B. Both DNA and RNA are polymers of four types of nucleotides. One base differs between DNA and RNA: Uracil occurs only in RNA, and thymine occurs only in DNA.

Function  DNA’s important but only role is to store a cell’s genetic information. By

contrast, cells make several kinds of RNA on an ongoing basis, and the different types have different functions. Ribosomal RNA (abbreviated rRNA) is the main component of ribosomes. Transfer RNA (tRNA) delivers amino acids to ribosomes, one by one, in the order specified by a messenger RNA (mRNA). Messenger RNA was named for its role as the “messenger” between DNA and protein. As you will see in Section 8.4, an mRNA carries a protein-building message in the sequence of its nucleotide bases. In an energy-intensive process called translation, that message guides the assembly of a polypeptide.

Information Flow During gene expression, information flows from DNA to RNA to protein: DNA

TRANSCRIPTION

RNA

TRANSLATION

ribose O HO

●●

HO

OH

OH

C. The sugar in an RNA nucleotide is a ribose; the sugar in a DNA nucleotide is a deoxyribose. Ribose has an additional hydroxyl group. Figure 8.3  Structure of RNA and DNA.

Table 8.1  Features of DNA and RNA

DNA Main form double helix

Information encoded in the sequence of nucleotides in DNA occurs in units called genes. In gene expression, information in a gene is converted to an RNA or protein product. Transcription copies a gene into RNA form. Translation converts protein-building information in an mRNA into a polypeptide.

RNA most are single-stranded

Monomers deoxyribonucleotides ribonucleotides Sugar

deoxyribose

ribose

Bases

adenine, guanine, cytosine, thymine

adenine, guanine, cytosine, uracil

Base pairing

A–T, G–C

A–U, G–C

Function

stores genetic information

protein synthesis, other roles depending on type

Take-Home Message 8.2 ●●

O OH

PROTEIN

Expression of genes that encode RNA products (such as tRNA and rRNA) involves transcription only. Expression of genes that encode protein products involves both transcription and translation. Directly or indirectly, a cell’s DNA contains all of the information required to make the other molecules of life. Transcription produces RNAs that interact in translation. Some of the resulting proteins have structural roles in the cell; others (enzymes in particular) assemble lipids and carbohydrates, replicate DNA, make RNA, and so on.

●●

deoxyribose OH

OH

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144  Unit 2 GENETICS noncoding strand

G

G

A

G

A

A

G

T

G

G

A

G

A

A

G

T

G

G

A

G

A

A

G

T

noncoding strand

coding strand

C

C

T

C

T

T

C

A

C

C

U

C

U

U

C

A

C

C

T

C

T

T

C

A

coding strand

C

A

C

C

U

C

U

U

C

A

new RNA

(transcription) C

A. Information encoded in a gene occurs on only one of the two strands of the DNA molecule: the coding strand. The other strand is noncoding.

C

T

C

T

T

B. During transcription, the noncoding DNA strand acts as a template for RNA synthesis.

Figure 8.4  How transcription produces an RNA copy of a gene.

C. The new RNA is complementary in sequence to the noncoding DNA strand—it is a copy of the coding strand.

8.3  Transcription: DNA to RNA Learning Objectives ●●

Describe the process of DNA transcription.

●●

Explain how a single gene can give rise to multiple forms of a protein.

Figure 8.5  Transcription.

Comparing Transcription and DNA Replication

Figure It Out: Does the DNA strand break during transcription?

Answer: No

gene

gene gene

gene

promoter promoter promoter RNA RNA polymerase RNA polymerase polymerase

s promoter. A. polymerase binds aa gene’s A. TheRNA enzyme RNA polymerase to apromoter. gene’s promoter. A. The The enzyme enzyme RNA polymerase binds to to binds gene’s promoter. transcription new new RNA RNA new RNA

transcription transcription transcription

Transcription, the process of copying a gene into RNA form, is similar in many ways to DNA replication (Section 7.5). Base-pairing rules are followed, for example. In DNA replication, cytosine pairs with guanine (C–G), and adenine pairs with thymine (A–T). The same base-pairing rules govern RNA synthesis in transcription, except that RNA, remember, has uracil instead of thymine. Uracil, like thymine, pairs with adenine (A–U). Transcription is also similar to DNA replication in that one strand of a nucleic acid serves as a template for synthesis of another. However, in DNA replication, both strands of the entire DNA molecule are used as templates for synthesis. In transcription, only part of one strand (a gene region) serves as the template. Thus, DNA replication produces two double-stranded DNA molecules; transcription produces one single-stranded RNA molecule.

Coding and Noncoding Strands DNA unwinding DNA winding up DNA unwinding DNA DNA winding winding up up DNA DNA unwinding unwinding

B. The RNA polymerase moves over the gene, unzipping B. polymerase moves over the B. The The RNA RNA polymerase the gene, gene, unzipping unzipping the double helixamoves to“transcription formover a “transcription bubble.” As it the double helix to form bubble.” As the doublemoves, helix totheform a “transcription bubble.” Asofitit RNA. The polymerase assembles aofstrand moves, the polymerase assembles a strand RNA. The moves, the polymerase strand of RNA. The DNA winds as up assembles again as theapolymerase passes. DNA DNA winds winds up up again again as the the polymerase polymerase passes. passes. C. Below, zooming in on the site C. in site C. Below, Below,ofzooming zooming in on on the the transcription, we site see that of transcription, we see that of transcription, we see nucleotides arethat linked in the nucleotides are linked the nucleotides are specified linked in in by thethe bases of U T order G order by bases of order specified specified by the the A bases the noncoding DNA of strand. TheC AA the DNA The A the noncoding noncoding DNAisstrand. strand. The A C new RNA complementary new RNA is complementary A new RNA in is sequence complementary to the noncoding U U in to noncoding RNA RNA in sequence sequence to the the A U strand, sononcoding it is an G RNA copyRNA of U RNA strand, so it is an RNA copy of strand, sothe it isgene. an RNA copy of G G the gene. the gene. G

A T T A

C

A

G

T

noncoding strand U U G CGA A C G C AU C C U UA C U T A U A U G G A A C

The information encoded in the DNA sequence of a gene occurs on only one of the two DNA strands—the coding strand. The sequence of other strand—the noncoding strand—is complementary to the gene sequence. During transcription, the noncoding strand acts as a template upon which a strand of RNA is assembled from nucleotides. A nucleotide can be added to the end of a growing RNA only if it base-pairs with the corresponding nucleotide of the template DNA. Thus, a new RNA is complementary in sequence to the DNA template—it is an RNA copy of the gene (Figure 8.4).

noncoding noncoding

noncoding U A T T strand C strand T C C strandA T GC C C AA C T A A C G A G CG A A A G A U G G C G U U C A C UU T C U G T A U A G A G G

A T C A A C T T C A CA ofA A direction T A A C A T G transcription C GC T G G T U C U CG U G G

direction of direction of transcription direction of transcription transcription C

G T T G G GT G T T T TG G T T G G C G AG AC T T G GG A A A T G TG G G G C C G G C AA G A A G G A G C A G T G T G C A G CA AA T A G A A G G T T A A A A A T AG G T T C C G G C GCA C C A A coding C G TT coding G T A C G U C G TT TU A C T C U G T Tcoding strand C G T T G C coding strand T T A strand U T T T A strand T T

T TA

C C G G

A AC A AT C CC T TG G GG

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T A

Gene Expression and Control  Chapter 8  145   gene in chromosomal DNA DNA DNA gene in gene chromosomal in chromosomal

exon exon 1 exon 1 1

exon exon 2 exon 2 2

ex e xo on e on 3xo ex on on e ex 3xo on 3 on

exon exon 4 exon 4 4

exon exon 5 exon 5 5

exon exon 4 exon 4 4

exon exon 5 exon 5 5

DNA DNA DNA transcription transcription transcription exon 1 exon 1 exon 1 RNA RNA RNA

exon exon 2 exon 2 2

exon e xo n e xo 3xo exon x on e exon 3xo xo n 3

alternative splicing alternative alternative splicing splicing

mRNAmRNA 1 mRNA 1 exon exon 11 exon 2 exon 3 1 2 exon 2 exon 52 exon 13 exon 3 4 1 exon 1 2 exon 2 exon 3 mRNA 3 mRNA 1 exon 1 2 exon exon 5 mRNA 5 mRNA 2 exon 3 mRNA 1 exon 1 exon 3 exon 3 exon 4 4 mRNA 2 exon 3 exon translation t tran translation translation t tran t tran

proteinprotein 1 protein 1 1

translation translation translation

translation translation translation

proteinprotein 2 protein 2 2

proteinprotein 3 protein 3 3

Figure 8.6  Alternative splicing.

RNA Synthesis RNA polymerase is the enzyme that carries out transcription. In eukaryotic cells,

the process occurs in the nucleus; in prokaryotes, it occurs in cytoplasm. Transcription begins when an RNA polymerase binds to a gene’s promoter, which is a special sequence of bases upstream from (in front of) the gene’s coding sequence (Figure 8.5A). After binding, the polymerase starts moving over the gene, unwinding the double helix to form an opening called a transcription bubble (Figure 8.5B). As the enzyme moves, it “reads” the base sequence of the noncoding DNA strand. That sequence serves as a template for the RNA polymerase to join free nucleotides into a new strand of RNA (Figure 8.5C). The double helix winds back up as the polymerase passes. When the polymerase reaches the end of the gene region, it releases the DNA and the new RNA.

Introns are removed from a newly transcribed eukaryotic RNA, and the remaining exons are spliced together. For some genes, exons are spliced together in different combinations, forming alternative mRNAs that code for different forms of a protein.

A New RNA Is Modified  Just as a dressmaker may snip off loose threads or add bows to a dress before it leaves the shop, so do eukaryotic cells tailor a new RNA before it leaves the nucleus. Introns, Exons, and Alternative Splicing  Most eukaryotic genes contain regions called introns that are removed in chunks from a newly transcribed RNA. Introns intervene between exons, which are regions that remain in the finished RNA.

Short base sequences at the ends of introns and exons mark their boundaries. The molecule that removes introns from RNA recognizes these boundaries as sites where exons are to be joined. This molecule also carries out alternative splicing, which means it can rearrange exons and splice them together in different combinations (Figure 8.6). Alternative splicing allows one gene to encode multiple versions of a protein. Poly(A) Tail  An RNA that will become an mRNA is further tailored after splic-

ing. For example, 50 to 300 adenines are added to the end of a new mRNA. This poly(A) tail helps regulate the timing and duration of the mRNA’s translation, and

exon  Gene segment that remains in an RNA after modification. intron  Gene segment that intervenes between exons and is removed from a new RNA. promoter  Special sequence of bases that functions as a binding site in DNA for RNA polymerase. RNA polymerase  Enzyme that carries out transcription.

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146  Unit 2 GENETICS first base U

second base C

A

UCU

UAU

U UUU

phe UUC

G

U

UGU

tyr UCC

third base

UAC

cys UGC

C

ser UUA

UCA

UAA

C

UGA

stop

A

UGG

trp

G

stop

leu UUG

UCG

UAG

CUU

CCU

CAU

CCC

leu

●●

●●

U

CGU

CAC

CGC

pro

CUA

CCA

arg CAA

During transcription, RNA polymerase assembles an RNA copy of a gene. The enzyme uses the noncoding strand of DNA as a template for RNA synthesis. Alternative splicing allows a cell to produce different forms of a protein from one gene.

C

CGA

A

gln CUG

CCG

CAG

CGG

G

AUU

ACU

AAU

AGU

U

asn AUC

ile

ACC

AAC

AUA

AGC

C

ACA

AAA

ACG

AAG

AGA AGG

G

GUU

GCU

GAU

GGU

U

GUC

GCC

GAC

lys AUG

met

arg

A

asp val

GGC

ala

gly

GUA

GCA

GAA

GUG

GCG

GAG

glu

8.4  RNAs in Translation Learning Objectives ●●

Describe codons and their function.

●●

Explain the function of a tRNA in terms of its structure.

●●

Give an overview of the roles of mRNA, rRNA, and tRNA in translation.

ser

thr

G

Take-Home Message 8.3

his CUC

A

in eukaryotes it is also a signal that allows the molecule to be exported from the nucleus.

C

GGA

A

GGG

G

A. Codon table. Each codon in mRNA is a set of three nucleotide bases. The left column lists a codon’s first base, the top row lists the second, and the right column lists the third. Sixty-one of the triplets encode amino acids; one of those, AUG, both codes for methionine and serves as a signal to start translation. Three codons are signals that stop translation.

ala alanine (A)

gly glycine (G)

pro proline (P)

arg arginine (R)

his histidine (H)

ser serine (S)

asn asparagine (N)

ile isoleucine (I)

thr threonine (T)

asp aspartic acid (D)

leu leucine (L)

trp tryptophan (W)

cys cysteine (C)

lys lysine (K)

tyr tyrosine (Y)

glu glutamic acid (E)

met methionine (M)

val valine (V)

gln glutamine (Q)

phe phenylalanine (F)

B. The amino acids. Names and abbreviations of the 20 naturally occurring amino acids specified by the genetic code (A).

Figure 8.7  The genetic code. Figure It Out: Which codons specify the amino acid lysine (lys)?

The Message in a Messenger RNA An mRNA is essentially a disposable copy of a gene; its job is to carry the gene’s protein-building information into translation. The protein-building message in an mRNA is encoded in its nucleotides, as a series of genetic “words” that occur one after another along its length. Like the sequence of words in a sentence, the sequence of nucleotide words in an mRNA forms a meaningful parcel of information: in this case, the sequence of amino acids that constitutes the primary structure of a protein. The Genetic Code  The protein-building information carried by an mRNA occurs in three-nucleotide units called codons. Each codon provides a specific instruction during translation: either “start,” “stop,” or “add a particular amino acid here.” The order of the three nucleotides in a codon determines the instruction it specifies. With four possible nucleotides (G, A, U, or C) in each of the three positions of a codon, there are a total of 64 (or 43) mRNA codons. These 64 codons constitute the genetic code (Figure 8.7). Most codons specify amino acids. For example, the codon UUU specifies the amino acid phenylalanine (phe), and UUA specifies leucine (leu). Note that different codons can specify the same amino acid: There are six codons that specify leucine, for example. Codons occur one after another along the length of an mRNA. When the mRNA is translated, the order of its codons determines the order of amino acids in the resulting polypeptide (Figure 8.8). The first AUG in a typical mRNA is a signal to start translation, so it is called a “start” codon. AUG is also the codon for methionine, so methionine is the first amino acid in typical new polypeptides. The codons UAA, UAG, and UGA do not specify an amino acid. These are signals that stop translation, so they are called “stop” codons. The genetic code is highly conserved, which means that all organisms use essentially the same code and probably always have. Bacteria, archaea, and a few eukaryotes use a few codons that differ from the standard code.

Answer: AAA and AAG

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anticodon  In a tRNA, set of three nucleotides that base-pairs with an mRNA codon.

a gene region in DNA A A

T

G

T

A

C

T

C

A

G

A

C

A

C

coding strand

codon  In an mRNA, three-nucleotide unit of information that specifies an instruction during translation.

T

A

C

A

T

G

A

G

T

C

T

G

T

G

noncoding strand

genetic code  Complete set of 64 mRNA codons.

transcription script mRNA U

codon

G

U

A

codon

C

U

C

codon

A

G

A

C

A

C

codon

Figure It Out: Which amino acid will follow asparagine (asp)?

translation

met

tyr

ser

asp

protein

Answer: Threonine (thr)

A

Figure 8.8  Correspondence between DNA, RNA, and protein. A gene region in DNA is transcribed into an mRNA. The codons in the mRNA specify the primary structure of a protein. Only a tiny portion of the gene is shown in this example.

So do mitochondria and chloroplasts—a clue that led to a theory of how these two organelles evolved (we return to this topic in Section 14.5).

The Translators: rRNA and tRNA rRNA  Ribosomes link amino acids into polypeptides. Each ribosome has two subunits, one large and one small, that consist of rRNA and structural proteins (Figure 8.9). When translation begins, a large and a small ribosomal subunit converge as an intact ribosome that can carry out protein synthesis. Ribosomal RNA is one example of RNA with enzymatic activity: The rRNA components of a ribosome (not the protein components) cause peptide bonds to form between amino acids. tRNA  Each tRNA has two attachment sites, one on each end of the molecule. One is an anticodon, which is a triplet of nucleotides that can base-pair with a particular mRNA codon. The second site can bind to a particular amino acid—the one

Figure 8.9  Ribosome structure. Each ribosome consists of a large and a small subunit. Protein components of both subunits are shown in green; rRNA components, in brown. Ribosomal subunits converge as an intact ribosome during translation. Data source: PDB ID: 4V7R. Ben-Shem, A., Jenner, L., Yusupova, G., Yusupov, M. Crystal structure of the eukaryotic ribosome. (2010) Science 330: 1203–1209

intact ribosome small ribosomal subunit

large ribosomal subunit

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148  Unit 2 GENETICS

U A C

anticodon

amino acid attachment site

specified by the mRNA codon (Figure 8.10). Transfer RNAs with different anticodons bind to different amino acids. During translation, tRNAs deliver amino acids to a ribosome, one after the next in the order specified by the codons in an mRNA. As the amino acids are delivered, the ribosome joins them into a new polypeptide. Thus, the order of codons in an mRNA—DNA’s protein-building message—becomes translated into a series of amino acids in a protein. The next section details this process.

Take-Home Message 8.4 ●● ●●

●●

Figure 8.10  tRNA structure.

●●

Each tRNA’s anticodon is complementary to an mRNA codon. Each also carries the amino acid specified by that particular codon. Data source: PDB ID: 1EVV. Jovine, L., Djordjevic, S., Rhodes, D. The crystal structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by Mg(2+) in 15-year old crystals. (2000) Journal of Molecular Biology. 301: 401–414

Figure It Out: What amino acid does this tRNA carry?

Messenger RNA, transfer RNA, and ribosomal RNA interact in protein synthesis. An mRNA carries a gene’s protein-building information into translation. The order of codons in the mRNA determines the order of amino acids in the polypeptide chain translated from it. Each tRNA has an anticodon that base-pairs with a codon in mRNA, and a binding site for the amino acid specified by that codon. During translation, tRNAs bring amino acids to a ribosome in the order specified by mRNA codons. The ribosome links the amino acids into a polypeptide.

8.5  Translation: RNA to Protein Learning Objectives ●●

Describe protein synthesis inside cells.

●●

Explain how an mRNA specifies the order of amino acids in a polypeptide.

Answer: Methionine (met)

Translation, the second part of protein synthesis, occurs in the cytoplasm of all cells (Figure 8.11). The process uses molecules abundant in cytoplasm: free amino acids, ribosomal subunits, and tRNAs 1.

Translation in Eukaryotic Cells In a eukaryotic cell, RNAs that participate in translation are produced in the nucleus, then transported through nuclear pores into cytoplasm 2. RNAs Converge  The process of translation begins when ribosomal subunits and

tRNAs converge on an mRNA 3. First, a small ribosomal subunit binds to the mRNA, and the anticodon of a tRNA base-pairs with the start codon—the first AUG in the mRNA. Then, a large ribosomal subunit joins the small subunit. The intact ribosome is now ready to carry out protein synthesis.

The Polypeptide Lengthens  The tRNA bound to the start codon carries methionine, so the first amino acid of new polypeptides is methionine. Another tRNA joins the complex of molecules when its anticodon base-pairs with the second codon in the mRNA 4. This tRNA brings with it the second amino acid. The ribosome joins the first two amino acids by way of a peptide bond. The ribosome moves to the next codon and releases the first tRNA 5. Another tRNA brings the third amino acid as its anticodon base-pairs with the third codon of the mRNA. The ribosome joins the second and third amino acids. The polypeptide lengthens as the ribosome continues moving along the mRNA, joining amino acids delivered by successive tRNAs 6. As the polypeptide lengthens, it begins to take on its three-dimensional shape 7.

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Gene Expression and Control  Chapter 8  149  

CLOSER LOOK Figure 8.11  Translation.

1 Cytoplasm contains many ribosomal subunits, tRNAs, and free amino acids. The anticodon of each tRNA can bind to the amino acid specified by the complementary mRNA codon. ribosomal subunits

free amino acids

tRNAs C U G

U A C

C U G

U A C

A G U

U G A

A U G

asp

G A G

tyr

ala

arg

asp

asn

cys

glu

gln

gly

his

ile

leu

lys

met

phe

pro

ser

thr

trp

tyr

val

2 In eukaryotes, mRNA is transcribed in the nucleus and transported to the cytoplasm for translation.

A G U

Figure It Out: Where do the tRNAs in eukaryotic cell cytoplasm originate?

ser

thr

A

G C U G

G G G

U

lys

tyr

ser

asp

thr

A

G

A

A

pro

U

t

me

tyr

asp ser

thr

lys t

yr tyr t me

as p ser

tyr

r se

thr

se

met

asp

yr

6 One after the next, tRNAs bind to successive codons in the mRNA. As they do, they bring amino acids to the ribosome. The ribosome joins the amino acids, one by one, into a polypeptide.

trp

lys

thr

asp

t

th r

r th

polypeptide

C U C

G

r th

3 Translation begins when ribosomal subunits and a tRNA converge on the start codon of an mRNA. The tRNA carries a methionine.

U G A U U U

C U G

U G A

C

pro

U

met

A U G

C U G U G A

thr

A G U

A U G

asp

C

r

U

me t

U

U A C

7 The ribosome adds more amino acids to the polypeptide as it moves along the mRNA. The polypeptide lengthens and begins to take on its threedimensional form.

Figure It Out: What is the start codon of this mRNA?

Answer: AUG

4

A G A A U G U A C U C A G A C

U A C A U G U A G

met

8 Many ribosomes can translate an mRNA at the same time. 9 When a ribosome reaches a stop codon, its subunits detach, and the mRNA and the new polypeptide are released.

tyr ser

Figure It Out: What does the yellow glow around the amino acids signify? Answer: Formation of a peptide bond

5

A G A A U G U A C U C A G A C

A U G A G U U

A C

G C U

met

tyr

ser asp

Figure Summary tRNAs deliver amino acids to ribosomes, in the order dictated by the order of codons in an mRNA. The ribosomes link the successive amino acids into a polypeptide. Models are not to scale.

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U C

U

G

met

U G A

Answer: In the nucleus

U G U

mRNA

150  Unit 2 GENETICS

Digging Into Data RIPs as Cancer Drugs 100 Cell Survival (%)

Researchers are taking a page from the structure–function rela­­­tion­ship of RIPs in their quest for cancer treatments. The most toxic RIPs, remember, have one domain that interferes with ribo­somes, and another that carries them into cells. Melissa Cheung and her colleagues incorporated a peptide that binds to skin cancer cells into the enzymatic part of an RIP, the E. coli Shiga-like toxin. The researchers created a new RIP that specifically kills skin cancer cells, which are notoriously resistant to established therapies. Some of their results are shown in Figure 8.12.

50

0

0.1

1.0

10

Concentration of RIP (µg/liter)

Figure 8.12  Effect of an engineered RIP on cancer cells.

1. At what concentration of RIP did 100 percent of all of the different kinds of cells survive? 2. Which cells survived best at 1 microgram per liter RIP? 3. Which cells had the greatest response to an increase in the concentration of the engineered RIP? 4. One cell type was much more sensitive to the engineered RIP than the others. What is the significance of this difference?

The model on the left shows the enzyme portion of E. coli  Shiga-like toxin engineered to carry a small sequence of amino acids (in blue) that targets skin cancer cells. (Red indicates the active site.) The graph on the right shows the effect of this engineered RIP on human cancer cells of the skin (●); breast (◆); liver (▲); and prostate (■). From Cheung, M. C., Revers, L., Perampalam, S., et al. An evolved ribosome-inactivating protein targets and kills human melanoma cells in vitro and in vivo, https://molecular-cancer.biomedcentral.com/articles/10.1186/1476-4598-9-28. 2019 Springer Nature.

Many ribosomes simultaneously translate the same mRNA, so many polypeptides form quickly 8. Translation Ends  Translation ends when the ribosome reaches a stop codon in the

mRNA. The ribosome releases the mRNA and the polypeptide, and its subunits separate from each other 9.

How RIPs Interfere with Translation Translation requires a lot of energy, and most of it is provided by the RNA nucleotide GTP. Phosphate-group transfers from GTP help the ribosome move from one codon to the next along an mRNA. Ricin and other RIPs you learned about in Section 8.1 are toxic because they remove a particular adenine base from one of the rRNAs in the ribosome’s large subunit. This adenine is part of a binding site for molecules that carry out the phosphate-group transfers. After it has been removed, the ribosome can no longer move along an mRNA.

Take-Home Message 8.5 ●●

●●

●●

●●

base-pair substitution  Type of mutation in which a single base pair changes.

Translation begins when ribosomal subunits and tRNAs converge on the start codon in an mRNA. Amino acids are delivered to the ribosome by tRNAs in the order dictated by successive mRNA codons. As the amino acids arrive, the ribosome joins them into a chain via peptide bonds, so a polypeptide forms. Translation ends when the ribosome reaches a stop codon and releases the new polypeptide.

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Gene Expression and Control  Chapter 8  151  

8.6  Products of Mutated Genes

A. Hemoglobin, an oxygenbinding protein in red blood cells. A molecule of hemoglobin has four polypeptides: two alpha globins (blue) and two beta globins (green). Each globin has a pocket that holds a heme (red). Oxygen molecules bind to the hemes.

Learning Objectives ●●

Describe three types of mutations.

●●

Explain how mutations can affect protein structure.

●●

Using an example, explain why some mutations are not harmful.

Harmful Mutations Are Rare Mutations—permanent changes in the DNA sequence of a chromosome (Section 7.6)—are relatively uncommon events in a normal cell. Consider that the DNA of a human somatic (body) cell consists of about 6 billion nucleotides, any of which may be copied incorrectly each time that cell divides. The mutation rate in human somatic cells has been measured: About five nucleotides change every time DNA replication occurs. Less than 2 percent of human DNA encodes gene products, however, so there is a low probability that any mutation will occur in a coding region. The redundancy of the genetic code offers an additional margin of safety for protein-coding genes. For example, a mutation that changes a codon from GUA to GUG may have no further effect, because both of these codons specify the same amino acid: valine.

16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 C

Base-Pair Substitutions Sickle-Cell Anemia  Sickle-cell anemia is the result of a particular mutation in the beta globin gene. The mutation changes one base pair to another, so it is called a base-pair substitution. In this case, the substitution results in a version of beta globin that has valine instead of glutamic acid as its sixth amino acid (Figure 8.13B,C). Hemoglobin assembled with this altered beta globin chain is called sickle hemoglobin, or HbS. Glutamic acid carries a negative charge, but valine carries no charge. As a result of that one base-pair substitution, a tiny patch of the beta globin polypeptide that is normally hydrophilic becomes hydrophobic. This change slightly alters the behavior of hemoglobin. Under certain conditions, HbS molecules stick together and form large, rodlike clumps. Red blood cells that contain the clumps are distorted into a crescent, or sickle shape (Figure 8.14, next page). Sickled cells clog tiny blood vessels, disrupting blood circulation throughout the body. Over time, repeated episodes of sickling can damage organs and eventually cause death.

U

A

G

pro

G

G

glu

A

G

A

glu

A

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U

lys

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ser

B. Part of the mRNA for normal human beta globin, and amino acids that result from its translation. Numbers indicate the nucleotide position in the coding sequence. 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 C

C

U

G

pro

Globins  Rare mutations change a gene’s product or interfere with its expres-

sion. Such mutations can have drastic effects. Consider hemoglobin, the oxygen-transporting protein in your red blood cells. Hemoglobin’s structure allows it to bind and release oxygen. In adult humans, a hemoglobin molecule consists of four polypeptides called globin chains or globins: two alpha globins and two beta globins (Figure 8.13A). Each globin chain folds around a heme, which is a type of cofactor (Section 4.4). Oxygen molecules bind to hemoglobin at those four hemes. Mutations that affect either globin chain also affect hemoglobin function, so they can cause conditions such as anemia, in which a person’s blood is deficient in hemoglobin or in red blood cells. Both outcomes limit the blood’s capacity to carry oxygen, and the resulting symptoms can range from mild to life-threatening.

C

U

G

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val

A

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A

glu

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C. A base-pair substitution replaces an adenine with a thymine in the beta globin gene. When the altered mRNA is translated, valine replaces glutamic acid as the sixth amino acid. Hemoglobin with this form of beta globin is called sickle hemoglobin, or HbS. A

16 17 18 19 21 22 23 24 25 26 27 28 29 30 31 C

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D. A deletion of one nucleotide shifts the reading frame for the rest of the mRNA, so a different protein forms. The outcome of this mutation is a type of beta-thalassemia. 16 17 18 19 20 21 22 23 24 25 26 27 C

C

pro

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E. An insertion of one nucleotide shifts the reading frame for the rest of the mRNA. The resulting protein is too short and does not assemble correctly into hemoglobin molecules. As in D, the outcome is beta-thalassemia. Figure 8.13  Examples of mutations. (A) 1BBB, A third quaternary structure of human hemoglobin A at 1.7-A resolution. Silva, M.M., Rogers, P.H., Arnone, A. (1992) J. Biological Chemistry 267: 17248–17256.

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152  Unit 2 GENETICS Hemoglobin C  Not all base-pair substitutions that change proteins are harmful.

Consider the sickle-cell anemia mutation shown in Figure 8.13C. A different mutation in the same codon, a base-pair substitution that changes the GAG to an AAG, results in a beta globin with lysine as its sixth amino acid instead of the normal valine. Hemoglobin assembled from this globin is called hemoglobin C, or HbC. Unlike HbS, HbC does not clump or distort red blood cells. It can cause a mild anemia, but most people who carry the mutation have no symptoms at all. These people are particularly resistant to infection by the parasite that causes a disease called malaria, so the mutation is helpful in malaria-ridden regions of the world.

normal cell

sickled cell

Deletions and Insertions Thalassemias  A deletion is a mutation in which one or more nucleotides is lost from the DNA. Most deletions cause the reading frame of mRNA codons to shift. A frameshift usually has drastic consequences because it garbles the genetic message, just as incorrectly grouping a series of letters garbles the meaning of words in a sentence:

Figure 8.14  Red blood cells from a person with sicklecell anemia.

The fat cat ate the sad rat.

A base-pair substitution gives rise to an abnormal beta globin that causes sickle-cell anemia. Hemoglobin assembled with the abnormal globin can form rodshaped clumps that distort normally round blood cells into a sickle shape. The sickled cells clog blood vessels.

[–] hef atc ata tet hes adr at.

Eye of Science/Science Source

Figure 8.15  Effect of a mutation in a regulatory site. A mutation that causes hairlessness in sphynx cats is a base-pair substitution in an intron–exon splice site. The altered site is no longer recognized during RNA processing, so the finished mRNA ends up with an intron in it. A stop codon in the intron sequence cuts short the protein translated from the mRNA. keratin gene

transcription and mRNA processing

exon 4

intron

exon 5

normal splice site: TGAAGCCGTAAGTCT

Deletions in globin genes can give rise to thalassemia, a type of anemia in which a person does not make enough globin. One form of thalassemia is caused by the loss of the 20th nucleotide in the coding region of the beta globin gene (Figure 8.13D). The frameshift caused by this deletion results in a polypeptide that is very different from beta globin, both in amino acid sequence and in length. The lack of normal beta globin is the source of the anemia. Beta-thalassemia can also be caused by an insertion, which is a mutation in which nucleotides are added to the DNA (Figure 8.13E). Insertions, like deletions, often cause frameshifts.

Mutations in Regulatory Sites Some mutations do not disrupt codons, but alter gene products nonetheless. Such mutations often occur in regulatory sites—binding sites for molecules that carry out processes of gene expression. Promoters and intron–exon boundary sequences are examples of regulatory sites. Consider a mutation that causes the hairless appearance of the sphynx cat (as shown in the chapter opening photo). This mutation, a base-pair substitution, occurs in a gene for keratin, a fibrous protein that makes up hair (Figure 8.15). The substitution alters a series of bases that normally marks an intron–exon boundary. Molecules that splice new RNAs don’t recognize the altered boundary, so they don’t remove the intron, and the finished mRNA ends up with a chunk of nonsense in the middle. The protein translated from this mRNA is too short and cannot properly assemble into hair. Cats that have the mutation still make hair, but it falls out before it gets very long.

altered splice site: TGAAGCCATAAGTCT

Take-Home Message 8.6

normal keratin mRNA exon 4 exon 5

●●

altered keratin mRNA

●●

exon 4 intron

exon 5

UAG (stop codon)

●●

Mutations that alter gene products or their expression can have dangerous effects on health, but they are uncommon in normal cells. A base-pair substitution can change an amino acid in a protein. Frameshifts change an mRNA’s codon reading frame, thus garbling its proteinbuilding instructions. They are an outcome of insertion and deletions.

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Gene Expression and Control  Chapter 8  153  

8.7  Control of Gene Expression

chromosome

Learning Objectives ●●

Explain gene expression control and why it is necessary.

●●

Explain how master regulators offer evidence of shared ancestry.

●●

Describe the use of knockouts.

●●

Use an example to explain how environmental factors can affect gene expression in offspring.

Molecular Switches All steps of gene expression are regulated, starting with loosening of chromosomal packing to make DNA available for transcription, and ending with delivery of an RNA or protein product to its final destination in the cell (Figure 8.16). Regulating gene expression does not involve changes to DNA sequence; rather, cells use molecules that act as “switches” to turn genes on or off. These molecules can increase or decrease the rate of individual steps of gene expression. For example, proteins called transcription factors affect whether and how fast a gene is transcribed by binding directly to regulatory sites in DNA. Some of these proteins enhance transcription by helping RNA polymerase bind to promoters; others inhibit transcription by preventing RNA polymerase from binding to a promoter, or by blocking its progress.

Unpacking DNA

Transcription new RNA

RNA modification mRNA

RNA transport

Why Cells Control Gene Expression Regulating gene expression is an important part of homeostasis, because it allows control over the kinds and amounts of substances that are present in a cell at any given time. By adjusting expression of particular genes, cells respond appropriately to changes in their internal and external environments. For example, bacteria alter gene expression based on changes in the availability of nutrient carbohydrates in their environment. When a bacterium encounters a preferred nutrient, it begins transcribing genes for enzymes that break it down. When the nutrient is no longer available, transcription of those genes stops. Thus, the cell does not waste energy and resources producing gene products that are not needed. Adjustments to gene expression also affect form and function in multicelled organisms. A typical differentiated body cell uses only about 10 percent of its genes at any given time. Some of the expressed genes affect structural features and metabolic functions common to all cells; others are used only by certain cells. For example, all of your body cells express genes for glycolysis enzymes, but only immature red blood cells express globin genes. Such differences begin early in embryonic development.

mRNA

Translation

polypeptide

Figure 8.16  Points of control over gene expression. Expression of a eukaryotic gene with a protein product is illustrated. Models are not to scale.

Master Regulators in Embryonic Development An animal body starts out as a tiny cluster of identical cells, all expressing the same genes. These cells divide repeatedly, and their descendants begin to differentiate as they start expressing different subsets of genes. As the cells diverge in form and function, they give rise to tissues, organs, and other body parts. Embryonic development is orchestrated by transcription factors that are produced in cascades of gene expression. In these cascades, the transcription factor product of one gene affects the expression of other transcription factor genes, whose products in turn affect the expression of others, and so on. Some of these genes are called master regulators. Expression of a master regulator begins a gene expression cascade that ultimately changes cells in a lineage from one type to other, more differentiated types—a bit like a master switch turns on a whole system with a single flip.

deletion  Mutation in which one or more nucleotides are lost from DNA. insertion  Mutation in which one or more nucleotides are inserted into DNA. master regulator  Gene whose expression triggers a gene expression cascade that ultimately changes cells in a lineage from one type to other, more differentiated types. transcription factor  Regulatory protein that influences transcription by binding directly to DNA.

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154  Unit 2 GENETICS

A. A normal fruit fly (left) has large, round eyes. A fly A. A anormal fruitinflyits(left) has gene large,(right) rounddevelops eyes. A fly with mutation eyeless A. A anormal fruit fly (left) has large, round eyes. A fly with mutation without eyes. in its eyeless gene (right) develops with a mutation without eyes. in its eyeless gene (right) develops without eyes. B. Eyes form wherever the B. Eyes gene form is wherever the eyeless expressed B. Eyes gene form is wherever the eyeless expressed in fly embryos: here, on the eyeless gene is here, expressed in fly and embryos: the head also on the on wing. in fly embryos: here, the head and also on the on wing. head and also wing. The PAX6 geneonofthe humans The PAX6 gene of humans and other animals is so The gene of humans and PAX6 other animals is soit similar to eyeless that and other animalsthat is so similar to eyeless similarly triggers eye it similar eyeless eye that it similarlytotriggers development in fruit flies. similarly triggers eyeflies. development in fruit development in fruit flies.

C. A normal human eye (left) has a colored iris surC. A normal eye (left) a colored iris surrounding thehuman pupil (dark area has where light enters). MutaC. A normal eye (left) has a colored iris surrounding thehuman pupil where light enters). Mutations in PAX6 cause(dark eyesarea to develop without an iris, a rounding the pupil (dark area where light enters). Mutations in PAX6 cause eyes(right). to develop without an iris, a condition called aniridia tions in PAX6 cause eyes(right). to develop without an iris, a condition called aniridia condition called aniridia (right). Figure 8.17  Eyes and eyeless. (A) © Jürgen Berger and Ralf Dahm, Max Planck Institute of Developmental Biology, Tübingen, Germany; (B) Meckes/Ottawa/Science Source; (C) Left, M. Bloch; Right, Courtesy of the Aniridia Foundation International, www.aniridia.net.

♀

♂

As an egg forms, maternal mRNAs are produced and delivered to specific regions of cytoplasm. These mRNAs are translated only after the egg is fertilized and begins to divide. Then, their protein products—transcription factors—diffuse away in gradients that span the whole embryo. The position of a cell in the embryo determines which and how much of these proteins it is exposed to. This in turn determines which of its own genes are turned on. The products of those genes also form gradients, and so on. This gene expression cascade results in differentiation of cells that give rise to the different regions of the developing body. Eventually, the cascade activates homeotic genes, which are master regulators whose expression results in the formation of specific body parts such as an eye. Knockouts  Most master regulators have been discovered via mutations that cause abnormal body form. The abnormalities are clues to the function of the gene’s product. Researchers who study gene function can use a technique called a knockout, in which a specific mutation is introduced into a gene in order to disable its expression in an organism. Gene expression cascades that sculpt development have been deciphered by knocking out genes one by one in fruit flies and other organisms. Mutations in master regulators can disrupt development, so these genes tend to change very little over evolutionary time. All multicelled eukaryotes that undergo development have at least a few of these genes in common, and some are even similar to transcription factor genes in yeast. Consider eyeless, a homeotic gene of flies. Flies with an eyeless knockout lack eyes (Figure 8.17A). Eyes form in fly embryos wherever eyeless is expressed, which is normally in tissues of the head. If eyeless is expressed in another part of the developing embryo, eyes form there too (Figure 8.17B). Humans have a gene called PAX6 that is very similar to eyeless, and mutations in this gene cause disorders of the eye (Figure 8.17C). If a PAX6 gene from a human is inserted into a fly embryo, it has the same effect as eyeless: An eye forms wherever it is expressed. (Because the PAX6 gene product is just a switch, the eye that forms is a fly eye, not a human eye.) X Chromosome Inactivation  In humans and most other mammals, almost all of

the genes on the X chromosome govern nonsexual traits such as blood clotting and color perception. These genes are expressed at the same level in males and females, even though a male has one copy of each gene and a female has two (one on each of her two X chromosomes). This equality occurs because the genes on only one X chromosome are expressed in the female’s cells. The other X chromosome remains highly condensed, a state that prevents transcription of all but a few genes. The inactivated chromosome is called a Barr body, after Murray Barr, who discovered these structures (Figure 8.18). X chromosome inactivation involves a long, noncoding RNA molecule that sticks to any X chromosome that expresses it. Once that RNA has been produced, the X chromosome condenses, and no further transcription of its genes can occur. The other X chromosome does not produce this RNA, so its genes remain available for transcription. X chromosome inactivation is required for proper development: Female animals in which this mechanism fails die shortly after birth.

Figure 8.18  The Barr body. These micrographs show nuclei of human cells. The white spot in the nucleus of the XX (female) cell on the left is a Barr body—the inactivated X chromosome. Most genes on this chromosome are not expressed. The nucleus of the XY (male) cell on the right has no Barr body. Left & Right, Copyright (2001) National Academy of Sciences, U.S.A. PNAS

DNA Methylations Adding methyl groups to (methylating) nucleotide bases in a gene’s promoter can shut down transcription of the gene in a more or less permanent way. When a base on one DNA strand becomes methylated, enzymes methylate the complementary base on the other strand. Thus, once a particular nucleotide has become methylated

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Gene Expression and Control  Chapter 8  155  

in a cell’s DNA, it will usually stay methylated in all of the DNA of the cell’s descendants (Figure 8.19). DNA methylation is a critical part of embryonic development. Genes actively expressed in cells of an embryo become silenced as their promoters get methylated, and this silencing is part of the changes in gene expression that drive differentiation.

DNA methyl group

Environmental Influences  Between 3 and 6 percent of the DNA is methylated in

normal, differentiated body cells, but which sites are methylated varies by the individual. This is because methylation is influenced by environmental factors encountered during an individual’s lifetime. For example, exposure to cigarette smoke alters DNA methylation in a person’s cells. Chemicals in the smoke change the methylation of certain promoters in a pattern that also occurs in cancer cells. Synthetic compounds such as BPA and phthalates (both found in plastics) alter methylation patterns of a number of genes, and this is thought to contribute to the adverse health effects associated with exposure to these chemicals. Methylation patterns also change depending on nutrition, starting at conception. For example, children conceived during a period of famine acquire a particular methylation pattern that differs dramatically from that of children conceived during a period of abundance. The resulting differences in gene expression give rise to differences in glucose and fatty acid metabolism in the adult. As another example, methylation patterns associated with cancer, obesity, and other health conditions can be reversed by molecules abundant in foods such as soybeans, kale, blueberries, turmeric, garlic, green tea, and even chocolate.

DNA replication

methylation

Epigenetics  Factors that influence DNA methylation patterns can have multigen-

erational effects. When an organism reproduces, it passes its DNA to offspring. Methylation of parental DNA is normally “reset” in gametes (eggs and sperm), with new methyl groups being added and old ones being removed. More methyl groups are removed just after fertilization occurs. However, this reprogramming does not remove all of the parental methyl groups, so some methylations acquired during an individual’s lifetime are passed to future offspring—as are their effects. For example, in humans, methylation patterns in hundreds of chromosomal regions change after exposure to lead (a toxic metal). These changes are passed to children, and to grandchildren. Potentially heritable modifications to DNA that affect gene expression without changing the DNA sequence are said to be epigenetic. DNA methylations are epigenetic, as are histone modifications. Epigenetic modifications are not considered to be evolutionary because they do not involve DNA sequence changes. However, epigenetic inheritance can adapt offspring to an environmental challenge much more quickly than evolution, and the changes can be reversed much more quickly after an environmental challenge has faded (Chapter 12 returns to evolution).

Figure 8.19  Replication of methylated DNA. If the parental strand is methylated (red balls), enzymes methylate the complementary base on the new strand too. This is why a methylation can persist in a cell’s descendants.

Take-Home Message 8.7 ●●

●●

●●

Regulating gene expression allows individual cells to respond appropriately to internal and external change. It is also the basis of differentiation during development. Mutations in master regulators can disrupt development, so these genes have changed little over evolutionary time. Exposure to environmental factors can change an individual’s DNA methylation patterns. The resulting changes in gene expression can persist for generations.

Barr body  Condensed, inactivated X chromosome in a body cell of a female mammal. The other X chromosome is active. epigenetic  Refers to potentially heritable modifications to DNA that affect gene expression without changing the DNA sequence. knockout  Technique of introducing a mutation that disables expression of a gene in an organism.

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156  Unit 2 GENETICS

Summary Section 8.1  The ability to make proteins is critical to all life processes. Ribosome-inactivating proteins (RIPs) have an enzyme domain that permanently disables ribosomes, but not all of these proteins can enter cells, so not all are toxic. Section 8.2  Information encoded within the nucleotide sequence of DNA occurs in subsets called genes. Cells use a gene’s coding sequence to produce an RNA or protein product. Gene expression is the conversion of information in a gene to an RNA or protein product. During gene expression, information flows from DNA to RNA to protein. Transcription produces several types of RNA. Messenger RNA (mRNA) carries a gene’s protein-building message into translation. Translation is the energy-intensive process that uses information encoded in an mRNA to assemble a polypeptide. Ribosomes, the organelles that carry out protein synthesis, consist mainly of ribosomal RNA (rRNA). Transfer RNA (tRNA) interacts with ribosomes and mRNA during translation. Section 8.3  During transcription, RNA polymerase binds to a gene’s promoter, then unwinds the DNA as it moves along the gene region. The polymerase uses the nucleotide sequence of the noncoding strand as a template to assemble a new RNA from free nucleotides. The new RNA is a copy of the gene in RNA form. In eukaryotes, newly transcribed RNA is modified before it leaves the nucleus. For example, intron sequences are removed, and the remaining exon sequences may be rearranged and spliced in different combinations. Section 8.4  The protein-building information in an mRNA consists of a series of codons. Most codons specify a particular amino acid during translation; some amino acids are specified by multiple codons. One codon is a signal to begin translation, and three stop translation. All 64 codons constitute the genetic code. Each tRNA has an anticodon that base-pairs with a codon, and it can bind to the amino acid specified by that codon. During translation, tRNAs bring amino acids to ribosomes. Proteins and rRNAs make up the two subunits of a ribosome. The rRNA components of a ribosome cause peptide bonds to form between amino acids during translation. Section 8.5  Translation is the process of linking amino acids into a polypeptide. The order of codons in an mRNA determines the order of amino acids in the polypeptide that forms. Translation begins when ribosomal subunits and tRNAs converge on an mRNA. Successive amino acids are delivered by tRNAs in the order specified by the codons in the mRNA. As the amino acids

arrive, the ribosome joins them via peptide bonds. Translation ends when the ribosome encounters a stop codon in the mRNA and releases the new polypeptide. Section 8.6  Deletions, insertions, and base-pair substitutions change the DNA sequence, and these mutations may affect gene products. Deletions and insertions in a protein-coding gene can cause frameshifts that garble codons in the mRNA transcribed from it. Mutations that occur in regulatory sites such as promoters can affect the production or form of gene products. Section 8.7  Mechanisms of adjusting gene expression are part of homeostasis in all cells, and they drive differentiation during embryonic development in multicelled eukaryotes. Different cells in an embryo differentiate—become specialized—as they begin to use different subsets of their genes. Cells use molecules such as transcription factors to adjust gene expression. Cascades of transcription factor gene expression that orchestrate animal development are triggered by master regulators. Master regulators function in similar ways among evolutionarily distant organisms. Those functions were discovered using knockouts, in which a gene is deliberately inactivated in an organism. In cells of typical female mammals, one of the two X chromosomes is condensed as a Barr body. The condensation prevents transcription of genes on this chromosome. Methylation of nucleotide bases in a promoter suppresses gene expression. DNA methylation patterns change during development, and also during an individual’s lifetime as a result of environmental factors. These patterns can be passed to offspring. Methylations and other potentially heritable modifications to DNA that affect gene expression without changing the DNA sequence are epigenetic.

Self-Quiz Answers in Appendix I 1. A chromosome contains many genes that are transcribed into different __________ . a. proteins c. RNAs b. polypeptides d. a and b 2. RNAs form by __________ ; proteins form by __________ . a. replication; translation c. transcription; translation b. translation; transcription d. replication; transcription

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Gene Expression and Control  Chapter 8  157  

4. The main function of a DNA molecule is to __________ . a. store heritable information b. carry a translatable message c. form peptide bonds between amino acids 5. The main function of an mRNA molecule is to __________ . a. store heritable information b. carry a translatable message c. form peptide bonds between amino acids 6. Where does transcription take place in a prokaryotic cell? c. the cytoplasm a. the nucleus b. ribosomes d. b and c are correct 7. Most codons specify a(n) __________ . a. protein c. amino acid b. polypeptide d. mRNA 8. Where does translation take place in a eukaryotic cell? a. the nucleus c. the cytoplasm b. ribosomes d. b and c are correct 9. A mutation called a(n) __________ often results in a frameshift that garbles the genetic message. a. deletion c. base-pair substitution b. insertion d. a or b 10. Gene expression does not vary by _______ . a. cell type c. stage of development b. extracellular conditions d. the genetic code 11. Muscle cells differ from bone cells because they __________ . a. have different genes c. are eukaryotic b. use different genes d. both a and b 12. A cell with a Barr body is __________ . a. prokaryotic c. from a female mammal b. a sex cell d. infected by Barr virus 13. Put the following processes in order of their occurrence during expression of a eukaryotic gene: a. mRNA processing c. transcription b. translation d. RNA leaves nucleus

14. Which of the following statements is not correct? a. Some gene expression patterns can be passed to an individual’s offspring. b. Expression of a master regulator triggers a gene expression cascade. c. X chromosome inactivation is necessary for normal development of male mammals. 15. Match each term with the most suitable description. a. cells become specialized methylation b. protein-coding segment insertion c. epigenetic promoter d. assembles amino acids genetic message e. read in threes differentiation f. extra nucleotides exon g. regulatory site ribosome

CRITICAL THinking 1. Toxic RIPs kill cells because they stop a process of gene expression. Many antibiotics used to treat bacterial infections in humans also target processes of gene expression. For example, rifampicin binds to RNA polymerase and physically blocks lengthening of a new RNA. Why do these antibiotics kill bacteria, but not humans? 2. An anticodon has the sequence GCG. What amino acid does this tRNA carry? What would be the effect of a mutation that changed the C of the anticodon to a G? 3. Use Figure 8.7 to translate the following sequence of bases in an mRNA into an amino acid sequence, starting at the first base. Use the one-letter abbreviations for the amino acids. GGUGAAAAUGAGACCAUUUGUAGU 4. Translate the base sequence in the previous question, starting at the third base. 5. Each position of a codon can be occupied by one of four (4) nucleotides. What is the minimum number of nucleotides per codon necessary to specify all 20 of the naturally occurring amino acids that are assembled into proteins? 6. The photo at right shows four Barr bodies in the nucleus of a cell from a human female. How can there be multiple Barr bodies in the same cell?

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Copyright (2001) National Academy of Sciences, U.S.A. PNAS

3. In cells, most RNA molecules are __________ , and DNA molecules are __________ . a. single-stranded; double-stranded b. double-stranded; single-stranded c. double-stranded; double stranded

9 How Cells Reproduce

9.1

Henrietta’s Immortal Cells  159

9.2

Multiplication by Division  160

9.3

Mitosis and Cytoplasmic Division  163

9.4

Cell Cycle Control  165

9.5

Sex and Alleles  169

9.6

Meiosis in Sexual Reproduction  171

This micrograph shows dividing cells making up an actively growing root tip of an onion plant. Chromosomes are stained blue. Cell divisions by mitosis are the basis of growth in multicelled eukaryotes.

Concept Connections Steve Gschmeissner/Science Photo Library/Getty Images

Mitosis is the basis of growth and tissue repair in multicelled eukaryotes (20.1, 20.6, 27.3, 28.6). Many single-celled eukaryotes can reproduce asexually by mitosis (14.6, 27.1), but sexual reproduction (27.2, 29.3) requires meiosis. Natural selection operates on variation in shared traits among members of a popula­­ tion (10.2, 13.2). This variation is an outcome of variations in DNA sequence (7.3) that arise by mutation (7.6). Mutations that disrupt regulatory molecules (8.7) governing cell division can lead to cancer (10.6, 11.1, 20.3, 24.3, 26.2, 27.8). This chapter also revisits the structure of cells (3.3–3.5) and chromosomes (7.4).

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How Cells Reproduce  Chapter 9  159 

Application 9.1  Henrietta’s Immortal Cells Each human starts out as a fertilized egg. By the time of birth, that single cell has given rise to about a trillion other cells, all organized as a human body. Even in an adult, billions of cells divide every day as new cells replace worn-out ones. As early as the mid-1800s, researchers were trying to coax human cells to keep dividing outside of the body. Immortal cell lineages—cell lines—would allow them to study human diseases (and potential cures) without experimenting on people. However, human cells grown in the laboratory tend to divide a limited number of times and die within weeks. The quest to create a human cell line continued unsuccessfully for over one hundred years. George and Margaret Gey had been trying for nearly thirty years when, in 1951, their assistant Mary Kubicek prepared a new sample of human cancer cells. Mary named the cells HeLa, after the first and last names of the patient from whom the cells had been taken. The HeLa cells began to divide, again and again. The cells were astonishingly vigorous, quickly coating the inside of their bottles and consuming their nutrient broth. Four days later, there were so many cells that the researchers had to transfer them to more bottles. Sadly, cancer cells in the patient were dividing just as fast. Only six months after she had been diagnosed with cervical cancer, malignant cells had invaded tissues throughout her body. Two months after that, Henrietta Lacks, a young woman from Baltimore, was dead. Even after Henrietta had passed away, her cells continued to divide, over and over, in the Geys’ laboratory. The Geys discovered how to grow poliovirus in HeLa cells, a practice that enabled them to determine which strains of the virus cause polio. That work was a critical step in the development of polio vaccines, which have since saved millions of lives. Frozen away in tiny tubes, HeLa cells continue to be shipped among laboratories all over the world. Their role in research has been invaluable, and they are still widely used to investigate cancer, viral growth, protein synthesis, the effects of radiation, and countless other processes important in medical research (Figure 9.1). HeLa cells helped several researchers win Nobel Prizes, and they even traveled into space for experiments on satellites. Understanding why cancer cells are immortal—and why we are not—begins with learning about the structures and mechanisms that cells use to divide.

A. Henrietta Lacks died of cancer in 1951, but her cells—HeLa cells—are still dividing in laboratories all over the world. For decades, they have been invaluable in research efforts that have saved countless lives.

B. A micrograph of HeLa cells reveals plasma membrane extensions that allow cancer cells to migrate through tissues. Inappropriate migration and other abnormal behaviors characteristic of cancer cells begin with defects in proteins that govern the timing of cell division. Figure 9.1  HeLa cells are a legacy of cancer victim Henrietta Lacks. (A) Henrietta Lacks (1920-1951) afro American woman, affected by cervical cancer, her cells were the first to be cultured and used in medical research (HeLa cells)/Rue Des Archives (RDA)/Bridgeman Images; (B) Courtesy of Tom Deerinck/National Institute of General Medical Sciences (NIGMS)/NIH

Discussion Questions 1. In the 1950s, it was common for doctors to experiment on patients without their knowledge or consent. Thus, the young physician treating Henrietta Lacks probably didn’t ask permission before taking a sample of her cancerous cervix. That sample was the one that the Geys used to establish the HeLa cell line. These days, patients’ tissues can be used for research only with their signed consent. Do you think Ms. Lacks would have given permission for her tissue to be used in research? Would you? Why or why not? 2. Cancer cells cultured from a person’s tissue sample may divide indefinitely when maintained properly in a laboratory, producing generation after generation of descendant cells. Do the descendant cells belong to the person from whom the tissue was taken, or to the laboratory that maintains them? 3. Cell lines such as HeLa are used as research tools to study human diseases. What are some of the benefits of using cell lines to study human diseases? What are some of the limitations?

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160  Unit 2 GENETICS

9.2  Multiplication by Division Learning Objectives ●●

Explain why we say that mitosis maintains the chromosome number.

●●

Identify two body processes that occur by mitosis.

A life cycle is a sequence of recognizable stages that occur during an organism’s lifetime. Multicelled organisms and free-living cells have life cycles, but what about cells that make up a multicelled body? Biologists consider such cells to be individually alive, each with its own lifetime (Figure 9.2). A eukaryotic cell’s life passes through a series of recognizable intervals and events collectively called the cell cycle (Figure 9.3).

The Cell Cycle

Figure 9.2  Cells are individually alive even as part of a multicelled organism. Cells in different regions of this five-day-old human embryo are at different stages of division, an indication that differentiation is already under way. DNA appears in red fluorescence; microtubules, in green. S.Ozkavukcu, Isik A, Cinar O & A. Can

Figure 9.3  A eukaryotic cell cycle. G1, S, and G2 are part of interphase. The length of these stages differs among cells.

inter

G2

5

4S 7 2 G1

1 A typical cell spends most of its life in interphase.

metaphase

2 Each cell starts out life in G1, during which it increases in size

anaphase

6

1

prophase

telophase cytoplasmic division

mitosis

ph

as

e

Built-in checkpoints can pause the cycle until certain conditions are met (see Section 9.3).

A typical cell spends most of its life in interphase, which is the interval between divisions 1. The cell increases in size, replicates its DNA, and prepares for division during interphase. Interphase proceeds in three major stages: G1, S, and G2. The G stands for “Gap”, and these stages were named because outwardly, they seem to be periods of inactivity, but they are not. A cell starts out life in G1 2. During this phase, the cell grows and produces the molecules it will need for DNA replication (Section 7.5). Cells in G1 may temporarily or permanently exit the cell cycle by entering a nondividing state called G0 3. Differentiated cells going about their metabolic business— muscle cells, nerve cells, and so on—are in G0. A cell that is going to divide continues in the cell cycle, and moves from G1 into the S phase, when DNA replication occurs 4. After the DNA has been replicated, the cell enters G2 5, when it makes the proteins and other cellular components needed for division. The remainder of the cell cycle consists of the division process. Because each cell arises by division of a preexisting cell (Section 3.2), the cycle begins and ends with division. The duration of cell cycle phases varies by the type of cell. For example, rapidly dividing human body cells spend about 11 hours in G1, 8 hours in S, and 4 hours in G2. Mitosis takes about an hour, so the entire cell cycle occurs in about 24 hours. By contrast, yeast cells can progress through their cell cycle in as little as 90 minutes.

and produces molecules required for DNA replication.

3 A cell in G1 may exit the cycle to temporarily or permanently

stay in a state called G0. A cell in G0 is going about its metabolic business and not preparing to divide.

4 During S, a cell copies its chromosomes by DNA replication. 5 During G2, the cell produces proteins and other components that are necessary for division.

6 The nucleus divides during mitosis. 3 G0

7 After mitosis, the cytoplasm divides. Each descendant cell begins the cycle anew, in G1.

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How Cells Reproduce  Chapter 9  161 

How Mitosis Maintains the Chromosome Number A eukaryotic cell reproduces by dividing, and each of its two cellular offspring receives DNA packaged in a nucleus. Thus, eukaryotic cell division necessarily includes a mechanism by which the nucleus divides. Mitosis 6 is the mechanism of nuclear division that maintains the chromosome number. Homologous Chromosomes  Consider how your body cells are diploid,

which means their nucleus contains two sets of chromosomes (Section 7.4). One complete set came from your mother; the other, from your father. Thus, your cells have two of each type of chromosome. Except for a pairing of nonidentical sex chromosomes (XY) in males, the chromosomes of each pair are homologous. Homologous chromosomes have the same length, shape, and genes (hom– means alike). Note that homologous chromosomes differ from sister chromatids, which are identical molecules of DNA produced by DNA replication. Sister chromatids are attached at the centromere to form one X-shaped chromosome: one pair of homologous chromosomes

A. Before DNA replication, each chromosome consists of one DNA molecule (and associated proteins). One chromosome of each homologous pair was inherited from each parent. B. After DNA replication, each chromosome consists of two molecules of DNA attached as sister chromatids.

sister chromatids sister chromatids

By contrast, the two homologous chromosomes of a pair are not identical. Each was inherited from two parents that differ genetically, so their DNA sequence differs slightly (Section 9.5 returns to this topic). One Diploid Cell to Two Diploid Cells  When a cell divides, it produces two cells.

Mitosis distributes a copy of each chromosome present in the parent cell to its offspring. Thus, if the parent cell is diploid, its offspring will be diploid too. When a cell is in G1, each of its chromosomes consists of one DNA molecule (Figure 9.4A). DNA replication occurs during S, so by G2, each chromosome consists of two identical DNA molecules attached as sister chromatids (Figure 9.4B). The sister chromatids stay attached until mitosis is almost over, and then they are pulled apart and packaged into two separate nuclei. As sister chromatids are pulled apart, each becomes an individual chromosome with one DNA molecule. Sister chromatids are identical, so the two new nuclei that form by mitosis contain the same number and types of chromosomes as the parent cell. When the cytoplasm divides 7, these nuclei are packaged into separate cells (Figure 9.4C).

Why Cells Divide by Mitosis In multicelled organisms, mitosis and cytoplasmic division are the basis of body formation and increases in size during development: Continuing mitotic divisions of embryonic cells as they differentiate produce tissues and body parts of the embryo. Juvenile development into the adult form also occurs by mitosis, as do ongoing replacements of damaged or dead cells. Scrape your knee, and mitotically dividing cells in your skin repair the wound. Skin cells and many other types of body cells are continually replaced by mitosis. In eukaryotes, mitosis is part of asexual reproduction, a reproductive mode in which offspring are produced by one parent only. Many plants can reproduce this way, for example when a stem breaks off and takes root in soil. Many singlecelled eukaryotes also reproduce asexually by mitosis. Prokaryotes reproduce by

C. Mitosis and cytoplasmic division separate the sister chromatids of each chromosome and package them in the nuclei of two new cells. Each new cell has the chromosome number of the parent. Figure 9.4  How mitosis maintains the chromosome number. For clarity, only one homologous pair of chromosomes is shown in a diploid cell.

asexual reproduction  Reproductive mode by which offspring arise from a single parent only. cell cycle  The collective series of intervals and events of a eukaryotic cell’s life, from the time it forms until it divides. homologous chromosomes  In a nucleus, chromosomes with the same length, shape, and set of genes. interphase  In a eukaryotic cell cycle, the interval between mitotic divisions when a cell grows, roughly doubles the number of its cytoplasmic components, and replicates its DNA. mitosis  Nuclear division mechanism that maintains the chromosome number.

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162  Unit 2 GENETICS

CLOSER LOOK Figure 9.5  Mitosis.

1 Interphase Interphase cells are shown for comparison, but interphase is not part of mitosis. The nuclear envelope is intact, and the loosened chromosomes are not easily visible under a light microscope. DNA replication occurs before mitosis begins, so each chromosome consists of two sister chromatids.

nuclear envelope breaking up

tightly packed chromosome

Mitosis in a plant cell

2 Prophase Mitosis begins. The duplicated chromosomes become visible as they pack into their most compact forms. The nuclear envelope breaks up as spindle microtubules assemble and bind to chromosomes at the centromere. Figure It Out: What is the chromosome number of the illustrated cell?

Answer: 4

Mitosis in an animal cell

spindle microtubule

3 Metaphase spindle pole

All of the chromosomes are aligned midway between the spindle poles. Microtubules of the spindle now attach sister chromatids of each chromosome to opposite spindle poles.

sister chromatids

4 Anaphase Sister chromatids separate and move toward opposite spindle poles. Each sister chromatid has now become an individual, unduplicated chromosome.

5 Telophase new nuclear nucl envelope enve chro chromosomes loosening loos

The chromosomes reach opposite sides of the cell and their packing loosens. Mitosis ends when a new nuclear envelope forms around each cluster of chromosomes. Figure It Out: At telophase, how many molecules of DNA does each chromosome have?

Answer: 1

Figure Summary Mitosis is a nuclear division process that maintains the chromosome number in cellular offspring. Micrographs show animal cells (fertilized egg of a worm, left) and plant cells (onion root, right). A diploid (2n) animal cell with two chromosome pairs is illustrated. ISM/Medical Images.com; Michael Clayton/University of Wisconsin

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How Cells Reproduce  Chapter 9  163 

dividing, but they do not have a nucleus and do not undergo mitosis (we discuss their reproduction in Section 14.4).

Take-Home Message 9.2 ●● ●●

●●

A cell’s life occurs in a series of intervals and events collectively called the cell cycle. Division of a eukaryotic cell occurs in two steps: nuclear division followed by cytoplasmic division. Mitosis, the nuclear division mechanism that maintains the chromosome number, is the basis of growth, tissue repair, and (in many species) asexual reproduction.

spindle pole

9.3  Mitosis and Cytoplasmic Division Learning Objectives ●●

Describe the role of microtubules in nuclear division.

●●

Explain the difference between cytoplasmic division in plants and animals.

Stages of Mitosis

Figure 9.6  The spindle.

When a cell is in interphase, its chromosomes are loosely packed to allow transcription and DNA replication (Figure 9.5). Loose packing makes chromosomes difficult to see under a light microscope 1. The events of mitosis proceed in four main stages: prophase, metaphase, anaphase, and telophase.

A spindle is visible in this cell, a fertilized egg (of a worm) undergoing mitosis. Microtubules appear in yellow; chromosomes, in blue.

Metaphase  By the end of prophase, one sister chromatid of each chromosome has

become attached to microtubules extending from one spindle pole, and the other sister chromatid has become attached to microtubules extending from the other spindle pole. The opposing sets of microtubules then begin a tug-of-war. By adding and losing tubulin subunits, the microtubules lengthen and shorten, pushing and pulling the chromosomes as they do. When all the microtubules are the same length, the chromosomes are aligned midway between spindle poles 3. The alignment marks metaphase. Anaphase  During anaphase, sister chromatids detach from one another and move toward opposite sides of the cell 4. When sister chromosomes separate, each becomes an individual, unduplicated chromosome. Telophase  Telophase begins when one set of chromosomes arrives at each spindle pole and forms a cluster 5. Each cluster has the same number and kinds of chromosomes as the parent cell nucleus had: two of each type of chromosome, if the parent

Figure It Out: In which stage of mitosis is this cell?

Answer: Prophase

Prophase  Mitosis begins with prophase. During prophase, the chromosomes pack into their most compact forms, which are visible under a light microscope 2. Tight packing keeps the chromosomes from getting tangled and breaking as the nucleus divides. “Mitosis” is from mitos, the Greek word for “thread,” after the threadlike appearance of chromosomes during the process. The nuclear envelope breaks up as microtubules lengthen from two regions on opposite sides of the cell and attach to the chromosomes at their centromeres. The microtubules form a spindle, a temporary structure that moves chromosomes during nuclear division (Figure 9.6). The areas where the spindle originates on both sides of the cell are called spindle poles.

© George von Dassow

anaphase  Stage of mitosis during which sister chromatids separate and move toward opposite spindle poles. metaphase  Stage of mitosis at which all chromosomes are aligned midway between spindle poles. prophase  Stage of mitosis during which chromosomes pack tightly and become attached to a newly forming spindle. spindle  Temporary structure that assembles and moves chromosomes during nuclear division; consists of microtubules that elongate from two spindle poles. telophase  Stage of mitosis during which chromosomes arrive at opposite spindle poles and become enclosed by a new nuclear envelope.

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164  Unit 2 GENETICS

1 A ring of microfilaments

cell was diploid. A new nuclear envelope forms around the clusters as the chromosomal packing loosens. At this point, mitosis is over.

and motor proteins (yellow) forms under the plasma membrane during anaphase. This contractile ring wraps around the cell.

Cytoplasmic Division Mitosis is usually followed by division of the cell’s cytoplasm. The mechanism of cytoplasmic division differs among eukaryotes, but in all cases it requires many molecules and structures that are in place well before mitosis ends.

2 After telophase, the

contractile ring pulls the plasma membrane inward, forming a cleavage furrow as it contracts. Spindle microtubules guide vesicles to the plane of division.

In Animal Cells  Cytoplasmic division in animal cells and many single-celled

cleavage furrow

3 When the contractile

ring is at its smallest diameter, spindle microtubules inside of it are cut. Vesicles fuse to form new membrane that partitions the two new cells.

Figure 9.7  Cytoplasmic division of an animal cell. The small blue dots represent vesicles.

1 Before mitosis, a

network of parallel microtubules (orange) condenses into a dense ring around the future plane of division.

2 During mitosis,

microtubules of the ring reorganize to form the spindle. In late anaphase, the microtubules guide vesicles to the plane of division. By telophase, the vesicles have begun to fuse and form a cell plate.

3 The cell plate expands along the plane of division as more vesicles merge with it. When the cell plate fuses with the plasma membrane, the cytoplasm is partitioned so two new cells form.

eukaryotes involves a mesh of cytoskeletal elements in the cell cortex, a region of cytoplasm that underlies the plasma membrane (Figure 9.7). During anaphase, these cytoskeletal elements reorganize to form a band of microfilaments and motor proteins that wraps around the cell 1. The band is called a contractile ring because it contracts after telophase. Contraction pulls the plasma membrane inward, forming an indentation called a cleavage furrow that is visible on the outside of the cell 2. Vesicles guided to the plane of division by spindle microtubules add membrane to the indented region, and this prevents the plasma membrane from stretching as the contractile ring shrinks. When the contractile ring reaches its smallest diameter, spindle microtubules inside the ring are cut, and more vesicles fuse to form new membrane that partitions the two new cells 3. In Plant Cells  A contractile ring minimizes the amount of new plasma membrane required to partition descendant cells, but this strategy works only in animal cells— which have no walls. Plant cells, by contrast, have a stiff cell wall around the plasma membrane (Section 3.6), so their strategy of cytoplasmic division necessarily differs (Figure 9.8). Before mitosis, a ring of parallel microtubules forms around the future plane of division 1. These microtubules reorganize during mitosis to form the spindle, and by late anaphase have guided vesicles to the plane of division. The vesicles contain polysaccharides and glycoproteins necessary for building cell wall material, and during telophase they fuse into a flat structure called a cell plate 2. The membranes of the merged vesicles will become the plasma membranes separating the two descendant cells, and the vesicles’ contents will be converted to walls. The cell plate expands at its edges as more vesicles merge, until it reaches and fuses with the cell’s plasma membrane 3.

Take-Home Message 9.3 ●●

●●

●●

●●

Figure 9.8  Cytoplasmic division of a plant cell. The small blue dots represent vesicles.

DNA replication occurs before mitosis. As mitosis begins, each chromosome consists of two identical DNA molecules attached at the centromere as sister chromatids. A spindle forms and attaches the sister chromatids of each chromosome to opposite spindle poles. The sister chromatids then separate and move to the spindle poles. At the moment of separation, each sister chromatid becomes an individual chromosome. A new nuclear envelope forms around the chromosomes clustering at each spindle pole, so two new nuclei form. Each nucleus has the same number and types of chromosomes as the parent. Cytoplasmic division after mitosis produces two descendant cells. The mechanism of cytoplasmic division differs among eukaryotes.

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How Cells Reproduce  Chapter 9  165 

9.4  Cell Cycle Control Learning Objectives ●●

Describe the role of checkpoints in the cell cycle.

●●

Explain the cell division limit.

●●

Explain why mutations can give rise to tumors.

●●

Use an example to describe tumor suppressors.

●●

Describe some characteristics of malignant cells.

Checkpoints The timing of cell division is determined by molecules that regulate gene expression (Section 8.2). Like the accelerator of a car, some of these molecules cause the cell cycle to advance. Others are like brakes that prevent the cycle from proceed­­ing. This control occurs at checkpoints built into the cell cycle (a few are marked in Figure 9.3). Protein products of “checkpoint genes” interact to ensure that cell division occurs only at appropriate times. Consider p53, a checkpoint gene product of humans and other animals. The p53 protein is a transcription factor that operates the checkpoint at the end of G1. If the cell’s DNA becomes damaged, p53 moves the cell cycle into G0 and activates repair proteins that can fix the damage. When repair is complete, the brakes are lifted, and the cell cycle advances to the S phase for DNA replication. If the DNA cannot be repaired, the cycle does not advance, and p53 triggers a series of events that cause the cell to self-destruct. By preventing replication of damaged DNA, p53 helps minimize the chance of replication errors that can lead to mutation (Section 7.6).

Figure 9.9  Effects of an oncogene. In this section of human breast tissue, a brown-colored tracer shows the active form of a growth factor receptor. The darker cells are part of a tumor; they have an overactive receptor that is constantly stimulating mitosis. Cells of most tumors have mutations that cause this particular receptor to be overproduced or overactive. Normal cells are lighter in color. From “Expression of the epidermal growth factor receptor (EGFR) and the phosphorylated EGFR in invasive breast carcinomas.” http://breast-cancer research.com/content/10/3/R49

Losing Control Some mutations can affect a checkpoint gene so that its protein product no longer works properly. Other mutations can disrupt the gene’s expression, so a cell makes too much or too little of its product. A cell with one of these mutations divides when it should not. The mutation is inherited by the cell’s descendants, so they divide abnormally too. In humans and other multicelled eukaryotes, a mutation that disrupts a cell cycle checkpoint can result in formation of a tumor. A tumor is a mass of abnormally dividing cells in a tissue. Almost all mutations arise in body cells. Those that arise in reproductive cells can be passed to offspring, which is why some types of tumors run in families. Oncogenes  Some mutations cause tumors because they increase the activity or number of molecules that stimulate mitosis. Genes in which such mutations can occur are called proto-oncogenes. A proto-oncogene that acquires a tumor-causing mutation becomes an oncogene. Oncogenes jam the accelerator on the cell cycle. Consider how most tumors in humans carry mutations resulting in an overactivity or overabundance of growth factor receptors (Figure 9.9). Growth factors are molecules that stimulate cell division, and most of your body cells have receptors for them. When these receptors bind to a growth factor, they trigger the cell cycle to advance, so the cell divides. Genes that encode growth factor receptors are proto-oncogenes, because mutations can turn them into oncogenes. Such mutations result in a receptor protein that triggers mitosis even in the absence of growth factor. Cells that have these mutations divide when they should not.

cleavage furrow  In a dividing animal cell, the indentation where cytoplasmic division will occur. oncogene  Gene that can transform a normal cell into a tumor cell. Carries a mutation that results in the inappropriate stimulation of mitosis. tumor  A mass of abnormally dividing cells in a tissue.

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166  Unit 2 GENETICS Tumor Suppressors  Some mutations cause tumors because they decrease the activ-

A. BRCA1 (red dots) repairs double-stranded breaks in DNA.

B. p53 (green dots) pauses the cell cycle when DNA is damaged.

Figure 9.10  Checkpoint gene products in action. These fluorescence micrographs show alternative views of the nucleus in the same cell. The cell was exposed to ionizing radiation, so its DNA is damaged. BRCA1 (red) and p53 (green) appear in the same places in the two photographs because they have clustered around the same sites of DNA damage. The integrated action of these and other proteins prevents DNA replication from occurring until the DNA breaks are fixed. © Phillip B. Carpenter, Department of Biochemistry and Molecular Biology, University of Texas - Houston Medical School.

1 Benign tumors

grow slowly and stay in their home tissue.

2 Malignant tumors grow

quickly, and their cells do not stay anchored in home tissue.

ity or number of molecules that inhibit mitosis. These molecules are called tumor suppressors, because tumors form when they are defective or missing. Tumor suppressors put the brakes on the cell cycle. The p53 protein is a tumor suppressor; so is a protein called BRCA1. Normally, BRCA1 suppresses expression of a particular growth factor receptor, so mutations that reduce its abundance cause a cell to make too many of these receptors. The cell becomes overresponsive to the growth factor, so it divides when it should not (an outcome associated with tumor formation). This is why mutations in the gene for BRCA1 are associated with an increased risk for breast and ovarian tumors. Tumors can also be caused by viruses that interfere with tumor suppressor function. For example, several types, or strains, of a virus called HPV (human papillomavirus) cause tumors. A cell infected with one of these HPV strains produces a protein that encourages the breakdown of p53. Mutations Lead to More Mutations  Like many other tumor suppressors, BRCA1 has multiple functions. In addition to inhibiting mitosis, BRCA1 plays a critical role in repairing double-stranded breaks in DNA (Figure 9.10). This type of DNA damage may not be repaired in cells that underproduce BRCA1. Normally, a cell with broken chromosomes will kill itself, an outcome of cell cycle regulation by the p53 protein. If a cell underproduces both BRCA1 and p53, however, its cell cycle can proceed into the S stage even when its chromosomes are broken. Replication of damaged DNA is highly error-prone (Section 7.6), so mutations accumulate in cells that continue dividing even when their DNA is damaged. As you will see shortly, this can have a dangerous outcome. The p53 protein operates as both a brake and an accelerator in the cell cycle, and mutations can disrupt either of these functions. Thus, p53 is a tumor suppressor, and the gene that encodes it is a proto-oncogene. This gene is mutated in most human tumor cells.

Pathological Mitosis

3 Malignant cells become attached to the wall of a

lymph vessel or blood vessel (as shown here). They release digestive enzymes that create an opening in the wall, then enter the vessel.

4 The cells move through the vessel, then exit the

same way they got in. Migrating cells may start growing in other tissues, a process called metastasis. Figure 9.11  Tumors and metastasis.

Some tumors are harmless, and others are not. Warts, which are growths caused by infection with some strains of HPV, are examples of benign (harmless) tumors. Benign tumors grow very slowly and stay properly anchored in their home tissue (Figure 9.11 1). By contrast, malignant tumors progressively worsen and are dangerous to health. Multiple mutations are required to transform a normal cell into a malignant one. Some of these mutations may be inherited, but DNA damage is their most common cause. Compromised repair mechanisms and failed cell cycle controls give rise to abnormalities characteristic of malignant cells. Following are a few examples. Malignant Cells Malfunction  Like cells of all tumors, malignant cells divide abnormally. Controls that usually keep cells from getting overcrowded in tissues are lost, so populations of malignant cells may reach extremely high densities with cell division occurring very rapidly. The cytoplasm and plasma membrane of malignant cells are altered; both are indications of cellular malfunction. The cytoskeleton may be shrunken, disorganized, or both. Malignant cells typically have an abnormal chromosome number, with some chromosomes present in multiple copies, and others missing or broken in pieces. The balance of metabolism is often shifted, as in ATP formation occurring mainly by fermentation rather than aerobic respiration.

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How Cells Reproduce  Chapter 9  167 

Figure 9.12  Telomeres. The bright dots at the end of each DNA strand in these (duplicated) chromosomes show telomere sequences. ISM/Medical Images.com

Metastasis  Malignant cells do not stay anchored properly in tissues 2 because

their plasma membrane adhesion proteins are defective or missing. This allows the cells to slip easily into and out of vessels of the circulatory and lymphatic systems 3. By migrating through these vessels, malignant cells can establish tumors elsewhere in the body 4. The process in which malignant cells break loose from their home tissue and invade other parts of the body is called metastasis. Cancer  Malignant tumors can disrupt body tissues, both physically and metabolically. Cancer is a group of diseases characterized by malignant cells—cells that are

abnormally dividing and have the potential to move to other body tissues. Unless chemotherapy, surgery, or another procedure eliminates malignant cells from the body, they can put an individual on a painful road to death. Each year, cancer causes 15 to 20 percent of all human deaths in developed countries. Prevention  Mutations that transform a normal cell into a malignant one may take a

lifetime to accumulate. Lifestyle choices such as not smoking and avoiding exposure of unprotected skin to sunlight reduce one’s risk of acquiring mutations in the first place. Some tumors can be detected with periodic screening such as gynecology or dermatology exams. If detected early enough, many types of malignant tumors can be removed before metastasis occurs.

The Role of Telomeres Triggering the suicide of a malfunctioning cell is one type of fail-safe defense against cancer. Another involves telomeres, which are regions of noncoding DNA at the ends of eukaryotic chromosomes (Figure 9.12). Telomeres consist of a short DNA sequence that is repeated hundreds or thousands of times. Proteins that bind to these repeats shield the ends of a chromosome from cellular processes that might damage them. Telomeres shorten every time a cell divides. When they get too short, the protective proteins can no longer bind to them, and DNA at the ends of the

cancer  Group of diseases characterized by malignant cells (abnormally dividing cells that can migrate to other body tissues). metastasis  The process in which cells of a malignant tumor spread from one part of the body to another.

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168  Unit 2 GENETICS

Digging Into Data HeLa Cells Are a Genetic Mess HeLa cells can vary in chromosome number. Defects in proteins that orchestrate cell division result in descendant cells with too many or too few chromosomes, an outcome that is one of the hallmarks of malignant cells. The karyotype in Figure 9.13, originally published in 1989, shows all of the chromosomes in a single HeLa cell. 1. What is the chromosome number of this HeLa cell? 2. How many extra chromosomes does this cell have, compared with a normal human body cell? 3. Can you tell that this cell came from a female? How?

Figure 9.13  Karyotype of HeLa showing chromosomes in one cell. Courtesy of Dr. Thomas Ried, NIH and the American Association for Cancer Research

chromosomes becomes exposed. An exposed end of a chromosome is targeted for repair as if it were a double-stranded DNA break: Checkpoint gene products bind to it, and p53 moves the cell cycle into G0. Senescence  Enzymes that repair DNA cannot fix short telomeres, so cell cycle arrest due to telomere shortening tends to be irreversible. Most cells in this state eventually die, but some become senescent, which means they are permanently stuck in G0—metabolically active but not functioning properly. The result can be dangerous. A senescent cell becomes progressively abnormal, for example enlarging and releasing too much of a protein that promotes inflammation. The cell will continue interacting dysfunctionally with other cells unless the immune system detects and eliminates it. The Cell Division Limit  Most body cells can divide only a certain number of times before they senesce, and that number—the cell division limit—varies by species. Typical human body cells, for example, can divide about 50 times before senescing. The cell division limit is a fail-safe mechanism in case a cell loses control over the cell cycle and begins to divide again and again. A limit on the number of divisions prevents these rogue cells from overrunning the body. Life Span  Telomere shortening may be the only physiological barrier to immortal-

ity, and it is a likely part of the mechanism that sets an organism’s life span. This is because, as an animal ages, the number of senescent cells increases in its tissues. When enough of these cells accumulate, they disrupt tissue and organ function: a common problem with advancing age.

Targeting Telomeres to Fight Cancer  A few cells in the adult body retain

alleles  Forms of a gene with slightly different DNA sequences; may encode different versions of the gene’s product.

the ability to divide indefinitely. These cells are called stem cells, and they are undifferentiated. A stem cell can remain inactive, idling in G0 until signals from other cells move it into a rapidly dividing state. The cell’s descendants can differentiate to repopulate tissues with replacement cells—for example, during injury repair. Stem cells are essentially immortal because they express genes for telomerase, an enzyme that lengthens telomeres. The lengthening means these cells have no cell

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How Cells Reproduce  Chapter 9  169 

division limit. Other body cells do not produce this enzyme, and their telomeres shorten every time they divide. Malignant cells, including the HeLa cells you learned about in Section 9.1, characteristically produce a lot of telomerase, which is why they can divide indefinitely. Cancer researchers have been developing treatments that target telomerase, with the goal of restoring mortality to malignant cells. One newly developed drug binds to the enzyme and prevents it from recognizing telomeres. The drug reduces the ability of malignant cells to maintain the length of their telomeres, so it shortens their life span. Another approach involves vaccines that elicit an immune response against telomerase. Immune cells produced in these responses recognize and kill cells that make the enzyme. (Chapter 23 returns to vaccines and immune responses.) Both approaches have shown positive results in clinical trials, and offer something that few current chemotherapies offer—high selective toxicity, meaning the drugs kill mainly cancer cells and have relatively little effect on healthy tissue.

Take-Home Message 9.4 ●●

●●

●●

●●

Built-in checkpoints that delay or stop the cell cycle ensure division occurs only at appropriate times. Tumors form when checkpoint mechanisms fail and cells begin dividing when they should not. Mutations in multiple checkpoint genes can give rise to a malignant tumor. Diseases called cancer are characterized by malignant cells. Telomere shortening imposes a limit on cell division—a fail-safe mechanism in case control over cell division is lost.

9.5  Sex and Alleles Learning Objectives ●●

Explain why homologous chromosomes of a sexually reproducing organism carry different alleles.

●●

List some differences between sexual reproduction and asexual reproduction.

●●

Describe some evolutionary advantages of sexual reproduction versus asexual reproduction.

A. Corresponding colored patches in this fluorescence micrograph indicate corresponding DNA sequences in a pair of homologous chromosomes.

Introducing Alleles Your body cells are diploid (2n)—they contain pairs of homologous chromosomes. The two chromosomes of each pair have the same genes, but their DNA sequence is not identical. This is because you inherited your chromosomes from two parents who differ genetically; unique mutations accumulated in their separate lines of descent over time. Thus, the DNA sequence of any of your genes may differ a bit from a corresponding gene on a homologous chromosome (Figure 9.14). Different forms of the same gene are called alleles.

B. Homologous chromosomes carry the same set of genes. The members of each pair of genes may be identical in DNA sequence, or they may differ slightly, as alleles (color variations represent DNA sequence variations).

Alleles and Shared Traits  New alleles arise by mutation. They may encode slightly

different forms of a gene’s product, and such differences influence the details of traits. Members of a species have the same traits because they have the same genes, but almost every shared trait varies a bit among individuals of a sexually reproducing species. For example, people normally have two eyes, but some people have brown eyes; others have blue; and so on. Alleles of shared genes are the basis of

Figure 9.14  Genes on homologous chromosomes. Different forms of a gene are called alleles. (A) Image courtesy of Carl Zeiss MicroImaging, Thornwood, NY

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170  Unit 2 GENETICS offspring

leaf of parent plant

offspring

parent

parent

offspring

A. Offspring of sexual reproducers differ from one another and from their parents. Figure 9.15  Different species use different modes of reproduction. (A) cynoclub/Shutterstock.com; (B) KYTan/Shutterstock.com

B. Asexual reproduction gives rise to genetically identical offspring.

this variation. As another example, consider the gene that encodes beta globin (Section 8.6). This gene has more than 700 alleles in humans: A few cause sicklecell anemia, several cause beta thalassemia, and so on. There are more than 20,000 human genes, and most of them have multiple alleles. (Chapter 10 returns to genetics and human traits.)

On the Advantages of Sex 

Table 9.1  Comparing Asexual and Sexual Reproduction

Mode:

Asexual

Sexual

Division

mitosis

meiosis, mitosis

Parent(s)

1

2

Parental cell(s)

one diploid or haploid cell

two haploid gametes

Parental genes

100% of one parent’s genes are passed to offspring

50% of each parent’s genes are passed to offspring

Offspring

genetically identical

not genetically identical

Advantage

does not require a partner

high genetic diversity

Disadvantage

low genetic diversity

requires a partner

You learned earlier in this chapter that mitosis and cytoplasmic division are part of asexual reproduction in eukaryotes, but only a few species use this reproductive mode exclusively. Most eukaryotes reproduce sexually (Figure 9.15). Sexual reproduction is the process in which offspring arise from two parents and inherit genes from both. Table 9.1 introduces some other differences between sexual and asexual reproduction. If the function of reproduction is the perpetuation of one’s genes, then an asexual reproducer would seem to win the evolutionary race. When it reproduces, it passes all of its genes to every one of its offspring. Only about half of a sexual reproducer’s genes are passed to each offspring. In addition, asexual reproduction tends to be faster than sexual reproduction because it requires no partner. So why is sex so widespread? Offspring of Asexual Reproducers Are Clones  Consider how all offspring of an asexual reproducer are clones: In the absence of new mutations, they have the same alleles as one another (and their one parent). This consistency is a good evolutionary strategy in a favorable, unchanging environment, because traits that help an organism survive and reproduce do the same for its offspring. However, most environments are constantly changing, and change is not always favorable. Individuals that are identical are equally vulnerable to environmental challenges. Offspring of Sexual Reproducers Are Diverse  In changing environments, sexual reproducers have the evolutionary edge because they carry different alleles. Sexual reproduction randomly mixes up the genetic information of two parents who

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How Cells Reproduce  Chapter 9  171 

have different alleles (and different forms of traits associated with those alleles). Offspring inherit new combinations of the alleles—and new combinations of the traits—so they differ from one another and from their parents. An environmental challenge may be unfavorable for some of these individuals, but others may be perfectly suited to the change. Thus, as a group, they have a better chance of surviving environmental challenges than clones. Weathering the Impact of Mutations  Another advantage of sexual reproduc-

tion involves the inevitable occurrence of moderately harmful mutations that can be passed to offspring. A population of sexual reproducers has a better chance of weathering the evolutionary effects of such mutations. With asexual reproduction, individuals bearing a mutation necessarily pass it to all of their offspring. This outcome is relatively rare with sexual reproduction, because each offspring of a sexual union has a 50 percent chance of inheriting a parent’s mutation. Thus, a moderately harmful mutation tends to spread more slowly through a population of sexual reproducers. (Chapter 13 returns to evolutionary processes.)

Take-Home Message 9.5 ●●

●● ●●

Paired genes on homologous chromosomes may vary slightly in DNA sequence, as alleles. Alleles arise by mutation. Alleles of shared genes are the basis of variation in shared traits. Offspring of sexual reproducers inherit new combinations of parental alleles, so they differ from one another and from their parents.

9.6  Meiosis in Sexual Reproduction Learning Objectives ●●

Describe the relationship between germ cells and gametes.

●●

Explain why sexual reproduction requires meiosis.

●●

Describe crossing over and how it fosters diversity among the offspring of sexual reproducers.

Most body cells are diploid (2n), with two copies of each chromosome—one inherited from each of two parents. A reproductive cell such as an egg or sperm is haploid (n), which means it has one copy of each chromosome. Meiosis is a nuclear division mechanism that halves the chromosome number, and it is essential to the formation of haploid cells.

Stages of Meiosis The process of meiosis is similar to mitosis in several ways. A cell replicates its DNA before either nuclear division process begins, so each chromosome consists of two sister chromatids. As in mitosis, a spindle forms, and its microtubules move the chromosomes. However, meiosis sorts the chromosomes into new nuclei not once but twice. The two consecutive nuclear divisions are called meiosis I and meiosis II. Figure 9.16 (next page) shows the stages of meiosis in a diploid (2n) cell. Meiosis I  The first stage of meiosis I is prophase I. During this stage, the chromo-

somes pack tightly, and homologous chromosomes align tightly and swap segments

haploid  Having one of each type of chromosome. meiosis  Nuclear division process that halves the chromosome number. Basis of sexual reproduction. sexual reproduction  Reproductive mode by which offspring arise from two parents and inherit genes from both.

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172  Unit 2 GENETICS

CLOSER LOOK Figure 9.16  Meiosis.

plasma membrane

spindle microtubule

spindle pole

nuclear envelope breaking up

pair of homologous chromosomes

MEIOSIS I: ONE DIPLOID CELL TO TWO HAPLOID CELLS

1 Prophase I

2 Metaphase I

3 Anaphase I

4 Telophase I

Homologous chromosomes pack tightly, pair up, and swap segments. Spindle microtubules assemble and bind to chromosomes as the nuclear envelope breaks up.

Homologous chromosome pairs are aligned midway between spindle poles. Microtubules of the spindle now attach the two chromosomes of each pair to opposite spindle poles.

Homologous chromosomes separate and move toward opposite spindle poles. This is the stage of meiosis in which the chromosome number becomes reduced.

A complete set of chromosomes clusters at each spindle pole. A nuclear envelope forms around each set as the chromosome packing loosens. Two haploid (n) cells form when the cytoplasm divides.

Figure Summary Two consecutive nuclear divisions, meiosis I (this page) and meiosis II (opposite), reduce the chromosome number. No DNA replication occurs between the two divisions. Meiosis in one diploid (2n) cell produces four haploid (n) cells. Illustrations show two pairs of chromosomes in an animal cell; homologous chromosomes are indicated in blue and pink. Micrographs show meiosis in a plant cell (lily). Bottom 1-8, With thanks to the John Innes Foundation Trustees, computer enhanced by Gary Head

Figure It Out: Which phase of meiosis reduces the chromosome number?

(more about this segment-swapping shortly). The nuclear envelope breaks up as the spindle forms 1. By the end of prophase I, microtubules of the spindle attach one chromosome of each homologous pair to one spindle pole, and the other chromosome to the opposite spindle pole. These microtubules grow and shrink, pushing and pulling the chromosomes as they do. At metaphase I 2, all of the microtubules are the same length, and the chromosomes are aligned midway between the spindle poles. During anaphase I 3, the homologous chromosomes of each pair move away from one another and toward opposite spindle poles. During telophase I, the two sets of chromosomes reach the spindle poles, and a new nuclear envelope forms around each set as the chromosomal packing loosens 4. The new nuclei are haploid (n), with one complete set of chromosomes. Each chromosome still consists of two sister chromatids. The cytoplasm divides at this point, so two haploid cells form.

Answer: Anaphase I

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How Cells Reproduce  Chapter 9  173 

No DNA replication

MEIOSIS II: TWO HAPLOID CELLS TO FOUR HAPLOID CELLS

5 Prophase II

6 Metaphase II

7 Anaphase II

8 Telophase II

The chromosomes pack tightly. Spindle microtubules assemble and bind to sister chromatids as the nuclear envelope breaks up.

The chromosomes are aligned midway between spindle poles. Microtubules of the spindle now attach sister chromatids to opposite spindle poles.

Sister chromatids separate and move toward opposite spindle poles. When sister chromatids separate, each becomes an individual chromosome.

A complete set of chromosomes clusters at each spindle pole. A nuclear envelope forms around each set as chromosomal packing loosens. Four haploid (n) cells form when the cytoplasm divides.

No DNA replication occurs between meiosis I and meiosis II. In some cells, a period of protein synthesis intervenes between the divisions; in other cells, meiosis II occurs immediately after meiosis I. Meiosis II  Meiosis II proceeds simultaneously in both nuclei that formed in

meiosis I. During prophase II 5, the chromosomes pack tightly, and the nuclear envelope breaks up as a new spindle forms. By the end of prophase II, spindle microtubules attach the sister chromatids of each chromosome to opposite spindle poles. These microtubules push and pull the chromosomes, aligning them midway between spindle poles at metaphase II 6. During anaphase II 7, all of the sister chromatids separate and move toward opposite spindle poles, thus becoming individual chromosomes. During telophase II 8, the chromosomes reach the spindle poles. New nuclear envelopes form around the clusters of chromosomes as their packing loosens. The

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174  Unit 2 GENETICS

new nuclei are haploid (n), with one complete set of chromosomes. Each chromosome has one molecule of DNA. The cytoplasm divides at this point, so four haploid cells form.

A. In this example, one gene has alleles A and a. The other gene has alleles B and b.

A

A

a

a

B

B

b

b

Crossing Over Early in prophase I of meiosis, all chromosomes in the cell pack tightly. When they do, each chromosome is drawn close to its homologous partner, so their corresponding chromatids align:

This tight, parallel orientation favors crossing over, a process by which a chromosome and its homologous partner exchange corresponding pieces of DNA during meiosis (Figure 9.17). Homologous chromosomes may swap any segment of DNA along their length, although crossovers tend to occur more frequently in certain regions.

B. Close contact between homologous chromosomes promotes crossing over: the exchange of corresponding pieces. Multiple crossovers are common.

C. After crossing over, paternal and maternal alleles have been mixed up on homologous chromosomes.

A

A

a

a

B

b

b

B

Crossing Over Shuffles Alleles  Exchanging segments of DNA shuffles alleles between homologous chromosomes. It breaks up the particular combinations of alleles that occurred on the parental chromosomes, and makes new ones on the chromosomes that end up in offspring. Thus, crossing over introduces novel combinations of alleles—and new combinations of traits—among offspring. It is a required process—meiosis will not finish unless it happens—but the rate of crossing over varies among species and among chromosomes. In humans, between 46 and 95 crossovers occur per meiosis, so each pair of homologous chromosomes crosses over two or three times, on average.

Figure 9.17  Crossing over. For clarity, we track only two genes on one pair of homologous chromosomes. Blue signifies the paternal chromosome, and pink, the maternal chromosome.

male germ cell (2n)

From Gametes to Offspring Germ Cells and Gametes  Meiosis is part of the process by which mature, haploid reproductive cells called gametes form. In multicelled eukaryotes, gametes arise

by division of immature reproductive cells called germ cells. In animals and plants, germ cells form in organs set aside for reproduction, but the two groups make gametes somewhat differently. In animals, germ cells are part of the germ line, which is a lineage of cells dedicated to producing gametes. Meiosis in diploid germ cells gives rise to eggs (female gametes) or sperm (male gametes). In plants, haploid germ cells (spores) form by meiosis. These cells divide by mitosis to form structures that produce or contain gametes.

male gamete (n)

meiosis

fertilization

meiosis zygote (2n) female germ cell (2n)

female gamete (n)

Figure 9.18  Meiosis halves the chromosome number, and fertilization restores it. Animal cells are illustrated. In animal cells, meiosis in diploid germ cells produces haploid gametes. At fertilization, two haploid gametes meet and form a diploid zygote.

Fertilization  We leave details of sexual reproduction in animals and plants for later chapters, but you will need to know a few concepts before then. A male gamete fuses with a female gamete at fertilization. The fusion of two haploid gametes at fertilization produces a diploid cell called a zygote, which is the first cell of a new individual. Thus, meiosis halves the chromosome number, and fertilization restores it (Figure 9.18). If meiosis did not precede fertilization, the chromosome number would double with every generation. An individual’s chromosomes are like a fine-tuned blueprint that must be followed exactly, in order to build a body that functions normally. If the chromosome number

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How Cells Reproduce  Chapter 9  175 

Digging Into Data BPA and Abnormal Meiosis In 1998, researchers at Case Western Reserve University were studying meiosis in mouse oocytes when they saw an unexpected and dramatic increase in abnormalities (Figure 9.19). Improper sorting of chromosomes into gametes is one of the main causes of human genetic disorders. The spike in abnormal meiosis events began shortly after the mouse facility started washing the animals’ plastic cages and water bottles in a new, alkaline detergent. The detergent had damaged the plastic, which as a result was leaching bisphenol A (BPA). BPA is a synthetic chemical that mimics estrogen, the main female sex hormone in animals. Though it has been banned for use in baby bottles, BPA is still widely used to manufacture other plastic items and epoxies (such as the coating on the inside of metal cans of food). BPA-free plastics are often manufactured with related compounds that have effects similar to BPA. 1. What percentage of mouse oocytes displayed abnormalities of meiosis with no exposure to damaged caging? 2. Which group had the highest percentage of abnormalities? 3. What is abnormal about metaphase I as it is occurring in the oocytes shown in B and C?

Caging materials

Total number of oocytes

Abnormalities

Control: New cages with glass bottles

271

5 (1.8%)

Damaged cages with glass bottles Mild damage Severe damage

401 149

35 (8.7%) 30 (20.1%)

Damaged plastic bottles

197

53 (26.9%)

58

24 (41.4%)

Damaged cages with damaged plastic bottles

A

B

C

Figure 9.19  Meiotic abnormalities associated with exposure to plastic. Fluorescent micrographs show the chromosomes (red) and spindle (green) in nuclei of mouse germ cells in metaphase I. A: Normal metaphase; B and C: abnormal metaphase. (A–C) Courtesy of Patricia Ann Hunt, Washington State University College of Veterinary Medicine

changes, so do the individual’s genetic instructions. As you will see in Chapter 10, such changes can have drastic consequences for health, particularly in animals. Fostering Diversity  Cells that give rise to human gametes have 23 pairs of homolo-

gous chromosomes. Each time a human germ cell undergoes meiosis, the four gametes that form end up with one of 8,388,608 (or 223) possible combinations of homologous chromosomes. In addition, any number of genes may occur as different alleles on the maternal and paternal chromosomes, and crossing over makes mosaics of that genetic information. Then, out of all the male and female gametes that form, which two actually get together at fertilization is a matter of chance. Are you getting an idea of why such fascinating combinations of traits show up among the generations of your own family tree?

Take-Home Message 9.6 ●●

●●

●●

During meiosis, the nucleus of a diploid (2n) cell divides twice. The process reduces the chromosome number to the haploid number (n) for forthcoming gametes. Crossing over—recombination between nonsister chromatids of homologous chromosomes—occurs during meiosis. It makes new combinations of parental alleles. The union of two haploid gametes at fertilization results in a diploid zygote, the first cell of a new individual.

crossing over  Process in which homologous chromosomes exchange corresponding segments during prophase I of meiosis. gamete  Mature, haploid reproductive cell; e.g., an egg or a sperm. zygote  Diploid cell that forms when two gametes fuse; the first cell of a new individual.

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176  Unit 2 GENETICS

Summary Section 9.1  An immortal line of human cells (HeLa) is a legacy of cancer victim Henrietta Lacks. For decades, these cells have been invaluable in research that has saved countless lives. Section 9.2  A eukaryotic cell reproduces by dividing: nucleus first, then cytoplasm. Mitosis is a mechanism of nuclear division that maintains the chromosome number. For example, mitosis in a diploid cell produces two diploid cells (with homologous chromosomes). Mitosis is the basis of asexual reproduction in many species, and development, growth, and tissue repair in multicelled organisms. DNA replication occurs during interphase, the interval of the cell cycle between divisions. Section 9.3  As mitosis begins, each chromosome consists of sister chromatids. During prophase, the chromosomes pack tightly and the nuclear envelope breaks up. Microtubules assemble into a spindle that attaches sister chromatids to opposite spindle poles. At metaphase, the chromosomes are aligned midway between spindle poles. During anaphase, the sister chromatids of each chromosome separate and move toward opposite spindle poles. During telophase, two new nuclei form, each with the parental chromosome number. In most cases, mitosis is followed by cytoplasmic division. In animal cells, a contractile ring pulls the plasma membrane inward (forming a cleavage furrow). Section 9.4  The products of checkpoint genes ensure that division occurs only at appropriate times. These molecules can pause the cell cycle until problems such as DNA damage are fixed. When checkpoint mechanisms fail, a cell loses control over its cell cycle, and its abnormally dividing descendants form a tumor. Mutations can turn some genes into tumor-causing oncogenes. Some tumors are benign; others are malignant. Cells of malignant tumors can break loose from their home tissues and colonize other parts of the body, a process called metastasis that is a hallmark of cancer. Telomere shortening limits the number of times that a normal cell can divide, a fail-safe mechanism against cancer. Section 9.5  Sexual reproduction mixes up the genetic information of two parents who differ in the details of shared, inherited traits. Offspring produced by sexual reproduction differ from one another and from the parents. Such variation can offer an evolutionary advantage in a changing environment. In cells of sexual reproducers, one chromosome of each homologous pair was inherited from the mother; the other, from the father. Homologous chromosomes carry the same set of

genes. Any gene may vary slightly in DNA sequence from the corresponding gene on the homologous chromosome. Different forms of the same gene are alleles. Alleles, which arise by mutation, are the basis of differences in shared traits among individuals of a sexually reproducing species. Section 9.6  Meiosis, the nuclear division mechanism that halves the chromosome number, is required for sexual reproduction in eukaryotes. DNA replication occurs before meiosis, so each chromosome has two sister chromatids. In meiosis I, homologous chromosomes exchange corresponding segments. This crossing over mixes up the alleles on maternal and paternal chromosomes. Crossing over gives rise to combinations of alleles not present in either parental chromosome, so it gives rise to combinations of traits not present in either parent. The homologous chromosomes are then moved apart and packaged in separate nuclei, so the chromosome number is reduced from diploid (2n) to haploid (n). Meiosis II occurs in both haploid nuclei that formed in meiosis I. Sister chromatids are separated and packaged in separate nuclei, so at the end of meiosis each chromosome consists of one molecule of DNA. Four haploid cells form. Meiosis is necessary for the production of haploid gametes. The fusion of two gametes at fertilization restores the diploid parental chromosome number in the zygote, the first cell of the new individual.

Self-Quiz Answers in Appendix I 1. Mitosis and cytoplasmic division function in . a. asexual reproduction of single-celled prokaryotes b. development and tissue repair in multicelled species c. sexual reproduction in plants and animals 2. A cell with two of each type of chromosome has a chromosome number that is . a. diploid c. tetraploid b. haploid d. abnormal 3. Homologous chromosomes are a. inherited from two parents b. sister chromatids c. different in size and length d. identical in DNA sequence

.

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How Cells Reproduce  Chapter 9  177 

4. After DNA replication, how many chromatids does a chromosome have? 5. Interphase is the part of the cell cycle when a. a cell ceases to function b. the spindle forms prior to nuclear division c. a cell grows and replicates its DNA

.

6. After mitosis, the chromosome number of a descendant cell is the parent cell’s. a. the same as c. rearranged compared to b. one-half of d. doubled compared to 7. One evolutionary advantage of sexual over asexual reproduction may be that it produces . a. more offspring per individual b. more variation among offspring c. less harmful mutations 8. Alternative forms of the same gene are a. gametes c. alleles d. oncogenes b. homologous

CRITICAL THinking

10. Crossing over mixes up parental . a. chromosomes c. zygotes b. alleles d. gametes .

12. Which of the following is one of the very important differences between mitosis and meiosis? a. Chromosomes align midway between spindle poles only in meiosis. b. Homologous chromosomes separate only in meiosis. c. Sister chromatids separate only in meiosis. 13. The cell illustrated on the right is in anaphase I, not anaphase II. I know this because . a. crossing over has already occurred b. sister chromatids have not separated c. a spindle has formed d. all of the above

15. Match each term with the best description. spindle a. shortens with division malignant tumor b. forms at fertilization contractile ring c. mash-up time gamete d. dangerous metastatic cells telomere e. consists of microtubules zygote f. haploid prophase I g. makes an indentation

.

9. Meiosis is a necessary part of sexual reproduction because it . a. divides one nucleus into four new nuclei b. reduces the chromosome number for gametes c. gives rise to new alleles

11. Sexual reproduction in animals requires a. meiosis c. gametes b. fertilization d. all of the above

14. Match each stage with the events listed. prophase a. sister chromatids move apart b. chromosomes pack tightly metaphase anaphase c. new nuclei form telophase d. DNA replication interphase e. chromosomes aligned midway between spindle poles

1. Persistent infection with one of two cancer-causing strains of HPV (HPV-16 and HPV-18) is the cause of most cervical cancers. HeLa cells still contain the remnants of HPV-18, the virus that transformed Henrietta Lacks’s normal cells into malignant cells. A different strain, HPV-11, causes benign genital warts, even though it has the same genes as HPV-18, and infected cells produce the same viral proteins. Speculate about why infection with different HPV strains leads to different clinical outcomes. 2. Mice that have had their telomerase enzyme knocked out age prematurely, with a life expectancy about half that of a normal mouse. When one of these knockout mice is close to the end of its shortened life span, rescuing the function of its telomerase enzyme results in lengthened telomeres. The rescued mouse also regains vitality: Worn-out tissue in the brain and other organs repairs itself and begins to function normally, and the once-geriatric individual even begins to reproduce again. Studies like these hint that increasing the activity of telomerase holds therapeutic promise for rejuvenating aged tissues. However, this approach can be dangerous. Why? 3. An error during meiosis gives rise to Down syndrome, a genetic disorder in which a person inherits three copies of chromosome 21 instead of two copies. What errors of meiosis could result in offspring inheriting the incorrect number of chromosomes, and in what phases would they occur? 4.   The eukaryotic cell in the photo on the left is in the process of cytoplasmic division. Is this cell from a plant or an animal? How do you know? ISM/Michel Delarue/Medical Images.com

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10 Patterns of Inheritance

10.1

Menacing Mucus  179

10.2

Tracking Traits  180

10.3

Mendelian Inheritance Patterns  183

10.4

Non-Mendelian Inheritance  185

10.5

Complex Variation in Traits  188

10.6

Human Genetic Analysis  190

10.7

Inheritance Patterns in Humans  192

10.8

Changes in Chromosome Number  196

10.9

Genetic Testing  198

The continuous range of variation in human eye color is the result of interactions among the products of multiple genes with multiple alleles, with added environmental effects.

Concept Connections

photoJS/Shutterstock.com; photoJS/Shutterstock.com; Andrey Armyagov/Shutterstock.com; Anemone/Shutterstock.com; Dimvix/Shutterstock.com; photoJS/Shutterstock. com; David Goodin; iStock.com/Adro_Hatxerre; Villedieu Christophe/Shutterstock.com; photoJS/Shutterstock.com; photoJS/Shutterstock.com; photoJS/Shutterstock.com; photoJS/Shutterstock.com; taffpixture/Shutterstock.com; Aaron Amat/Shutterstock.com; vaaka/Shutterstock.com; Anemone/Shutterstock.com; photography/Shutterstock. com; photoJS/Shutterstock.com; photoJS/Shutterstock.com; photoJS/Shutterstock.com; Jason Salmon/Shutterstock.com; Tatiana Makotra/Shutterstock.com; Lotus_studio/Shutterstock.com; l i g h t p o e t/Shutterstock.com; photoJS/Shutterstock.com; photoJS/Shutterstock.com

In this chapter, you will use your knowledge of chromosomes (Section 7.4), gene expression (8.2–8.5), alleles (9.5), and processes of sexual reproduction (9.6) as you learn about inheritance (1.3). Inheritance is part of evolution (12.3, 12.6–12.7, 13.3–13.4, 13.6–13.7), and mutations (7.6, 8.6) are the raw materials of evolutionary processes (13.2). You will encounter examples of environmental cues that alter body form and function (27.6, 29.5) by triggering changes in gene expression (8.7), and revisit sampling error (1.6), amyloid fibrils (2.9), the endomembrane system (3.5, 3.6), the nuclear lamina (3.5), osmosis (4.5), active transport (4.6), and growth factor receptors and BRCA1 (9.4).

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Patterns of Inheritance  Chapter 10  179  

Application 10.1  Menacing Mucus Cystic fibrosis (CF), the most common fatal genetic disorder in the United States, is characterized by severe damage to the lungs and other organs. Symptoms can vary, but all patients have persistent lung infections and other respiratory problems. The disorder arises from mutations in CFTR, a gene for an active transport protein that moves chloride ions across cell membranes. In the respiratory system, the CFTR protein is produced mainly by cells called ionocytes, which are minor components of the tissue that lines the airways to the lungs (Figure 10.1). The CFTR protein pumps chloride ions out of ionocytes, and this increases the solute concentration of the fluid on the surface of the tissue. Water then diffuses out of the tissue (by osmosis, Section 4.5). This twostep process maintains a thin, watery film on the interior surfaces of tubes of the respiratory system airways. Mucus slides easily through the wet tubes. The allele most commonly associated with CF has a deletion of three base pairs. One codon is missing from the mRNA translated from this allele, so the protein product is missing one amino acid. A CFTR protein that lacks this amino acid misfolds in a tiny region. A cellular quality control mechanism recognizes the misfolded region and destroys the protein before it leaves the ER. Thus, CFTR proteins with the missing amino acid are produced, but not installed in the plasma membrane. Ionocyte membranes that lack the CFTR protein cannot transport chloride ions. Too few chloride ions leave these cells, and not enough water leaves the tissues they occur in. Thus, the airways of the respiratory system are too dry. Mucus that normally slips through these tubes sticks to their walls instead. Thick globs of mucus accumulate, and breathing becomes difficult as the mucus clogs the airways to the lungs. In addition to its role in chloride ion transport, the CFTR protein also helps alert the immune system to the presence of disease-causing bacteria in the respiratory airways. It functions as a receptor by binding directly to the bacteria and causing them to be taken into the cell by endocytosis—a mechanism that triggers an immune response targeting the bacteria. This early alert system gives the body a head start in producing bacteria-fighting molecules. When cells lack CFTR, bacteria have time to multiply and establish infections before being detected by the immune system. Thus, chronic bacterial infections of the lungs are a hallmark of cystic fibrosis. Drugs help control infections, but there is no cure for the disorder. With the best of care, people who are affected may reach middle age. Most die when their tormented lungs fail.

interior surface of the airway cilia

sheet of epithelial cells

20 µm

Figure 10.1  CFTR and cystic fibrosis. Top, difficulty breathing is a hallmark of cystic fibrosis. Bottom, a sheet of epithelial cells lines the interior surface of respiratory airways (here, the trachea, or windpipe). Some of these cells are ionocytes. CFTR in ionocyte plasma membranes keeps the surface of the cell sheet moist, so mucus slides easily over it. Cilia can sweep the mucus away from the lungs. Mutations that alter CFTR can result in epithelial cell sheets that are too dry. Mucus accumulates and clogs the airways, making it difficult to breathe. Top, iStock.com/Steve Debenport; Bottom, Jose Luis Calvo/Shutterstock.com

Discussion Questions 1. Genetic screening is commonly used in diagnosing cystic fibrosis. Thousands of different mutations that affect CFTR can cause the disorder, and which mutation(s) a patient carries factors into the treatment plan. Why? 2. CFTR regulates the amount of fluid on the linings of respiratory airways. It has the same function in the reproductive system, digestive tract, and urinary system. Aside from breathing difficulty, what other physiological outcomes of the CF mutation can you think of? 3. CF occurs in all ethnic groups, but it is more common in some. For example, in the United States, the disease affects about one in 3,000 newborns of northern European descent, and one in 31,000 newborns of Asian descent. Why do you think the incidence of CF varies among ethnic groups?

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180  Unit 2 GENETICS

10.2  Tracking Traits LEARNING OBJECTIVES ●● ●●

●●

Explain Gregor Mendel’s contribution to the study of inheritance. Describe the difference between a homozygous and heterozygous genotype, and represent each symbolically with an example. Use an example to describe dominant and recessive alleles.

Early Thoughts about Heredity In the nineteenth century, people thought that hereditary material must be some type of fluid, with fluids from both parents blending at fertilization like milk into coffee. However, the idea of “blending inheritance” failed to explain what people could see with their own eyes. Children sometimes have traits such as freckles that do not appear in either parent, for example. A cross between a black horse and a white one does not produce gray offspring. At the time, no one knew that hereditary information is divided into discrete units (genes), an insight that is critical to understanding how traits are inherited. Around 1850, Gregor Mendel began an extended series of experiments breeding pea plants, which vary in traits such as flower color, height, and so on. Mendel, an Austrian monk, crossed thousands of plants, and kept careful records of the traits of parents and offspring. Through these experiments, he gained insight into the nature of inheritance.

Mendel’s Pea Plants   Mendel cultivated the garden pea (Figure 10.2). This species is naturally selffertilizing, which means its flowers produce male and female gametes 1 that form viable seeds when they meet up. In order to study inheritance, Mendel had to carry out controlled matings (crosses) between individuals with specific traits. First, he removed the pollen-bearing parts (anthers) from pea flowers 2. Removing anthers from a pea flower prevents it from self-fertilizing. Second, he cross-fertilized the flowers by brushing their egg-bearing parts (carpels) with pollen from other plants 3. Third, he collected seeds 4 that formed from the cross-fertilized flowers, planted them, and recorded the traits of the resulting pea plant offspring 5. Many of Mendel’s experiments started with plants that “breed true” for particular traits such as white flowers or purple flowers. Breeding true for a trait means that, new mutations aside, all offspring have the same form of the trait as the parent(s), generation after generation. For example, all offspring of pea plants that breed true for white flowers also have white flowers. As you will see in the next section, Mendel cross-fertilized pea plants that breed true for different forms of a trait, and discovered that the traits of the offspring often appear in predictable patterns. Mendel’s meticulous work breeding pea plants and tracking their traits led him to conclude (correctly) that hereditary information passes from one generation to the next in distinct units. He published his work in 1866, but apparently it was read by few and understood by no one at the time. In 1871 he was promoted, and his pioneering experiments ended. When he died in 1884, he did not know that his work with pea plants would be the starting point for modern genetics.

Inheritance in Modern Terms  Today, we know that Mendel’s “hereditary units” are genes. Individuals of a species share certain traits because their chromosomes carry the same genes.

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Patterns of Inheritance  Chapter 10  181  

CLOSER LOOK Figure 10.2  Breeding experiments with the garden pea. Bottom left; Moravian Museum

2 Mendel cut off the pollen-producing anthers from flowers to prevent them from self-fertilizing. In this example, anthers are removed from a white flower. carpel (♀)

Figure It Out: Why does removing anthers prevent self-fertilization? Answer: It removes the source of male gametes (pollen). anther (♂) ovary

3 Mendel then cross-fertilized the de-anthered flowers. Using a brush, he transferred pollen from a different flower onto their carpels.

1 Pollen grains that form in anthers of flowers produce male gametes. Female gametes form in ovaries, which are part of carpels.

Figure It Out: In this cross, which flower is the source of female gametes, the white flower or the purple flower?

Male and female gametes meet up (fertilization) when pollen lands on a carpel. Embryos develop in the flower’s ovary, and each becomes encased in a seed.

Answer: The white flower

4 Later, seeds develop inside pods of the cross-fertilized plant.

Garden pea plants can self-fertilize, which means viable seeds can form if a flower’s pollen lands on its carpel.

Gregor Mendel

5 When the seeds are planted, the embryo in each develops into a new plant. In this example, every plant that arises from the cross has purple flowers.

Figure Summary Gregor Mendel carefully controlled the transfer of hereditary material from one pea plant to another, and recorded the traits of the offspring of these crosses. He saw predictable patterns of inheritance—evidence of how inheritance works.

Each gene occurs at a specific location on a particular chromosome (Figure 10.3, next page). Diploid cells have pairs of homologous chromosomes (Section 9.2), so they have two copies of each gene; in most cases, both copies are expressed at the same level. The two copies of any gene may be identical, or they may be different alleles (Section 9.5).

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182  Unit 2 GENETICS interleukin-6 cytochrome c

7

EGF receptor elastin calcitonin receptor collagen I alpha-2: osteogenesis imperfecta CFTR: cystic fibrosis leptin: obesity blue cone opsin: bluedeficient colorblindness trypsin: pancreatitis

TYRP1 interferons galactosemia alcohol dehydrogenase, cytoplasmic: alcohol flushing reaction Friedreich ataxia fructose intolerance

Genetic disorders that result from mutations in the genes are indicated in red. The number or letter below a chromosome is its name. Characteristic banding patterns appear after staining. A similar map of all 23 chromosomes is in Appendix III. Figure It Out: On which chromosome does the allele most commonly associated with cystic fibrosis occur?

Answer: Chromosome 7

genotype

phenotype

testosterone receptor: androgen insensitivity neuroligin 3: autism IL2RG: SCID, X-linked XIST

GH releasing hormone: acromegaly

Tay-Sachs disease 15

Figure 10.3  Locations of a few genes on a few human chromosomes.

antidiuretic hormone oxytocin prion protein: CreutzfeldtJakob disease

fibrillin: Marfan syndrome

ABO blood group 9

dystrophin: Duchenne muscular dystrophy MAO-B

rRNA gene repeats 3 Prader-Willi/ Angelman syndrome antibody heavy chain variable region gene cluster

20

X

factor IX: hemophilia B fragile X syndrome red cone opsin: red-deficient colorblindness green cone opsin: green-deficient colorblindness incontinentia pigmenti factor VIII: hemophilia A

Homozygous and Heterozygous  An individual with the same allele of a gene on both homologous chromosomes is homozygous for the allele (homo- means “the

same”). Organisms breed true for a trait because they are homozygous for alleles governing the trait. By contrast, an individual with different alleles of a gene is heterozygous for the allele (hetero- means “different”). A hybrid is a heterozygous individual produced by a cross or mating between parents that breed true for different forms of a trait. Genotype and Phenotype  Homozygous and heterozygous describe genotype, the particular set of alleles that an individual carries. Genotype is the basis of phenotype, which refers to the individual’s observable traits. “White-flowered” and “purple-flowered” are examples of pea plant phenotypes that arise from differences in genotype. Dominant and Recessive  The phenotype of a heterozygous individual depends on

PP (homozygous

for dominant allele P)

pp (homozygous

for recessive allele p)

Pp (heterozygous for alleles P and p)

Figure 10.4  Genotype gives rise to phenotype. In this example, the dominant allele P specifies purple flowers; the recessive allele p, white flowers.

how the products of its two different alleles interact. In many cases, the product of one allele influences the effect of the other, and the outcome of this interaction is reflected in the individual’s phenotype. An allele is dominant when its effect masks that of a recessive allele paired with it. A dominant allele is often represented by an uppercase italic capital letter such as A; a recessive allele, with a lowercase italic letter such as a. Consider the purple- and white-flowered pea plants that Mendel studied. In these plants, the allele that specifies purple flowers (let’s call it P) is dominant over the allele that specifies white flowers (p). Thus, a pea plant homozygous for the dominant allele (PP) has the dominant trait: purple flowers. A plant homozygous for the recessive allele (pp) has the recessive trait: white flowers. A heterozygous plant—one with both the dominant and recessive allele (Pp)—has the dominant trait, which is purple flowers (Figure 10.4).

Take-Home Message 10.2

Tamara Kulikova/Shutterstock.com ●●

Figure It Out: Which individual is a hybrid? ●●

Answer: The heterozygous one

●●

Genotype refers to the particular set of alleles that an individual carries. Genotype is the basis of phenotype, which refers to the individual’s observable traits. A homozygous individual has two identical alleles of a gene. A heterozygous individual has two nonidentical alleles. A dominant allele masks the effect of a recessive allele paired with it in a heterozygous individual.

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Patterns of Inheritance  Chapter 10  183  

DNA replication

P–

parent cell ( pp)

parent cell (PP)

1 An individual –P

meiosis I

P– –P

DNA replication

2 An individual

homozygous for a dominant allele can make only gametes that carry the dominant allele.

homozygous for a recessive allele can make only gametes that carry the recessive allele.

P–

P–

p–

–p

Figure It Out: What percentage of the offspring of this cross will be homozygous for allele P?

meiosis I

p– –p

P– –P meiosis II

P–

p– –p

Answer: 0 percent

P– –P

p– –p meiosis II

P–

male gametes (P)

fertilization

female gametes ( p)

3 If these two individuals are crossed, the

union of any of their gametes at fertilization produces a zygote (Section 9.6) with both alleles. All offspring will be heterozygous.

–p

–p

–p

–p

4 The outcome of crosses like this P – –p

one can be predicted by making a grid called a Punnett square (right).

zygote (Pp)

female gametes

male gametes

p

p

P

Pp

Pp

P

Pp

Pp

offspring

Figure 10.5  Segregation of genes on homologous chromosomes into gametes. Homologous chromosomes separate during meiosis, so the genes they carry separate too. Each of the resulting gametes carries one of the two members of each gene pair. For clarity, only one set of chromosomes is illustrated.

10.3  Mendelian Inheritance Patterns LEARNING OBJECTIVES ●●

●●

Describe a monohybrid cross and how it can reveal a dominant–recessive relationship between alleles. Explain why Mendel concluded that hereditary material passes to offspring in discrete units.

Segregation of Genes into Gametes Meiosis separates the homologous chromosomes of a pair and packages each in a different gamete (Section 9.6). Thus, alleles on the homologous chromosomes end up in different gametes. Let’s use our pea plant alleles for purple and white flowers in an example (Figure 10.5). A plant homozygous for the dominant allele (PP) can only make gametes that carry the dominant allele P 1. A plant homozygous for the recessive allele (pp) can only make gametes that carry the recessive allele p 2. If the two homozygous plants are crossed (PP × pp), only one outcome is possible: A gamete carrying allele P meets up with a gamete carrying allele p 3. All offspring of this cross will have both alleles—they will be heterozygous (Pp). A grid called a Punnett square is helpful for predicting the outcome of crosses like this one 4.

dominant  Refers to an allele that masks the effect of a recessive allele on the homologous chromosome. Also used to describe a trait associated with a dominant allele. genotype  The particular set of alleles that occurs in an individual’s chromosomes. heterozygous  Describes a genotype in which homologous chromosomes have different alleles of a gene. homozygous  Describes a genotype in which homologous chromosomes have the same allele of a gene. phenotype  An individual’s observable traits. Punnett square  Diagram used to predict the genotypic and phenotypic outcomes of a cross. recessive  Refers to an allele with an effect that is masked by a dominant allele on the homologous chromosome. Also used to describe a trait associated with a recessive allele.

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184  Unit 2 GENETICS parent plant true-breeding for purple flowers (PP) one type of gamete

p

×

P

Monohybrid Crosses  Mendel did not know what alleles were, but he discov-

parent plant true-breeding for white flowers (pp) one type of gamete

F1 hybrid offspring (Pp) P

p

two types of gametes

P

p

A. A cross between parents that breed true for different forms of a trait produces F1 (first-generation) offspring that are identically heterozygous for alleles governing the trait (Pp). These hybrid offspring make two types of gametes: P and p. A cross between F1 hybrids is a monohybrid cross (Pp 3 Pp): monohybrid cross P

p

×

P

p

F2 offspring p

P P

p

PP

Pp

Pp

pp

B. The two types of gametes made by F1 hybrids can meet up four possible ways at fertilization. In this example, three of the four combinations include the dominant allele P, so there will be about three purple-flowered plants for every white-flowered plant (3:1) among the F2 (second-generation) offspring. Figure 10.6  A monohybrid cross. In this example, P is a dominant allele for purple flowers, and the recessive allele p specifies white flowers.

dihybrid cross  Cross between two individuals identically heterozygous for alleles of two genes. incomplete dominance  Inheritance pattern in which one allele is not fully dominant over another, so the heterozygous phenotype is an intermediate blend between the two homozygous phenotypes. monohybrid cross  Cross between two individuals identically heterozygous for alleles of one gene.

ered that they segregate into gametes and recombine in offspring. Experiments called monohybrid crosses were key to this discovery. A monohybrid cross is a cross between individuals that are identically heterozygous for alleles of one gene (Aa × Aa, for example). The experiment begins with a cross between individuals that breed true for different forms of a trait. The cross produces F1 (first-generation) hybrid offspring (Figure 10.6A). A cross between two of these F1 individuals is the monohybrid cross, and it produces F2 (secondgeneration) offspring. The frequency at which the two forms of the trait appear among the F2 offspring offers information about a dominance relationship between alleles governing the trait. A cross between two purple-flowered heterozygous plants (Pp × Pp) offers an example of a monohybrid cross. Each of these plants makes two types of gametes: gametes that carry a P allele, and gametes that carry a p allele. The two types of gametes can meet up in four possible ways at fertilization (Figure 10.6B). Three of the four possible combinations include the dominant allele P. In other words, each time fertilization occurs, there are three chances in four that the resulting zygote will have a P allele (and the individual will make purple flowers). There is one chance in four that the zygote will have two p alleles (and the individual will make white flowers). Thus, among F2 offspring, there will be roughly three purple-flowered plants for every white-flowered plant. A phenotype ratio of 3:1 among F2 offspring in a monohybrid cross means that the alleles governing the phenotypes have a dominant–recessive relationship. This pattern is so predictable that it can be used to investigate dominance relationships among unknown alleles. Mendel realized its significance: Hereditary information that governs traits is passed from one generation to the next in discrete units.

Independent Assortment of Genes into Gametes When the members of a pair of homologous chromosomes separate during meiosis, either chromosome can end up in either of the two new nuclei that form. This assortment is random, and it happens independently for each pair of homologous chromosomes. Thus, alleles of genes on one pair of homologous chromosomes tend to assort into gametes independently of alleles of genes on other chromosomes. What about genes on the same chromosome? There may be hundreds or thousands of genes on a chromosome, and most are far enough apart that crossing over almost always occurs in regions between them. Thus, alleles of these genes tend to assort into gametes independently, just as if the genes were on different chromosomes. By contrast, some genes are very close together on a chromosome. Alleles of these genes usually do not assort independently into gametes because crossing over rarely occurs in the region between them. Thus, for genes that are close together on a chromosome, gametes usually end up with a parental combination of alleles. Dihybrid Crosses  An individual heterozygous for alleles of two genes (AaBb, for example) is called a dihybrid, and a cross between two such individuals is a dihybrid cross. Mendel’s dihybrid crosses led him to discover that hereditary units for differ-

ent traits (alleles of different genes) often assort independently into gametes. A dihybrid is an offspring of individuals that breed true for different forms of two traits. Let’s say one parent plant breeds true for purple flowers and tall stems, and the other breeds true for white flowers and short stems. P and p are dominant and recessive alleles for purple and white flowers; T and t, dominant and recessive alleles for tall and short stems. A cross between the purple-flowered, tall

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Patterns of Inheritance  Chapter 10  185  

plant (PPTT) and the white-flowered, short plant (pptt) produces F1 dihybrid offspring (PpTt), all with purple flowers and tall stems (Figure 10.7A). A cross between two of these F1 dihybrids is the dihybrid cross (PpTt × PpTt). The PpTt dihybrids make four types of gametes, and these can meet up in sixteen possible ways at fertilization (Figure 10.7B). Nine of the sixteen combinations would give rise to tall plants with purple flowers; three, to short plants with purple flowers; three, to tall plants with white flowers; and one, to short plants with white flowers. Thus, the ratio of phenotypes among the F2 offspring in this dihybrid cross would be 9:3:3:1. A phenotype ratio of 9:3:3:1 among F2 offspring in a dihybrid cross has two implications. First, the alleles for both traits have a clear dominant– recessive relationship. Second, the alleles that govern one trait assort into gametes independently of alleles that govern the other.

one type of gamete

×

PT

●●

●●

●●

Predictable patterns of inheritance offer observable evidence of how alleles pass to offspring. A diploid cell has two copies of every gene (on homologous chromosomes), and the two copies may vary as alleles. Meiosis separates the two chromosomes of a homologous pair and packages them in different gametes. Thus, alleles end up in different gametes. In most cases, alleles of one gene are distributed into gametes independently of alleles of other genes.

PT

Pt

Explain how one gene may influence multiple traits.

●●

Describe a trait that is influenced by multiple genes.

The previous section discussed Mendelian inheritance, in which one gene gives rise to one trait, and alleles of the gene are either dominant or recessive. Other, more complex relationships between alleles and traits are more common. Following are some examples.

Incomplete Dominance in Snapdragons In an inheritance pattern called incomplete dominance, one allele is not fully dominant over the other, so the heterozygous phenotype is an intermediate blend of the two homozygous phenotypes. Alleles of a gene that influences flower color in snapdragon plants offer an example. One allele encodes an enzyme that makes a red pigment. Plants homozygous for this allele make a lot of red pigment, so they have red flowers. A different allele has a mutation, and the enzyme it encodes cannot make any pigment. Plants homozygous for the mutated allele make no pigment, so their flowers are white. Heterozygous plants make only enough pigment to tint their flowers pink.

PT

Pt

pT

pt

Pt

pT

×

pt

PT

Pt

pT

pt

F2 offspring PT

LEARNING OBJECTIVES

●●

four types of gametes

pt

dihybrid cross

10.4  Non-Mendelian Inheritance Use examples to explain the difference between codominance and incomplete dominance.

pT

A. A cross between parents that breed true for different forms of two traits produces F1 (first generation) offspring that are identically heterozygous for alleles governing the traits (PpTt). These dihybrid offspring make four types of gametes: PT, Pt, pT, and pt. A cross between F1 dihybrids is a dihybrid cross (PpTt 3 PpTt).

PT

●●

one type of gamete

pt

F1 dihybrid offspring (PpTt)

Take-Home Message 10.3 ●●

parent plant true-breeding for white flowers and short stems ( pptt)

parent plant true-breeding for purple flowers and long stems (PPTT )

pT

Pt

pt

PT

PPTT

PPTt

PpTT

PpTt

Pt

PPTt

PPtt

PpTt

Pptt

pT

PpTT

PpTt

ppTT

ppTt

pt

PpTt

Pptt

ppTt

pptt

B. The four types of gametes made by F1 dihybrids can meet up in 16 possible ways at fertilization. In this example, 9 of the combinations will result in plants that are purple-flowered and tall; 3, purple-flowered and short; 3, white-flowered and tall; and 1, white-flowered and short. Thus, the ratio of phenotypes is 9:3:3:1. Figure 10.7  An example of a dihybrid cross. In this example, P and p are dominant and recessive alleles for purple and white flower color; T and t are dominant and recessive alleles for tall and short stems.

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186  Unit 2 GENETICS

Codominance and Blood Type AA

Genotype:

or

AB

A

AB

AO

Phenotype:

BB or

OO

B

O

BO

Figure 10.8  Combinations of alleles (genotypes) that are the basis of blood type (phenotypes). Source: Anne Cavanagh

With codominance, traits associated with two alleles are fully and equally apparent in heterozygous individuals; neither allele is dominant or recessive. Alleles of the ABO gene offer an example. This gene encodes an enzyme that modifies a carbohydrate on the surface of human red blood cells. Two alleles of the gene, A and B, encode slightly different versions of the enzyme, which in turn modify the carbohydrate differently. A third allele, O, has a mutation that causes a frameshift (Section 8.6). The protein encoded by this allele has no enzymatic activity, so the carbohydrate remains unmodified. The alleles of the ABO gene that you carry determine the form of the carbohydrate on your blood cells, so they are the basis of your ABO blood type (Figure 10.8). The A and B alleles are codominant when paired. If your genotype is AB, then you have both modified versions of the carbohydrate, and your blood type is AB. The O allele is recessive when paired with either the A or B allele. If your genotype is AA or AO, your blood type is A. If your genotype is BB or BO, it is type B. If you are OO, it is type O. Blood Transfusions  Receiving incompatible blood in a transfusion can be danger-

EB

Eb

eB

eb

EB

EEBB

EEBb

EeBB

EeBb

Eb

EEBb

EEbb

EeBb

Eebb

eB

EeBB

EeBb

eeBB

eeBb

eb

EeBb

Eebb

eeBb

eebb

Figure 10.9  Polygenic inheritance: coat color in Labrador retrievers. Interactions among the products of two genes affect fur color in these dogs. Dogs with a dominant allele of both genes (E and B) have black fur. Those with the dominant E and two recessive b alleles have brown fur. Dogs homozygous for the recessive e allele have yellow fur. Top, Susan Schmitz/Shutterstock.com

ous because the immune system attacks any cell bearing molecules that do not occur in one’s own body. An immune attack causes red blood cells to clump or burst, with potentially fatal results. Almost everyone makes the unmodified carbohydrate, so type O blood does not trigger an immune response in most transfusion recipients. People with type O blood are called universal donors because they can donate blood to anyone. However, because their body is unfamiliar with the modified forms of the carbohydrate made by people with type A, B, or AB blood, they can receive type O blood only. People with type AB blood can receive a transfusion of any ABO blood type, so they are called universal recipients.

Pleiotropy and Marfan Syndrome In an inheritance pattern called pleiotropy, a single gene influences multiple traits. Mutations that affect the gene’s product or its expression affect all of the traits. Some complex genetic disorders, including sickle-cell anemia and cystic fibrosis, are caused by mutations in single genes. Marfan syndrome, another example, is a result of mutations in the gene for fibrillin. Long fibers of this protein are part of elastic tissues that make up the heart, skin, blood vessels, tendons, and other body parts. In people who carry these mutations, body tissues form with defective or insufficient fibrillin. The largest blood vessel leading from the heart, the aorta, is particularly affected. Without a proper scaffold of fibrillin, the aorta’s thick wall is not as elastic as it should be, and it eventually stretches and becomes leaky. Thinned and weakened, the aorta can rupture during exercise, causing immediate death. About 1 in 5,000 people have Marfan syndrome. There is no cure, but the risk of dangerous complications can be minimized by receiving regular medical care and avoiding certain activities.

Polygenic Inheritance codominance  Inheritance pattern in which the full and separate phenotypic effects of two alleles are apparent in heterozygous individuals. pleiotropy  Inheritance pattern in which a single gene affects multiple traits. polygenic inheritance  Pattern of inheritance in which multiple genes affect one trait.

In a pattern called polygenic inheritance, alleles of two or more genes collectively affect a single trait. Hundreds of genes may be involved, with each making a small contribution to the phenotype. Fur Color in Dogs  The color of animal fur arises from two pigments: eumelanin, which ranges in color from brown to black, and pheomelanin, which is reddish. The relative amount of the two melanins determines the color of the fur.

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Patterns of Inheritance  Chapter 10  187  

Digging Into Data The allele most commonly associated with CF is at least 50,000 years old and very common: 1 in 25 people carry it in some populations. Researchers think the CF allele has persisted at such a high frequency because it offers heterozygous individuals an advantage in surviving certain deadly infectious diseases. These people have a somewhat greater risk of respiratory illness than the general population, but are otherwise healthy. The cells of a heterozygous person make half of the normal amount of CFTR protein, which is enough to prevent cystic fibrosis. The CFTR protein triggers endocytosis when it binds to bacteria, and this function is an important part of the respiratory tract’s immune defenses against common Pseudomonas bacteria. Pseudomonas infections of the lungs are a chronic problem in patients with cystic fibrosis, in part because their cells lack the CFTR protein and cannot take up bacteria by endocytosis. Endocytosis triggered by CFTR is also the way that Salmonella typhi bacteria enter epithelial cells in the gastrointestinal tract. Uptake of S. typhi by these cells is the cause of a disease called typhoid fever. Symptoms include extreme fever and diarrhea, and the resulting dehydration causes delirium that may last several weeks. If untreated, it kills up to 30 percent of those infected. Every year, around 600,000 people—most of whom are children—die from the disease. Gerald Pier and his colleagues compared the uptake of S. typhi by different types of epithelial cells: those homozygous for the normal allele of

Number of bacteria internalized by the cells

The Cystic Fibrosis Allele and Typhoid Fever Normal cells

106

Cells heterozygous for the CF allele

105

104

Ty2

167

7251

Strain of Salmonella typhi

Figure 10.11  Effect of the CF mutation on uptake of three strains of Salmonella typhi bacteria by epithelial cells. the CFTR gene, and those heterozygous for the CF allele (cells that are homozygous for the allele do not take up any S. typhi bacteria). Some of the results are shown in Figure 10.11. 1. Regarding the Ty2 strain of S. typhi, about how many more of these bacteria were able to enter normal cells than cells heterozygous for the CF allele? 2. Which strain of bacteria entered normal epithelial cells most easily? 3. Entry of all three S. typhi strains into CF heterozygous epithelial cells was inhibited. Is it possible to tell from this graph which strain was most inhibited?

The products of multiple genes interact to make and deposit melanin in fur as it grows. In dogs called Labrador retrievers, alleles of two genes determine whether the individual has black, brown, or yellow fur (Figure 10.9). The product of one gene helps make eumelanin. A dominant allele (B) of the gene results in production of the black form of this pigment; a recessive allele (b) results in a brown form. The product of a second gene determines whether eumelanin is produced at all. Individuals with the dominant allele (E) of this gene make eumelanin, so they have black or brown fur. Individuals homozygous for the recessive allele (e) make only the reddish pheomelanin, so they have yellow fur.

Figure 10.10  Polygenic inheritance: human skin color. Twins Kian and Remee are shown with their parents. Both of the children’s grandmothers are of European descent, and have pale skin. Both of their grandfathers are of African descent, and have dark skin. The twins inherited different alleles of some genes that affect skin color. Gary Roberts/worldwidefeatures.com

Human Skin Color  Human skin color is also inherited in a polygenic pattern (Figure 10.10). At least 350 gene products affect this trait, which begins with melanosomes—organelles that make melanins. Most people have about the same number of melanosomes in their skin cells. Variations in skin color arise from differences in the size, shape, and cellular distribution of melanosomes in the skin, as well as in the kinds and amounts of melanins they make. These variations have a genetic basis. Consider one gene that encodes a transport protein in melanosome membranes. Nearly all people of African, Native American, or East Asian descent carry the same allele of this gene. A mutation that occurred between 6,000 and 12,000 years ago gave rise to a different allele. The mutation, a single base-pair substitution, results in less melanin—and lighter skin color—than

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188  Unit 2 GENETICS

the original African allele does. Today, nearly all people of European descent are homozygous for the mutated allele.

Take-Home Message 10.4 ●●

●●

●●

A. Under low-oxygen conditions, a water flea (Daphnia) switches on genes involved in producing hemoglobin. Making this red protein enhances the individual’s ability to take up oxygen from water. The water flea on the left has been living in water with a normal oxygen content; the one on the right, in water with a low oxygen content.

Mendel studied traits that arise from single genes with alleles that have a clear dominant–recessive relationship. Other, more complex patterns are more common. With incomplete dominance, the heterozygous phenotype is an intermediate blend of the two homozygous phenotypes. With codominance, both homozygous phenotypes appear in the heterozygous phenotype. With pleiotropy, one gene influences multiple traits. With polygenic inheritance, multiple genes influence one trait.

10.5  Complex Variation in Traits LEARNING OBJECTIVES ●●

Explain the phrase “nature versus nurture.”

●●

Give examples of environmental factors that affect phenotype by altering gene expression.

●●

Use examples to explain continuous variation and its causes.

We know that variation in traits begins with alleles, but in many cases this relationship is difficult to determine. Environmental cues influence the form of many traits, for example, and some traits do not have distinct forms. Tracking traits with complex variation presents a special challenge, which is why the genetic basis of many of them has not yet been completely unraveled.

B. The color of the snowshoe hare’s fur varies by season. A hare’s summer fur is brown (left); its winter fur is white (right). Both color forms offer seasonally appropriate camouflage from predators.

Nature and Nurture The phrase “nature versus nurture” refers to a centuries-old debate about whether human behavioral traits arise from one’s genetics (nature) or from environmental factors (nurture). Today, we know that both play a substantial role. The environment affects the expression of many genes, which in turn affects phenotype—including behavioral traits. We can summarize this thinking with an equation: genotype 1 environment

C. In many plants, seasonal patterns of growth are triggered by seasonal changes in the length of night. Figure 10.12  Some environmental effects on phenotype. (A) From Science 4 February 2011: Vol. 331 no. 6017 pp. 555–561. Reprinted with permission from AAAS; (B) left, JupiterImages Corporation; right, age fotostock/Superstock; (C) mandritoiu/Shutterstock.com

phenotype

Epigenetics research is revealing that the environment has an even greater contribution to this equation than most biologists had suspected (Section 8.7). Environmental cues trigger cell-signaling pathways that in turn trigger changes in gene expression (you will learn more about such pathways in later chapters). Some cell-signaling pathways methylate particular regions of DNA, so they suppress gene expression in those regions. In humans and other animals, DNA methylation patterns can be affected by diet, stress, and exercise, and also by exposure to drugs and toxins such as tobacco and alcohol.

Examples of Environmental Effects on Phenotype Mechanisms that adjust phenotype in response to external cues are part of an individual’s normal ability to adapt to its environment, as the following examples illustrate.

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Patterns of Inheritance  Chapter 10  189  

Water Fleas  Water fleas (Daphnia) are tiny aquatic animals that inhabit seasonal

ponds and other standing pools of fresh water. Daphnia have a striking flexibility of phenotype. Environmental cues trigger adjustments in gene expression that change an individual’s form and function to suit its current environment. Consider how warm water at the top of a still summer pond contains more dissolved oxygen than cool water at the bottom. A water flea that swims to the bottom of a pond can survive the low oxygen conditions there by turning on expression of genes involved in the production of hemoglobin—and turning red (Figure 10.12A). Hemoglobin is a (red) protein that carries oxygen (Section 8.6), and making it enhances the individual’s ability to absorb oxygen from the water. Many other environmental factors affect water flea phenotype. For example, the presence of insect predators causes water fleas to form a protective pointy helmet and lengthened tail spine. Individual water fleas can also switch between asexual and sexual modes of reproduction. During early spring, food and space are typically abundant, and competition for these resources is minimal. Under these conditions, water fleas reproduce asexually, giving birth to large numbers of female offspring that quickly fill ponds. Later in the season, competition intensifies as pond water becomes warmer, saltier, and more crowded. Then, some of the water fleas start giving birth to males, and the population begins to reproduce sexually. The increased genetic diversity of sexually produced offspring offers an advantage in the more challenging environment (Section 9.5). Seasonal Changes in Coat Color  In many mammals, seasonal changes in tem-

perature and the length of day affect production of pigments that color fur. These species have different color phases in different seasons (Figure 10.12B). Hormonal signals triggered by the seasonal changes cause fur to be shed, and new fur grows back with different types and amounts of pigments deposited in it. The resulting change in phenotype provides these animals with seasonally appropriate camouflage from predators. Plant Development  In animals, most development occurs before adulthood. By contrast, plant development continues throughout the individual’s lifetime (Figure 10.12C). Changes in temperature, gravity, night length, availability of water and nutrients, and the presence of pathogens or herbivores trigger changes in gene expression, which in turn trigger changes in patterns of growth. Section 29.7 returns to developmental flexibility in plants.

Continuous Variation  Some traits occur in a range of small differences that is called continuous variation. Continuous variation is often an outcome of polygenic inheritance, in which multiple genes affect a single trait. Traits that arise from genes with a lot of alleles may also vary continuously. For example, in dogs, continuous variation in face length is an outcome of a homeotic gene with 12 alleles. The gene has a short tandem repeat, which is a region in which a series of 2 to 6 nucleotides is repeated many times in a row. The number of short tandem repeats can spontaneously increase or decrease during DNA replication and repair, and the resulting expansion or contraction of the repeat region may be preserved as an allele. In this case, alleles with more repeats are associated with longer dog faces (Figure 10.13). How do we know that a particular trait varies continuously? First, we divide the total range of phenotypes into measurable categories. The number of individuals in each category reveals the frequencies of phenotypes across the range of values.

Figure 10.13  Face length varies continuously in dogs. A gene with 12 alleles influences this trait; all arose by spontaneous expansion or contraction of a short tandem repeat region. Variation in the number of repeats correlates with variation in face length: The more repeats, the longer the face. Willee Cole Photography/Shutterstock.com

continuous variation  A range of small differences in forms of a trait. short tandem repeat  In chromosomal DNA, region in which a sequence of a few nucleotides is repeated multiple times in a row.

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190  Unit 2 GENETICS

When the data are plotted as a bar chart, a graph line around the top of the bars shows the distribution of values for the trait. If the line is a bell-shaped curve, or bell curve, then the trait varies continuously (Figure 10.14).

Take-Home Message 10.5 ●● ●●

63 64 65 66 67 68 69 70 71 72 73 74 75 76 77

A. Male biology students at the University of Florida lined up according to height (in inches).

Environmental cues can alter phenotype by altering gene expression patterns. Traits that occur in a continuous range of variation are often an outcome of multiple genes, multiple alleles, or both.

10.6  Human Genetic Analysis LEARNING OBJECTIVES

Number of individuals 15

●●

Explain why pedigrees are used to study human inheritance patterns.

●●

Differentiate between a genetic disorder and a genetic abnormality.

Studying Inheritance in Humans 10

5

63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 Measured values

B. A characteristic bell curve results from graphing the distribution of values for a trait that varies continuously. Height of male biology students in A provided the data for this graph. Figure 10.14  Continuous variation in human height. (A) Courtesy of Ray Carson, University of Florida News and Public Affairs

bell curve  Bell-shaped curve; typically results from graphing frequency versus distribution for a trait that varies continuously. pedigree  Chart that marks the appearance of a phenotype through generations of a family tree.

Surprisingly few easily observed human traits are inherited in a Mendelian pattern. As in other organisms, polygenic traits are common, and many phenotypes have epigenetic and environmental contributions. Studying complex inheritance patterns in humans presents a special challenge. Consider how pea plants and fruit flies are ideal for genetics research. Breeding them in a controlled manner poses few ethical problems. They reproduce quickly, so it does not take long to follow a trait through many generations. Humans, however, live under variable conditions, in different places, and we live as long as the geneticists who study us. Most of us choose our own mates and reproduce if and when we want to. Most human families are small, so sampling error (Section 1.6) is unavoidable. Pedigrees  Because of the challenges involved in studying human inheritance,

geneticists often use historical records to track traits through past generations of a family. They make and use pedigrees, which are charts that mark the appearance of a trait among generations of family members. A pedigree is constructed in a standard way, with individuals represented as polygons and relationships between them as lines (Figure 10.15). Males are represented as squares; females, as circles. A filled-in polygon indicates an individual with the trait being studied. A mating or marriage is signified by a line between parents, with offspring of the match connected to this line. Every generation appears in a row designated by a roman numeral (I, II, III, and so on). A pedigree allows geneticists to estimate the probability that a phenotype will reappear in future generations. It can also reveal whether a trait is associated with a dominant or recessive allele, and whether the allele is on an autosome or a sex chromosome (Section 7.4).

Genetic Disorders and Abnormalities Our understanding of inheritance patterns in humans comes mainly from research involving genetic disorders, which are health conditions that arise from alleles. A genetic disorder can be inherited, or it can arise spontaneously—for example, as a result of a mutation that occurs during gamete formation. Genetic abnormalities

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Patterns of Inheritance  Chapter 10  191  

Discovering a Breast Cancer Gene It has long been known that breast cancer arises more frequently in some families than in others. In the 1970s, Mary-Claire King proposed that the elevated risk of breast cancer in these families is due to inherited mutations. Today, the link between genetics and cancer is well accepted, but King’s idea was radical at a time when cancer was assumed to be caused solely by external factors such as viruses. King tested her hypothesis by developing mathematical models that predicted the theoretical incidence of cancer from genetic causes, and from nongenetic causes. By comparing these predictions against a large set of patient data being collected by the National Cancer Institute (NCI), King’s group discovered that a “breast cancer trait” arising from a dominant allele on an autosome could explain all cases of familial early-onset breast cancer. This striking result set the stage for a major shift in the focus of cancer biology research toward genetic causes. In 1990, King’s lab succeeded in identifying their cancer-causing gene: BRCA1. This gene encodes a tumor suppressor (Section 9.4), and mutations in it confer susceptibility to breast cancer. Since then, the group has continued their work on the genetic basis of cancer and other diseases. Among their discoveries: Half of all women with oncogenic BRCA1 mutations have no family history of breast cancer—an outcome of sampling error (these women often come from small families). Early detection allows early treatment, so it can save lives. Some women who discover they have one of these mutations are opting for preventive treatments before cancer develops.

Take-Home Message 10.6 ●●

●●

●●

●●

Human inheritance patterns are often studied by tracking genetic disorders in families. A pedigree is a chart that marks the appearance of a trait through generations of family members. Most human traits have a complex pattern of inheritance. We have a better understanding of inheritance of single-gene disorders. A genetic disorder causes medical problems that often occur in a syndrome. A genetic abnormality is a rare but harmless form of a trait.

A. Polydactyly is a genetic abnormality characterized by extra fingers, toes, or both.

I II

*Gene not expressed in this carrier.

5,5 6,6

*

III IV

5,5 6,6

6,6 5,5

6,6 5,5

5,5 6,6 5,5 6,6

5,5 6,6

5,5 6,6

5,6 6,7

V

6,6 6,6

B. This pedigree tracks polydactyly through five generations (I–V) of a family tree. The number of fingers on each hand is indicated in black; toes on each foot, in red. Symbol legend is given below. male

female

individual with the trait being studied

unknown gender

marriage/mating

offspring

generation

I, II, III, IV...

Figure 10.15  A pedigree for polydactyly. Dominant alleles give rise to polydactyly on its own. The abnormality also occurs in genetic disorders such as Ellis–van Creveld syndrome, and in these cases it arises from recessive alleles. (A) Courtesy of Irving Buchbinder, DPM, DABPS, Community Health Services, Hartford, CT

Figure It Out: In this family, does polydactyly arise from a dominant or recessive allele? Answer: A recessive allele

arise the same way. A genetic abnormality is a rare or uncommon version of a trait, such as having six fingers on a hand, or a web between two toes. Genetic abnormalities are not inherently life-threatening, and how you view them is a matter of opinion. By contrast, a genetic disorder sooner or later causes medical problems that may be quite severe. Even though single-gene traits (one gene → one trait) are the least common kind in humans, we actually know most about inheritance of single-gene disorders. This is partly an outcome of relative complexity. Genetic disorders typically have multiple symptoms (a syndrome) that vary among affected individuals. Diabetes, asthma, obesity, cancers, heart disease, multiple sclerosis, and many other disorders can be inherited, but in patterns so complex that their genetic underpinnings remain unclear despite decades of research. For example, mutations associated with an increased risk of autism (a developmental disorder) have been found on almost every chromosome, but most people who have these mutations do not have autism.

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192  Unit 2 GENETICS

10.7  Inheritance Patterns in Humans LEARNING OBJECTIVES ●●

●●

Table 10.1  Some Autosomal Dominant Abnormalities and Disorders in Humans

Disorder/Abnormality

Main Symptom(s)

Achondroplasia

Dwarfism

Aniridia

Defects of the eyes

Huntington’s disease

Degeneration of the nervous system

Marfan syndrome

Cardiovascular system malfunction

Polydactyly

Extra fingers or toes

Progeria

Drastic premature aging

Use diagrams to explain the autosomal dominant and autosomal recessive inheritance patterns. Explain why X-linked recessive disorders are more common in men than in women.

Human genetic disorders inherited in a Mendelian pattern are typically categorized by the chromosome of origin (autosome or sex chromosome) and whether alleles associated with them are dominant or recessive.

The Autosomal Dominant Pattern A trait associated with a dominant allele on an autosome (an autosomal dominant trait) appears in heterozygous people as well as those who are homozygous. Table 10.1 lists a few examples. Such traits can appear in every generation of a family, and they occur with equal frequency in both sexes. When one parent is heterozygous for a dominant allele, and the other is homozygous for the recessive allele, each of their children has a 50 percent chance of inheriting the dominant allele and having the associated trait (Figure 10.16A). Achondroplasia  A form of hereditary dwarfism called achondroplasia is an

autosomal dominant disorder. Mutations associated with achondroplasia occur in a gene for a growth factor receptor (Section 9.4), the activity of which inhibits growth and differentiation of cells that give rise to bone. The mutations result in

Figure 10.16  Examples of autosomal dominant inheritance. People heterozygous for a dominant allele on an autosome have the associated trait. (B) © Newcastle Photos and Ivy and Violet Broadhead and family; (C) Photo courtesy of The Progeria Research Foundation

normal mother

affected father

aa

Aa

3 meiosis and gamete formation A

a

a

Aa

aa

a

Aa

aa

affected child normal child A

disorder-causing allele (dominant)

A. In this example, an affected father is heterozygous for the dominant allele. Each child has a 50 percent chance of inheriting the allele and having the trait.

B. Achondroplasia affects Ivy (left), as well as her brother, father, and grandfather.

C. Symptoms of Hutchinson–Gilford progeria are already apparent in Megan at age 5.

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Patterns of Inheritance  Chapter 10  193  

a receptor that is overly active, so bone development is inappropriately dampened during periods of growth. As a result, adults affected by the disorder have an unusually short stature, with arms and legs that are short relative to torso size (Figure 10.16B). About 1 in 10,000 people is heterozygous for an allele associated with achondroplasia. These alleles can be passed to children because their expression does not interfere with reproduction, at least in heterozygous people. The homozygous condition results in severe skeletal malformations that are lethal before birth or shortly after. Huntington’s Disease  An autosomal dominant disorder called Huntington’s

disease is caused by expansions of a short tandem repeat in the gene for huntingtin, a protein that participates in DNA damage repair. The version of huntingtin encoded by the expanded gene has a region in which one amino acid (glutamine) is repeated 40 or more times. The altered huntingtin resists cellular mechanisms that destroy defective proteins, so it accumulates to high levels, particularly in brain cells involved in movement, thinking, and emotion. Cellular functioning is hampered, and a stress response is triggered that eventually causes the cell to die. Glutaminerich protein fragments accumulate in amyloid fibrils, so amyloid plaques form in the brain (Section 2.9). In the most common form of Huntington’s, symptoms do not start until after the age of 30. Voluntary muscle control gradually gives way to involuntary jerking, twitching, and writhing movements. Eventually, serious problems with swallowing cause many patients to die from choking or malnutrition in their 40s or 50s. With this and other late-onset disorders, people tend to reproduce before symptoms appear, so an allele is often passed unknowingly to children.

Hutchinson–Gilford Progeria  Drastically accelerated aging characterizes an autoso-

mal dominant disorder called Hutchinson–Gilford progeria. Most cases of the disorder are caused by a base-pair substitution in the gene for lamin A, a protein subunit of intermediate filaments that make up the nuclear lamina (Section 3.5). Cells that carry this mutation make an abnormal, toxic version of the protein. Their nucleus is grossly abnormal, with nuclear pore complexes that do not assemble properly and membrane proteins localized to the wrong side of the nuclear envelope. The function of the nucleus as protector of chromosomes is severely impaired. DNA damage accumulates quickly, and the cell enters early senescence (Section 9.4). The gene for lamin A affects multiple traits (an example of pleiotropy), and the effects of the progeria mutation are widespread. Outward symptoms begin to appear before age two, as skin that should be plump and resilient starts to thin, muscles weaken, and bones soften (Figure 10.16C). Most people with the disorder die in their early teens as a result of a stroke or heart attack brought on by hardened arteries, a condition typical of advanced age. Affected people are not known to reproduce. In almost all cases, the disorder is an outcome of a new mutation that occurs during gamete formation or fertilization.

The Autosomal Recessive Pattern  A trait associated with a recessive allele on an autosome (an autosomal recessive trait) appears only in homozygous individuals. Heterozygous individuals are called carriers because they have the allele but not the trait. Table 10.2 lists a few examples. Such traits appear in both sexes at equal frequency, and they tend to skip generations. Any child of two carriers has a 25 percent chance of inheriting the allele from both parents—and developing the trait (Figure 10.17).

Table 10.2  Some Autosomal Recessive Abnormalities and Disorders in Humans

Disorder/Abnormality

Main Symptom(s)

Albinism

Absence of pigmentation

Cystic fibrosis

Difficulty breathing, lung infections

Ellis–van Creveld syndrome

Dwarfism, heart defects, polydactyly

Friedreich’s ataxia

Progressive loss of motor and sensory function

Hereditary methemoglobinemia

Blue skin coloration

Phenylketonuria (PKU)

Mental impairment

Sickle-cell anemia

Anemia, swelling, frequent infections

Tay–Sachs disease

Deterioration of mental and physical abilities; early death

carrier mother

carrier father

Aa

Aa

3 meiosis and gamete formation A

a

A

AA

Aa

a

Aa

aa

affected child carrier child normal child a

disorder-causing allele (recessive)

Figure 10.17  Autosomal recessive inheritance pattern. Only people homozygous for a recessive allele on an autosome (red) have the associated trait. In this example, both parents are carriers. Each of their children has a 25 percent chance of inheriting two alleles and having the trait.

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194  Unit 2 GENETICS Albinism  Albinism is an autosomal recessive phenotype characterized by an

Disorder/Abnormality

Main Symptom(s)

Androgen insensitivity syndrome

XY individual but having some female traits; sterility

Red–green color blindness

Inability to distinguish red from green

Hemophilia

Impaired blood clotting

Muscular dystrophies

Progressive loss of muscle function

X-SCID

Severe immune system deficiency

carrier mother XX

normal father XY

3 meiosis and gamete formation X

Y

X

XX

XY

X

XX

XY

BSIP SA/Alamy Stock Photo

Table 10.3  Some X-Linked Recessive Abnormalities and Disorders of Humans

abnormally low level of melanin. Mutations associated with albinism affect proteins involved in melanin synthesis. Skin, hair, or eye pigmentation may be reduced or missing. In the most dramatic form, the skin is very white and does not tan, and the hair is white. The irises of the eyes appear red because the lack of pigment allows underlying blood vessels to show through (left). Melanin also plays a role in the retina, so vision problems are typical. In skin, melanin acts as a sunscreen; without it, the skin is defenseless against UV radiation. Thus, people with the albino phenotype have a very high risk of skin cancer. Tay–Sachs Disease  Alleles associated with Tay–Sachs disease are inherited in an autosomal recessive pattern. In the general population, about 1 in 300 people is a carrier for one of these alleles, but the incidence is ten times higher in some groups, such as Jews of eastern European descent. The gene altered in Tay–Sachs encodes a lysosomal enzyme responsible for breaking down a particular type of lipid. Mutations that cause the most common form of the disease result in a misfolded enzyme that becomes destroyed, so cells make the lipid but cannot break it down. The lipid accumulates to high levels in cells of the brain and spinal cord, damaging the cells and eventually killing them. Newborns homozygous for a Tay–Sachs allele seem normal, but within three to six months they become irritable, listless, and may have seizures as the lipid accumulates in their nerve cells. Blindness, deafness, and paralysis follow. Affected children usually die by age five.

The X-Linked Recessive Pattern

normal daughter or son carrier daughter X

affected son

X

X chromosome with recessive allele

Figure 10.18  X-linked recessive inheritance pattern. In this example, the mother carries a recessive allele on one of her two X chromosomes (red). Figure It Out: What is the chance that a female child of this union will be a carrier?

Traits inherited in an X-linked pattern (X-linked traits) arise from genes on the X chromosome. Table 10.3 lists a few examples. Most X chromosome alleles that cause genetic disorders are recessive, and these leave two inheritance clues. First, an affected father never passes one of these alleles to a son, because all children who inherit their father’s X chromosome are female (Figure 10.18). Second, the disorder appears more often in males than females. Having only one X chromosome, a male must inherit only one allele to be affected by the disorder; a female must inherit two, and inheriting two disorder-causing alleles is statistically less likely than inheriting one. An X-linked recessive disorder can have uneven effects in heterozygous females because of X chromosome inactivation (Section 8.7). About half of the cells making up the body of a heterozygous female express the recessive allele on one X chromosome; the other half express the dominant allele on the other X chromosome. Mild symptoms may appear if the effect of the recessive allele on her body is not fully masked by that of the dominant allele. Duchenne Muscular Dystrophy  Progressive muscle degeneration characterizes a

severe genetic disorder called Duchenne muscular dystrophy (DMD). The disorder is caused by mutations in the X chromosome gene for dystrophin, a rod-shaped, flexible protein that imparts strength to skeletal and heart (cardiac) muscle. Mutations associated with DMD result in defective or missing dystrophin. Without dystrophin, muscle cell plasma membranes are easily damaged during contraction, and the cells become flooded with calcium ions. Calcium ions act as potent messengers in cells, so their concentration in cytoplasm is normally kept very low (Section 4.6). Among other negative effects, a chronic calcium ion overload causes mitochondrial malfunction (Section 6.1). Muscle cell mitochondria produce too

Answer: 50 percent

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Patterns of Inheritance  Chapter 10  195  

little ATP to support normal cellular function, so muscles are abnormally weak. Free radicals accumulate and kill the cells. Eventually, the tissue’s capacity to regenerate is overwhelmed by rapid cell turnover, and it becomes replaced by fat and connective tissue. DMD affects about 1 in 3,500 people, almost all of them boys. Symptoms begin around age four and progress very quickly. Anti-inflammatory drugs can slow the progression of DMD, but there is no cure. When an affected boy is about 10 years old, he will begin to need a wheelchair and his heart will start to fail. Even with the best care, he will probably die before the age of 30, from a heart disorder or respiratory failure. Red–Green Color Blindness  Color blindness refers to a range of genetic abnormali-

ties in which an individual cannot distinguish among some or all colors of visible light. These conditions are typically inherited in an X-linked recessive pattern, because most of the genes involved in color vision are on the X chromosome. Human eyes normally sense differences between 150 colors, and this perception depends on receptors that respond to red, blue, or green light. Mutations can result in abnormal or defective receptors. The brain distinguishes colors by comparing signals between receptors, so color vision requires at least two types of working receptors. People with mutations that affect two (or three) types of receptors see no color at all, but this is the rarest form of color blindness. The more common red–green color blindness is caused by mutations that alter receptors for red light, or receptors for green light (Figure 10.19). Blue–yellow color blindness is caused by mutations that alter receptors for blue light.

Hemophilia  Hemophilias are genetic disorders in which the blood does not clot properly. Most people have a blood-clotting mechanism that quickly stops bleeding from minor injuries. That mechanism involves two proteins called clotting factors that are products of X chromosome genes. Mutations in these two genes cause two types of hemophilia (A and B, respectively). Males who carry one of these mutations have prolonged bleeding, as do homozygous females (heterozygous females make about half the normal amount of the clotting factor, but this is generally enough to sustain normal clotting). Affected people bruise easily, but internal bleeding is their most serious problem. Repeated bleeding inside the joints disfigures them and causes chronic arthritis. In the nineteenth century, the incidence of hemophilia was relatively high among European and Russian royals, in part because a centuries-old practice of inbreeding among close relatives kept the alleles circulating in royal families. Today, about 1 in 7,500 people in the general population is affected. That number may be rising because the disorder is now treatable, so more affected people are living long enough to transmit an allele to children.

A. The photo on the left shows how a person with red– green color blindness sees the photo on the right. The perception of blues and yellows is normal; red and green appear similar.

B. Part of a standardized test for color blindness. A set of 38 of these circles is commonly used to diagnose deficiencies in color perception. You may have one form of red–green color blindness if you see a 7 instead of a 29 in the circle on the left. You may have another form of red–green color blindness if you see a 3 instead of an 8 in the circle on the right. Figure 10.19  A view of red–green color blindness. Red–green color blindness is inherited in an X-linked recessive pattern. Many people do not realize they are affected by this abnormality until they encounter a standardized test in an introductory biology class. (A) Gary L. Friedman, www.FriedmanArchives.com; (B) Life Nature Library, The Primates 1965 by Sarel Eimerl and Irven DeVore

Take-Home Message 10.7 ●●

●●

●●

A trait associated with a dominant allele on an autosome may appear in every generation. Everyone with the allele has the trait. A trait associated with a recessive allele on an autosome tends to skip generations. Only people homozygous for the allele have the trait. Traits associated with recessive alleles on the X chromosome appear more frequently in men than in women.

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196  Unit 2 GENETICS

10.8  Changes in Chromosome Number Metaphase I

LEARNING OBJECTIVES ●●

Distinguish between polyploidy and aneuploidy.

●●

Explain nondisjunction and its potential effects.

Polyploidy and Aneuploidy Anaphase I

Telophase I

Metaphase II

Individuals of some species have three or more complete sets of chromosomes, a condition called polyploidy. About 70 percent of flowering plant species are polyploid, as are some insects, fishes, and other animals—but not humans. In our species, inheriting more than two full sets of chromosomes is invariably fatal. A few babies survive with too many or too few copies of a particular chromosome, a condition called aneuploidy. Aneuploidy is usually an outcome of nondisjunction, the failure of chromosomes to separate properly during nuclear division. Nondisjunction during meiosis produces gametes with an abnormal number of chromosomes (Figure 10.20), so it can affect the chromosome number at fertilization. Suppose a normal gamete (n) fuses with a gamete that has an extra chromosome (n+1). The resulting zygote will have three copies of one type of chromosome and two of every other type (2n+1), an aneuploid condition called trisomy. If a normal gamete (n) fuses with a gamete missing a chromosome (n−1), the new individual will have one copy of one chromosome and two of every other type (2n−1), a condition called monosomy. Syndromes associated with some forms of aneuploidy are listed in Table 10.4.

Down Syndrome  Anaphase II

Telophase II

Figure 10.20  An example of nondisjunction. Of the two pairs of homologous chromosomes shown here, one fails to separate during meiosis. The chromosome number is abnormal in the resulting gametes. Figure It Out: During which stage of meiosis does nonjunction occur in this example?

Answer: Anaphase I

aneuploidy  Condition of having too many or two few copies of a particular chromosome. nondisjunction  Failure of chromosomes to separate properly during mitosis or meiosis. polyploidy  Condition of having three or more of each type of chromosome characteristic of the species.

In most cases, autosomal aneuploidy in humans is fatal before birth or shortly thereafter. An important exception is trisomy 21. A person born with three copies of chromosome 21 will have Down syndrome and a high likelihood of surviving infancy. Mild to moderate mental impairment and health problems such as heart disease are hallmarks of Down syndrome. Other phenotypic effects may include a somewhat flattened facial profile, a fold of skin that starts at the inner corner of each eyelid, white spots on the iris (Figure 10.21), and one deep crease (instead of two shallow creases) across each palm. The skeleton grows and develops abnormally, so older children have short body parts, loose joints, and misaligned bones of the fingers, toes, and hips. Muscles and reflexes are weak, and motor skills such as speech develop slowly. With medical care, affected individuals live about 55 years. Early training can help these individuals learn to care for themselves and to take part in normal activities. Alzheimer’s disease, a condition of progressive mental deterioration, is associated with Down syndrome. A gene on chromosome 21 is the culprit. Having three of these chromosomes, a person with Down syndrome makes an excess of the gene’s product, a protein that forms the main component of amyloid fibrils (Section 2.9) characteristic of Alzheimer’s. All people with Down syndrome will have these fibrils in their brain by the age of 40. Down syndrome occurs in about 1 of 700 live births, and the risk increases with maternal age.

Sex Chromosome Aneuploidy  About 1 in 400 human babies is born with an atypical number of sex chromosomes. Such alterations often lead to mild difficulties in learning and impaired motor skills, but these problems may be very subtle.

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Patterns of Inheritance  Chapter 10  197  

Turner Syndrome  Individuals with Turner syndrome have an X chromosome and

no corresponding X or Y chromosome (XO). The syndrome is thought to arise most often as an outcome of inheriting an unstable Y chromosome from the father. The zygote starts out being genetically male, with an X and a Y chromosome. Sometime during early development, the Y chromosome breaks up and is lost, so the embryo continues to develop as a female. Fewer people are affected by Turner syndrome than by other chromosome abnormalities: Only about 1 in 2,500 newborns has it. A person who has the syndrome will grow up well proportioned but short, with an average height of 4 feet 8 inches (1.4 meters). In most cases, the ovaries do not develop properly, so the individual does not make enough sex hormones to become sexually mature or to develop secondary sexual traits such as enlarged breasts.

XXX Syndrome  A female may inherit multiple X chromosomes, a condition called triple X syndrome or trisomy X. This syndrome occurs in about 1 of 1,000 births. As with Down syndrome, the risk increases with maternal age. Because of X chromosome inactivation (Section 8.7), only one X chromosome is typically active in female cells. Thus, having extra X chromosomes usually does not cause physical or medical problems, but mild mental impairment may occur.

Table 10.4  A Few Effects of Aneuploidy in Humans

Cause

Syndrome

Main Symptom(s)

Trisomy 21

Down

Mental impairment; heart defects

XO

Turner

Abnormal ovaries and sexual traits

XXY

Klinefelter

Sterility; mild mental impairment

XXX

Trisomy X

Minimal abnormalities

XYY

Jacob’s

Mild mental impairment or no effect

Klinefelter Syndrome  About 1 out of every 500 males has two or more X chro-

mosomes (XXY, XXXY, and so on). The result—Klinefelter syndrome—develops at puberty. As adults, affected males tend to be overweight and tall, with small testes. Underproduction of the hormone testosterone interferes with sexual development and can result in sparse facial and body hair, a high-pitched voice, enlarged breasts, and infertility. Testosterone injections during puberty can minimize these traits. XYY Syndrome  About 1 in 1,000 males is born with an extra Y chromosome

(XYY), a result of nondisjunction of the Y chromosome during sperm formation. Adults with the resulting Jacob’s syndrome tend to be taller than average, with mild mental impairment and an increased vulnerability to psychological problems. Men with XYY syndrome were once thought to be predisposed to a life of crime. This misguided view was based on sampling error (too few cases in narrowly chosen groups such as prison inmates) and bias (the researchers who gathered the karyotypes also took the personal histories of the participants). That view has since been disproven: Men with XYY syndrome are only slightly more likely to be convicted for crimes than unaffected men. Researchers now believe this slight increase can be explained by poor socioeconomic conditions related to psychological problems.

Take-Home Message 10.8 ●●

●●

●●

Polyploidy is the condition of having multiple complete sets of chromosomes. Many organisms are polyploid, but the condition is fatal in humans. Aneuploidy, the condition of having too many or too few copies of a particular chromosome, often arises from nondisjunction. Sex chromosome aneuploidy typically has milder effects on health than autosomal aneuploidy, which is usually fatal in humans. Trisomy 21, which causes Down syndrome, is an exception.

Karyotypeofofananindividual individual with with three A. A. Karyotype threecopies copiesofofchrochromosome 21 and Down syndrome. mosome 21 and Down syndrome.

B. A person with Down syndrome typically has a somewhat flattened facial profile, and a fold of skin that B. starts A person Down syndrome typically hastissue a at thewith inner corner of each eyelid. Excess deposits flattened on the irisfacial also give rise to a ring of starlike somewhat profile, and a fold of skin that white starts at speckles. the inner corner of each eyelid. Excess tissue

deposits on the iris also give rise to a ring of starlike white speckles. Figure 10.21  Down syndrome.

(A) Science Photo Library/Science Source; (B) Michelle Harmon

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198  Unit 2 GENETICS

10.9  Genetic Testing LEARNING OBJECTIVES ●●

Explain how early genetic screening can help a baby.

●●

Discuss the benefits and risks of three prenatal diagnosis methods.

Tests for Newborns

A. Conventional ultrasound.

Studying human inheritance patterns has given us many insights into how genetic disorders arise and progress, and how to treat them. Surgery, prescription drugs, hormone replacement therapy, and dietary controls can minimize and in some cases eliminate the symptoms of a genetic disorder. Some disorders can be detected early enough to start countermeasures before symptoms develop; thus, most hospitals in the United States now screen newborns for mutations that cause phenylketonuria, or PKU. The mutations affect an enzyme that converts one amino acid (phenylalanine) to another (tyrosine). Without this enzyme, the body becomes deficient in tyrosine, and phenylalanine accumulates to high levels. The imbalance inhibits protein synthesis in the brain, which in turn results in permanent intellectual disability. Restricting all intake of phenylalanine can slow the progression of PKU, so routine early screening has resulted in fewer individuals suffering from the symptoms of the disorder.

Tests for Prospective Parents The probability that a future child will inherit a genetic disorder can be estimated by testing the parents for associated alleles. Karyotypes and pedigrees are also useful in this type of screening, which can help prospective parents make informed decisions about family planning.

Prenatal Tests B. 4D ultrasound.

C. Fetoscopy. Figure 10.22  Three ways of imaging a human fetus. (A) Mediscan/Corbis; (B) Dr. Benoit/Mona Lisa/ LookatSciences/Medical Images.com; (C) SPL/ Science Source

Genetic screening is also done postconception, in which case it is called prenatal diagnosis (prenatal means before birth). Prenatal diagnosis checks a fetus for physical abnormalities and genetic disorders. Dozens of genetic conditions are detectable prenatally, including aneuploidy, hemophilia, Tay–Sachs disease, sicklecell anemia, muscular dystrophy, and cystic fibrosis. If a fetus has a treatable disorder, early detection can allow the newborn to receive prompt and appropriate medical care. A few conditions are even surgically correctable before birth. Ultrasound Imaging  As an example of how prenatal diagnosis works, consider a woman who becomes pregnant at age 35. Her doctor will probably perform a procedure called obstetric sonography, in which ultrasound waves directed across the woman’s abdomen form images of the fetus’s limbs and internal organs (Figure 10.22A,B). If the images reveal a physical defect that may be the result of a genetic disorder, a more invasive technique such as fetoscopy would be recommended for further diagnosis. With fetoscopy, sound waves pulsed from inside the mother’s uterus yield images much higher in resolution than ultrasound (Figure 10.22C). Samples of tissue or blood are often taken at the same time, and some corrective surgeries can be performed. Sampling Fetal Cells  Human genetics studies show that our 35-year-old woman

has about a 1 in 80 chance that her baby will be born with a chromosomal abnormality, a risk more than six times greater than when she was 20 years old. Thus, even if no abnormalities are detected by ultrasound, she probably will be

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Patterns of Inheritance  Chapter 10  199  

offered an additional diagnostic procedure in which a few fetal cells are harvested for karyotyping and testing for genetic disorders. With amniocentesis, a small sample of fluid is drawn from the amniotic sac enclosing the fetus (Figure 10.23A). The fluid contains cells shed by the fetus, and those cells are tested. Chorionic villus sampling (CVS) can be performed earlier than amniocentesis. With this technique, a few cells from the chorion are removed and tested (the chorion is a membrane that surrounds the amniotic sac).

amniotic sac

Risks  An invasive procedure often carries a risk to the fetus. The risks vary by the

procedure. Amniocentesis has improved so much that, in the hands of a skilled physician, it no longer increases the risk of miscarriage. CVS occasionally disrupts the placenta’s development, and thus causes underdeveloped or missing fingers and toes in 0.3 percent of newborns. Fetoscopy raises the miscarriage risk by a whopping 2 to 10 percent, so it is rarely performed unless surgery or another medical procedure is required before the baby is born.

Reproductive Interventions Couples who discover they are at high risk of having a child with a genetic disorder may opt for reproductive interventions such as in vitro fertilization (IVF). With this procedure, sperm and eggs taken from the prospective parents are mixed in a test tube. If an egg becomes fertilized, cell divisions will transform the resulting zygote into an embryo. After about 48 hours, the embryo consists of a ball of eight undifferentiated cells (Figure 10.23B). One cell can be removed and its genes analyzed. The withdrawn cell will not be missed. If the embryo has no detectable genetic defects, it is inserted into the woman’s uterus to develop. Most of the resulting “test-tube babies” are born in good health.

chorion

A. With amniocentesis, fetal cells that have been shed into amniotic fluid are tested for genetic disorders. Chorionic villus sampling tests cells of the chorion, which is part of the placenta.

Take-Home Message 10.9 ●●

●●

●●

Studying inheritance patterns for genetic disorders has helped researchers develop treatments for some of them. Genetic testing can provide prospective parents with information about the health of their future children. Symptoms of some genetic disorders can be minimized or eliminated with early detection and treatment.

B. About 48 hours after fertilization, a human embryo is a tiny ball of eight identical cells. This micrograph shows how one of the cells is removed for genetic analysis during IVF. The remaining seven cells can continue development. Figure 10.23  Testing cells of embryos. (A) Lennart Nilsson/Bonnierforlagen AB; (B) Benoît Rajau/Science Source

Summary Section 10.1  Symptoms of cystic fibrosis are pleiotropic effects of mutations in the CFTR gene. The allele associated with most cases persists at high frequency despite its devastating effects in homozygous people. Section 10.2  Gregor Mendel indirectly discovered the role of genes and alleles in inheritance by breeding pea plants and carefully tracking traits of the offspring over many generations.

Genotype (an individual’s alleles) is the basis of phenotype (the individual’s observable traits). Each gene occurs at a particular location on both homologous chromosomes. If both homologous chromosomes have the same allele of a gene, the individual is homozygous for the allele. If the homologous chromosomes have nonidentical alleles, the individual is heterozygous. A dominant allele masks the effect of a recessive allele in a heterozygous individual.

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200  Unit 2 GENETICS

Summary (Continued) Section 10.3  With Mendelian inheritance, one gene gives rise to one trait, and alleles of the gene have a clear dominant–recessive relationship. A diploid cell has homologous chromosomes, so it has two copies of every gene. The two copies of a gene (which may differ as alleles) separate from each other during meiosis, and they end up in different gametes. Crossing individuals that breed true for two forms of a trait yields offspring that are heterozygous for alleles governing the trait. A cross between individuals identically heterozygous for alleles of one gene is a monohybrid cross. The frequency at which the two forms of the trait appear among the offspring of a monohybrid cross can reveal a dominance relationship between the alleles. Crossing individuals that breed true for two forms of two traits yields offspring that are heterozygous for alleles governing both traits. A cross between individuals identically heterozygous for alleles of two genes is a dihybrid cross. Unless the two genes are close together on a chromosome, alleles of one will assort into gametes independently of alleles of the other. A Punnett square can be useful for determining the probability that certain genotypes (and phenotypes) will appear among the offspring of a monohybrid cross or a dihybrid cross.

the trait appears in everyone who has the allele (homozygous or heterozygous). The trait occurs in both sexes, and may appear in every generation of a family. In an autosomal recessive pattern, a recessive allele associated with a trait occurs on an autosome, and the trait appears only in homozygous people. The trait occurs in both sexes, and it can skip generations. In an X-linked inheritance pattern, an allele associated with a trait occurs on the X chromosome. Alleles that cause most X-linked disorders are recessive, and these tend to appear in men more often than in women. A male child can inherit one of these alleles from his mother only.

Section 10.4  Patterns of inheritance that differ from the Mendelian model are common. With incomplete dominance, the phenotype of heterozygous individuals is an intermediate blend of the two homozygous phenotypes. With codominance, heterozygous individuals have both homozygous phenotypes. With polygenic inheritance, multiple genes affect one trait. With pleiotropy, one gene affects multiple traits.

Section 10.9  Genetic testing can reveal the presence of a genetic disorder in newborns. Prospective parents can be tested to determine their risk of transmitting a harmful allele to offspring. Amniocentesis and other methods of prenatal testing can reveal a genetic disorder before birth.

Section 10.5  Environmental factors influence phenotype by altering gene expression. Many traits occur in a range of small increments of phenotype (continuous variation). A bell curve in the range of values is typical of a trait that varies continuously. Multiple alleles such as those that arise in short tandem repeat regions can give rise to continuous variation.

Self-Quiz

Section 10.6  Few easily observed human traits have a Mendelian pattern of inheritance; most are polygenic. Pedigrees can reveal inheritance patterns for alleles associated with genetic abnormalities or disorders. Genetic disorders, unlike abnormalities, cause mild or severe medical problems that often occur as a syndrome. Section 10.7  In an autosomal dominant inheritance pattern, a dominant allele associated with a trait occurs on an autosome, so

Section 10.8  Chromosome number change is usually an outcome of nondisjunction, in which chromosomes fail to separate properly during nuclear division. Having three or more complete sets of chromosomes is a condition called polyploidy. Polyploidy is lethal in humans, but not in flowering plants and some animals. Aneuploidy is the condition of having too many or too few copies of a particular chromosome. In humans, most cases of autosomal aneuploidy are lethal. Trisomy 21, which causes Down syndrome, is an exception. Sex chromosome aneuploidy may result in minor impairment in learning and motor skills.

Answers in Appendix I 1. A heterozygous individual has __________ . a. the same allele on both homologous chromosomes b. two different alleles of a gene c. a haploid condition, in genetic terms 2. An organism’s observable traits constitute its __________ . a. phenotype c. genotype b. variation d. pedigree 3. The offspring of the cross AA × aa are __________ . a. all AA c. all Aa b. all aa d. half are AA and half are aa

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Patterns of Inheritance  Chapter 10  201  

4. The probability of a crossover occurring between two genes on the same chromosome __________ . a. is unrelated to the distance between them b. decreases with the distance between them c. increases with the distance between them 5. If one parent is heterozygous for a dominant allele on an autosome and the other parent does not carry the allele, any child of theirs has a __________ chance of being heterozygous. 25 percent   b. 50 percent   c. 75 percent a. 6. True or false? All traits are inherited in a Mendelian pattern. 7. One gene that gives rise to three traits is an example of __________ . a. polygenic inheritance  b. codominance  c. pleiotropy 8. __________ in a trait is indicated by a bell curve. a. An epigenetic effect c. Incomplete dominance b. Nondisjunction d. Continuous variation 9. Pedigree analysis is necessary when studying human inheritance patterns because __________ . a. humans have approximately 20,000 genes b. of ethical problems with experimenting on humans c. inheritance in humans is more complicated than it is in other organisms d. genetic disorders occur only in humans 10. A female child inherits one X chromosome from her mother and one from her father. What sex chromosome does a male child inherit from each of his parents? 11. Nondisjunction at meiosis can result in __________ . a. base-pair substitutions c. crossing over b. aneuploidy d. pleiotropy 12. True or false? An individual with three or more complete sets of chromosomes is polyploid. 13. Klinefelter syndrome (XXY) is most easily diagnosed by __________ . a. pedigree analysis c. karyotyping b. aneuploidy d. a Punnett square 14. Match each example with the best description. dihybrid cross a. bb monohybrid cross b. AaBb × AaBb homozygous c. Aa heterozygous d. Aa × Aa

15. Match the terms appropriately. a. symptoms of a genetic disorder polyploid b. extra sets of chromosomes syndrome c. caused by a short tandem repeat aneuploidy d. one extra chromosome Mendelian e. dominant > recessive genotype f. an individual’s alleles Huntington’s disease

CRITICAL THinking 1. Cystic fibrosis is inherited in an autosomal recessive pattern, and it has pleiotropic effects. Chronic respiratory problems are characteristic of the disorder, but so are other symptoms: extremely salty sweat, chronic diarrhea, malnutrition, bowel obstructions, diabetes, cirrhosis of the liver, and infertility, for example. The incidence and severity of these symptoms varies dramatically, however. Why does the disease manifest itself differently in different patients? 2. Assuming that genes assort independently during meiosis, how many type(s) of gametes will form in individuals with the following genotypes? a. AABB   b. AaBB   c. Aabb   d. AaBb 3. Marfan syndrome is inherited in an autosomal dominant pattern. What is the chance that a child will have the syndrome if one parent does not carry the associated allele, and the other is heterozygous for it? 4. Which pattern of inheritance best describes each of the following scenarios? a. In mice, alleles of the agouti gene determine the distri­­­ bution of pigment in the individual’s fur. The dominant allele A of this gene gives rise to banded fur; the recessive allele a, to solid fur. Pigment production is controlled by alleles of the TYR gene. b. Cats with a dominant allele of the KIT gene have white fur, blue eyes, and they are deaf. c. In Andalusian chickens, a mating between an individual with black feathers and an individual with white feathers produces offspring with gray feathers. d. In cattle, a mating between an individual with red hair and an individual with white hair may yield offspring with roan coloration (an even distribution of red hair and white hair). e. A cross between a true-breeding pea plant with green pods and a true-breeding plant with yellow pods produces offspring with green pods.

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11 Biotechnology

11.1

Personal Genetic Testing  203

11.2

Working with DNA  204

11.3

Studying DNA  207

11.4

Genetic Engineering  211

11.5

Editing Genomes  214

Mice transgenic for multiple pigments (“brainbow mice”) are allowing researchers to map the complex neural circuitry of the brain. In this fluorescence micrograph, individual nerve cells in the brain stem of a brainbow mouse are visible in different colors.

Concept Connections

Courtesy of Dr. Jean Levit. The Brainbow technique was developed in the laboratories of Jeff W. Lichtman and Joshua R. Sanes at Harvard University. This image has received the Bioscape imaging competition 2007 prize.

In this chapter, you will use your knowledge of DNA structure (Sections 7.3 and 7.4) and replication (7.5) as you learn about how researchers manipulate DNA, for example when they produce clones (7.1) and knockouts (8.8). Researchers use techniques such as PCR and DNA sequencing to study organisms and their evolutionary relationships (12.7). Be sure you understand the relationship between genotype and phenotype (10.2), including alleles (9.5) and the effects of mutations (8.6). The chapter also revisits tracers (2.2), lipids (2.8), plasmids (3.4), Alzheimer’s disease (3.5), bacteriophage (7.2), proto-oncogenes (9.4), and short tandem repeats (10.5).

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Biotechnology  Chapter 11  203 

Application 11.1  Personal Genetic Testing About 99 percent of your DNA is exactly the same as everyone else’s. The shared part is what makes you human; the differences make you a unique member of the species. If you compared your DNA with your neighbor’s, about 2.97 billion nucleotides of the two sequences would be identical. The nonidentical nucleotides are sprinkled throughout your chromosomes, but the sprinkling is not entirely random: Some regions vary less than others. When one of these regions does vary among people, the variation tends to be in single nucleotides at a particular location. A one-nucleotide DNA sequence variation carried by a measurable percentage of a population, usually above 1 percent, is called a single-nucleotide polymorphism, or SNP (pronounced “snip”). Variations carried by less than 1 percent of a population are just called mutations. Alleles of most genes differ by single nucleotides—SNPs—and differences in alleles are the basis of the variation in human traits that makes each person unique. Thus, SNPs account for differences in the way humans appear, and they also have a lot to do with differences in the way our bodies work: how we age, respond to drugs, weather assaults by pathogens and toxins, and so on. If you want to know your genotype, a genetic testing company can extract DNA from a few drops of spit or a cheek swab, then analyze its sequence for SNPs and mutations. Results may include the likelihood of having traits associated with these variations. For example, the test will probably determine whether you are homozygous for a particular SNP in the MC1R gene. If you are, then you have red hair. Few SNPs have such a clear effect, however. A genetic test can accurately determine an individual’s DNA sequence variations, but it cannot reliably predict the effect of most of those variations on the individual. Consider how your risk of developing Alzheimer’s disease depends on which alleles of the APOE gene you have. APOE encodes apolipoprotein E, a protein component of lipoprotein particles that carry fats and cholesterol through our bloodstreams (Section 2.9). Most people are homozygous for an APOE allele called E3. A different allele, E4, has a SNP in which a cytosine replaces the more common thymine at a particular location. How this substitution affects the function of the protein is not yet clear, but we do know that having the allele increases one’s risk of developing Alzheimer’s disease. About one in seven people are heterozygous for the E4 allele. If you are, a DNA testing company cannot tell you whether you will develop Alzheimer’s. However, it may report your lifetime risk of developing the disease, which is about 47 percent, as compared with about 20 percent for someone who is homozygous for the E3 allele. What, exactly, does a 47 percent lifetime risk mean? The number is a probability statistic: It means, on average, 47 of every 100 people who have one E4 allele eventually get the disease. However, a risk is just that. Not everyone who has the allele develops Alzheimer’s, and not everyone who develops the disease has the allele. Our understanding of the genetic underpinnings of many health conditions is incomplete, but we are at a tipping point. Physicians now use genetic testing to determine a patient’s ability to respond to certain drugs prior to treatment, and to tailor cancer treatments for individuals and their tumor cells. Preventive treatments based on genotype are becoming mainstream (Figure 11.1).

Figure 11.1  Preventive treatment based on genotype. Genetic testing revealed that celebrity Angelina Jolie inherited a BRCA1 mutation associated with an 87 per­­­­­­­cent lifetime risk of developing breast cancer. Even though she did not yet have cancer, Jolie underwent a double mastectomy. Doing so reduced her breast cancer risk to 5 percent. Preventive surgery based on high-risk genotype has since become common. WENN Rights Ltd./Alamy Stock Photo

SNP  Single-nucleotide polymorphism. A onenucleotide DNA sequence variation carried by a measurable percentage of a population.

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204  Unit 2 GENETICS

Discussion Questions 1. Can you think of potential drawbacks to the widespread public availability of personal genetic testing? 2. Imagine that you owned a genetic testing company. Would you provide clients with their estimated risk of developing certain health conditions based on their genotype? Explain your rationale. 3. Would you want to know whether you had a high risk of developing a dangerous health condition? What factors might influence your decision? Eco RI recognition site C

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11.2  Working with DNA Learning Objectives

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Explain the use of probes in screening a DNA library.

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Describe PCR.

Restriction Enzymes

A. The restriction enzyme Eco RI recognizes and cuts a specific nucleotide sequence in DNA (GAATTC). Eco RI leaves single-stranded tails (“sticky ends”) at the cuts.

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Describe restriction enzymes and explain why their discovery was important for DNA research.

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C. DNA ligase joins hybridized DNA fragments to produce a molecule of recombinant DNA. Figure 11.2  Restriction enzymes and recombinant DNA. Figure It Out: Why does the enzyme cut both strands of DNA?

In the 1950s, excitement over the discovery of DNA’s structure gave way to frustration, because no one could determine the sequence of DNA in a chromosome. Identifying single nucleotides among thousands or millions of others turned out to be a huge technical hurdle. Research in a seemingly unrelated field yielded a solution when Werner Arber, Hamilton Smith, and their coworkers discovered how some bacteria resist infection by bacteriophage (Section 7.2). These bacteria have enzymes that chop up any injected viral DNA. The enzymes restrict viral replication, so they are called restriction enzymes. A restriction enzyme cuts DNA wherever a specific nucleotide sequence occurs. For example, the enzyme EcoRI (named after E. coli, the bacteria from which it was isolated) cuts DNA at the nucleotide sequence GAATTC (Figure 11.2A). Other restriction enzymes cut at different sequences.

Recombinant DNA The discovery of restriction enzymes allowed researchers to cut chromosomal DNA into manageable chunks. It also allowed them to combine DNA fragments from different organisms. How? Many restriction enzymes, including EcoRI, leave single-stranded tails on DNA fragments. Because the chemical structure of DNA is the same in all organisms, complementary tails will base-pair regardless of the source of DNA (Figure 11.2B). The tails are called “sticky ends,” because two DNA fragments stick together when their matching tails base-pair, or hybridize (Section 7.5). The gaps between hybridized sticky ends can be sealed with an enzyme called DNA ligase, so continuous DNA strands form (Figure 11.2C). Thus, using appropriate restriction enzymes and DNA ligase, DNA from different sources can be cut and pasted together. The result, a hybrid molecule that consists of genetic material from two or more organisms, is called recombinant DNA.

DNA Cloning Making recombinant DNA is the first step in DNA cloning, a set of laboratory methods that uses living cells to mass-produce specific DNA fragments. Researchers clone a fragment of DNA by inserting it into a vector, which in this context

Answer: Because the recognition sequence occurs on both strands.

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Biotechnology  Chapter 11  205 

CLOSER LOOK Figure 11.3  An example of cloning.

5 The cell is cultured. 4 The recombinant

vector is inserted into a host bacterial cell.

chromosomal DNA

With every division, each descendant cell (clone) receives a copy of the recombinant vector.

fragments of chromosomal DNA

1 A restriction enzyme ( ) cuts chromosomal DNA. The enzyme’s recognition sequence occurs many times in the DNA, so the DNA is cut into many fragments.

plasmid cloning vector

recombinant vector

cut vector

3 The cut vector is mixed with the

chromosomal DNA fragments, and the matching sticky ends base-pair. DNA ligase seals one of the fragments into the vector.

2 The same restriction enzyme ( )

cuts a plasmid cloning vector.

Figure It Out: How many times does the enzyme’s recognition sequence occur in this vector? Answer: Once

is a molecule or virus that can carry foreign DNA into host cells. Plasmids may be used as cloning vectors in bacteria, yeast, and other cells (Figure 11.3). When a cell reproduces, its offspring inherit a full complement of genetic information— chromosome(s) plus plasmid(s). A recombinant plasmid gets replicated and distributed to descendant cells just like other plasmids. In a typical procedure, the DNA to be cloned is cut into fragments with a restriction enzyme 1. The cloning vector is cut with the same enzyme 2 and mixed with the DNA fragments so their sticky ends can base-pair. DNA ligase seals a DNA fragment into a vector 3. The resulting recombinant vector is inserted into a host cell 4.

6 The hosted DNA fragment is harvested from the clones and purified.

Figure Summary In this example, a fragment of chromosomal DNA is cloned by inserting it into a plasmid. The recombinant plasmid is then delivered into a bacterial host cell, which is cultured to produce many descendants.

Why Clone DNA?  Researchers clone DNA to study and manipulate it, because

doing so requires some quantity of purified material. A cell that hosts a recombinant vector can be grown in the laboratory (cultured) to yield a huge population of genetically identical cells 5. Each of these clones contains at least one copy of the vector and its foreign DNA fragment. The DNA fragment can be harvested in large quantities from the clones and purified 6. Cloning a DNA fragment separates it from chromosomal DNA, and allows it to be produced in essentially unlimited quantities. This was a key step in the quest to understand the information DNA encodes, which is why Arber and Smith won a 1978 Nobel Prize for the discovery of restriction enzymes. The use of these enzymes opened the door on a new era of research, because it enabled researchers to determine the sequence of DNA (Section 11.4 returns to this topic).

DNA cloning  Set of methods that uses living cells to mass-produce targeted DNA fragments.

DNA Libraries  The entire set of genetic material—the genome—of most organisms consists of thousands of genes. To study or manipulate a single gene, researchers must first separate it from all of the other genes in a genome. They may begin

vector  In DNA cloning, a virus or molecule that can accept foreign DNA and be replicated inside a host cell.

genome  An organism’s complete set of genetic material. recombinant DNA  A hybrid DNA molecule; contains genetic material from more than one organism. restriction enzyme  Type of enzyme that cuts DNA at a specific nucleotide sequence.

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206  Unit 2 GENETICS

1 DNA (blue) with a targeted sequence (gray) is mixed with primers (pink), nucleotides, and heat-tolerant Taq DNA polymerase.

template DNA

2 Round 1. When the mixture is heated, the DNA

separates into single strands. When the mixture is cooled, primers base-pair with the DNA at opposite ends of the targeted sequence.

round: copies:

1 2

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4 16

5 32

30 1 billion

Figure 11.5  Exponential amplification of DNA by PCR. Thirty rounds of PCR can result in a billion-fold amplification of a DNA fragment.

3 Taq polymerase begins DNA synthesis at the

primers, so it produces complementary strands of the targeted DNA sequence.

by cutting an organism’s DNA into fragments, and then cloning all the fragments simultaneously. The result is a set of clones that collectively contain all of the DNA in a genome. This and any other set of cells that collectively host various cloned DNA fragments is called a DNA library. Probes  In DNA libraries, a cell that contains a particular DNA fragment of interest

4 Round 2. The mixture is heated again, so the DNA

separates into single strands. When it is cooled, primers base-pair with the targeted sequence in the original template DNA and in the new DNA strands.

is often mixed up with thousands or millions of others that do not—a needle in a genetic haystack. One way to find that cell among all of the others involves the use of a probe, which is a fragment of DNA or RNA labeled with a tracer (Section 2.2). For example, to find a cell that hosts DNA with a particular gene in a library, a researcher may assemble radioactive nucleotides into a short, single strand of DNA complementary in sequence to the gene. The probe will hybridize with DNA containing the gene, but not with other DNA. Thus, the researcher can pinpoint a cell that hosts the targeted DNA by detecting radioactivity coming from the probe. The cell is isolated and cultured, and the DNA is extracted from the cultured cells.

PCR

5 Each cycle (round) of heating and cooling can double the number of copies of the targeted DNA section. Figure 11.4  PCR.

The polymerase chain reaction, or PCR, is a technique that mass-produces copies of (amplifies) a particular section of DNA. PCR can quickly transform a needle in a haystack—that one-in-a-million fragment of DNA—into a huge stack of needles with a little hay in it. The starting material for PCR is any sample that contains at least one molecule of DNA. It might be extracted from a mixture of 10 million different clones, a sperm, a hair left at a crime scene, or a mummy—essentially any sample that has DNA in it. PCR is based on DNA replication (Section 7.5), and it requires two synthetic primers designed to base-pair at opposite ends of a targeted section of DNA (Figure 11.4). Researchers mix these primers with the template DNA (DNA to be amplified), nucleotides, and DNA polymerase 1. Then, they expose the mixture to repeated cycles, or rounds, of high and low temperatures. A few seconds at high

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Biotechnology  Chapter 11  207 

temperature disrupts the hydrogen bonds that hold the two strands of a DNA double helix together (Section 7.3), so every molecule of DNA unwinds and becomes single-stranded. As the temperature of the reaction mixture is lowered, the primers hybridize with DNA strands that have the targeted sequence 2. The DNA polymerases of most organisms denature at the high temperature required to separate DNA strands. PCR makes use of Taq polymerase, an enzyme isolated from Thermus aquaticus bacteria. These bacteria live in hot springs and hydrothermal vents, so their DNA polymerase necessarily tolerates heat. Like other DNA polymerases, Taq polymerase recognizes hybridized primers as places to start DNA synthesis. The enzyme begins assembling a complementary strand of DNA based on the sequence of nucleotides in the template strand 3. The newly synthesized DNA is a copy of the targeted section. The reaction proceeds until the second round of PCR, when the temperature rises and the DNA once again separates into single strands 4. When the mixture is cooled, primers hybridize, and DNA synthesis begins again. Each cycle of heating and cooling takes only a few minutes, but it can double the number of copies of the targeted section of DNA 5. Thirty rounds of PCR can make a billion copies of a targeted section of DNA (Figure 11.5).

Take-Home Message 11.2 ●●

●●

●●

●● ●●

In DNA cloning, researchers use restriction enzymes to cut DNA into fragments, and DNA ligase to seal fragments from different sources together. Recombinant DNA results. Cloning vectors carry foreign DNA into host cells that can be cultured. Foreign DNA carried by a recombinant vector can be extracted from cultured cells in quantity. A probe can be used to identify a cell that hosts a targeted DNA fragment among many others in a DNA library. A genome comprises an organism’s complete set of genetic material. PCR quickly mass-produces copies of (amplifies) a targeted section of DNA.

11.3  Studying DNA Learning Objectives ●●

Describe the use of electrophoresis in DNA sequencing.

●●

Give an example of the types of information yielded by genome comparisons.

●●

Explain how and why individuals can be identified by their DNA.

Sequencing Determining the order of nucleotide bases in a DNA molecule (its sequence) is called DNA sequencing. In a sequencing method based on DNA replication, DNA polymerase is mixed with a primer, nucleotides, and a template—the DNA to be sequenced. Starting at the primer, the polymerase joins the nucleotides into a new strand of DNA, in the order dictated by the sequence of the template. Millions of DNA fragments of different lengths are produced, each a partial copy of the template DNA. Electrophoresis  The newly synthesized DNA fragments are then separated by length. In a technique called electrophoresis, an electric field pulls the fragments through a semisolid gel. Fragments of different sizes move through the gel at different rates. The shorter the fragment, the faster it moves, because shorter fragments

DNA library  Collection of cells that host different fragments of foreign DNA, often representing an organism’s entire genome. DNA sequencing  Method of determining DNA sequence. electrophoresis  Technique that separates DNA fragments by size. PCR  Polymerase chain reaction. Technique that rapidly amplifies (generates many copies of) a specific section of DNA. probe  Short fragment of DNA labeled with a tracer; designed to hybridize with a nucleotide sequence of interest.

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208  Unit 2 GENETICS DNA profiling  Identifying an individual by the unique parts of his or her DNA. genomics  The study of genome structure and function.

DNA movement through electrophoresis gel

human DNA sequence data

Figure 11.6  DNA sequencing. Sequencing uses an electrophoresis gel to separate DNA fragments by length. The shorter the fragment, the faster it moves through the gel. Fragments of the same length gather into bands. The nucleotide at the end of each DNA fragment has been labeled with a colored tracer: A (green), T (red), G (yellow), or C (blue). The order of the colored bands in each vertical “lane” represents part of the DNA sequence.

slip through the tangled molecules of the gel faster than longer fragments do. All fragments of the same length move through the gel at the same speed, so they gather into bands. The nucleotide at the end of each fragment is labeled with one of four colored tracers, with the color depending on the base. These tracers impart colors to the bands. Successive bands consist of fragments that differ in length by one nucleotide, so the order of the colors in the bands reflects the DNA sequence (Figure 11.6).

The Human Genome Project The sequencing method we have just described was invented in 1975. Ten years later, it had become so routine that scientists began to consider sequencing the entire human genome—all 3 billion nucleotides. Proponents of the idea said it could provide huge payoffs for medicine and research. Opponents said this daunting task would divert attention and funding from more urgent research. Given the existing methods, sequencing 3 billion bases would take at least 50 years. However, the methods continued to improve rapidly, and with each improvement more nucleotides could be sequenced in less time. Automated (robotic) DNA sequencing and PCR had just been invented. Both were still too cumbersome and expensive to be useful in routine applications, but they would not be so for long. Waiting for faster, cheaper technologies seemed the most efficient way to sequence the genome, but just how fast did they need to be before the project should begin? A few privately owned companies decided not to wait, and started sequencing. One of them intended to determine the genome sequence in order to patent it. The idea of patenting the human genome provoked widespread outrage, but it also spurred commitments in the public sector. In 1988, the National Institutes of Health (NIH) hired James Watson (of DNA structure fame) to head an official Human Genome Project, and provided $200 million per year to fund it. A partnership formed between the NIH and international institutions that were sequencing different parts of the genome. Amid ongoing squabbles over patent issues, Celera Genomics formed in 1998. With biologist Craig Venter at its helm, the company intended to commercialize human genetic information. Celera invented faster sequencing techniques, because the first company to complete the genome sequence had a legal basis for patenting it. The competition motivated the international partnership to accelerate its efforts. Then, in 2000, U.S. President Bill Clinton and British Prime Minister Tony Blair jointly declared that the sequence of the human genome could not be patented. Celera kept sequencing anyway, and, in 2001, the competing governmental and corporate teams published about 90 percent of the sequence. In 2003, fifty years after the discovery of the structure of DNA, the sequence of the human genome was officially completed. The sequence is freely accessible worldwide (see www.ncbi.nlm.nih.gov/genome). Anyone can search it and see current statistics (Table 11.1). From start to finish, the Human Genome Project required about 16 years and $2.7 billion to complete, but it spurred development of much more efficient technologies for sequencing and data analysis. Today, an entire genome can be sequenced in a few days, for less than $1,000.

Genomics

(Right) Patrick Landmann/Science Source

Figure It Out: What is the sequence indicated by the colored bands in the gel on the left, starting at the bottom?

It will take time before we understand all of the information coded within the human genome. Some of it has been deciphered by comparing genomes of different species, the premise being that all organisms are descended from shared ancestors, so all genomes are related to some extent. We see evidence of such genetic

Answer: TACCATGTGAACCTA

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Biotechnology  Chapter 11  209  758 752 751 754 782 758 823 763

GATAATCCTGTTTTGAACAAAAGGTCAAATTGCTGAATAGAAA–GTCTTGATTAACTAAAAGATGTACAAAGTGGAATTA GATAATCCTGTTTTGAACAAAAGGTCAAATTGCTGAATAGAAA–GTCTTGATTAACTAAAAGATGTACAAAGTGGAATTA GATAATCCTGTTTTGAACAAAAGGTCAAATTGCTGAATAGAAA–GTCTTGATTAACTAAAAGATGTACAAAGTGGAATTA GATAATCCTGTTTTGAACAAAAGGTCAAATTGCTGAATAGAAA–GTCTTGATTAACTAAAAGATGTACAAAGTGGAATTA GATAATCCTGTTTTGAACAAAAGGTCAAATTGCTGAATAGAAA–GTCTTGATTAACTAAAAGATGTACAAAGTGGAATTA GATAATCCTGTTTTGAACAAAAGGTCAAATTGCTGAATAGAAA–GTCTTGATTAAGTAAAAGATGTACAAAGTGGAATTA GATAATCCTGTTTTGAACAAAAGGTCAGATTGCTGAATAGAAAAGGCTTGATTAAAGCAGAGATGTACAAAGTGGACGCA GATAATCCTGTTTTGAACAAAAGGTCAAATTGTTGAATAGAGACGCTTTGATAAAGCGGAGGAGGTACAAAGTGGGACC–

836 830 829 832 860 836 902 841

Human Mouse Rat Dog Chicken Frog Zebrafish Pufferfish

Figure 11.7  Alignment of a section of genomic DNA from various species. This is a region of the gene for a DNA polymerase. Nucleotides that differ from those in the human sequence are highlighted in color. The chance that any two of these sequences would randomly match is 1 in 1046.

Table 11.1  Some Human Genome Statistics

Chromosomes (number of)*

relationships simply by aligning the sequences, which, in some regions of DNA, are extremely similar across many species (Figure 11.7). Comparing genome sequences is part of genomics, the study of genome structure and function. Similarities among genomes allow us to discover the function of human genes by studying their counterparts in other species. For example, by comparing human and mouse genomes, researchers discovered a human version of a mouse gene called APOA5, which encodes a lipoprotein (Section 2.9). Mice with an APOA5 knockout have four times the normal level of triglycerides in their blood. The researchers then looked for—and found—a correlation between APOA5 mutations and high triglyceride levels in humans. High triglycerides are a risk factor for coronary artery disease.

Nucleotides (number of)*

Even though 99 percent of your DNA is exactly the same as everyone else’s, unique differences in the remaining 1 percent can be used to identify you. Identifying an individual by his or her DNA is called DNA profiling. SNP Genotyping  One DNA profiling method is based on SNPs. Analyzing an

individual’s DNA for SNPs involves DNA microarray chips, which are tiny glass plates with thousands of microscopic spots of DNA stamped on them. Each spot contains a short, synthetic single strand of DNA with a unique SNP sequence. When an individual’s DNA is washed over a chip, it hybridizes only with spots that have a matching SNP. Tracers reveal where the individual’s DNA has hybridized—and which SNPs are in it (Figure 11.8). A standard DNA profiling kit used in population studies tests an individual’s DNA for 52 SNPs. The chance that two people who are not identical twins would have the same set of these SNPs is less than one in 1021. Personal genetic testing companies will test your DNA for about 700,000 SNPs—far more than are necessary to identify you among all others on the planet. Microsatellite Analysis  You learned in Section 10.5 that short tandem repeats are regions of DNA in which a series of two to six nucleotides is repeated many times in a row. Short tandem repeats are also called microsatellites, and there are thousands of them in the human genome. The number of times a sequence is repeated in a given microsatellite differs among individuals. For example, in a microsatellite that consists of the repeated nucleotide sequence TTTTC, one person may have 15 repeats of this sequence, another may have 4, and so on. DNA polymerases stutter or slip over the repeated sequences during DNA replication, so the number of repeats can increase or decrease from one generation to the next.

3,547,121,844

Genes Protein-coding genes (number of)*

20,313

Non-protein-coding genes (number of)*

25,180

Pseudogenes (gene duplications, number of)*

14,453

Exons (number of) Average exon length (base pairs) Introns (number of)

DNA Profiling

24

Average intron length (base pairs)

381,122 163 378,089 5,849

Variation Short tandem repeats (number of)

741,587

Single-nucleotide polymorphisms (number of)‡

87,339,846

*Ensembl release 84.38 ‡ NCBI dbSNP build 146

Figure 11.8  A DNA microarray. Each microscopic spot is a region where an individual’s DNA has hybridized with a SNP. A red or green spot means the individual is homozygous, with the same SNP on both homologous chromosomes. A combined signal (yellow spot) means the individual is heterozygous, with different SNPs. Andre Nantel/Shutterstock.com

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210  Unit 2 GENETICS A. Gray boxes show the names of the six microsatellites that were tested. D5S818

11.0 14.0

D13S317

11.013.0

D7S820

7.0

13.0

D16S539

CSF1PO

13.013.0

12.0

Penta D

12.0

14.0

B. The number of repeats is shown in a box below each peak. (Peak size reflects amount of DNA produced by the PCR reaction.) Figure 11.9  A partial DNA profile. This one is based on microsatellites (short tandem repeats). Double peaks appear on a profile when the two members of a chromosome pair carry a different number of repeats. Figure It Out: How many repeats does this individual have at the Penta D region?

A common method of DNA profiling uses PCR to amplify 13 to 20 microsatellites. PCR produces DNA fragments whose length depends on the number of repeats, and electrophoresis is used to determine the length of the fragments. A graph of the results constitutes the individual’s DNA profile (Figure 11.9). Unless two people are identical twins, the chance that they would have an identical number of repeats at 13 microsatellites is less than one in a quadrillion (1015), which is more than the number of people who have ever lived. Thus, an individual’s array of short tandem repeats is, for all practical purposes, unique. DNA profiles based on microsatellite analysis are routinely used as evidence in criminal cases. Within the context of a criminal investigation, DNA profiling is called DNA fingerprinting. By 2019, the database of DNA fingerprints maintained by the Federal Bureau of Investigation (FBI) contained the short tandem repeat profiles of almost 14 million convicted offenders, and had been used in more than 400,000 criminal investigations.

Answer: 12 on one chromosome, and 14 on the other

A Killer Application  SNPs and mutations are a built-in genetic record of family

history, so they are a great way to discover your roots. People who are related have similar patterns of these DNA sequence variations, with closer relatives having more similarities than distant relatives. Thus, genetic testing companies can help you understand your ethnic origins—where your ancestors hailed from, hundreds or even thousands of years ago. The companies can also help you find living relatives whose DNA data has been shared in genealogy (family history) databases. Genealogy databases are also helping investigators find criminals. In 2018, police arrested a man suspected of murdering 12 people and raping 51 others in a series of crime sprees in the 1970s and 1980s. The killer’s DNA had been collected from many crime scenes, but it did not match any DNA in the FBI’s criminal database. However, when investigators uploaded the man’s DNA profile into a public genealogy database, they identified several of his relatives. Within a few months, a genealogist had constructed a family tree that brought investigators to the killer’s front door.

Take-Home Message 11.3 genetic engineering  Process by which deliberate changes are introduced into a genome, with the intent of modifying phenotype. genetically modified organism (GMO)  Organism whose genome has been modified by genetic engineering. transgenic  Refers to a genetically modified organism that carries a gene from a different species.

●●

●●

●●

Sequencing reveals the order of nucleotides in DNA. Improved sequencing technologies are the result of worldwide efforts to sequence the human genome. All genomes are related to some extent. We have deciphered the function of many human genes by comparing our genome with that of other species. Aside from identical twins, each person has a unique pattern of short tandem repeats and SNPs. Using these patterns to identify an individual is called DNA profiling.

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Biotechnology  Chapter 11  211 

11.4  Genetic Engineering Learning Objectives ●●

Explain the difference between a GMO and a transgenic organism.

●●

Describe some genetically engineered organisms and their uses.

GMOs Traditional crossbreeding methods can alter genomes, but only if individuals with the desired traits will interbreed. Genetic engineering takes gene swapping to an entirely different level. Genetic engineering is a process by which deliberate changes are introduced into a genome, with the intent of modifying phenotype. An individual whose genome has been engineered is a genetically modified organism (GMO). Some GMOs are transgenic, which means a gene from a different species has been inserted into their DNA.

Modified Microorganisms  Most GMOs are yeast (single-celled fungi) and bacteria (Figure 11.10). Both types of cells are easily engineered, and they have the metabolic machinery to make complex organic molecules—including medically important proteins. People with a life-threatening form of diabetes were among the first beneficiaries of such organisms. These people do not make the hormone insulin, so they require insulin injections. The insulin was once extracted from animals, but some people have allergic reactions to animal insulin. Human insulin, which does not provoke allergic reactions, has been produced by transgenic E. coli since 1982. Genetically engineered microorganisms also make proteins used in food production. For example, we use enzymes produced by modified microorganisms to improve the taste and clarity of beer and fruit juice, to slow bread staling, and to modify fats. Cheese is traditionally made with an enzyme (chymosin) extracted from calf stomachs. Today, almost all cheese is made with calf chymosin produced by transgenic yeast.

Figure 11.10  E. coli bacteria transgenic for a fluorescent jellyfish protein. Variation in fluorescence among these genetically identical E. coli cells reveals differences in gene expression that may help us understand why some bacteria become dangerously resistant to antibiotics, and others do not. Photo Courtesy of Systems Biodynamics Lab, P. I. Jeff Hasty, UCSD Department of Bioengineering, and Scott Cookson

A. The genetically modified plants that produced the corn on the left are resistant to insect damage because they carry a gene from the bacterium Bacillus thuringiensis (Bt). Compare the corn from unmodified plants on the right. No pesticides were used on either crop.

Designer Plants  As crop production expands to keep pace with human population growth, farmers are relying more and more on transgenic crop plants. Some genetically modified plants carry genes that impart resistance to diseases or pests. Consider that farmers who grow organic produce often spray their crops with spores of Bt (Bacillus thuringiensis), a species of bacteria that makes a protein toxic only to some insect larvae. The gene for the Bt protein has been transferred into crop plants such as soy and corn. Larvae that feed on these engineered plants die shortly after eating their first (and only) GMO meal. Farmers can use much less pesticide on crops that make their own (Figure 11.11A). Transgenic crop plants are also being developed for impoverished regions of the world. Genes that confer drought tolerance and enhanced nutritional value have already been introduced into plants such as corn, rice, beans, sugarcane, cassava, cowpeas, banana, and wheat. For example, rice plants were engineered to overproduce β-carotene, an orange photosynthetic pigment that is remodeled into vitamin A by cells of the small intestine. These rice plants carry two genes in the β-carotene synthesis pathway: one from corn, the other from bacteria. One cup of their seeds—grains of Golden Rice (Figure 11.11B)—has enough β-carotene to satisfy a child’s daily need for vitamin A.

B. Plants that make Golden Rice (on the right) carry two genes that upregulate their synthesis of β-carotene, a pigment that is remodeled by the body into vitamin A. This crop was approved in the U.S. for human consumption in 2018. Figure 11.11  Examples of GMO crops. (A) The Bt and Non-Bt corn photos were taken as part of field trial conducted on the main campus of Tennessee State University at the Institute of Agricultural and Environmental Research. The work was supported by a competitive grant from the CSREES, USDA titled Southern Agricultural Biotechnology Consortium for Underserved Communities, (2000-2005). Dr. Fisseha Tegegne and Dr. Ahmad Aziz served as Principal and Co-principal Investigators respectively to conduct the portion of the study in the State of Tennessee; (B) Erik De Castro/REUTERS

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212  Unit 2 GENETICS

Worldwide, more than 330 million acres are currently planted in GMO crops, the majority of which are corn, sorghum, cotton, soy, canola, and alfalfa genetically engineered for resistance to the herbicide glyphosate. Rather than tilling the soil to control weeds, farmers can spray their fields with glyphosate, which kills the weeds but not the GMO crops. Crop Controversy  Crops genetically engineered to resist glyphosate have been

used in conjunction with the herbicide since the mid-1970s, and the practice is still controversial. The scientific consensus is that GMO crops are as nutritious as other crops, and eating them poses no threat to human health. However, their impact on wild plants and other environmental factors is less clear. Genes that confer glyphosate resistance are now appearing in weeds and other wild plants, as well as in unmodified crops—which means that recombinant DNA can (and does) escape into the environment. Glyphosate resistance genes can be transferred from transgenic plants to nontransgenic ones via pollen carried by wind or insects. Issues surrounding the use of GMO crops are complicated and involve multiple constituencies—consumers, farmers, biotech companies, regulatory agencies, and so on. Understanding the science behind these crops is the first step toward forming your own educated opinions.

A. Zebrafish genetically modified to glow in places where BPA, an endocrine-disrupting chemical, is present. The fish are literally illuminating where this pollutant acts in the body—and helping researchers discover what it does when it gets there.

B. These transgenic goats produce human antithrombin, an anticlotting protein. Antithrombin harvested from their milk is used as a drug during surgery or childbirth to prevent blood clotting in people with hereditary antithrombin deficiency. This genetic disorder carries a high risk of life-threatening clots. Figure 11.12  Examples of transgenic animals. (A) © Charles Tyler/University of Exeter; (B) © LFB S.A.

Biotech Barnyards Genetically modified mice are used extensively in research, for example as models of human metabolism, disease, and anatomy (the chapter opening photo shows an example). Consider how researchers inactivated the genes involved in the control of glucose metabolism, one by one, in mice. Studying the effects of these knockouts resulted in much of our current understanding of how diabetes works in humans. We have discovered the function of many other human genes (including the APOA5 gene discussed in Section 11.3) by knocking out their counterparts in mice. Genetically engineered animals other than mice are also useful in research (Figure 11.12), and some make molecules that have medical and industrial applications. Transgenic goats produce proteins used to treat blood-clotting disorders, cystic fibrosis, heart attacks, and even nerve gas exposure. Goats transgenic for a spider silk gene produce the silk protein in their milk; researchers can spin this protein into nanofibers that have applications in medicine and electronics. Transgenic rabbits make human interleukin-2, a protein that can be used as a cancer drug because it triggers immune cells to divide. Livestock are engineered to add or improve desirable traits such as hardiness, disease resistance, accelerated growth, and nutritional value. Genetic engineering has given us pigs with heart-healthy fat and environmentally friendly low-phosphate feces, extra-meaty trout, chickens that do not transmit bird flu, and cows that do not get mad cow disease, for example. Milk from goats transgenic for lysozyme, an antibacterial protein in human milk, may protect infants and children in developing countries from acute diarrheal disease; dairy cattle engineered to carry additional human proteins produce milk that is even more similar to human breast milk. In 2015, the FDA approved the first GMO animal for use as human food: a transgenic Atlantic salmon called AquAdvantage Salmon. These fish have been engineered to carry a promoter from ocean pout (a type of fish) governing a growth hormone from a Chinook salmon, and they grow to full size about twice as fast as their unmodified counterparts.

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Biotechnology  Chapter 11  213 

Digging Into Data Enhanced Spatial Learning Ability in Mice Engineered to Carry an Autism Mutation

1. In the first test, how long did it take unmodified mice to learn to find the hidden platform within 10 seconds? 2. Did the modified or the unmodified mice learn the location of the platform faster in the first test? 3. Which mice learned faster the second time around? 4. Which mice had the greatest improvement in performance? 5. What implication, if any, does this experiment have for our understanding of autism in humans?

submerged platform wading pool

before learning

after learning

A. Water maze. How quickly swimming mice learn the location of a submerged (invisible) platform is a measure of their spatial learning ability.

Days of training required to reach platform in 10 sec

Autism is a neurobiological disorder with symptoms that include impaired social interactions and repetitive, stereotyped patterns of behavior. Around 10 percent of affected people also have an extraordinary skill or talent such as greatly enhanced memory. Mutations in the gene for neuroligin 3, an adhesion protein that connects brain cells, have been associated with autism. In 2007, Katsuhiko Tabuchi and his colleagues introduced one of these mutations into the neuroligin 3 gene of mice. The researchers discovered that the genetically modified mice had impaired social behavior and superior spatial learning ability. Spatial learning in mice is tested with a water maze, which consists of a pool of water with a small platform in it (Figure 11.13A). The platform is submerged just under the surface of the water, so it is invisible to swimming mice. Mice do not particularly enjoy swimming, so they try to locate the hidden platform as quickly as they can. When tested in the same maze again, they remember the platform’s location by checking visual cues around the edge of the pool. How quickly they remember is a measure of their spatial learning ability (Figure 11.13B).

6

wild-type R451C

5 4 3 2 1 0

First test

Second test

B. Mice genetically modified to carry a mutation in neuroligin (R451C ) were tested in a water maze. Graph compares their performance in the maze with that of unmodified (wild-type) mice. Figure 11.13  Spatial learning ability in mice genetically modified to have a mutation associated with autism.

Ethical Concerns  Manipulating genes in animals raises a host of ethical dilemmas.

Consider animals genetically engineered to carry mutations associated with human disorders such as multiple sclerosis, cystic fibrosis, diabetes, cancer, or Huntington’s disease. Researchers produce these animals to study the disorders (and potential treatments) without experimenting on humans. However, the research is controversial because the modified animals often suffer the same terrible symptoms of the condition as humans do.

Take-Home Message 11.4 ●●

●●

●●

Genetic engineering is the directed alteration of a genome, and it results in a genetically modified organism (GMO). A transgenic organism carries a gene from a different species. These organisms are used in research, medicine, and industry. Most GMO crops have been engineered for resistance to pests. Widespread use of these crops is having unintended environmental effects.

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214  Unit 2 GENETICS

11.5  Editing Genomes Learning ObjectiveS ●●

Describe two ways of editing genomes.

●●

Explain some applications of CRISPR gene editing.

Gene Therapy Drugs and other treatments can minimize the symptoms of some genetic disorders, but gene therapy is the only cure. Gene therapy is the transfer of a gene into an individual’s body cells, with the intent to correct a genetic disorder or treat a disease. Gene therapy is a compelling reason to embrace the idea of genetically modifying people. It is being tested as a treatment for AIDS, muscular dystrophy, heart attack, sickle-cell anemia, cystic fibrosis, hemophilia A, Parkinson’s disease, Alzheimer’s disease, inherited diseases of the eye, the ear, and the immune system, and several types of cancer. For example, a viral vector has been used to insert a gene into immune cells extracted from patients with leukemia, a potentially fatal cancer of bone marrow cells). When the modified cells are reintroduced into the patients’ bodies, the inserted gene directs the destruction of cancer cells (Figure 11.14). The therapy seems to work astonishingly well: In one patient, all traces of the leukemia vanished in eight days.

Figure 11.14  To save a child. In 2012, Emily was six years old and just days from death when she underwent an experimental gene therapy for acute lymphocytic leukemia. She remains cancer-free to this day. Courtesy of the Emily Whitehead Foundation

Risks  Despite the successes, manipulating a gene within the context of a living individual can be unpredictable. Consider SCID-X1, a genetic disorder that stems from a mutation in the IL2RG gene. The gene encodes a receptor for an immunesignaling molecule. Without treatment, people affected by this disorder can survive only in germ-free isolation tents because they cannot fight infections (a diminished life in a sterile isolation tent was the source of the term “bubble boy”). In the late 1990s, researchers used a genetically engineered virus to insert unmutated copies of IL2RG into cells taken from the bone marrow of 20 boys with SCID-X1. Each child’s modified cells were infused back into his bone marrow. Within months of their treatment, 18 of the boys left their isolation tents. Gene therapy had repaired their immune systems. However, 5 of the boys later developed leukemia and died. Developers of the gene therapy could not have known that the very gene targeted for repair, especially when combined with the virus that delivered it, could cause cancer. The recombinant viral vector preferentially inserted the gene into chromosomes at a site near a proto-oncogene (Section 9.4). The insertion triggered inappropriate transcription of the gene, and that is how the leukemia began.

CRISPR Gene Editing A new method of editing chromosomal DNA has profoundly changed conversations about gene therapy. The technique is based on CRISPR-Cas9, a system of molecules that prokaryotes use to defend themselves against viral infection. In this system, a special restriction enzyme is guided to DNA by an RNA molecule. The enzyme cuts the DNA wherever its “guide” RNA hybridizes (Figure 11.15A). With gene editing, a researcher designs the guide RNA to target a specific part of a cell’s genome, and delivers it into a living cell along with the enzyme. The resulting chromosomal cut can be repaired by the cell’s DNA polymerases. A separate DNA molecule is required as a template for the repair (Section 7.6), and researchers can customize this molecule to introduce specific changes at the location of the cut (Figure 11.15B). Any part of the genome in a living cell can be edited in any way, and the change will be passed to the cell’s descendants.

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Biotechnology  Chapter 11  215 

CRISPR is more accurate, efficient, and powerful than any other method of altering genomes. Accordingly, it is now in widespread use. The technique is not flawless (for example, it sometimes cuts DNA in unexpected places), but the problems are being worked out quickly. Products of some CRISPR-modified crops will soon be sold in U.S. markets. These crops are not subject to the same regulations as other GMOs because they contain no DNA from other species (genes or remnants of cloning vectors), so in theory they could have been produced by traditional breeding methods. For example, a mutation that disabled an enzyme involved in browning resulted in an extended shelf life for white button mushrooms. This mutation could have occurred naturally, but researchers used CRISPR to make it deliberately. Hundreds of other gene-edited food crops are being brought to market, including low-gluten wheat, allergy-free peanuts, and disease-resistant bananas. As of this writing, CRISPR-edited animals are not used for food, but a huge number of them have been produced as models for studying human development, diseases, and genetic disorders. The resulting explosion of research holds phenomenal promise in thousands of applications. For example, CRISPR has been used to edit HIV out of infected animals; in patients, this approach may prevent the relapse of AIDS symptoms after remission. CRISPR has also been used to repair mutations causing muscular dystrophy, achondroplasia, and cancer in cells taken from human patients—the first step toward permanently curing these genetic disorders in people. Several clinical trials are now under way testing the use of CRISPR or CRISPRmodified cells, for example as treatments for sickle-cell anemia and β-thalassemia (Section 8.6); several types of cancer; and infection by HIV, HPV, and norovirus. Germline Alterations  CRISPR is currently being used to alter human gametes and embryos for research purposes. Altered embryos could be implanted to complete their development just like other test-tube babies, in which case the alterations would become part of the human germline and pass to subsequent generations. The practice is illegal in many countries, but at this writing one alleged violation has already occurred. A researcher in China announced that he used CRISPR to alter human embryos, with the goal of producing HIV-resistant children. HIV enters cells by binding to a particular receptor, and CRISPR was used to change the structure of the receptor so the virus could no longer bind to it. The researcher claimed that two baby girls, children of a man who is HIV positive, were born in 2018 with this edit to their genome. The effect of the edit on the children is currently unknown, but based on experiments in animals, it may have an impact on their cognitive function and lifespan. This experiment has been generally condemned as a monstrous ethical violation, but it illustrates the point that we as a society are on a slippery slope: Our ability to tinker with genetics may have surpassed our ability to understand the impact of the tinkering. In this brave new world, the questions before you are these: What are the risks of taking such bold risks? What do we stand to lose if serious risks are not taken? And, do we have the right to impose potential consequences on people who would choose not to take those risks?

“guide” RNA chromosomal DNA

Cas-9 enzyme

T

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A. The Cas9 enzyme cuts both strands of chromosomal DNA wherever a “guide” RNA hybridizes. The guide RNA can be customized to target any sequence in the DNA.

chromosomal DNA T

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template DNA used for repair

B. Repairing a double-strand break in a chromosome requires a DNA template, and a eukaryotic cell normally uses the homologous chromosome for this purpose. With CRISPR gene editing, researchers design a fragment of DNA that serves as the template for repair. The sequence of the fragment can be customized to include, for example, an insertion or deletion. This template includes an insertion of a stop codon (TAA).

altered chromosomal DNA T

A

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C. After the chromosome is repaired, its sequence includes the change introduced by the researcher. When the cell divides, the altered chromosome is replicated and passed to descendant cells. Figure 11.15  An example of CRISPR gene editing.

Take-Home Message 11.5 ●● ●●

Genetic engineering can be used to correct genetic defects or treat diseases in humans. CRISPR gene editing is used to alter DNA in living cells.

gene therapy  Treating a genetic defect or disorder by transferring a gene into the affected individual.

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216  Unit 2 GENETICS

Summary Section 11.1  Alleles of shared genes make individuals unique members of a species. Alleles often differ in single nucleotide bases—single-nucleotide polymorphisms (SNPs). Personal genetic testing, which reveals SNPs and mutations in an individual’s DNA, is widely available, and individualized medical care based on these variations is becoming more common. Personal treatment plans can be based on DNA variations that have been linked to drug responsiveness and health risks, but it is not yet possible to accurately predict most future health problems based on genotype. Section 11.2  In DNA cloning, researchers use restriction enzymes to cut a sample of DNA into fragments, and then insert the fragments into plasmids or other cloning vectors. The resulting molecules of recombinant DNA are delivered into host cells such as bacteria or yeast. Division of host cells produces huge populations of genetically identical descendant cells (clones), each with at least one copy of the recombinant vector. The DNA fragment can be harvested from the host cells in quantity. A DNA library is a collection of cells that host different fragments of DNA, often representing an organism’s entire genome. Researchers can use probes to identify cells in a library that carry a specific fragment of DNA. PCR, the polymerase chain reaction, uses primers and a heatresistant Taq DNA polymerase to rapidly amplify (mass-produce copies of) a targeted section of DNA. Section 11.3  Worldwide efforts to determine the sequence of the human genome led to advances in DNA sequencing technologies. A common sequencing method uses DNA polymerase to partially replicate a DNA template, and electrophoresis to separate the resulting DNA fragments by length. Genomics gives us insights into genome function. For example, similarities between the human genome and genomes of other organisms have revealed the function of many human genes. DNA profiling identifies individuals by the unique parts of their DNA. Aside from identical twins, every individual has a unique array of short tandem repeats (microsatellites) and SNPs. Within the context of a criminal investigation, a DNA profile is called a DNA fingerprint. Section 11.4  Recombinant DNA technology is the basis of genetic engineering, the directed modification of genotype with the intent to modify phenotype. An organism whose genome has been modified by genetic engineering is called a genetically modified organism (GMO). A genetically modified organism that carries a gene from a different species is transgenic.

Bacteria and yeast, the most common genetically modified organisms, produce proteins that have medical and industrial value. Transgenic crops are in widespread, worldwide use. Most have been modified for resistance to pests and pathogens; some have enhanced hardiness or nutritional value. Most genetically modified animals are mice used as models of human systems in research. Some produce medically relevant proteins. Section 11.5  With gene therapy, a gene is transferred into body cells to correct a genetic defect or treat a disease. CRISPR is an efficient, powerful method of editing the genome of a living organism.

Self-Quiz Answers in Appendix I 1.

cut(s) DNA molecules at specific sites. a. DNA polymerase c. Restriction enzymes b. DNA probes d. DNA ligase

2. A is a molecule that can be used to carry a fragment of DNA into a host organism. a. cloning vector c. GMO b. chromosome d. PCR 3. For each species, all chromosomes is the a. mutations; DNA profile b. DNA; genome

in the complete set of . c. SNPs; genome d. genomes; genotype

4. A set of cells that host various DNA fragments collectively representing an organism’s entire set of genetic information is called a . a. genome c. clone d. polymorphism b. DNA library 5. PCR is often used a. in DNA profiling b. to modify a human genome c. as a cloning vector

.

6. Fragments of DNA can be separated by electrophoresis according to . a. sequence c. species b. length d. SNPs

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Biotechnology  Chapter 11  217 

7. Taq polymerase is used for PCR because it . a. tolerates the high temperature needed to separate DNA strands b. is an enzyme from a bacterium c. does not require primers d. is genetically modified 8.

is a technique to determine the order of nucleotides in a fragment of DNA. a. PCR c. Electrophoresis b. DNA sequencing d. Nucleic acid hybridization

9. An individual’s unique set of DNA profiling. a. DNA sequences b. short tandem repeats

can be used in c. SNPs d. all of the above

10. Put the following tasks in the order they would occur during a cloning experiment. a. Using DNA ligase to seal DNA fragments into vectors b. Using a probe to identify a clone in the library c. Sequencing the DNA of the clone d. Making a DNA library of clones e. Using restriction enzymes to cut chromosomal DNA into fragments 11. A transgenic organism . a. carries a gene from another species b. has been genetically modified c. both a and b 12. True or false? Some transgenic organisms can pass their foreign genes to offspring. 13.

can correct a genetic defect. a. Sequencing an individual’s DNA c. Gene therapy b. Cloning a gene d. Electrophoresis

14. True or false? Some humans are genetically modified. 15. Match the terms with the most suitable description. DNA profile a. carries a foreign gene genomics b. alleles commonly have them CRISPR c. a person’s unique collection SNP of short tandem repeats transgenic d. gene editing GMO e. genetically modified f. study of genomes

CRITICAL THinking 1. Some health care providers are offering personal genetic testing as part of routine preventive care for healthy clients. Individuals are not informed if they have SNPs associated with untreatable conditions (such as APOE alleles associated with Alzheimer’s). Clients who have SNPs associated with treatable conditions are given preventive treatment and guidance for making lifestyle changes that can prevent or delay the onset of symptoms, or reduce their severity. What are some potential pros and cons of this approach? 2. In 1918, an influenza pandemic that originated with avian flu killed 50 million people. Researchers isolated samples of that virus from bodies of infected people preserved in Alaskan permafrost since 1918. From the samples, they sequenced the viral genome, then reconstructed the virus. The reconstructed virus is 39,000 times more infectious than modern influenza strains, and 100 percent lethal in mice. Understanding how this virus works can help us defend ourselves against other strains that may arise. For example, discovering what makes it so infectious and deadly would help us design more effective vaccines. Critics of the research are concerned: If the virus escapes the containment facilities (even though it has not done so yet), it might cause another pandemic. Or, the published DNA sequence and methods to make the virus could be used for criminal purposes. Do you think this research makes us more or less safe? 3. The results of a paternity test using short tandem repeats are listed in the following table. Who’s the daddy? How sure are you? Microsatellite

DNA Samples Tested Mother

Baby

Alleged Father #1

Alleged Father #2

15, 17

17, 23

23, 27

17, 15

9, 9

9, 9

9, 12

9, 12

THO1

29, 29

29, 27

27, 28

29, 28

TPOX

14, 18

18, 20

15, 20

17, 22

VWA

14, 14

14, 14

14, 14

14, 16

D3S1358

11, 14

14, 16

12, 16

14, 20

D5S818

11, 13

10, 13

8, 10

18, 18

D7S820

7, 13

13, 13

13, 19

13, 13

D8S1179

13, 13

13, 15

12, 15

10, 12

D13S317

12, 12

10, 12

8, 10

12, 17

D16S539

CSF1PO FGA

12, 14

14, 12

14, 14

18, 25

D18S51

5, 6

6, 22

22, 6

5, 22

D21S11

15, 17

17, 22

15, 22

22, 22

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12 Evidence of Evolution

12.1

Reflections of a Distant Past  219

12.2

Old Beliefs, New Discoveries  220

12.3

Natural Selection  223

12.4

Fossil Evidence  225

12.5

Changes in the History of Earth  229

12.6

Evidence in Form and Function  234

12.7

Molecular Evidence  236

Fossil skeleton of Dorudon atrox, an extinct whale-like mammal, in Wadi Al-Hitan, Egypt—a desert region that was once at the bottom of a prehistoric ocean. Fossils are stone-hard evidence of ancient life, and biologists study them to make inferences about evolution.

Concept Connections Zhao Dingzhe/Xinhua/Alamy Stock Photo

You may wish to review critical thinking (Section 1.5) before reading this chapter, which discusses a clash between belief and science (1.7). What you know about mutations (8.6), genes (9.2), and alleles (9.5) will help you understand natural selection. The next chapter details evolutionary processes, including how natural selection works (13.1–13.4), and how tectonic plate movements influence evolution (13.6). Chapter 26 returns to animal development. This chapter also revisits species discoveries (1.4), the scientific process (1.6), radioisotopes (2.2), the genetic code (8.4), master regulators (8.7), and genomics (11.3).

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Evidence of Evolution  Chapter 12  219  

Application

U.S. Geological Survey.

12.1  Reflections of a Distant Past How do you think about time? Perhaps you can conceive of a few hundred years of human events, maybe a few thousand, but how about a few million? Envisioning the very distant past requires an intellectual leap from the familiar to the unknown. One way to make that leap involves, surprisingly, asteroids. Asteroids are space rocks—chunks of rock or metal hurtling through space— that range in size from a few meters to hundreds of kilometers in diameter. Millions of them orbit the sun between Mars and Jupiter—cold, stony leftovers from the formation of our solar system. Space rocks enter Earth’s atmosphere by the ton, but most of them burn up before they hit the ground. Those that do reach Earth’s surface are called meteorites, and big ones can cause significant damage at the site of impact. Consider Meteor Crater, a mile-wide hole in the desert sandstone near Flagstaff, Arizona (Figure 12.1A). This crater formed 50,000 years ago, when an asteroid 45 meters in diameter slammed into Earth. The impact was 150 times more powerful than the bomb that leveled Hiroshima—so much energy that most of the meteorite and part of the ground vaporized instantly. There were no humans in North America to witness anything 50,000 years ago, so how could anyone know what happened at Meteor Crater? We often reconstruct history by studying physical evidence of events that took place in the past. Geologists were able to infer the most probable cause of the crater by analyzing tons of rocky clues at the site. For example, in addition to meteorite fragments, the crater contains shocked quartz (left) and glass nodules called tektites—structures that form when quartz or sand (respectively) undergoes a sudden, violent application of extreme pressure. The only processes on Earth Shocked quartz known to produce shocked quartz and tektites are nuclear explosions and asteroid impacts. Similar evidence points to impacts of even larger asteroids. Consider how fossil hunters have long known about a mass extinction that occurred 66 million years ago. The event is marked by an unusual, worldwide layer of rock called the ​K–Pg boundary (Figure 12.1B). The layer serves as a geological signature because the rock above and below it differs dramatically in fossil content. Rock layers below the boundary contain plenty of dinosaur fossils. Above the boundary, in layers of rock that were deposited more recently, there are no dinosaur fossils, anywhere. Researchers studying the composition of the K–Pg boundary layer discovered that it is rich in iridium, an element rare on Earth’s surface but common in asteroids. They began searching for evidence of an asteroid impact massive enough to cover Earth’s entire surface with extraterrestrial debris. Twenty years later, they found it: a gigantic impact crater buried under Chicxulub, Yucatán. The Chicxulub crater is 180 kilometers wide and 20 kilometers deep; to make it, an asteroid 15 kilometers in diameter must have hit Earth with a force a billion times more powerful than the Hiroshima bomb—enough to cause an ecological catastrophe of sufficient scale to wipe out the dinosaurs and most other life on Earth.

A. What made Meteor Crater? This photo was taken from an airplane; the buildings to the left of the crater give an idea of size. Geologists used rocky evidence at the site to infer that the impact of a 300,000-ton asteroid made the crater 50,000 years ago.

B. The K–Pg boundary. This unusual layer of rock (white, marked with a red pocket-knife for scale) formed worldwide, 66 million years ago. It marks an abrupt transition in the fossil record, and contains far too much iridium to have originated on Earth. The impact of an asteroid big enough to blanket the planet with its debris would have had catastrophic effects on life at the time. Figure 12.1  Evidence to inference. (A) © Brad Snowder; (B) © David A. Kring, NASA/Univ. Arizona Space Imagery Center.

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220  Unit 3  EVOLUTION AND DIVERSITY

You are about to make an intellectual leap through time, to places that were not even known a few centuries ago. We invite you to launch yourself from this premise: Natural phenomena that occurred in the past can be explained by the same physical, chemical, and biological processes operating today. The premise is the foundation for scientific research into the history of life, and it is supported by a vast amount of data from many disciplines. Researching the history of life involves a shift from experience to inference—from the known to what can only be surmised—and it gives us astonishing glimpses into the distant past.

Discussion Questions 1. What disciplines (other than geology or evolutionary biology) use evidence to make inferences about events no one witnessed? 2. Most scientists accept the hypothesis that the Chicxulub asteroid impact played a major role in the mass extinction 66 million years ago, but exactly how the impact could have caused the extinctions is still hotly debated. Can you think of a possible ecological effect of the impact that would have harmed life worldwide? What evidence would you look for to support your hypothesis? 3. Fossil evidence shows that the global extinction rate returned to normal levels about 32,000 years after the Chicxulub impact, but it took millions of years for ecosystems to recover their diversity. Why do you think the recovery period was so long?

12.2  Old Beliefs, New Discoveries Learning Objective ●●

Using appropriate examples, explain how three types of observations of the natural world challenged traditional European belief systems in the 1800s.

Figure 12.2  Similar-looking, related animals native to distant geographic realms.

The Great Chain of Being

These birds are unlike most others in several unusual features, including their large size; long, muscular legs; and an inability to fly. All are native to open grassland regions about the same distance from the equator.

About 2,300 years ago, the Greek philosopher Aristotle described nature as a continuum of organization, from lifeless matter through complex plants and animals. Aristotle’s work greatly influenced later European thinkers, who adopted his view of

(A) Rebecca Yale/Moment/Getty Images; (B) Novarc Images/Alamy Stock Photo; (C) Earl and Nazima Kowall/Encyclopedia/Corbis

A. Ostrich, native to Africa.

B. Rhea, native to South America.

C. Emu, native to Australia.

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Evidence of Evolution  Chapter 12  221  

Heritage Image Partnership Ltd./Alamy Stock Photo

nature and modified it in light of their own beliefs. By the fourteenth century, Europeans generally believed that a “great chain of being” extended from the lowest form of life (plants), up through animals, humans, and spiritual beings. Each link in the chain was a species, and each was said to have been forged at the same time, in one place, and in a perfect state. The chain was complete. Because everything that needed to exist already did, there was no room for change.

Aristotle

New Evidence In the 1800s, European naturalists embarked on globe-spanning survey expeditions and brought back tens of thousands of plants and animals from Asia, Africa, North and South America, and the Pacific Islands. Each newly discovered species was carefully cataloged. Biogeography  The European explorers began to see patterns in where species live and similarities in body plans, and they started to think about how natural forces might affect life. These explorers were pioneers in biogeography, the study of patterns in the geographic distribution of species and communities. Some biogeographical patterns raised questions that could not be answered within the framework of existing belief systems. For example, some plants and animals looked suspiciously similar to species living on the other side of impassable mountain ranges, or across vast expanses of open ocean. Consider the emu, rhea, and ostrich. These birds share a set of unusual features, but each is native to a different continent (Figure 12.2). Alfred Wallace, an explorer interested in the geographic distribution of animals, thought that the shared traits might mean the flightless birds descended from a common ancestor (and he was correct), but how could they have ended up on widely separated continents? Comparative Morphology  Naturalists were also having trouble classifying organisms that are very similar in some features, but different in others. For example, both plants shown in Figure 12.3 live in hot deserts where water is seasonally scarce. Both have rows of sharp spines that deter herbivores, and both store water in their thick, fleshy stems. However, their reproductive parts are very different, so these plants cannot be (and are not) as closely related as their outward appearance might suggest. Comparative morphology is the study of anatomical patterns: similarities and differences among the body plans of organisms. Today, comparative morphology is only one of several aspects of taxonomy (Section 1.4), but in the nineteenth century it was the only way to distinguish species. In some cases, comparative morphology revealed anatomical details (such as body parts with no apparent function) that added to the mounting confusion. If every species had been created in a perfect state, then why were there “useless” parts such as wings in birds that do not fly, eyes in moles that are blind, or remnants of a tail in humans (Figure 12.4)?

Figure 12.3  Similar-looking, unrelated species. Left, saguaro cactus (Carnegiea gigantea ), native to the Sonoran Desert of Arizona. Right, an African milk barrel plant (Euphorbia horrida ), native to the Great Karoo desert of South Africa. Left, Marka/Superstock; right, © Richard J. Hodgkiss, www.succulent-plant.com

coccyx (tailbones)

Figure 12.4  Human tailbones. Nineteenth-century naturalists were well aware of—but had trouble explaining—body structures such as human tailbones that had apparently lost most or all function. SPL/Science Source

New Ideas As discoveries in biogeography and comparative morphology accumulated, nineteenthcentury naturalists struggled to wrap prevailing beliefs around the increasing evidence that life on Earth had changed over time. Key insights about natural forces that could drive the change emerged from their arguments and efforts to make sense of the new information.

biogeography  Study of patterns in the geographic distribution of species and communities. comparative morphology  Scientific study of similarities and differences in body plans.

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222  Unit 3  EVOLUTION AND DIVERSITY Lamarckian Inheritance  In the early 1800s, Jean-Baptiste

Lamarck proposed the idea that a species gradually improved over generations because of an inherent drive toward perfection, up the chain of being. The drive directed an unknown “fluida” into body parts needing change. By Lamarck’s hypothesis, environmental pressures cause an internal requirement for change in an individual’s body, and the resulting change is inherited by offspring. Lamarck Lamarck’s understanding of how inheritance works was incomplete, but he was the first to propose a mechanism for evolution, or change in a line of descent. A line of descent is also called a lineage. Catastrophism  Georges Cuvier, an expert in the new field of comparative morphology, vehemently rejected Lamarck’s hypothesis. Like most others of his time, Cuvier was a proponent of catastrophism, the idea that Earth’s current landscape had been shaped by periodic, violent geologic events unlike any in recorded history. Cuvier had been studying newly unearthed fossil skeletons of gigantic dinosaurs and other animals that had no living repreCuvier sentatives. If these animals were perfect at the time of creation, then what had happened to them? Cuvier dismissed a popular idea that the missing animals were somehow hidden in large forests or unexplored regions of the world. Instead, he proposed a different idea that was startling for the time: Many species had been killed off during the violent geologic events. Cuvier thought that new species were created after each event, and that there was not enough time between catastrophes for these species to change. He argued that evidence for change did not exist: No one had yet discovered any fossils representing intermediate forms between the gigantic animals and living species. Uniformitarianism  The geologist Charles Lyell thought that

global catastrophes were not necessary to explain Earth’s current landscape. He was a proponent of uniformitarianism, the idea that gradual, everyday geologic processes such as erosion shaped Earth’s surface. Lyell had seen plenty of evidence to support uniformitarianism. For many years, geologists had been chipping away at different types of rock formations all over the world, Lyell and they knew that each formation’s composition and structure provided a physical record of its history. Lyell realized that ordinary geologic processes that sculpt rock formations in the present could have also sculpted rock formations in the past—if they took place over millions of years. This idea challenged the prevailing belief that Earth was thousands of years old, but Lyell’s thorough documentation of rocky evidence in support of geologic continuity led to its general acceptance by other naturalists.

Take-Home Message 12.2 ●●

●●

evolution  Change in a line of descent.

In the nineteenth century, increasingly extensive observations of nature did not fit into the framework of prevailing beliefs. Cumulative findings led naturalists to question traditional ways of interpreting the natural world. Many of the naturalists realized that Earth—and life—had changed over time. New thoughts emerged about forces that could drive such change.

lineage  Line of descent.

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Evidence of Evolution  Chapter 12  223  

Plymouth Azores Tenerife 0

(km)

5000

0

(mi)

3000

Cape Verde

Galapagos

Cocos (Keeling) Isl.

Bahia Callao Lima Valparaiso

Rio de Janeiro Montevideo

Mauritius Cape Town

Falkland Islands

Sydney King George's Sound

Hobart

Figure 12.5  Voyage of the HMS Beagle. The path of the ship’s 1831 survey expedition is shown from red to blue. Charles Darwin’s detailed observations of the geology, fossils, plants, and animals he encountered on this expedition helped shape his ideas about evolution.

12.3  Natural Selection Learning Objectives ●●

Explain Darwin’s hypothesis of evolution by natural selection.

●●

Discuss the relationship between evolutionary adaptations and fitness. A. A modern armadillo. This one is about 11 inches long.

Painting by George Richmond

Darwin and the HMS Beagle  Lamarck, Cuvier, and Lyell influenced the thinking of another naturalist, Charles Darwin. Darwin had earned a theology degree from Cambridge after an attempt to study medicine. All through school, however, he had spent most of his time with faculty members and other students who embraced natural history. In 1831, Darwin joined a five-year survey expedition on a ship named the Beagle (Figure 12.5). During the expedition, the Darwin young man found many unusual fossils, and he saw diverse species living in environments that ranged from the sandy shores of remote islands to plains high in the Andes. After returning to England, Darwin pondered his notes and fossils, and reflected on what he had seen during his travels. Along with other naturalists of the time, he had recognized evidence that life had changed over time, and was thinking about forces that could have caused such change. Descent with Modification  Among the thousands of specimens Darwin collected

on his voyage were fossil glyptodonts. These armored mammals are extinct, but they have many unusual traits in common with modern armadillos (Figure 12.6). Armadillos also live only in places where glyptodonts once lived. Could the odd

B. Fossil of a glyptodont, a huge mammal that existed from 2 million to 15,000 years ago. This one is about 11 feet long. Figure 12.6  Ancient relatives: armadillo and glyptodont. These animals are widely separated in time, but they share a restricted distribution and unusual traits, including a shell and helmet of keratin-covered bony plates—a material similar to crocodile and lizard skin. Their similarities are evidence of shared ancestry. (A) Joel Sartore/National Geographic Image Collection/Getty Images; (B) The Natural History Museum/Alamy Stock Photo

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224  Unit 3  EVOLUTION AND DIVERSITY

shared traits and restricted distribution mean that glyptodonts were ancient relatives of armadillos? If so, perhaps traits had changed in the line of descent that led to armadillos. But why would such changes have occurred? The Struggle for Limited Resources  Darwin read an essay by

Observations About Populations ✔ Natural populations have an inherent capacity to increase in size over time. ✔ As a population expands, resources that are used by its members (such as food and living space) eventually become limited. ✔ Members of a population compete for resources that are limited. Observations About Genetics ✔ Individuals of a species share certain traits. ✔ Members of a natural population vary in the details of shared traits. ✔ Shared traits have a heritable basis, in genes. Slightly different forms of those genes (alleles) give rise to variation in shared traits. Inferences ✔ A certain form of a shared trait may make its bearer better able to survive. ✔ Members of a population that are better able to survive tend to leave more offspring. ✔ Thus, an allele associated with an adaptive trait tends to become more common in a population over time.

De Agostini Picture Library/ Getty Images

Table 12.1  Natural Selection

economist Thomas Malthus, who had proposed that famine, disease, and war limit the size of human populations. When people reproduce beyond the capacity of their environment to sustain them, they run out of food and start competing for resources that become limited. Some survive this struggle for existence, Malthus and some do not. Darwin realized that Malthus’s ideas had wider application: Individuals of all populations, not just human ones, struggle for existence by competing for limited resources. Variation in Traits  Reflecting on his journey, Darwin started thinking about small

differences in traits that distinguish closely related species. He saw such variation among finch species he discovered on isolated islands of the Galápagos archipelago. These islands are separated from South America by 550 miles (900 kilometers) of open ocean, so most species living there had no opportunity to interbreed with mainland populations. The Galápagos island birds resembled finch species in South America, but had unique traits suited to their particular island environments.

Fitness  Darwin was familiar with variations in traits that selective breeding could produce in pigeons, dogs, and horses. He reasoned that natural environments could similarly “select” certain traits. Having a particular form of a shared trait might give an individual an advantage over competing members of its species. In any population, some individuals have forms of shared traits that make them better suited to their environment than others. In other words, individuals of a natural population vary in fitness. Today, we define fitness as the degree of adaptation to a specific environment, and measure it by relative genetic contribution to future generations. An evolutionary adaptation, or adaptive trait, is a form of a heritable trait that enhances fitness. Natural Selection  Darwin realized that individuals best adapted to a particular

adaptation  Adaptive trait. adaptive trait  A form of a heritable trait that enhances an individual’s fitness. An evolutionary adaptation. fitness  Degree of adaptation to an environment, as measured by an individual’s relative genetic contribution to future generations. fossil  Physical evidence of an organism that lived in the ancient past. natural selection  Differential survival and reproduction of individuals of a population based on differences in shared, heritable traits.

environment would tend to leave more offspring than their less fit rivals, a process he named natural selection. Natural selection causes a population to change over time. Table 12.1 summarizes this reasoning: If an individual has an adaptive trait that makes it better suited to an environment, then it is better able to survive. If an individual is better able to survive, then it has a better chance of living long enough to produce offspring. If individuals with an adaptive trait produce more offspring than other individuals, then the frequency of the adaptive trait in the population will increase over successive generations (the population will evolve). If Earth was millions of years old (as Lyell had proposed), then there had been ample time for natural selection to have driven evolution.

Great Minds Think Alike  Darwin came up with his hypothesis of evolution by natural selection in the late 1830s, but did not publish it right away. He spent a decade collecting evidence, focusing on other projects, and battling ill health before starting to compile a book on the subject. Meanwhile, Alfred Wallace, who was studying wildlife in the Amazon Basin and the Malay Archipelago, wrote to Darwin about patterns in the geographic distribution of species. When he was ready to publish his own ideas about evolution,

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Evidence of Evolution  Chapter 12  225  

he sent them to Darwin for advice. To Darwin’s shock, Wallace had come up with the same hypothesis: that evolution can be driven by natural selection. In 1858, the hypothesis of evolution by natural selection was presented at a scientific meeting. Darwin and Wallace were credited as authors, but neither attended the meeting. The next year, Darwin published On the Origin of Species, which laid out detailed Wallace evidence in support of the hypothesis. By that time, many people had accepted the idea of descent with modification (evolution). However, there was a fierce debate over the idea that natural selection drives the process. Decades would pass before experimental evidence from the field of genetics led to its widespread acceptance by the scientific community.

Take-Home Message 12.3 ●●

●●

●●

Darwin’s observations of species in different parts of the world led him to propose natural selection as a driving force of evolution (change in a line of descent). With natural selection, individuals of a population survive and reproduce with differing success depending on the details of their shared, heritable traits. An evolutionary adaptation (an adaptive trait) enhances fitness, so it tends to become more common in a population over time.

12.4  Fossil Evidence Learning Objectives ●●

Explain why fossils are relatively rare.

●●

Give examples of information that fossils provide about past life.

●●

Explain how researchers determine the age of ancient materials.

Fossils Fossils are the remains or traces of organisms that lived long ago (Figure 12.7). Most fossils consist of mineralized bones, teeth, shells, seeds, spores, or other durable body parts. Trace fossils such as footprints and other impressions, nests, burrows, trails, eggshells, or feces are evidence of activities. Fossilization  The process of fossilization typically begins when an organism or its

traces become covered by sediments, mud, or ash. Groundwater then seeps into the remains, filling spaces around and inside of them. Minerals dissolved in the water gradually replace minerals in bones and other hard tissues, and they can crystallize inside cavities and impressions to form detailed imprints of internal and external structures. Sediments that slowly accumulate on top of the site exert increasing pressure, and, after a very long time, extreme pressure transforms the mineralized remains into rock.

A. Fossil skeleton of an ichthyosaur that lived about 200 million years ago. These marine reptiles were about the size of modern porpoises, breathed air like them, and probably swam as fast, but the two groups are not closely related.

B. Extinct wasp encased in amber (ancient tree sap). This 9-mm-long insect lived about 20 million years ago.

C. Fossilized leaf from a 260-million-year-old Glossopteris, a type of plant called a seed fern.

D. Theropod footprints. Theropods were carnivorous dinosaurs that arose 250 million years ago; Tyrannosaurus rex was one. Each footprint is about 18 inches (45 centimeters) long.

E. Coprolite (fossilized feces) excreted by a foxlike animal. Fossilized food remains and parasitic worms in coprolites offer clues about diet and health.

Sedimentary Rock  Most fossils are found in sedimentary rock. Sedimentary rocks

form as rivers wash silt, sand, volcanic ash, and other materials from land to sea. Mineral particles in the materials settle on seafloors in horizontal layers that often vary in thickness and composition. After millions of years, the layers of sediments

Figure 12.7  Examples of fossils. (A) Jonathan Blair; (B) © Dr. Michael Engel, University of Kansas; (C) © Martin Land/Science Source; (D) Pixtal/Superstock; (E) Courtesy of Stan Celestian/Glendale Community College Earth Science Image Archive

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226  Unit 3  EVOLUTION AND DIVERSITY

Digging Into Data Discovery of Iridium in the K–Pg Boundary In the late 1970s, geologist Walter Alvarez was investigating the composition of the K–Pg boundary layer in different parts of the world. He asked his father, Nobel Prize–winning physicist Luis Alvarez, to help him analyze the elemental composition of the layer. The Alvarezes and their colleagues tested the K–Pg boundary layer in Italy and Denmark, and discovered that it contains a much higher amount of iridium than the surrounding rock layers (Figure 12.9). Iridium belongs to a group of elements that are much more abundant in asteroids and other solar system materials than they are in Earth’s crust, so the Alvarez group concluded that the K–Pg boundary layer must have originated with extraterrestrial material. 1. What was the iridium content of the K–Pg boundary layer? 2. What was the difference in iridium content between the boundary layer and the sample taken 0.7 meters above the layer?

58 million years old

Figure 12.8  Sequence of fossil foraminifera. Foraminifera are single-celled protists; most of the 4,000 known species alive today are found at the bottom of the ocean. All secrete a durable shell of calcium carbonate. After the organism dies, the shell may become fossilized as sediments accumulate on top of it. Researchers found these representative shells of ancient foraminifera in cylindrical sections (core samples) of the ocean floor, each in a successive layer of stacked rock. Courtesy of Daniel C. Kelley, Anthony J. Arnold, and William C. Parker, Florida State University Department of Geological Science

64.5 million years old

half-life  Characteristic time it takes for half of a quantity of a radioisotope to decay.

Sample Depth

Average Abundance of Iridium (ppb)

+ 2.7 m + 1.2 m + 0.7 m boundary layer – 0.5 m – 5.4 m

< 0.3 < 0.3 0.36 41.6 0.25 0.30

Figure 12.9  Abundance of iridium in and near the K–Pg boundary. The table indicates iridium content of rock samples above, below, and at the K–Pg boundary in Stevns Klint, Denmark. Sample depths are given as meters above or below the boundary layer (ppb, parts per billion). The photo shows Luis and Walter Alvarez next to the K–Pg boundary layer in Stevns Klint. The iridium content of an average Earth rock is 0.4 ppb. The average meteorite contains about 550 ppb iridium. Lawrence Berkeley National Laboratory

become buried and compacted into layers of rock. Geologic processes can tilt sedimentary rock and lift it far above sea level, where erosion can expose the layers and reveal fossils in them. Biologists study sedimentary rock formations to understand the historical context of ancient life. For example, the deepest layers in a formation were the first to form, and those closest to the surface formed most recently. Thus, in general, the deeper the layer, the older the fossils it contains (Figure 12.8). The composition of each layer also reflects environmental conditions that prevailed as it formed.

The Fossil Record  We have fossils for more than 250,000 known species. Considering the current range of biodiversity, there must have been many millions more, but we will never know all of them. Why not? For us to know about a species that existed long ago, we have to find evidence of it—a fossil. Relatively few individuals of a species become fossilized in the first place. Typically, when an organism dies, its remains are obliterated by scavengers. Organic materials decompose in the presence of moisture and oxygen, so remains that escape scavenging can endure only if they dry out, freeze, or become encased in an air-excluding material such as sap, tar, or mud. Fossils that do form are often crushed or scattered by erosion and other geologic assaults. Of those that remain intact, many are inaccessible—buried deeply in rock or other places where they are difficult to find. Most ancient species had no hard parts to fossilize, so we do not find much evidence of them. For example, there are many fossils of bony fishes and mollusks with hard shells, but few fossils of the jellyfishes and soft worms that were probably much more common. Also think about relative numbers of organisms. Fungal spores and pollen grains are often released by the millions. By contrast, the earliest humans lived in small bands and few of their offspring survived. The odds of finding even one fossilized human bone are much smaller than the odds of finding a fossilized fungal

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Evidence of Evolution  Chapter 12  227  

spore. Finally, imagine two species, one that existed only briefly and the other for a hundred million years. Which one is more likely to be represented in the fossil record?

Finding a Missing Link   The discovery of intermediate forms of cetaceans (an order of animals that includes whales, dolphins, and porpoises) offers an example of how fossil finds can be used to reconstruct evolutionary history of current lineages. Skeletons of modern cetaceans have remnants of a pelvis and hind limbs, so evolutionary biologists had long thought that the ancestors of this group walked on land. The hypothesis was supported by the discovery of intact fossil skeletons of Dorudon atrox, a whalelike animal with hind limbs that lived about 37 million years ago. However, Dorudon’s hind limbs were too tiny to have supported its huge body out of water, so it must have been fully aquatic. No one had found other fossils with intermediate skeletal features that would have accompanied a transition from terrestrial to aquatic life, so the rest of the story remained speculative. Genome comparisons in the early 1990s suggested that modern cetaceans are more related to artiodactyls than to other groups. Artiodactyls are hooved mammals with an even number of toes (two or four) on each foot; modern members of the lineage include hippopotamuses, antelopes, and sheep. The discovery was controversial because the ancestors of artiodactyls resembled tiny deer with long tails (Figure 12.10). A seemingly unimaginable number of skeletal and physiological changes would have been required for these small, land-based animals to evolve into whales with gigantic bodies suited to deep ocean swimming. Then, in 2000, Philip Gingerich and his colleagues discovered intact fossil skeletons of two other ancient cetaceans in a 47-million-year-old rock formation in Pakistan. Both Artiocetus clavis and Rodhocetus balochistanensis had whalelike skulls and robust hind limbs. Their bodies were built to swim with their feet (not their tails as whales do), and their ankle bones had clearly distinctive features of artiodactyls. Neither was a direct ancestor of modern whales, but they were relatives. Both were offshoots of the artiodactyl-to-modern-whale lineage as it transitioned from land to water.

Radiometric Dating  How do we know the age of a fossil? The answer involves radioisotopes (Section 2.2). Radioactive decay is not influenced by temperature, pressure, chemical bonding state, or moisture. Thus, like the ticking of a perfect clock, a radioisotope decays at a constant rate into predictable products—daughter elements. The time it takes for half of the atoms in a sample of a radioisotope to decay is called a half-life (Figure 12.11, next page). Each radioisotope has a characteristic half-life. Dating a Fossil  Carbon isotopes can be used to determine the age of fossils that still contain organic material. Almost all of the carbon on Earth is in the form of 12 C, so almost all of the carbon dioxide molecules on Earth contain this carbon isotope. A tiny number of CO2 molecules contain 14C instead of 12C. Carbon 14 is a radioisotope, so it decays at a constant rate, but it also forms at a constant rate in the atmosphere. Thus, the ratio of 14C to 12C in atmospheric CO2 is essentially stable. Carbon dioxide is life’s main source of carbon, so the same ratio occurs in the body of a living organism. As long as an organism lives, it continues to acquire carbon, and both isotopes become incorporated into its tissues in the same proportions. However, after the organism dies, no more carbon is assimilated, and the ratio of 14C to 12C in its remains declines over time as the 14C decays. The half-life of 14C is

50 cm

A. Pakicetus attocki. Considered one of the earliest cetaceans, this small animal lived about 50 million years ago. It was semiaquatic, but its body was specialized for running. Pakicetus belonged to the artiodactyl lineage, and it had traits unique to cetaceans.

50 cm

B. Rodhocetus balochistanensis. This cetacean lived about 47 million years ago. It was capable of walking (or dragging itself) on land, but its body was built more for swimming. Distinctive ankle bones indicate a close evolutionary connection to artiodactyls. Artiodactyls have a unique “doublepulley” shape of the bone (right) that forms the lower part of the ankle joint.

ankle bones

Rodhocetus

antelope

50 cm

C. Dorudon atrox. This cetacean lived about 37 million years ago. Its hind limbs worked, but they were tiny and not connected to the backbone, so they would not have supported the weight of the animal’s huge body on land. Thus, Dorudon had to be fully aquatic.

2m

D. Modern cetaceans such as the sperm whale have remnants of a pelvis and leg, but they do not walk. Figure 12.10  Comparison of cetacean skeletons. The ancestor of whales was an artiodactyl that walked on land. Over millions of years, the lineage transitioned from life on land to life in water, and as it did, bones of the hind limb (highlighted in blue) became smaller. © Philip Gingerich/University of Michigan

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228  Unit 3  EVOLUTION AND DIVERSITY

Parent isotope remaining (%)

parent isotope daughter elements

100

newly formed rock or recent remains

A. Long ago, 14C and 12C were incorporated into the tissues of a nautilus. Both carbon isotopes were part of organic molecules in the animal’s food. 12C

is stable and 14C decays, but the proportion of the two isotopes in the nautilus’s tissues remained the same. Why? The nautilus continued to gain both types of carbon atoms in the same proportions from its food.

75 after one half-life

50

25

Half-lives:

B. The nautilus stopped eating when it died, so its body stopped gaining carbon. The 12C atoms in its tissues were stable, but the 14C atoms (represented as red dots) were decaying into nitrogen atoms. Thus, over time, the amount of 14C decreased relative to the amount of 12C.

after two half-lives

1

2

3

4

After 5,730 years, half of the 14C had decayed; after another 5,730 years, half of what was left had decayed, and so on.

Figure 12.11  Half-life. Figure It Out: How much of any radioisotope remains after two half-lives?

C. Fossil hunters discover the fossil and measure its content of 14C and 12C. They use the ratio of these isotopes to calculate how many half-lives have passed since the organism died.

Answer: 25 percent

For example, if its 14C to 12C ratio is one-eighth of the ratio in living organisms, then three half-lives (½)3 must have passed since it died. Three half-lives of 14C is 17,190 years.

Figure 12.12  Carbon dating. Carbon 14 (14C) is a radioisotope of carbon that decays into nitrogen. It forms in the atmosphere and combines with oxygen to become carbon dioxide (CO2), which enters food chains by way of photosynthesis. (A) PhotoDisc/Getty Images

known (5,730 years) so the ratio of 14C to 12C in the organism’s remains can be used to calculate how long ago it died (Figure 12.12). We have just described radiometric dating, a method that can reveal the age of a material by measuring its radioisotope content. Carbon isotope dating can be used to find the age of a biological material less than 60,000 years old, but essentially no 14C remains in older material. The age of older fossils can be estimated by dating volcanic rocks in lava flows above and below the fossil-containing layer of sedimentary rock. Dating a Rock  Determining the age of a rock also involves radiometric dating.

The original source of most rock on Earth is magma, a hot, molten material under Earth’s surface. Atoms swirl and mix in it. When magma cools, for example after reaching the surface as lava, it hardens and becomes rock. As this occurs, the atoms in it join and crystallize as different kinds of minerals, each with a characteristic structure and composition. Consider zircon, a mineral that consists mainly of zirconium silicate molecules (ZrSiO4 ). Some of the molecules in a newly formed zircon crystal have uranium

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Evidence of Evolution  Chapter 12  229  

atoms substituted for zirconium atoms, but never lead atoms. Uranium is a radioactive element with a half-life of 4.5 billion years. It decays into lead, a stable element. Over time, uranium atoms disappear from a zircon crystal, and lead atoms accumulate in it. The ratio of uranium atoms to lead atoms in a zircon crystal can be measured and used to calculate how long ago the crystal formed (its age). Using this technique, scientists determined that the oldest known terrestrial rock, a tiny zircon crystal from the Jack Hills in Western Australia, is 4.404 billion years old (Figure 12.13).

Take-Home Message 12.4 ●● ●●

●●

Fossils are physical evidence of organisms that lived in the remote past. The fossil record will never be complete. It is slanted toward hard-bodied species that lived in large populations and persisted for a long time. The predictability of radioisotope decay can be used to determine the age of fossils and ancient rocks.

Figure 12.13  The oldest Earth rock. Dr. Simon Wilde holds a 4.4 billion-year-old speck of zircon embedded in protective plastic. AP Images/Andy Manis

12.5  Changes in the History of Earth Learning Objectives ●●

Explain how tectonic plate movements could have influenced the history of life.

●●

Describe the geologic time scale in terms of life’s history.

Continents Drift Wind, water flow, and other natural processes continuously sculpt Earth’s surface, but they are only part of a much bigger picture of geologic change. Earth itself also changes. For example, all continents were once part of a bigger supercontinent called Pangaea that split into fragments and drifted apart about 200 million years ago. The idea that continents move around, originally called continental drift, was proposed in the early 1900s to explain why the Atlantic coasts of South America and Africa seem to “fit” like jigsaw puzzle pieces. The concept of continental drift also explained why the magnetic poles of gigantic rock formations point in different directions on different continents. As magma solidifies into rock, some iron-rich minerals in it become magnetic, and their magnetic poles align with Earth’s poles when they do. If the continents never moved, then all of these ancient rocky magnets should be aligned north to south, like compass needles. They are not. Magnetic poles of rocks in each formation are aligned with one another, but the alignment is not always north to south. Either Earth’s magnetic poles veer dramatically from their north–south axis, or the continents have wandered.

Plate Tectonics

Pangaea  Supercontinent that began to form about 300 million years ago, and broke up 100 million years later.

Despite the evidence in support of continental drift, the concept was first greeted with intense skepticism because there was no known mechanism for continents to move. Then, in the late 1950s, deep-sea explorers found huge ridges and trenches stretching thousands of kilometers across the seafloor. The discovery led to a mechanism for continental drift, which became a theory called plate tectonics. By the plate tectonics theory, Earth’s outer layer of rock is cracked into huge plates, like a gigantic cracked eggshell. Magma welling up at an undersea

radiometric dating  Method of estimating the age of a rock or fossil by measuring the content and proportions of a radioisotope and its daughter element(s).

plate tectonics theory  Theory that Earth’s outermost layer of rock is cracked into plates, the slow movement of which conveys continents to new locations over geologic time.

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230  Unit 3  EVOLUTION AND DIVERSITY

2 trench

1 ridge

3 hot spot

4 archipelago

continental crust magma

oceanic crust

2 trench

continental crust

magma

Figure 12.14  Plate tectonics. Huge pieces of Earth’s outer layer of rock (crust) slowly drift apart and collide. As these tectonic plates move, they convey continents around the globe.

1 At oceanic ridges, magma (red) welling up from Earth’s interior drives the movement of tectonic plates. New crust spreads outward as it forms on the surface, forcing adjacent tectonic plates away from the ridge and into trenches elsewhere. 2 At trenches, the advancing edge of one plate plows under an adjacent plate and buckles it. 3 Magma ruptures a tectonic plate at “hot spots.” 4 An archipelago forms as a tectonic plate moves over a

hot spot. The Hawaiian Islands have been forming from magma that continues to erupt from a hot spot under the Pacific Plate.

ridge (Figure 12.14 1)  or continental rift at one edge of a plate pushes old rock at the opposite edge into a trench 2. The movement is like that of a giant conveyor belt that slowly transports continents on top of it to new locations. The plates move no more than 10 centimeters (4 inches) per year, but it is enough to carry a continent all the way around the world after about 200 million years. Geologic Evidence  Evidence of tectonic plate movement is all around us, in geologic

features. Consider volcanic hot spots, which are places where plumes of magma well up from deep inside Earth and rupture its crust 3. Volcanic island chains (archipelagos) form as a plate moves across an undersea hot spot 4. As another example, faults are cracks in Earth’s crust that often occur where plates meet (Figure 12.15).

Fossil Evidence  The fossil record also provides evidence in support of plate tectonics. Consider an unusual geological formation that occurs in a belt across Africa. The formation consists of a complex sequence of rock layers that is very unlikely to have formed more than once, but identical sequences also occur in huge belts spanning India, South America, Madagascar, Australia, and Antarctica. Across all of these continents, the layers are the same ages, and they hold fossils found

Figure 12.15  The San Andreas Fault. Faults are ruptures in Earth’s crust that mark the boundary between tectonic plates. This one extends 800 miles through California. Kevin Schafer/Corbis Documentary/Getty Images

geologic time scale  Chronology of Earth’s history. Gondwana  Supercontinent that existed before Pangaea, more than 500 million years ago.

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Evidence of Evolution  Chapter 12  231  

nowhere else—remains of the seed fern Glossopteris (pictured in Figure 12.7C), which lived 299 to 252 million years ago, and an early reptile called Lystrosaurus that existed 270 to 225 million years ago. The layers must have been deposited on a single continent that later broke up.

0 mya

Supercontinents  At least five supercontinents formed and split up again since

Earth’s outer layer of rock solidified 4.55 billion years ago. One of them, a supercontinent called Gondwana, existed about 540 million years ago. Over the next 260 million years, Gondwana drifted across the south pole, then north until it merged with another supercontinent 300 million years ago to form Pangaea (Figure 12.16). Most of the landmasses currently in the southern hemisphere as well as India and Arabia were once part of Gondwana. Some modern species, including the birds pictured in Figure 12.2, live only in these places. Tectonics and Life’s History  Geologic changes brought on by plate tectonics had a

profound impact on life. For example, when two continents collided into one, they brought together populations of organisms that had been living apart on the separate landmasses, and physically separated ocean-dwelling populations. Continental breakups separated land-based populations, and allowed contact between aquatic populations that had previously been separated. Events like these have been a major driving force of evolution, as you will see in the next chapter.

The Geologic Time Scale Georges Cuvier, the proponent of catastrophism, could not have imagined how plate tectonics changed Earth’s landscape over millions of years. Charles Lyell, the proponent of uniformitarianism, never knew about asteroid impacts that permanently altered the course of life in a geologic instant. Today, we understand that Earth’s history has been shaped both by gradual processes and by catastrophic events. The chronological history of Earth can be represented as a geologic time scale that correlates layers of rock with great intervals of time (Figure 12.17, on the next page). The composition of each layer holds information about environmental conditions that prevailed during the time it was deposited; fossils in it are a record of life during the same period. The layers differ in composition and fossil content, and these differences imply transitions in Earth’s history. Consider two major formations of sedimentary rock that stretch across the western United States. Hermit Shale consists mainly of compacted mud and silt with abundant fossils of land plants and insects, so this formation was probably deposited by a river system that stretched across a broad, wet coastal plain. Coconino Sandstone, which was deposited on top of Hermit Shale, consists mainly of compacted, weathered sand. Ripple marks and reptile tracks are the only fossils in it. These and other characteristics indicate that it accumulated as a vast sand desert similar to the modern Sahara. Thus, a major climactic shift must have occurred between the deposition of Hermit Shale and Coconino Sandstone.

120 mya

240 mya

Pangea

300 mya

400 mya

Gondwana

450 mya

660 mya

Take-Home Message 12.5 ●●

●●

Over geologic time, movements of Earth’s crust have caused dramatic changes in continents and oceans. The changes profoundly influenced the course of life’s evolution. The geologic time scale is a chronology of Earth’s history that correlates layers of rock with great intervals of time.

Figure 12.16  A series of reconstructions of drifting continents. mya: million years ago.

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232  Unit 3  EVOLUTION AND DIVERSITY

CLOSER LOOK Figure 12.17  Slices of time: the geologic time scale correlated with sedimentary rock in the Grand Canyon. Eon

Era

Period

Phanerozoic

Cenozoic

Quaternary Neogene Paleogene

Mesozoic

Cretaceous

Holocene Pleistocene Pliocene Miocene Oligocene Eocene Paleocene

mya*

Major Geologic and Biological Events

0.01 0.0 .01 1 2.6 5.3 5 3 23.0 33.9 33 9 56.0 56 56. 60 66.0

Modern humans evolve. Major extinction event is now under way.

Upper

100.5 Lower

145.0 Jurassic

201.3

252

299

359

Major extinction event

High atmospheric oxygen level fosters giant arthropods. Spore-releasing plants dominate. Age of great lycophyte trees; vast coal forests form. Ears evolve in amphibians; penises evolve in early reptiles (vaginas evolve later, in mammals only). Major extinction event Land tetrapods appear. Explosion of plant diversity leads to tree forms, forests, and many new plant groups including lycophytes, ferns with complex leaves, seed plants.

419 443

Ordovician

Cambrian

Major extinction event

Supercontinent Pangea and world ocean form. Adaptive radiation of conifers. Cycads and ginkgos appear. Relatively dry climate leads to drought-adapted gymnosperms and insects such as beetles and flies.

Devonian

Silurian

Climate very warm. Dinosaurs continue to dominate. Important modern insect groups appear (bees, butterflies, termites, ants, and herbivorous insects including aphids and grasshoppers). Flowering plants originate and become dominant land plants.

Recovery from the major extinction at end of Permian. Many new groups appear, including turtles, dinosaurs, pterosaurs, and mammals.

Permian

Carboniferous

Major extinction event Flowering plants diversify; sharks evolve. All dinosaurs and many marine organisms disappear at the end of this epoch.

Age of dinosaurs. Lush vegetation; abundant gymnosperms and ferns. Birds appear. Pangea breaks up.

Triassic

Paleozoic

Tropics, subtropics extend poleward. Climate cools; dry woodlands and grasslands emerge. Adaptive radiations of mammals, insects, birds.

Radiations of marine invertebrates. First appearances of land fungi, vascular plants, bony fishes, and perhaps terrestrial animals (millipedes, spiders). Major extinction event Major period for first appearances. The first land plants, fishes, and reef-forming corals appear. Gondwana moves toward the South Pole and becomes frigid.

485

Earth thaws. Explosion of animal diversity. Most major groups of animals appear (in the oceans). Trilobites and shelled organisms evolve.

541 Precambrian

Proterozoic

Oxygen accumulates in atmosphere. Origin of aerobic metabolism. Origin of eukaryotic cells, then protists, fungi, plants, animals. Evidence that Earth mostly freezes over in a series of global ice ages between 750 and 600 mya.

2,500 Origin of bacteria and archaea.

Archean

4,000 Hadean

Origin of Earth’s crust, first atmosphere, first seas.

~4,600 *International Commission on Stratigraphy, 2018

Figure Summary Opposite, layers of sedimentary rock in the Grand Canyon have been exposed by erosion. Visible layers are correlated with the geologic time scale above. Red triangles mark mass extinctions; “first appearance” refers to appearance in the fossil record, not necessarily first appearance on Earth. mya: million years ago.

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Evidence of Evolution  Chapter 12  233  

Ka Kaibab Limestone Ka

To

Toroweap Formation

To

Permian

Co He Co Coconino Sandstone

Es We Ma Wa

He Hermit Shale Es Esplanade Sandstone

Re Te

We Wescogame Formation

Carboniferous

Mu Ma Manakacha Formation Br Wa Watahomigi Formation Ta

Vi Re Redwall Limestone Te

Temple Butte Formation

Proterozoic

Cambrian

Mu Muav Limestone

Br

Bright Angel Shale

Ta

Tapeats Sandstone

†

Ch

†

Na

†

p on ou ati Gr rm o F ap we

r ua o

nk

r ka

p

ou Gr

Un

Vi

Vishnu Basement Rocks

?

Figure It Out: Which formation in the photo is marked with the

Answer: Tapeats sandstone

Layers not visible in this view

†

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© Michael Pancier

12.6  Evidence in Form and Function

analogous structures  Similar body parts that evolved independently in different lineages (by convergent evolution).

Learning Objectives

convergent evolution  Evolutionary pattern in which similar body parts evolve separately in different lineages. divergent evolution  Evolutionary pattern in which lineages descended from a common ancestor diverge.

●●

Describe how body form and function can offer clues about evolutionary relationships.

●●

Distinguish between divergent and convergent evolution.

●●

Use examples to explain the difference between analogous and homologous structures.

In general, species with closer evolutionary relationships have more traits in common. Comparative morphology can reveal evidence of such relationships in body form and function.

homologous structures  Body structures that may appear different in different lineages, but are derived from a common ancestral form.

Homologous Structures Descendants of a common ancestor may evolve in different ways in response to different environmental pressures. The divergence of lineages descended from a common ancestor is called divergent evolution. Divergent evolution can give rise to homologous structures, which are body parts that may appear different in different lineages, but are derived from a common ancestral form. Figure 12.18  Homologous structures: vertebrate forelimbs. The number and position of many skeletal elements were preserved when these diverse animals evolved from a stem reptile (the photo shows a fossilized stem reptile of the genus Captorhinus). Notice the bones of the forearms. Certain bones were lost over time in some of the lineages (compare the digits numbered 1 through 5). Drawings are not to scale. Richard Paselk, Humboldt State University Natural History Museum

stem reptile

1

2

3

4

1

3

4

5

5

23 4 4

3

3

5

1 4

2

2

5

1 2 3

2 2 1

2

1

3

3

1

4 5

chicken

penguin

dolphin

bat

Figure It Out: What is the evolutionary pattern that gave rise to these homologous structures?

human

elephant Answer: Divergent evolution

pterosaur

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Evidence of Evolution  Chapter 12  235  

Vertebrate Forelimbs  The forelimbs of vertebrate animals are examples of homolo-

gous structures (Figure 12.18). Although the limbs vary in size, shape, and function, they are alike in the structure and positioning of internal elements such as bones, nerves, blood vessels, and muscles. A family of ancient “stem reptiles” with five-toed limbs was ancestral to many vertebrates. Over millions of years, descendants of this ancestral group diversified into different lineages that eventually gave rise to modern reptiles, birds, and mammals. During this process of divergent evolution, fivetoed limbs became adapted for appropriate purposes. For example, human forelimbs are arms with hands that have four fingers and an opposable thumb. Forelimbs of dolphins and other cetaceans are pectoral fins (flippers) useful for swimming; in bats and most birds, they are wings that allow flight.

Analogous Structures  Structures that appear similar in different species are not always homologous. Similarities sometimes evolve independently in lineages subject to the same environmental pressures, a pattern called convergent evolution. Convergent evolution can give rise to analogous structures, which are similar body parts that evolved independently in different lineages. Wing Surfaces  The wings of birds, bats, and insects all perform the same function,

which is flight. However, several clues tell us that the wing surfaces are not homologous. All three types of wings have adaptations for the same physical constraints that govern flight, but the adaptations differ. In the case of birds and bats, the limbs themselves are homologous, but other structures that make those limbs useful for flight are not. The surface of a bat wing is a thin, membranous extension of the animal’s skin. By contrast, the surface of a bird wing is a sweep of feathers, which are specialized structures derived from skin. Insect wings differ even more. An insect wing forms as a saclike extension of the body wall. The sac flattens and fuses into a thin membrane around sturdy, forked veins that structurally support the wing. Unique adaptations for flight are evidence that wing surfaces of birds, bats, and insects are analogous structures that evolved after the ancestors of these modern groups diverged (Figure 12.19A).

Insects wings

Bats

Humans

wings

Birds

Crocodiles

wings

limbs with 5 digits ancient common ancestor

A. Adaptations that make an insect wing, a bat wing, and a bird wing useful for flight differ. The diagram shows how the evolution of wings (red dots) occurred independently in the three lineages.

Plant Form  Homologous structures of the African milk barrel plant and the

saguaro cactus (shown in Figure 12.3) are adaptations to harsh desert environments where rain is scarce. Accordion-like pleats allow the plant body to swell with water when rain does fall; water stored in the plants’ tissues allows them to survive long dry periods. As the stored water is used, the plant body shrinks, and the folded pleats provide some shade in an environment that typically has none. Despite these similarities, a closer look reveals differences that indicate the two types of plants are not closely related (Figure 12.19B). For example, cactus spines are simple modified leaves that arise from dimpled structures. By contrast, the spines on an African milk barrel plant are dried flower stalks that project smoothly from the plant surface.

Take-Home Message 12.6 ●●

●●

Body parts may become modified for different purposes in different lineages as they diverge from a common ancestor. Such body parts are homologous structures. Body parts that appear alike may have evolved independently in lineages that have faced similar environmental pressures. Such body parts are analogous structures.

B. Spines of a saguaro cactus (left) are modified leaves. Spines of an African milk barrel plant (right) are dried flower stalks. Figure 12.19  Analogous structures. Similar structures that evolve independently in separate lineages are an outcome of similar environmental pressures. (A) Top, © iStockphoto.com/DanCardiff; middle, © Taro Taylor, www.flickr.com/photos/tjt195; bottom, Alberto J. Espiñeira Francés - Alesfra/Getty Images; (B) Left, George Burba/Shutterstock .com; right, James C. Gaither, www.flickr.com/people/jim-sf/

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236  Unit 3  EVOLUTION AND DIVERSITY

12.7  Molecular Evidence Learning ObjectiveS ●●

●●

Describe the way similarities between protein sequences (or between DNA sequences) are used as a measure of relative relatedness. Explain why similarities in patterns of embryonic development can be used as evidence of an evolutionary relationship.

Similarities in DNA and Proteins Over generations, inevitable mutations change the DNA sequence of a lineage’s genome. Most of these mutations are neutral, which means they have no effect on an individual’s survival or reproduction. Thus, we can assume that neutral mutations accumulate in a lineage’s genome at a constant rate. Mutations accumulate independently in the genomes of separate lineages. When two lineages start to diverge from a common ancestor, very few mutations differentiate their genomes. Over many generations, the genomes diverge as separate mutations accumulate in them. The more recently two lineages diverged, the less time there has been for unique mutations to accumulate in their DNA. Thus, similarities in the nucleotide sequence of a shared gene (or in the amino acid sequence of a shared protein) are often used as evidence of an evolutionary relationship. Molecular comparisons like these may be combined with morphological comparisons to provide data for hypotheses about shared ancestry.

Figure 12.20  Example of a protein comparison. This is an alignment of part of the amino acid sequence of the same protein (cytochrome b) from 19 species. The sequence is identical in 10 species of honeycreeper; amino acids that differ in the other species are highlighted in red. Dashes reflect insertions or deletions. See Figure 8.7 for amino acid codes.

Comparing DNA  Among species that diverged relatively recently, many proteins

have identical amino acid sequences. Nucleotide sequence differences may be

...CRDVQFGWLIRNLHANGASFFFICIYLHIGRGIYYGSYLNK--ETWNIGVILLLTLMATAFVGYVLPWGQMSFWG... ...CRDVQFGWLIRNLHANGASFFFICIYLHIGRGIYYGSYLNK--ETWNVGIILLLALMATAFVGYVLPWGQMSFWG... ...CRDVQFGWLIRNIHANGASFFFICIYLHIGRGLYYGSYLYK--ETWNVGVILLLTLMATAFVGYVLPWGQMSFWG... ...CRDVNYGWLIRYMHANGASMFFICLFLHVGRGMYYGSYTFT--ETWNIGIVLLFAVMATAFMGYVLPWGQMSFWG... ...CRDVHYGWIIRYMHANGASMFFICLFMHVGRGLYYGSYLLS--ETWNIGIILLFTVMATAFMGYVLPWGQMSFWG... ...CRDVNYGWLIRNLHANGASFFFICIYLHIGRGLYYGSYLYK--ETWNIGVVLLLLVMGTAFVGYVLPWGQMSFWG... ...TRDVNYGWIIRYLHANGASMFFICLFLHIGRGLYYGSFLYS--ETWNIGIILLLATMATAFMGYVLPWGQMSFWG... ...MRDVEGGWLLRYMHANGASMFLIVVYLHIFRGLYHASYSSPREFVWCLGVVIFLLMIVTAFIGYVLPWGQMSFWG... ...ETDVMNGWMVRSIHANGASWFFIMLYSHIFRGLWVSSFTQP--LVWLSGVIILFLSMATAFLGYVLPWGQMSFWG... ...MRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVIIFTLTIATAFLGYCCVYGQMSHWG...

Figure It Out: By this comparison, which species is the closest relative of honeycreepers?

Answer: The song sparrow

honeycreepers (10) song sparrow Gough Island finch deer mouse Asiatic black bear bogue (a fish) human thale cress (a plant) baboon louse baker’s yeast

Comparing Proteins  Evolutionary biologists often compare a protein’s sequence among species, and use the number of amino acid differences as a measure of relative relatedness (Figure 12.20). The amino acids that differ also offer clues. For example, a leucine to isoleucine change may not affect the function of a protein very much, because both amino acids are nonpolar, and both are about the same size. By contrast, the substitution of a lysine (which is basic) for an aspartic acid (which is acidic) will dramatically change the character of a protein, which in turn may affect phenotype. Most mutations that affect phenotype are selected against, but occasionally one proves adaptive. Thus, the longer it has been since two lineages diverged, the more of these nonconservative amino acid substitutions we are likely to see when comparing their proteins.

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Evidence of Evolution  Chapter 12  237  

Figure 12.21  Comparing vertebrate embryos.

instructive in such cases, because the genetic code has a lot of redundancies (Section 8.4). Even if the amino acid sequence of a protein is identical, the nucleotide sequence of the gene that encodes the protein may differ. Getting useful information from comparing DNA requires more data than protein comparisons. This is because chance matches are statistically more likely to occur with DNA comparisons—there are only 4 nucleotides in DNA versus 20 amino acids in proteins. However, DNA sequencing has become so fast that there is a lot of data available to compare. Genomics studies with such data have shown us (for example) that about 86 percent of the mouse genome sequence is identical with the human genome, as is 51 percent of the bee genome, 19 percent of the thale cress genome, and 9 percent of the bacterial genome.

All vertebrates go through an embryonic stage in which they have a tail and divisions called somites along their back. From left to right: human, mouse, lizard, turtle, chicken. From left, Lennart Nilsson/ Bonnierforlagen AB; Courtesy of Anna Bigas, IDIBELL-Institut de Recerca Oncologica, Spain; Catherine May; Catherine May; Courtesy of Prof. Dr. G. Elisabeth Pollerberg, Institut für Zoologie, Universität Heidelberg, Germany

Similarities in Development  In general, the more closely related animals are, the more similar is their development. For example, all vertebrates go through a stage during which a developing embryo has a tail and a series of somites—divisions of the body that give rise to the backbone and associated skin and muscle (Figure 12.21). Animals have similar patterns of embryonic development because the same master regulators direct the process (Section 8.7). Because a mutation in a master regulator can completely unravel development, these genes tend to be highly conserved. Even among lineages that diverged a very long time ago, many master regulators retain similar sequences and functions. Hox Genes  Consider a group of highly conserved master regulators called Hox.

Hox genes are homeotic, so they trigger formation of specific body parts during embryonic development. Insects have a Hox gene called antennapedia that causes legs to form wherever it is expressed, which is normally in the midsection of the body (the thorax). Humans and other vertebrates have a version of antennapedia called Hoxc6. Expression of Hoxc6 in a vertebrate embryo causes ribs to develop on a vertebra. Vertebrae of the neck and tail normally develop with no Hoxc6 expression, and no ribs (Figure 12.22).

Figure 12.22  Differences in body form arise from differences in master regulator expression. Expression of the Hoxc6 gene, indicated by the purple tracer in two vertebrate embryos, chicken (left) and garter snake (right), causes a vertebra to develop ribs as part of the back. Chickens have 7 vertebrae in their back and 14 to 17 vertebrae in their neck; snakes have upwards of 450 back vertebrae and essentially no neck. Courtesy of Ann C. Burke, Wesleyan University

Take-Home Message 12.7 ●●

●●

Species that are more closely related tend to share more similarities in their DNA (and their proteins). Similarities in patterns of embryonic development are the result of master regulators that have been conserved over evolutionary time.

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238  Unit 3  EVOLUTION AND DIVERSITY

Summary Section 12.1  Events of the ancient past can be explained by the same physical, chemical, and biological processes that operate today. The dinosaurs disappeared 66 million years ago in a mass extinction that was probably caused by a catastrophic asteroid impact. The impact left physical traces in a worldwide sedimentary rock formation called the K–Pg boundary. Section 12.2  Expeditions in the nineteenth century yielded new observations of organisms, fossils, and their distribution (biogeography). Comparative morphology yielded new observations of similarities and differences between organisms and fossils. Taken together, the accumulating evidence implied that Earth and life on it had changed over time, an idea that could not be explained within the framework of existing belief systems. Attempts to reconcile traditional beliefs with physical evidence of evolution, which is change in a lineage over time, led to new ways of thinking about the natural world. Section 12.3  Charles Darwin’s voyage on the Beagle set the stage for his ideas about evolution. He and Alfred Wallace independently realized that evolution can occur as a result of natural selection, explained here in modern terms: A natural population tends to grow until it exhausts environmental resources. As that happens, competition for those resources intensifies among the population’s members. Individuals with forms of shared, heritable traits that make them more competitive for the limited resources tend to produce more offspring. These adaptive traits (adaptations) impart greater fitness, so they tend to become more common in a population over generations. Section 12.4  Fossils—mineralized remains or traces of ancient organisms—are typically found in layers of sedimentary rock, which forms from sand, silt, and other materials deposited on the bottom of seas and other bodies of water. Geologic processes can lift and tilt sedimentary rock formations far above sea level. The fossil record will always be incomplete. Even so, we have discovered enough fossils to reconstruct the evolutionary history of many ancient and modern species. Each radioisotope has a characteristic half-life. The constancy of radioactive decay allows us to determine the age of rocks and fossils with radiometric dating. Section 12.5  By the plate tectonics theory, Earth’s crust is cracked into giant plates that carry landmasses to new positions as they move. The course of life’s evolution has been profoundly influenced by this movement, for example as populations were brought together or split up during the formation and breakup of supercontinents

such as Gondwana and Pangaea. The geologic time scale, a chronology of Earth’s history, correlates layers of rock with great intervals of time. Section 12.6  Comparative morphology can reveal evidence of evolutionary connections among lineages. With divergent evolution, homologous structures are modified differently in lineages diverging from a common ancestor. Analogous structures are body parts that appear similar in different lineages, but did not evolve in a common ancestor. Rather, they evolved separately after the lineages diverged (convergent evolution). Analogous structures reflect adaptations to similar environmental constraints. Section 12.7  Similarities between protein or DNA sequences of different species are evidence of evolutionary relationships. In general, these sequences are more similar among lineages that diverged more recently. Master regulators tend to be highly conserved, so similarities in patterns of embryonic development reflect shared ancestry that can be evolutionarily ancient.

Self-Quiz Answers in Appendix I 1. The number of species on an island usually depends on the size of the island and its distance from a mainland. This statement would most likely be made by __________ . a. an explorer c. a geologist b. a biogeographer d. a philosopher 2. Evolution __________ . a. is change in a line of descent b. is the same as natural selection c. is the goal of natural selection d. explains the origin of life 3. A trait is adaptive if it __________ . a. arises by mutation c. is passed to offspring b. increases fitness d. occurs in fossils 4. The process in which environmental pressures result in the differential survival and reproduction of individuals of a population is called __________ . a. catastrophism c. natural selection b. evolution d. genetics

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Evidence of Evolution  Chapter 12  239  

7. True or false? Wrinkly textures in rock that formed from ancient biofilms living in marine sediments are fossils. 8. If the half-life of a radioisotope is 20,000 years, then a sample in which three-quarters of that radioisotope has decayed is __________ years old. a. 15,000 c. 30,000 b. 26,667 d. 40,000 9. Forces that cause geologic change include __________ (select all that are correct). a. movement of water d. tectonic plate movement b. natural selection e. wind c. volcanic activity f. asteroid impacts 10. Did Pangaea or Gondwana form first? 11. The dinosaurs disappeared about __________ million years ago. 12. Through __________, a body part of an ancestor is modified differently in different lines of descent. a. homologous structures c. analogous structures b. convergent evolution d. divergent evolution

CRITICAL THinking 1. In the late 1800s, a biologist studying animal embryos coined the phrase “ontogeny recapitulates phylogeny,” meaning that the physical development of an animal embryo (ontogeny) seemed to retrace the changing form of the species during its evolutionary history (phylogeny). The idea is incorrect, but why would he have thought that development retraces evolution? 2. Radioactive decay is a random event, which means we cannot determine when an individual atom of a radioisotope will decay. However, we can accurately determine the average rate of decay among a large number of atoms in a sample of a radioisotope. We measure this rate in terms of half-life. Why not “full-life”? 3. Natural selection makes an adaptive trait more common in a population. After many generations, will all individuals in the population have the same adaptive trait? 4. If you think of geologic time spans as minutes, life’s history might be plotted on a clock such as the one shown below. According to this clock, the most recent epoch started in the last 0.1 second before noon. Where does that put you? 11:37:18 A.M. flowering plants 11:21:10 A.M. mammals, dinosaurs 10:40:57 A.M. early fishes

Ph

11

12:00:00 A.M. Earth’s crust solidifies

c

12

1

ch

9

3

ter

o Pr

8

4 7

6

d earl ier n an

2

10

ea

14. __________ are highly conserved because mutations in them can unravel development. a. Derived traits c. Homologous structures b. Master regulators d. Fossils

an

zoi e ro

11:59:59 A.M. first humans

Ar

13. All of the following data types can be evidence of shared ancestry except similarities in __________ . a. amino acid sequences b. embryonic development c. DNA sequences d. fossil morphologies e. form due to convergent evolution

a. does not affect fitness b. line of descent c. human arm and bird wing d. survival of the fittest e. characteristic of a radioisotope f. insect wing and bird wing g. evidence of ancient life

lineage fossils natural selection neutral mutation half-life homologous structures analogous structures

ic

6. In which type of rock are you more likely to find a fossil? a. basalt, a dark, fine-grained volcanic rock b. limestone, composed of sedimented calcium carbonate c. slate, a volcanically melted and cooled mudstone d. granite, which forms by crystallization of magma cooling below Earth’s surface

15. Match each term with the most suitable description.

ozo

5. Darwin and Wallace proposed the hypothesis that __________ . a. natural selection drives evolution b. change occurs in a line of descent c. new species arise after geologic events d. dinosaurs perished in the aftermath of an asteroid impact

2:05:13 A.M. archaea, bacteria

5

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5:28:41 A.M. eukaryotes

13 Processes of Evolution

13.1

Farming Superbugs  241

13.2

Alleles in Populations  242

13.3

Patterns of Natural Selection  245

13.4

Natural Selection and Diversity  248

13.5

Nonselective Evolution  250

13.6

Speciation  253

13.7

Macroevolution  257

13.8

Phylogeny  260

Variation in shared traits is apparent among individuals of the species Polymita picta, a land snail native to Cuba. The adaptive value of their colorful shells has changed because humans now value them for making jewelry. The species is now endangered.

Concept Connections Nature Picture Library/Alamy Stock Photo

With natural selection (Section 12.3), environmental pressures operate on variation in shared traits (1.4, 10.4–10.5) among members of a population (1.2). Mutations (7.6, 8.6) give rise to alleles (9.5) that are the basis of the variation (10.2). Form and function are shaped by such processes (12.6), as are interactions among species in communities (18.3). This chapter also revisits the process of science (1.5–1.7), harmful bacteria (3.1), coenzymes (4.4), pigments (5.3), master regulators (8.7), clotting factors (10.7), polyploidy (10.8), SNPs (11.1), transgenic plants (11.4), evidence to inference (12.1), plate tectonics and the geologic time scale (12.5), and sequence comparisons (12.7).

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Processes of Evolution  Chapter 13  241  

Application 13.1  Farming Superbugs Scarlet fever, tuberculosis, and pneumonia once caused a quarter of the annual deaths in the United States. Since the 1940s, we have been relying on antibiotics to fight these and other dangerous bacterial diseases. We have also been using them in other, less dire circumstances. For an unknown reason, cattle, pigs, poultry, and even fish grow more quickly when fed antibiotics on a regular basis. The agricultural industry uses a lot of antibiotics for this purpose. An FDA ruling that went into effect in January 2017 ended the use of medically important antibiotics (those important for human medicine) for promoting growth in livestock, but these antibiotics can still be used to prevent or treat livestock illnesses. Medically important antibiotics constituted almost half of the 11 million kilograms of antibiotics sold for use in food-producing animals in the United States in 2017. Farms where antibiotics are regularly given to livestock (Figure 13.1) are hot spots for the evolution of antibiotic-resistant bacteria and their spread to humans. People who work with animals on these farms tend to have more antibiotic-resistant bacteria in their bodies, as do neighbors living within a mile radius. The bacteria spread much farther than that, however. For example, bacteria on an animal’s skin or in its digestive tract can easily contaminate its meat during slaughter, and contaminated meat ends up in restaurant and home kitchens. Bacteria in meat can be killed by the heat of cooking, but it is almost impossible to prevent them from spreading to kitchen surfaces—and to people—during the food preparation process. A large proportion of chicken, ground turkey, pork chops, and ground beef sold in U.S. grocery stores has antibiotic-resistant bacteria in it. Most of these bacteria are not inherently harmful, but some are human pathogens. For example, the FDA found Salmonella in about 6 percent of retail chicken meat samples they tested in 2015. More than half of these bacteria were resistant to at least one antibiotic, and about one in a hundred chicken samples contained Salmonella “superbugs”—bacteria resistant to three or more antibiotics. Salmonella causes an estimated 1.2 million cases of food poisoning each year. Meat-eaters are not the only people exposed to superbugs. Bacterial contamination of fresh produce is thought to cause the majority of food poisoning incidents in the United States. Superbugs are now commonly found on fresh fruits and vegetables in grocery stores; most of this contamination comes from soil or irrigation water that contacts the crop during growth. A natural population of bacteria can evolve astonishingly fast. Consider how each cell division is an opportunity for mutation. Bacteria such as Salmonella can divide every 20 minutes, so even if a population starts out as clones, its cells can diversify quickly. When a natural population of bacteria is exposed to an antibiotic, some cells are likely to survive because they carry an allele that offers resistance. As susceptible cells die and the survivors reproduce, the frequency of the antibiotic-​resistance allele in the population increases. A two-week course of treatment with antibiotics can exert selection pressure on hundreds of generations of bacteria. The pressure drives genetic change

Figure 13.1  A hot spot for antibiotic-resistant bacteria. The vast majority of “free-range” chickens raised for meat in the United States spend their lives in gigantic flocks that crowd huge buildings like this one. Growthpromoting antibiotics are given to the entire flock in food or water, a practice that pressures bacterial populations to become antibiotic-resistant. Bob Nichols/USDA photo

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242  Unit 3 EVOLUTION AND DIVERSITY

in bacterial populations so they become composed mainly of antibiotic-resistant cells. Thus, using antibiotics on an ongoing basis effectively guarantees the production of antibiotic-resistant bacterial populations. We have only a limited number of antibiotic drugs, and developing new ones is much slower than bacterial evolution. As resistant bacteria become more common, the number of antibiotics useful for treating infections in humans dwindles. Using a particular antibiotic only in animals, or only in humans, is not a universal solution because there are only a few mechanisms by which these drugs kill bacteria; resistance to one antibiotic can confer resistance to others. For example, bacteria that become resistant to Flavomycin (an antibiotic used only in animals) also resist vancomycin (an antibiotic used only in humans). In addition, even distantly related bacteria can swap genes, so alleles that offer resistance in one bacterial species are quickly acquired by others. Superbugs that are resistant to most currently available antibiotics are turning up at a very alarming rate. In humans, an infection with multidrug-resistant bacteria tends to be longer, more severe, and more likely to be deadly than one more easily treatable with antibiotics. Antibiotic-resistant bacteria cause more than 2 million cases of serious illness each year in the United States alone, and outright kill more than 150,000 people. Many more die because the infection complicates another, preexisting illness.

Discussion Questions 1. If you were in charge of a task force to revise current policy on the use of antibiotics in agriculture, what would you recommend and why? 2. Feeding antibiotics to livestock is only one way in which we have fostered antibiotic-resistant bacteria. Can you think of other practices that lead to antibiotic resistance? 3. Exposure to an antibiotic can increase the proportion of antibioticresistant individuals in a population of bacteria. After exposure ends, the proportion of resistant bacteria declines. Why?

13.2  Alleles in Populations Learning Objectives ●●

Using appropriate examples, explain variation in shared traits among individuals of a population.

●●

Explain allele frequency.

●●

Describe microevolution.

Variation in Shared Traits Remember from Section 1.2 that a population is a group of interbreeding individuals of the same species in some specified area. Individuals of a population (and a species) have the same genes, so they share certain features. Humans, for example, normally have a short neck, a thumb on each hand, and so on. These are examples of morphological traits (morpho– means “form”). Individuals of a population also share physiological traits, such as details of metabolism, and they respond the same way to certain stimuli (behavioral traits). Sexual reproduction produces offspring with different combinations of alleles (Section 9.5), so almost every shared trait varies among members of a sexually

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Processes of Evolution  Chapter 13  243  

Figure 13.2  Sampling morphological variation among humans.

reproducing population (Figure 13.2). Many traits have two or more distinct forms, or morphs. A trait with two forms is called a dimorphism. Flower color in the pea plants that Gregor Mendel studied is an example of a dimorphic trait (Section 10.2). In these plants, two alleles with a clear dominance relationship give rise to the dimorphism: purple or white flowers. A trait with three or more distinct forms is called a polymorphism. ABO blood type in humans, which is determined by the codominant alleles of the ABO gene, is an example. Most other traits are complex, as is their genetic basis. Any of the genes that influence such traits may have multiple alleles. In earlier chapters, you learned that alleles arise by mutation. Other events shuffle them among offspring (Table 13.1). To understand the potential scope of variation that results from these events, consider our own species. Humans have more than 20,000 genes, all with multiple alleles. Unless you have an identical twin, it is essentially impossible that another person with your particular complement of alleles has ever lived, or ever will.

An Evolutionary View of Mutations  Mutations—the original source of new alleles—are the raw material of evolution. We cannot predict when or in which individual a particular gene will mutate. We can, however, measure the average mutation rate of a species, which is the probability that a mutation will occur in a given interval. In our species, that rate is about 1.2 × 10−8 mutations per nucleotide per generation. In other words, each child is born with an average of 64 new mutations—64 DNA sequence variations that did not occur in either parent.

Variation in shared traits is an outcome of alleles that influence those traits. Top row (left to right), © Roderick Hulsbergen/http://www.photography.euweb.nl; V.S.Anandhakrishna/Shutterstock.com; FXQuadro/Shutterstock.com; Rasstock/Shutterstock .com; Michael Jung/Shutterstock.com; BestPhotoStudio/Shutterstock.com; bottom row (left to right), violetblue/Shutterstock.com; wong sze yuen/Shutterstock.com; NinaMalyna/ Shutterstock.com; cheapbooks/Shutterstock.com; TS/Adobe Stock; Gelpi/Shutterstock.com

Table 13.1  Some Sources of Variation in Human Traits

Genetic Event

Effect

Mutation

Original source of new alleles

Crossing over at meiosis I

Mixes up maternal and paternal alleles on homologous chromosomes for forthcoming gametes

Independent assortment at meiosis I

Randomly distributes homologous chromosomes into gametes

Fertilization

Combines alleles from two parents

Beneficial Mutations  Mutations that are beneficial tend to become more common

in a population over time, even if they bestow only a slight advantage. With natural selection, remember, environmental pressures result in an increase in the frequency of an adaptive form of a trait in a population over generations (Section 12.3).

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244  Unit 3 EVOLUTION AND DIVERSITY

Mutations have been altering genomes for billions of years, and they continue to do so. Cumulatively, they have given rise to Earth’s staggering biodiversity. Think about it: The reason you do not look like an avocado or an earthworm or even your neighbor began with mutations that occurred in different lines of descent. Neutral Mutations  Most mutations are neutral, which means they neither help nor hurt the individual. Mutations that affect the extent of attachment of your earlobes to your head offer an example. Having earlobes that are entirely attached or entirely free swinging has no effect on survival or reproduction, so natural selection does not operate on variations in this trait (Figure 13.3). free earlobe

attached earlobe

Figure 13.3  Variation in earlobe attachment. Mutations that affect the degree of attachment of the earlobe to the head do not affect an individual’s survival or reproduction, so these mutations are neutral. Note that this trait varies continuously in humans. Left, Tatjana Romanova/Shutterstock.com; right, BLACKDAY/Shutterstock.com

Harmful Mutations  Some mutations give rise to structural, functional, or behav-

ioral changes that reduce an individual’s chances of surviving and reproducing. Consider what happens if a gene for collagen mutates. Collagen is a protein component of the skin, bones, tendons, lungs, blood vessels, and other vertebrate organs, so a mutation that alters its function affects the entire body, typically in a negative way. Natural selection operates on traits with a genetic basis, so mutations that reduce fitness tend to become less common in a population over time. Some mutations change phenotype so drastically that they result in death, in which case they are called lethal mutations.

Allele Frequency  Together, all the alleles of all the genes of a population constitute a pool of genetic resources—a gene pool. Members of a population breed with one another more often than they breed with members of other populations, so their gene pool is more or less isolated. Allele frequency is the proportion of one allele relative to all copies of the gene in a population—the fraction of chromosomes that have the allele. For example, if half the members of a population are homozygous for a particular allele, then the allele’s frequency is 50 percent, or 0.5. If half of the population is heterozygous for the allele, then its frequency is 25 percent, or 0.25. Remember, diploid organisms have two copies of each chromosome (Section 9.2). Microevolution  Allele frequency can change over time, and this change is called microevolution. Microevolution is always occurring in natural populations because

natural selection and other processes that drive evolution are always in play. As you learn about these processes, remember an important point: Evolution is not purposeful. It simply fills nooks and crannies of opportunity. allele frequency  Abundance of a particular allele in a population’s gene pool. directional selection  Pattern of natural selection in which a form of a trait at one end of a range of variation is adaptive. disruptive selection  Pattern of natural selection in which forms of a trait at both ends of a range of variation are adaptive, and intermediate forms are not.

Take-Home Message 13.2 ●●

●●

gene pool  All alleles of all genes in a population; a pool of genetic resources.

●●

microevolution  Change in allele frequency.

●●

stabilizing selection  Pattern of natural selection in which an intermediate form of a trait is adaptive, and extreme forms are not.

●●

●●

Individuals of a population share morphological, physiological, and behavioral traits characteristic of the species. Details of most shared traits vary among members of a sexually reproducing population. Alleles, the basis of this variation, arise by mutation. All alleles of all genes in a population make up the population’s gene pool. An allele’s abundance in the gene pool is called its allele frequency. A change in an allele’s frequency is called microevolution. Microevolution is always occurring in natural populations because processes that drive it are always operating.

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13.3  Patterns of Natural Selection Learning Objectives ●●

Describe three patterns of natural selection.

●●

Explain how natural selection drives microevolution.

●●

Use an example to explain how a change in the environment can favor a mutation that had previously been harmful.

Natural selection is one of several mechanisms by which microevolution occurs. By operating on forms of a trait that differ among members of a population, natural selection affects the frequency of alleles that influence the trait. This process may occur in recognizable patterns (Figure 13.4). With directional selection, a form of a trait at one end of a range of variation is adaptive. With stabilizing selection, an intermediate form of a trait is adaptive, and extreme forms are selected against. With disruptive selection, forms of a trait at both ends of a range of variation are adaptive, and intermediate forms are selected against. The following examples illustrate these three patterns of natural selection.

Number of individuals in population

Processes of Evolution  Chapter 13  245  

Range of values for the trait

A. Population before selection occurs. Directional Selection

Directional Selection  Warfarin Resistance in Rats  Rats thrive in urban centers where garbage is plentiful and natural predators are not. Part of their success stems from an ability to reproduce very quickly: Rat populations can expand within weeks to match the amount of garbage available for them to eat. For decades, people have been using poisons to fight rat infestations. Baits laced with warfarin, an organic compound that interferes with blood clotting, became popular in the 1950s. Warfarin binds to and inhibits the function of an enzyme called VKOR. This enzyme regenerates vitamin K, which functions as a coenzyme in the production of clotting factors (Section 10.7). When vitamin K is not regenerated, clotting factors are not properly produced, and clotting cannot occur. Rats that eat warfarin baits die within days after bleeding internally or losing blood through cuts or scrapes. The use of warfarin increased over time because it was more effective than other poisons, and it had less impact on nonpest species. By 1980, however, about 10 percent of rats in urban areas were resistant to warfarin. Why? Exposure to the poison drives microevolution in rat populations. Rats that are resistant to warfarin have alleles with mutations in the gene for VKOR. These mutations alter the enzyme in a way that prevents warfarin binding. Rats with the normal allele die after eating warfarin; the lucky ones with a mutated allele survive and pass it to offspring. The populations recover quickly, and with each onslaught of warfarin, the frequency of mutated alleles increases. Mutations that confer warfarin resistance also reduce the activity of the VKOR enzyme, so resistant rats require extra vitamin K—a lot of it. Rats with warfarinresistance alleles cannot easily obtain enough of the vitamin to sustain normal blood clotting and bone formation. This outcome is not so bad when compared with being dead from rat poison, but rats with the alleles are at a serious disadvantage when warfarin is not present. Thus, when warfarin exposure ends, the frequency of the alleles declines in rat populations—another example of microevolution driven by directional selection. Coat Color in Rock Pocket Mice  Directional selection also affects the coat color of

rock pocket mice, which are small mammals that inhabit rocky deserts in Arizona

B. With directional selection, a form of a trait at one end of a range of variation is adaptive.

Stabilizing Selection

C. With stabilizing selection, extreme forms of a trait are eliminated, and an intermediate form is maintained.

Disruptive Selection

D. With disruptive selection, a midrange form of a trait is eliminated, and extreme forms are maintained. Figure 13.4  Comparing three modes of natural selection. In these examples, blue arrows indicate which forms of the trait are adaptive; red arrows show forms that are selected against.

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246  Unit 3 EVOLUTION AND DIVERSITY

Digging Into Data Resistance to Rodenticides in Wild Rat Populations Beginning in 1990, rat infestations in northwestern Germany started to intensify despite continuing use of rat poisons. Michael H. Kohn and his colleagues tested wild rat populations around Muenster. In five towns, they trapped and tested wild rats for resistance to warfarin and the more recently developed poison bromadiolone. The results are shown in Figure 13.5. 1. In which of the five towns were most of the rats susceptible to warfarin? 2. Which town had the highest percentage of poison-resistant wild rats? 3. What percentage of rats in Olfen were warfarin resistant? 4. In which town do you think the application of bromadiolone was most intensive?

Figure 13.6  Adaptive value of two color forms of the peppered moth. J. A. Bishop, L. M. Cook

A. Light moths (left) on a lichen-covered tree trunk are hidden from predators. Black moths (right) stand out.

B. On lichen-free tree trunks, the black color (left) provides more camouflage than the light color (right).

21% 58% 21%

not resistant to warfarin or bromadiolone

Olfen 5% 8%

Germany 87%

Stadtlohn

5% 5%

56% 44%

Dorsten

100%

Ludwigshafen

warfarin resistant resistant to warfarin and bromadiolone

90%

Drensteinfurt

Figure 13.5  Poison resistance in wild rats in Germany, 2000.

and New Mexico. These environments are dominated by light brown granite, with widely separated patches of dark basalt. Both types of rock are colonized by populations of rock pocket mice. Individual mice have no preference for the basalt or the granite, but a population’s predominant coat color depends on the type of rock it inhabits. Almost all of the mice inhabiting the patches of dark basalt have black coats, and almost all of the mice inhabiting the light brown granite have light brown coats. The difference arises because mice that match the rock color in each habitat are camouflaged from their natural predators. The mice forage for seeds mainly at night, when they are visible to night-flying owls. Owls use their keen sense of vision to find prey, and they preferentially catch and eat easily seen mice. In this environment, coat color that matches rock color is an adaptive trait, and predation by owls exerts directional selection on populations of mice living in each type of rock. This natural selection is driving microevolution. Remember from Section 10.4 that the products of several genes interact to determine fur color in animals. Populations of black mice have a high frequency of alleles with mutations that affect melanin production; populations of brown mice do not. Color Forms of the Peppered Moth  A well-documented case of directional selection involves coloration changes in the peppered moth in England. These insects feed and mate at night, then rest on trees during the day. In 1850, the vast majority of peppered moths were light with black speckles, and a very small number were black. At the time, the air was clean, and light-gray lichens grew on the trunks and branches of most trees. Light moths that rested on lichen-covered trees were well camouflaged, but black moths were not (Figure 13.6A). By 1900, black moths had become much more common than light moths. Scientists suspected that predation by birds was the selective pressure that shaped moth coloration in local populations. The industrial revolution had begun, and smoke emitted by coal-burning factories was killing lichens. The black moths were better camouflaged from predatory birds on lichen-free, soot-darkened trees (Figure 13.6B). H. B. Kettlewell set out to test this hypothesis in the 1950s. He bred both color morphs in captivity, marked them for easy identification, then released them in

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Processes of Evolution  Chapter 13  247  

400 Number of survivors

sociable weavers

300 200 100 0 35.5

34.5

33.5

32.5

31.5

30.5

29.5

28.5

27.5

26.5

25.5

24.5

23.5

Body mass (grams)

Figure It Out: According to this graph, what is the optimal weight of a sociable weaver? Answer: About 29 grams

Figure 13.7  Stabilizing selection in sociable weavers.

several areas. His team recaptured more of the black moths in the polluted areas, and more of the light moths in the less polluted areas. The researchers also observed predatory birds eating more light moths in soot-darkened forests, and more black moths in cleaner, lichen-rich forests. Black moths were clearly at a selective advantage in industrialized areas. Pollution controls went into effect in 1952. As a result of improved environmental standards, tree trunks gradually became free of soot, and lichens made a comeback. Kettlewell observed that moth phenotypes shifted too: Wherever pollution decreased, the frequency of dark moths decreased as well. Later research confirmed Kettlewell’s results. In peppered moths, having a color form that matches tree color is an adaptive trait, and directional selection for this trait drives microevolution in local populations. Moth color is determined by a single gene. Individuals with a dominant allele of the gene are black, and those homozygous for a recessive allele are light. Populations of moths living in polluted forests have a higher frequency of the dominant allele; populations in clean forests have a higher frequency of the recessive allele.

The graph shows the number of birds (out of 977) that survived a breeding season. Compare Figure 13.4C. Left, JMx Images/Shutterstock.com

Stabilizing Selection in the Sociable Weaver Most populations are at least fairly well adapted to their environments, so stabilizing selection is thought to be the most common form of natural selection. Consider how environmental pressures maintain intermediate body mass in populations of birds called sociable weavers that build large communal nests in the African savanna. Between 1993 and 2000, Rita Covas and her colleagues investigated selection pressures that operate on sociable weaver body mass, which has a genetic basis. The results of this study indicated that optimal body mass in sociable weavers is a trade-off between the risks of starvation and predation. Big birds are less likely to starve than small birds, but they also spend more time eating, which in this species means foraging in open areas where they are easily accessible to predators. Big birds are also more attractive to predators and not as agile when escaping. Thus, predators are agents of selection that eliminate the biggest individuals. Intermediate body size is an adaptive trait in this environment, so medium-sized birds make up the bulk of sociable weaver populations (Figure 13.7).

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248  Unit 3 EVOLUTION AND DIVERSITY

Disruptive Selection in the Black-Bellied Seedcracker 

lower bill 12 mm wide

lower bill 15 mm wide

Figure 13.8  Bill size dimorphism in black-bellied seedcrackers. Competition for scarce food during dry seasons favors birds with bills that are either 12 millimeters wide (left) or 15 to 20 millimeters wide (right). Birds with bills of intermediate size are selected against. © Thomas Bates Smith

Disruptive selection maintains a dimorphism in black-bellied seedcrackers, colorful birds native to Cameroon, Africa. The beak (bill) of a typical black-bellied seedcracker, male or female, is either 12 millimeters wide, or 15 to 20 millimeters wide (Figure 13.8). Birds with a bill size between 12 and 15 millimeters are uncommon. It is as if every human adult were 4 feet or 6 feet tall, with no one of intermediate height. Large-billed and small-billed African seedcrackers inhabit the same geographic range, and they breed randomly with respect to bill size. The dimorphism has a genetic basis, and it is maintained by environmental factors that affect feeding performance. The birds feed mainly on the seeds of two types of grasslike plants. One plant produces hard seeds; the other produces soft seeds. Small-billed birds are better at opening the soft seeds, but large-billed birds are better at cracking the hard ones. Both hard and soft seeds are abundant during Cameroon’s semiannual wet seasons. At these times, all seedcrackers feed on both seed types. During the region’s dry seasons, the seeds become scarce. As competition for food intensifies, each bird focuses on eating the seeds that it opens most efficiently: Small-billed birds feed mainly on soft seeds, and large-billed birds feed mainly on hard seeds. Birds with intermediate-sized bills cannot open either type of seed as efficiently as the other birds, so they are less likely to survive the dry seasons.

Take-Home Message 13.3 ●●

●●

●● ●●

●●

Natural selection drives microevolution. By operating on different forms of a shared trait, natural selection affects the frequency of alleles associated with the trait. Natural selection can occur in different patterns depending on the organisms and environmental pressures. With directional selection, a form of a trait at one end of a range of variation is adaptive. With stabilizing selection, an intermediate form of a trait is maintained, and extreme forms are eliminated. With disruptive selection, an intermediate form of a trait is eliminated, and extreme forms are maintained.

13.4  Natural Selection and Diversity Learning Objectives ●●

Use examples to explain sexual selection and its outcomes.

●●

Describe a balanced polymorphism and how it can be maintained.

●●

Explain why a harmful allele can persist at high frequency in a population.

Survival of the Sexiest 

sexual selection  Type of natural selection in which some individuals outreproduce others of a population because they are better at securing mates.

Not all evolution is driven by selection for traits that enhance survival. Competition for mates is another selective pressure that can shape form and behavior. Consider how individuals of many sexually reproducing species have a distinct male or female phenotype (a trait that differs between males and females is called a sexual dimorphism). Individuals of one sex are more colorful, larger, or more aggressive than individuals of the other sex. These traits can seem puzzling because they take energy and time away from activities that enhance survival, and some actually hinder an individual’s ability to survive. Why, then, do they persist?

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Processes of Evolution  Chapter 13  249  

The answer is sexual selection, a type of natural selection in which the evolutionary winners outreproduce others of a population because they are better at securing mates. With sexual selection, adaptive traits help individuals defeat rivals for mates, or are most attractive to the opposite sex. For example, the females of some species cluster in defensible groups when they are sexually receptive, and males compete for sole access to the groups. Competition for the ready-made harems favors brawny, combative males (Figure 13.9A). Males or females that are choosy about mates act as selective agents on their own species. The females of some species shop for a mate among males that display species-specific cues such as a highly specialized appearance or courtship behavior (Figure 13.9B). The cues often include flashy body parts or movements, traits that tend to attract predators and in some cases are a physical hindrance. However, in terms of reproductive success, the ability to command the sexual attention of females can offset a survival handicap imposed by flashiness. Selected males pass alleles for their attractive traits to the next generation of males, and females pass alleles that influence mate preference to the next generation of females. Highly exaggerated traits can be an evolutionary outcome (Figure 13.9C).

A. These male elephant seals are engaged in bloody combat. Males of this species compete fiercely for access to clusters of females.

Maintaining Multiple Alleles  The following examples illustrate how natural selection may maintain two or more alleles at relatively high frequency in a population’s gene pool, a state called balanced polymorphism. Eye Color in Fruit Flies  Sexual selection maintains multiple alleles that govern eye color in populations of Drosophila fruit flies. Female flies prefer to mate with males whose eye color is unusual in the population. When white-eyed males are uncommon, they leave more offspring than red-eyed males. Once white-eyed males become more common than red-eyed males, red-eyed males are preferred. Sickle Cell Anemia and Malaria  Balanced polymorphisms often occur in environments that favor heterozygous individuals. Consider the gene that encodes the beta globin chain of hemoglobin (Section 8.6). HbA is the normal allele; people homozygous for the HbS allele have sickle-cell anemia. Without treatment, the vast majority of these individuals die in early childhood, an outcome of body damage caused by the abnormal sickle shape of their red blood cells. Despite being so harmful, the HbS allele persists at very high frequency among the human populations in tropical and subtropical regions of Asia, Africa, and the Middle East. Why? Populations with the highest frequency of the HbS allele also have the highest incidence of malaria. Mosquitoes transmit Plasmodium, the parasitic protist that causes malaria, to human hosts. Plasmodium multiplies in the liver and then in red blood cells, which rupture and release new parasites during recurring bouts of severe illness. The HbA and HbS alleles are codominant, so heterozygous people make both normal and sickle hemoglobin. Red blood cells of these individuals can sickle under some circumstances, but not enough to cause severe symptoms. One of the circumstances under which sickling occurs is infection with Plasmodium. The abnormal shape brings infected cells to the attention of the immune system, which destroys them along with the parasites they harbor. The action of the immune system can prevent the infection from spreading to other red blood cells, so heterozygous individuals are more likely to survive malaria than individuals homozygous for the normal HbA allele. Plasmodium-infected red blood cells of people who

B. A male bird of paradise engaged in a flashy courtship display has caught the eye (and, perhaps, the sexual interest) of a female. Females are choosy; a male mates with any female that accepts him.

C. Mating stalk-eyed flies. Females of this species prefer to mate with males that have the longest eyestalks, a trait that provides no known selective advantage other than sexual attractiveness. Figure 13.9  Sexual selection in action. (A) Jeremy Richards/Shutterstock.com; (B) Tim Laman/National Geographic Image Collection; (C) Minden Pictures/Superstock

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250  Unit 3 EVOLUTION AND DIVERSITY

Gabon

A. Distribution of people who have one HbS allele. Yellow indicates regions where more than 10 percent of the population are heterozygous for the allele. White indicates regions where less than 10 percent of the population are carriers.

make only normal hemoglobin do not sickle, so the parasite may remain hidden from the immune system. In areas where malaria is common, the persistence of the HbS allele is a matter of relative evils. Malaria and sickle-cell anemia are both potentially deadly. Heterozygous individuals may not be completely healthy, but they do have a better chance of surviving malaria than people homozygous for the normal allele (HbA/HbA). With or without malaria, people who have both alleles (HbA/HbS) are more likely to live long enough to reproduce than individuals homozygous for the sickle allele (HbS/HbS). Thus, populations native to malaria-ridden regions of the world tend to have a high proportion of people heterozygous for the HbS allele (Figure 13.10).

Take-Home Message 13.4 ●●

●●

Sexual selection is a form of natural selection in which adaptive traits offer an advantage in securing mates. It can result in exaggerated form or behavior. Environmental pressures that favor heterozygous individuals can maintain a balanced polymorphism.

13.5  Nonselective Evolution Gabon

Learning Objectives ●●

B. Distribution of malaria cases. Yellow indicates regions where more than 30 percent of the population have malaria. In the white regions, less than 30 percent of the population have the disease. Figure 13.10  Frequency of the HbS allele and incidence of malaria in Gabon, Africa, in 2014.

fixed  Refers to an allele for which all members of a population are homozygous. founder effect  After a small group of individuals found a new population, allele frequencies in the new population differ from those in the original population. genetic drift  Change in allele frequency due to chance alone. population bottleneck  Reduction in population size so severe that it reduces genetic diversity.

With suitable examples, explain how allele frequency can change independently of natural selection.

●●

Explain why smaller populations are more vulnerable to the loss of genetic diversity.

●●

Describe the way gene flow stabilizes allele frequency.

Natural selection is a major driver of evolution, but it is not the only one. Other evolutionary mechanisms operate without respect to adaptive traits.

Genetic Drift  Members of a natural population survive and reproduce with differing success, and the differences are not always an outcome of natural selection. By chance, a perfectly fit and healthy individual may not pass its alleles to offspring, for example by dying in a random event before the opportunity to reproduce arises. Such events can change a population’s allele frequencies. Change in allele frequency brought about by chance alone is called genetic drift (Figure 13.11A). Genetic drift occurs in all populations, but it makes small populations particularly vulnerable to the loss of genetic diversity (Figure 13.12). To understand why, imagine a hypothetical gene with two alleles, neither of which confers a selective advantage. These alleles (let’s call them A and a) occur at a frequency of 95 percent and 5 percent, respectively. In a population with 10 members, one individual would be heterozygous (Aa), and the remaining nine would be homozygous (AA). A random event that eliminates the heterozygous individual from the population before it reproduces also eliminates allele a from the population’s gene pool. If this occurs, the other allele (A) becomes fixed, which means all individuals of the population are homozygous for it. A fixed allele remains that way until a new mutation occurs, or an individual bearing another allele enters the population. Now imagine that our population with alleles A and a consists of 100 members instead of 10. Five individuals in this larger population would be heterozygous (Aa).

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Processes of Evolution  Chapter 13  251  

For allele a to be lost from the population’s gene pool, all five would have to be eliminated before they reproduce. The chance of random events eliminating all heterozygous individuals is smaller in the larger population. This is a simplified example of a general effect: The loss of genetic diversity is possible in all populations, but it is more likely to occur in small ones.

A. Genetic drift. Allele frequency changes because of a random event. In this example, the two individuals who have an allele (red) are eliminated from the population.

Population Bottlenecks   A population bottleneck is a drastic reduction in population size, and it can reduce the population’s genetic diversity (Figure 13.11B). Consider how overhunting during the late 1890s left only about 10 northern elephant seals alive. Since then, hunting restrictions have allowed the population to recover, but genetic diversity among its members remains greatly reduced. The bottleneck and subsequent genetic drift eliminated many alleles. Every gene that has been tested in these animals was affected.

B. Bottleneck. A severe reduction in population size alters allele frequency.

The Founder Effect A loss of genetic diversity can also occur when a small group of individuals establishes a new population. If the founding group is not representative of the original population in terms of allele frequencies, then the new population will not be representative of it either. This outcome is called the founder effect (Figure 13.11C). Consider the ABO alleles for blood type that you learned about in Section 10.4. All three alleles of this gene are common in most human populations. Native Americans are an exception, with the majority of individuals being homozygous for the O allele. Native Americans are descendants of early humans that migrated from Asia between 14,000 and 21,000 years ago, across a narrow land bridge that once connected Siberia and Alaska. Analysis of DNA from ancient skeletal remains reveals that most early Americans were also homozygous for the O allele. Modern Siberians have all three alleles. Thus, the humans who first populated the Americas were probably members of a small group that had reduced genetic diversity compared with the general population.

C. The founder effect. A group that founds a new population is not genetically representative of the original population, so allele frequencies differ between the new and the old populations. Figure 13.11  Some evolutionary processes that do not involve natural selection.

Figure 13.12  Genetic drift in flour beetle populations (a flour beetle is shown at left on a flake of cereal). Twelve populations of beetles heterozygous for alleles b+ and b were maintained for 20 generations. In one experiment (A), each population consisted of 10 individuals; in another (B), each population consisted of 100 individuals. Graph lines in B are smoother than in A, which means that less genetic drift occurred in the larger populations. Notice that the average frequency of allele b+ rose at the same rate in both groups, an indication that natural selection was at work too: Allele b+ was weakly favored. Photo, Peggy Greb/USDA

100% Frequency of b+ allele

Frequency of b+ allele

100%

50%

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A. In these experiments, population size was maintained at 10 beetles. Allele b became fixed in one population; allele b+ became fixed in six others.

50%

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20

B. In these experiments, population size was maintained at 100 beetles. Genetic drift was less pronounced in these populations than in the 10-beetle populations in A. Neither allele became fixed.

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252  Unit 3 EVOLUTION AND DIVERSITY

Inbreeding Small founding populations and those that have undergone a severe bottleneck are necessarily inbred. Inbreeding is breeding or mating between close relatives, and it can have negative effects on a population with low genetic diversity. Closely related individuals tend to share more harmful recessive alleles than nonrelatives, and inbreeding increases the likelihood that an individual will inherit the same harmful allele from both parents. Thus, inbred populations often have an unusually high incidence of genetic disorders. This outcome is minimized in human populations that discourage or forbid incest (mating between parents and children or between siblings). The Old Order Amish in Lancaster County, Pennsylvania, offer an example of the effects of inbreeding. Amish people marry only within their community. Intermarriage with other groups is not permitted, and no “outsiders” are allowed to join the community. As a result, Amish populations are moderately inbred, and many of their individuals are homozygous for harmful recessive alleles. The Lancaster community has an unusually high frequency of a recessive allele that causes Ellis–van Creveld syndrome, a genetic disorder characterized by dwarfism, heart defects, and polydactyly (extra fingers or toes), among other symptoms. This allele has been traced to a man and his wife, two of a group of 400 Amish people who immigrated to the United States in the mid-1700s. As a result of the founder effect and inbreeding since then, about 1 of 8 people in the Lancaster community is now heterozygous for the allele, and 1 in 200 is homozygous (Figure 13.13). Figure 13.13  Ellis–van Creveld syndrome. An allele that causes this genetic disorder occurs at high frequency in the gene pool of the Lancaster Amish—a result of the founder effect and moderate inbreeding since then. Outward indications of the disorder (polydactyly and dwarfism) appear in this Amish baby. © Dr. Victor A. McKusick

Gene Flow  Individuals tend to mate or breed most frequently with other members of their own population. However, not all populations of a species are completely isolated from one another, and nearby populations may interbreed. Also, individuals sometimes leave one population and join another. Gene flow, the movement of alleles between populations, occurs in both cases. Gene flow can keep populations genetically similar. By stabilizing allele frequencies, it counters genetic drift. Gene flow is common among populations of animals, but it also occurs in less mobile organisms. Consider acorns dispersed by jays gathering nuts for the winter. Every fall, these birds visit acorn-bearing oak trees repeatedly, then bury the acorns in the soil of territories as much as a mile away. The jays transfer acorns (and the alleles carried by these seeds) among populations of oak trees that may otherwise be genetically isolated. Gene flow also occurs when wind or an animal transfers pollen from one plant to another, and this can occur over great distances. Many opponents of genetic engineering cite the movement of engineered genes from transgenic crop plants into wild populations via pollen.

Take-Home Message 13.5 ●● ●●

gene flow  The movement of alleles between populations.

●●

inbreeding  Mating among close relatives. reproductive isolation  The end of gene flow between populations.

●●

Evolution can occur by mechanisms that do not involve natural selection. Genetic drift, or change in allele frequency that occurs by chance alone, makes small populations particularly vulnerable to the loss of genetic diversity. Loss of genetic diversity can be the result of a population bottleneck or the founder effect. Gene flow stabilizes allele frequencies between populations, so it counters genetic drift.

speciation  Emergence of a new species.

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Processes of Evolution  Chapter 13  253  

Learning Objectives ●●

Describe speciation in terms of reproductive isolation.

●●

Use examples to explain two models by which speciation occurs.

With divergent evolution, lineages descended from a common ancestor evolve in different ways (Section 12.6). When two populations of a species do not interbreed, the number of genetic differences between them increases because mutation, natural selection, and genetic drift occur independently in each gene pool. Over time, the populations may become so different that we consider them to be different species. The emergence of a new species—the splitting of one lineage into two—is called speciation. Evolution is a dynamic, extravagant, messy, and ongoing process that can be challenging for people who like clear categories. Speciation offers a perfect example, because it rarely occurs at a precise moment in time. Populations often continue to interbreed even as they are diverging, and populations that have already diverged may come together and interbreed again. As you learn about speciation, remember that it occurs in a continuum of geographic, genetic, and ecological contexts. Categories are useful as models, but the relationship between pattern and process is rarely simple.

Reproductive Isolation  Every time speciation happens, it happens in a unique way, which means that each species is a product of a unique set of evolutionary events. However, reproductive isolation, the end of gene flow between populations, is always part of the process by which sexually reproducing species achieve and maintain separate identities. Several mechanisms of reproductive isolation prevent successful interbreeding, and thus reinforce differences between diverging populations (Figure 13.14).

Gerry Bishop/Shutterstock.com

2265524729/Shutterstock.com

Temporal Isolation  Differences in the timing of repro-

duction can prevent interbreeding. Consider the periodical cicada (left). Larvae of these insects feed on roots as they mature underground, then the adults emerge to reproduce. Three cicada species reproduce every 17 years. Each has a sibling species with nearly identical form and behavior, except that the siblings emerge on a 13-year cycle instead of a 17-year cycle. Sibling species have the potential to interbreed, but they can only get together once every 221 years!

Ecological Isolation  Adaptation to life in different environments can prevent interbreeding. For example, populations of pea aphids (left) living on red clover plants do not interbreed with populations living on alfalfa plants, even if the two types of plants are closely intermingled. Individual aphids that migrate to a different plant species have a low survival rate, so these sap-sucking insects reproduce exclusively on plants where they are born. As another example, two species of manzanita, a plant native to the Sierra Nevada

CLOSER LOOK Figure 13.14  How reproductive isolation prevents interbreeding. Different species form and . . . Reproduction occurs at different times (temporal isolation). Living in different environments prevents meeting up for sex (ecological isolation). Cues required for sex differ (behavioral isolation).

Physical incompatibilities prevent sex (mechanical isolation). Mating occurs and . . . Fertilization does not occur (gamete incompatibility). Zygotes form and . . . Hybrid individuals or their offspring have reduced fitness (hybrid inviability). Hybrid individuals cannot produce offspring (hybrid sterility). Interbreeding is successful

Figure Summary The details of speciation differ every time it occurs, but reproductive isolation is always part of the process. Several mechanisms prevent interbreeding between populations. Most occur before zygotes form. Figure It Out: In how many of these mechanisms are offspring produced?

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Answer: Two

13.6  Speciation

254  Unit 3  EVOLUTION AND DIVERSITY

Figure 13.15  Courtship displays in peacock spiders. This male peacock spider is signaling his intent to mate with the female by raising and waving colorful flaps, and moving his legs in time with abdominal vibrations. If his species-specific courtship display fails to impress her, she may eat him. © Jürgen Otto

Mountain range, rarely hybridize. One species that lives on dry, rocky hillsides is better adapted for conserving water. The other species, which requires more water, lives on lower slopes where water stress is not as intense. The physical separation makes cross-pollination rare. Behavioral Isolation  Differences in behavior can prevent interbreeding, for

example when specific cues required for sex are not recognized by members of other species. Species-specific physical traits such as coloration and patterning are typical cues. Males and females of many animal species also engage in courtship displays. In a typical pattern, the female recognizes the sounds and movements of a male of her species as an overture to sex (Figure 13.15).

A. Black sage is pollinated mainly by honeybees and other small insects that touch the reproductive parts of the flowers as they sip nectar.

Mechanical Isolation  Differences in the size or shape of reproductive parts may

prevent interbreeding. For example, closely related species of damselflies cannot interbreed because anatomical differences in mating structures prevent males from grasping females of other species. As another example, two closely related species of sage plants grow in the same areas, but their flowers are specialized for different pollinators, so cross-pollination rarely occurs and hybrids rarely form (Figure 13.16). Gamete Incompatibility  Even if gametes of different species do meet up, they often

have molecular incompatibilities that prevent a zygote from forming. For example, the molecular signals that trigger pollen germination in flowering plants differ by species (we return to flowering plant reproduction in Section 29.3). Gamete incompatibility may be the primary speciation route among animals that release their eggs and free-swimming sperm into water. B. The flowers of black sage are too delicate to support larger insects. Big insects such as this carpenter bee access the nectar of small sage flowers by piercing from the outside. When they do so, they avoid touching the flower’s reproductive parts. Figure 13.16   Pollinator specialization in sage. (A) Courtesy of Dr. James French; (B) Courtesy of Ron Brinkmann, www.flickr.com/photos /ronbrinkmann

Hybrid Inviability  Hybrid offspring form in some cases, but most have reduced fit-

ness. Chromosomes of species that diverged even recently may be different enough that a hybrid zygote ends up with extra or missing genes, or genes with incompatible products. Such outcomes typically disrupt embryonic development. Hybrid individuals that do survive embryonic development often have reduced fitness. For example, hybrid offspring of lions and tigers have more health problems and a shorter life expectancy than individuals of either parent species. If hybrids live long enough to reproduce, their offspring often have lower fitness with each successive

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generation. Incompatible nuclear and mitochondrial DNA may be the cause (mitochondrial DNA is inherited from the mother only).

allopatric speciation  Speciation pattern in which a physical barrier arises and ends gene flow between populations.

Hybrid Sterility  Some interspecies matings produce robust but sterile hybrid offspring. For example, mating between a female horse (64 chromosomes) and a male donkey (62 chromosomes) produces a mule (63 chromosomes: 32 from the horse, and 31 from the donkey). Mules are healthy, but their chromosomes cannot pair up properly for crossing over during meiosis, so this animal makes few viable gametes.

Allopatric Speciation  Reproductive isolation sometimes begins when a physical barrier arises between members of a population and interrupts gene flow between them. Whether the barrier slows or prevents gene flow depends on the barrier and the species—how it travels (such as by swimming, walking, or flying), and how it reproduces (for example, by internal fertilization or by pollen dispersal). If gene flow is sufficiently hampered, genetic changes accumulate independently in the two new populations. The divergences may cause the populations to remain reproductively isolated even if the barrier is removed. This pattern, in which speciation occurs after a physical barrier interrupts gene flow between populations, is called allopatric speciation. A geographic barrier can arise in an instant, or over an eon. The Great Wall of China is an example of a barrier that arose abruptly. When it was built about 600 years ago, the wall interrupted gene flow among nearby populations of insectpollinated plants. Today, genetic divergences are occurring between populations of plants living on opposite sides of the wall. Other barriers to gene flow arose over much longer periods of time. For example, it took millions of years of tectonic plate movements to bring the two continents of North and South America close enough to collide. The land bridge where the two continents now connect is called the Isthmus of Panama. When this isthmus formed about 3 million years ago, it cut off the flow of water—and gene flow among populations of aquatic organisms—as it separated one large ocean into what are now the Pacific and Atlantic Oceans. Pacific and Atlantic populations of many of these organisms diverged so much that they are now reproductively isolated, separate species (Figure 13.17).

Figure 13.17  Example of allopatric speciation.

Atlantic Ocean

Mexico

When the Isthmus of Panama formed about 3 million years ago, it cut off gene flow among ocean-dwelling populations of snapping shrimp. Alpheus nuttingi (Atlantic)

Isthmus of Panama

Ocean

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1500

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Colombia

Alpheus millsae (Pacific)

Today, shrimp species on opposite sides of the isthmus are so similar that they might interbreed, but they are reproductively isolated. Instead of mating when they are brought together, they snap their claws at one another aggressively. The photos show two of the many closely related species that live on opposite sides of the isthmus. Right, © Arthur Anker.

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256  Unit 3 EVOLUTION AND DIVERSITY

ancestral species

Triticum urartu AA

Aegilops speltoides BB

1

Male Pundamilia nyererei. This species breeds in deep water, where the ambient light is reddish.

Male Pundamilia pundamilia. This species breeds in shallow water, where the ambient light is mainly blue.

Figure 13.19  Red fish, blue fish: Sympatric speciation of Lake Victoria cichlids.

2 Triticum turgidum AABB

Aegilops tauschii DD

Mutations that affect female cichlids’ perception of the color of ambient light in deeper (red) or shallower (blue) regions of the lake also affect their choice of mates. Female cichlids prefer to mate with males that they perceive to be most brightly colored. The outcome of this sexual selection: Species that inhabit different regions of the lake match the color of ambient light. Two of hundreds of species are pictured. Kevin Bauman, www.african-cichlid.com.

3

Sympatric Speciation  In a pattern called sympatric speciation, genetic changes that lead to reproductive isolation occur within a single population, in the absence of a physical barrier to gene flow.

Triticum aestivum AABBDD

Figure 13.18  Sympatric speciation in wheat. The wheat genome occurs in several slightly different forms: A, B, D, and so on.

1  About 5.5 million years ago, a diploid (2n) einkorn

grass, Triticum urartu (AA), hybridized with a diploid goatgrass, Aegilops speltoides (BB). The union produced diploid A. tauschii (DD).

2  A few million years later, the same two parental spe-

cies hybridized again, this time producing the tetraploid (4n) emmer wheat T. turgidum (AABB).

3  Our hexaploid (6n) bread wheat, T. aestivum

(AABBDD), is the offspring of a hybridization between T. turgidum (AABB) and A. taushii (DD). The match is shown for scale.

Photos by © J. Honegger, courtesy of S. Stamp, E. Merz, www.sortengarten/ethz.ch.

Wheat  Sympatric speciation after chromosome number changes is a common way for plants to speciate. Individuals of different taxa sometimes hybridize, and the offspring of the union inherit all of the chromosomes of both parents. Our common bread wheat, Triticum aestivum, arose this way. T. aestivum is hexaploid (6n), having inherited its three distinct sets of chromosomes by way of multiple hybridizations between grasses of different genera (Figure 13.18). African Cichlids  More than 500 species of cichlid fishes arose by sympatric speciation in the shallow waters of Lake Victoria. This large freshwater lake sits isolated from river inflow on an elevated plain in Africa’s Great Rift Valley. Lake Victoria has dried up completely several times during its 400,000-year history. DNA sequence comparisons indicate that almost all of the cichlid species in this lake arose since it was last dry, about 12,400 years ago. How could 500 species of fish arise so quickly in the same body of water? In this case, the answer involves sexual selection. Consider how the color of ambient light differs in different parts of a lake. The light in the lake’s shallower, clear water is mainly blue; light that penetrates the deeper, muddier water is redder. Cichlid species vary in color (Figure 13.19). Female cichlids prefer to mate with brightly colored males. Their preference has a genetic basis, in alleles that encode light-sensitive pigments of the retina (part of the eye). Retinal pigments made by species that live mainly in shallow areas of the lake are more sensitive to blue light. The males of these species are also the bluest. Retinal pigments made by species that prefer deeper areas of the lake are more sensitive to red light. Males of these species are redder. In other words, the colors that a female cichlid sees best are the same colors displayed by males of her species. This is unlikely to be a coincidence. Mutations

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that affect color perception would affect a female’s choice of mates, so they are probably the way sympatric speciation occurs in cichlids.

Take-Home Message 13.6 ●●

●●

●●

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Populations that are not interbreeding diverge genetically. The divergences may result in different species. Speciation occurs within a continuum of geographic, ecological, and genetic contexts, but reproductive isolation is always part of the process in sexual reproducers. With allopatric speciation, a physical barrier arises and interrupts gene flow between two populations. The populations then diverge genetically and become different species. Sympatric speciation occurs with no barrier to gene flow; genetic divergence within a population leads to reproductive isolation.

macroevolution  Patterns of evolutionary change in taxa above the species level. sympatric speciation  Speciation pattern in which genetic divergence within a population leads to reproductive isolation; occurs in the absence of a physical barrier to gene flow.

13.7  Macroevolution Learning Objectives ●●

Explain the difference between microevolution and macroevolution.

●●

Use examples to describe some patterns of macroevolution.

Macroevolutionary Patterns Microevolution is change in allele frequency within a population. Macroevolution refers to patterns of evolutionary change that we see in higher taxa. Patterns of macroevolution include large-scale trends such as land plants evolving from green algae, the disappearance of the dinosaurs, and so on. Stasis  Very little change occurs in some lineages over a very long period of time.

Consider coelacanths, an ancient order of lobe-finned fish. In its unique form and other traits, modern coelacanth species are similar to fossil specimens hundreds of millions of years old (Figure 13.20).

Notochord

This tough, elastic tube, which is partially hollow and filled with fluid, is ancestral to the spinal cord.

Lobed fins

These fleshy fins retain a few of the ancestral bones that gave rise to legs and arms in other lineages.

Figure 13.20  The coelacanth, a living fossil. Until a fisherman caught one in 1938, coelocanths were thought to have become extinct 70 million years ago. Left, compare a 320-million-year-old fossil found in Montana with a live fish. Right, a few of the coelacanth’s unusual features that have been lost in almost all other fish lineages over evolutionary time. Top left, Courtesy of The Virtual Fossil Museum/www.fossilmuseum.net; bottom left, Alessandro Zocc/Shutterstock.com; right, Raul Martin Domingo/National Geographic Image Collection

Long gestation

Coelacanths give birth to litters of up to 26 fully developed “pups” after gestation of more than a year.

Rostral organ

A sensory organ that responds to electrical impulses in water, it probably helps the fish locate prey in dark ocean depths.

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258  Unit 3 EVOLUTION AND DIVERSITY

'Akepa (Loxops coccineus)

Nihoa finch (Telespiza ultima )

'Akikiki (Oreomystis bairdi)

‘Alawi (Loxops mana)

'I'iwi (Drepanis coccinea)

'Akohekohe (Palmeria dolei)

'Apapane (Himatione sanguinea)

'Akiapola'au (Hemignathus wilsoni)

Kiwikiu (Pseudonestor xanthophrys)

Maui 'Alauahio (Paroreomyza montana)

Kaua'i 'Amakihi (Chlorodrepanis stejnegeri)

Hawai'i 'Amakihi (Chlorodrepanis virens)

Figure 13.21  Adaptive radiation of Hawaiian honeycreepers. The photos above show a small sampling of the unique traits that adapt each Hawaiian honeycreeper species to life in a particular part of the archipelago. All Hawaiian honeycreepers are descended from Eurasian rosefinches (below) that were blown to the Hawaiian archipelago (right) by a massive storm about 7 million years ago. Thousands of miles of open ocean prevented gene flow with mainland populations, and the birds’ descendants diverged into hundreds of new species.

Hawaiian archipelago

Top from left: US Fish and Wildlife Service; Jack Jeffrey Photography; Eric VanderWerf; Carter T. Atkinson/U.S. Geological Survey; Jim Denny; Douglas Peebles Photography/Alamy Stock Photo; Eric VanderWerf; Jack Jeffrey/Minden Pictures; Maui Forest Bird Recovery Project; Jack Jeffrey Photography; Eric VanderWerf; James A. Hancock/Science Source; Bottom: Andrzej Sliwinski/Shutterstock.com

Rosefinch (Carpodacus)

Adaptive Radiations  With adaptive radiation, one lineage rapidly diversifies into multiple species. Adaptive radiation can occur after a geologic or climatic event that eliminates some species from a habitat; species that survive the event then have access to resources from which they had previously been excluded. For example, the disappearance of the dinosaurs 66 million years ago in the aftermath of an asteroid impact (Section 12.1) allowed mammals to undergo a spectacular adaptive radiation. Adaptive radiation can also occur after a population colonizes a new environment that has a variety of different habitats and few competitors. Multiple speciations occur as adaptations to the different habitats evolve. The Hawaiian honeycreepers arose this way; all are descendants of a Eurasian rosefinch (Figure 13.21). Rosefinches can migrate far outside of their normal range when food becomes scarce in a preferred overwintering spot, traveling in flocks of thousands or even tens of thousands of individuals. About 7 million years ago, one of these flocks was migrating through southern Asia when it became caught in the winds of a huge

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Processes of Evolution  Chapter 13  259  

storm. The birds were blown at least 6,000 miles (9,600 kilometers) across the open ocean to the Hawaiian archipelago. Enough individuals survived the journey to found a new population. The birds’ arrival had been preceded by insects and plants, but no bird-eating predators, so their descendants thrived. Isolated from gene flow with mainland bird populations, the island colonizers diverged. Local environments on the Hawaiian islands vary dramatically: from lava beds, rain forests, and grasslands to dry woodlands and snowcapped peaks. Selection pressures differ within and between these habitats, and, over many generations, populations of birds living in the different environments became hundreds of separate species. Key Innovations  Adaptive radiation may occur after a key innovation evolves. A key innovation is an adaptive trait that allows its bearer to exploit its environ-

ment more efficiently or in a novel way. The evolution of lungs offers an example, because lungs were a key innovation that opened the way for an adaptive radiation of vertebrates on land.

A. This Myrmica sabuleti ant is stroking a Maculinea arion caterpillar. The beguiled ant is preparing to carry the honey-exuding, hunched-up caterpillar back to its nest, where the caterpillar will feed on ant larvae for the next 10 months until it becomes a pupa.

Repurposing  Major evolutionary novelties often stem from the adaptation of an

existing structure for a completely new purpose. The feathers that allow modern birds to fly, for example, are derived from dinosaur feathers, which could not have sustained flight when they first evolved. The earliest feathers probably served as insulation, and may have been useful for courtship displays or camouflage. Extinctions  By current estimates, more than 99 percent of all species that ever lived are now extinct, which means they no longer have living members. In addition

to ongoing extinctions of individual species, the fossil record indicates that there have been more than 20 mass extinctions, which are simultaneous losses of many lineages. These include five catastrophic events in which the majority of species on Earth disappeared (see Figure 12.17).

Coevolution  Two species that have close ecological interactions may evolve jointly, a pattern called coevolution. One species acts as an agent of selection on the other,

and each adapts to changes in the other. Over evolutionary time, the two species may become so interdependent that they can no longer survive without one another. Relationships between coevolved species can be quite intricate. Consider the large blue butterfly (Maculinea arion), a parasite of ants. After hatching, the butterfly larvae (caterpillars) feed on wild thyme flowers and then drop to the ground. An ant that finds a caterpillar strokes it, which makes the caterpillar exude honey. The ant eats the honey and continues to stroke the caterpillar, which secretes more honey. This interaction continues for hours, until the caterpillar suddenly hunches itself up into a shape that appears (to an ant) very much like an ant larva (Figure 13.22). The deceived ant then carries the caterpillar back to its nest, where, in most cases, other ants kill it—except if the ants are of the species Myrmica sabuleti. The caterpillar secretes the same chemicals as Myrmica sabuleti larvae, and makes the same sounds as their queen—behaviors that trick the ants into adopting the caterpillar and treating it better than their own larvae. The adopted caterpillar feeds on ant larvae for about 10 months, then undergoes metamorphosis, changing into a butterfly that emerges from the ground to mate. Eggs are deposited on wild thyme near another M. sabuleti nest, and the cycle starts anew. This relationship between ant and butterfly is typical of coevolved species in that it is extremely specific. Any increase in the ants’ ability to identify a

B. Maculinea arion butterflies emerge from pupae to feed, mate, and lay eggs on wild thyme flowers. Larvae that hatch from the eggs will survive only if a colony of Myrmica sabuleti ants adopts them. Figure 13.22  Coevolved species: butterfly and ant. (A) Natural Visions; (B) Roger Meerts/Shutterstock.com

adaptive radiation  Macroevolutionary pattern in which a lineage undergoes a rapid burst of genetic divergences that gives rise to many species. coevolution  The joint evolution of two closely interacting species; each species is a selective agent for traits of the other. extinct  Refers to a species that no longer has living members. key innovation  An evolutionary adaptation that gives its bearer the opportunity to exploit its environment more efficiently or in a new way.

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260  Unit 3 EVOLUTION AND DIVERSITY

caterpillar in their nest selects for caterpillars that better deceive the ants, which in turn select for ants that can better identify the caterpillars. Each species exerts directional selection on the other.

Evolutionary Theory  Biologists do not doubt that macroevolution occurs, but many disagree about how it occurs. However we choose to categorize evolutionary processes, the very same genetic change may be at the root of all evolution—fast or slow, large-scale or smallscale. Dramatic jumps in form, if they are not artifacts of gaps in the fossil record, may be the result of mutations in master regulators (Section 8.7). Macroevolution may include more processes than microevolution, or it may not. It may be an accumulation of many microevolutionary events, or it may be an entirely different process. Evolutionary biologists may disagree about these and other hypotheses, but all of them are trying to explain the same thing: how all species are related by descent from common ancestors.

Take-Home Message 13.7 ●●

●●

●●

Macroevolution includes evolutionary trends and patterns that we see in taxa above the species level. A key innovation or mass extinction can lead to adaptive radiation, a pattern in which one lineage rapidly diversifies into many. Two species with close ecological interactions may evolve jointly, a pattern called coevolution.

13.8  Phylogeny Learning Objectives ●●

Explain the difference between a trait and a derived trait.

●●

Describe cladistics, and compare it to Linnaean taxonomy.

Reconstructing Evolutionary History Today’s biologists work from the premise that all species are related if you look back far enough in time. Grouping species according to evolutionary relationships is a way to fill in the details of this bigger picture of evolution. Thus, reconstructing phylogeny, the evolutionary history of a species or a group of species, is a priority. Phylogeny is a kind of genealogy that follows evolutionary relationships. Derived Traits  Humans were not around to witness the evolution of most species, clade  A group that includes a species in which a derived trait evolved, together with all of its descendants. cladistics  Method of making hypotheses about evolutionary relationships. Involves grouping species into clades based on derived traits. cladogram  Evolutionary tree diagram that shows how a group of clades are related. phylogeny  Evolutionary history of a species or group of species.

but there is plenty of evidence to help us understand ancient evolutionary events. Consider how each species bears traces of its own unique evolutionary history in its traits. Evolutionary biologists determine common ancestry by looking for a derived trait—one that is present in a group of species under consideration, but not in any of the group’s ancestors.

Cladistics  Derived traits are central to cladistics, a method of making hypoth-

eses about evolutionary relationships. Cladistics differs from Linnaean taxonomy (Section 1.4) even though both are based on shared traits. Taxonomy is a system of naming species and categorizing them into taxa based on similarities; cladistics

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Processes of Evolution  Chapter 13  261  

focuses on the ancestral relationships that gave rise to the similarities in the first place. In cladistics, species are grouped into clades based on derived traits. A clade is a group that includes a species in which a derived trait evolved, together with all of its descendants. It is the relative newness of a derived trait that defines a clade. Consider that humans, mice, and bacteria use some of the same proteins to repair DNA, but so do almost all other organisms on Earth. Both humans and mice, however, make proteins such as keratin (a component of hair) that bacteria do not. Thus, humans and mice share a more recent ancestor than they share with bacteria. Other relationships may not be as obvious. Alligators, for example, look a lot more like lizards than birds. In this case, the similarity in appearance does indicate shared ancestry, but it is a more distant relationship than alligators have with birds. A unique set of traits that include a gizzard and a four-chambered heart evolved in the lineage that gave rise to alligators and birds, but not in the lineage that gave rise to lizards. Note that many taxa are equivalent to clades—flowering plants, for example, constitute both a phylum and a clade—but this is not always the case. For example, the traditional Linnaean class Reptilia (“reptiles”) includes crocodiles, alligators, tuataras, snakes, lizards, turtles, and tortoises, but these groups would not constitute a clade unless birds are included. Taxa that do not include all descendants of the last shared ancestor are not clades. Cladograms  A cladogram is an evolutionary tree diagram that visually summarizes a hypothesis about how a group of clades are related (Figure 13.23). Each line is a lineage, which may branch into two lineages. A branch point (node) represents a common ancestor, and the two lineages that emerge from it are called sister groups. Any complete branch that can be cut from a cladogram—including the smallest branch possible (a species)—is a clade.

earthworm tuna lizard mouse human

node sister groups

A. A line in a cladogram represents a lineage. Sister groups emerge from a node, which represents a common ancestor. earthworm

multicellular

tuna

multicellular with a backbone

lizard

multicellular with a backbone and legs

mouse

Studies of phylogeny reveal how species relate to one another and to species that are now extinct. The following examples illustrate how deciphering these evolutionary connections informs our efforts to preserve endangered species, and helps us track ongoing evolutionary processes. Conservation Biology  Hawaiian honeycreepers are so diverse in form and behav-

ior that their close evolutionary relationships remained controversial until recent DNA comparisons. More than 50 species of these colorful songbirds were thriving on the Hawaiian Islands when the first Polynesians arrived, sometime before A.D. 1000. Europeans followed in 1778. Hawaii’s rich ecosystem was hospitable to the newcomers as well as their livestock, pets, and crops. Escaped livestock began to eat and trample rain forest plants that had provided the honeycreepers with food and shelter. Entire forests were cleared to grow imported crops, and plants that escaped cultivation began to crowd out native plants. Mosquitoes accidentally introduced in 1826 spread diseases such as avian malaria from imported songbirds to native birds. Stowaway rats ate their way through populations of native birds and their eggs; mongooses deliberately imported to eat the rats preferred to eat birds and bird eggs. The isolation that had fostered the adaptive radiation of honeycreepers also made them vulnerable to extinction. Divergence from the ancestral finch species had led to the loss of unnecessary traits such as defenses against mainland predators and diseases. Traits that had been adaptive—such as a long, curved beak matching

multicellular with a backbone, legs, and hair

human

B. A cladogram can be viewed as “sets within sets” of derived traits. Each set (an ancestor together with all of its descendants) is a clade. Figure 13.23  Cladograms. A cladogram is a diagram of evolutionary connections. Any complete branch that can be “cut” from a cladogram is one clade. Top, National Geographic/SuperStock

Figure It Out: Which groups in this cladogram diverged most recently?

Answer: Human and mouse

Applications  

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262  Unit 3 EVOLUTION AND DIVERSITY

A. Palila (Loxioides bailleui ). Palila feed on seeds of a native Hawaiian plant that are toxic to most other birds. The one remaining population is declining because these plants are being trampled and eaten by domestic livestock. Between 1997 and 2018, the number of Palila dropped from 4,396 to 1,051.

the flower of a particular coevolved plant—became hindrances when the birds’ environment suddenly changed or disappeared. Today, only 18 Hawaiian honeycreeper species remain, and 16 of them are in immediate danger of extinction (Figure 13.24). Nonnative predators and competitors are an ongoing threat, as is the rise in global temperature. As Hawaii’s average temperature rises, mosquitos are expanding their range into high-altitude environments that were previously too cold for them. Mosquitos carry bird diseases such as avian malaria, so the expansion of their range has been decimating populations of high-altitude honeycreepers that had previously avoided these diseases. As honeycreeper species become extinct, the group’s reservoir of genetic diversity dwindles. The lowered diversity means the group as a whole is less resilient to change, and more likely to suffer catastrophic losses. As you will see in later chapters, the stability of a natural community depends on its biodiversity— the diversity of organisms that make it up. The disappearance of one species affects other species in the community, and may unravel it entirely. Funding for conservation efforts continues to decrease, so understanding phylogeny allows us to focus available resources on species whose extinction would have the greatest impact on biodiversity. Studying Viral Transmission  Researchers often study the evolution of viruses by

B. ‘Akeke’e (Loxops caeruleirostris). An offset lower bill allows these little green birds to pry open buds that harbor insects. Avian malaria is wiping out the last population of the species. Between 2007 and 2012, the number of ‘Akeke’e dropped from 3,536 to 945.

grouping them into clades based on biochemical traits. Even though viruses are not alive, they can mutate every time they infect a host, so their genetic material changes quickly. Consider the H5N1 strain of influenza (flu) virus, which infects birds and other animals. H5N1 has a very high mortality rate in humans, but human-to-human transmission has been rare to date. The virus replicates in pigs without causing symptoms. Pigs transmit the virus to other pigs—and apparently to humans too. A cladistic analysis of H5N1 isolated from pigs showed that the virus “jumped” from birds to pigs at least three times since 2005, and that one of the isolates had acquired the potential to be transmitted among humans. Our increased understanding of the evolutionary history of this virus is helping us develop strategies to prevent it from spreading to humans again.

Forensic Phylogenetics  In 1998, a series of people who had undergone minor sur-

C. Po’ouli (Melamprosops phaeosoma). This male— rare, old, and missing an eye—died in 2004 from avian malaria. There were two other Po’ouli alive at the time, but neither has been seen since then. Figure 13.24  Three honeycreepers: going, going, and gone. The genetic diversity of Hawaiian honeycreepers is dwindling along with their continued extinctions. Deciphering their evolutionary connections may help us preserve the remaining species. (A) Jack Jeffrey/Minden Pictures; (B) Courtesy of Lucas Behnke; (C) Bill Sparklin/Ashley Dayer

gery at a private hospital in Valencia, Spain, became infected with hepatitis C virus. A massive public health investigation revealed that all were patients of anesthesiologist Juan Maeso, who also had hepatitis C. Maeso insisted that he had contracted hepatitis C from his patients (not the other way around). Because the epidemiological evidence was circumstantial, evolutionary biologists were asked to study the case. The biologists isolated samples of the virus from 322 people thought to be infected during the outbreak. Sequencing the genome of each viral sample allowed the researchers to sort the infections into clades based on patterns of change in regions of the viral genome that mutate most frequently. They also used the known mutation rate of the virus as a molecular clock that could be used to pinpoint the time of infection. Correlating surgery dates with the cladogram allowed the biologists to determine that Maeso was responsible for infecting 275 people with hepatitis C. Just before administering morphine to his patients, Maeso had been secretly injecting himself with part of their dose, then using the same needle to inject the patients with the remainder. Phylogenetic analysis of viral strains helped convict him of malpractice. He was sentenced to 1,933 years in prison.

Tracing the Origin of Superbugs  Studies that elucidate our role in the evolution

of antibiotic-resistant bacteria are an important foundation for government and

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Processes of Evolution  Chapter 13  263  

medical policies regarding the use of antibiotics. Consider a superbug called ST131, a strain of Escherichia coli bacteria that is a major human pathogen threatening public health on a global scale. ST131 is the main pathogenic form of E. coli, causing millions of infections of the blood, lungs, urinary tract, abdominal cavity, and skin every year. It is everywhere: in companion animals and livestock; in seawater and sediments of Italian coastlines and Swiss lakes; in birds of prey in Portugal, seagulls in Sweden, and penguins in the Antarctic; and so on. Researchers sequenced the genomes of thousands of ST131 samples taken from clinical, environmental, and veterinary sources. Cladistics based on SNPs (single-nucleotide polymorphisms, Section 11.1) in the sequences revealed the stepwise evolution of the bacterial lineage as it acquired resistance to antibiotics (Figure 13.25). One ST131 subgroup called H30 is resistant to fluoroquinone antibiotics, and it emerged just after the introduction of these antibiotics in clinical medicine in the 1980s. H30 acquired resistance to cephalosporin antibiotics in the 1990s, then spread explosively around the world in the early 2000s. At the time, fluoroquinolones and cephalosporins were the standard first-line treatments for bacterial infections, especially urinary tract infections, which are typically caused by E. coli infections. Despite receiving these antibiotics, patients with urinary tract infections worsened and many died. H30 is a descendant of another ST131 subgroup called H22, which is established in poultry populations worldwide. H22 is a common contaminant of supermarket chicken and turkey. It also causes serious, invasive urinary tract infections in humans. Cladistic analysis of H22 samples suggests that these infections can arise as a result of eating contaminated poultry meat.

Take-Home Message 13.8 ●●

●●

Evolutionary biologists study phylogeny to understand how all species are connected by shared ancestry. Among other applications, phylogeny research can help us prioritize efforts to preserve endangered species, and to understand the spread of infectious diseases.

ST131-H22 (ancestral strain)

1970s ST131-H30 clade C fluoroquinoloneresistance mutations

1980s

cephalosporinresistance plasmid

1990s

2000s

ST131-H30 clade C1 resistant to fluoroquinolones

ST131-H30 clade C2 resistant to fluoroquinolones and cephalosporins

clinical introduction of fluoroquinolones

Figure 13.25  Evolution of a superbug. ST131 is a pathogenic strain of Escherichia coli that spread rapidly around the world in the early 2000s, after the lineage acquired resistance to fluoroquinolone and cephalosporin antibiotics. It continues to be a major human pathogen, causing millions of antibiotic-resistant infections annually. Today, H30 is the major subgroup of ST131; H22 is ancestral to H30.

Summary Section 13.1  Populations tend to change along with the selection pressures that operate on them. The use of antibiotics exerts directional selection favoring resistant bacterial populations, which are now common in the environment. We are running out of antibiotics effective as human drugs. Section 13.2  Mutations are the source of new alleles, and they can be neutral, harmful or lethal, or adapative. Alleles are the basis of differences in the forms of traits shared by a species. All alleles of all genes in a population constitute a gene pool. Allele frequency is the abundance of an allele among all copies of the gene in a gene pool (the proportion of chromosomes with the allele).

Microevolution, or change in allele frequency, is always occurring in natural populations because processes that drive it are always operating. Section 13.3  Natural selection is one mechanism that drives evolution, and it can occur in different patterns depending on the environmental pressures. Directional selection is a pattern of natural selection in which a form of a trait at one end of a range of variation is adaptive. An intermediate form of a trait is adaptive in stabilizing selection. In disruptive selection, extreme forms of a trait are adaptive and midrange forms are eliminated.

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264  Unit 3 EVOLUTION AND DIVERSITY

Summary (Continued) Section 13.4  Sexual dimorphism can be an outcome of sexual selection, a type of natural selection in which traits that make their bearers better at securing mates are adaptive. Natural selection can maintain multiple alleles at relatively high frequency in a population. Section 13.5  Evolution can occur by mechanisms that do not involve natural selection. Genetic drift, which is change in allele frequency due to chance alone, can lead to the loss of genetic diversity. Particularly in small populations, genetic drift can cause alleles to become fixed. Gene flow keeps populations genetically similar. By stabilizing allele frequencies, it can counter genetic drift. A population bottleneck may reduce a population’s genetic diversity. Allele frequencies in a population founded by a small group of individuals may differ from those of other populations (the founder effect). Populations in which inbreeding is common tend to have a higher than normal incidence of genetic disorders. Section 13.6  Speciation is the splitting of one lineage into two. Reproductive isolation, the end of gene flow between populations, is always a part of the process in sexual reproducers. We can model speciation patterns, but the process is rarely as simple as these models suggest. Each speciation event is unique, and it occurs within a continuum of geographic, genetic, and ecological factors. With allopatric speciation, a geographic barrier arises and interrupts gene flow between populations. The interruption allows genetic divergences to occur independently in each population, and this can result in separate species. Speciation can also occur in the absence of a barrier to gene flow. Sympatric speciation occurs by genetic divergence within a population. Polyploid species of many plants have originated this way. Section 13.7  Macroevolution refers to patterns of evolution that occur in taxa above the species level. A lineage may change very little over evolutionary time. Some body structures have been repurposed for a new use during evolution. A key innovation can result in an adaptive radiation, or rapid splitting of one lineage into many. Coevolution occurs when two species act as agents of selection upon one another. A lineage with no more living members is extinct; in a mass extinction, many lineages become extinct simultaneously. Section 13.8  Evolutionary biologists reconstruct evolutionary history (phylogeny) based on the premise that all life is

interconnected by shared ancestry. Species are grouped based on derived traits. A clade consists of an ancestor in which a derived trait evolved, together with all of its descendants. Making hypotheses about the evolutionary history of a clade is called cladistics. These hypotheses are often represented as cladograms, which are branching diagrams of evolutionary connections among clades. Each line in a cladogram represents a lineage. A branch point (node) represents a shared ancestor, and the two lineages that emerge from it are called sister groups. Phylogeny research informs conservation efforts by revealing a clade’s diversity. We use it to prioritize allocation of limited funding on species whose extinction will have the greatest impact. The loss of a single species from a community can unravel the connections that stabilize an ecosystem. We can use phylogeny to study the spread of viruses and other agents of infectious disease.

Self-Quiz Answers in Appendix I 1. __________ is the original source of new alleles. a. Mutation d. Gene flow b. Natural selection e. Speciation c. Genetic drift f. Microevolution 2. Which is required for evolution to occur in a population? a. genetic diversity c. gene flow b. selection pressure d. none of the above 3. Match the pattern of natural selection with its best description. stabilizing     a. eliminates extreme forms of a trait disruptive     b. eliminates mid-range forms of a trait 4. Sexual selection frequently influences aspects of body form and can lead to __________ . a. a sexual dimorphism c. exaggerated traits d. all of the above b. male aggression 5. The persistence of the sickle allele at high frequency in a population is a case of __________ . a. bottlenecking c. the founder effect b. balanced polymorphism d. inbreeding

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Processes of Evolution  Chapter 13  265  

6. __________ tends to keep populations similar to one another. c. Mutation a. Genetic drift b. Gene flow d. Natural selection 7. The theory of evolution by natural selection does not explain __________ . a. genetic drift d. how mutations arise b. the founder effect e. inheritance c. gene flow f. any of the above 8. Which of the following is not part of how we define a species? a. Its individuals appear different from other species. b. It is reproductively isolated from other species. c. Its populations can interbreed. d. Fertile offspring are produced. 9. Which of the following statements is correct? a. Genetic drift occurs only in small populations. b. Inbreeding increases genetic diversity. c. Gene flow can reintroduce alleles into a population. 10. After fire devastates all of the trees in a wide swath of forest, populations of a species of tree-dwelling frog on either side of the burned area diverge to become separate species. This is an example of __________ . a. allopatric speciation c. an evolutionary bottleneck b. adaptive radiation d. genetic drift 11. In many bird species, sex is preceded by a courtship dance. If a male’s dance is unrecognized by the female, she will not mate with him. This is an example of __________ . c. sexual selection a. a sexual dimorphism b. disruptive selection d. coevolution 12. __________ is a way of reconstructing evolutionary history based on derived traits. a. Natural selection c. Adaptive radiation b. Linnaean taxonomy d. Cladistics 13. The evolution of wings helped Pterygota, the winged insect clade, to be very successful. In this example, wings are a(n) __________ . a. derived trait c. key innovation b. adaptive trait d. all of the above 14. In cladograms, sister groups are __________ . a. inbred c. represented by nodes b. the same age d. in the same family

15. Match the evolution concepts. a. outcome can be interdependence gene flow b. changes in allele frequencies sexual selection due to chance alone derived trait c. alleles enter or leave a population extinct d. evolutionary history genetic drift e. adaptive traits make their bearers coevolution better at securing mates cladogram f. burst of divergences from one adaptive radiation lineage into many phylogeny g. no more living members h. diagram of sets within sets i. present in a group but not in its ancestors

CRITICAL THinking 1. Does the use of antibiotics cause antibiotic resistance in bacteria? Explain your answer. 2. In 2019, the U.S. Environmental Protection Agency (EPA) approved the use of two medically important antibiotics to treat citrus greening, a bacterial disease of plants that has been decimating the citrus industry in Florida since arriving there in 2005. Tiny sucking insects called psyllids harbor and transmit the bacteria that cause the disease. Infected trees produce misshapen, bitter fruits, and die within a few years. There is no known cure. Growers apply pesticides to control psyllid populations, but these chemicals have limited effectiveness because the infection passes very quickly from insect to plant, and the insects are vulnerable during only a portion of their seasonal life cycle. Thanks to the new ruling, desperate citrus growers in Florida are expected to spray hundreds of thousands of kilograms of streptomycin and oxytetracycline per year on their trees. Spraying won’t cure or eradicate citrus greening, but growers hope it may delay the spread of the disease. Ongoing antibiotic treatment may also help infected trees live longer. Antibiotics have been used on crops for decades to treat bacterial diseases, but on a much smaller scale. Explain why environmental and consumer groups are unhappy with the EPA’s decision. 3. Two species of antelope, one from Africa, the other from Asia, are put into the same enclosure in a zoo. To the zookeeper’s surprise, individuals of the different species begin to mate and produce healthy, hybrid baby antelopes. Explain why a biologist might not view these offspring as evidence that the two species of antelope are in fact one.

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14 Prokaryotes, Protists, and Viruses

14.1

The Human Microbiota  267

14.2

Origin of Cellular Life  268

14.3

Early Life  271

14.4

Modern Bacteria and Archaea  273

14.5

Origin of Eukaryotes  277

14.6

Protists  279

14.7

Viruses  286

A variety of microbes live in and on us. Feces (shown in this colorized micrograph) consists largely of bacteria from our intestine.

Concept Connections

Scimat Scimat/Science Source/Getty Images

The history of life on Earth extends back billions of years (Section 13.2). Through the evolutionary processes described in Chapter 12, new lineages arose and became adapted to Earth’s diverse environments. This chapter describes the divergences that gave rise to the three domains (Section 1.4) and considers how features of eukaryotic cells (Section 3.5) arose. It draws on your knowledge of organic monomers (Section 2.6), osmosis (4.5), oxygen-producing photosynthesis (5.3), and aerobic respiration (6.3). Protists, which we discuss in this chapter, include the ancestors of plants, fungi, and animals—groups that we discuss in Chapters 15 and 16.

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Prokaryotes, Protists, and Viruses  Chapter 14  267  

Application 14.1  The Human Microbiota Vast numbers of microscopic organisms live in and on your body; a healthy human adult is home to somewhere between 30 and 50 trillion bacteria. This means your body has as at least as many bacteria as it does human cells. In addition to bacteria, you host archaea, protists, viruses, and fungi. Taken together, these microbes account for about 3 percent of your body weight. The many types of microbes capable of living in or on humans constitute the human microbiota (or the human microbiome). A microbiota is a community of microorganisms that can live in a specific environment, in this case the human body. In the 1860s, scientists discovered that some microorganisms cause disease. A disease-causing organism is called a pathogen, and identifying pathogens was a major focus of twentieth-century microbiology. About 1,400 types of human pathogens have now been described. They include bacteria, fungi, viruses, and protists. Pathogens are the most well-studied members of our microbiota, but they constitute only a tiny fraction of it. The overwhelming majority of species in the human microbiota are either harmless or helpful. The composition of the microbiota varies among individuals and among human populations. To date, the Yanomami people, who live as hunter-gatherers in the Amazon rain forest, have the most diverse microbiota ever examined. Subsistence farmers in New Guinea also have a highly diverse microbiota. In industrialized countries, the diversity of the human microbiota is much lower. This lower diversity likely results from the use of antibiotics, limited time spent outdoors, a diet low in fiber, and improved hygiene and sanitation. The reduced microbiota diversity observed in industrialized nations may have negative health effects. By one hypothesis, the human immune system, which evolved in the presence of a diverse microbiota, becomes disordered when microbial diversity declines. This disorder could explain the rise in immune-related disorders such as asthma, food allergies, and inflammatory bowel disease. Such disorders are much more common in developed countries than in less-developed ones. Experimental studies have shown how different diets can select for different intestinal microbes. In one six-day study, volunteers ate only animal products (meat, eggs, and cheese) or only plant products (grains, legumes, fruits, and vegetables). The diet of animal products increased the proportion of bile-tolerant bacteria in the subjects’ feces (Figure 14.1). (Bile is a fluid that is produced by the liver and plays a role in the digestion of fats.) It also decreased the proportion of bacteria that ferment plant polysaccharides. Human digestive enzymes cannot break down these compounds, but some bacteria can. If sustained, the shift toward bile-tolerant bacteria observed in this study could cause health problems. These bacteria release metabolic by-products that promote liver cancer and encourage inflammatory bowel disease. The plants-only diet had the opposite effect. It decreased the proportion of bile-tolerant bacteria and increased the proportion of plant polysaccharide fermenters. Compounds released by bacterial fermentation of these

Figure 14.1  Human intestinal bacteria. Bilophila wadsworthia is a species most abundant in people who eat a lot of animal fat. Dr. Fred Hossler/Visuals Unlimited, Inc.

microbiota  Collection of microorganisms that can live in a specific environment. pathogen  Disease-causing agent.

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268  Unit 3  EVOLUTION AND DIVERSITY

polysaccharides promote health by suppressing the growth of pathogens, dampening inflammation, and serving as energy sources for the in the lining of the intestines. This study and others demonstrate the benefits of foods containing prebiotics—polysaccharides that cannot be broken down by human digestive enzymes but can be fermented by beneficial bacteria. Eating plant foods that contain prebiotic compounds keeps the beneficial bacteria in your digestive tract well fed. Think of eating fruits and vegetables as a way of feeding some particularly useful pets.

Discussion Questions 1. Probiotics are foods or other formulations that contain potentially beneficial microbes. Why are probiotics most effective when combined with a diet rich in prebiotics? 2. Most antibiotics are now given orally. To minimize the negative effects of antibiotics on the gut microbiota, some physicians propose replacing oral antibiotics with antibiotic injections whenever possible. Discuss the advantages and disadvantages of this proposal. 3. A change in diet can alter the relative proportions of bacterial species in the human intestines. Is such a shift in species composition an example of evolution?

14.2  Origin of Cellular Life Learning Objectives ●●

Describe conditions on the early Earth.

●●

List three possible sources for the organic building blocks of Earth’s first life.

●●

Describe the proposed steps that led to the first cellular life.

No one was present to witness the origin of life on Earth, and time has erased all traces of the earliest cells. To investigate this first chapter in life’s history, scientists propose and test hypotheses about how life began.

Conditions on the Early Earth 

hydrothermal vent  Underwater opening from which mineral-rich water heated by geothermal energy streams out.

Earth formed about 4.6 billion years. At first, the planet’s surface was molten rock, and water existed only as a vapor. Over the next billion years or so, the planet cooled, and by 4.3 billion years ago liquid water had begun to pool on its surface. Liquid water is considered essential to life because all the metabolic reactions that sustain life take place in water-based solutions. Today, any iron exposed to air or water will rust, meaning it will react with oxygen to form iron oxides. However, Earth’s most ancient iron-containing rocks do not contain iron oxides. This lack of rust indicates that there was little or no oxygen gas present when these rocks formed. An oxygen-free environment may have made life’s origin possible. Formation and accumulation of small organic molecules was probably the first step on the road to life. Had oxygen been present, it would have reacted with and broken down these molecules as soon as they formed.

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Prokaryotes, Protists, and Viruses  Chapter 14  269  

The Building Blocks of Life

Lightning-Fueled Atmospheric Reactions  In 1953, Stanley Miller and Harold

Urey proposed that lightning-powered reactions among inorganic gases in Earth’s early atmosphere could have produced the organic building blocks of life. To test this hypothesis, they built a glass reaction apparatus and filled it with a mixture designed to mimic the early atmosphere: gaseous ammonia (NH4), methane gas (CH4), hydrogen gas (H2), and water vapor (H2O). As this mixture circulated through the apparatus, sparks from electrodes simulated lightning (Figure 14.2). Within a week, this process produced simple organic compounds, including five of the amino acids present in living organisms. We now know that the mixture of gases in this first experiment did not accurately represent the atmosphere of the early Earth. However, this work remains notable because it was the first experimental test of a hypothesis about life’s origin. Later experimental variations using the same sort of apparatus and mixtures of gases that better simulate Earth’s early atmosphere also produced amino acids.

Delivery from Space  Modern-day meteorites that fall to Earth sometimes contain amino acids, sugars, and nucleotide bases, indicating that these compounds form in outer space. Thus, it is possible that some of the many meteorites that fell on the early Earth carried organic monomers. Some scientists have even suggested that life could have originated on another planet such as Mars and been carried to Earth on meteorites. Keep in mind that during Earth’s early years, meteorites fell to Earth thousands of times more frequently than they do today.

electrodes CH4  NH4  gases H2 

spark simulates lightening



condenser (cools steam, so water forms)

boiling water

organic compounds accumulate here

Figure 14.2  Stanley Miller’s experimental apparatus. It was used to test whether lightning-fueled reactions could have formed organic monomers in Earth’s early atmosphere. Water vapor, hydrogen gas (H2), methane (CH4), and ammonia (NH4) circulated in a glass chamber to simulate the atmosphere. Sparks provided by an electrode simulated lightning. Figure It Out: Why didn’t Miller include oxygen (O2) in the mix of gases?

Answer: Earth’s early atmosphere lacked oxygen.

All organisms consist of the same organic subunits: amino acids, fatty acids, nucleotides, and simple sugars. What process produced the building blocks of the first life? We consider three possible mechanisms. Keep in mind that these mechanisms are not mutually exclusive. Most likely, they all contributed to an accumulation of simple organic compounds on the early Earth.

Reactions at Hydrothermal Vents  Heat from hydrothermal vents may have supplied the energy required to produce organic subunits from components in Earth’s early seas. A hydrothermal vent is like an underwater geyser, a place where mineral-rich water heated by geothermal energy streams out through a rocky opening in the seafloor (Figure 14.3). Amino acids and other organic monomers form spontaneously in a simulated hydrothermal vent environment.

Origin of Metabolism Modern cells selectively take up small organic molecules, concentrate them, and assemble them into larger organic polymers. Before there were cells, a nonbiological process that concentrated organic subunits would have increased the likelihood of polymer formation. By one hypothesis, organic polymers formed spontaneously on clay-rich tidal flats. Clay particles have a slight negative charge, so positively charged molecules in seawater stick to them and thus become locally concentrated. At low tide, evaporation would have concentrated the subunits even more, and energy from sunlight might have induced the formation of polymers. Amino acids do form short chains under simulated tidal flat conditions. An alternative hypothesis proposes that early metabolic reactions took place in rocks around hydrothermal vents. These rocks are rich in iron sulfide

Figure 14.3  A hydrothermal vent on the seafloor. At such vents, mineral-rich water heated by geothermal energy streams out into cold ocean water. Courtesy of the University of Washington

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270  Unit 3  EVOLUTION AND DIVERSITY

minerals, and they are porous, with many tiny chambers about the size of cells. Metabolism may have begun when the iron sulfide in the rocks donated electrons to dissolved carbon monoxide (CO), setting in motion reactions that led to formation of larger organic compounds. The products of these reactions would then have accumulated in the cell-sized chambers. A universal requirement for iron–sulfur cofactors in modern organisms may be a legacy of life’s rocky beginnings.

Origin of Genetic Material  DNA is the genetic material in all modern cells. Cells pass copies of their DNA to descendant cells, which use instructions encoded in DNA to build proteins. Some of these proteins function in the synthesis of new DNA, which is passed along to descendant cells, and so on. Protein synthesis depends on DNA, which is built by proteins. How did this cycle begin? According to the RNA world hypothesis, there was an early interval during which RNA served a dual role, functioning both as a genome and as an enzyme. RNA is a simpler molecule than DNA, and thus is more likely to have formed by nonbiological processes. Evidence that some RNAs (called ribozymes) can function as enzymes is cited as evidence for the RNA world hypothesis. For example, some ribozymes cut noncoding bits (introns) out of newly formed RNAs (Section 8.3), and the rRNA in ribosomes speeds formation of peptide bonds (Section 8.5). If early genetic systems were RNA-based, why do all cells now have a genome of DNA? The difference in stability of the two nucleic acids was probably a factor. Compared to a double-stranded DNA molecule, a single-stranded RNA breaks more easily and is more prone to replication errors. Thus, a switch from RNA to DNA would have made larger, more stable genomes possible.

Origin of Cell Membranes 

Figure 14.4  Illustration of a laboratory-produced protocell. A bilayer membrane of fatty acids encloses strands of RNA. © Janet Iwasa

archaea  Members of a prokaryotic lineage that is more closely related to eukaryotes than to bacteria. bacteria  The most diverse prokaryotic lineage; branched off from the lineage leading to archaea and eukaryotes early in the history of life. protocell  Membranous sac that contains interacting organic molecules; hypothesized to have formed prior to the earliest cells. RNA world hypothesis  Hypothesis that RNA served as the first material of inheritance.

Self-replicating molecules and products of synthetic reactions would have floated away from one another unless something enclosed them. In modern cells, a plasma membrane serves this function. It is possible that vesicle-like structures may have functioned in a similar manner before there were cells. Such vesicles form spontaneously when polar lipids mix with water. A membrane-enclosed collection of interacting molecules that can take up material and replicate is called a protocell. Protocells are hypothesized to be the ancestors of cellular life. Membranes of early protocells probably consisted of a variety of fatty acids, rather than the phospholipids that make up the bulk of modern cell membranes (Section 3.3). Like phospholipids, fatty acids are polar and self-assemble as vesicles when mixed with water. However, fatty acids are structurally simpler than phospholipids and would have been more abundant on early Earth. Experiments that simulate protocell formation provide insight into how cellular life could have originated. Some of these experiments have produced vesicle-like spheres in which a bilayer of fatty acids surrounds molecules of RNA (Figure 14.4).

Defining Plausible Pathways Simulations and experiments such as those described in this section cannot prove how life or cells began. However, they help scientists determine the likelihood that any proposed step on the pathway to life could have occurred. A variety of investigations by many researchers tell us this: Chemical and physical processes that operate today can produce simple organic compounds, concentrate them, and allow them to

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Prokaryotes, Protists, and Viruses  Chapter 14  271  

assemble as protocells. Billions of years ago, the same processes may have led to the first life (Figure 14.5).

inorganic molecules . . . self-assemble on Earth and in space

Take-Home Message 14.2 ●●

●● ●● ●●

organic monomers

Small organic subunits could have formed on the early Earth or formed in space and fallen to Earth on meteorites. Complex organic molecules can self-assemble from simpler ones. The first genetic material may have been RNA rather than DNA. Protocells—chemical-filled membranous sacs that grow and divide—may have been the ancestors of the first cells.

. . . self-assemble in aquatic environments on Earth organic polymers . . . interact in early metabolism . . . self-assemble as vesicles . . . become the first genome protocells in an RNA world

14.3  Early Life

. . . are subject to selection that favors a DNA genome

Learning Objectives ●●

Describe the likely characteristics of the last common ancestor of all life.

●●

Explain how scientists discovered that there are two prokaryotic domains.

●●

Describe some fossils of early life and the habitats in which they formed.

●●

Explain the role of prokaryotic cells in the oxygenation of Earth’s atmosphere and the biological consequences of the increase in oxygen.

DNA-based cells

Figure 14.5  Proposed sequence for the evolution of cells. Scientists carry out experiments and simulations that test the feasibility of each step.

The Last Common Ancestor of All Life The processes described in Section 14.2 may have produced cellular life more than once. If so, all but one of those early lineages have become extinct. Similarities among modern genomes indicate that all living species descended from a common single-celled ancestor, a species that lived perhaps as early as 4 billion years ago. There was little or no oxygen on the early Earth, so that ancestral species must have been anaerobic (capable of living without oxygen). Given fossil evidence and what we know about relationships among modern species, this ancestor was most likely prokaryotic, meaning it did not have a nucleus.

An Early Divergence Scientists have historically classified all prokaryotic cells as bacteria. Then, in the late 1970s, Carl Woese began trying to construct an evolutionary tree for the prokaryotes. To determine the relationships among prokaryotic species, Woese compared their sequences for a gene that encodes a ribosomal RNA. To his surprise, some prokaryotes had a ribosomal RNA gene unlike that of any known bacteria. In fact, the sequence data from these cells indicated that they were more closely related to eukaryotes than to bacteria. Woese named the newly recognized prokaryotic lineage the archaea, and he proposed a classification system with three domains: Bacteria, Archaea, and Eukaryotes (Figure 14.6). We now define bacteria as members of a prokaryotic lineage that branched off from the lineage leading to archaea and eukaryotes early in the history of life. Archaea are members of a prokaryotic lineage that is more closely related to eukaryotes than to bacteria.

Bacteria

Archaea

Eukaryotes

Figure 14.6  The three-domain classification system.

Fossil Evidence of Prokaryotic Cells Prokaryotic species were the only life on Earth for billions of years but finding and identifying fossils of these cells poses a challenge. Prokaryotic cells are microscopic and

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272  Unit 3  EVOLUTION AND DIVERSITY

10 µm

Figure 14.7  Fossil cells from an ancient beach. Microscopic 3.4-billion-year-old fossil cells nestle among sand grains in sandstone. They resemble bacteria that live in modern mudflats. (Background), tratong/Shutterstock.com; (inset) David Wacey

most have no hard parts to fossilize. In addition, most of the ancient rocks that could hold early fossils have either been destroyed or modified by geologic processes. An additional problem is that structures formed by nonbiological mechanisms sometimes resemble fossils. To avoid mistaking such material for a genuine fossil, scientists constantly reanalyze purported fossils and they often question one another’s conclusions. At this time, the oldest purported fossil cells come from Canadian rocks that formed about 3.77 billion years ago on the ocean floor. The rocks contain tubes and filaments that resemble those formed by prokaryotic cells near modern deep-sea hydrothermal vents. Another possible fossil of early life comes from Australian sandstone rocks that date back 3.4 billion years. These rocks include spherical fossils nestled among sand grains from an ancient beach (Figure 14.7). The most widespread evidence of early cellular life comes from fossil stromatolites. A stromatolite is a rocky layered structure that forms in shallow sunlit water when a biofilm of prokaryotic cells traps minerals and sediment. New layers are added to the stromatolite when the cells at its apex grow up through the accumulated sediment and trap more sediment. Scientists can observe this process in modern stromatolites such as those in Australia’s Shark Bay (Figure 14.8). The oldest undisputed stromatolite fossils date to 2.8 billion years ago, but other structures that may be fossil stromatolites date to 3.4 billion years ago. Taken together, the variety of early fossils indicates that by about 3 billion years ago, prokaryotic life was widespread in Earth’s waters, from sandy shorelines to the deep ocean floor.

The Great Oxygenation Event Figure 14.8  Modern stromatolites in Australia’s Shark Bay.

Bacteria and archaea arose when Earth had little or no oxygen, so the earliest members of these lineages were anaerobic. Then, about 2.7 billion years ago, a lineage of

Michael Aw/Lonely Planet Images/Getty Images

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Prokaryotes, Protists, and Viruses  Chapter 14  273  

bacteria called the cyanobacteria began to carry out photosynthesis by the noncyclic pathway. This pathway produces oxygen as a by-product. As cyanobacteria became increasingly abundant, oxygen began to accumulate in the air and water. The increase in oxygen created a new selective pressure, putting species that could not tolerate oxygen at a disadvantage. Such species were harmed by oxygen because reactions with oxygen damaged their biological molecules, and unlike aerobic cells, they had no enzymes to repair such damage. As time went by, these species became restricted to the limited low-oxygen environments that remained. Today, anaerobic bacteria and archaea live only in oxygen-poor environments such as aquatic sediments and the animal gut. As oxygen accumulated, the pathway of aerobic respiration evolved and became widespread. This energy-releasing pathway requires oxygen, and it is far more efficient at releasing energy from organic molecules than other pathways. As another effect, some oxygen atoms combined as ozone gas (O3), which accumulated as the ozone layer in the upper atmosphere. Ozone absorbs UV radiation, so formation of the ozone layer reduced the level of UV radiation at Earth’s surface. This reduction made life on land possible. UV radiation is a mutagen; it can damage DNA and other biological molecules. Water screens out UV light, so aquatic life was possible even without the ozone layer. However, before the ozone layer formed, UV radiation would have destroyed any life that ventured onto land.

Take-Home Message 14.3 ●●

●● ●●

●●

The last common ancestor of all modern life may have arisen as early as 4 billion years ago; it was anaerobic and prokaryotic. An early divergence gave rise to two prokaryotic domains (Archaea and Bacteria). Fossil evidence indicates that by about 3 billion years ago prokaryotic cells were living in a variety of aquatic environments. After cyanobacteria began carrying out oxygen-producing photosynthesis, the amount of oxygen in Earth’s air and waters increased and a protective ozone layer formed.

DNA cytoplasm with ribosomes plasma membrane cell wall capsule

flagellum

14.4  Modern Bacteria and Archaea

pilus

Learning Objectives ●●

List some structural and functional traits shared by bacteria and archaea.

●●

Describe how prokaryotic cells reproduce, and the mechanisms by which they can share genes.

●●

Explain the roles bacteria play in ecosystems.

●●

Using appropriate examples, explain how bacteria affect human health.

●●

Describe two extreme habitats in which archaea are found.

Figure 14.9  Generalized structure of a prokaryotic cell.

Structural Traits Bacteria and archaea are typically much smaller than eukaryotic cells, and they do not have a nucleus (Figure 14.9). Although some do have internal membranes, none have the membrane-enclosed organelles typical of eukaryotes. Their single circular chromosome (a ring of DNA) lies in the cytoplasm, as do the ribosomes. Nearly all bacteria and archaea secrete a porous cell wall around their plasma membrane, although the composition of the wall differs between the two groups. (Most bacterial cell walls contain a polymer called peptidoglycan; archaea do not make peptidoglycan.) A cell wall gives the cell its shape, which is most commonly

cyanobacteria  Bacteria that carry out photosynthesis by the oxygen-producing noncyclic pathway. ozone layer  Atmospheric layer with a high concentration of ozone that prevents much UV radiation from reaching Earth’s surface. stromatolites  Dome-shaped structures composed of layers of prokaryotic cells and sediments; form in shallow seas.

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274  Unit 3  EVOLUTION AND DIVERSITY

1 A typical bacterial cell has one circular chromosome suspended in the cytoplasm. 2 Enzymes in the center of the cell replicate the chromosome. Replication usually begins at a single point. 3 After chromosome

duplication, membrane and cell wall are deposited between the two daughter chromosomes.

4 The result is two

identical daughter cells.

spherical, spiral, or rod-shaped. A spherical cell is a coccus, a spiral-shaped one is a spirillum, and a rod-shaped one a bacillus. Many bacteria and archaea have a flagellum that allows them to move about. Many also have hairlike filaments called pili (singular, pilus) at their cell surface. Some cells use pili to stick to surfaces. Another type of pilus is retractable; it draws cells together for gene exchanges.

Reproduction Bacteria and archaea most commonly replicate by binary fission, a mechanism of asexual reproduction that yields two equal-sized, genetically identical descendant cells (Figure 14.10). The process begins when the cell replicates its single chromosome, which is suspended in the cytoplasm 1. DNA replication typically begins at a single point. It is carried out by enzymes at the center of the cell 2. Once the chromosome has been replicated, plasma membrane and cell wall material are deposited across the cell’s midsection 3. This material partitions the cell, eventually yielding two genetically identical descendant cells 4.

Gene Exchanges Figure 14.10  Asexual reproduction by binary fission.

Bacteria and archaea do not reproduce sexually, so reproduction does not produce new gene combinations. However, prokaryotes can transfer genetic material among existing individuals. Three mechanisms permit such exchanges: 1. With transformation (Figure 14.11A), a prokaryote takes up free DNA, such as that from a dead cell, from its environment. 2. With transduction (Figure 14.11B), a virus picks up DNA from one host and passes it along to another. 3. With conjugation (Figure 14.11C), one cell donates a small circle of DNA called a plasmid to another. A plasmid is a circle of double-stranded DNA with a few genes.

Figure 14.11  Mechanisms of gene exchange between prokaryotic cells. binary fission  Method of asexual reproduction in which a prokaryote divides into two identical descendant cells.

donor cell tube through which the plasmid is transferred

conjugation  Mechanism of gene transfer in which one prokaryotic cell directly transfers a plasmid to another. decomposer  Organism that feeds on organic wastes and remains, breaking these materials down into their inorganic building blocks. nitrogen fixation  Process of combining nitrogen gas with hydrogen to form ammonia.

transduction  Mechanism of gene transfer in which a virus moves genes from one host cell to another. transformation  Mechanism of gene transfer in which a prokaryotic cell takes up and uses DNA from its environment.

recipient cell

A. Transformation: taking up DNA from the environment.

B. Transduction: transfer of DNA by means of a virus.

C. Conjugation: direct transfer of a plasmid between cells.

Figure It Out: Which of these processes doubles the number of cells? Answer: None of them. All are means of gene exchange, not reproduction.

plasmid  Of many prokaryotes, a small ring of nonchromosomal DNA.

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Prokaryotes, Protists, and Viruses  Chapter 14  275  

Ecology and Diversity of Bacteria We share the planet with an estimated 5 million trillion trillion bacterial cells. Bacteria live just about everywhere, and they play essential roles in all ecosystems. Bacteria as Producers  In any ecosystem, energy flow begins when autotrophs (pro-

ducers) capture energy from their environment. There are two types of autotrophs. You are already familiar with photoautotrophs; they capture light energy and carry out photosynthesis. Chemoautotrophs, by contrast, obtain energy by removing electrons from inorganic materials. Photosynthesis evolved in many bacterial lineages, so photoautotrophic bacteria are important producers in well-lit aquatic environments (Figure 14.12). Most bacteria carry out photosynthesis by the cyclic pathway, which does not produce oxygen. The oxygen-producing pathway of photosynthesis evolved only once, in the cyanobacteria. As you will learn in Section 14.5, chloroplasts are descended from cyanobacteria. Thus, we have cyanobacteria and their chloroplast descendants to thank for nearly all the oxygen in Earth’s atmosphere. No eukaryotes are chemoautotrophs, so chemoautotrophic bacteria and archaea are the main producers in dark places, such as the ocean floor. They are especially abundant near hydrothermal vents, where they meet their energy needs by pulling electrons from rocks and from dissolved minerals in the water near the vent.

Nutrient Cycling  Recall that heterotrophs obtain carbon and energy by breaking

down organic compounds. Heterotrophic bacteria are the main decomposers on land and in aquatic environments. A decomposer feeds on organic wastes and remains, breaking these materials down into their inorganic building blocks. Some of the nutrients released by this process escape into the environment, where producers can take them up and use them to meet their own nutritional needs. Bacteria also aid eukaryotic producers by carrying out nitrogen fixation, a process that incorporates nitrogen from the air into organic compounds such as ammonia (NH3). Plants and photosynthetic protists need nitrogen to grow, but they cannot use nitrogen gas (N2) because they do not have an enzyme that can break that molecule’s triple bond. They can, however, take up ammonium, which forms when the ammonia produced by nitrogen fixation dissolves in water. A variety of bacterial species, including many cyanobacteria, can fix nitrogen. Nitrogen-fixing bacteria in the genus Rhizobium play an important role in agriculture. These bacteria form a mutually beneficial partnership with legumes, which are plants such as peas and beans. The bacteria live inside a root nodule (a swelling on the root’s surface). The bacteria provide the plant with nitrogen, and it provides them with shelter and photosynthetically produced sugar.

nitrogenfixing cell

A

Figure 14.12  Aquatic cyanobacteria. This species grows as long chains of cells connected by a secreted mucous sheath. Some cells in the chain are specialized for nitrogen fixation. Michael Abbey/Visuals Unlimited, Inc.

Research and Industrial Uses  Bacteria are frequently used in scientific research

and in industry. The most well-studied and widely grown prokaryote is Escherichia coli, which normally lives in the mammalian intestines. More than a dozen Nobel Prizes have been awarded for studies that made use of this species. E. coli is also widely used in industrial biotechnology. Recombinant E. coli now make hormones and other proteins for medical use. Bacteria that carry out fermentation reactions are used to make foods such as sauerkraut and yogurt (Figure 14.13). The bacteria ferment sugars and produce lactate (lactic acid), which gives these foods their sour taste.

Figure 14.13  Lactate-fermenting bacteria used to produce yogurt. SCIMAT/Science Source

Bacteria and Human Health Bacteria have major effects—both positive and negative—on human health.

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276  Unit 3  EVOLUTION AND DIVERSITY Normal Microbiota  The microorganisms that live on or in us without causing

disease are called our normal microbiota (or normal flora). The normal microbiota of our skin and our body’s internal linings helps protect us from pathogens. For example, lactate-producing bacteria in the vagina keep the pH too low for pathogens to thrive. In the intestines, beneficial bacteria synthesize essential vitamins and break down toxic compounds from food. They also ferment plant carbohydrates to produce short-chain fatty acids (SCFAs). These compounds feed the cells of the intestinal lining, discourage growth of colon cancers, promote immune function, and have beneficial effects on metabolism throughout the body.

Table 14.1  Examples of Bacterial Diseases

Disease

Description

Whooping cough

Childhood respiratory disease

Tuberculosis

Respiratory disease

Impetigo, boils

Blisters, sores on skin

Strep throat

Sore throat, can damage heart

Cholera

Diarrheal illness

Syphilis

Sexually transmitted disease

Gonorrhea

Sexually transmitted disease

Chlamydia

Sexually transmitted disease

Lyme disease

Rash, flulike symptoms

Botulism, tetanus

Muscle paralysis by bacterial toxin

Bacterial Pathogens  Bacteria cause many common diseases (Table 14.1). Most

pathogenic bacteria harm us by producing toxins that disrupt our health. The toxin may be a substance that bacteria release into their environment or a molecule integral to the cell’s wall. Some bacterial diseases are infectious, meaning they are spread by contact with an infected individual or their body fluids. Whooping cough, tuberculosis, and sexually transmitted diseases such as gonorrhea are infectious. Other bacterial diseases are spread by an animal vector. For example, the bacteria that cause Lyme disease are spread by ticks. Pathogenic bacteria can also enter the body in contaminated food or water (as with cholera) or through a wound (as with tetanus). Some soil bacteria, including those that cause the diseases tetanus and anthrax, produce an especially resilient resting structure called an endospore. An endospore is a stripped-down, dehydrated bacterial cell within a thick protective covering. Unlike metabolically active cells, endospores withstand heating, freezing, and drying out. Disease arises when endospores enter the body and germinate (resume activity).

Antibiotics We are fortunate to live at a time when nearly all bacterial infections can be cured by an antibiotic. Prior to the 1940s, there was no effective treatment for bacterial diseases. Penicillin, one of the earliest antibiotics, was first isolated from a fungus (Penicillium) that lives in the soil. Penicillin acts by the most common antibiotic mechanism—inhibiting synthesis of bacterial cell walls. Other antibiotics such as tetracyclines and streptomycins disable bacterial ribosomes. Eukaryotic ribosomes, which have a different structure, remain unaffected. As noted in Section 13.1, our widespread use of antibiotics favors bacterial strains that can survive in the presence of these drugs. Genes that confer resistance can arise through mutation or be acquired through horizontal gene transfer.

The Archaea  endospore  Spore (resting structure) formed by some soil bacteria; contains a dormant cell and is highly resistant to adverse conditions. extreme halophile  Organism that lives where the salt concentration is high. extreme thermophile  Organism that lives where the temperature is very high. methanogen  Organism that produces methane gas as a metabolic by-product.

Archaea differ from bacteria in many respects. Their cell wall does not contain peptidoglycan, and their cell membrane contains lipids not found in bacteria. Like eukaryotes, archaea organize their DNA around histone proteins, whereas bacteria do not have histones. Many archaea thrive in seemingly hostile environments. They include extreme thermophiles, which thrive at high temperatures. For example, archaea have been found in scalding hot water near deep-sea hydrothermal vents and in thermal springs (Figure 14.14A). Other archaea are extreme halophiles, meaning they live in highly salty environments (Figure 14.14B).

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Prokaryotes, Protists, and Viruses  Chapter 14  277  

Some archaea, including some extreme halophiles and thermophiles, are methanogens. Methanogens produce methane, an odorless flammable gas, as a by-product of their metabolic reactions. Methane-producing archaea cannot tolerate oxygen, but they abound in sewage, marsh sediments, and the animal gut (Figure 14.14C). Cattle have methanogens in their stomach and they release methane gas primarily by belching. About a third of the human population has significant numbers of methanogens in their intestine, so their flatulence (farts) contains methane. As biologists continue to explore archaeal diversity, they are finding that archaea are not restricted to extreme environments. They live alongside bacteria nearly everywhere. So far, scientists have not found any archaea that pose a major threat to human health. However, some that live in the mouth may encourage gum disease, and some that live in the intestines may encourage weight gain.

A. Thermally heated waters. Pigmented archaea color rocks in waters of this Nevada hot spring.

Take-Home Message 14.4 ●●

●●

●●

Bacteria and archaea are cells that do not have a nucleus. They reproduce mainly by binary fission and they swap genes by conjugation and other processes. Bacteria benefit other organisms by releasing oxygen, fixing nitrogen, and serving as decomposers. We use them to produce foods and in biotechnology. Some bacteria that live in and on us promote our heath, but others are pathogens. Archaea are the most recently discovered prokaryotic domain. They are closer to eukaryotes than to bacteria. Many archaea live in extremely hot or salty habitats.

14.5  Origin of Eukaryotes Learning Objectives ●● ●●

B. Highly salty waters. Salt-tolerant archaea color the brine in this California lake.

Describe the process by which nucleus likely evolved. Explain why some components of eukaryotes are similar to archaea and others are similar to bacteria.

Fossil Eukaryotes Nuclei and other organelles are almost never preserved during fossilization, but other traits can indicate that a fossilized cell was eukaryotic. Eukaryotic cells are generally larger than prokaryotic ones. A cell wall with complex patterns, spines, or spikes also indicates that a cell is most likely eukaryotic. At this time, the oldest fossils that most scientists agree are eukaryotic date to about 1.8 billion years ago. The age of these fossils is consistent with genetic studies that date the origin of eukaryotes to between 1.9 and 1.7 billion years ago. Such studies use the degree of genetic differences among existing lineages to estimate how long ago the lineages shared a common ancestor.

A Mixed Heritage Eukaryotes are similar to archaea in terms of how they store their DNA (wrapped around histone proteins) and in some details of how they transcribe, replicate, and repair their DNA. On the other hand, many eukaryotic genes, especially those involved in energy metabolism, are more like bacterial genes than archaeal ones. The mix of archaeal and bacterial traits in eukaryotes indicates that this group has a composite heritage.

C. The digestive tract of many animals. Cattle belch to expel methane produced by archaea in their digestive system.

Figure 14.14  Environments of archaea. (A) © Savannah River Ecology Laboratory; (B) Courtesy of Benjamin Brunner; (C) TonyV3112/Shutterstock.com

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278  Unit 3  EVOLUTION AND DIVERSITY Origin of the Nucleus  The defining feature of eukaryotes is their nucleus. The

ancestral archaeal cell

DNA

3 Aerobic 1 Portions

of the plasma membrane fold inward.

2 Infoldings

evolve into the nuclear envelope and the endomembrane system.

bacteria enter and live inside an archaeal cell.

4 Over generations, the

aerobic bacteria evolve into mitochondria.

5 Photosynthetic

bacteria enter an early eukaryote and, over generations, evolve into chloroplasts.

Figure 14.15  Evolution of eukaryotic organelles. The nuclear envelope and endomembrane components are derived from infoldings of the plasma membrane. Mitochondria and chloroplasts evolved from bacteria that lived inside a host cell.

colonial organism  Organism composed of many behaviorally integrated cells, each capable of surviving and reproducing on its own. contractile vacuole  In freshwater protists, an organelle that collects and expels excess water. endosymbiont hypothesis  Mitochondria and chloroplasts evolved from free-living bacteria that entered and lived inside another cell. foraminiferan  Heterotrophic single-celled protist that secretes a calcium carbonate shell. multicellular organism  Organism composed of interdependent cells that have a division of labor; each cell is unable to survive and reproduce on its own. plankton  Community of mostly microscopic drifting or swimming organisms. protist  General term for eukaryote that is not a fungus, plant, or animal.

evolution of a nucleus probably began in the archaeal ancestor of eukaryotes when portions of the plasma membrane folded inward (Figure 14.15). Over time, some of this now internal membrane came to surround the DNA, forming the first version of the nuclear membrane 1. Other portions of internalized membrane gave rise to additional components of the endomembrane system 2.

The Endosymbiont Hypothesis The endosymbiont hypothesis states that mitochondria and chloroplasts evolved from bacteria. (Endosymbiosis means “living inside” and refers to a relationship in which one organism lives inside another.) A variety of evidence supports this hypothesis. Mitochondria and chloroplasts resemble bacteria in size and shape, and they replicate independently of the eukaryotic cell that holds them. Like bacteria, they have a single circular chromosome and their ribosomes resemble bacterial ribosomes. They also have at least two outer membranes, and their innermost membrane is similar to a bacterial plasma membrane. Nearly all eukaryotic lineages have mitochondria or mitochondria-like organelles, but not all have chloroplasts. Thus, biologists think that the two types of organelles were acquired independently in the sequence illustrated in Figure 14.15. Evolution of Mitochondria  A high degree of similarity among all modern mitochondrial genomes indicates that all mitochondria are descendants of the same bacterial ancestor. The evolution of mitochondria by endosymbiosis most likely began when aerobic bacteria were taken in by an archaeal cell 3. When the host cell divided, it passed some “guest” bacteria, referred to as endosymbionts, along to its offspring. As the host and its bacterial endosymbionts lived together over many generations, both evolved. The endosymbionts lost the capacity to build structures they no longer needed, such as a cell wall. Some metabolism-related genes from the endosymbiont moved into the host’s genome. Redundant genes were eliminated; a gene could become nonfunctional in one partner if a similar gene carried by the other partner still worked. Eventually, the host and endosymbiont became incapable of living independently. At that point, the endosymbionts had become mitochondria 4. Evolution of Chloroplasts  An endosymbiosis between a host eukaryote and its guest cyanobacteria gave rise to the first chloroplasts 5. The result of this first endosymbiotic event was a green alga, a type of protist. Later, some photosynthetic protists would be taken up by other protists and evolve into chloroplasts inside their hosts. Thus, although chloroplasts evolved independently in several different lineages, all chloroplasts ultimately trace their ancestry to the same cyanobacterial ancestor.

Take-Home Message 14.5 ●● ●●

●●

Eukaryotes evolved after prokaryotes, and they have a mixed ancestry. The nuclear envelope and endomembrane system probably evolved from membrane infoldings in an ancestral archaeal cell. Mitochondria and chloroplasts are descended from bacteria.

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Prokaryotes, Protists, and Viruses  Chapter 14  279   Flagellated protozoans

Learning Objectives

Foraminiferans

●●

Give examples of single-celled, colonial, and multicellular protists.

●●

Describe the ecological roles played by protists.

●●

List some human diseases caused by protists and describe the protists that cause them.

●●

Describe the protist group that is most closely related to plants and the group that is most closely related to animals.

prokaryotic ancestor

14.6  Protists

Ciliated protozoans Dinoflagellates Apicomplexans Water molds Diatoms Brown algae

A eukaryote that is not a fungus, plant, or animal is referred to as a protist. The protists are a collection of lineages, rather than a valid biological group (a clade) because no shared trait defines them. Some protists are more closely related to plants, fungi, or animals than to other protists (Figure 14.16). The vast majority of protists live as single cells. However, colonial protists exist, and multicellularity evolved independently in several lineages. Cells of a colonial organism live together and behave in an integrated fashion, but remain self-sufficient. Each retains the traits required to survive and reproduce on its own. By contrast, the cells of a multicellular organism have a division of labor and rely on one another for survival. In a multicellular organism, only specialized cells produce gametes. Being eukaryotes, protists form gametes by meiosis.

Red algae Green algae Land plants Amoebas Slime molds Fungi

Cell Structure Protists are eukaryotes, so they all have a nucleus. Most have all other standard eukaryotic organelles such as endoplasmic reticulum (ER) and Golgi bodies. Almost all protists have at least one mitochondrion, or a modified mitochondrion that functions in anaerobic energy production. The eukaryotic organelles can be seen in Figure 14.17, which illustrates the body plan of the single-celled, freshwater protist Euglena. The cytoplasm of Euglena is saltier than its freshwater habitat, so water tends to diffuse into the cell by osmosis. To keep from bursting, Euglena and other freshwater protists have contractile vacuoles, organelles that collect excess water from the cytoplasm, then contract and expel it from the cell through a pore. Euglena is photosynthetic, with chloroplasts that evolved from a green alga. An eyespot allows Euglena to detect light, and a flagellum allows it to move to a well-lit area. Other single-celled protists move with the help of cilia or by extending lobes of cytoplasm called pseudopods.

Free-Living Aquatic Cells Most protists are free-living aquatic cells. Protists are an important component of the plankton, the community of tiny organisms that swim or drift through Earth’s waters. They are represented both among the phytoplankton (the photosynthetic species) and the zooplankton (the species that are consumers). Protists are also abundant among the sediments at the bottom of lakes and seas, where they act as tiny predators and decomposers. Chalky-Shelled Foraminifera  The foraminifera (singular, foraminiferan) are

single-celled predators that secrete a shell containing calcium carbonate. Including its shell, an individual foraminiferal cell can be as big as a grain of sand. Threadlike cytoplasmic extensions protrude through openings in the shell. Most foraminifera live on the seafloor, where they use their cytoplasmic extensions to

Choanoflagellates Animals

Figure 14.16  Evolutionary tree for the eukaryotes. Orange boxes indicate the protist lineages.

long flagellum chloroplast

contractile vacuole

mitochondrion

eyespot ER nucleus pellicle

Golgi body

Figure 14.17  Euglena, a freshwater flagellated protozoan. The species depicted here has chloroplasts that evolved from a green alga.

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280  Unit 3  EVOLUTION AND DIVERSITY

200 µm

Figure 14.18  A planktonic foraminiferan. The yellow dots are algae that live in its cytoplasm. Courtesy of Allen W. H. Bé and David A. Caron

Silica-Shelled Diatoms  Some diatoms live in moist soil, but most float near the surface of seas or lakes. A diatom is a nonmotile, single-celled photosynthetic protist

that secretes a two-part silica shell. The upper and lower parts of the glassy shell fit together like a shoe box and its lid (Figure 14.19). Diatoms are closely related to the multicellular brown algae, and like these algae, they have chloroplasts with a brownish accessory pigment that tints them olive green, golden, or dark brown. Diatom cells contain a large amount of oil, which serves as a store of energy and helps them stay afloat in sunlit waters. (Oil floats on water.) Like foraminifera, marine diatoms have lived and died in the oceans for many millions of years, and their remains form vast deposits on the seafloor. In some places, deposits of ancient diatom oil have been transformed into petroleum, which we extract to produce gasoline. In other places, ancient diatom shells have been transformed into a silicarich powder called diatomaceous earth. This material is quarried for use in filters, abrasive cleaners, and as an insecticide that is not harmful to vertebrates.

Figure 14.19  Diatom. Chloroplasts are visible through the cell’s silica shell. Barbol/Shutterstock.com

beltlike flagellum that encircles cell chloroplast nucleus flagellum

10 µm

Figure 14.20  Photosynthetic dinoflagellate. Bob Andersen and D. J. Patterson

probe the water and sediments for prey. Others are part of the marine plankton. Many planktonic foraminifera have photosynthetic protists living in their cytoplasm (Figure 14.18). Foraminifera have lived and died in the oceans for more than 500 million years, so remains of countless cells have fallen to the seafloor. Over time, geologic processes transformed some accumulations of these shells into chalk and limestone, two types of calcium carbonate–rich sedimentary rock. The giant blocks of limestone that make up the great pyramids in Egypt consist mainly of the shells of ancient foraminifera. Modern foraminifera play an important role in the global carbon cycle. By taking up carbon dioxide from seawater and incorporating it into their shells, foraminifera lower the ocean’s carbon dioxide concentration and allow the seawater to absorb more carbon dioxide from the air. Removing carbon dioxide from the air is important because the increasing atmospheric concentration of this gas contributes to global climate change.

Whirling Dinoflagellates  The name dinoflagellate means “whirling flagellate.” These single-celled protists typically have two flagella, one at the cell’s tip and the other running in a groove around the middle of the cell like a belt (Figure 14.20). Combined action of the two flagella causes the cell to rotate as it moves forward. The vast majority of dinoflagellates are part of the marine plankton, and they are especially abundant in warm climates. In tropical seas, dinoflagellates are the most common source of bioluminescence, light produced by a living organism. When disturbed, dinoflagellates produce a blue or blue-green glow by means of an ATP-requiring reaction. A few photosynthetic dinoflagellate species live in the tissues of reef-building corals, which are invertebrate animals. The dinoflagellates supply the coral with oxygen needed for aerobic respiration and with photosynthetically produced sugar. The coral provides the protists with nutrients, shelter, and the carbon dioxide necessary for photosynthesis. Without its dinoflagellate partners, a reef-building coral will die. Ciliates  The ciliates are unwalled single-celled protists that use cilia to move and

feed. Most ciliates are predators in seawater or freshwater. They eat bacteria, algae, and one another. Paramecium is a freshwater ciliate commonly found in ponds (Figure 14.21). The cilia that cover its entire surface function in feeding and locomotion. They sweep water laden with bacteria, algae, and other food particles into an oral groove at the cell surface, and then to a gullet. Enzyme-filled vesicles digest food in the gullet.

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Prokaryotes, Protists, and Viruses  Chapter 14  281   food vacuole

empty contractile vacuole

gullet

nucleus

cilia

full contractile vacuole

Figure 14.22  Amoeba proteus, a freshwater amoeba.

shape. A compact blob of a cell can extend lobes of cytoplasm called pseudopods (Section 3.6) to move about and to capture food. Amoebas are common bottomdwellers in both freshwater and marine environments. Amoeba proteus (Figure 14.22) creeps along the bottom of well-oxygenated ponds and streams, where it engulfs and digests bacteria and smaller protists. A few species of amoebas live in animal bodies.

stipe

iStock.com/Micro_Photo

blade

Figure 14.21  The freshwater ciliate Paramecium.

Shape-Shifting Amoebas  Amoebas are unwalled cells that continually change

bladder

Figure 14.23  Structure of a giant kelp. Dr. Fred Hossler/ Visuals Unlimited, Inc.

holdfast

Algae Algae is a common term for the lineages of mostly multicellular photosynthetic protists that live in lakes and seas. We consider three lineages here: brown algae, red algae, and green algae. Brown Algae  The brown algae are multicellular photosynthetic protists that live mainly in temperate and cool seas. As previously noted, brown algae are close relatives of the diatoms. Like diatoms, they are colored brown by an accessory pigment in their chloroplasts. In size, brown algae range from microscopic filaments to the largest protists—giant kelps that stand 100 feet (30 meters) tall (Figure 14.23). Giant kelps dominate the forestlike underwater community that thrives along the coast of the northwestern United States. Like trees in a forest, kelps shelter a wide variety of other organisms. A compound extracted from the cell walls of brown algae is used to produce algins, which we use as thickeners, emulsifiers, and suspension agents. Algins are used to manufacture ice cream, pudding, jelly beans, toothpaste, cosmetics, and other products.

Figure 14.24  Red algae. Image courtesy of FGBNMS/UNCW-NURC

Red Algae and Green Algae  Red algae, green algae, and land plants share a variety

of unique traits, indicating a close evolutionary relationship among them. The red and green algae share a protist ancestor that had chloroplasts descended from cyanobacteria. After these two algal lineages diverged, land plants evolved from one lineage of green algae. Some red algae are single cells, but most are multicellular (Figure 14.24). Coralline algae (red algae with cell walls hardened by calcium carbonate) are a component of tropical coral reefs. Red algae are tinted red to black by accessory pigments called phycobilins. These pigments absorb the blue-green light that penetrates deep into water. Phycobilins allow red algae to carry out photosynthesis at greater depths than other algae. Red algae have many commercial uses. Nori, the sheets of seaweed used to wrap some sushi, is a red alga that is grown commercially. Agar and carrageenan are valuable products extracted from the cell walls of red algae. Agar keeps baked goods and cosmetics moist, helps jellies set, and is used to make capsules that hold medicines. Carrageenan is added to soy milk, dairy foods, and the fluid that is sprayed on airplanes to prevent ice formation.

amoeba  Solitary heterotrophic protist that feeds and moves by extending pseudopods. bioluminescence  Light produced by a living organism. brown alga  Multicelled, photosynthetic protist with brown accessory pigments. ciliate  Unwalled, single-celled protist with many cilia. diatom  Single-celled nonmotile photosynthetic protist with brown accessory pigments and a two-part silica shell. dinoflagellates  Single-celled, aquatic protist typically with cellulose plates and two flagella; may be heterotrophic or photosynthetic. red alga  Single-celled or multicelled photosynthetic protist with red accessory pigment.

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282  Unit 3  EVOLUTION AND DIVERSITY

20 µm

A. Chlorella, a single-celled green alga.

B. Volvox, a colonial, freshwater green alga.

C. Sheets of sea lettuce (Ulva), a multicelled marine green alga.

Figure 14.25  Green algae. (A) iStock.com/Nnehring; (B) Charles Krebs/SuperStock; (C) Sompraaong0042/Shutterstock.com

Green algae include single-celled, colonial, and multicellular species. Most live

in freshwater, but some are marine, and some grow on soil, trees, or other damp surfaces. A few single-celled species of green algae partner with a fungus to form a lichen. The single-celled alga Chlorella (Figure 14.25A) is common in ponds and lakes worldwide. It is also grown commercially, dried, and sold in powdered or pill form as a nutritional supplement. Chlorella is also a promising candidate for biofuel production because it has a high oil content and is easily cultivated. In the 1960s, Melvin Calvin used laboratory-grown Chlorella to carry out his Nobel Prize– winning studies on the steps in the Calvin Benson cycle. Volvox is a colonial freshwater green alga. Hundreds to thousands of flagellated cells are joined together by thin cytoplasmic strands to form a whirling, spherical colony (Figure 14.25b). Daughter colonies form inside the parental sphere, which eventually ruptures and releases them. Wispy sheets of the green alga Ulva cling to coastal rocks worldwide (Figure 14.25C). In some species, sheets grow longer than your arm, but are less than 40 microns thick.

Protists in the Human Body A. Giardia attached to the intestinal wall.

flagellum attached to the cell body by a membrane red blood cell

B. Trypanosoma in human blood. Figure 14.26  Flagellated protozoans that parasitize humans. (A) CDC/Dr. Stan Erlandsen; (B) Oliver Meckes/Science Source

In terms of species and number of cells, bacteria dominate the human microbiota. However, a wide variety of protist lineages can infect us. Infections by protists are most common in developing nations where cysts excreted in feces contaminate drinking water. A protistan cyst is a dormant cell enclosed within a thick protective wall. The protist most commonly found in the human body is Blastocystis, a singlecelled, nonphotosynthetic organism related to diatoms and brown algae. Blastocystis infects the human intestines. It is not clear whether Blastocystis is pathogenic. Most infected people show no symptoms, but others report cramps, aches, and bloody diarrhea. Whether the adverse symptoms arise from specific strains of Blastocystis or from other causes remains to be determined. Similar adverse symptoms occur when the ciliate Balantidium coli or the amoeba Entamoeba infect the human intestines. Flagellated Pathogens  The flagellated protozoans are single-celled protists with

one or more flagella. A variety of flagellated protozoans cause human disease. Giardia lamblia attaches to the intestinal lining of mammals, including humans, and sucks out nutrients (Figure 14.26A). Like other protist pathogens that infect the intestines, it causes cramps, nausea, and diarrhea. Infected people excrete cysts of G. lamblia in their feces. Another flagellated protozoan causes trichomoniasis, a sexually transmitted disease commonly called “trich.” Trichomoniasis currently affects an estimated 3.7 million people in the United States. Untreated infections damage the urinary tract, cause infertility, and increase risk of HIV (human immunodeficiency virus) infection.

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A trypanosome is a flagellated protozoan that has a finlike, membrane-enclosed flagellum (Figure 14.26B). Biting bugs transmit the trypanosome that causes Chagas disease, which can damage the heart and other organs if untreated. About 8 million people are infected, most of them in Central and South America. Other trypanosomes cause African sleeping sickness, which affects the brain and impairs the sleep cycle. If untreated, African sleeping sickness is typically fatal.

apicomplexan  Parasitic protist that enters and lives inside the cells of its host. green alga  Single-celled, colonial, or multicelled photosynthetic protist belonging to the group most closely related to land plants.

Apicomplexans and Malaria  All apicomplexans are parasitic protists that spend

part of their life inside cells of their hosts. Their name refers to a complex of microtubules at their apical (top) end that allows them to enter a host cell. In most species, the life cycle is complicated, with multiple hosts and several forms. The most well studied apicomplexans belong to the genus Plasmodium and cause the disease malaria (Figure 14.27). Of all protist diseases, malaria is responsible for the greatest number of deaths. When a female mosquito carrying the infectious form of Plasmodium (called a sporozoite) bites a human, the sporozoite enters the human bloodstream 1. The sporozoite travels through blood vessels to the liver, where it reproduces asexually, producing offspring called merozoites 2. Some of the resulting offspring enter red blood cells and produce more merozoites by asexual reproduction 3. Other merozoites enter into red blood cells and develop into immature gametes, or gametocytes 4. When a mosquito bites an infected person, it takes up gametocytes along with blood. The gametocytes mature in the mosquito’s gut, then fuse to form zygotes 5. Zygotes develop into new sporozoites that migrate to the insect’s salivary glands, where they await transfer to a new vertebrate host 6. Malaria symptoms usually start a week or two after a mosquito bite, when infected liver cells rupture and release Plasmodium cells and cellular debris into the blood. Shaking, chills, a burning fever, and sweats result. After the first episode, symptoms may subside for weeks or even months. However, an ongoing infection damages the liver, spleen, kidneys, and brain. If untreated, malaria nearly always results in death. Each year, almost a half million people die of malaria, most of them in Africa.

zygote

4 gametocytes

gametocytes in gut

Figure 14.27  Life cycle of Plasmodium, the protist that causes malaria.

1 Infected mosquito bites a human. Sporo-

5 asexual blood cycle

3 6

1

2 Sporozoites reproduce asexually in liver

cells, then mature into merozoites. Merozoites leave the liver and enter the bloodstream, where they infect red blood cells.

sporozoites

sporozoites in salivary glands

merozoites

mosquito takes up gametocytes or injects sporozoites

zoites enter the blood, which carries them to the liver.

2 liver stage

3 Inside some red blood cells, merozoites reproduce asexually. These cells burst and release more merozoites into the bloodstream.

4 Inside other red blood cells, merozoites

develop into male and female gametocytes.

5 A female mosquito bites and sucks blood

from the infected person. Gametocytes in red blood cells enter her gut and mature into gametes, which fuse to form zygotes.

6  Zygotes develop into sporozoites that Based on Fig. 1 from “Genetic linkage and association analyses for trait mapping in Plasmodium falciparum,” by Xinzhuan Su, Karen Hayton & Thomas E. Wellems, Nature Reviews Genetics 8, 497–506 (July 2007).

migrate to the mosquito’s salivary glands.

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284  Unit 3  EVOLUTION AND DIVERSITY

Digging Into Data How Plasmodium Summons Mosquitoes

1. On average, which group of children was the most attractive to mosquitoes? 2. Did carrying the noninfectious, asexual form of Plasmodium make children more attractive to mosquitoes than uninfected children? 3. Did the data support the hypothesis that the presence of infectious Plasmodium cells (gametocytes) makes an individual more attractive to mosquitoes? 4. Why would it be it beneficial for Plasmodium gametocytes to make their host attractive to mosquitoes?

12 Number of mosquitoes

Parasites sometimes alter their host’s behavior in a way that increases their chances of transmission to another host. Plasmodium (the protists that causes malaria) would benefit by making its human host more attractive to hungry mosquitoes when immature gametes (gametocytes) are present in the host’s blood. Such gametocytes are taken up by the mosquito along with blood, and they mature into gametes inside the mosquito’s gut. Dr. Jacob Koella and his associates performed an experiment to see whether infection by Plasmodium makes a person more attractive to mosquitoes. The researchers recorded the response of mosquitoes to the odor of Plasmodium-infected children and uninfected children over the course of 12 trials on 12 separate days. They also recorded which form of Plasmodium the infected children were carrying at the time. Figure 14.28 shows their results.

10 8 6 4 2 0

uninfected children

children with asexual stage

children with gametocytes

Figure 14.28  Number of mosquitoes (out of 100) attracted to uninfected children, children with asexual stages of Plasmodium (sporozoites, merozoites), and children with gametocytes. The bars show the average number of mosquitoes attracted to that category of child over the course of 12 separate trials.

Slime Molds

cellular slime mold  Heterotrophic protist that usually lives as a single-celled, amoeba-like predator. With unfavorable conditions, cells aggregate into a cohesive group that can form a fruiting body. choanoflagellates  Heterotrophic protists with a collared flagellum; protist group most closely related to animals. plasmodial slime mold  Heterotrophic protist that moves and feeds as a multinucleated mass; forms a fruiting body when conditions are unfavorable.

Slime molds are unusual among protists in that they all live on land. They are especially common on the floor of temperate forests. Slime molds are related to the amoebas and are sometimes described as “social amoebas.” There are two types: cellular slime molds and plasmodial slime molds. Cellular slime molds spend the bulk of their existence as individual amoeboid (amoeba-like) cells. Consider the life cycle of Dictyostelium discoideum (Figure 14.29), a species that is widely studied. Each cell eats bacteria and reproduces by mitosis 1. When food runs out, thousands of cells aggregate to form a multicelled mass 2. Environmental gradients in light and moisture induce the mass to crawl along as a cohesive unit often referred to as a “slug” 3. When the slug reaches a suitable spot, its component cells differentiate to form a spore-bearing structure called a fruiting body. Some cells become a stalk, and others become spores atop the stalk 4. When a spore germinates, it releases a cell that starts the life cycle anew 5. Plasmodial slime molds are usually encountered as a multinucleated mass called a plasmodium (Figure 14.30). The plasmodium forms when a diploid cell divides its nucleus repeatedly by mitosis but does not undergo cytoplasmic division. The resulting mass can be as big as a dinner plate. It streams out along the forest floor feeding on microbes and organic matter. When food supplies dwindle, a plasmodium develops into spore-bearing fruiting bodies. Later, after the spores disperse, a cell will emerge from each spore.

Protist Relatives of Animals Our closest relatives among the protists are the choanoflagellates, a small group of aquatic heterotrophic protists. They are not considered ancestors of animals, but rather a group that shared a common single-celled ancestor with animals long ago.

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Prokaryotes, Protists, and Viruses  Chapter 14  285  

5 Spores give rise

to amoeboid cells.

4 A fruiting

body forms with resting spores atop a stalk. Mature fruiting body

1 Cells feed

and multiply by mitosis.

2 When food

is scarce, cells aggregate.

Figure 14.29  Life cycle of the cellular slime mold Dictyostelium discoideum. Carolina Biological Supply Company

Migrating slug stage

3 The cells form a

slug. It may start to develop as a fruiting body right away, or migrate about. In the slug, cells become prestalk (red) and prespore (tan) cells.

Choanoflagellate means “collared flagellate.” Each choanoflagellate cell has a long flagellum surrounded by a ring (or collar) of tiny filaments reinforced with the protein actin (Figure 14.31A). Movement of the flagellum creates a current that draws water through the filaments. After tiny bits of food become entrapped, the cell extends pseudopods to capture them. The food is then digested within the cell body. As you will learn in Section 16.3, the feeding cells of sponges have a similar structure and function. Most choanoflagellates live as single cells, but some form colonies (Figure 14.31B). The colonies arise when cells divide and the descendant cells stick together with the help of adhesion proteins similar to those that hold cells together in an animal body.

Figure 14.30  Plasmodial slime mold on a log. This multinucleated mass (the plasmodium) streams along at a rate of about a millimeter an hour, engulfing any food it encounters. As the plasmodium travels, it lays down a trail of slime. If it later happens across its own trail, it will move off in a different direction. In this way, the slime mold “remembers” where it has been and avoids revisiting areas where it has already depleted its food supply. Edward S. Ross

actin-reinforced filaments of collar

flagellum

A. Structure of a solitary choanoflagellate.

Take-Home Message 14.6 ●●

●● ●●

●●

●●

The protists are a diverse collection of eukaryotic lineages, some of which are only distantly related to one another. Most protists live as single cells, but there are colonial and multicelled species. Protists include both producers and consumers. They live in freshwater, seas, and damp places on land. Some protists also live inside other eukaryotes, including humans. Protist diseases are spread by insect bites, by water contaminated with cysts, and by sexual contact. Green algae are the closest protist relatives of land plants, and choanoflagellates are the closest protist relatives of animals.

B. AA colonial colonialchoanoflagellate. choanoflagellate.

Figure 14.31  Choanoflagellates, the modern protist group most closely related to animals. (B) Courtesy of Damian Zanette

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286  Unit 3  EVOLUTION AND DIVERSITY

14.7  Viruses Learning Objectives

RNA

protein coat

●●

Explain how viruses replicate.

●●

Compare the structure of a bacteriophage and the human immunodeficiency virus (HIV).

●●

Explain how new combinations of viral genes can arise.

Although viruses are not cells, they are considered part of the human microbiota. A virus is a noncellular infectious particle that replicates only inside a living cell. We do not know how viruses are related to cellular life. The fact that they can only replicate inside cells suggests that they may have evolved from cells. Alternatively, viruses may be remnants of a time before cells. Viruses infect and replicate in all organisms, no matter how simple or complex. A viral infection often decreases a host’s ability to survive and reproduce, so viruses affect ecological interactions among species throughout the biosphere.

Viral Structure A. Tobacco mosaic virus, a helical virus that infects tobacco and related plants.

polyhedral “head”

DNA helical sheath tail fiber

A free viral particle (one that is not inside a cell) always includes a viral genome enclosed within a protein coat. The viral genome may be RNA or DNA, and it may be single-stranded or double-stranded. The viral coat consists of many protein subunits that self-assemble in a repeating pattern to produce a helical rod (Figure 14.32A) or many-sided (polyhedral) structure (Figure 14.32B). The coat protects the viral genetic material and plays a role in infection. In all viruses, components of the viral coat bind to proteins at the surface of a host cell. The specificity of this binding ensures that each type of virus can infect on only one species or a group of related species. In addition to the viral genome, the coat may also enclose viral enzymes that will act within the host. In many animal-infecting viruses, the protein coat is enclosed within a viral envelope (Figure 14.32C). The viral envelope is layer of cell membrane derived from the host cell in which the viral particle formed.

Viral Replication B. Bacteriophage, a bacteria-infecting virus with DNAfilled polyhedral head. lipid bilayer of envelope (derived from former host) glycoprotein spike matrix proteins coat proteins

Viral replication cycles vary in their details, but nearly all include the following steps. The virus first attaches to an appropriate host cell by binding to a specific protein or proteins in the host’s plasma membrane. Once a virus comes into contact with and attaches to a host cell, the viral genome, and in some cases other viral components, enter into that cell. A viral infection is like a cellular hijacking. Viral genes take over a host’s cellular machinery and direct it to replicate the viral genome and to build viral proteins. These viral components self-assemble to form new viral particles. The particles may be released when the infected host cell bursts (lyses) or they may bud from the host cell, taking a bit of host plasma membrane with them.

RNA

HIV—The AIDS Virus  HIV (human immunodeficiency virus) is an enveloped

viral enzyme

C. HIV (human immunodeficiency virus), an enveloped virus that infects humans. The envelope is derived from a host cell. Figure 14.32  Examples of virus structure. (A) After Stephen L. Wolfe; (B) Source: © Dr. Richard Feldmann/National Cancer Institute; (C) © Russell Knightly/Science Source

RNA virus that replicates inside human white blood cells (Figure 14.33). It attaches to a cell via a glycoprotein that extends out beyond the viral envelope 1. After attachment, the viral envelope fuses with the blood cell’s plasma membrane, releasing viral enzymes and RNA into the cell 2. A viral enzyme called reverse transcriptase uses viral RNA as a template to synthesize a double-stranded DNA 3. This DNA enters the nucleus together with another viral enzyme that inserts the DNA into one of the host’s chromosomes 4. Once integrated, the viral DNA is

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Prokaryotes, Protists, and Viruses  Chapter 14  287  

CLOSER LOOK Figure 14.33  Replication of HIV, an enveloped RNA virus.

1 Viral protein binds to proteins at the surface of a white blood cell.

2 Viral RNA and enzymes enter the cell. 3 Viral reverse transcriptase uses viral RNA to make double-

HIV DNA

2 3

4 reverse transcription

5

stranded viral DNA.

4 Viral DNA enters the nucleus and becomes integrated into

transcription

the host genome.

5 Transcription produces viral RNA. 6 Some viral RNA is translated to produce viral proteins. 7 Other viral RNA forms the new viral genome. 8 Viral proteins and viral RNA self-assemble at the host

HIV RNA

6 HIV

translation

7

plasma membrane.

1 9 8

9 Virus buds from the host cell, with an envelope of host plasma membrane.

Figure It Out: What is the product of reverse tran­ scription of HIV RNA?

Answer: Double-stranded DNA

1 Viral protein binds to proteins at the surface of a white blood cell. 2 Viral RNA and enzymes enter the cell. 3 Viral reverse transcriptase uses viral RNA to make double-stranded viral DNA. enters the nucleus and becomes into the genome. 4 Viral DNAand replicated transcribed along with theintegrated host genome 5.host Some of the resulting produces into viral viral RNA. proteins 6, and some becomes the genetic mate5 Transcription viral RNA is translated viral RNAparticles is translated to produce viralself-assemble proteins. 6 Some rial of new HIV 7. The particles at the plasma membrane 8. Other viral RNA forms the new viral genome. 7 As the virus buds from the host cell, some of the host’s plasma membrane becomes and9. viralEach RNAnew self-assemble the host plasma membrane. 8 Viral the viralproteins envelope virus canatthen infect another white blood cell. buds from the hostare cell, withproduced an envelope of host membrane. 9 Virus New HIV-infected cells also when an plasma infected cell replicates. The

Figure Summary HIV enters human white blood cells and replicates inside them. The process requires a viral enzyme, as well as the host's transcription and translation machinery.

disease AIDS (acquired immunodeficiency syndrome) arises as a result of HIV’s detrimental effects on the immune system. We consider these effects in detail in Chapter 23. Drugs that fight HIV take aim at steps in viral replication. Some interfere with the way HIV binds to a host cell. Others impair reverse transcription or assembly of new virus particles. These antiviral drugs lower the number of HIV particles, so a person stays healthier. Lowering the concentration of HIV in body fluids also reduces the risk of passing the virus to others.

Bacteriophage Replication  Bacteriophages, sometimes called phages, are nonenveloped viruses that infect bacteria. You learned earlier how Hershey and Chase used one type of bacteriophage to identify DNA as the genetic material of all organisms (Section 7.2). This bacteriophage, called lambda, has a complex structure. The “head” of the virus consists of a polyhedral protein coat and the viral DNA inside it. A hollow helical “tail” extends from the head. Bacteriophages replicate in bacteria by two pathways. Both pathways begin when a bacteriophage attaches to a bacterial cell and injects its DNA (Figure 14.34). In the lytic pathway, viral genes are expressed immediately. The infected host first produces viral components that self-assemble as virus particles. Then a viralencoded enzyme breaks down the host’s cell wall. Breakdown of the cell wall kills the cell and releases viral particles into the environment.

bacteriophage  Virus that infects bacteria. HIV (human immunodeficiency virus)  Enveloped RNA virus that causes AIDS. viral envelope  A layer of cell membrane derived from the host cell in which an enveloped virus was produced. virus  A noncellular infectious particle with a protein coat and a genome of RNA or DNA; replicates only in living cells.

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288  Unit 3  EVOLUTION AND DIVERSITY Virus injecting its DNA (red) into a bacterium

Lysis of the host cell releases the viral particles.

Lytic pathway Viral DNA directs the host to copy viral DNA and make viral proteins.

Viral DNA and proteins self-assemble as viral particles.

Host replicates, passing chromosome with viral DNA to its descendants.

Reactivation of the viral DNA in the descendant cells, as in response to an increase in bacterial population density, puts the cells on the lytic pathway.

Lysogenic pathway bacterial chromosome

Viral DNA is integrated into the host’s chromosome but is not expressed.

Figure 14.34  The two bacteriophage replication pathways.

In the lysogenic pathway, viral DNA becomes integrated into the host cell’s genome and viral genes are not immediately expressed, so the cell remains healthy. When the cell reproduces, viral DNA is copied and passed to the cell’s descendants along with the host’s genome. Like miniature time bombs, the viral DNA inside the new cells awaits a signal to enter the lytic pathway. Some bacteriophages can only replicate by the lytic pathway. They always kill their host cell quickly and are not passed from one bacterial generation to the next. Others embark upon either the lytic or lysogenic pathway, depending on conditions in the host cell.

Viruses and Human Health 

Figure 14.35  Cold sore.

Some viruses have a beneficial effect on human health. For example, some bacteriophages in the mucus that coats our airways and the lining of our diges­ t­ ive tract help keep bacterial pathogens from infecting us. Other viruses are themselves human pathogens. Most of these viruses produce mild symptoms and trouble us only briefly. For example, some rhinoviruses infect membranes of our upper respiratory system and cause common colds. The infection ends when the immune system eliminates all the virus-infected cells. A minority of viral diseases are more persistent. For example, after an initial infection, herpes simplex viruses can remain latent in the body and reawaken periodically to cause symptoms. As a result, the herpes simplex virus that causes chicken pox during childhood can also cause shingles in adults. Other herpes simplex viruses cause intermittent reappearances of sores on the genitals or “cold sores” on the edge of the lips (Figure 14.35). Some viruses can cause cancer. A few strains of human papillomavirus (HPV) can cause cancers of the cervix, penis, anus, or mouth. Infection by some hepatitis viruses increases the risk of liver cancer.

Evidence of an active herpes simplex virus 1 infection. Fluid rich in viral particles leaks from the open sore.

Emerging Viral Diseases  An emerging disease is a disease that has only recently

CDC/Dr. Hermann

been detected in humans or is now expanding its range.

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Prokaryotes, Protists, and Viruses  Chapter 14  289  

AIDS is the emerging viral disease caused by HIV. The virus was identified in 1981, but it probably entered the human population in the early 1900s. HIV evolved from SIV, a virus that infects African primates. After SIV entered and survived inside a human host, it mutated to become HIV. Sexual contact is now the main mode of HIV transmission. Ebola hemorrhagic fever is caused by an enveloped RNA virus first discovered in Africa in 1976. The virus causes flulike symptoms, followed by a rash, vomiting, diarrhea, and bleeding from all body openings. Contact with body fluids transmits the virus, and about half of those infected die. Until recently, Ebola outbreaks occurred only in limited regions of Africa and affected fewer than 500 people. However, an outbreak that began in Guinea in 2013 killed more than 11,000 people before ending in 2016. Sporadic African outbreaks have occurred since and are likely to continue. Zika virus is mosquito-borne RNA virus that can also be transmitted sexually. It was discovered in Africa during the 1950s and has since been observed in 90 countries, mostly in the tropics or subtropics. The majority of infections produce mild flulike symptoms, but some cause temporary or permanent paralysis. An infection during pregnancy raises the risk of miscarriage and of nervous system birth defects. In 2016, small outbreaks of Zika occurred in Florida and Texas. Mosquito control eliminated the virus in these states, so that by 2017 there were no locally contracted cases of Zika in the United States.

Viral Mutation and Recombination  Like living organisms, viruses have genomes that can be altered by mutation. RNA viruses such as HIV and influenza virus mutate especially quickly. New viral strains arise both through mutation and by viral reassortment, the swapping of genes between related viruses that infect a host at the same time (Figure 14.36). Consider the influenza viruses, which are enveloped RNA viruses that cause seasonal flus. To keep up with the ongoing evolution of influenza viruses, scientists create a new flu shot every year. The flu shot is a vaccine designed to protect against the influenza strains that scientists predict are most likely to pose a threat during the upcoming flu season. Unfortunately, determining which flu strains will be circulating in the future is not an exact science. Even after a flu shot, a person remains susceptible to a virus that differs from the strains targeted by the vaccine.

1 Two strains of influenza virus (shown here as red and blue) infect a host at the same time.

3 A mix of genes is packaged into each new viral particle that buds from the host cell.

viral genes

2 Inside the host cell, viral genes are copied and the copies mix.

Figure 14.36  Viral reassortment. When a host cell is infected by two viruses of the same type, such as two influenza viruses, viral genes recombine to form viruses with new gene combinations.

Take-Home Message 14.7 ●●

●●

●●

Viruses are noncellular particles that consist of genetic material wrapped in a protein coat. They replicate only inside living cells, and each type of virus infects and replicates inside a specific type of host. A virus harms and eventually kills a host cell. Viral genes direct the host cell’s metabolic machinery to produce new viral particles. Viral genomes can be altered by mutation. Viruses with new combinations of genes also arise as a result of viral reassortment.

viral reassortment  Two viruses of the same type infect an individual at the same time and swap genes.

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290  Unit 3  EVOLUTION AND DIVERSITY

Summary Section 14.1  The human microbiota includes all the microbes that can live on or in the human body. Some of these are pathogens, but most are harmless or beneficial. The composition of the microbiota differs among cultures and among individuals. People in industrialized cultures tend to have a less diverse microbiota than hunter-gathers or subsistence farmers. A diet rich in prebiotics helps maintain helpful bacteria in the digestive tract. Section 14.2  Scientists carry out experiments to test hypotheses about how life began. These experiments attempt to mimic conditions on the early Earth, such as the lack of free oxygen. Laboratory simulations show that organic subunits can self-assemble under certain conditions, including those near hydrothermal vents. Experiments also show how complex organic compounds and protocells may have formed on the early Earth. The RNA world hypothesis holds that the first genome was RNA-based. Section 14.3  The first life was prokaryotic and anaerobic. Fossil stromatolites are the most widespread evidence of early life. After an early divergence separated the bacteria from the archaea, production of oxygen by cyanobacteria altered Earth’s atmosphere and produced the protective ozone layer. Section 14.4  Archaea and bacteria are prokaryotic cells, meaning they lack a nucleus. They reproduce asexually by binary fission, and exchange genes through transformation, transduction, and conjugation (direct transfer of a plasmid). Bacteria are producers in many environments. Some are photoautotrophs that carry out photosynthesis. Others are chemoautotrophs that obtain energy by stripping electrons from inorganic molecules. Bacteria make nutrients available to other organisms by acting as decomposers and carrying out nitrogen fixation. Bacteria are used in scientific research, food production, and biotechnology. Some bacteria are part of our normal microbiota. Others are pathogens. Some pathogens produce resistant endospores. Archaea include heat-loving extreme thermophiles or salt-loving extreme halophiles. Others live in less extreme environments, such as the human gut. Some people have archaea that produce methane (methanogens) in their gut. Section 14.5  Eukaryotes arose about 1.8 billion years ago. They have a composite ancestry with both bacterial and archaeal components. According to the endosymbiont hypothesis, mitochondria and chloroplasts evolved from bacteria. Section 14.6  Protists are a diverse collection of lineages. Most lineages are single-celled, but some include colonial organisms

or multicellular organisms. Nearly all protists live in water or in moist habitats, including host tissues. A contractile vacuole allows single-celled, freshwater protists such as Euglena to expel excess water. Foraminifera are single-celled heterotrophs with calcium carbonate shells. They live on the seafloor or drift as marine plankton. Shells of foraminifera contribute to limestone and chalk. Diatoms are single-celled, silica-shelled, aquatic producers. Ciliates are single-celled heterotrophs that use cilia to move and feed. Amoebas are shape-shifting cells that extend pseudopods to feed and move. Dinoflagellates are single cells that move with a whirling motion and can be heterotrophs or photosynthetic. Some light up the seas with their bioluminescence. Brown algae include the giant kelps, which are the largest protists. Red algae can live at greater depths than other algae. Red algae share a common ancestor with green algae. Land plants evolved from a green alga. Some protists live in the human body. Giardia, Trichomoniasis, and some trypanosomes, are flagellated protozoans that cause disease. Apicomplexans, such as the species that cause malaria, are parasites that spend part of their life in cells of their host. Plasmodial slime molds feed as a giant multinucleated mass, then form a spore-bearing fruiting body when food runs out. The cellular slime molds spend part of their life as a single cell and part in a cohesive group that can migrate and differentiate to form a fruiting body. The choanoflagellates are the protists most closely related to animals. Section 14.7  Viruses consist of RNA or DNA inside a protein coat. Some also have a viral envelope. Viruses replicate only in living cells, as when bacteriophages multiply in bacteria. Mutation and viral reassortment produce new types of viruses. HIV (human immunodeficiency virus) is an enveloped RNA virus that infects human cells and causes acquired immunodeficiency syndrome (AIDS). HIV, Ebola virus, and Zika virus cause emerging diseases.

Self-Quiz Answers in Appendix I 1. Evolution of __________ led to an accumulation of oxygen in Earth’s atmosphere. a. aerobic respiration c. chemoautotrophs b. lactate fermentation d. the noncyclic pathway of photosynthesis

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Prokaryotes, Protists, and Viruses  Chapter 14  291  

2. Stanley Miller’s experiment demonstrated __________ . a. the great age of Earth b. that amino acids self-assemble under some conditions c. that oxygen is necessary for all life d. the feasibility of the endosymbiont hypothesis 3. The universal need for iron–sulfur cofactors is taken as evidence that metabolism may have begun __________ . a. on a meteorite b. on a mudflat c. on a rock near a hydrothermal vent 4. Mitochondria are descendants of ___________ . a. methanogenic archaea c. cyanobacteria b. aerobic bacteria d. green algae 5. __________ take up carbon dioxide from seawater and use it to make a chalky shell. c. Foraminifera a. Ciliates b. Diatoms d. Cyanobacteria 6. All __________ are parasitic eukaryotes that live in other cells. a. bacteriophages c. archaea b. apicomplexans d. diatoms 7. Oil-rich remains of ancient __________ are the main source of the petroleum that we use to make gasoline. a. diatoms c. foraminifera b. ciliates d. red algae 8. Some __________ live in corals and supply them with sugars. a. ciliates c. kelps b. viruses d. dinoflagellates 9. The closest protistan relatives of animals are the __________ . c. ciliates a. amoebozoans b. choanoflagellates d. foraminifera 10. Some __________ make nitrogen available to producers by carrying out nitrogen fixation. a. green algae c. bacteria b. diatoms d. viruses 11. Genetic material of a __________ can be either DNA or RNA. a. bacteria c. ciliate b. dinoflagellate d. virus 12. The genetic material of HIV is ___________ . a. protein c. RNA b. DNA d. ATP

13. Viral transfer of genes between bacteria is called ___________ . a. conjugation c. transduction b. viral reassortment d. transformation 14. Archaea ___________ . a. are more closely related to eukaryotes than to bacteria b. were the first prokaryotes c. commonly cause human disease d. live only in hot or salty environments 15. Match these terms with the appropriate definition. a. oxygen-producing prokaryote green algae b. social amoeba virus c. whirling cell methanogen d. noncellular infectious agent brown algae e. include the largest protists bioluminescence f. flagellate with chloroplasts euglena g. closest relative of plants cyanobacteria h. layered prokaryotes and sediment dinoflagellate i. biologically produced light slime mold j. methane producer stromatolite

CRITICAL THinking 1. The human virome is the collection of viruses that can live on and in a human body. Explain why the human virome includes both viruses that infect prokaryotic cells and viruses that infect eukaryotic cells. 2. The herbicide glyphosate works by inhibiting a plant enzyme that speeds production of amino acids. Some bacteria also make this same enzyme, raising the concern that the herbicide could have unforeseen ecological effects. Recently scientists found that exposure of honeybees to glyphosate alters the array of bacteria in their gut. How might the herbicide cause this change and what negative effects might it have on the bees’ health? 3. Which groups of protists are most likely and least likely to be found as fossils? Why? 4. Viruses that do not have a lipid envelope tend to remain infectious outside the body longer than enveloped viruses. “Naked” viruses are also less likely to be rendered harmless by soap and water. Can you explain why? 5. The apicomplexan that causes malaria had a photosynthetic ancestor and contains an organelle that evolved from its ancestral chloroplast. The organelle no longer functions in photosynthesis, but it does carry out some essential metabolic tasks. Why would targeting this organelle yield an antimalarial drug that would be likely to have minimal side effects?

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15 Plants and Fungi

15.1

Fungal Threats to Crops  293

15.2

Plant Traits and Evolution  294

15.3

Nonvascular Plants  296

15.4

Seedless Vascular Plants  298

15.5

Rise of the Seed Plants  301

15.6

Gymnosperms  302

15.7

Angiosperms—Flowering Plants  303

15.8

Fungal Traits and Diversity  307

15.9

Ecological Roles of Fungi  310

Plants and fungi in a Canadian forest. The fungus feeds on plant remains and releases nutrients that the living plants need to grow.

Concept Connections Ferenc Cegledi/Shutterstock.com

Most land ecosystems run on sunlight energy that plants capture through photosynthesis (Chapter 5). Energy flows through an ecosystem, but nutrients are recycled (Section 1.3), and fungi are essential to that recycling. We return to the ecological roles of plants and fungi in Chapter 18. Plants and fungi are eukaryotes that evolved from ancestral protists (Chapter 14), and both carry out mitosis and meiosis (Chapter 9). We will return to plant structure and function in Chapters 28 and 29.

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Plants and Fungi  Chapter 15  293 

Application 15.1  Fungal Threats to Crops Plants are the main producers on land and thus serve as an important food source for both animals and fungi. As a result, we often find ourselves competing with fungi for plant foods. For example, wheat is both an important agricultural crop and the host for wheat stem rust fungus (Puccinia graminis). This fungus is an obligate plant parasite, meaning it can grow and reproduce only in a living plant. The wheat stem rust fungus disperses by releasing microscopic spores that travel on the wind. A wheat stem rust infection begins when a fungal spore lands on a wheat plant. As fungal filaments extend through the plant’s tissues, they rob the plant of photosynthetic sugars. The loss of nutrients stunts the plant, so it produces few or no seeds. About a week after infection, rust-colored spore sacs appear on the stem of the infected plant (Figure 15.1). Each of the thousands of spores that form can disperse and infect a new plant. Outbreaks of wheat stem rust disease routinely destroyed wheat crops worldwide until the 1960s, when a plant breeding program produced resistant strains of wheat. Planting these wheat strains prevented outbreaks of wheat stem rust infection for decades. Then, in 1999, scientists discovered a new strain of wheat stem rust in Uganda. This strain, called Ug99, has mutations that allow it to infect almost all the wheat varieties that were previously resistant to wheat stem rust. Ug99 is now spreading. As of 2018, wind-borne spores of Ug99 had reached Kenya, Ethiopia, and Sudan, crossed the Red Sea to Yemen, and from there crossed the Persian Gulf to Iran. Given the prevailing winds, India, the Figure 15.1  Wheat stem rust fungus. world’s second largest wheat producer, will probably be affected soon. Most Wheat stem, with rust-colored fungal spore-producing likely, winds will eventually distribute Ug99 worldwide. Fungicides can ministructures on its surface. The inset micrograph shows mize the damage but are too expensive for farmers in developing nations. spores (red) escaping. The threat fungal diseases pose to crop plants is heightened by current Background, Photo by Yue Jin/US Department of Agriculture; inset, Courtesy of Charles Good, Ohio State University at Lima agricultural practices. Farmers often plant a single variety of a crop in dense stands that cover an extensive area. The proximity of many genetically identical host plants allows a fungus to spread quickly through a field. In addition, farmers in different parts of the world often buy seeds from the same large companies and plant the same few varieties of a crop. Protecting our food supply from the threat of plant diseases requires maintaining the genetic diversity of both crop plants and their wild relatives. Having many varieties of a crop increases the likelihood that at least one variety will be immune to any given disease. That variety can be planted or used to create new disease-resistant varieties, either through traditional plant breeding or by using genetic engineering to transfer disease-resistance genes. Wild relatives of crop plants can also provide disease-resistance genes. Discussion Questions For example, researchers have discov1. Identify at least two reasons why farmers prefer to plant a single variety of a crop. ered genes that confer Ug99 resistance 2. Imagine that you are a scientist advising farmers on sustainable agriculture. Sustainable in a wild grass related to wheat, and agriculture involves practices that demonstrate long-term feasibility. Why would you advise in a primitive wheat. Transferring these farmers not to plant a single variety of a crop? genes into widely used bread wheats 3. What specific steps can you take in your everyday life to support sustainable agriculture? could help ensure the safety of the world’s wheat supply.

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294  Unit 3  EVOLUTION AND DIVERSITY

Nonvascular Plants

Seedless vascular plants

Gymnosperms

Angiosperms

• No xylem or phloem

• Vascular tissue present

• Vascular tissue present

• Vascular tissue present

• Gametophyte predominant

• Sporophyte predominant

• Sporophyte predominant

• Sporophyte predominant

• Water required for fertilization

• Water required for fertilization

• Pollen grains; water not required for fertilization

• Pollen grains; water not required for fertilization

• Seedless

• Seedless

• “Naked” seeds

• Seeds form in a floral ovary that becomes a fruit

liverworts hornworts mosses

club mosses, spike mosses

whisk ferns, horsetails, ferns

gnetophytes, ginkgos, conifers, cycads

monocots, eudicots, and relatives

ancestral alga

Figure 15.2  Traits of modern plant groups and relationships among them. Photos, Courtesy of Christine Evers

15.2  Plant Traits and Evolution Learning Objectives

diploid phase

m

haploid phase

sis ito

Sporophyte plant (2n)

zygote (2n) Fertilization

Meiosis

m

to

spores (n)

i

s is

Describe the trait that defines land plants as a distinct lineage.

●●

Explain how plant life cycles differ from those of animals.

●●

List traits that adapt plants to life on land.

Plants are a lineage of land-dwelling, multicelled, typically photosynthetic eukaryotes. They evolved from freshwater green algae (a charophyte algae) and share many traits with this group. The defining trait that sets plants apart is a multicelled embryo that forms, develops within, and is nourished by the parent plant. For this reason, the clade of land plants is referred to as the embryophytes. Figure 15.2 summarizes the relationships among modern plants and their defining traits. The story of plant evolution is one of adaptation to increasingly drier environments. An aquatic green alga lives surrounded by water, so it can absorb water and dissolved nutrients across its entire surface. Water buoys the alga’s parts, thus helping it stand upright. On land, plants face the constant threat of drying out, and they have to hold themselves upright. Adapting to these new challenges involved changes in life cycle, structure, and altered mechanisms of reproduction and dispersal.

s is

gametes (n)

●●

Gametophyte plant (n)

mi

to

Figure 15.3  Plant life cycle (alternation of generations).

Life Cycles Plant life cycles differ from those of animals. Recall that animals are diploid and produce haploid gametes by meiosis (Section 9.5). By contrast, plants have an alternation of generations, a life cycle in which a diploid generation alternates with a haploid generation (Figure 15.3). The diploid plant body, called the sporophyte,

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Plants and Fungi  Chapter 15  295 

produces spores by meiosis. A plant spore is a single haploid cell that undergoes mitosis and develops into a multicellular, haploid body. This haploid body, called the gametophyte, produces gametes by mitosis. Gametes unite at fertilization to form a zygote that develops into a new diploid sporophyte. The relative size, complexity, and longevity of the haploid and diploid generations varies among the land plants. In the earliest plants, the gametophyte generation was “dominant,” meaning it was larger, longer-lived, and structurally more complex than the sporophyte. As time went by, new adaptive traits arose in the sporophytes of some lineages. Environmental pressures favoring these traits produced an evolutionary trend toward sporophyte dominance. Most modern plants are members of lineages in which the sporophyte generation is dominant.

Structural Adaptations Cuticle and Stomata  All land plants lose water to evaporation. In most, a layer of waxy secretions called a cuticle helps reduce water

loss from leaves and stems (Figure 15.4). Adjustable openings called stomata (singular, stoma) extend across the cuticle and allow gases to pass into and out of plant parts. Depending on environmental conditions, stomata either open to allow gas exchange or close to conserve water. Vascular Tissues  The oldest plant lineages have threadlike structures to hold them

in place, but these structures do not supply water and dissolved minerals to other parts of the plant. By contrast, the sporophytes of vascular plants have specialized tissues that serve as internal pipelines. There are two types of vascular tissues. Xylem is the vascular tissue that distributes water and mineral ions. Phloem is the vascular tissue that distributes sugars produced by photosynthetic cells. More than 90 percent of modern plants have xylem and phloem and thus are classified vascular plants. Older lineages that lack these tissues are known as nonvascular plants. In addition to distributing materials, vascular tissue provides structural support. Organic compounds called lignins stiffen the walls of xylem. Stems with lignin-stiffened tissue allow vascular plants to stand taller than nonvascular plants and to branch. Most vascular plants also have leaves. Leaves are flattened, above­ ground organs that increase the surface area available for capturing sunlight and for gas exchange. They contain veins of vascular tissue.

Reproduction and Dispersal Novel reproductive traits evolved in the lineage of vascular plants known as seed plants. Nonvascular plants and seedless vascular plants disperse by releasing spores, but seed plants disperse by releasing seeds. A seed consists of an embryo sporophyte and food to support it, enclosed within a protective coat. All nonvascular plants and seedless vascular plants have flagellated sperm. These sperm swim through droplets of water in their environment to reach an egg. As a result, these plants can only reproduce in a damp environment. By contrast, seed plants produce pollen grains. A pollen grain is a walled, immature male gametophyte. Wind or animals can convey pollen grains between plants, so seed plants can reproduce even in dry environments.

(vascular tissues) xylem

stoma (adjustable opening)

phloem

cuticle (layer of waxy secretions)

Figure 15.4  Cross section of a vascular plant leaf, showing some traits that adapt plants to land.

alternation of generations  A life cycle that alternates between a diploid spore-producing generation (the sporophyte) and a haploid, gamete-producing one (the gametophyte). cuticle  Secreted covering at a body surface. In plants it is waxy and helps conserve water. gametophyte  Haploid gamete-forming body in a plant life cycle. lignin  Compound that stiffens walls of some cells (including xylem) in vascular plants. phloem  Vascular tissue that distributes dissolved sugars. plant  Multicellular, typically photosynthetic organism; develops from an embryo that forms within the parent plant and is nourished by it. pollen grain  Immature male gametophyte of a seed plant. seed  Embryo sporophyte of a seed-bearing plant packaged with nutritive tissue inside a protective coat. seed plant  Vascular plant that produces seeds; an angiosperm or gymnosperm. sporophyte  Diploid spore-forming body in a plant life cycle. stomata  Adjustable openings that extend across a plant cuticle and allow gas exchange. vascular plants  Plant lineages that have xylem and phloem; include ferns, gymnosperms, and angiosperms. xylem  Vascular tissue that distributes water and dissolved mineral ions.

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296  Unit 3  EVOLUTION AND DIVERSITY

There are two kinds of seed plants, gymnosperms and angiosperms. Angiosperms are the only plants that make flowers and disperse their seeds inside of fruits.

Take-Home Message 15.2 ●●

●●

●●

●●

Plants are multicellular, photosynthetic eukaryotes that protect and nourish their multicelled embryos on their body. The plant life cycle alternates between two multicellular generations: a haploid gametophyte generation and a diploid sporophyte generation. Structural adaptations to life on land include a waxy cuticle with stomata, and vascular tissues that distribute materials and provide structural support. Evolution of pollen grains and seeds gave seed plants the capacity to live in drier places than other plants.

15.3  Nonvascular Plants Learning Objectives ●●

Explain why nonvascular plants tend to be low growing.

●●

Describe the life cycle of a moss.

●●

Give an example of an economically important moss.

All nonvascular plants (plants that lack xylem and phloem) were traditionally grouped together as bryophytes. The term “bryophyte” is still used as an informal designation for a nonvascular plant. However, biologists now recognize three distinct nonvascular lineages: the mosses, liverworts, and hornworts. Nonvascular plants are the only plants in which the gametophyte is larger and longer-lived than the sporophyte. However, even the gametophytes of these plants tend to be low growing. One constraint on their size is their lack of vascular tissue. Without internal pipelines, materials cannot move efficiently through a tall plant body. Reproductive factors also keep nonvascular plants small. All nonvascular plants produce flagellated sperm that must swim to eggs. The low, mat-like growth form of their gametophytes minimizes the distance that sperm must swim to reach an egg.

Moss Life Cycle

nonvascular plants  Plant lineages that lack xylem and phloem; for example, the mosses. rhizoid  At the base of a moss gametophyte, threadlike structures that hold it in place.

Mosses are the largest group of the nonvascular plants and the most familiar, so they will be our main focus here. As an example of a nonvascular plant life cycle, consider the life of the haircap moss (Figure 15.5). Haploid gametophytes of this moss are present year-round as small, free-living plants. The gametophyte has leaflike photosynthetic parts arrayed around a central stalk. Threadlike structures called rhizoids extend from the base of the gametophyte and hold it in place. Moss sporophytes appear only periodically. They lack chloroplasts and spend their life attached to and dependent on a gametophyte. The sporophyte body is diploid and consists of an unbranched stalk with a spore-producing organ (a sporangium) at its tip. Meiosis of cells inside a spore chamber yields haploid spores 1. The sporophyte releases its spores, then degenerates. After a moss spore is released, it germinates (becomes active) and develops into a gametophyte 2. Gametes form in multicellular organs (called gametangia) at the tips of each gametophyte. The moss we are using as our example has separate sexes, with each gametophyte producing either eggs or sperm. Rain triggers the release of flagellated sperm that swim through a film of water to eggs 3. Fertilization occurs inside the egg chamber and produces a zygote 4.

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Plants and Fungi  Chapter 15  297 

CLOSER LOOK Figure 15.5  Life cycle of a moss (Polytrichum).

1 Meiosis of cells in the spore capsule 2 Released spores develop into haploid gametophytes.

Figure It Out: Are cells of a rhizoid haploid or diploid?

5 zygote

sporophyte (2n)

4

Answer: Diploid

of the diploid sporophyte produces haploid spores.

3 Gametophytes produce gametes by mitosis.

Fertilization

Meiosis

4 A sperm swims to an egg and fertilizes it, forming a diploid zygote.

5 The zygote develops into a diploid sporophyte that remains attached to the gametophyte.

rhizoids

1

gametophyte (n) spore (n)

Figure Summary In mosses, as in all nonvascular plants, the haploid gametophye is the larger and longer-lived generation.

male gametophyte

sperm

3

egg

2 female gametophyte

haploid phase diploid phase

The zygote grows and develops into a new sporophyte while still attached to the gametophyte 5. In addition to reproducing sexually by producing spores, many mosses reproduce asexually by fragmentation. Fragmentation occurs when a piece of gametophyte breaks off and develops into a new gametophyte.

Diversity and Ecology With about 14,000 named species, mosses are the most diverse nonvascular plants. Many mosses colonize rocky areas where the lack of soil prevents other plants from becoming established. Over time, decomposition of dead moss helps to create a layer of soil in which vascular plants can take root. The 350 or so species of moisture-loving peat mosses (Sphagnum) are of notable ecological and commercial importance. Peat mosses are the dominant plants in peat bogs that cover hundreds of millions of acres in high-latitude regions of Europe, Asia, and North America. Many peat bogs have existed for thousands of years. Over that time, layer upon layer of partially decayed plant remains have become compressed to form deposits of a carbon-rich material called peat. People cut and dry blocks of peat for use as a clean-burning fuel (Figure 15.6). Freshly harvested peat moss is also an important commercial product. It is dried and added to planting mixes to help soil retain moisture. Liverworts and hornworts often live alongside mosses. Liverworts are so named because some liverwort gametophytes are flat and multilobed like a human liver.

Figure 15.6  Peat moss (Sphagnum). Blocks of dead, compacted peat moss are cut from long-established peat bogs and dried for use as fuel. The photo at the lower right shows the live moss. Background, DrimaFilm/Shutterstock.com; inset, AaronKitching/Shutterstock.com

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298  Unit 3  EVOLUTION AND DIVERSITY

Hornwort gametophytes are ribbonlike. Their common name refers to the hornlike spore capsule that the sporophyte produces.

Take-Home Message 15.3 ●● ●● ●●

Mosses and other nonvascular plants are low growing and lack vascular tissue. Nonvascular plants have flagellated sperm and disperse by releasing spores. Nonvascular plants are the only modern plants in which the gametophyte dominates the life cycle and the sporophyte is dependent upon it.

15.4  Seedless Vascular Plants Learning Objectives ●●

List some traits that seedless vascular plants share with nonvascular plants.

●●

Compare the structure of a fern sporophyte and fern gametophyte.

●●

Explain the role that nonvascular plants played in formation of coal.

Seedless vascular plants include three lineages: ferns, horsetails, and lycophytes. Like nonvascular plants, these plants have flagellated sperm that require a film of water to swim to eggs. Seedless vascular plants also are similar to nonvascular plants in that they disperse by releasing spores. Seedless vascular plants differ from nonvascular plants in other aspects of their life cycle and structure. Their gametophyte is reduced in size and is relatively shortlived. Although the sporophyte develops on the gametophyte body, it survives on its own after the gametophyte dies. Lignin stiffens a sporophyte’s body, and a system of vascular tissue distributes water, sugars, and minerals through it. These innovations in support and plumbing allow seedless vascular sporophytes to be large and structurally complex, with roots, stems, and leaves.

Ferns

epiphyte  Plant that grows on the trunk or branches of another plant but does not withdraw nutrients from it. ferns  Most diverse lineage of seedless vascular plants. rhizome  Stem that grows horizontally along or just below the ground. sorus (plural, sori)  Cluster of spore-forming chambers on a fern frond.

We begin our survey of the seedless vascular plants with the most diverse and familiar lineage, the ferns. Figure 15.7 shows the life cycle of a common North American fern. The leafy plant we envision when we think of a fern is a sporophyte 1. Fern leaves (referred to as fronds) have veins of vascular tissue running through them. In most ferns, the stem is a rhizome, a type of stem that grows along or just below the ground. Fronds and roots develop from the rhizome. Spores form by meiosis in spore-forming capsules on the underside of fronds 2. The spore-forming capsules are arranged in clusters called sori (singular, sorus). A spore capsule pops open to release the spores, which are dispersed by the wind. A spore germinates, then develops into a photosynthetic gametophyte that is just a few centimeters wide—much smaller than the sporophyte. Eggs and sperm form by mitosis in chambers on the underside of the gametophyte 3. In the fern we are discussing, eggs and sperm form on the same gametophyte. In some other ferns, each gametophyte produces either sperm or eggs. Sperm must swim to eggs to fertilize them 4. After fertilization, the resulting zygote develops into a new sporophyte 5. The sporophyte is initially attached to its parental gametophyte, but it continues to live and grow even after the gametophyte dies. Note that seedless vascular plants are the only plants in which both the sporophyte and the gametophyte are photosynthetic and free living. In many ferns, asexual reproduction occurs more frequently than sexual reproduction. New shoots and roots develop from a rhizome as it grows through the soil.

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Plants and Fungi  Chapter 15  299 

CLOSER LOOK Figure 15.7  Life cycle of a fern (Woodwardia). sporophyte (2n)

haploid phase

1 A diploid sporophyte produces haploid spores by meiosis. The spores form in sori on the underside of fronds.

diploid phase

young sporophyte (2n)

5

sori on underside of frond

2 Released spores grow into

tiny haploid gametophytes.

3 Gametophytes produce

eggs and spores by mitosis. zygote (2n)

4 Sperm swim to an egg and

fertilize it, forming a diploid zygote.

5 The sporophyte begins its

development attached to the gametophyte, but it continues to grow and live independently after the gametophyte dies.

4

1

rhizome

Fertilization

Meiosis egg (n)

Photo, A. & E. Courtesy of Christine Evers

Figure Summary In nonvascular plants such as ferns, both generations are photosynthetic, but the sporophyte is dominant.

2 gametophyte (n)

spore (n)

3

sperm (n)

Figure It Out: Do fern gametes form by meiosis? Answer: No. They form by mitosis on a haploid gametophyte.

Eventually the connection to the parent plant breaks, and that segment of rhizome becomes an independent plant. Fern sporophytes vary enormously in their size and form. Some float on freshwater ponds and have fronds less than a centimeter wide. Many tropical ferns are epiphytes, plants that live attached to the trunk or branches of another plant but do not withdraw nutrients from it. The largest ferns are tree ferns that grow up to 82 feet (25 meters) high.

Horsetails and Lycophytes  Horsetails (Equisetum) are close relatives of ferns. They thrive along streams and roadsides, and in disturbed areas. A horsetail sporophyte has rhizomes and hollow stems with tiny nonphotosynthetic leaves at the joints (Figure 15.8A). Photosynthesis occurs in stems and leaflike branches. The stems contain silica, a gritty mineral that helps the plant fend off insects and snails. Before the invention of modern abrasive cleansers, silica-rich stems of some Equisetum species were used to scrub pots and polish metals. Depending on the species, spore-bearing structures form either at tips of photosynthetic stems or on specialized reproductive stems that do no have chlorophyll. Most lycophytes belong to the group commonly known as club mosses, although they are not true mosses. Club mosses are common on the floor of temperate forests. Sporophytes of the club moss Lycopodium resemble miniature pine trees and are sometimes called ground pines (Figure 15.8B). Roots and upright stems covered by tiny, scalelike leaves grow from a rhizome. Each leaf has a single unbranched vein.

A. Horsetail

B. Club moss B. Club moss

Figure 15.8  Seedless vascular plants. (A) Matteo Gabrieli/Shutterstock.com; (B) © Martin LaBar, www.flickr.com/photos/martinlabar

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300  Unit 3  EVOLUTION AND DIVERSITY

Figure 15.9  Coal forest. An artist’s depiction of a swamp forest during the Carboniferous period. An understory of ferns 1 is shaded by tree-sized club mosses 2 and horsetails 3 .

3

2

1

When a Lycopodium plant is several years old, spore-bearing structures form at the tips of its stems. The spores have a waxy coating and ignite easily when suspended in the air. In the past, they were used as a flash powder for photography and they are still used for special effects such as simulating explosions.

Coal Forests 

coal  Fossil fuel consisting primarily of the carbonrich remains of seedless vascular plants. megaspore  In seed plants, a haploid cell that gives rise to a female gametophyte. microspore  In seed plants, a haploid cell that gives rise to a pollen-producing gametophyte. ovule  Chamber in an ovary of a seed-bearing plant; gives rise to an egg-containing gametophyte. Develops into a seed after fertilization. pollen sac  Of seed plants, chamber in which microspores form and develop into male gametophytes (pollen grains).

Ferns are currently the most diverse seedless vascular plants, but during the Carboniferous period (359 to 299 million years ago), swamp forests were filled with giant relatives of modern club mosses (Figure 15.9). Some of these plants stood more than 130 feet (40 meters) high. After the swamp forests appeared, climates changed, and the sea level rose and fell many times. When the waters receded, the forests flourished. After the sea moved back in, submerged trees became buried in sediments that protected them from decomposition. As layers of sediments accumulated one on top of the other, their weight squeezed the water out of the saturated, undecayed plant remains, and the compaction generated heat. Over time, pressure and heat transformed the compacted organic remains into coal. It took millions of years of photosynthesis, burial, and compaction to form coal. When you hear about annual production of coal or other fossil fuels, keep in mind that we do not really “produce” these materials, we only extract them. No new fossil fuels can form as quickly as we use the existing reserves, so these are nonrenewable sources of energy.

Take-Home Message 15.4 ●● ●●

pollination  Delivery of a pollen grain to the eggbearing part of a seed plant. wood  Lignin-reinforced tissue produced by secondary growth of some seed plants.

●●

Seedless vascular plants include ferns, horsetails, and club mosses. These plants disperse by releasing spores, and their life cycle is dominated by a sporophyte that has lignin-reinforced vascular tissue. The gametophyte is small and relatively short-lived. Like nonvascular plants, seedless vascular plants have flagellated sperm that must swim through a film of water to reach eggs.

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Plants and Fungi  Chapter 15  301 

Learning Objectives ●●

●●

Explain how the reproductive traits of seed plants put them at an advantage in dry environments. Describe the two types of spores that seed plants produce, where those spores form, and their roles in reproduction.

Seed plants evolved from a lineage of seedless vascular plants during the Carboniferous. They survived alongside nonvascular plants and seedless vascular plants until the late Carboniferous, then rose to dominance as the climate became drier. Unique traits of seed plants give them a competitive advantage over seedless plants in places where water can be scarce.

Seed Formation

2n

1

ovule diploid cell in pollen sac

diploid cell in ovule

2n

meiosis

meiosis and unequal cytoplasmic division

3

microspores (n) megaspore

n

2

4

pollen grains (male gametophytes)

egg egg-producing female gametophyte

po llin io

5

at n

Gametophytes of seedless vascular plants are free-living, meaning they develop from spores that were released into the environment. By contrast, gametophytes of seed plants develop within the protection of a spore-forming chamber (a pollen sac or an ovule) on a sporophyte (Figure 15.10). All seed plants produce two types of spores that differ in size. Meiosis of a cell inside a chamber called a pollen sac produces four microspores 1. Each microspore develops into a pollen grain, which is the sperm-producing gametophyte 2. In ovules, meiosis and unequal cytoplasmic division produce three small cells that disintegrate and one large megaspore 3. The megaspore develops into an egg-producing gametophyte 4. A seed plant releases its pollen grains but holds on to its eggs. Pollination is the delivery of a pollen grain to the egg-bearing part of a seed plant 5. In most seed plants, wind or animals transfer pollen from one plant to the pollen-receiving parts of another. Sperm of seed plants do not need to swim through a film of water to reach an egg-bearing plant, so seed plants can reproduce in dry times. After pollination, a pollen tube extends outward from the pollen grain into the ovule, where it delivers a sperm to the egg 6. Fertilization produces a zygote within the ovule, which then matures to become a seed 7.

pollen sac

6 seed coat stored food embryo

7 seed

pollen tube sperm cell

fertilization, development

Figure 15.10  How seeds form. This diagram shows the process in gymnosperms. The process is slightly different in angiosperms, as described in Section 15.7. Figure It Out: Do pollen sacs form on sporophytes or on gametophytes?

Answer: Pollen sacs form on sporophytes. They produce spores that develop into male gametophytes.

15.5  Rise of the Seed Plants

Seed Dispersal Dispersing by releasing seeds puts seed plants at an advantage over plants that disperse by releasing spores. A seed contains a multicelled embryo sporophyte and stored food that the embryo can draw on during early development. By contrast, a plant spore is a single cell that does not have any food reserves. In addition, seeds often also have adaptations that aid in their long-distance dispersal. For example, the seed may have a winglike structure that helps it catch the wind.

Wood Production Structural traits also give seed plants an advantage. Some seed plants undergo secondary growth during which their parts produce wood and thicken. Wood is lignin-stiffened tissue that strengthens and protects older stems and roots. The giant

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302  Unit 3  EVOLUTION AND DIVERSITY

seedless vascular plants that lived in Carboniferous forests did not produce wood. Instead, their trunks were supported by overlapping leaf bases. As a result, their trunks were softer and more flexible than those of woody seed plants. No nonwoody plants ever grew as tall as the tallest modern trees.

Take-Home Message 15.5 ●● ●●

●●

●●

Figure 15.11  Composite photo of one of the world’s tallest trees. This coast redwood (Sequoia sempervirens) stands 379 feet (116 meters) high in a northern California forest.

Seed plant spores develop into gametophytes while protected by the sporophyte body. Male gametophytes are pollen grains that can be carried to egg-bearing ovules even in dry environments. A seed contains a plant embryo and a food supply that the embryo can draw upon during its early development. Some seed plants undergo secondary growth (they thicken) and become woody.

15.6  Gymnosperms Gymnosperms are seed plants that produce seeds on the surface of ovules. Their

seeds are said to be “naked,” because unlike seeds of angiosperms, they are not inside a fruit. (Gymnos means naked and sperma is taken to mean seed.) However, many gymnosperms enclose their seeds in a fleshy or papery covering.

Conifers

James Balog/Aurora Photos

angiosperm  Seed plant that produces flowers and fruits. conifer  Woody gymnosperm with needlelike leaves. deciduous plant  Plant that sheds all its leaves in preparation for a seasonal dormancy. evergreen plant  Plant that has leaves throughout the year. flower  Specialized reproductive shoot of a flowering plant. gymnosperm  Seed plant that produces “naked” seeds (seeds that are not encased within a fruit).

Conifers are the most diverse gymnosperms with more than 600 species. All are woody trees or shrubs with needlelike or scalelike leaves. Most conifers are evergreen plants, meaning they have leaves throughout the year. Evergreen conifers are the main plants in cool northern hemisphere forests. A conical shape helps many conifers shed snow easily. Needlelike leaves with a heavy wax coating help a conifer minimize water loss during a long winter when soil is frozen, or during a dry hot season. Conifers include redwoods (Figure 15.11), which are the world’s tallest trees. They also include the longest-lived plants; some bristlecone pines are more than 4,000 years old. Conifers are of great economic importance. We mulch our gardens with fir bark, flavor gin with juniper “berries,” use oils from cedar in cleaning products, and eat the seeds, or “pine nuts,” of some pines. Pines provide lumber for building homes and furniture. Some pines make a sticky resin that deters insects from boring into them. We use this resin to make turpentine, a paint solvent. A pine tree’s life cycle is typical of conifers. The tree is a sporophyte and its cones are specialized spore-bearing structures. There are two types of cones: small, soft pollen cones and large, woody, seed cones (Figure 15.12). Both have scales (modified leaves) arranged around a central axis. Each scale of a pollen cone contains pollen sacs, and each scale of a seed cone contains ovules. Pollen released by a pollen cone drifts on the wind. Seed cones produce a sticky substance that traps the wind-borne pollen. After a pollen grain is trapped on the scale of a seed cone, a pollen tube grows toward one of the two ovules inside that scale. Fertilization occurs when the pollen tube delivers a nonmotile sperm cell to an egg in the ovule. The pollen tubes of pines grow very slowly, so fertilization can occur as long as a year after pollination. Fertilization produces a zygote that will develop into an embryo sporophyte. A conifer seed is a mature ovule that contains an embryo sporophyte.

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Plants and Fungi  Chapter 15  303 

Cycads and Ginkgos Cycads (phylum Cycadophyta) and ginkgos (phylum Ginkgophyta) are ancient gymnosperm lineages that were at their most diverse when dinosaurs walked the Earth. They are the only modern seed plants that have flagellated sperm. The sperm swim through a pollen tube to reach an egg inside an ovule. About 130 species of cycads survive, and they live mainly in tropical and subtropical regions. Cycads resemble palms or ferns but, being seed plants, they are not close relatives of either (Figure 15.13A). “Sago palms” commonly used in landscaping and as houseplants are actually cycads. All cycads form a mutually beneficial partnership with nitrogen-fixing cyanobacteria. The cyanobacteria live in specialized cycad roots that grow at the surface of the soil, where there is enough light for the bacteria to carry out photosynthesis. Because the bacteria supply their host with nitrogen, cycads can live in soils that have too little nitrogen to sustain other plants. In addition to nitrogen, the cyanobacteria produce a neurotoxic chemical that the cycad takes up and incorporates into its tissues. The level of this toxin is especially high in cycad seeds. Before the effects of this toxin were understood, people living on the Pacific island of Guam used cycad seeds to make flour and routinely ate bats that fed on cycad seeds. As a result of this dietary exposure, the population of Guam had an unusually high incidence of nervous system disorders. The only living ginkgo species is Ginkgo biloba, the maidenhair tree. It is native to China, but its pretty fan-shaped leaves (Figure 15.13B) and resistance to air pollution make it popular in many cities in the United States. Typically, male trees are planted because female trees make seeds with a fleshy covering that has a strong, unpleasant odor. Ginkgos are deciduous plants, meaning they shed all their leaves at the end of their growing season and spend the winter leafless and dormant.

Take-Home Message 15.6 ●●

●●

●●

needlelike leaf

seed cone pollen cone

Figure 15.12  Pine needles and cones. Pines have needlelike leaves and produce two types of cones: seed cones and pollen cones. This photo shows two seed cones and a cluster of pollen cones. Michael Giannechini/Science Source

A. Cycad with palmlike leaves and fleshy seeds.

Gymnosperms are one of the two lineages of seed-bearing vascular plants. Their seeds are not enclosed within a fruit. Conifers, the most diverse gymnosperm group, are evergreen trees with needlelike leaves. They are the most abundant trees in cool, high-latitude forests. Cycads and ginkgos are two ancient angiosperm lineages. They are the only living seed plants that produce flagellated sperm.

15.7  Angiosperms—Flowering Plants

B. Ginkgo tree with fan-shaped leaves and fleshy seeds.

Learning Objectives

Figure 15.13  Modern representatives of ancient gymnosperm lineages.

●●

Describe the components of a flower and the roles they play in reproduction.

●●

Explain the importance of animals in the reproduction and dispersal of flowering plants.

●●

Give examples of how humans use angiosperms.

(A) W. K. Fletcher/Science Source; (B) (Left) KPG_Payless/Shutterstock.com, (Right) picturepartners/Shutterstock.com

Floral Structure and Function Angiosperms are seed plants, and the only plants that make flowers and fruits. A flower is a specialized reproductive shoot that consists of modified leaves arranged

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304  Unit 3  EVOLUTION AND DIVERSITY stamen filament

carpel

anther

stigma

style

petal

ovary

ovule (forms within ovary)

sepal

in concentric whorls (Figure 15.14). Sepals, which usually have a green leaflike appearance, ring the base of a flower and enclose it until it opens. Just inside the sepals is a ring of petals, which are often brightly colored. Inside the petals are stamens, a flower’s pollen-producing parts. In most flowers, each stamen consists of a tall stalk (called the filament) topped by an anther that holds four pollen sacs. The carpel at the center of the flower captures pollen and produces eggs. A carpel has a sticky stigma, a region specialized for receiving pollen, at its tip. The stigma is located atop a stalk called the style. At the base of the style is an ovary, a chamber that contains one or more egg-producing ovules. After fertilization, an ovule matures into a seed and the ovary becomes the fruit. The name angiosperm refers to the fact that seeds form within the protection of the ovary; angio– means enclosed chamber, and sperma, seed.

Flowering Plant Life Cycle receptacle

Figure 15.15 shows a generalized life cycle for a flowering plant. A flower forms on the sporophyte body. Pollen sacs in the anthers hold diploid cells 1 that produce microspores by meiosis 2. The microspores develop into pollen grains

Figure 15.14  Floral structure.

1 An anther contains

four pollen sacs, each containing diploid cells that give rise to microspores.

haploid phase pollen sac ovule

4 An ovule forms on the

ovary wall. It contains a diploid cell that will undergo meiosis.

2n

seed coat (2n)

9 The ovule

develops into a seed.

Meiosis

embryo (2n) endosperm (3n)

seed

Meiosis

Double Fertilization

2 Meiosis

produces microspores.

diploid phase

microspores (n)

5 Meiosis megaspore (n)

3 Microspores develop into pollen grains.

pollen grain (n)

pollination

7 Pollination oc-

curs when a pollen grain reaches a receptive stigma. The pollen grain mature male germinates, and a gametophyte pollen tube grows through the ovary to the ovule, where it releases two sperm.

pollen tube delivers 2 sperm to ovule

pollen tube sperm

8 Double fertilization. One sperm

and unequal cytoplasmic division produce a megaspore.

mature female gametophyte in ovule

cell with 2 nuclei egg

6 A megaspore develops into a female gametophyte that includes an egg, a central cell with two nuclei, and five additional cells.

fertilizes the egg; the other fertilizes the cell that has two nuclei.

Figure 15.15  Angiosperm life cycle.

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Plants and Fungi  Chapter 15  305 

(immature male gametophytes) 3. Ovules form on the wall of an ovary at the base of a carpel 4. Meiosis of cells in ovules yields haploid megaspores 5. A megaspore develops into a female gametophyte consisting of a haploid egg, a cell with two nuclei, and a few other cells 6. Pollination occurs when a pollen grain arrives on a receptive stigma, the uppermost part of the carpel 7. The pollen grain germinates, and a pollen tube grows through the style (the structure that elevates the stigma) to the ovary at the base of the carpel. Two nonflagellated sperm form inside the pollen tube as it grows. Double fertilization occurs when a pollen tube delivers the two sperm into the ovule 8. One sperm fertilizes the egg to create a zygote. The other sperm fuses with the cell that has two nuclei, forming a triploid (3n) cell. After double fertilization, the ovule matures into a seed 9. The zygote develops into an embryo sporophyte and the triploid cell develops into endosperm, a nutritious tissue that will serve as a source of food for the developing embryo.

Angiosperm Success Flowering plants constitute 90 percent of all modern plant species. What accounts for angiosperm success? For one thing, they tend to grow faster than gymnosperms. Think of how a plant like a dandelion or a grass can grow from a seed and produce seeds of its own within a few months. In contrast, most gymnosperms take years to mature and produce seeds. Evolution of flowers gave angiosperms a selective advantage by encouraging animal-assisted pollination. After pollen-producing plants evolved, some insects began feeding on the plants’ highly nutritious pollen. Plants gave up some pollen but gained a reproductive edge when insects unknowingly moved pollen, thus facilitating pollination. Animals that facilitate pollination by moving pollen from one plant to another are called pollinators. Insects are the most common pollinators (Figure 15.16), but birds, bats, and other animals also serve in this role. Many traits of flowers are adaptations that attract pollinators. For example, producing sugary nectar encourages more pollinator visits, thus improving pollination rates and enhancing seed production. Brightly colored petals make flowers easier for pollinators to locate. A variety of fruit structures help angiosperms disperse their seeds. The structure of some fruits helps them ride the winds or stick to animal fur. Other fruits entice animals to eat them and release seeds in their feces. Gymnosperm seeds have less diverse dispersal mechanisms.

Monocots and Eudicots  The vast majority of flowering plants belong to one of two lineages. The monocots include orchids, palms, lilies, and grasses, such as rye, wheat, corn, rice, sugarcane, and other important crop plants. Eudicots include most herbaceous (nonwoody) plants such as tomatoes, cabbages, roses, and daisies; most

Figure 15.16  A pollinator. A bee unknowingly transfers pollen among flowers as it gathers pollen and sips nectar. Courtesy of Christine Evers

anther  Part of the stamen that contains pollen sacs. carpel  Ovule-containing part of a flower. double fertilization  In flowering plants, one sperm fertilizes the egg to form the zygote, and another fertilizes a cell that has two nuclei, forming a triploid cell that will give rise to endosperm. endosperm  Nutritive tissue in an angiosperm seed. fruit  Mature ovary that encloses a seed or seeds. ovary  Of flowering plants, a floral chamber that holds one or more ovules. pollinator  Animal that moves pollen from one plant to another, thus facilitating pollination. stamen  Pollen-producing part of a flower. Consists of an anther that contains pollen sacs, atop a filament. stigma  Pollen-receiving part of a carpel. style  Elongated portion of a carpel that holds the stigma above the ovary.

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306  Unit 3  EVOLUTION AND DIVERSITY

flowering shrubs and trees; and cacti. Monocots and eudicots derive their group names from the number of seed leaves (cotyledons) in the embryo. Monocots have one seed leaf, and eudicots have two. The two lineages also differ in many structural details. For example, some eudicots produce wood, but no monocots do. Section 28.2 describes the differences between eudicots and monocots in more detail.

Ecological and Economic Importance

A. Mechanized harvesting of wheat.

B. A field of cotton ready for harvest. Figure 15.17  Angiosperms as crops. (A) US Department of Agriculture; (B) Scott Bauer/USDA/ARS

It would be nearly impossible to overestimate the importance of angiosperms. As the most numerous and diverse plants in nearly all land habitats, they provide food and shelter for land animals. They also supply many products that meet human needs (Figure 15.17). Angiosperms provide nearly all human food, either directly or as feed for livestock. Cereal crops are the most widely planted. In the United States, more acreage is devoted to corn than to any other plant. Worldwide, rice feeds the greatest number of people. Wheat, barley, and sorghum are other widely grown grains. All are grasses (a type of monocot). Legumes are the second most important source of human food. They can be paired with grains to provide all the amino acids the human body needs to build proteins. Soybeans, lentils, peas, and peanuts are examples of legumes. Name a part of a plant, and humans eat it. In addition to the seeds of grains and legumes, we dine on leaves of lettuce and spinach, stems of asparagus, developing flowers of broccoli, modified roots of carrots and beets, and fruits of tomatoes, apples, and blueberries. Stamens of crocus flowers provide the spice saffron, and the bark of a tropical tree provides cinnamon. Fibers used to make clothing come from two main sources, petroleum and plants. Plant fibers include cotton, flax, ramie, and hemp. We also use fibers from flowering plants to weave rugs, and in many places to thatch roofs. Oak and other hardwoods derived from angiosperms provide flooring and furniture. We extract medicines and psychoactive drugs from angiosperms too. Aspirin is derived from a compound discovered in willows. Digitalis from foxglove strengthens a weak heartbeat. Coffee, tea, and tobacco are widely used plantderived stimulants. Worldwide, cultivation of opium poppies (the source of heroin) and coca (the source of cocaine) have wide-reaching health, economic, and political effects.

Take-Home Message 15.7 ●● ●●

●● ●●

Angiosperm seeds develop inside ovaries that become fruits. Angiosperms are the most diverse plant lineage. Adaptations that contributed to their success include a short life cycle, flower traits that attract pollinators, and a variety of fruit structures that aid in dispersal of seeds. There are two major angiosperm lineages: monocots and eudicots. Most plants grown as crops are angiosperms.

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15.8  Fungal Traits and Diversity

eudicots  Largest lineage of angiosperms; includes herbaceous plants, flowering trees, and cacti.

Learning Objectives

fungus  Single-celled or multicelled eukaryotic consumer that breaks down material outside its body, then absorbs nutrients released from the breakdown.

●● ●●

Explain how fungi feed. Describe the feeding structure and reproductive structure of a mushroom-producing fungus.

monocots  Angiosperm lineage that includes grasses, orchids, and palms.

With this section, we begin our survey of another major lineage of eukaryotes, the fungi. A fungus is a eukaryotic heterotroph that secretes digestive enzymes onto its food, then absorbs the resulting breakdown products. Most fungi are decomposers that feed on organic wastes and remains, but some live on or in other living organisms. Mushrooms are the most familiar fungi. They may seem similar to plants because, like plants, they spend their lives fixed in place. However, fungi are more closely related to animals than to plants. Table 15.1 compares some characteristics of fungi, plants, and animals.

Structure of a Fungus Fungi have a variety of growth habits. Some live as single cells and are referred to as yeasts (Figure 15.18A). However, most fungi are multicellular. Molds, mildews, and mushrooms are multicellular fungi (Figure 15.18B–D). Table 15.1  Comparison of Plants, Fungi, and Animals

Level(s) of Organization

Mode of Nutrition

All multicellular

Autotrophs Produce spores by (photosynthetic) meiosis

Kingdom

Cell Wall

Plants

Present (cellulose)

Fungi

Present (chitin Most multicellular, and glucan) some single-celled

Heterotrophs

Produce spores by mitosis or meiosis

Animals

Absent

Heterotrophs

Do not produce spores

All multicellular

Spore Formation

Figure 15.18  Variety of fungal forms. (A) Dr. John D. Cunningham/Visuals Unlimited, Inc.; (B) Scott Bauer/US Department of Agriculture; (C) Nigel Cattlin/Science Source; (D) Robert C. Simpson/Nature Stock

A. Yeast (single-celled fungus).

B. Mold growing on a grapefruit.

C. Mildew growing on leaves.

D. Mushrooms on a forest floor.

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308  Unit 3  EVOLUTION AND DIVERSITY

fruiting body hyphae

mycelium

pore in cross-wall

septate hypha

Figure 15.19  Hyphae as the basic units of a fungus. All parts of a multicellular fungus are composed of hyphae. Garry T. Cole, University of Texas, Austin/BPS. From Russell/Wolfe/Hertz/Starr, Biology, 3e, © Cengage Learning®.

Figure 15.20  Black bread mold, a zygote fungus. The fungus usually grows as a mass of hyphae that produces spores asexually (by mitosis). The inset micrograph shows a zygospore. Background, Micrograph J. D. Cunningham/Visuals Unlimited, Inc.; inset, © Ed Reschke

The body of a multicellular fungus is composed of many tiny filaments called hyphae (singular, hypha). Each fungal hypha is thinner than a human hair. In most familiar fungi, each hypha consists of walled cells arranged one after the other (Figure 15.19). However, hyphae of some fungi do not have internal walls. In these fungi, each hypha is like a bag of cytoplasm and nuclei. In all fungi, cell walls consist primarily of two complex carbohydrates: chitin and glucan. By contrast, plant cell walls consist mainly of cellulose. A fungus grows by adding cells to the tips of its hyphae. As fungal hyphae grow through soil or over organic material, they form a branching network called a mycelium (plural, mycelia). Fungi do not have vascular tissue; however, material can move within their hyphae. Any walls that exist between hyphal cells are porous, so nutrients or water taken up in one part of the mycelium can be shared with cells in other regions. Some mycelia are enormous. One honey mushroom fungus in Oregon has a mycelium that extends across about 3.4 square miles (8.8 square kilometers). This fungus is one of the largest living organisms and is at least 2,400 years old. Although the mycelium of a honey mushroom fungus is constantly present in the soil, honey mushrooms appear only seasonally. The mycelium is a feeding structure, whereas a mushroom is a reproductive structure. Like a mycelium, a mushroom is composed of tightly packed hypha.

Lineages and Life Cycles Scientists estimate there are more than a million species of fungus. Most fungi belong to one of five phyla: chytrid fungi (phylum Chytridiomycota), zygote fungi (Zygomycota), glomeromycete fungi (Glomeromycota), sac fungi (Ascomycota), and club fungi (Basidiomycota). All fungi disperse by producing spores. Recall that in plants, spores form by meiosis. Among fungi, by contrast, spores can form either asexually (by mitosis) or sexually (by meiosis). The details of spore formation differ among fungal groups and are one of the ways in which these groups are defined. Chytrid fungi are the only fungi that produce flagellated spores. Most chytrids are aquatic decomposers. However, some live in or on other organisms. When zygote fungi reproduce, they produce a thick-walled diploid structure called a zygospore. Some zygote fungi are molds, meaning they usually grow on organic material as a mass of asexually reproducing hyphae. Black bread mold is an example. When a spore of this zygote fungus lands on a piece of bread, the spore germinates and gives rise to a mycelium composed of haploid hyphae. As the mycelium grows over the bread, it produces specialized hyphae. These hyphae make haploid spores asexually, by mitosis of cells at their tips. Sexual reproduction of black bread mold usually occurs when food supplies run low. In all multicellular fungi, sexual reproduction begins with the fusion of haploid hyphae from two individuals of different mating strains. In zygote fungi, this fusion leads to formation of a thick-walled diploid structure—the zygospore (Figure 15.20). Meiosis of cells inside the zygospore yields haploid cells that give rise to a new haploid mycelium.

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Plants and Fungi  Chapter 15  309 

4 zygote (2n) in spore-forming cell

Figure 15.21  Generalized life cycle for a club fungus.

Fusion of nuclei

Meiosis

Colored dots in the hyphae indicate nuclei.

1 A haploid spore germinates and gives rise to a haploid mycelium.

spore-forming cell at gill edge (n+n)

2 When mycelia of two mating strains meet, cytoplasmic fusion produces a dikaryotic (n+n) mycelium.

5 spores (n)

gill

3A mushroom composed of dikaryotic hyphae develops. 4 Fusion of nuclei in cells of the mushrooms produces diploid

3

2

1

fruiting body (n+n)

mycelium (n+n)

mycelium (n)

(2n) zygotes.

5 Meiosis of a zygote produces haploid (n) spores. Figure It Out: Are cells that make up the stalk of a mushroom haploid, diploid, or dikaryotic?

Answer: Dikaryotic

Cytoplasmic fusion haploid

dikaryotic

diploid

A club fungus usually produces spores by meiosis of club-shaped cells. In many club fungi, these cells are part of a structurally complex fruiting body. The common button mushroom is an example of a club fungal fruiting body (Figure 15.21). After a club fungus spore germinates, mitotic divisions produce a haploid mycelium 1. If haploid hyphae of two club fungus individuals meet in the soil, cytoplasmic fusion may produce a dikaryotic cell. Dikaryotic means “having two haploid nuclei,” being (n+n). Mitotic divisions produce a dikaryotic mycelium 2. Multicelled club fungi spend most of their life cycle growing as a dikaryotic mycelium. When conditions favor reproduction, a sudden burst of hyphal growth produces a mushroom that emerges above the ground. A typical mushroom has a stalk and a cap, with thin sheets of tissue called gills on the cap’s underside 3. Fusion of haploid nuclei in the dikaryotic cells at the edges of the gills yields diploid zygotes 4. Each zygote undergoes meiosis, producing haploid spores 5. Each spore can give rise to a new haploid mycelium. Like club fungi, some sac fungi form complex fruiting bodies (Figure 15.22). However, sac fungus spores do not form in club-shaped cells. Instead, sac fungi form spores by meiosis inside a saclike cell. Hence the name “sac” fungus.

Figure 15.22  Morels, edible fruiting bodies of a sac fungus. unverdorben jr/Shutterstock.com

chytrid fungus  Fungus that produces flagellated spores; most are aquatic decomposers. club fungus  Fungus that produces spores by meiosis in club-shaped cells.

Take-Home Message 15.8 ●●

●● ●●

Fungi are heterotrophs that absorb nutrients from their environment. They live as single cells or as a multicelled mycelium and disperse by producing spores. Zygote fungi grow as molds that most often produce spores asexually. Mushrooms are spore-producing fruiting bodies of club fungi. Some sac fungi also produce similarly large fruiting bodies.

hypha (plural, hyphae)  In a multicellular fungus, a single filament of the fungal mycelium. mycelium (plural, mycelia)  Mass of threadlike filaments (hyphae) that compose the body of a multicelled fungus. sac fungus  Fungus that produces spores by meiosis in saclike cells. zygote fungus  Fungus that forms a thick-walled zygospore during sexual reproduction.

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310  Unit 3  EVOLUTION AND DIVERSITY

15.9  Ecological Roles of Fungi Learning Objectives ●●

●●

Using appropriate examples, describe the mechanisms by which fungi can help or harm other organisms. List some of the ways in which humans make use of fungi.

Decomposers Most fungi provide an important ecological service by breaking down complex compounds in organic wastes and remains. When a fungus secretes digestive enzymes onto these materials, some soluble nutrients escape into nearby soil or water. Plants and other producers can then take up these nutrients to meet their own nutritional needs. Bacteria also serve as decomposers, but they tend to grow mainly on surfaces. By contrast, fungal hyphae can extend deep into a bulky food source such as a dead log and break it down from the inside (Figure 15.23). Figure 15.23  Fungi as decomposers.

Fungal Infections of Plants

A coral fungus (a type of club fungus) is growing through this log. The white structure is the fungal fruiting body.

Some fungi are plant parasites. Powdery mildews (which are sac fungi) and rusts and smuts (which are club fungi) grow only in living plants. Wheat stem rust is an example. Hyphae of mildews, rusts, and smuts extend into cells of stems and leaves, where they suck up photosynthetically produced sugars. The resulting loss of nutrients stunts the plant, reduces its ability to form seeds, and may eventually kill it. However, a plant usually does not die before the fungus has produced spores on the surface of its infected parts. Other pathogenic fungi produce toxins that kill plant tissues, then feed on the resulting remains. The club fungus Armillaria causes root rot by infecting trees and

Timothy D. Kramp/Shutterstock.com

Digging Into Data The club fungus Armillaria ostoyae infects living trees and acts as a parasite, withdrawing nutrients from them. When the tree dies, the fungus continues to dine on its remains. Fungal hyphae grow out from the roots of infected trees and roots of dead stumps. If these hyphae contact roots of a healthy tree, they can invade and cause a new infection. Canadian forest pathologists hypothesized that removing stumps after logging fungus-killed trees could help prevent additional tree deaths. To test this hypothesis, they carried out an experiment. In half of a forest, they removed stumps after logging. In a control area, they left stumps behind. For more than 20 years, they recorded tree deaths and whether A. ostoyae caused them. Figure 15.24 shows the results. 1. Which tree species was most often killed by A. ostoyae in control forests? Which was least affected by the fungus? 2. For the species most affected, what percentage of deaths did A. ostoyae cause in control and in experimental forests? 3. Do the overall data support the hypothesis that stump removal helps protect living trees from infection by A. ostoyae?

Percent cumulative mortality resulting from A. ostoyae

Removing Fungus-Infected Stumps to Save Trees 30

experimental forest control forest

25 20 15 10 5 0

Birch Larch Spruce Douglas Pine Cedar fir Figure 15.24  Results of a long-term study of how logging practices affect tree deaths caused by the fungus A. ostoyae. In the experimental forest, whole trees—including stumps—were removed (gold bars). The control half of the forest was logged conventionally, with stumps left behind (blue bars). After graph from www.pfc.forestry.ca.

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Plants and Fungi  Chapter 15  311 

woody shrubs in forests worldwide. Once an infected tree dies, the fungus decomposes the stumps and logs left behind.

Fungal Infections of Animals Animals are less vulnerable to fungal infections than plants and, among animals, those with a high body temperature are least susceptible. About 50,000 species of fungus can infect insects, whereas only a few hundred can infect mammals. Like insects, amphibians do not maintain a high body temperature, and many amphibian species are currently threatened by one pathogenic chytrid that has been spread worldwide by humans. In mammals, fungi seldom cause fatal infections. White-nose syndrome, a fungal disease currently decimating North American bats, is an exception (Figure 15.25). The disease was first discovered in upstate New York in 2006. By 2018, infected bats had been reported in 33 states and millions of North American bats had died of the disease. The fungus kills bats during the winter, when they go into hibernation and their body temperature drops. The presence of the fungus irritates the bat’s skin, causing the bat to come out of hibernation. Awakening and fidgeting during winter, when no food or water is available, causes infected bats to waste away, so many do not survive until spring.

Fungal Infections in Humans Human fungal infections most frequently involve body surfaces. Typically, a fungus feeds on the outer layers of skin, secreting enzymes that dissolve keratin, the main skin protein. Infected areas become raised, red, and itchy, as when fungi infect skin between the toes and on the sole of the foot, causing “athlete’s foot.” Fungi also cause the skin infection commonly known as “ringworm.” No worm is involved. A ringshaped lesion is caused by the growth of hyphae outward from the initial infection. Fungal vaginitis (a vaginal yeast infection) occurs when single-celled fungi that normally live in the vagina in low numbers undergo a population explosion. Symptoms of the infection include itching or burning sensations; a thick, odorless, whitish vaginal discharge; and pain during intercourse. Fungi seldom cause systemwide disease in otherwise healthy people. However, fungal infections can be life-threatening in people whose immune system is impaired, as by AIDS or chemotherapy.

Fungal Partnerships Nearly all plants form mutually beneficial relationships, or mutualisms, with fungi. For example, many soil fungi take part in a mycorrhiza (plural, mycorrhizae), a mutually beneficial relationship with plant root cells (Figure 15.26). In mycorrhizae that involve glomerocyte fungi, hyphae penetrate the root cell wall and share space with the cell. An estimated 80 percent of vascular plants have a glomeromycete partner. Some zygote fungi, sac fungi, and club fungi also take part in mycorrhizae. In these groups, the hyphae grow into a root and between its walled cells, rather than penetrating the cell wall. Hyphae of all mycorrhizal fungi functionally increase the absorptive surface area of their plant partner. Hyphae are thinner than even the smallest roots and can grow more easily between soil particles. The fungus shares water and nutrients taken up by its hyphae with root cells. In return, the plant supplies the fungus with photosynthetically produced sugar. Fungal partners also enhance the nutrition of some animals. Chytrid fungi that live in the stomachs of grazing hoofed mammals such as cattle, deer, and moose

Figure 15.25  White-nose syndrome. Affected bats have white filaments of a parasitic sac fungus on their wings, ears, and muzzle. NPS

sporangium

plant root hypha branching inside a root cell wall

Figure 15.26  A mycorrhiza. Specialized hyphae of glomeromycete fungus enter and branch inside the cell wall of a plant root cell.

mutualism  Species interaction that benefits both species. mycorrhiza  Fungus–plant root partnership.

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312  Unit 3  EVOLUTION AND DIVERSITY

photosynthetic cell

fungal hyphae

Figure 15.27  Structure of a leaflike lichen. Przemyslaw Muszynski/Shutterstock.com

aid their hosts by breaking down otherwise indigestible cellulose. Similarly, fungal partners of leafcutter ants serve as an external digestive system. The ants bring bits of leaves to their nest, where the leaf bits serve as food for a fungus. The primary food of the ants is not the leaves (which they cannot digest), but rather specialized hyphae produced by their farmed fungi. Lichens are composite organisms consisting of a fungus and a single-celled photosynthetic species, either a green alga or a cyanobacterium. The fungus makes up most of the lichen’s mass and shelters the photosynthetic species, which shares nutrients with the fungus. Lichens grow on many exposed surfaces (Figure 15.27). They are ecologically important as colonizers in places that are too hostile for other organisms. By releasing acids and retaining water that freezes and thaws, lichens help break down rocks and form soil.

Human Uses of Fungi

Figure 15.28  Products made with the help of fungi. Sac fungal yeasts carry out fermentation necessary to make bread and wine. The blue material in “blue cheese” is hyphae of a sac fungal mold. iStock.com/Cameron Whitman

Some fungi are important as human food crops. Mushroom farms produce many varieties of club fungi by inoculating sterilized compost with spores of the desired crop species. Mycorrhizal fungi, including chanterelles, morels, and truffles, cannot be easily cultivated, so they are most commonly gathered from the wild. If you are considering mushroom hunting, keep in mind that many edible species have poisonous look-alikes. Mushrooms taken from the wild should always be identified by an experienced mushroom forager before they are eaten. In addition to eating fungi, we make use of fungal fermentation reactions to produce food and drinks (Figure 15.28). A package of baker’s yeast contains spores of a sac fungus (Saccharomyces cerevisiae). Set bread dough out to rise, and yeast cells carry out fermentation reactions that produce carbon dioxide, causing the dough to expand (rise). Other strains of Saccharomyces help us produce beer and wine. Geneticists and biotechnologists also make use of the yeast S. cerevisiae. Like E. coli bacteria, S. cerevisiae grows readily in laboratories and it offers the added advantage of being eukaryotic like us. Checkpoint genes that regulate the eukaryotic cell cycle (Section 9.3) were first discovered in S. cerevisiae. This discovery was the first step toward our current understanding of how mutations of these genes cause

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human cancers. Genetically engineered S. cerevisiae and other yeasts are also now used to produce proteins that serve as vaccines or other medicines. Some medicines and psychoactive drugs are compounds first isolated from fungi. Most famously, the initial source of the antibiotic penicillin was the sac fungal mold Penicillium. Fungi have also yielded drugs that we use to lower blood pressure, reduce cholesterol levels, or to prevent rejection of transplanted organs. Lysergic acid, a precursor to the hallucinogen LSD, was first isolated from ergot, a club fungus that infects grains. So-called magic mushrooms contain compounds called psilocybins that induce a dreamlike state.

lichen  Composite organism consisting of a fungus and photosynthetic cells (either green algae or cyanobacteria).

Take-Home Message 15.9 ●●

●●

●●

Mycorrhizal fungi live in or on plant roots in a mutually beneficial relationship. Fungi also live with single-celled photosynthetic cells as lichens. Fungi benefit other organisms when they feed on wastes and remains, releasing nutrients into the soil. They harm other organisms, including humans, by infecting and feeding on their tissues. We use fungi as food, as sources of drugs, and as a model for studying genetic processes.

Summary Section 15.1  Plants are food for both people and fungi. Winds spread spores of fungal pathogens, so outbreaks of fungal disease can spread often over a wide area. Section 15.2  Plants evolved from freshwater green algae. Their life cycle, an alternation of generations, includes two multicelled forms, a haploid gametophyte and a diploid sporophyte. The gametophyte dominates the life cycle of nonvascular plants, but the sporophyte dominates in vascular plants. Key adaptations to dry habitats include a waterproof cuticle with stomata, and internal pipelines of xylem and phloem. Xylem reinforced by lignin helps vascular plants stand upright. Seeds and male gametophytes that can be dispersed without water (pollen grains) evolved in seed plants. Section 15.3  Nonvascular plants (bryophytes) include three lineages of low-growing plants: mosses, liverworts, and hornworts. The photosynthetic moss gametophyte is held in place by threadlike rhizoids. Flagellated sperm swim to eggs. The sporophyte remains attached to and often dependent upon the gametophyte even when mature. Section 15.4  Ferns are seedless vascular plants. Sporophytes dominate their life cycle and produce spores in sori. Gametophytes

produce eggs and flagellated sperm. Ferns grow from rhizomes (horizontal stems). Some live on trees as epiphytes. Other seedless vascular plants include club mosses and horsetails. Coal formed from the remains of ancient nonvascular seed plants. Section 15.5  Seed-bearing vascular plants make two types of spores. Microspores give rise to pollen grains in a pollen sac. Megaspores form in ovules and give rise to egg-producing female gametophytes. Even in the absence of water, winds or pollinators can move pollen, thus facilitating pollination. The seed is a mature ovule, with an embryo sporophyte and some nutritive tissue inside it. Some seed plants undergo secondary growth and produce wood. Section 15.6  Conifers, cycads, and ginkgos are among the gymnosperms. They are adapted to dry climates and bear seeds on exposed surfaces of spore-bearing structures. In conifers, these spore-bearing structures are distinctive cones. Conifers tend to be evergreen plants. Ginkgos are deciduous plants. Section 15.7  Angiosperms are the dominant land plants. They alone have flowers. Pollen forms in a flower’s anthers, the part of a stamen that holds pollen sacs. Many flowering plants coevolved with pollinators that deliver pollen to a receptive

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314  Unit 3  EVOLUTION AND DIVERSITY

Summary (Continued) stigma. After pollination, a pollen tube grows through a style of the flower’s carpel to the ovary at its base, and double fertilization occurs. The ovary becomes a fruit containing one or more seeds. A flowering plant seed includes an embryo sporophyte and endosperm, a nutritious tissue. Most crops are angiosperms. There are two main lineages of flowering plants. Monocots include grasses and palm trees. Eudicots include most flowering trees and shrubs, as well as most herbaceous plants. Section 15.8  Fungi are single-celled or multicelled heterotrophs. They secrete enzymes onto organic material and absorb the resulting breakdown products. Multicelled fungi grow as a mycelium composed of many filaments called hyphae. Fungi produce spores both sexually and asexually. A mushroom is a spore-producing body of a club fungus. Fungi of some sac fungi are also used as food. Bread mold is an example of a zygote fungus. Section 15.9  Most fungi are decomposers. A mycorrhiza is a mutualism between a fungus and plant root cells. Fungi also partner with photosynthetic cells to form lichens. Some fungi infect plants or animals, causing disease. We eat fungi and use them to produce foods, drinks, and medicines.

Self-Quiz Answers in Appendix I 1. Which of the following statements is not correct? a. Angiosperms produce pollen and seeds. b. Mosses are nonvascular plants. c. Ferns and angiosperms are vascular plants. d. Only gymnosperms produce fruits. 2. Which does not apply to all seed plants? a. Vascular tissues b. Diploid dominance c. Single spore type d. All of the above 3. Mosses have independent __________ and dependent __________ . a. sporophytes; gametophytes b. gametophytes; sporophytes

4. Ferns and horsetails are__________ plants. a. flowering b. nonvascular c. seedless vascular d. seed-bearing vascular 5. Unlike ferns, conifers have __________ . a. vascular tissue b. seeds c. flagellated sperm d. fruits 6. The __________ produced in the male cones of a conifer develop into pollen grains. a. ovules b. ovaries c. megaspores d. microspores 7. A seed is a(n) __________ . a. female gametophyte b. mature ovule c. mature pollen tube d. immature megaspore 8. Match the terms appropriately. gymnosperm sporophyte fern moss gametophyte stomata angiosperm

a. gamete-producing body b. help control water loss c. “naked” seeds d. spore-producing body e. nonvascular plant f. seedless vascular plant g. flowering plant

9. All fungi __________ . a. are multicelled b. form flagellated spores c. are heterotrophs d. produce multicellular fruiting bodies 10. Fungal decomposers derive nutrients from __________ . a. organic wastes and remains b. living plants c. living animals d. photosynthesis

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Plants and Fungi  Chapter 15  315 

11. A mushroom is __________ . a. the food-absorbing part of a fungus b. the food-producing part of a fungus c. a reproductive structure that releases sexual spores d. the only part of the fungal body not made of hyphae 12. Human fungal infections most commonly involve __________ . a. the brain b. the heart c. the digestive system d. body surfaces 13. A __________ is a composite organism composed of a fungus and a single-celled photosynthetic species. a. mycorrhiza b. lichen c. decomposer d. ringworm 14. Cell walls of fungi are composed of __________ . a. cellulose b. keratin c. lignin d. chitin 15. Match the terms appropriately. decomposer     a. food-absorbing filament yeast        b. club fungus fruiting body mushroom      c. fungus with flagellated spores chytrid       d. mesh of fungal filaments hypha       e. root-fungus partnership mycelium      f. single-celled fungus mycorrhiza      g. breaks down organic matter

CRITICAL THinking 1. Early botanists admired ferns but found their life cycle perplexing. In the 1700s, they learned to propagate them by sowing what appeared to be tiny dustlike “seeds” from the undersides of fronds. Despite many attempts, the scientists could not find the pollen source, which they assumed must stimulate the “seeds” to develop. Imagine you could write to one of these botanists. Compose a note that would clear up their confusion. 2. Consider a cherry pit, which is a seed containing an embryonic cherry tree sporophyte. Trace the paternal ancestry of that embryo. Explain how the sperm that fathered that embryo came to unite with the egg, and the process by which that sperm formed. 3. When infected by a parasitic fungus such as wheat stem rust, some plants produce chitinase (an enzyme that breaks down chitin) and/or glucanase (an enzyme that breaks down glucan). Explain how production of these enzymes could help a plant fend off a fungal parasite. What mechanisms might allow the rust fungus to overcome these plant defenses? 4. Fungal skin diseases are persistent, in part because fungi can penetrate deeper layers of skin than can ointments and creams used as the first line of defense against these infections. There are fewer oral antifungal medications than antibacterial ones. Reflect on the evolutionary relationships among bacteria, fungi, and humans. Why it is harder to develop oral medications against fungi than bacteria? 5. Recently discovered fossils from the Canadian Arctic may be evidence of early fungi. The fossils consist of spheres that resemble fungal spores and filaments that resemble fungal hyphae. In addition, chemical analysis of the fossils suggests that they are the remains of organisms that contained chitin. The fossils date back about a billion years, which is hundreds of thousands of years before plants or animals arose. Given that fungi living a billion years ago could not have been decomposing plant or animal material, how do you think they met their nutritional needs?

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16 Animal Evolution

16.1

Medicines from the Sea  317

16.2

Traits and Evolutionary Trends  318

16.3

Sponges and Cnidarians  321

16.4

Flatworms, Annelids, and Mollusks  323

16.5

Roundworms and Arthropods  326

16.6

Echinoderms and Chordates  332

16.7

Fishes and Amphibians  335

16.8

Escape from Water—Amniotes  338

16.9

Primate and Human Evolution  341

A coral reef. Reefs are centers of diversity, for both vertebrate and invertebrate animals.

Concept Connections Andrey Armyagov/Shutterstock.com

The form and diversity of modern animals is the result of evolutionary processes such as mutation (Section 13.2), morphological divergence (12.6), speciation (13.6), adaptive radiation (13.7), and extinction (Sections 12.1 and 13.7). The study of fossils (12.4) forms the basis for much of what we know about animal phylogeny (13.8) and allows us to place the major events in animal evolution on geologic time scale (12.5). We return to the structure and function of animals, especially vertebrates, in Chapters 20 to 27.

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Animal Evolution  Chapter 16  317  

Application 16.1  Medicines from the Sea Animal life began in the sea, and Earth’s oceans still hold more animal phyla than the land does. In the sea, as on land, the majority of animals are invertebrates, meaning they do not have a backbone. Of all animals, only about 5 percent have a backbone and thus are described as vertebrates. Many marine invertebrates produce compounds that are toxic to other organisms. Such toxins can protect an animal from predators, help it fend off pathogens, or assist in the capture of prey. Some invertebrate toxins also have effects in the human body, and these can be useful as medicines. Consider the venom that some fish-eating cone snails use to subdue their prey (Figure 16.1). The snail’s venom anesthetizes and paralyzes a fish, thus preventing the fish from struggling and possibly harming the snail. Human nerves and fish nerves use the same chemical communication signals. Thus, a toxin that acts on fish nerves also affects the function of the human nervous system. A person accidentally stung by a fish-eating cone snail may become numb at the site of venom injection, suffer from temporary paralysis, or even die. The painkiller ziconotide (sold under the brand name Prialt) is a synthetic version of a peptide in the venom of one cone snail. Ziconotide is injected into the spinal cord to suppress pain that cannot be controlled by other means. Additional peptides isolated from cone snail venom are being tested as treatments for epilepsy, diabetes, and cancer. Compounds derived from other marine invertebrates are also in use. AZT (azidothymidine), the first drug successfully used to treat AIDS, is a synthetic version of a molecule discovered in a sponge. Other compounds discovered in sponges can be used to treat infections caused by herpes viruses. Sea whips, which are relatives of sea anemones, produce a variety of anti-inflammatory compounds, one of which is used in face creams. Finding a compound that might have medicinal value is only the first step in developing a new drug. For a compound to be used in clinical tests, researchers must obtain a sufficient amount of it. This can be difficult because many compounds of interest occur only at very low concentrations in animals. Consider the drug eribulin, which is now used to treat some advanced-stage breast cancers. Sponges synthesize the compound on which eribulin is modeled, but only in tiny amounts. Obtaining 300 milligrams of the sponge compound—enough to test it for anticancer activity—required processing more than a metric ton of sponge tissue. Once the structure of a useful compound has been determined, chemists can usually manufacture that compound or one with similar properties. The cancer drug eribulin is a synthetic molecule similar to the molecule first

Figure 16.1  Cone snail with its fish prey. After administering a toxin that puts the fish into a stupor, the snail engulfs and devours it. K. S. Matz

invertebrate  Animal without a backbone. vertebrate  Animal with a backbone.

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318  Unit 3  EVOLUTION AND DIVERSITY

extracted from sponges. Use of synthetically produced compounds prevents overharvesting of the species in which the compound was discovered.

Discussion Questions 1. The Census of Marine Life was a 10-year-long project that involved scientists from more than 80 countries. The goal of the project was to document what lives in Earth’s oceans and where. How might the general public benefit this from project? Why is it especially useful to have scientists from many nations take part in projects that involve the oceans? 2. The painkiller ziconotide is a peptide (a short chain of amino acids). Peptides can be produced synthetically, so researchers could make peptides with random amino acid sequences, then test those peptides for medically useful activity. Why is testing peptides isolated from animal venoms a more promising way to find new drugs? 3. Searching for economically valuable compounds in natural organisms is called bioprospecting. One criticism of bioprospecting is that it often allows companies in developed nations to profit from the biodiversity of less-developed regions. For example, venom from a cone snail native to the Philippines was the basis for ziconotide, a drug currently manufactured in Ireland. Do people in less-developed regions have a right to share in jobs and profits made possible by exploration of their country’s biological diversity? How would such profit sharing encourage people to maintain biodiversity?

16.2  Traits and Evolutionary Trends Learning Objectives ●●

List some traits that all animals share.

●●

Explain the colonial hypothesis for animal origins.

●●

Describe the body form of animals with bilateral symmetry and radial symmetry.

●●

List some factors that may have encouraged the great adaptive radiation during the Cambrian.

Animals are multicellular consumers that take food into their body, where they digest it and absorb the released nutrients. An animal body consists of a few to hundreds of types of cells, all of them unwalled. All animals are motile (can move from place to place) during part or all of their life cycle. Most animals can reproduce sexually, and some reproduce asexually as well.

Animal Origins The colonial theory of animal origins states that animals evolved from a heterotrophic protist that formed colonies. At first, all cells in the colony were identical, and each could survive and reproduce on its own. Later, mutations resulted in cells that specialized in some tasks and did not carry out others. Perhaps some cells captured food more efficiently, but did not make gametes, whereas others made gametes but did not catch food. The division of labor among interdependent cells made colonies more efficient, because it allowed them to collectively obtain more food and produce more offspring. Over time, cells became increasingly interdependent, and more specialized cell types evolved. The first animals were the result of these evolutionary processes.

Evolutionary Tree of Animals  Figure 16.2 shows relationships among the animal groups covered in this book, and we will use it to discuss evolutionary trends and variations in body plan.

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Animal Evolution  Chapter 16  319  

Cnidarians

Flatworms

Annelids

5

3

Mollusks

4 2

Arthropods

Protostome Development

Radial Symmetry

1

Roundworms

Echinoderms

6

Chordates

Deuterostome Development

Bilateral Symmetry

Tissues

Multicellularity Ancestral protist

Cells and Tissues  Genetic analyses indicate that all animals are descendants of the

same protist ancestor 1. The earliest animals were aggregations of cells, and this level of organization persists in sponges. In all animals more complex than sponges, cells are organized as tissues 2. A tissue consists of one or more types of cells that are organized in a specific pattern and collectively carry out a particular task. The first tissues that form in an animal embryo are called germ layers. The embryo of a cnidarian such as a jelly or sea anemone has two germ layers: an outer layer called ectoderm and an inner layer called endoderm. In more complex animals, the embryo has three germ layers. In these animals, a middle germ layer, called mesoderm, forms between the ectoderm and the endoderm. Symmetry  Sponges, the animals with the simplest structural organization, are asymmetrical, meaning their body cannot be divided into two halves that are mirror images. Cnidarians such as jellies have radial symmetry, meaning their body parts are repeated around a central axis, like the spokes of a wheel 3. Radial animals have no front or back end. Most attach to an underwater surface or drift along, so their food can arrive from any direction. Animals with a three-layered embryo typically have bilateral symmetry, meaning they have a right and left half, with body parts repeated on either side of the body 4. They also have a distinctive “head end” that has a concentration of nerve cells and sensory structures. Protostomes and Deuterostomes  There are two lineages of bilateral animals and they are defined in part by developmental differences. In protostomes, the first

opening that forms on an embryo becomes the mouth 5. Proto- means “first,” and stoma means “opening.” All protostomes are invertebrates. Protostomes include flatworms, annelids, mollusks, roundworms, and arthropods. In deuterostomes, the mouth develops from the second embryonic opening 6. Deutero- means “second.” Deuterostomes include both invertebrates (echinoderms, invertebrate chordates) and all vertebrates.

Figure It Out: What type of body symmetry do the arthropods have?

Answer: Bilateral symmetry

Sponges

Figure 16.2  Family tree for major animal phyla based on body form and genetic comparisons. Vertebrates (animals with a backbone) are a subgroup of the chordates.

animal  A motile, multicellular eukaryotic consumer that has multiple types of unwalled cells and digests food inside its body. bilateral symmetry  Having right and left halves with similar parts. colonial theory of animal origins  Wellaccepted hypothesis that animals evolved from a colonial protist. deuterostomes  Animal lineage with a three-layer embryo in which the mouth is the second opening to form; includes echinoderms, invertebrate chordates, and vertebrates. germ layer  Embryonic tissue layer; endoderm, mesoderm, or ectoderm. protostomes  Animal lineage with a three-layer embryo in which the first opening to form is the mouth; includes flatworms, annelids, mollusks, roundworms, and arthropods. radial symmetry  Having parts arranged around a central axis, like spokes around a wheel. tissue  One or more types of cells that are organized in a specific pattern and that carry out a specific task.

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320  Unit 3  EVOLUTION AND DIVERSITY epidermis (from ectoderm)

coelom

epidermis (from ectoderm)

pseudocoelom

epidermis (from ectoderm)

mesentery tissues, organs (from mesoderm)

gut tissue (from endoderm)

gut cavity

A. Flatworm, with no body cavity other than the gut. Figure 16.3  Variations in body plans among bilateral animals. Diagrams show a cross section through the body. Relative width of tissue layers is not to scale. Figure It Out: Which of the animals shown develops from an embryo with three tissue layers?

tissues, organs (from mesoderm)

tissues, organs (from mesoderm)

gut cavity

gut tissue (from endoderm)

B. Annelid, with a fluid-filled coelom.

gut cavity

gut tissue (from endoderm)

C. Roundworm, with a pseudocoelom.

Body Cavity  A mass of tissues and organs surrounds a flatworm’s gut (Figure 16.3A).

However, most bilaterally symmetrical animals have a “tube within a tube” body plan. Their gut runs through a coelom, a fluid-filled body cavity that is completely lined with tissue derived from mesoderm. Earthworms have this type of body plan (Figure 16.3B). Sheets of tissue (called mesentery) suspend the gut in the center of a coelom. Roundworms and a few other invertebrates have a pseudocoelom, which has only a partial mesodermal lining (Figure 16.3C). Evolution of a fluid-filled body cavity provided a number of benefits. First, materials can diffuse through coelomic fluid to body cells. Second, muscles can redistribute the fluid to alter the shape of body parts in ways that allow movement. Finally, because internal organs of animals with a coelom are not hemmed in by a mass of tissue, the organs could, over evolutionary time, become larger and shift position relative to one another.

Answer: All three do.

Early Animals  Genetic comparisons indicate that the animal lineage may have arisen as early as 850 million years ago. However, we have no fossil evidence of the earliest animals. Most likely they were microscopic and, like the protist from which they evolved, had no hard parts likely to fossilize. The oldest known fossil animal is Dickonsonia, which was an oval, pancake-like bottom dweller that lived in the sea 570 million years ago (Figure 16.4). We know that Dickonsonia was an animal because a chemical analysis of fossilized remains showed that the organism contained a large amount of cholesterol. Other types of organisms produce little or no cholesterol. Dickonsonia is one of a large group of soft-bodied aquatic organisms collectively referred to as Ediacarans because their fossils were found in Australia’s Ediacara Hills. On the geologic time scale, the Ediacaran period runs from 635 to 540 million years ago. We do not know how the Ediacaran lineages are related to modern animals, although some may be early representatives of modern animal lineages. For example, Dickonsonia may have been an early jellyfish or annelid worm.

Cambrian Adaptive Radiation 

Figure 16.4  Fossil of an Ediacaran, an early animal. Dickonsonia lived in the sea about 570 million years ago. De Agostini Picture Library/Getty Images

On the geologic time scale, the Ediacaran period is followed by the Cambrian (541 to 485 million years ago). A great adaptive radiation of animals occurred during the Cambrian. By the end of this period, all major animal lineages that we are familiar with were living in the seas. Environmental and biological factors encouraged the diversification. During the Cambrian, global climate warmed and the amount of oxygen in the seas increased, making the environment more hospitable to animal life. (With rare

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exceptions, animals require oxygen.) During the same period, the supercontinent Gondwana underwent a dramatic rotation. Movement of this landmass interrupted gene flow between populations, increasing the likelihood of allopatric speciation. Biological factors also encouraged diversification. After predatory animals arose, defensive traits evolved in their prey. These defenses in turn selected for predators capable of overcoming them. Mutations in homeotic genes probably facilitated the emergence of novel structures, because such changes can alter body plans.

coelom  A body cavity completely lined by tissue derived from mesoderm. sponge  Aquatic invertebrate that has no tissues or organs and filters food from the water.

Take-Home Message 16.2 ●●

●●

●●

●●

Animals are multicellular consumers that digest food inside their body and move at some point in their life. Animals evolved from a protist ancestor. They underwent a great adaptive radiation during the Cambrian period. Early animals were asymmetrical aggregations of cells, but most animals develop distinct tissues and have either radial or bilateral body symmetry. The two lineages of bilateral animals, protostomes and deuterostomes, differ in the details of their development, but both develop from an embryo with three tissue layers.

16.3  Sponges and Cnidarians Learning Objectives ●●

Describe the types of cells in a sponge body, and explain how they interact to keep the animal alive.

●●

Compare and contrast the two cnidarian body plans.

●●

Discuss how cnidarians capture, ingest, and digest their food.

Sponges  Sponges (phylum Porifera) are aquatic animals that do not have tissues or organs. An adult sponge is sessile, meaning it does not move from place to place, but rather lives attached to some surface. The sponge body has many pores (Figure 16.5). Flattened cells cover a sponge’s outer body surface, and flagellated collar cells line its internal cavities. Collar cells are named for the collar of filaments at the base of their flagellum. A jellylike extracellular matrix lies between the two cell layers. In many species, cells in the matrix secrete fibrous proteins or glassy spikes. These materials structurally support the body and discourage predators by making the sponge difficult to eat and digest. Sponges are the only animals in which digestion is intracellular. Most sponges are filter feeders, meaning they filter bits of food from the surrounding water. By moving their flagella, collar cells cause water to flow inward through pores in the body, then outward through a large central opening. As water flows past collar cells, the cells capture food in the filaments of their collar and engulf it. The food is then digested in vesicles inside the cell. Collar cells share the breakdown products of digestion with amoeba-like cells in the matrix, which then distribute these nutrients to other cells in the sponge body.

water out

glasslike structural elements amoeboid cell pore semifluid matrix

central cavity

flattened surface cells collar cell water in

A. Body plan of a glass sponge. Arrows indicate the direction of water flow.

B. Natural bath sponge.

Figure 16.5  Sponges, animals without body symmetry or tissues. (B) ultimathule/Shutterstock.com

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322  Unit 3  EVOLUTION AND DIVERSITY Medusa

A typical sponge is a hermaphrodite: an individual that produces both eggs and sperm. Most sponge species release their sperm into the water but retain eggs on their body. After fertilization, the zygote develops into a ciliated larva. A larva (plural, larvae) is a sexually immature animal that has a different body form than the adult. Sponge larvae exit the parental body, swim briefly, then settle and develop into adults. Many sponges can reproduce asexually when small buds or fragments break away and grow into new sponges. Sponges also have an amazing ability to regenerate. Some can even reassemble as a functional sponge after being broken into individual cells by a blender.

Polyp outer tissue layer

gastrovascular cavity

jellylike matrix inner tissue layer gastrovascular cavity

A. Structure of the two body plans.

Cnidarians 

B. Jelly, a medusa.

C. Sea anemone, a polyp.

Figure 16.6  Cnidarian body plans. (B) Ted M. Kinsman/Science Source; (C) Ethan Daniels/Shutterstock.com

cnidarian  Radially symmetrical invertebrate with two tissue layers; uses tentacles with stinging cells to capture food. flatworm  Bilaterally symmetrical invertebrate with organs but no body cavity; for example, a planarian or tapeworm.

Cnidarians (phylum Cnidaria) are aquatic, radially symmetrical animals with stinging tentacles. The two common body plans, medusa and polyp, both consist of two tissue layers (endoderm and ectoderm) with a secreted jellylike matrix between them (Figure 16.6A). A bell-shaped medusa (plural, medusae) swims or drifts about. Jellies (jellyfish) are medusae (Figure 16.6B). A polyp, such as a sea anemone, is tubular, and has one end attached to some surface (Figure 16.6C). In both polyps and medusae, tentacles surround the entrance to the gastrovascular cavity, a saclike structure that takes in and digests food, expels wastes, and also functions in gas exchange. An animal with a gastrovascular cavity must fully digest a meal and excrete any resulting wastes before it can ingest the next meal. Nutrients and oxygen taken in to the gastrovascular cavity reach body cells by diffusion. The phylum name Cnidaria is derived from cnidos, the Greek word for nettle, a kind of stinging plant. The name refers to unique stinging cells (cnidocytes) at the surface of cnidarian tentacles. The cells have a capsule-like organelle (called a nematocyst) that contains a coiled threadlike structure. Touch causes the capsule to pop open, forcing the thread outward. The thread then entangles prey or pierces it and delivers venom. Tentacles push the captured prey through the mouth into the gastrovascular cavity, where digestive enzymes secreted by gland cells break it down. Reef-building corals are polyps that capture prey with their tentacles, but also rely on sugars made by photosynthetic protists (dinoflagellates) that live in their tissues. Each coral polyp secretes a hard, calcium carbonate–rich skeleton around its base. Over time, skeletal remains of many generations of polyps accumulate as a reef, with a layer of living polyps at its surface. Coral reefs are of great ecological importance because they provide food and shelter for many types of animals.

gastrovascular cavity  Of some invertebrates, a saclike structure with a single opening that functions in digestion and respiration. hermaphrodite  Individual animal that makes both eggs and sperm.

Take-Home Message 16.3

larva  Sexually immature animal that has a different body form than the adult.

●●

medusa  Bell-shaped, free-swimming cnidarian body form. polyp  In cnidarians, tubular, typically sessile, cnidarian body form.

●●

Sponges have an asymmetrical body without tissues or organs. As adults they are filter feeders that digest food inside their cells. Cnidarians have a radially symmetrical body with two tissue layers. There are two body forms: medusa and polyp. Both use tentacles with stinging cells to capture food, which is then digested in a gastrovascular cavity.

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Animal Evolution  Chapter 16  323  

16.4  Flatworms, Annelids, and Mollusks Learning Objectives ●●

Compare the body plan of a flatworm and an earthworm.

●●

Give examples of parasitic flatworms and annelids.

●●

Using appropriate examples, name the three major mollusk groups and the traits that define them.

With this section, we begin our survey of protostomes, one of the two lineages of bilaterally symmetrical animals. All protostomes develop from an embryo that has three germ layers, and all have organs and organ systems. An early evolutionary branching produced two protostome lineages. Flatworms, together with annelids and mollusks, are members of one protostome lineage and are the focus of this section. Roundworms and arthropods are members of the other protostome lineage and are covered in Section 16.5.

Flatworms  Flatworms (phylum Platyhelminthes) have a flat body with an array of organ

systems, but no body cavity other than a gastrovascular cavity. Most free-living flatworms are aquatic. Parasitic flatworms live inside animals. Planarians (Figure 16.7) are free-living flatworms common in ponds. Three muscle layers and a ciliated body surface allow a planarian to swim and to glide along surfaces. A planarian’s mouth is at the end of a muscular tube (called a pharynx) that opens onto a highly branched gastrovascular cavity. Nutrients released by digestion diffuse from the fine branches of this cavity to body cells. The front end of a planarian has chemical receptors for detecting food, light-detecting eyespots, and clusters of nerve cells that serve as a simple brain. Tapeworms are parasitic flatworms that live in the vertebrate gut. The head end of the worm has hooks for attaching to the host, but no mouth. A tapeworm absorbs nutrients across its body wall. The tapeworm body consists of units called proglottids, and it grows in length by adding new proglottids. Figure 16.8 shows the life cycle of the beef tapeworm, which can infect people who eat undercooked beef.

muscular tube that sucks up food and expels waste

branching gastrovascular cavity

Figure 16.7  Body plan of a planarian.

Figure 16.8  Life cycle of the beef tapeworm. Andrew Syred/Science Source

1 A person eats undercooked beef that contains

5 The larval

a cyst (resting stage) of a tapeworm.

tapeworm forms a cyst in cattle muscle tissue.

proglottid

scolex

2 In the human intestine, the

beef with larval tapeworm

cyst develops into an adult tapeworm that uses barbed headparts (a scolex) to attach to the intestinal wall. The worm grows by adding new body units. Over time, it can become many meters long.

3 Each body unit makes

eggs and sperm, which combine. Proglottids containing fertilized eggs exit the body in feces.

4 Cattle eat grass

contaminated with proglottids or early larvae.

larva

proglottid with fertilized eggs

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324  Unit 3  EVOLUTION AND DIVERSITY

anus

blood vessel excretory organ coelom gut cavity

Annelids  secretory region (clitellum)

nerve cord

one of five nerve hearts cord

Flukes are also internal parasites of snails and vertebrates. Some tropical freshwater snails carry blood flukes that can infect humans and cause schistosomiasis. People become infected when they wade in water containing the larval flukes, which enter the body through a cut. Once inside, the flukes live in blood vessels and damage organs throughout the body. Untreated infections can be fatal.

gut

brain

mouth

A. Body plan of an earthworm, an oligochaete.

B. Sandworm B. Sandworm (Nereis), (Nereis), a marine a marine polychaete. polychaete.

Annelids are bilateral worms with a coelom and conspicuous segmentation, both inside and out. Segmentation refers to a body plan in which similar units are repeated one after the other along a body’s main axis. There are three annelid lineages: oligochaetes, polychaetes, and leeches. Earthworms  The most familiar annelids are earthworms, which are oligochaetes that live in soil. Rings visible at an earthworm’s surface correspond to internal segmentation (Figure 16.9A). Each body segment has a fluid-filled coelomic chamber with paired excretory organs that remove waste from the fluid. A simple brain at the worm’s front end connects to a nerve cord that extends along the lower length of the body. The brain coordinates locomotion and receives sensory information. Earthworms can sense light (which they avoid), detect touch and vibration, and recognize specific odors emitted by their food. An earthworm eats its way through the soil, digesting the organic material that it takes in. A complete digestive tract extends the length of the body inside the coelom. A complete digestive tract is a tubular gut with an opening at either end. Different parts of the digestive tract specialize in taking in food, digesting food, absorbing nutrients, or compacting waste. Unlike a gastrovascular cavity, a tubular gut can carry out all of these tasks simultaneously. Gas exchange occurs across the body surface, and gases and nutrients are distributed through the body by a circulatory system. Annelids have a closed circulatory system, in which blood is always in either a heart or a blood vessel. In this type of circulatory system, all exchanges between blood and body tissues take place across the wall of a blood vessel. Earthworms have five hearts that pump blood through the blood vessels. Earthworms are hermaphrodites. Mucus produced by a secretory region called the clitellum glues worms together while they exchange sperm. Later, the clitellum secretes a silky case for the fertilized eggs that the worm deposits in the soil. Polychaetes and Leeches  Most marine annelids are polychaetes, a lineage of

annelids that typically have many bristles per segment. (Poly- means “many,” and chaete means “bristle.”) Some polychaetes, including the sandworms often sold as bait, are active predators (Figure 16.9B). Others remain fixed in place and have feathery appendages specialized for filtering food from currents. Leeches typically live in freshwater, although some are found in damp places on land. Most are scavengers and predators of invertebrates. An infamous few suck blood from vertebrates (Figure 16.9C). Leech saliva has a protein that keeps blood from clotting while the leech feeds. For this reason, doctors who reattach a severed finger or ear sometimes apply leeches to the reattached body part. The presence of the feeding leeches prevents clots from forming inside the newly reconnected blood vessels.

C. Leech sucking blood from a human hand.

Figure 16.9  Annelids. (B) Darlyne A. Murawski/National Geographic Image Collection/Getty Images; (C) Martin Pelanek/Shutterstock.com

Mollusks  Mollusks (phylum Mollusca) have a soft, unsegmented body, a complete digestive tract, and a reduced coelom. Mulluscus is Latin for “soft.” The mantle, a skirtlike

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Animal Evolution  Chapter 16  325   excretory organ

gill

anus

heart

mantle cavity

digestive gland stomach shell foot

edge of mantle that covers organs

A. Body plan of an aquatic snail (a gastropod).

radula

B. Scallop, a bivalve with a two-part, hinged shell.

C. Octopus, a cephalopod.

Figure 16.10  Three types of mollusks. (B) Frank Park/ANT Photo Library; (C) NURC/UNCW and NOAA/FGBNMS

extension of the upper body wall, drapes over the internal organs (Figure 16.10A). In most mollusks, the outermost layer of the mantle secretes a hard shell rich in calcium carbonate. Unlike the invertebrate groups discussed previously, mollusks have respiratory organs. Aquatic mollusks have one or more gills that facilitate gas exchange with the water. Some mollusks that live on land have a lung, which is a saclike respiratory organ that facilitates gas exchanges with the air. Among animals, mollusks are second only to arthropods in diversity. There are three major groups: gastropods, bivalves, and cephalopods. Gastropods  With 60,000 species of snails and slugs, gastropods are the largest

mollusk subgroup. Gastropod means “belly foot,” and members of this group glide about on a broad muscular foot that makes up most of their lower body mass. The gastropod shell, when present, is one piece and usually coiled. Most gastropods scrape up algae with a radula, a tonguelike organ hardened with a tough polysaccharide called chitin. Gastropods include the only land-dwelling mollusks. Glands on the foot of a land snail or slug continually secrete mucus that protects the animal as it moves across dry, abrasive surfaces. Most mollusks have separate sexes, but land dwellers are typically hermaphrodites. Gastropods and bivalves have an open circulatory system. In an open circulatory system, fluid leaves vessels and seeps among tissues before returning to the heart. An open system requires less energy to operate than a closed circulatory system, but it moves materials more slowly. Bivalves  The distinguishing trait of bivalves is a hinged, two-part shell (Figure 16.10B). Bivalves live in both freshwater and the seas. Some, such as mussels, attach to a surface whereas others, such as clams, burrow into sediments. A bivalve does not have a distinct head, and it does not have a radula. Most feed by drawing water into the mantle cavity and filtering out bits of food. Cephalopods  Cephalopod means “head-footed,” and in all cephalopods the foot has been modified into tentacles and/or arms that extend from the head. Cuttlefish, squids, nautiluses, and octopuses are examples of cephalopods (Figure 16.10C). Most are predators, and have beaklike, biting mouthparts in addition to a radula. Cephalopods move by jet propulsion. They draw water into their mantle cavity, then force it out through a funnel-shaped siphon. A closed circulatory system

annelid  Segmented worm with a coelom, complete digestive system, and closed circulatory system; an earthworm, polychaete, or leech. bivalve  Mollusk with a hinged two-part shell. cephalopod  Mollusk with a foot modified to form arms or tentacles; moves by jet propulsion. closed circulatory system  Circulatory system in blood flows through a continuous system of vessels and exchanges with cells take place across vessel walls. complete digestive tract  Tubular gut with two openings. gastropod  Mollusk that moves about on its enlarged foot. mantle  Skirtlike extension of tissue in mollusks; covers the internal organs and secretes the shell (if there is one). mollusk  Invertebrate with a reduced coelom, complete digestive system, and a mantle that, in some groups, secretes a shell; a gastropod, bivalve, or cephalopod. open circulatory system  Circulatory system in which the circulatory fluid leaves open-ended vessels and flows among tissues before returning to the heart. radula  Tonguelike organ of many mollusks.

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326  Unit 3  EVOLUTION AND DIVERSITY

supports their high activity level. Remember that a closed circulatory system circulates blood more quickly than an open one.

Take-Home Message 16.4 ●●

●●

●●

●●

Flatworms, annelids, and mollusks belong to the same protostome lineage. All have organ systems. Flatworms include free-living planarians and the parasitic tapeworms and flukes. They have a gastrovascular cavity and no coelom. An earthworm is an annelid, a segmented worm with a complete digestive tract. Multiple hearts pump blood through an earthworm’s closed circulatory system. Polychaetes and leeches are also annelids. Mollusks have a skirtlike mantle that secretes a shell in some species. Gills or lungs allow gas exchange. The circulatory system is open in gastropods and bivalves but closed in cephalopods such as octopuses.

16.5  Roundworms and Arthropods  Learning Objectives ●●

List traits that roundworms and arthropods share.

●●

Explain why roundworms are used as models in scientific studies.

●●

List the traits that contribute to the diversity of arthropods.

●●

Give examples of roundworms and insects that have a negative effect on human health.

Molting is the characteristic trait of the protostome lineage that includes roundworms and arthropods. In this context, molting refers to the periodic shedding of a secreted body covering that would otherwise constrain growth. Both roundworms and arthropods have a complete digestive tract, excretory organs, and a nervous system.

Roundworms  Roundworms, or nematodes (phylum Nematoda), are cylindrical, unsegmented

worms with a pseudocoelom (Figure 16.11). They do not have circulatory or respiratory organs. Roundworms secrete a flexible, protein-rich cuticle that is molted and replaced as the worm grows. Free-Living Roundworms  Roundworms live in the seas, in freshwater, and in

soil. Most of the nearly 20,000 species are free-living decomposers less than a millimeter long. Caenorhabditis elegans, a soil roundworm that is easily grown in the lab, is often used in scientific studies. C. elegans has the same tissue types

Figure 16.11  Body plan of a free-living roundworm. arthropod  Invertebrate with jointed legs and a hardened exoskeleton that is periodically molted. exoskeleton  External skeleton. roundworm  Unsegmented worm with a pseudocoelom and a cuticle that is molted as the animal grows.

pharynx

intestine

pseudocoelom

eggs in uterus

gonad

muscular body wall

anus

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Animal Evolution  Chapter 16  327  

as more complex organisms, but it is transparent and has fewer than 1,000 body cells. Such traits make it easy for scientists to monitor each cell’s fate during development. Several scientists have made Nobel Prize–winning discoveries while studying C. elegans, and it was the first multicellular organism to have its genome sequenced. Roundworms as Parasites  A few types of parasitic roundworms infect people. In the tropics, mosquitoes transmit parasitic roundworms that enter human lymph vessels. The worms injure valves in these vessels, so lymph collects in the lower limbs. The resulting condition is called elephantiasis, because affected people have fluid-swollen “elephant-like” legs (Figure 16.12A). The swelling is permanent because lymph vessels remain damaged even after the worms have been eliminated. In the United States, pinworms (Enterobius vermicularis) are the most common parasitic roundworms. Most infections occur in children. The worms, about the size of a staple, live in the rectum. Females emerge at night and lay eggs on the skin around the anus, causing itching. Scratching puts eggs onto fingertips, from which they can be transferred to other surfaces. Each egg can cause a new infection if ingested. Parasitic roundworms also infect our livestock, pets, and crops. A roundworm that infects pigs can also infect humans. Eating undercooked pork that contains this parasite causes trichinosis. Dogs are susceptible to heartworms transmitted by mosquitoes. Cats can become infected by an intestinal roundworm after eating an infected rodent. Roundworms that infect roots are important agricultural pests (Figure 16.12B). A roundworm infection stunts plant growth and lowers crop yields.

A. A man with elephantiasis of his left leg. The swelling arises after roundworms damage lymph vessels.

Arthropods Traits  Arthropods (phylum Arthropoda) are invertebrates with jointed legs. Unlike

roundworms, they have a coelom, an open circulatory system, and respiratory organs. There are currently an estimated 5 to 10 million arthropod species, making arthropods the most diverse animal phylum. A variety of traits have contributed to the evolutionary success of arthropods. Hardened Exoskeleton with Jointed Appendages  Arthropods secrete a cuticle that contains chitin, the same polysaccharide that hardens the mollusk radula. The arthropod cuticle serves as an external skeleton, or exoskeleton. It helps fend off predators and serves as a point of attachment for muscles. In land arthropods, the exoskeleton also helps conserve water and supports the animal’s weight. A hard exoskeleton does not restrict growth, because, like roundworms, arthropods periodically molt their cuticle. A new cuticle forms under the old one, which is shed. If an arthropod’s cuticle were uniformly hard like a plaster cast, it would prevent movement. However, the cuticle is thinner at joints, where two hard body parts meet. Arthropod means “jointed leg.” Body parts move when the muscles that attach to the exoskeleton on either side of a joint contract. Specialized Segments  In early arthropods, there were many similar body segments

and all appendages were alike. As later groups evolved, segments became fused into structural units such as a head, thorax, and abdomen (Figure 16.13). In some groups, specialized appendages such as wings developed on certain segments.

B. Plant-infecting roundworm entering a root. Figure 16.12  Parasitic roundworms. (A) Courtesy of Emily Howard Staub and The Carter Center; (B) William Wergin and Richard Sayre. Colorized by Stephen Ausmus.

antenna

head

thorax

abdomen

compound eye

Figure 16.13  Grasshopper body plan. The body has three distinct regions. Compound eyes and a pair of antennae on the head provide sensory information. From Russell/Wolfe/Hertz/Starr, Biology, 1e. © 2008 Cengage Learning®.

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328  Unit 3  EVOLUTION AND DIVERSITY adult female with mass of fertilized eggs first earlystage larva

juvenile

metamorphosis late-stage larva

fifth earlystage larva

Figure 16.14  Development of a Dungeness crab (a crustacean arthropod). Fertilized eggs develop into planktonic larvae that grow and molt. Metamorphosis (change in body form) occurs during the molt from a late-stage larva to a juvenile with the adult form. Additional growth and molting produces a sexually mature adult. Sensory Organs  Most arthropods have paired eyes. Insects and crustaceans have compound eyes that consist of many units, each with a lens. Compound eyes excel at detecting movement. Many arthropods also have one or two pairs of antennae

(singular, antenna), which are sensory structures on the head that detect touch, odor, and vibrations.

Development  The body plan of many arthropods changes during the life cycle. Individuals undergo metamorphosis, a dramatic remodeling of body form during

the transition from larva to adult. For example, crab larvae swim near the ocean surface and filter food from the water, but adults are bottom-feeders (Figure 16.14). Having different body forms and ways of life helps prevent adults and juveniles from competing with one another for resources.

Arthropod Lineages  Arthropod subgroups are defined largely by differences in body form, such as their types and numbers of appendages. Figure 16.15  Atlantic horseshoe crab (Limulus). Ethan Daniels/Shutterstock.com

antennae  Of some arthropods, sensory structures on the head that detect touch, odors, and vibrations. arachnids  Arthropods with palps, four pairs of walking legs and no antennae; most live on land (for example, spiders, scorpions, or ticks). compound eye  Eye that consists of many individual units, each with its own lens. metamorphosis  Dramatic remodeling of body form during the transition from larva to adult.

Horseshoe Crabs  We know from fossils that horseshoe crabs have lived in Earth’s oceans for at least 470 million years. All four modern species of horseshoe crabs are bottom-feeders that live in shallow, nearshore waters (Figure 16.15). Their common name refers to the fused head and thorax segments (the cephalothorax), which in this group is horseshoe-shaped. A long spike that extends from the last abdominal segment looks dangerous; however, it does not contain venom and has no defensive function. The animal uses the spike to dig and to turn over if it is flipped over by a wave. Each spring, horseshoe crabs venture onto damp sands along North America’s east coast to mate and lay their eggs. The billions of eggs they leave behind are an essential food source for migratory shorebirds. Arachnids  Despite their common name, horseshoe crabs are not true crabs. Rather, they are close relatives of the arachnids. Arachnids have four pairs of

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Animal Evolution  Chapter 16  329  

Digging Into Data Sustainable Use of Horseshoe Crabs

Control Animals Mark Thiessen/National Geographic Image Collection

The Atlantic horseshoe crab, Limulus polyphemus, is an economically important species. The horseshoe crab’s blue blood (right) is used to test for the presence of potentially deadly bacteria in injectable drugs and on medical implants. Because of its scarcity and medical importance, a liter of horseshoe crab blood sells for about $16,000. To keep horseshoe crab populations stable, blood is extracted from captured animals, which are then returned to the wild. Concerns about the survival of animals after bleeding led researchers to do an experiment. They compared survival of animals captured and maintained in a tank with that of animals captured, bled, and kept in a similar tank. Figure 16.16 shows the results.

Trial

Number that Died

Number of Crabs

Number that Died

1

10

0

10

0

2

10

0

10

3

3

30

0

30

0

4

30

0

30

0

5

30

1

30

6

6

30

0

30

0

7

30

0

30

2

8

30

0

30

5

200

1

200

16

Total

1. In which trial did the most control crabs die? In which did the most bled crabs die? 2. Looking at the overall results, how did the mortality of the two groups differ? 3. Based on these results, would you conclude that bleeding harms horseshoe crabs more than capture alone does?

Number of Crabs

Bled Animals

Figure 16.16  Mortality of young male horseshoe crabs kept in tanks for the two weeks after their capture. Blood was drawn from half of the animals on the day of their capture. Control animals were handled, but not bled. The experiment was repeated eight times with eight different sets of horseshoe crabs. Source data: Walls, E., Berkson, J., Fish. Bull. 101:457–459 (2003).

walking legs, a pair of touch-sensitive appendages called palps, and no antennae. They include spiders, scorpions, ticks, and mites. Spiders and scorpions are venomous predators. Spiders deliver venom through fanglike mouthparts. They have a two-part body, with the cephalothorax (fused head and thorax) separated from the abdomen by a narrow “waist” (Figure 16.17A). The abdomen contains silk-making glands. Scorpions catch their prey with clawlike palps and subdue it with a venom-producing stinger on the final abdominal segment (Figure 16.17B). They eat insects, spiders, and even small lizards. Ticks suck blood from vertebrates (Figure 16.17C). Some serve as vectors for bacterial diseases, such as Lyme disease. A closely related group, the mites, are the

abdomen

cephalothorax

Figure 16.17  Arachnids. (A) Eric Isselee/Shutterstock.com; (B) wacpan/Shutterstock.com; (C) Sarah2/Shutterstock.com

unfed

A. Spider (tarantula), a predator.

B. Scorpion, a predator.

after a blood meal

C. Tick, a parasite of vertebrates.

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330  Unit 3  EVOLUTION AND DIVERSITY

smallest arachnids. Most species are less than a millimeter long. Many mites are scavengers, but some are parasites. Scabies in humans and mange in dogs are both caused by mites that burrow beneath the skin. Some larval mites, commonly called chiggers, crawl into a human hair follicle and cause an itchy rash.

B. Millipede, a scavenger of decaying plant material. Figure 16.18  Centipede and millipede. Eric Isselee/Shutterstock.com

eyes abdomen cephalothorax (two)

antennae (two pairs)

mouthparts

tail swimmerets fan

first leg walking legs (five pairs)

A. Body plan of an American lobster.

Centipedes and Millipedes  Centipedes and millipedes are nocturnal (active at night) ground dwellers with an elongated body composed of many similar segments (Figure 16.18). Their head has one pair of antennae. Centipedes are venomous predators with a flat, low-slung body and one pair of legs per segment. Most millipedes eat plant material. Their cylindrical body has two legs per segment and their cuticle is hardened with calcium carbonate. Crustaceans  The crustaceans are a lineage of mostly marine arthropods that have two pairs of antennae and at least five pairs of legs. Many, such as shrimps, crabs, and lobsters (Figure 16.19A), are harvested as human food. Other animals also depend on crustaceans for food. Shrimplike crustaceans called krill abound in cool ocean waters (Figure 16.19B). Each is only a few centimeters long, but krill are so abundant and nutritious that a 100-ton blue whale can subsist almost entirely on the krill that it filters from seawater. Barnacles are marine crustaceans that secrete a calcium-rich external shell (Figure 16.19C). Barnacle larvae swim, then settle and develop into adults that attach to a surface. Adults filter food from seawater with their feathery legs. Some barnacles are notable for the length of their penis, which can be eight times that of their body. Isopods are a mostly marine group of crustaceans, but some live in damp places on land. The species commonly known as pill bugs or sow bugs defend themselves from threats by rolling into a ball (right). Insects  The most diverse group of arthropods is the insects, which have three

B. Krill swimming in Antarctic waters.

C. Barnacle filtering food from the water with its feathery legs.

Figure 16.19  Marine crustaceans. (B) NOAA NMFS SWFSC Antarctic Marine Living Resources (AMLR) Program; (C) Joe Belanger/ Shutterstock.com

pairs of legs and one pair of antennae. An estimated 90 percent of arthropods are insects. Genetic data indicate that insects are descended from freshwater crustaceans. Early insects were wingless, ground-dwelling scavengers that did not undergo metamorphosis. Modern bristletails and silverfish retain this body form and development. However, most modern insects have wings and undergo metamorphosis. Insects are the only invertebrates that can fly. In insects with incomplete metamorphosis, the juvenile that hatches from an egg is called a nymph. The nymph looks a bit different from the adult, and it develops the adult form over the course of several molts. Cockroaches, grasshoppers, and dragonflies develop in this way. In insects that undergo complete metamorphosis, a larva grows and molts without altering its form, then undergoes pupation. A pupa is a nonfeeding body in which larval tissues are remodeled into the adult form. Flies, beetles, and butterflies all have two pairs of wings on the thorax and undergo complete metamorphosis (Figure 16.20). Insects play important ecological roles. They serve as pollinators to many flowering plants (Figure 16.21A). They also serve as food for a variety of wildlife. For example, larval moths and butterflies (caterpillars) feed songbird nestlings. Aquatic larvae of dragonflies and mayflies serve as food for fish. Most amphibians and reptiles feed mainly on insects. Insects also dispose of wastes

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Chris Howey/ Shutterstock.com

A. Centipede, a speedy predator.

Animal Evolution  Chapter 16  331  

and remains. Flies and beetles are quick to find an animal corpse or a pile of feces (Figure 16.21B). They lay eggs in or on this organic material, and the larvae that hatch devour it. By their actions, these insects help distribute nutrients through the ecosystem. On the other hand, some insects negatively affect humans. Insects are our main competitors for plant foods. For example, Mediterranean fruit flies, or medflies, damage citrus crops (Figure 16.21C). Insects also transmit dangerous diseases. Mosquitoes spread malaria and carry parasitic roundworms between human hosts. Fleas can transmit plague, and lice can transmit typhus. Bedbugs (Figure 16.21D) do not transmit disease, but their bites itch, and infestations can have severe psychological and economic effects.

Larva (leaf-eating, wingless caterpillar)

Pupa (remodeling stage)

Adult (winged nectar feeder)

Figure 16.20  Complete metamorphosis in a butterfly. Left and middle, Jacob Hamblin/Shutterstock.com; right, Laurie Barr/Shutterstock.com

Take-Home Message 16.5 ●● ●●

●●

●●

Roundworms and arthropods are protostomes that molt. Roundworms are unsegmented worms that have a pseudocoelom. Most are freeliving decomposers, but some are parasites of plants or animals. Arthropods are the most diverse animal group. A hard, jointed exoskeleton, specialized body segments, sensory structures such as eyes and antennae, and a body plan that includes multiple forms contributed to their evolutionary success. Insects are the most diverse arthropod group and the only invertebrates that fly. Most play important ecological roles, but some are pests.

A. Bee serving as a pollinator.

B. Dung beetle gathering feces.

Figure 16.21  Ecological roles of insects. (A) Photo by Jack Dykinga, USDA, ARS; (B) Michael Potter11/Shutterstock.com; (C) Scott Bauer/USDA; (D) CDC/Piotr Naskrecki

crustaceans  Mostly marine arthropods with two pairs of antennae and at least five pairs of legs; for example, a shrimp, crab, lobster, or barnacle.

C. Medfly, a threat to citrus.

D. Bedbug, a human parasite.

insects  Land-dwelling arthropods with a pair of antennae, three pairs of legs, and—in the most diverse groups—wings.

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16.6  Echinoderms and Chordates 

chordates  Animal phylum characterized by a notochord, dorsal nerve cord, pharyngeal gill slits, and a tail that extends beyond the anus. Includes invertebrate and vertebrate groups.

Learning Objectives Describe the structure and function of a sea star, and explain the function of the echinoderm water-vascular system.

echinoderms  Invertebrates with a water-vascular system and an endoskeleton made of calcium carbonate plates and spines.

●  

● 

endoskeleton  Internal skeleton.

List the traits that characterize chordates. Describe the two groups of invertebrate chordates and their evolutionary relationship to the vertebrates.

●  

lancelets  Invertebrate chordates that have a fishlike shape and retain their defining chordate traits into adulthood.

● 

Explain which trait defines vertebrates.

notochord  Stiff rod of connective tissue that runs the length of the body in chordate larvae or embryos.

With this section, we begin our survey of deuterostomes, another lineage of bilaterally symmetrical animals. Echinoderms and chordates are the two deuterostome subgroups.

tunicates  Invertebrate chordates that produce a secreted body covering as adults; the only chordate trait of adults is the pharynx with gill slits.

Echinoderms  Echinoderms (phylum Echinodermata) include about 6,000 marine invertebrates

such as sea stars, sea urchins, and sea cucumbers (Figure 16.22). Their phylum name means spiny-skinned and refers to interlocking spines and plates of calcium carbonate embedded in their skin. The plates form an internal skeleton called an endoskeleton. Echinoderm adults are radially symmetrical. Sea stars (sometimes called starfish) are the most familiar echinoderms (Figure 16.22A). They do not have a brain, but they do have a decentralized nervous system. Eyespots at the tips of their arms detect light and movement. A typical sea star moves about on tiny, fluid-filled tube feet. Tube feet are part of a watervascular system, a system of fluid-filled tubes unique to echinoderms. The system includes a central ring and fluid-filled canals that extend into the arms. In each arm, branches from the main canal deliver coelomic fluid into muscular bulbs (called ampullae) that function like the bulb on a medicine dropper. Contraction of a bulb forces fluid into the attached tube foot, extending the foot. A sea star glides along as coordinated contraction and relaxation of the bulbs redistribute fluid among hundreds of tube feet. Most sea stars prey on bivalve mollusks. To feed, the sea star slides its stomach out through its mouth and into a bivalve’s shell. The stomach secretes acid and enzymes that kill the mollusk and begin to digest it. Partially digested food enters

water-vascular system  Of echinoderms, a system of fluid-filled tubes and tube feet that function in locomotion.

Figure 16.22  Echinoderms. (B) naturediver/iStock/Getty Images; (C) Andrew David, NOAA/NMFS/SEFSC Panama City, Lance Horn, UNCW/NURC-Phantom II ROV operator

anus

upper stomach

lower stomach

gonad

spine

coelom digestive gland eyespot

spine

ossicle (tiny skeletal structure)

A. Body plan of a sea star.

ampullae

tube feet

B. Sea urchin.

C. Sea cucumber.

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Animal Evolution  Chapter 16  333  

the stomach, and digestion is completed with the aid of enzyme-secreting digestive glands in the arms. A sea star’s reproductive organs are also in its arms. A sea star larva is ciliated and bilaterally symmetrical. It swims about briefly, then develops into an adult. The bilateral symmetry of echinoderm larva, along with evidence from genetic studies, indicates that the ancestor of echinoderms was a bilateral animal.

single eyespot pharynx with gill slits dorsal nerve cord

Chordates

notochord

Four embryonic traits define the chordates (phylum Chordata): (1) A notochord, a rod of stiff but flexible connective tissue, extends the length of the body and provides support; (2) a dorsal, hollow nerve cord parallels the notochord; (3) gill slits open across the wall of the pharynx (throat region); and (4) a muscular tail extends beyond the anus. Depending on the chordate group, some, all, or none of these traits persist in the adult.

anus

Invertebrate Chordates 

tail that extends beyond the anus

There are two groups of invertebrate chordates, tunicates and lancelets. Both are marine filter feeders that strain food from currents of water that pass through the gill slits in their pharynx. Lancelets (subphylum Cephalochordata) have a fishlike shape and are 1.2 to 2.8 inches (3 to 7 centimeters long) (Figure 16.23). Lancelets retain all characteristic chordate traits as adults. The dorsal nerve cord extends into the head, where a single eyespot at its tip detects light. However, the head does not have a true brain or any paired sensory organs similar to those of fishes. Tunicates (subphylum Urochordata) are named for the secreted carbohydraterich covering or “tunic” that encloses the adult body (Figure 16.24A). Larval tunicates have all the typical chordate traits (Figure 16.24B). They swim about briefly, then undergo metamorphosis to the adult form. Of the four typical chordate traits, the adult retains only the pharynx with gill slits. Most adult tunicates attach to an undersea surface and filter food from the water. Which invertebrate chordate is most closely related to vertebrates? An adult lancelet looks more like a fish than an adult tunicate does, but such superficial similarities are sometimes deceiving. Studies of developmental processes and gene sequences indicate that tunicates are the closest invertebrate relatives of vertebrates. Keep in mind that neither tunicates nor lancelets are ancestors of vertebrates. All three groups evolved from a now extinct invertebrate chordate ancestor; each has unique traits that put it on a separate branch of the animal family tree.

Figure 16.23  Lancelet. These marine invertebrates retain all chordate traits (labeled with bold text) into adulthood. Lancelets live in sandy sediments, and filter food from the water with their pharynx.

water flows in water flows out

Figure 16.24  Tunicate body plans. Larval tunicates are free-swimming and have all the characteristic chordate features. After metamorphosis, the adult retains only the pharynx with gill slits.

pharynx with gill slits secreted “tunic”

dorsal nerve cord

notochord

postanal tail

pharynx with gill slits

A. Adult tunicate.

B. Free-swimming tunicate larva.

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334  Unit 3  EVOLUTION AND DIVERSITY

Chordates Vertebrates Tetrapods Amniotes

Lancelets

Tunicates

Cartilaginous fishes

Jawless fishes

Ray-finned fishes

Lobe-finned fishes

Amphibians

Reptiles (with birds)

Mammals

6 Amniote eggs 5 Four limbs 4 Bony appendages 3 Swim bladder or lung(s)

Vertebrate Traits and Trends Vertebrates (subphylum Vertebrata)

are the third major chordate subgroup. All vertebrates have a distinct head with a brain, and most have a pair of eyes. Their circulatory system is closed, with a single heart, and there is a complete digestive tract. Paired organs called kidneys filter blood, adjust its volume and solute composition, and eliminate wastes. Figure 16.25 shows the chordate family tree and notes the key innovations that define various lineages. Vertebrates 1 are named for the vertebral column (backbone) that replaces the notochord as a vertebrate embryo develops. This flexible but sturdy structure encloses the spinal cord that develops from the nerve cord. The vertebral column is part of the vertebrate endoskeleton. Jaws are hinged skeletal elements used in feeding 2. They evolved by modification of bony structures that supported the gills of jawless fishes. Evolution of jaws opened up new feeding opportunities, allowing an adaptive radiation. The vast majority of modern fishes have jaws. Internal air sacs evolved in some jawed fishes 3. In some species, such a sac functioned as a simple lung, a respiratory organ in which blood exchanges gases with the air. One lineage of fish with lungs also had bony paired fins 4. Bony paired limbs evolved in their descendants, which were the first tetrapods, or four-legged walkers 5. A special type of egg (the amniote egg) allowed one tetrapod group to lay eggs on land 6. Members of that lineage, the amniotes (reptiles, birds, and mammals), are the most successful tetrapods on land with regard to number of species. 2 Jaws

1 Backbone

ancestral chordate

Figure 16.25  The chordate family tree. The vast majority of chordates are vertebrates. Figure It Out: Do the cartilaginous fishes have a backbone?

Answer: Yes

cartilaginous fish  Fish that has jaws, paired fins, and a skeleton made of cartilage; for example, a shark. jawless fish  Fish that has a skeleton of cartilage, but no jaws or paired fins; for example, a lamprey. kidney  Organ of the vertebrate urinary system that filters blood, adjusts its composition, and eliminates wastes.

Take-Home Message 16.6 ●●

lung  Saclike organ inside which blood exchanges gases with the air. scales  Hard, flattened elements that cover the skin of reptiles and some fishes. tetrapod  Vertebrate that has four limbs or is descended from a four-limbed ancestor. vertebral column  Backbone. vertebrate  Animal with a backbone; a fish, amphibian, reptile, bird, or mammal.

●●

●●

●●

Echinoderms are invertebrates that are radial as adults but have bilateral larvae. The adult has a “spiny skin” with many embedded hard plates and it walks about on tiny tube feet that are part of a water-vascular system. The earliest chordates were invertebrates, and two groups of invertebrate chordates (tunicates and lancelets) still exist. They are aquatic filter feeders. Vertebrates evolved from an invertebrate chordate ancestor. All have a vertebral column, or backbone. Jaws, lungs, limbs, and waterproof eggs were key innovations that led to the adaptive radiation of vertebrates, first in the seas and then on the land.

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Animal Evolution  Chapter 16  335  

16.7  Fishes and Amphibians Learning Objectives ●●

Compare the body form of jawless fishes, cartilaginous fishes, and bony fishes.

●●

Describe some of the anatomical changes that occurred as vertebrates moved onto land.

●●

Give examples of modern amphibians, and explain why many amphibian populations are currently in decline.

We devote the remainder of this chapter to a survey of vertebrate diversity, beginning here with the fishes and amphibians.

Jawless Fishes  The earliest vertebrates were jawless fishes. Modern jawless fishes have a smooth, elongated body without paired fins. Like lancelets, they move by wriggling their body. The skeleton of a jawless fish is made of cartilage, the same type of connective tissue that supports your nose and ears. Figure 16.26 shows the distinctive mouth of one jawless fish, a lamprey. As adults, most lampreys feed on other fish. Lacking jaws, a lamprey cannot bite. Instead, it attaches to a fish using an oral disk ringed by horny teeth made of the protein keratin. Once attached, the lamprey secretes enzymes and scrapes up bits of its host’s flesh with a tooth-covered tongue.

Figure 16.26  Lamprey, a jawless fish. A lamprey has no paired fins and its gill slits are visible at the body surface. It attaches to other fishes with its oral disk and scrapes at their flesh. Gena Melendrez/Shutterstock.com

A. Ancestral jawless fish

B. Jawed fish

Jawed Fishes  Jaws evolved from gill arches, which are skeletal elements that support a fish’s gills (Figure 16.27). Most modern jawed fishes have paired fins and scales: hard, flattened structures that grow from and often cover the skin. There are two groups of jawed fishes: cartilaginous fishes and bony fishes (Figure 16.28). Cartilaginous Fishes  As their name implies, cartilaginous fishes are jawed

gill slits

gill support

jaw, derived from gill supports

Figure 16.27  Evolution of jaws from gill supports.

fishes with a skeleton made of mineral-hardened cartilage. They include 850 species of rays, skates, and sharks, with sharks being the best known. Some sharks such as great white sharks are predators that swim in upper ocean waters (Figure 16.28A). Others strain plankton from the water or suck up food from the seafloor.

Figure 16.28  Jawed fishes. (A) wildestanimal/Shutterstock.com

swim bladder

anus

A. Cartilaginous fish with jaws and paired fins. A. Cartilaginous fish with paired fins. This great white shark is ajaws swiftand predator. This great white shark is a swift predator.

kidney spinal cord brain

ovary

intestine stomach liver heart

gills

B. Bony fish body plan. This is a perch.

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336  Unit 3  EVOLUTION AND DIVERSITY

Shark attacks on humans receive a lot of attention, but they are rare. Worldwide, sharks kill about five people a year. For comparison, dogs kill about 30 people each year in the United States alone.

A. Goldfish (carp), a ray-finned bony fish. Its fins consist of a web of skin supported by thin spines.

pelvic fin

pectoral fin

B. Lungfish, a lobe-finned bony fish. Its thick, fleshy fins have sturdy bony supports inside them. Figure 16.29  Two types of fins in bony fishes. (A) iStock.com/GlobalP; (B) Wernher Krutein/Photovault.com

Bony Fishes  In bony fishes, an embryonic skeleton of cartilage develops into an adult skeleton consisting mainly of bone. Both cartilaginous fishes and bony fishes have paired fins, but those of bony fish have a much greater range of motion. Bony fishes also differ from other fishes in having their gill slits hidden beneath a gill cover. In jawless and cartilaginous fish, gill slits are visible at the body surface. There are two lineages of bony fishes: ray-finned fishes and lobe-finned fishes. Ray-finned fishes have flexible fins supported by thin rays derived from skin. A gas-filled swim bladder helps them adjust their buoyancy. With about 30,000 species, ray-finned fishes constitute nearly half of the vertebrates. They include most familiar freshwater fish (Figure 16.29A) as well as marine species such as tuna, halibut, and cod. Lobe-finned fishes have thick, fleshy pelvic and pectoral fins with internal bony supports. Modern lobe-finned fishes include coelacanths (Section 13.7) and lungfishes (Figure 16.29B). As their name suggests, lungfishes have one or two lungs in addition to their gills. The fish inflates its lungs by gulping air, then air in the lungs exchanges gases with blood. Having lungs in addition to gills allows lungfishes to survive in low-oxygen waters. Tetrapods (vertebrates with limbs) descended from an ancestral lobe-finned fish. Genome comparisons indicate that lungfishes are their closest living relatives.

Amphibians Amphibians are scaleless vertebrates that generally spend time on land but require water to breed. Fertilization is typically external. Eggs and sperm are released into water through a cloaca, a body opening that also serves as the exit for urinary and digestive wastes. (Sharks, reptiles, birds, and egg-laying mammals also have a cloaca.) Amphibian larvae are aquatic and have gills. Most species lose their gills and develop lungs during the transition to adulthood. The Transition to Land  Amphibians were the first tetrapods. Looking at fossils,

amphibian  Tetrapod with a scaleless skin that typically develops in water, then lives on land as a carnivore with lungs. bony fish  Jawed fish with a skeleton composed mainly of bone. cloaca  Of some vertebrates, body opening that releases urinary and digestive waste, and also functions in reproduction. lobe-finned fish  Bony fish that has bony supports inside its fins. ray-finned fish  Bony fish with fins supported by thin rays derived from skin.

we can see the skeletal changes that occurred as fishes, with bodies adapted to swimming, evolved into the four-legged walkers (Figure 16.30). Amphibian limb bones and the bones of a lobe-finned fish’s pelvic and pectoral fins are homologous structures (Section 12.6). During the transition to land, these bones became larger and better able to bear weight. Ribs also enlarged. In addition, a distinct neck emerged, allowing the head to move independently of the rest of the body. Adapting to life on land was not simply a matter of skeletal changes. Lungs became larger and more complex. Division of the previously two-chambered fish heart into three chambers allowed blood to flow in two circuits, one to the body and one to those increasingly important lungs. Changes to the inner ear improved detection of airborne sounds. Evolution of eyelids prevented delicate eye tissues from drying out. What was the advantage of living on land? An ability to survive out of water is useful in seasonally dry places. Individuals on land were also safe from aquatic predators and had access to a new food—insects—which had recently evolved.

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Animal Evolution  Chapter 16  337  

3

1 Fish (Eusthenopteron) with fins and no ribs.

2 1

2 Fish (Tiktaalik ) with ribs and modified fins.

3 Early amphibian (Ichthyostega) with ribs and limbs. Figure 16.30  Fossil species from the late Devonian show how vertebrates made the transition from water to land. (A) P. E. Ahlberg; (B) Illustration by © Kalliopi Monoyios; (C) P. E. Ahlberg

Modern Amphibians  Modern amphibians include salamanders, frogs, and toads. As adults, nearly all are carnivores, feeding on mainly insects and worms. Of all amphibians, the 530 or so species of salamanders and newts most closely resemble early tetrapods in body form. Their forelimbs and back limbs are similarly sized, and they have a long tail (Figure 16.31A). Salamander larvae look like small adults, except for the presence of gills. Frogs and toads belong to the most diverse amphibian lineage, with more than 5,000 species. Long, muscular hind limbs allow adult frogs to swim, hop, and make spectacular leaps (Figure 16.31B). The much smaller forelimbs help absorb the impact of landings. Compared with frogs, toads have a stubbier body and their hind legs are proportionately shorter. Toads can hop, but more often they walk. The larvae of frogs and toads differ markedly from adults. The larvae, commonly called tadpoles, have gills and a tail but no limbs (Figure 16.31C).

Declining Amphibian Populations  Amphibians are in decline worldwide, with an estimated 30 to 50 percent of species now at risk of extinction. Most species declines are the result of human activities.

B. Frog, with long, muscular legs and short forelimbs.

Figure 16.31  Amphibians. All have a scaleless body. (A) James Bettaso, US Fish and Wildlife Service; (B) Stephen Dalton/Science Source; (C) Steve Byland/Shutterstock.com

A. Salamander, with equal-sized front and back limbs.

C. Tadpole, a swimming frog larva with gills and a tail.

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338  Unit 3  EVOLUTION AND DIVERSITY

People destroy amphibian breeding areas by filling low-lying areas where seasonal rains would otherwise pool. Amphibians are also highly sensitive to water pollution. Their thin skin allows waste carbon dioxide to diffuse out of their body, but it also allows chemical pollutants to move inward. Another factor is the spread of pathogens, most notably the chytrid fungus Batrachochytrium dendrobatidis (Bd). Humans have spread this lethal fungus worldwide by shipping amphibians for use as pets, food, and medical testing. Declines of at least 400 frog species have been attributed to the spread of the Bd fungus.

Take-Home Message 16.7 A. Python Python emerging emergingfrom fromegg. egg.

●●

●●

●●

Like the earliest fishes, modern lampreys are jawless and do not have paired fins or scales. Cartilaginous fishes and bony fishes have jaws, scales, and paired pins. Bony fishes, the most diverse fish lineage, have paired movable fins. One subgroup, the lobe-finned fishes, gave rise to the tetrapods. Amphibians are tetrapods with a scaleless body. They lay their eggs in water and produce gilled larvae.

16.8  Escape from Water—Amniotes Komododragon, dragon,the thelargest largestlizard. lizard. B. Komodo

Learning Objectives ●● ●●

D. Crocodile Crocodilewith withits itsfish fishprey. prey.

Figure 16.32  Diversity of nonbird reptiles. (A) Heiko Kiera/Shutterstock.com; (B) OutdoorWorks/Shutterstock.com; (C) Joel Sartore/ National Geographic Image Collection/Getty Images; (D) Johan Swanepoel/Shutterstock.com

Using appropriate amniote examples, explain the difference between endotherms and ectotherms.

●●

Explain how birds are related to dinosaurs.

●●

Give examples of structural and physiological traits that adapt birds to flight.

●●

C. Turtle Turtle in inaadefensive defensiveposture. posture.

List the traits that adapt amniotes to land.

Describe the traits that define mammals and the differences among the three mammalian lineages.

During the Carboniferous period, amphibians were the dominant animals on land. Late in that period, the first amniotes evolved from an amphibian ancestor. Reptiles (including birds) and mammals are amniotes. The defining trait of amniotes is a unique type of egg that allows them to reproduce on land. Inside an amniote egg, the embryo develops enclosed within protective membranes and surrounded by fluid. In most lineages, females lay eggs that have a hard or leathery shell (Figure 16.32A), but in some mammals development takes place inside the mother’s body. Other traits also adapt amniotes to life away from water. Amniote skin is rich in keratin, a protein that makes it waterproof. A pair of well-developed kidneys help conserve water, and fertilization takes place inside the female’s body. The ability to regulate internal body temperature evolved in some early amniotes, including the ancestors of birds and of mammals. Amphibians, turtles, lizards, and snakes are ectotherms, which means “heated from outside.” Ectotherms adjust their internal temperature by altering their behavior. They can, for example, bask on a warm rock to heat up, or retreat into a burrow to cool off. In contrast, birds and mammals are endotherms that maintain their body temperature by varying their production of metabolic heat. Endotherms use energy staying warm, so they require more food than ectotherms. A bird or mammal requires far more calories than a lizard or snake of the same weight.

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Animal Evolution  Chapter 16  339  

However, because endotherms warm themselves, they can remain active at lower temperatures than ectotherms.

Reptiles An early branching of the amniote lineage separated the ancestors of mammals from those of the reptiles: Mammals

Lizards, snakes Turtles

Crocodilians

Birds

Reptiles

Note that biologists use the term “reptile” somewhat differently than the general public. In biology, reptiles (members of the clade Reptilia) include not only the lizards, snakes, turtles, crocodilians, and the extinct dinosaurs, but also the birds. Lizards and Snakes  Lizards and snakes have overlapping scales, and they periodically shed their skin as they grow. All have teeth, and most are active hunters. The largest lizard, the Komodo dragon (Figure 16.32B), is a predator that grows up to 10 feet (3 meters) long. Its saliva contains a slow-acting venom. The dragon bites a prey animal, then follows it for hours or days until the poisoned animal collapses. Snakes evolved from lizards during the Cretaceous, and some snakes such as pythons retain bony remnants of ancestral hind limbs. All snakes are predators, but only some have fangs. Rattlesnakes and other fanged snakes bite and subdue prey with venom they produce in modified salivary (saliva-making) glands. Other snakes are constrictors that wrap around a prey animal and suffocate it. Venoms from lizards and snakes, like venom from marine invertebrates, contain compounds that can have medical benefits. ACE inhibitors, a class of drugs used to treat high blood pressure, are synthetic versions of a peptide from Brazilian viper venom. Venom from the Gila monster (a type of lizard) contains a compound that is now synthesized for treatment of diabetes. Komodo dragon venom contains compounds that inhibit blood clotting and may point the way to a new blood-thinning drug. Turtles and Crocodilians  Turtles have a bony, protective shell attached to their backbone (Figure 16.32C). Modern turtles do not have teeth. Instead, a thick layer of the protein keratin covers their jaws and forms a horny beak. Most turtles live either in the sea or in freshwater. Those that live entirely on land are commonly called tortoises. Crocodilians live in or near water and include crocodiles, alligators, and caimans. They are predators with powerful jaws, a long snout, and sharp teeth (Figure 16.32D). Like birds, all crocodilians have a highly efficient four-chambered heart. They are the closest living relatives of birds. Dinosaurs  Unique skeletal features such as the anatomy of the pelvis and hips

define the dinosaurs. During the Jurassic and Cretaceous periods (201 to 66 million years ago), dinosaurs underwent a great adaptive radiation and became the dominant animals on land. One dinosaur lineage, the theropods, included many

amniote  Vertebrate adapted to life on land by amniote eggs such as a reptile (including birds) or a mammal. ectotherm  Animal that gains heat from its environment and adjusts its internal temperature by altering its behavior. endotherm  Animal that maintains its body temperature by varying its production of metabolic heat. reptiles  Amniote clade that includes modern lizards, snakes, turtles, crocodilians, and birds, as well as some extinct groups such as dinosaurs.

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340  Unit 3  EVOLUTION AND DIVERSITY

feathered species. About 160 million years ago, this lineage gave rise to the first birds. Dinosaurs became extinct at the end of the Cretaceous (65 million years ago), most likely as a result of an asteroid impact (Section 12.1). Birds   Birds are the only modern animals with feathers, which are modified

Figure 16.33  Bird in flight. Birds flap their wings to fly. The downstroke provides lift. Eric Isselee/Shutterstock.com

yolk sac embryo

amnion

chorion

allantois

egg white (albumen)

hardened shell

scales. Flight feathers and other traits adapt the bird body to flight. Bird wings are homologous to our arms. Contraction of one set of muscles produces a powerful downstroke that lifts the bird (Figure 16.33). A less powerful set of muscles contracts to raise the wing. Birds have the most efficient respiratory system of any vertebrate. This system ensures a steady supply of the oxygen to flight muscles, which produce ATP by aerobic respiration. A four-chambered heart pumps oxygen-poor blood to the lungs and oxygen-rich blood to the rest of the body in separate circuits. Flying also requires good eyesight and a great deal of coordination. Compared to a lizard of a similar body mass, a bird has much larger eyes and a larger brain. Most birds are surprisingly lightweight. Air cavities inside a bird’s bones keep its body weight low, as does the lack of a bladder (an organ that stores urinary waste in many other vertebrates). Rather than heavy, bony teeth, bird jaws are covered with a lightweight beak made of keratin. In birds, as in other reptiles, fertilization is internal. Unlike most male reptiles, male birds do not typically have a penis. Thus, to inseminate a female, a male bird must press his cloaca against hers, in a maneuver poetically described as a cloacal kiss. A female bird lays an egg that has four membranes characteristic of amniote eggs (Figure 16.34A). Nutrients from the egg’s yolk and water from the egg white (albumen) sustain the developing embryo. Like some turtles and all crocodilians, birds encase their eggs within a rigid shell hardened by calcium carbonate. In nearly all bird species, one or both parents incubate the eggs until they are ready to hatch. Many birds hatch in a relatively undeveloped state and require extensive parental care before they can live on their own (Figure 16.34B).

A. Developing embryo inside an egg.

Mammals  Mammals are the amniotes in which females nourish their offspring with milk

B. Newly hatched parrots. Figure 16.34  Bird development. (B), Jane Burton/Nature Picture Library

secreted from mammary glands. The group name is derived from the Latin mamma, meaning breast. Mammals are also the only animals that have hair or fur. Like feathers, hair and fur are modifications of scales. Mammals are endotherms, and a coat of fur or head of hair helps them maintain their core temperature. Mammals have distinctive skeletal and dental traits. Compared to other vertebrates, they have a larger skull and brain for their body size, and they are the only vertebrates with three bones in their middle ear. Most mammals have multiple types of teeth, whereas in other jawed vertebrates all teeth are similarly shaped. Having a variety of different kinds of teeth allows mammals to eat a wider variety of foods than most other vertebrates. Mammals evolved early in the Jurassic, and early mouselike species coexisted with dinosaurs. By 130 million years ago, three lineages had evolved: monotremes (egg-laying mammals), marsupials (the pouched mammals), and placental mammals (mammals in which an organ called the placenta provides nutrients to developing offspring). Figure 16.35 shows a member of each group. Only five species of monotremes survive, four species of echidnas (spiny anteaters) and one species of platypus. All live in Australia or on nearby islands. Marsupials are more diverse, with about 300 species such as kangaroos and opossums in or near Australia, and about 100 species (mostly opossums) in South America.

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Animal Evolution  Chapter 16  341  

B

A

C

Placental mammals are the most diverse and abundant mammalian lineage, with about 4,000 species and a worldwide distribution. What gives placental mammals their competitive edge? They have a higher metabolic rate, better body temperature control, and a more efficient way to nourish embryos. Compared to other mammals, placental mammals develop to a far more advanced stage inside their mother’s body. Rats and bats are the most diverse mammals. About half the 4,000 species of placental mammals are rodents and, of those, about half are rats. The next most diverse group is the bats, with about 375 species. Bats are the only flying mammals. Although some may look like flying mice, bats are more closely related to carnivores such as wolves and foxes than to rodents. Humans are primates. The next section explores the unique adaptations of this order of placental mammals and the history of the human lineage.

Figure 16.35  Mammal mothers and young. A. Egg-laying mammal, the platypus. Her young hatched from eggs laid outside her body. They lick milk that oozes from her skin. B. Marsupial, a kangaroo. Her young developed to an early stage in her body, then climbed into a pouch on her belly to nurse and complete development. C. Placental mammal, a bear. Her young developed to a late stage inside her body. After birth, they suck milk from nipples on her chest and belly. (A) JACANA/Science Source; (B) iStock.com/Craig Dingle; (C) Sergey Gorshkov/Nature Picture Library

Take-Home Message 16.8 ●●

●●

●●

Amniotes are vertebrates that are adapted to life on land by their unique eggs, waterproof skin, and highly efficient kidneys. One amniote lineage includes snakes, lizards, turtles, and crocodiles as well as the birds. Birds are the only amniotes with feathers. Like mammals, birds are endotherms; metabolic heat maintains their internal temperature. Mammals are amniotes that nourish their young with milk. Most have hair or fur. The three lineages are egg-laying monotremes, pouched marsupials, and placental mammals. Placental mammals are the most widespread and diverse.

16.9  Primate and Human Evolution Learning Objectives ●● ●●

●● ●●

Describe the traits that characterize primates. Compare the bodies of an Old World monkey, a New World monkey, and an ape, giving examples of each. Detail the evidence that our species originated in Africa. Describe what is known about Neanderthals and about the other recently discovered members of our genus.

bird  Modern amniote with feathers. mammal  Vertebrate that nourishes its young with milk from mammary glands. marsupial  Mammal in which offspring complete development in a pouch on the mother’s body. monotreme  Egg-laying mammal. placental mammal  Mammal in which developing offspring are nourished within the mother’s body by way of a placenta.

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anthropoids  Primate subgroup that includes monkeys, apes, and humans.

Figure 16.36  Adapted to climbing.

bipedalism  Habitually walking upright. hominin  Bipedal primates; humans and extinct humanlike species.

A female orangutan (an Asian ape) demonstrates her wide range of shoulder motion and the grasping ability of her hands and feet. Eyes situated at the front of her face provide excellent depth perception.

primate  Mammalian group with grasping hands; includes lemurs, tarsiers, monkeys, apes, and humans.

Sergey Uryadnikov/Shutterstock.com

Figure 16.37  Evolutionary tree for modern primates, with subgroup names in blue.

Lemurs, lorises, galagos

Tarsiers

New World monkeys

Old World monkeys

Primates are an order of placental mammals that includes humans, apes, monkeys, and their close relatives. Primates first evolved in tropical forests, and many of the group’s characteristic traits arose as adaptations to life among the branches. Primate shoulders have an extensive range of motion that facilitates climbing (Figure 16.36). Unlike most mammals, a primate can extend its arms out to its sides, reach above its head, and rotate its forearm at the elbow. Both hands and feet are capable of grasping. Many types of mammals have claws, whereas the tips of primate fingers and toes typically have touch-sensitive pads protected by flattened nails. Compared to other mammals, primates have a large brain for their body size. The regions of the brain devoted to vision and to information processing are expanded, and the area devoted to smell is reduced. Most mammals have widely spaced eyes set toward the side of the skull, but primate eyes tend to be at the front of the head. As a result, both eyes view the same area, each from a slightly different vantage point. The brain integrates the differing signals it receives from the two eyes to produce the three-dimensional view that you see. A primate’s excellent depth perception adapts it to a life spent leaping or swinging from limb to limb.

Gibbons

Orangutans

Gorillas

Chimpanzees, bonobos

Humans Hominins

Hominoids

Anthropoids Dry-nosed

Figure It Out: Which modern primates are human ancestors? Answer: None of them. All species ancestral to humans are extinct. We share a common ancestor with chimpanzees and bonobos.

Wet-nosed

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Animal Evolution  Chapter 16  343  

Most primates spend their life in a social group that includes adults of both sexes. Females usually give birth to only one or two young at a time and provide care for an extended period after birth.

Primate Origins and Diversification  Figure 16.37 shows the relationships among modern primate subgroups. Primates most likely arose before the demise of the dinosaurs, sometime between 85 and 66 million years ago. Lemurs are members of the oldest existing primate lineage. Like dogs and most other mammals, lemurs are “wet-nosed”; they have a moist nose and an upper lip that attaches tightly to the underlying gum (Figure 16.38A). A dry nose and a movable, noncleft upper lip evolved in the common ancestor of tarsiers (Figure 16.38B) and all other modern primates. This innovation gave dry-nosed primates a wider range of facial expressions and allowed more complex vocalizations. Anthropoids include monkeys, apes, and humans; anthropoid means “humanlike.” Nearly all anthropoids are diurnal (active during the day) and have good eyesight, including color vision. New World monkeys (Figure 16.38C) eat fruits in the forests of Central and South America. (The Americas are sometimes referred to as the New World, with Eurasia and Africa being the Old World.) New World monkeys have a flat face and a nose with widely separated nostrils. A long tail helps them maintain balance. In many species, the tail is prehensile, meaning it grasps things. Old World monkeys live in Africa, the Middle East, and Asia. They tend to be larger than New World monkeys, with a longer nose and closely set nostrils. Some are tree-climbing forest dwellers. Others, such as baboons (Figure 16.38D), spend most of their time on the ground in grasslands and deserts. Not all Old World monkeys have a tail, but in those that do the tail is typically short and never prehensile. Tailless nonhuman primates are commonly called apes. About 15 species of small apes called gibbons inhabit Southeast Asian forests. Gibbons are sometimes referred to as “lesser apes,” in comparison with the larger apes, or “great apes.” The only surviving Asian great ape is the orangutan, which climbs trees in the forests of Sumatra and Borneo. All other great apes (gorillas, chimpanzees, and bonobos) are native to central Africa and spend most of their time on the ground. When walking, African apes lean forward and support their weight on their knuckles (Figure 16.38E). Gorillas, the largest living primates, live in forests and feed mainly on leaves. Chimpanzees (Figure 16.38F) and the bonobos are our closest living relatives. The chimpanzee/bonobo lineage and the lineage leading to humans diverged 6 to 13 million years ago.

Early Hominins  Humans and their closest extinct relatives are now grouped together as hominins (previously called hominids). The defining trait of hominins is bipedalism—habitual upright walking. Thus, researchers interested in human origins look for fossil evidence that a species walked upright. Some fossils of primates that may have been bipedal date back as long as 7 million years ago. However, the fossil record of these species is patchy, and little is known about them.

A. Lemur, with a wet nose and cleft upper lip.

C. Squirrel monkey (New World monkey), with a flat face and prehensile tail.

E. Gorilla, the largest living great ape.

B. Tarsier, with a dry nose and uncleft upper lip.

D. Baboon (Old World monkey), with a long nose and short tail.

F. Chimpanzee, one of our two closest living relatives.

Figure 16.38  Diversity of modern, nonhuman primates. (A) iStock.com/Toos; (B) iStock.com/Roc8jas; (C) Primates.com; (D) iStock.com/Jason R. Warren; (E) © Dallas Zoo, Robert Cabello; (F) Abeselom Zerit/Shutterstock.com

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344  Unit 3  EVOLUTION AND DIVERSITY

The best-known early hominins are the australopiths, who lived in Africa from about 4 million to 1.2 million years ago. One australopith genus, Australopithecus, includes several species considered likely human ancestors. The fossil history of australopiths shows trends toward smaller teeth and improvements in the ability to walk upright, but little increase in brain size. Fossil footprints in Tanzania document the passage of a bipedal species 3.6 million years ago (Figure 16.39A). The prints reveal that the walkers’ feet had a pronounced arch and a big toe in line with the other toes—both adaptations to upright walking. The prints were probably made by Australopithecus afarensis, an australopith that lived in Tanzania and other parts of eastern Africa from 3.9 to 3 million years ago. An A. afarensis skeleton known as Lucy (Figure 16.39B) is the best-known representative of this species. A. afarensis is considered a possible human ancestor.

Early Humans  Humans are members of the genus Homo.

A. 3.6-million-year-old footprints of a bipedal species.

B. A. afarensis fossil (Lucy) from 3.5 million years ago.

Figure 16.39  Evidence of early hominins. (A) Louise M. Robbins; (B) Dr. John D. Cunningham/Visuals Unlimited, Inc.

Homo habilis  Fossils of the oldest species in this genus, Homo habilis, date from 2.3 million years to 1.4 million years before the present. The species was named based on a fossil discovered in Kenya in 1964. The name Homo habilis, which means “handy man,” is a reference to the stone tools found near the fossil. At the time of the fossil’s discovery, the ability to make stone tools was considered a distinctly human trait. We now know that hominins used sharp stone edges to scrape meat from bones as early as 3.4 million years ago. Given the age of the bones, these early tool users were most likely australopiths. Classification of H. habilis continues to inspire debate. The species is australopith-like in its body proportions and brain size, so some scientists think it should be reclassified as a species of Australopithecus. Other scientists argue for the species’ inclusion in the genus Homo, pointing out that the hands and arms were similar to those of modern humans. Homo erectus  The first known hominin with body proportions like modern humans was Homo erectus, which arose in Africa by about 2 million years ago. The

australopiths  Informal name for a lineage of chimpanzee-sized hominins that lived in Africa between 4 million and 1.2 million years ago.

species name means “upright man,” and like us, H. erectus stood on legs that were longer than its arms. The most complete H. erectus fossil found thus far is a skeleton of a young male who lived about 1.5 million years ago in Kenya (Figure 16.40A). This individual, informally known as Turkana boy, was under age 14 when he died. However, he was already 5 feet 2 inches (1.60 meters) tall and his brain was twice the size of a chimpanzee’s. H. erectus is the first hominin for which we have evidence outside of Africa. Fossils of this species have been found in China (Figure 16.40B) and the Eurasian country of Georgia. At the same time that some Homo erectus was becoming established in new locations, African Homo erectus populations continued to thrive. An African population of Homo erectus is considered the most likely ancestor of our own species and of Neanderthals.

Homo erectus  Human species that dispersed out of Africa; likely ancestor of Homo sapiens.

Homo sapiens 

Homo habilis  Earliest named human species.

Homo sapiens is the species name for anatomically modern humans such as you.

Homo neanderthalensis  Neanderthals. Closest extinct relatives of modern humans; had large brain, stocky body. Homo sapiens  Anatomically modern humans. humans  Members of the genus Homo.

Compared to H. erectus, H. sapiens has a higher, rounder skull, a larger brain, and a flatter face with smaller jaw and teeth. H. sapiens is also the only hominin with a chin, a protruding area of thickened bone in the middle of the lower jawbone. Exactly when H. sapiens arose remains a matter of investigation. Two 195,000-year-old skull fossils from Ethiopia have long been considered the oldest

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Animal Evolution  Chapter 16  345  

A. Fossil of a male who lived in Kenya 1.5 million years ago.

B. Reconstruction based on a 700,000-year-old skull discovered in China.

Figure 16.40  Homo erectus, the first hominin species to leave Africa. (A) Science VU/NMK/Visuals Unlimited, Inc.; (B) LOOK AT SCIENCES/Science Source

representatives of our species. However, a Homo sapiens jaw fossil from Morocco was recently analyzed and found to date to 300,000 years ago. The oldest H. sapiens fossils are all from Africa, indicating that our species originated there. Genetic analyses also support the African origin hypothesis. Modern Africans are more genetically diverse than people of any other region. This diversity indicates that African populations have existed for a very long time—long enough to accumulate a very large number of random mutations compared with other populations. Furthermore, most genetic variations seen in people native to regions outside of Africa are subsets of the variation found in Africa. This pattern is evidence that a series of founder effects occurred as small groups of people left their homeland to colonize the rest of the world. Recently discovered H. sapiens fossils from Greece indicate that small groups began to venture out of Africa as early as 210,000 years ago. Other fossils found in China may be H. sapiens and date to 100,000 years ago. However, genetic studies of modern humans indicate that most non-African populations are descendants of individuals who left Africa in a mass migration 70,000 to 60,000 years ago. Our species expanded its range over many generations, as small groups ventured beyond from their place of birth. Human pioneers traveled along the coasts of Africa, then Eurasia and Australia. By about 40,000 years ago they were creating art on rocks in Europe and in Indonesia. By 13,000 years ago, they were leaving footprints along a beach in British Columbia on the west coast of North America.

Neanderthals and Denisovans  Neanderthals (Homo neanderthalensis) have long been considered our closest extinct relatives. A recent reconstruction of a Neanderthal male, based on material from multiple fossils, stands about five foot four inches (164 centimeters) tall (Figure 16.41).

Homo neanderthalensis

Homo sapiens

Figure 16.41  Skeletal comparison of Neanderthal and modern human males. The Neanderthal skeleton is a reconstruction based on multiple fossils. Each color denotes a different fossil. Courtesy of @ Blaine Maley, Washington University, St. Louis

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346  Unit 3  EVOLUTION AND DIVERSITY

CLOSER LOOK 1 Perhaps as long as 700,000 years ago, a divergence

2

Denisovan

3

Neanderthals

Melanesian

Asian

European

African

Figure 16.42  One current model of human evolution. separated the ancestors of modern humans from the lineage leading to Neanderthals and Denisovans.

2 About 60,000 years ago, Neanderthals living in

the Middle East mated with modern humans who were venturing out of Africa.

3 About 40,000 years ago, ancestors of the modern

humans who would later populate New Guinea and Australia mated with Denisovans.

Modern Human Lineage

Neanderthal Lineage

1

Figure It Out: Did modern humans and Neanderthals interbreed in Africa?

Figure Summary Some modern human populations contain DNA sequences inherited from Neanderthal or Denisovan ancestors.

Answer: No

Neanderthals first appeared about 230,000 years ago, and they left an extensive fossil record in the Middle East, Europe, and central Asia. The common conception of Neanderthals as brutish cavemen with poor posture arose from an early reconstruction based on a fossil of an individual deformed by arthritis. More recent reconstructions reveal Neanderthals were shorter than modern humans but stood upright. They lived in regions where winters are cold, and a short, stocky body minimizes the surface area available for heat loss. Modern Arctic peoples have a similar body shape. The Neanderthal braincase was longer and lower than that of modern humans, but their brain was as big as or bigger than ours. Their face had pronounced browridges, a large nose with widely spaced nostrils, and no chin. Fossils of Neanderthal individuals who survived despite disabilities such as the loss of a limb suggest they had a compassionate social structure. Some simple burials suggest possible symbolic thought. Several lines of evidence suggest Neanderthals were able to speak. The most recent Neanderthal remains date to about 40,000 years ago. Why did they die out? Neanderthals may have been outcompeted by newly arrived H. sapiens or killed by diseases these migrants brought with them. Climate change may have contributed to their demise by altering the abundance of the animals they hunted. The existence of Denisovans was discovered when researchers sequenced DNA extracted from a fossil pinky (small finger) bone discovered in Denisova Cave in Siberia. The researchers expected to find typical Neanderthal DNA. Instead, the finger’s DNA contained unique sequences never seen before. As a result, the fossil was assigned to a group—the Denisovans—named for the site of its discovery. Analysis of another finger bone from the same region indicated this bone was from a young girl who had a Neanderthal mother and a Denisovan father. At this writing, Denisovans do not have a formal species name.

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Animal Evolution  Chapter 16  347  

As early modern humans left Africa and expanded their range to Eurasia, they met and interbred with Neanderthals and Dennisovans (Figure 16.42). These three hominin groups shared an ancestor between 500,000 and 700,000 years ago 1. About 60,000 years ago, as some modern humans ventured into the Middle East, they met up with and interbred with Neanderthals (Homo neanderthalensis) 2. As a result of this interbreeding, modern human populations native to regions outside of Africa have distinctive Neanderthal alleles that are rare among populations native to Africa. A second interbreeding event took place about 40,000 years ago somewhere in Asia. Here, humans interbred with Denisovans 3. As a result, we find unique Denisovan alleles in some mod-ern Asians. Melanesians, such as people of Papua New Guinea, have an especially high percentage of Denisovan DNA.

Take-Home Message 16.9 ●●

●●

●●

●●

Humans, like other primates, have grasping hands and shoulders adapted to climbing. Unlike most primates, they walk upright. Australopiths are a group of upright-walking species that include likely human ancestors. They evolved in Africa by about 4 million years ago. The first humans, or members of the genus Homo, also arose in Africa. Homo erectus migrated out of Africa and into Europe and Asia. Modern humans (Homo sapiens) and the extinct Neanderthals are descendants of Homo erectus. By the currently favored model, modern humans evolved in Africa, then migrated worldwide.

Summary Section 16.1  Invertebrates (animals without a backbone) are the most diverse animal group. They far outnumber vertebrates. Some compounds that invertebrates produce can be used as medicines.

The radially symmetrical cnidarians have two tissue layers. There are two body types: medusa (as in jellies) and polyp (as in sea anemones and corals). Stinging cells help cnidarians capture prey.

Section 16.2  Animals are multicelled heterotrophs that ingest food and move about during at least part of their life. The colonial theory of animal origins states that they evolved from a colonial protist. In most animals, cells are organized as tissues and the body shows either radial symmetry or bilateral symmetry. Animals with bilateral symmetry are either deuterostomes or protostomes. Both of these lineages develop from an embryo that has three germ layers. However, other details of their development differ. Most members of both lineages have a coelom around their gut.

Section 16.4  Flatworms, annelids, and mollusks belong to one protostome lineage. Flatworms have simple organ systems, a gastrovascular cavity, and no coelom. Planarians are free-living flatworms, whereas the tapeworms and flukes are parasites. Annelids are segmented worms that have a coelom. The soil-dwelling earthworms have a complete digestive tract and a closed circulatory system. The annelid lineage also includes polychaetes and leeches. Mollusks have a mantle, a skirtlike extension of the body. In many groups, the mantle secretes a shell. Gastropods (snails and slugs) and cephalopods (such as octopuses) have a head with a radula used in feeding. Bivalves such as clams are filter feeders. Most mollusks have an open circulatory system, but cephalopods have a closed system.

Section 16.3  Sponges are sessile filter feeders with no body symmetry or tissues. Each individual is a hermaphrodite that makes both eggs and sperm. The sponge larva is free-swimming.

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348  Unit 3  EVOLUTION AND DIVERSITY

Summary (Continued) Section 16.5  Roundworms and arthropods are protostomes that molt. Roundworms (nematodes) are unsegmented worms with a complete gut and an incompletely lined coelom. They may be freeliving or parasitic. Arthropods have a jointed exoskeleton. Horseshoe crabs are marine bottom-feeders. Arachnids include spiders, mites, ticks, and scorpions. Most crustaceans, such as lobsters, krill, and barnacles, are aquatic. Centipedes and millipedes have an elongated body and live on land. Insects, which have paired antennae and compound eyes, are the most diverse animals and the only winged invertebrates. Most insects undergo metamorphosis. Section 16.6  Echinoderms and chordates are deuterostomes. Echinoderms such as sea stars have calcium carbonate endoskeleton components of spines and plates. A water-vascular system allows adults to move about on tiny tube feet. Adult echinoderms are radial, but larvae are bilateral. The existence of bilateral larvae indicates that the group has a bilateral ancestor. Four embryonic traits define the chordates: a notochord, a dorsal hollow nerve cord, a pharynx with gill slits, and a tail extending past the anus. Depending on the group, some or all of the features persist in adults. Lancelets and tunicates are invertebrate chordates. Most chordates are vertebrates; they have a vertebral column of cartilage or bone. Jaws, lungs, limbs, and waterproof eggs are innovations that made the adaptive radiation of vertebrates possible. Tetrapods have four limbs. All vertebrates have a complete digestive system, closed circulatory system, and kidneys. Section 16.7  The earliest fishes were jawless fishes. Cartilaginous fishes and bony fishes have jaws, scales, and paired fins. Jaws evolved from gill supports. The two bony fish lineages are the highly diverse ray-finned fishes, which includes most familiar fishes, and the lobe-finned fishes. Amphibians evolved from a lobe-finned fish and require water to reproduce. Existing amphibian groups include salamanders, frogs, and toads. Fertilization is external. Eggs and sperm exit the body through a cloaca that also expels digestive and urinary wastes. Section 16.8  Amniotes were the first vertebrates that did not need external water for reproduction. Their skin and kidneys conserve water, and they produce eggs in which the embryo is surrounded by membranes and fluid. Mammals are one amniote lineage. Reptiles, including birds, are another. Most reptiles are ectotherms, but birds and mammals are endotherms; they

maintain their temperature by metabolic production of heat. There are three lineages of mammals: egg-laying monotremes, pouched marsupials, and placental mammals. Placental mammals are the most diverse group. Section 16.9  Primates are a lineage adapted to climbing, and all have hands capable of grasping. Lemurs have a moist, doglike snout, and tarsiers and anthropoids (monkeys, apes, humans) have a dry nose and movable upper lip. Our closest living relatives are the chimpanzees and bonobos. Bipedalism defines the hominins, which include humans and their extinct close relatives. Australopiths were early hominins, and some are considered likely human ancestors. The first named members of our genus, Homo habilis, resembled australopiths. Homo erectus had a larger brain and some populations became established outside of Africa. Modern humans (Homo sapiens) arose in Africa. As modern humans dispersed, some interbred with typical Neanderthals (Homo neanderthalensis) or with Denisovans. As a result, some human genomes contain alleles that can be traced to these groups.

Self-Quiz Answers in Appendix I 1. The first animals __________ . a. arose during the Cambrian b. had an embryo with three tissue layers c. lived in the sea d. had an open circulatory system. 2. The colonial hypothesis of animal origins states that __________ . a. animals colonized the land during the Cambrian b. animals evolved from a colonial protist c. the earliest animals lived in colonies d. most animals live in social groups 3. A __________ functions in both digestion and gas exchange. a. pseudocoelom c. complete digestive tract b. coelom d. gastrovascular cavity 4. Most animals have a body that is __________ . a. radially symmetrical b. bilaterally symmetrical c. asymmetrical

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Animal Evolution  Chapter 16  349  

5. Earthworms are most closely related to __________ . a. insects c. leeches d. roundworms b. tapeworms 6. The __________ include the only winged invertebrates. c. arthropods a. flatworms b. annelids d. cnidarians

15. Arrange the events in order, from most ancient to most recent. a. Cambrian explosion of diversity 1 b. Origin of animals 2 c. Tetrapods move onto the land 3 d. Extinction of dinosaurs 4 e. Homo erectus leaves Africa 5 f. First jawed vertebrates evolve 6

7. List the four distinguishing chordate traits. Which of these traits are retained by an adult tunicate? 8. All modern fishes have __________ . a. jaws c. scales b. a cartilage skeleton d. a closed circulatory system 9. All vertebrates are __________, but only some are __________ . a. tetrapods; mammals c. amniotes; hominins b. chordates; amniotes d. bipedal; australopiths 10. Amniote eggs __________ . a. enclose a developing embryo inside multiple membranes b. are typically released into water c. define the protostome lineage d. allowed the first tetrapods to move onto land 11. Birds and placental mammals __________ . a. are endotherms b. are descended from dinosaurs c. have mammary glands d. have an open circulatory system 12. True or false? Bipedalism is the defining trait of primates. 13. Homo erectus is a likely ancestor of H. sapiens and __________ . a. Homo habilis c. the great apes b. australopiths d. Neanderthals 14. Match the organisms with the appropriate description. a. most diverse vertebrates sponges b. no true tissues, no organs cnidarians c. jointed exoskeleton flatworms d. mantle over body mass roundworms e. segmented worms annelids f. tube feet, spiny skin arthropods g. have specialized stinging cells mollusks h. lay amniote eggs echinoderms i. feed young secreted milk amphibians j. unsegmented, molting worms fishes k. first terrestrial tetrapods birds l. tailless primates mammals m. bilateral with a saclike gut apes

CRITICAL THinking 1. Much research on animal venoms focuses on compounds that have potential as medicines. However, components of venom can also be useful in other contexts. For example, the recently developed insecticide Spear-T contains a synthetic version of a compound from the venom of an Australian spider. The insecticide paralyzes the muscles of plant-sucking pests such as aphids and spider mites but does not harm beneficial insects such as honeybees and ladybird beetles. It also is nontoxic to vertebrates. Explain why spider venom is an especially rich source of insecticidal compounds. Why are compounds isolated from spider venom less likely to harm humans than components of cone snail venom or snake venom? 2. As human activities put more and more carbon dioxide (CO2) into the air, the ocean takes up more CO2 and becomes increasingly acidic. Increased ocean acidity makes it more difficult for marine animals to produce their calcium-rich hard parts. List three types of invertebrates that are likely to be adversely affected by an increase in ocean acidity. 3. One subgroup of ray-finned fishes, the teleosts, is exceptionally diverse. It includes about half of all vertebrate species. Early in their evolution, teleosts underwent a duplication of their entire genome. By one hypothesis, this event opened the way to their diversification. Explain why such a duplication might make the evolution of new traits more likely. 4. Climate change resulting from greenhouse gas emissions is expected to increase the number and length of droughts. Why do prolonged droughts pose a greater threat to amphibians than to lizards?

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17 Population Ecology

17.1

Managing Canada Geese  351

17.2

Characteristics of Populations  352

17.3

Models of Population Growth  355

17.4

Life History Patterns  359

17.5

Human Populations  362

Canada geese in flight. Most members of this species belong to a migratory population.

Concept Connections David Hoffmann Photography/Shutterstock.com

Most species consist of multiple populations, each with a somewhat different collection of alleles, and subject to different selective pressures (Chapter 13). Scientists study natural populations by creating and testing models and carrying out experiments as described in Chapter 1. We return to the species interactions that influence populations in Chapter 18, and consider the effects of human population growth on other species in Chapter 19.

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Population Ecology  Chapter 17  351  

Application 17.1  Managing Canada Geese Visit a grassy park or a golf course and you may need to watch where you step. Wide expanses of grass with a nearby body of water attract large numbers of Canada geese, or Branta canadensis (Figure 17.1). Geese prefer to poop on land and each of these plant-eating birds excretes up to three pounds of slimy, green feces every day. Large deposits of goose feces make an area unappealing to human visitors, but geese also cause more serious problems. When goose feces contaminate a lake or pond, nutrients added by the feces can cause an overgrowth of bacteria and algae. Overgrowth of these microbes can harm other aquatic organisms. Goose feces can also introduce eggs of a parasitic fluke (a schistosome) into a body of water. The infectious form of this fluke can penetrate and inflame human skin, causing “swimmer’s itch.” Those affected can suffer from intense itching for up to two weeks. In flight, Canada geese can pose a risk to air traffic. Between 2010 and 2016, nearly 600 Canada goose– airplane collisions were reported in the United States. The 2016 movie Sully: Miracle on the Hudson dramatizes a 2009 incident in which both engines of a commercial airliner failed after Canada geese were sucked into the engines. Fortunately, the pilot was able to land the plane in the nearby Hudson River and all 155 people aboard were rescued. Migratory birds are protected under federal law and by international treaties. However, problems caused by increasing numbers of Canada geese have led the U.S. Fish and Wildlife Service to exempt this species from some protections. Controlling the number of Canada geese remains a challenge because several different Canada goose populations spend time in the United States. A population is a group of organisms of the same species that lives in a specific location and breeds with one another more often than they breed with members of other populations. In the past, nearly all Canada geese seen in the United States were migratory. They nested in northern Canada, flew to the United States for the winter, then returned to Canada to breed. Most Canada geese still migrate north to breed, but some populations have become nonmigratory. Geese breed where they grew up, and the nonmigratory birds are generally descendants of geese deliberately introduced to a park or hunting preserve. Life is more difficult for migratory geese than for nonmigratory ones. Flying to and from a northern breeding area takes lots of energy and is dangerous. A bird that does not migrate can devote more energy to producing young than a migratory one can. If the nonmigrant lives in a suburban or urban area, it also benefits from an unnatural abundance of food (grass) and a lack of predators. Not surprisingly, the greatest increases in Canada geese have been among nonmigratory populations that live where humans are plentiful.

Figure 17.1  Canada geese overrun a California park. Courtesy of Joel Peter

population  A group of organisms of the same species who live in a specific location and breed with one another more often than they breed with members of other populations.

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352  Unit 4 ECOLOGY

Wildlife managers want to reduce nonmigratory populations of Canada geese, without unduly harming migratory birds. To do so, these biologists need to know about the traits that characterize different goose populations, as well as how these populations interact with one another, and with other species. These sorts of questions are the focus of the science of ecology, the study of interactions among organisms, and between organisms and their physical environment. Ecology is not the same as environmentalism, which is advocacy for protection of the natural environment. However, environmentalists often cite the results of ecological studies when drawing attention to environmental concerns.

Discussion Questions 1. Efforts to control Canada geese generally focus on resident, nonmigratory populations. Why do you think this is? 2. What kind of population data would be helpful in designing humane ways to control goose populations? 3. Picture a golf course in southern California that is overrun by Canada geese every winter. Why are the migratory and nonmigratory geese that mingle here considered different populations even though they are the same species and are in the same area?

17.2  Characteristics of Populations Learning Objectives ●●

Provide examples of quantifiable characteristics of populations.

●●

Describe two methods of estimating population size.

The total geographic area occupied by all populations of a species is that species’ range. Each population occupies some subset of the species’ range and is influenced by and adapted to the unique conditions in that area. As a result, populations of a species typically differ in some characteristics such as population size, density, distribution, and age structure. Ecological studies often involve collecting data about these quantifiable characteristics.

Population Size and Density  ecology  Scientific study of interactions among organisms, and between organisms and their environment. environmentalism  Advocacy for protection of the natural environment. population density  Number of members of a population in a given area. population distribution  The way in which members of a population are arrayed in their environment. population size  Number of individuals in a population. range  Of a species, the total geographic area where its members live.

Population size refers to the number of individuals of a species in a population. Population density is the number of individuals in some specified area or volume,

such as the number of frogs per acre of rain forest or the number of amoebas per liter of pond water.

Population Distribution   Population distribution describes where individuals are relative to one another. Members of a population may clump together, be distributed in a near-uniform manner, or be randomly distributed. Clumped Distribution  Most populations have a clumped distribution, meaning

members of the population are closer to one another than would be predicted by

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Population Ecology  Chapter 17  353  

chance alone. Often, a patchy distribution of an essential resource draws individuals together, as when hippopotamuses gather in muddy river shallows (Figure 17.2A). Similarly, a cool, damp, north-facing slope may be covered with ferns, whereas an adjacent drier, south-facing slope has none. Limited dispersal ability increases the likelihood of a clumped distribution: For example, some plants such as poppies drop their seeds to the ground beneath them. Asexual reproduction can also result in clumping. A female aphid that reproduces asexually during the summer produces many female offspring that will live beside her. Similarly, asexual reproduction produces large stands of trees such as aspens. Social behavior brings animals together, so it too can cause a clumped distribution. Benefits of living in a social group include improved detection of predators, cooperative defense, and an enhanced ability to locate and utilize food resources. Near-Uniform Distribution  Competition for resources among members of a population can produce a near-uniform distribution, with individuals more evenly spaced than would be expected by chance. Creosote bushes in deserts of the American Southwest grow in this pattern. Competition for water among the plants’ root systems prevents them from growing near one another. Seabirds in breeding colonies often show a near-uniform distribution too. Each bird repels others that get within reach of its beak as it sits on its nest (Figure 17.2B). Random Distribution  A random population distribution is rare in nature. Random

distribution arises when resources are uniformly available, and proximity to others neither benefits nor harms individuals. For example, when wind-dispersed dandelion seeds land on the uniform environment of a suburban lawn, dandelions grow in a random pattern (Figure 17.2C).

Effects of Scale and Timing  The observed pattern of distribution can be influenced by scale of the area observed and timing of the observations. For example, although seabirds may be spaced almost uniformly at a nesting site, nesting sites are clustered along a shoreline. Also, these birds crowd together in the breeding season, but disperse at other times. Figure 17.2  Population distributions. (A) iStock.com/Rocket k; (B) JHVEPhoto/Shutterstock.com; (C) Emmoth/Shutterstock.com

A. Clumped distribution of hippopotamuses.

B. Near-uniform distribution of nesting seabirds. C. Random distribution of dandelions.

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354  Unit 4 ECOLOGY

Age Structure  The distribution of individuals among various age categories defines a population’s age structure. The number of males and females in each age category is often measured. Age structure of a population is useful information for predicting the size of the population in the future. A population with a large proportion of young individuals who have not begun to breed has a greater potential for growth than one composed mainly of older individuals. The effects of age structure on human population growth are covered in Section 17.5.

Collecting Population Data  Scientists use a variety of methods to determine the size of a population and the characteristics of its members. Direct Counts  For small, well-defined population such as waterfowl on a lake,

scientists can count all the individuals in the population. Aerial photography can be used to measure the number of antelope in a grassland area or the number of whales in a bay. Use of drone-mounted cameras can lower the cost of photographic surveys and minimize the likelihood of disturbing animals. Many populations are too large or dispersed for scientists to directly collect data on all the members of a population. Under these circumstances, scientists sample a population, then use data from that sample to estimate characteristics of the population as a whole. For organisms that live on land, plot sampling can be used to estimate the total number of individuals in an area on the basis of direct counts in a marked area. For example, to determine the number of daisies in a prairie or clams in a mudflat, ecologists begin by measuring the number of individuals in several 1-meter-by1-meter-square plots. They then multiply the average number of individuals in the sample plots by the number of plots in the area that the population inhabits. This gives an estimate of the total population size. Plot sampling is most accurate for organisms that do not move about and live in an area where conditions are uniform.

Indirect Counts  For mobile animals that cannot be counted directly, mark–recapture sampling is often used to estimate population size. Researchers capture animals, mark them, then release them. Sometime later, the researchers repeat the capture procedure. The proportion of marked animals in the second captured sample is then taken to be representative of the proportion marked in the whole population. The following equation is used: marked individuals in sampling at time 2 total captured in sampling 2

age structure  Of a population, the distribution of individuals among various age groups. per capita growth rate  The number of individuals added during some interval divided by the initial population size.

=

marked individuals in sampling at time 1 total population size

Suppose, for example, that scientists capture, mark, and release 100 deer. Later, they return and once again capture 100 deer. Of these, 50 are marked. The proportion of marked deer in the second sample (50 percent) indicates that half of the deer in the population have been marked. Thus the 100 deer initially marked must be members of a population of 200 deer. Information about the traits of individuals in a sample plot or captured group can also be used to infer properties such as age structure or sex ratio. For example, if a third of the deer recaptured in a mark–recapture study are of reproductive age, a third of the population is assumed to share this characteristic.

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Population Ecology  Chapter 17  355  

Digging Into Data Monitoring Iguana Populations

1. Which island had more marked iguanas at the time of the first census? 2. How much did the population size on each island change between the first and second census? 3. Wikelski concluded that changes on Santa Fe were the result of the oil spill, rather than sea temperature or other climate factors common to both islands. How would the census numbers be different from those he observed if an adverse event had affected both islands?

180 Number of marked iguanas

In 1989, Martin Wikelski started a long-term study of marine iguana populations in the Galápagos Islands. He marked the iguanas on two of the islands—Genovesa and Santa Fe—and collected data on how their body size, survival, and reproductive rates varied over time. The iguanas have no predators, so deaths are usually the result of food shortages, disease, or old age. His studies showed that the iguana populations decline during El Niño events, when water surrounding the islands heats up. In January 2001, an oil tanker ran aground and leaked a small amount of oil into the waters near Santa Fe. Figure 17.3 shows the number of marked iguanas that Wikelski and his team counted on the islands just before the oil spill and the number that they counted about a year later.

150 120 90 60 30 0

Jan Dec

Jan Dec

Genovesa Island

Santa Fe Island

Figure 17.3  Shifting numbers of marked marine iguanas on two Galápagos Islands. An oil spill occurred near Santa Fe just before the January 2001 census (blue bars). A second census was carried out in December 2001 (yellow bars). (Right), Bruce Coleman/Photoshot

Any study that draws conclusions based on only a sample of a population is susceptible to sampling error (Section 1.7). The larger the sample size, the more likely that conclusions drawn from that sample will be accurate.

Take-Home Message 17.2 ●●

●●

Populations can be described in terms of their size, density, and how their members are distributed through their environment. Population studies typically utilize sampling methods. Such methods run the risk of sampling error, which can be minimized by using a large sample size.

17.3  Models of Population Growth Learning Objectives ●●

●●

Give the equation that describes exponential growth, and explain what the terms in the equation mean. Explain the conditions required for a population to undergo exponential growth.

A population grows when its birthrate exceeds its death rate. Ecologists measure births and deaths per capita, which means per individual. For example, if the birthrate in a population of 2,000 mice is 1,000 young per month, then the per capita birthrate is 1,000/2,000, or 0.5 births per mouse per month. Subtract the per capita death rate from the per capita birthrate and you have the per capita growth rate.

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356  Unit 4 ECOLOGY Starting Size of Population 2,000 2,800 3,920 5,488 7,683 10,756 15,058 21,081 29,513 41,318 57,845 80,983 113,376 158,726 222,216 311,103 435,544 609,762 853,667

3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3

Net Monthly Increase r r r r r r r r r r r r r r r r r r r

5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5

New Size of Population

800 1,120 1,568 2,195 3,073 4,302 6,023 8,432 11,805 16,527 23,138 32,393 45,350 63,490 88,887 124,441 174,218 243,905 341,467

2,800 3,920 5,488 7,683 10,756 15,058 21,081 29,513 41,318 57,845 80,983 113,376 158,726 222,216 311,103 435,544 609,762 853,667 1,195,134

A. Increases in size over time. Note that the net increase becomes larger with each generation. 1,200,000 1,100,000

Number of individuals (N )

1,000,000 900,000 800,000 700,000 600,000 500,000 400,000 300,000

If the death rate in the population of 2,000 mice is 200 per month (0.1 per mouse per month), then the per capita growth rate is 0.5 minus 0.1 equals 0.4 per mouse per month.

Exponential Growth  The exponential model of population growth describes how a population would change in size over time if its per capita growth rate was constant and its resources were unlimited. Under these conditions, the population growth in any interval (G) can be calculated as follows: N (number of individuals)

×

r (per capita growth rate)

=

G (population growth per unit time)

Suppose we apply this to our population of 2,000 mice with their per capita growth rate of 0.4 per month. In the first month, the population grows by 2,000 mice × 0.4. This brings the size to 2,800. In the next month, 2,800 × 0.4, or 1,120 mice, are added, and so on. At this growth rate, the number of mice would rise from 2,000 to more than a million in less than two years! Plotting the size of this population against time produces a J-shaped, or “hockey stick,” curve, characteristic of exponential growth (Figure 17.4). Exponential population growth is analogous to compounding interest on a bank account that pays a fixed rate of return. Although the interest rate does not change, each year the amount of interest paid increases. The annual interest paid into the account adds to the size of the balance, and the following year’s interest payment is based on that higher balance. The exponential model of population growth cannot accurately predict the long-term growth of real populations because it assumes that resources are unlimited. However, it does provide insight into the expected short-term growth of a population with plentiful resources. For example, when a few individuals of a species colonize a new habitat, the resulting population often grows exponentially for a period.

200,000

Density-Dependent Limiting Factors 

100,000 0

2

4

6

8

10 12 14 16 18 20

Time (months)

B. Graphing numbers over time yields a J-shaped curve. Figure 17.4  Exponential growth in population of mice with a per capita growth rate (r) of 0.4 per mouse per month and an initial population size of 2,000.

No population can grow exponentially forever. As population size increases, densitydependent limiting factors cause birthrates to slow and/or death rates to rise. Intraspecific competition, or competition among members of the same species, is an important density-dependent limiting factor. Essential resources for which members of an animal population might compete include food, water, hiding places, and nesting sites. Plants compete for nutrients, water, and access to sunlight. Parasitism, contagious disease, and predation are also density-dependent limiting factors. The closer individuals are to one another, the more easily parasites and pathogens can spread. Predation increases with density, because predators often concentrate their efforts on the most abundant prey species.

Carrying Capacity  The maximum population size that an environment can sustain indefinitely is called the carrying capacity. By “sustain indefinitely,” we mean sustain without environmental degradation that would prevent the species from living in the environment in the future. Note that carrying capacity is both environment-specific and species-specific. An acre with regular rains can support more grass plants than an acre of desert, and the rainy acre can support more grass plants than oak trees.

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Population Ecology  Chapter 17  357  

CLOSER LOOK Figure 17.5  An example of logistic growth. Consider what happens when a few deer are introduced to a new habitat with finite resources:

Figure It Out: At which numbered point is the growth rate highest?

Population Size

Answer: 1

1 When the population is small, individu-

3 2

als have access to all the resources they require, and the population grows exponentially.

2 As population size increases, densitydependent limiting factors begin to have an effect, so the growth rate slows.

3 Eventually, population size levels off. Population size plotted against time produces an S-shaped curve.

1 Time

Figure Summary Logistic growth occurs when densitydependent factors come into play.

The carrying capacity of an environment for a particular species can also change over time. For example, the carrying capacity for a plant species decreases when nutrients in the soil become depleted.

Logistic Growth  The logistic model of population growth describes how population growth changes as the size of the population approaches carrying capacity. Unlike the exponential growth model, this model incorporates the effects of density-dependent limiting factors. With logistic growth, the rate of population growth does not remain constant, but rather declines as population density increases. When there are few individuals relative to the amount of resources, the population grows exponentially (Figure 17.5 1). As the number of individuals rises, density-dependent limiting factors begin to put the brakes on growth. As a result of these factors, population growth begins to slow 2. Population growth continues until population size levels off at the environment’s carrying capacity 3.

Density-Independent Factors  Sometimes, natural disasters or man-made events affect population size. A volcanic eruption, hurricane, flood, or oil spills can decrease the size of a population. Such events are described as density-independent limiting factors, because crowding does not influence how likely they are to occur or the magnitude of their effect.

Combined Effects of Limiting Factors  In nature, density-dependent and density-independent factors interact to determine the fate of a population. Consider what happened after the 1944 introduction of 29 reindeer to St. Matthew Island, an uninhabited island off the coast of Alaska.

carrying capacity  The maximum number of individuals of a particular species that a population’s environment can support indefinitely. density-dependent limiting factor  Factor whose negative effect on growth is felt most in dense populations; for example, infectious disease or intrapecific competition for resources. density-independent limiting factor  Factor that limits growth in populations regardless of their density; for example, a natural disaster or harsh weather. exponential model of population growth  Model for population growth when resources are unlimited. Per capita growth rate remains constant as population size increases. intraspecific competition  Competition among members of the same species. logistic model of population growth  Model for growth of a population limited by density-dependent factors; numbers increase exponentially at first, then the growth rate slows and population size levels off at carrying capacity.

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358  Unit 4 ECOLOGY

When biologist David Klein first visited the island in 1957, he found 1,350 wellfed reindeer munching on lichens (Figure 17.6). When Klein returned in 1963, he counted 6,000 reindeer. The population had soared far above the island’s carrying capacity. Remember that carrying capacity is the maximum sustainable size for a population. Although a population can temporarily exceed the carrying capacity of its environment, the high density will degrade the environment and cannot be maintained. Klein observed that density-dependent negative effects were already apparent. For example, the average body size of the reindeer had decreased. When Klein returned in 1966, only 42 reindeer survived and only one of them was male. There were no fawns. Klein figured out that thousands of reindeer had starved to death during the winter of 1963–64. That winter was unusually harsh, with low temperatures, high winds, and 140 inches of snow. Most reindeer, already in poor condition as a result of increased competition, starved when deep snow covered their food. A population decline had been expected—a population that exceeds the carrying capacity of an environment must eventually shrink and fall below that capacity— but bad weather magnified the extent of the crash. By the 1980s, there were no reindeer on the island.

Population size

6,000

4,500

3,000

1,500

0

carrying capacity 1944

1956 1963

1980

Year

Figure 17.6  Changes in the size of a reindeer population. The reindeer were introduced to an island off the coast of Alaska in 1944. Top, Jacques Langevin/Sygma/Corbis

Human Effects on Carrying Capacity Human activities sometimes decrease an environment’s carrying capacity for a species. Consider what has happened to horseshoe crabs and red knot sand­ pipers in the Delaware Bay region. Humans harvest horseshoe crabs for use as bait and for their blood, which is used to test the safety of drugs (Section 16.5). In the past 15 years, the Delaware Bay population of horseshoe crabs has declined dramatically as a result of overharvesting and degradation of their environment. The reduction in horseshoe crab numbers has lowered the region’s carrying capacity for red knot sandpipers, a type of migratory shorebird. Each spring, all the horseshoe crabs in Delaware Bay take part in a mass spawning event, leaving their fertilized eggs to develop in damp sand along the shore. For thousands of years, red knot sandpipers have fed on those eggs as they migrated north through the Delaware Bay region. When fewer horseshoe crabs are present, there is less food for the sandpipers, and fewer of these birds survive their northward migration.

Take-Home Message 17.3 ●●

biotic potential  Maximum possible population growth under optimal conditions.

●●

cohort  Group of individuals born during the same interval. life history traits  Set of heritable traits related to growth, survival, and reproduction such as life span, age-specific mortality, age at first reproduction, and number of breeding events. survivorship curve  Graph showing the decline in numbers of a cohort over time.

●●

●●

The exponential model of population growth describes the growth of a population with unlimited resources. In this idealized circumstance, per capita growth rate remains constant, but the population grows faster and faster. The logistic model of population growth describes the growth of a population affected by density-dependent limiting factors. Such a population grows exponentially at first, then its growth rate declines as a result of competition for resources, infectious disease, and other negative effects of crowding. A population undergoing logistic growth levels off at the environment’s carrying capacity for that species. Density-independent factors such as harsh weather are not addressed by models for population growth, but they too affect natural populations.

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Population Ecology  Chapter 17  359  

17.4  Life History Patterns ●●

Give some examples of life history traits.

●●

Distinguish between opportunistic and equilibrium species.

●●

Describe the three types of survivorship curves.

Table 17.1  Life Table for an Annual Plant*

Age Interval

Biotic Potential  The maximum growth rate for a species under ideal conditions is its biotic potential. This is the theoretical value that would hold if shelter, food, and other essential resources were unlimited and there were no predators or pathogens. Populations seldom reach their biotic potential because of limiting factors. Biotic potential is determined by life history traits, which are a set of heritable traits such as average rate of growth, age at first reproduction, number of breeding events, and life span. In this section, we look at how such life history traits vary and the evolutionary basis for this variation.

Describing Life Histories  One way to gather information about the life history traits of a population is to focus on a cohort, a group of individuals that are all born at about the same time. Table 17.1 shows data from a cohort study of phlox, a type of annual plant. (An annual plant grows from a seed, blooms, produces seeds, and dies within a single growing season.) Information about age-specific death rates can also be illustrated by a survivorship curve, a plot that shows how many members of a cohort remain alive over time. Ecologists describe three generalized types of survivorship curves. A type I curve is convex (bulges outward), indicating survivorship is high until late in life (Figure 17.7A). This pattern is characteristic of humans and other large mammals that produce one or two young and care for them.

“Birth” Rate Survivorship Death Rate in Interval Number (number (number of (number Dying surviving during dying/number seeds per at start of plant) surviving) Interval interval)

0–63

996

328

0.329

0

63–124

668

373

0.558

0

124–184

295

105

0.356

0

184–215

190

 14

0.074

0

215–264

176

  4

0.023

0

264–278

172

  5

0.029

0

278–292

167

  8

0.048

0

292–306

159

  5

0.031

0.33

306–320

154

  7

0.045

3.13

320–334

147

 42

0.286

5.42

334–348

105

 83

0.790

9.26

348–362

 22

 22

1.000

4.31

362–

  0

  0

0

0

996 *Phlox drummondii; data from W. J. Leverich, and D. A. Levin. “Age-Specific Survivorship and Reproduction in Phlox drummondii.” American Naturalist 113 (1979): 881–903.

Figure 17.7  Types of survivorship curves. Blue lines are theoretical curves. Red dots are data from field studies. Figure It Out: Which type of curve best fits the plant mortality data shown in Table 17.1?

10

0

50

100

Percentage of life span

A. Type I curve. Mortality is highest very late in life. Data are for Dall sheep (Ovis dalli).

1 million

Number surviving

Number surviving

Number surviving

1,000

100

0

Answer: Type III. Mortality is highest early in life.

1,000

100

10

0

0

50

Percentage of life span

100

10,000

100

0

0

50

100

Percentage of life span

B. Type II curve. Mortality does not vary with age. C. Type III curve. Mortality is highest early in life. Data are for a small lizard (Eumeces fasciatus). Data are for a desert shrub (Cleome droserifolia).

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360  Unit 4 ECOLOGY

A type II curve is diagonal, indicating that the death rate of the population does not vary much with age (Figure 17.7B). A type II curve is characteristic of lizards, small mammals, and large birds. In these groups, old individuals are as likely to die of disease or predation as young ones. A type III curve is concave (bulges inward), indicating that the death rate for a population is highest early in life (Figure 17.7C). Marine animals that release eggs into water have this type of curve, as do plants that release enormous numbers of tiny seeds.

Adaptive Value of Life History Traits  When producing offspring, an individual uses resources that it could otherwise use to grow and maintain itself. We refer to these resources as parental investment. Note that parental investment occurs even in species that do not provide parental care. Parental investment includes resources used to produce gametes, as well as resources used to nurture developing young in or on a parental body. Species differ in the way in which they distribute their parental investment among offspring and over the course of a lifetime. Some invest little in each of many offspring; others invest a lot in only a few offspring. Some reproduce once, others many times. The sequence of growth, development, and reproductionrelated events that occurs over an individual’s lifetime is called a life history. Life histories vary continuously, but ecologists have described two theoretical extremes at either end of this continuum (Figure 17.8). Both allow an individual to maximize the number and survival of its offspring, but each is adaptive under different environmental conditions.

Opportunistic Life History 

Figure 17.8  Opportunistic versus equilibrial life histories. A, B. Dandelions and flies are opportunists. C, D. Whales and coconut palms are equilibrial species.

When a species lives where conditions vary in an unpredictable manner, its populations seldom reach their carrying capacity. As a result, there is usually little competition for resources among members of the same species. Such conditions favor an opportunistic life history, in which individuals produce as many offspring as possible, as quickly as possible. Because parental investment is spread across many offspring, each offspring receives a relatively small share. Opportunistic species (also called r-selected species) tend to have a small body and to reach the age of reproduction quickly. Opportunistic species usually have a type III survivorship curve, with mortality heaviest early in life. Annual plants such as dandelions (Figure 17.8A) have an opportunistic life history. They mature within weeks, produce many tiny seeds, then die. Flies are opportunistic animals. A female

(A) blueeyes/Shutterstock.com; (B) Richard Baker; (C) Tono Balaguer/Shutterstock.com; (D) Florida Fish and Wildlife Conservation Commission/NOAA

Opportunistic life history shorter development early reproduction

A

B

Equilibrial life history longer development later reproduction

fewer breeding episodes, many young per episode

more breeding episodes, few young per episode

less parental investment per young

more parental investment per young

higher early mortality, shorter life span

low early mortality, longer life span

C

D

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Population Ecology  Chapter 17  361  

fly can lay hundreds of small eggs (Figure 17.8B) in a temporary food source such as a rotting tomato or a pile of feces.

Equilibrial Life History  When a species lives in a stable environment, its populations are often near their carrying capacity for that environment. Under these circumstances, interspecific competition for resources can be fierce, and an equilibrial life history, in which parents produce a few, high-quality offspring, is more common. Species with an equilibrial life history (also called K-selected species) tend to have a large body and a long generation time. Consider a coconut palm, which grows for years before beginning to produce a few coconuts at a time (Figure 17.8C). Large mammals such as elephants and whales have this sort of life history too. They take years to reach adult body size and begin reproduc­ ing. A mature female whale typically produces only one large calf at a time (Figure 17.8D), and she continues to invest in the calf by nursing it after its birth. In both coconut palms and whales, a mature individual produces young for many years. Some species such as century plants (a type of agave) and bamboo are large and long-lived but reproduce only once. Such a strategy evolves when cost of successful reproduction exceeds a certain fraction of a species’ resources, thus making future reproductive value small. Under these circumstances, fitness is maximized by one reproductive episode. In century plants and bamboo, climate conditions that allow reproduction are rare, so expending all available energy when these conditions do arise is selectively advantageous.

Predation and Life History Evolution  Often, different populations within a species live in slightly different environments, and their life history traits reflect these differences. Consider one long-term study in which biologists David Reznick and John Endler documented the evolutionary effects of predation on the life history traits of guppies, a type of small freshwater fish. The study involved fieldwork in the mountains of Trinidad, an island in the southern Caribbean Sea. Here, guppies live in shallow freshwater streams (Figure 17.9). Waterfalls in the streams function as barriers that keep guppies from moving from one part of the stream to another. As a result, there are a number of separate guppy populations along each stream. Two kinds of fish prey on guppies in the streams. Killifish are relatively small, and they prey on small, juvenile guppies but ignore full-grown adults. Pike cichlids are larger. They pursue large, mature guppies, while ignoring juveniles. Because waterfalls restrict the movement of the predatory fishes, different guppy populations face different predators. Reznick and Endler suspected that predation shapes guppy life history patterns through natural selection, and they devised an experiment to test this hypothesis. They found a pool that held guppies and pike cichlids, but no killifish. Some guppies from this pool were left in place as a control group. Others (the experimental group) were moved from this pool to a part of the stream where killifish were the only predators. After 11 years, life history traits of the two groups had diverged. Compared to the control population, guppies in the experimental population grew faster, reproduced when larger, and produced bigger offspring. Selective pressure exerted

Guppy

Figure 17.9  Studying effects of predation on guppy life history. Biologist David Reznick at his study site, a freshwater stream in Trinidad that is home to guppies and their predators. (Background), Helen Rodd; (inset), David Reznick/University of California-Riverside; computer enhanced by Lisa Starr

equilibrial life history  Life history favored in stable environments; individuals grow large, then invest a lot in each of a few offspring. opportunistic life history  Life history favored in unpredictable environments; individuals reproduce while young and invest little in each of many offspring.

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362  Unit 4 ECOLOGY

by predation on the smallest fishes favored individuals that put their energy into growth rather than reproduction, until they reached the size at which they were too big to be eaten.

Effects of Humans as Predators 

Figure 17.10  Fishermen with a prized catch, a large Atlantic codfish. Both sport fishermen and commercial fishermen preferentially harvested the largest codfish. Bruce Bornstein, www.captbluefin.com.

Just as guppies evolved in response to predators, a population of Atlantic codfish (Gadus morhua) evolved in response to human fishing pressure. From the mid1980s to early 1990s, the number of boats fishing for cod in the North Atlantic increased. As the yearly catch increased, so did the proportion of fish that reproduced while young and small. Such individuals were at an advantage because both commercial fisherman and sport fishermen preferentially caught and kept larger fish (Figure 17.10). Fishing pressure continued to rise until 1992, when declining cod numbers caused the Canadian government to ban cod fishing in some areas. That ban, and later restrictions, came too late to stop the Atlantic cod population from crashing. In some areas, the population declined by 97 percent and has not recovered. Looking back, scientists determined that the observed shift toward earlier reproduction was an early sign that human fishing was exerting a strong selective pressure on the North Atlantic cod population. By monitoring life history data for other economically important fishes, fisheries managers hope to prevent similar overfishing-induced population crashes in the future.

Take-Home Message 17.4 ●●

●●

●●

Life history traits such as the age at which an organism first reproduces, the number of offspring produced at a time, and potential life span have a heritable basis. Rapid production of many offspring is adaptive when environmental factors keep population density low. Producing offspring that are fewer in number but better able to compete is adaptive if populations are often near carrying capacity. Predator preferences can influence the life history traits of their prey.

17.5  Human Populations Learning Objectives ●●

Describe the factors that allowed a rapid increase in the human population during the past 200 years.

●●

Explain why replacement fertility rate varies among regions.

●●

Explain how population growth is influenced by age structure.

Population Size and Growth Rate  For most of its history, the human population grew very slowly (Figure 17.11). The growth rate began to pick up about 10,000 years ago, and during the past two centuries, it soared. A worldwide decline in death rates without an equivalent drop in birthrates is responsible for the ongoing explosion in human population size. It took more than 100,000 years for the human population to reach a billion in number. Since then, the rate of increase has risen steadily. The population is now about 7 billion, and it is expected to reach 9 billion by 2050.

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Population Ecology  Chapter 17  363  

2011

7

1999

6

10,440 years ago

5 million

By 1804

1 billion

By 1927

2 billion

By 1960

3 billion

By 1974

4 billion

By 1987

5 billion

By 1999

6 billion

By 2011

7 billion

5

1975

4

3

2 domestication of plants, animals 9000 B.C. (about 11,000 years ago)

14,000 13,000 12,000 11,000 10,000

9000

8000

agriculturally based urban societies

7000

6000

5000

4000

beginning of industrial, scientific revolutions

3000

2000

1000

B.C. A.D.

1000

Number of individuals (billions)

Estimated human population

1

2011

Figure 17.11  Growth curve (red) for the world human population. The gray box lists how long it took for our number to increase from 5 million to 7 billion. Source: NASA

Three trends have contributed to human population growth. First, humans migrated into new habitats and expanded into new climate zones. Second, they developed technologies that increased the carrying capacity of existing habitats. Third, they sidestepped some limiting factors that typically restrain population growth. Expansion into New Habitats  Modern humans evolved in Africa approximately

200,000 years ago, and about 60,000 years ago they began to spread out across the globe. A large brain and the capacity to master a variety of skills gave humans an unmatched ability to live in a broad range of habitats. Humans learned how to start fires, build shelters, make clothing, manufacture tools, and cooperate in hunts. With the advent of language, knowledge of such skills did not die with the individual. Increased Carrying Capacity  The invention of agriculture about 11,000 years ago

provided a more dependable food supply than traditional hunting and gathering. A pivotal factor was the domestication of wild grasses, including species ancestral to wheat and rice. In the middle of the eighteenth century, people learned to harness energy in fossil fuels to operate machinery. This innovation opened the way to high-yielding mechanized agriculture and improved food distribution systems. Food production was further enhanced in the early 1900s, when the invention of synthetic nitrogen fertilizers increased crop yields. The invention of synthetic pesticides in the mid1900s also contributed to increased food production.

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364  Unit 4 ECOLOGY

Post-reproductive

Reproductive Pre-reproductive Increasing growth (Nigeria)

Stable (United States)

Decreasing Growth (Japan)

Figure 17.12  Age structure diagrams for three countries. The width of each bar represents the number of individuals in a 5-year age group. Ages 0 to 15 are prereproductive, 16 to 45 are reproductive, and over 45 are post-reproductive. The left side of each chart indicates males; the right side, females. Based on 2016 data. Source: Japan pyramid is here: https://www.cia.gov/library/publications/the-world-factbook /geos/ ja.html; Nigeria pyramid is: https://www.cia.gov/library/publications/the-world -factbook/geos/ni.html; United States pyramid: https://www.cia.gov/library/publications /the-world-factbook/geos/ us.html

Figure It Out: Which country has the largest proportion of its population in the pre-reproductive category?

Removal of Limiting Factors  Disease has historically dampened human

population growth. Beginning in the mid-1800s, an increased understanding of the link between microorganisms and illness led to improvements in food safety, sanitation, and medicine. People began to pasteurize foods and drinks, heating them to reduce the numbers of harmful bacteria. Doctors began to wash their hands between patients and before surgery. People also began to protect their water supply. The first modern sewer system was constructed in London, England, in the late 1800s. By diverting wastewater downstream of the city’s water source, the system lowered the incidence of waterborne diseases such as cholera and typhoid fever. In the early 1900s, most industrial nations began sterilizing drinking water, causing a further decline in deaths from these diseases. Vaccines and antibiotics also helped lower death rates. Vaccinations became widespread in developed countries during the 1800s. Antibiotics are a more recent development. Large-scale production of penicillin, the first antibiotic to be widely used, began in the 1940s.

Answer: Nigeria

Fertility Rates and Future Growth 

demographic transition model  Model describing the changes in human birth and death rates that occur as a region becomes industrialized. ecological footprint  Area of Earth’s surface required to sustainably support a particular level of development and consumption. total fertility rate  Average number of children born to females of a population over the course of their lifetimes.

A population’s total fertility rate is the average number of children that women of that population produce over the course of their childbearing years. In 1950, the worldwide total fertility rate averaged 6.5 children per woman. In 2018, it was just below 2.5. The total fertility rate remains above the replacement level, which is the number of children a woman must bear to ensure that two children grow to maturity and replace her and her partner. At present, this replacement level is 2.1 for developed countries and as high as 3 in some developing countries. (It is higher in developing countries because more female children die before reaching the age when they can reproduce.) Age structure affects a population’s growth rate. Compare the age structure for Nigeria, the United States, and Japan (Figure 17.12). Notice especially the size of the age groups that will be reproducing during the next 15 years. The broader the base of an age structure diagram, the greater the proportion of young people, and the greater the expected growth. Even if every couple now alive were to produce only two children, world population growth will not slow for many years, because more than a third of the world population is now in the broad pre-reproductive base. About 1.9 billion people are about to enter the reproductive age bracket.

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Population Ecology  Chapter 17  365  

Effects of Industrial and Economic Development  Industrial and economic development affect the growth rate of human populations. The most highly developed countries have the lowest fertility rate, the lowest infant mortality, and the highest life expectancy. The demographic transition model describes how birth and death rates change over the course of four stages of development. In the preindustrial stage, before technological and medical advances come into widespread use, birth and death rates are both high, so a population’s growth rate is low. As industrialization begins, food production and health care improve so the death rate falls. The birthrate declines too, but more slowly. As a result, the population growth rate increases rapidly. Nigeria is in this stage. Once industrialization is in full swing, the birthrate moves closer to the death rate, and the population grows less rapidly. The United States is currently in this stage. In the postindustrial stage, a population’s growth rate becomes negative. The birthrate falls below the death rate, and population size slowly decreases. In some developed countries such as Japan, the decreasing total fertility rate and increasing life expectancy have resulted in a high proportion of older adults.

Country

Hectares per Capita

United States Canada Russia Germany Japan China Brazil Mexico Nigeria India World Average

8.4 8.0 5.6 5.1 4.7 3.7 3.1 2.5 1.1 1.1 2.8

* Data from www.footprintnetwork.org

Figure 17.13  Ecological footprints. A nation’s ecological footprint estimates the amount of Earth’s surface that a nation uses at its current level of development and consumption. (Background), Konstantin Christian/Shutterstock.com

Industrial Development and Resource Consumption  Increased resource consumption is one of the side effects of industrialization. Ecological footprint analysis can be used to illustrate this effect. An ecological footprint is the amount of Earth’s surface required to support a particular level of development and resource consumption in a sustainable fashion. It includes the area needed to secure food and manufacture products, as well as the natural area needed to take up any excess carbon dioxide produced by human activities. Figure 17.13 shows per capita global footprint data for a few nations. Note that the average person in the United States has an ecological footprint nearly three times that of an average world citizen, and more than eight times that of an average person living in India or Nigeria. The United States accounts for about 4.6 percent of the world’s population, yet it uses about 25 percent of the world’s minerals and energy supply. Billions of people living in India, China, and other less industrialized nations would like to own the same kinds of goods that people in highly industrialized countries enjoy. However, given current technology, Earth does not have the resources to make that possible. Finding ways to meet the wants and needs of expanding populations on a planet with finite resources will be a challenge.

Take-Home Message 17.5 ●●

●● ●●

Through expansion into new regions, invention of agriculture, and technological innovation, the human population has sidestepped environmental resistance to growth. Its size has been skyrocketing since the industrial revolution. Death rates and birthrates fall as nations have become more industrialized. Earth’s resources are limited, so the current exponential growth of the human population is unsustainable.

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366  Unit 4 ECOLOGY

Summary Section 17.1  A population is a group of individuals that live in a given area and tend to mate with one another. Human actions have influenced the growth of some Canada goose populations. The study of populations is one aspect of the field of biology known as ecology. Ecological studies are sometimes cited in support of environmentalism, which is advocacy for protection of the natural environment. Section 17.2  Each population occupies some portion of its species’ range. Populations vary in characteristics such as population size, population density, population distribution, and age structure. In most populations, individuals have a clumped distribution because of limited dispersal, a need for resources that are clumped, and/or the benefits of living in a social group. Section 17.3  Birth and death rates determine how fast a population grows. The exponential model of population growth describes what happens with a constant, positive per capita growth rate. The population increases by a fixed percentage of the whole with each successive interval, so a plot of numbers over time produces a J-shaped curve. The logistic model of population growth describes how population growth is affected by density-dependent limiting factors such as disease or intraspecific competition for resources. The population slowly increases in size, goes through a rapid growth phase, then stabilizes once carrying capacity is reached. Carrying capacity is the maximum number of individuals that can be sustained indefinitely by the resources available in the environment. Extreme weather events and other density-independent limiting factors can affect any population regardless of its size. Section 17.4  The maximum theoretical rate of population growth is the biotic potential. Limiting factors prevent populations from attaining this potential. Biotic potential is affected by aspects of an organism’s life history traits such as age at maturity, number of reproductive events, offspring number per event, and life span. Life histories are often studied by following a cohort, a group of individuals that were born in the same time interval. Three types of survivorship curves are common: a high death rate late in life, a constant rate at all ages, or a high rate early in life. Life histories have a genetic basis and are subject to natural selection. Depending on the environment, a population may be more successful if its individuals reproduce once, or many times. At low population density, an opportunistic life history, in which individuals make many offspring fast, is advantageous. At a higher population density, an equilibrial life history, in which individuals invest more in fewer, higher-quality offspring, is

most adaptive. Predation can affect life history patterns because predators (including humans) act as selective agents that affect the traits of prey populations. Section 17.5  The human population has now surpassed 7 billion. Expansion into new habitats and the invention of agriculture opened the way to early increases. Later, improved sanitation and technological innovations such as the invention of synthetic fertilizer raised the carrying capacity and minimized limiting factors that adversely affect other species. Globally, the average number of children born to women during their reproductive years is declining but it remains above the replacement rate. A population’s age structure influences its growth. The pre-reproductive base of the human population is so large that the population is expected to grow for many years. The demographic transition model describes how population growth rates change during industrialization. Developed nations have a lower growth rate than developing nations, but they also have a larger ecological footprint. Given existing technology, Earth does not have enough resources to support the current population in the style of the most developed nations.

Self-Quiz Answers in Appendix I 1. Most commonly, individuals of a population have a __________ distribution. a. clumped c. nearly uniform b. random d. none of the above 2. All populations of a species __________ . a. have the same distribution pattern b. have the same age structure c. live within the species’ range d. constitute a cohort 3. The exponential model of population growth assumes __________ . a. the death rate declines as population density increases b. per capita growth rate does not change c. industrialization causes a fall in birthrates d. resources are limited 4. Disease and intraspecific competition for resources are __________ controls on population growth rates. a. density-independent b. density-dependent

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Population Ecology  Chapter 17  367  

5. For a given species, the maximum rate of population increase under ideal conditions is the __________ . a. biotic potential b. carrying capacity c. opportunistic strategy d. density control 6. An increase in the population of a prey species would most likely __________ the carrying capacity for that species’ predators. a. increase b. decrease c. not affect d. stabilize 7. Members of a species with an __________ life history have many offspring and invest little in each one. a. equilibrial b. opportunistic 8. The logistic model of population growth takes into account __________ , but not __________ . a. density-dependent factors; density-independent factors b. density-independent factors; density-dependent factors 9. The human population is now about __________ . a. 7 billion c. 70 billion b. 7 million d. 70 million 10. Compared to the less industrialized nations, the highly industrialized ones have a higher __________ . a. death rate   b. birthrate    c. total fertility rate d. ecological footprint 11. Carrying capacity __________ . a. total fertility rate is the same for all species that share a habitat b. total fertility rate is constant for a given species regardless of its habitat c. total fertility rate varies among both species and habitats d. total fertility rate is constant over time 12. The total fertility rate of a population is __________ . a. total fertility rate always higher than the replacement fertility rate b. total fertility rate the average number of children that females have over the course of their reproductive years c. total fertility rate the maximum number of children a woman could have if her resources were unlimited

13. If an exponentially growing population of 1,000 mice has a per capita growth rate (r) of 0.3 mice per month, how many mice will there be one month from now? a. 3,000 c. 1,300 b. 3,300 d. 300 14. Human population growth was encouraged by __________ . a. invention of agriculture c. improved sanitation b. medical advances d. all of the above 15. Match each term with its most suitable description. a. change in birth and death rates with carrying industrialization capacity b. group of individuals born during the logistic same period of time growth c. population growth plots out as an exponential S-shaped curve growth d. largest number of individuals demographic sustainable by the resources in a given transition environment limiting e. population growth plots out as a factor J-shaped curve cohort f. essential resource that restricts population growth when scarce

CRITICAL THinking 1. A biologist is hired to assess the population of Canada geese at a city park near Baltimore, Maryland. She captures 50 geese on August 1st, marks them, and then releases them. She returns in November and again catches 50 geese. Ten of them are marked. Does she have enough data to calculate an accurate estimate of the size of the local Canada goose population? Why or why not? 2. We know from fossils that horseshoe crabs have been spawning on Earth’s beaches for 400 million years. Explain how, given what we know of the history of life, we can be sure that egg predation by birds had no effect on the population size of these first horseshoe crabs. 3. Bluebirds are native North American songbirds that nest in cavities in trees. House sparrows introduced from Europe use the same type of nesting site. Explain why the arrival of house sparrows affected the carrying capacity of environments for bluebirds. 4. Give examples of density-dependent and density-independent factors that limit the growth of modern human populations.

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18 Communities and Ecosystems

18.1

Invasion of the Red Imported Fire Ants  369

18.2

Community Structure  370

18.3

Direct Species Interactions  371

18.4

How Communities Change  377

18.5

The Nature of Ecosystems  379

18.6

The Water, Nitrogen, and Phosphorus Cycles  383

18.7

The Carbon Cycle and Climate Change  387

Sunlight energy captured by a plant is transferred to a caterpillar that feeds on its leaves.

Concept Connections iStock.com/Sinenkiy

All organisms require energy and nutrients (Chapter 1), and most rely directly or indirectly on sunlight energy captured through photosynthesis (Chapter 5). Interactions among species influence population size (Section 17.3) and can result in directional selection (12.3) and coevolution (13.7). In this chapter, you will revisit the properties of chemical bonds (Section 2.3) and see how the movement of tectonic plates (12.5) influences nutrient cycling. We will also consider the effects of burning fossil fuels, such as the coal formed from ancient plants (15.4) and petroleum from diatoms (14.6). These and other adverse effects of human activities are discussed in greater detail in Chapter 19.

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Communities and Ecosystems  Chapter 18  369  

Application 18.1  Invasion of the Red Imported

Fire Ants Each year in the United States, an estimated 14 million people are stung by red imported fire ants (Solenopsis invicta). Accidentally step on one of their nests, and you will quickly realize your mistake. Fire ants defend their nest by stinging, and their venom causes a burning sensation that gives the ants their common name (Figure 18.1A). S. invicta is native to South America. The species first arrived in the southeastern United States in the 1930s, probably on a cargo ship. Since then, it has gradually expanded its range across the south and was accidentally transported to California and New Mexico. Fifteen states now have well-established S. invicta populations. The ongoing spread of S. invicta has important economic effects. A high density of S. invicta nests reduces the value of land by making it inhospitable to humans, pets, and livestock. In addition, efforts to prevent the spread of S. invicta rely on quarantines that prohibit moving soil from a region where the ants are present to one where they are not. Thus, the arrival of S. invicta can put commercial plant growers out of business. The introduced ants also pose a threat to North America’s native species. S. invicta competes with native ants, causing their populations to shrink. Because the native ants play a variety of ecological roles, a decline in these ants causes other species to decline in turn. For example, in Texas, the S. invicta–induced decline of native harvester ants threatens the Texas horned lizard. Harvester ants are a staple of this lizard’s diet, and it cannot eat the red imported fire ants that have largely replaced them. Red imported fire ants threaten native birds too. The ants prey on insects that songbirds need to feed to their young. In addition, the ants eat birds’ eggs and nestlings. Ground-nesting birds are at special risk (Figure 18.1B). Even native plants can be affected. The ants interfere with pollination by displacing or preying on native pollinators such as ground-nesting bees. They interfere with plant dispersal by displacing native harvester ants that would otherwise spread the plants’ seeds. Given all the problems that S. invicta causes in the United States, you might wonder what happens in South America, where this species evolved. In fact, the ants are not much of a problem there, in part because they are not particularly abundant. In S. invicta’s native environment, parasites and predators help keep the species in check. The S. invicta that left South America benefited by leaving their many natural enemies behind. In the absence of these natural controls, S. invicta becomes more abundant and widespread than it would be in its native environment. As this example illustrates, the types of species that live in an area and the population size of each species are determined not only by physical characteristics of an area, but also by species interactions. As a result, when a new

A. One red imported fire ant worker. A colony can contain thousands of such workers, each with a stinger.

B. Red imported fire ants destroy eggs and kill nestlings of ground-nesting birds such as quail. Figure 18.1  Red imported fire ant (Solenopsis invicta), an introduced threat to native species. (A) Alex Wild/Visuals Unlimited, Inc.; (B) James Mueller

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370  Unit 4 ECOLOGY

species enters an area, its arrival can alter the array of species there in complex and often unpredictable ways.

Discussion Questions 1. Global trade and travel have the potential to inadvertently move species such as red imported fire ants from one region to another. Suggest precautions that could help prevent the introduction of other nonnative species into the United States. 2. Most species that are accidently introduced to a new region fail to survive there. What factors might make a successful introduction more or less likely? 3. Use of pesticides to fight red imported fire ants is most effective when the pesticide is applied in a coordinated fashion across a wide area. Discuss the reasons why such coordinated action is most useful and why it can be difficult to accomplish.

18.2  Community Structure Learning Objectives

community  All populations of all species in some area. habitat  The type of environment in which a species lives. interspecific competition  Two species compete for a limited resource and both are harmed by the interaction. niche  The role of a species in its community; the conditions it requires and the interactions it takes part in. species diversity  The number of species and their relative abundance within a community.

●●

Using appropriate examples, describe factors that influence community structure.

●●

Distinguish between the two components of species diversity.

●●

Explain the difference between a species habitat and its niche.

In biology, the term community refers to all populations of all organisms that live in a particular area. Biological communities vary in size and often are nested one inside another. For example, we find a community of microbial organisms inside the gut of a termite. That termite is part of a larger community of organisms that live on a fallen log. This community is in turn part of a still larger forest community. Even communities that are similar in scale differ in their species diversity. There are two components to species diversity: The first, species richness, refers to the number of species that are present; the second is species evenness, or the relative abundance of each species. A pond that contains similar numbers of five species of fish has a higher species evenness, and thus a higher species diversity, than a pond with one abundant fish species and four rare ones. Community structure refers to the types of species and their abundances within a community, as well as the interactions among them. It is influenced by a combination of nonbiological and biological factors, and it can change over time.

Nonbiological Factors  Factors related to geography and climate affect community structure. These factors include soil quality, sunlight intensity, rainfall, and temperature. Nonbiological factors vary with latitude (distance from the equator) and elevation (distance above sea level). In aquatic environments, they also vary with depth. Tropical regions (regions near the equator) receive the most sunlight energy and have the most even temperature. For most plants and animal groups, the number of species is greatest in the tropics and declines as you move toward the poles. For example, tropical forest communities contain a greater variety of species than

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Communities and Ecosystems  Chapter 18  371  

forest communities in temperate regions. Similarly, tropical coral reef communities are more diverse than comparable marine communities farther from the equator.

Biological Factors  The evolutionary history and adaptations of the species in a community also influence community structure. Each species evolved in and is adapted to a specific habitat, the type of place where it typically occurs. Although many species in a community may share the same habitat, each has a unique ecological role that sets it apart. This role is the species’ niche, which we describe in terms of the conditions, resources, and interactions necessary for survival and reproduction. Aspects of an animal’s niche include temperatures it can tolerate, the kinds of foods it can eat, and the types of places where it can breed or hide. A description of a plant’s niche would include details of its requirements for soil, water, light, and pollinators. Species interactions also affect community structure. The presence of one species often enhances or inhibits the population growth of another species. In some cases, the effect is indirect. For example, when songbirds eat caterpillars, the birds indirectly benefit the trees that the caterpillars feed on. Other interactions are direct, meaning one species actively helps or harms another. Such direct interactions are the subject of the next section.

Take-Home Message 18.2 ●●

●●

Communities vary in their species diversity as a result of nonbiological factors such as differences in incoming sunlight, temperature, and soil quality. Biological factors such as species requirements for survival and reproduction, as well as interactions with other species, also influence community structure.

18.3  Direct Species Interactions Learning Objectives ●●

Using appropriate examples, describe the types of benefits that partners in a mutualism can exchange.

●●

Compare the processes of competitive exclusion and resource partitioning.

●●

Distinguish among predators, parasites, and parasitoids.

●●

Define symbiosis and give examples.

We can categorize direct interspecific interactions by their effects on the participating species (Table 18.1). Interactions that have a negative effect on a species reduce its abundance in a community, whereas those with a positive effect increase its abundance.

Interspecific Competition  Intraspecific competition, competition among members of the same species, is one of the density-dependent factors that limits population growth. Interspecific competition is competition between members of different species. Like intraspecific competition, it has a negative effect on both competitors. Competition between species takes two forms: interference and exploitation. With interference competition, members of one species actively prevent members of another species from using a resource. For example, scavengers such as eagles

Table 18.1  Direct Interspecific Interactions

Type of Interaction

Effect on Species 1

Effect on Species 2

Competition

Negative

Negative

Antagonism  Predation  Herbivory  Parasitism

Positive

Negative

Mutualism

Positive

Positive

Commensalism

Positive

None

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372  Unit 4 ECOLOGY

Figure 18.2  Active competition among scavengers. After facing off over a carcass (left), an eagle attacked a fox with its talons (right). The fox then retreated, leaving the eagle to exploit the carcass. Pekka Komi

and foxes sometimes fight over a carcass (Figure 18.2). Some plants actively interfere with their competitors too, as when a sagebrush plant secretes chemicals that prevent other plant species from growing nearby. With exploitative competition, neither species tries to fend off the other. Instead, both competitors scramble to obtain what they need, thus reducing the amount of resource available to the other. For example, wolf spiders and carnivorous plants called sundews both capture and eat flies (Figure 18.3). Each fly captured and eaten by one species reduces the number of flies available to the other. Species compete most intensely when the supply of a shared resource is the main limiting factor for both. In the early 1930s, the Russian scientist Georgy Gause described the principle of competitive exclusion: Species that require the same limited resources and access them in the same way cannot coexist indefinitely. Gause studied interactions between two species of ciliated protists (Paramecium) that eat the same bacteria. He grew the species separately and together (Figure 18.4). In the mixed cultures, population growth of one species always outpaced the other, which eventually died out. When resource needs of two species overlap somewhat, the presence of each reduces the carrying capacity of the habitat for the other. Over time, the result may be resource partitioning, an evolutionary process in which traits of two species that compete for a limited resource come to differ a way that minimizes competition. Resource partitioning occurs because, in each species, individuals that are least similar to the competing species experience the least competition and thus leave the most offspring.

Predation Figure 18.3  Scramble competition between members of different kingdoms. Sundew plants (top) and wolf spiders (bottom) compete for food. Both feed on flies and other insects. Top, scaners3d/Shutterstock.com; bottom, Cathy Keifer/Shutterstock.com

In antagonistic interactions, one species benefits by extracting resources from another, which is harmed as a result. Predation is an antagonistic interaction in which one species captures, kills, and eats another (Figure 18.5). Predators exert selective pressure on prey, putting prey individuals with the best antipredator defenses at an advantage. In turn, prey defenses favor the predatory individuals best able to overcome those defenses. As a result, predators and prey

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Communities and Ecosystems  Chapter 18  373  

Paramecium

0

A

4

8

12

16

Time (days)

20

24

0

B

4

8

12

16

Both species together

Relative population density

P. aurelia alone

Relative population density

Relative population density

P. caudatum alone

20

24

Time (days)

0

C

4

8

12

16

20

24

Time (days)

Figure 18.4  Competitive exclusion.

Left, Michael Abbey/Science Source

Figure It Out: Which species of Paramecium was driven to extinction?

Figure 18.5  Predation. Predators such as this lynx catch, kill, and devour their prey, in this case a snowshoe hare. Ed Cesar/Science Source

mimicry  Two or more species come to resemble one another. predation  One species (the predator) captures, kills, and feeds on another (its prey).

Figure 18.6  Warning coloration and mimicry. (A) Kletr/Shutterstock.com; (B) Marco Uliana/Shutterstock.com

A. The coloration of this yellow jacket wasp warns predators that it can sting.

Two species of the ciliated protozoan Paramecium, P. caudatum and P. aurelia, both feed on bacteria. When grown in separate test tubes, each does well A, B. When grown together C, one species drives the other to extinction.

Answer: P. caudatum

may engage in an evolutionary arms race that continues over many generations. Consider that cheetahs, the fastest land animals, are capable of brief sprints at up to 70 miles (114 kilometers) per hour. That evolved capacity for speed is essential because Thomson’s gazelles, the cheetah’s preferred prey, can run 50 miles (80 kilometers) per hour. You have already learned about some other defensive adaptations of prey. Many prey species have hard or sharp parts that make them difficult to eat. Think of a snail’s shell or a porcupine’s quills. Other prey species contain chemicals that taste bad or sicken predators. Consider that monarch butterfly caterpillars feed only on milkweed and store toxins from milkweed in their body. If a bird eats a monarch caterpillar or butterfly, the plant-derived chemicals will sicken it. Monarch caterpillars are not sickened by the toxin because they have an evolved resistance to its effect. Warning coloration is a conspicuous pattern or color that predators learn to avoid. For example, stinging wasps and bees typically have black and yellow stripes (Figure 18.6A). The similar appearance of these stinging insects is one type of mimicry, an evolutionary pattern in which species comes to resemble one another. Stinging wasps and bees benefit from their similar appearance, because a predator that is stung by any one of these insects is likely to avoid others with similar coloration. In another type of mimicry, a species that lacks a defense mimics a better-defended species. For example, some flies that cannot sting resemble stinging bees or wasps (Figure 18.6B). Such flies benefit when predators avoid them after an encounter with the better-defended look-alike species. Startling or distracting a predator is another form of defense. Section 1.5 described how some butterflies protect themselves from predators by flicking their wings open to expose startling eyespots. A lizard’s tail may detach from the body and wiggle a bit, distracting a predator while the lizard runs off. Skunks and some beetles defend themselves by squirting foul-smelling, irritating repellents at predators.

B. This fly, which cannot sting, benefits by mimicking the color pattern of wasps.

principle of competitive exclusion  Species that require the same limited resources and access them in the same way cannot coexist indefinitely in an environment. resource partitioning  Evolutionary process in which traits of competing species come to differ as a result of the selective pressure imposed by the competition between them. warning coloration  Distinctive color or pattern that makes a well-defended prey species easy to recognize.

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374  Unit 4 ECOLOGY Camouflage is a body shape, color pattern, or behavior that allows an indi-

vidual to blend into its surroundings and avoid detection (Figure 18.7). Prey benefit when they have camouflage that allows them to hide from predators, and predators benefit from camouflage that makes them less visible to prey.

Herbivory  Herbivory is an antagonistic interaction in which an animal feeds on a plant, which

may or may not die as a result. Some plants can withstand loss of their parts and quickly grow replacements. For example, grasses are seldom killed by herbivores. They have a fast growth rate and store enough resources in their roots to replace the shoots lost to grazers. Other plants have traits that fend off herbivores. Physical deterrents include spines, thorns, and fibrous, difficult-to-chew leaves. Plants can also produce compounds that taste bad to herbivores or sicken them. Capsaicin, a compound that makes some peppers “hot,” defends seeds against seed-eating mammals. Rodents find capsaicin-rich pepper fruits unpalatable, leaving them to be eaten by birds, which cannot detect capsaicin. A pepper benefits by deterring rodent seed eaters because rodents chew up and kill seeds, whereas birds eat seeds whole, and excrete them alive and intact.

Parasitism Figure 18.7  Camouflage. When frightened, a least bittern points its bill upward and sways with the wind to better blend in with marsh vegetation. Menno Schaefer/Shutterstock.com

An interspecific interaction in which two species have a permanent or long-lasting, physically close association is called a symbiosis. Parasitism, commensalism, and mutualism are symbioses. With parasitism, a parasite withdraws nutrients from a living individual of another species (its host). Some bacteria, protists, and fungi are parasites. Parasitic invertebrates include tapeworms and flukes, fleas, and ticks (Figure 18.8A). Even a few plants are parasitic (Figure 18.8B). Parasites that cause disease symptoms are referred to as pathogens. However, even parasites that do not cause obvious illness can lower their host’s fitness. The presence of a parasite can weaken a host, making it more vulnerable to predation or less attractive to potential mates. Some parasitic infections cause sterility or shift the sex ratio among the host’s offspring. Adaptations to a parasitic lifestyle include traits that allow the parasite to locate hosts and to feed undetected. For example, ticks locate mammals and birds

brood parasite  An animal that tricks another species into raising its young. camouflage  Body shape, pattern, or behavior that helps a plant or animal blend into its surroundings. commensalism  Species interaction that benefits one species and has no effect on the other. herbivory  An animal feeds on a plant, which may or may not die as a result. parasitism  Species interaction in which one species (the parasite) lives and feeds on another (the host). parasitoid  An insect that lays eggs in or on another insect, and whose young devour their host from the inside. symbiosis  Interspecific interaction in which two species have a permanent or long-lasting, physically close association.

A. Ticks sucking blood from a finch.

B. Dodder (Cuscuta). Roots that extend from the leafless golden stems withdraw water and nutrients from another plant.

Figure 18.8  Parasites. (A) Bill Hilton, Jr., Hilton Pond Center; (B) Courtesy of Christine Evers

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Communities and Ecosystems  Chapter 18  375  

by moving toward sources of heat and exhaled carbon dioxide. When the tick bites, a chemical in its saliva acts as a local anesthetic, preventing the host from noticing it. Parasites that live inside other organisms often have adaptations that help them evade a host’s immune defenses. Hosts’ defenses against parasites include immune responses (a topic we consider in detail in Chapter 23) and behavioral responses. For example, many primates take turns removing ticks and other parasites from one another. Birds kill external parasites by preening their feathers. Coloration can also provide defense against parasites. For example, stripes have long been thought to protect zebras against parasitic flies, and a recent experiment supports this hypothesis. When researchers outfitted horses in black, white, or zebra-striped coats, biting flies landed on the single-color coats significantly more often than the striped coats. The stripes seem to interfere with the flies’ depth perception. Brood Parasites  Animals that deplete their hosts’ resources by stealing parental care are called brood parasites. A brood parasite tricks an animal of a different species into raising its young. For example, North American cowbirds (Figure 18.9) lay their eggs in the nests of other birds. When a cowbird egg hatches, the foster parents care for the young cowbird as if it were their own. Freed from the constraints imposed by parental care, a female cowbird can lay as many as 30 eggs in a single season. Some other birds, fish, and insects are also brood parasites.

Figure 18.9  Brood parasite. A cowbird chick with its foster parent. A female cowbird minimizes her cost of parental care by laying her eggs in the nests of other bird species. E. R. Degginger/Science Source

Parasitoids  Parasitoids take the concept of forcing another to care for one’s young to an even higher level. A parasitoid is an insect that is free-living as an adult but lays its eggs in or on another insect. The eggs hatch into larvae that devour their host from the inside, eventually killing it. Figure 18.10  Parasitoid.

Biological Pest Control Predators, parasites, and parasitoids of pest species can be used in biological pest control. Use of a pest’s natural enemies provides an alternative to chemical pesticides that can kill or harm a wide variety of nontarget species. Species chosen for use as biological pest control agents target only a specific type of host or prey. For example, scientists have imported parasitoid flies from Brazil for use as a biological control against red imported fire ants (Figure 18.10). The flies lay their eggs on fire ants, then the flies’ grublike larva feeds on the ant’s internal tissues. Eventually, the larva moves into the ant’s head, causes the head to fall off, and thus kills the ant. The fly larva then undergoes metamorphosis inside the now hollowed-out head. Introduced parasitoid flies are not expected to kill off all red imported fire ants in affected areas. Rather, the hope is that the flies will reduce the density of the invaders’ colonies. Ecologists are also exploring other biological control agents, such as pathogens that infect red imported fire ants but not native ants.

A phorid fly attempting to lay an egg on a red imported fire ant. If the fly succeeds, a fly larva will grow inside the ant, eventually killing it. Photo by Sanford Porter/USDA

Commensalism With commensalism, one species benefits and the other is unaffected. For example, some orchids that live attached to a tree trunk or branch (Figure 18.11) benefit by having a perch in the sun, while the tree that provides this support is unaffected. Many animals, including humans, have commensal bacteria that live in their digestive tract. The bacteria benefit by having a warm, nutrient-rich place to live, and their presence neither helps nor harms their host.

Figure 18.11  Commensalism. This tree provides orchids with an elevated perch from which they can capture sunlight. The presence of the orchids has no effect on the tree. joloei/Shutterstock.com

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376  Unit 4 ECOLOGY

Mutualism An interspecific interaction that benefits both species is a mutualism. In most animals, the digestive tract contains mutualistic bacteria, as well as commensal ones. The mutualistic species assist their host by aiding in digestion or synthesizing vitamins. Flowering plants and their pollinators are other examples of mutualism. In some cases, coevolution of plants and their pollinators result in a mutual dependence. For example, several species of yucca plant, each pollinated by a single species of yucca moth, have larvae that develop on that plant species alone (Figure 18.12A). More often, mutualistic relationships are less exclusive. Most flowering plants have more than one pollinator, and most pollinators service more than one species of plant. Many mutualisms involve a nutritional benefit to one or both partners. Photosynthetic organisms often supply sugars to their partners, as when plants lure pollinators with nectar or produce sugary fruits that attract seed-dispersing animals. Plants also provide sugars to mycorrhizal fungi and nitrogen-fixing bacteria. The plants’ fungal or bacterial symbionts return the favor by supplying their host with other essential nutrients. Similarly, photosynthetic dinoflagellates provide sugars to corals, and photosynthetic bacteria or algae feed their fungal partner in a lichen (Figure 18.12B). Mutualisms can also involve defense. A pink anemonefish will be eaten by a predator unless it has a sea anemone to hide in (Figure 18.12C). The anemone’s tentacles are covered by stinging cells that do not bother the anemonefish, but help fend off predators that would eat the fish or its eggs. The anemone can survive on its own, but partnering with an anemonefish is beneficial because the fish chases away animals that eat anemone tentacles. From an evolutionary standpoint, mutualism is best considered as reciprocal exploitation. Each participant increases its own fitness by extracting a resource, such as protection or food, from its partner. If taking part in the mutualism has a cost, individuals who minimize that cost will be at a selective advantage. Consider nectar production, which is energetically costly for a flower, but serves as a necessary payoff to pollinators. Plants that produce the minimum amount of nectar required

Figure 18.12  Mutualism. (A) Bob and Miriam Francis/ Tom Stack & Associates; (B) Sergey Uryadnikov/Shutterstock.com; (C) Thomas W. Doeppner

A. Yucca moth on a yucca flower. The yucca plant benefits by being pollinated. The moth benefits by laying eggs that develop within the yucca’s fruit.

B. Lichen. It consists of a fungus and a green alga. The fungus supports and shelters the alga, which shares the sugar it makes with the fungus.

C. Anemonefish nestles among the tentacles of a sea anemone. In this mutually beneficial partnership, each species protects the other.

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to attract pollinators will be able to produce more seeds than plants that expend additional energy to produce a more generous serving of nectar.

Take-Home Message 18.3 ●●

●●

●● ●●

Interspecific competition for resources has a negative effect on both competitors. It causes directional selection that favors individuals whose resource needs are least similar to those of the competing species. Over time, competition can lead to resource partitioning. With predation, herbivory, and parasitism, one species benefits by extracting resources from another, which is harmed as a result. In commensalism, one species benefits and the other is unaffected. In mutualism, two species exploit one another in a way that benefits both.

ecological succession  A change in community structure, in which the array of species shifts gradually. mutualism  Species interaction that benefits both species. pioneer species  Species that can colonize a new habitat. primary succession  Ecological succession that occurs in an area where there was previously no soil. secondary succession  Ecological succession occurs in an area where a community previously existed and soil remains.

18.4  How Communities Change Learning Objectives ●●

Distinguish between primary and secondary succession.

●●

Explain why the exact course of succession can be unpredictable.

●●

Describe how addition or subtraction of a single species can dramatically alter community structure.

Ecological Succession  Community structure changes constantly. In a process called ecological succession, the array of species shifts gradually as organisms alter their own

habitat. One array of species is replaced by another, which is in turn replaced by another, and so on. Primary succession occurs in habitats that lack soil and thus have few or no existing species. For example, a rocky area exposed by retreat of a glacier undergoes primary succession (Figure 18.13). At first, no multicellular organisms are present 1. The community begins to change as pioneer species gain a foothold 2. Pioneer species colonize new or vacated habitats. Lichens, mosses, and hardy annual plants with wind-dispersed seeds are often pioneer species. As generations of pioneers live and die, they help build and improve the soil. In doing so, they set the stage for their own replacement. Seeds of shrubby species take root in the soil and overgrow the pioneers 3. Over time, organic wastes and remains build up, and by adding volume and nutrients to soil, this material allows tall trees to take hold 4. Secondary succession occurs after a natural or human disturbance removes the natural array of species, but leaves the soil in place. We observe this kind of succession after a fire destroys a forest or a field is cultivated and then abandoned. In such cases, an array of different species will move in and take over. Scientists now recognize that three types of factors affect succession: (1) physical factors such as climate, (2) chance events 1 such as the order in which pioneer species arrive, and (3) the frequency and extent of disturbances. Because the sequence of species arrivals and the frequency and extent of disturbances vary

Figure 18.13  Artist’s depiction of how primary succession in a previously glaciated area can lead to establishment of a forest community.

4

3 2

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378  Unit 4 ECOLOGY

Figure 18.14  Ecological succession after a volcanic eruption. (A) R. Barrick/USGS; (B) USGS

A. Mount Saint Helens erupted in 1980. Volcanic ash completely buried the community that had previously existed at the base of this volcano.

Figure 18.15  A keystone species. The sea star Pisaster lives along rocky shores. Remove it, and the species diversity of this community declines.

B. In less than a decade, numerous pioneer species had become established.

in unpredictable ways, it is difficult to predict exactly how the composition of any particular community will change. The 1980 eruption of Mount Saint Helens, a volcano in Washington State, gave scientists an opportunity to observe succession in action (Figure 18.14). The eruption showered the area around the volcano with volcanic rock and ash, wiping out the existing plant life and covering the soil. Since then, plant life has colonized the area and succession is under way.

lauraslens/Shutterstock.com

The Role of Disturbance  In communities that frequently undergo a particular type of physical disturbance, individuals that withstand or benefit from such disturbance have a selective advantage. For example, some plants in areas subject to periodic fires produce seeds that germinate only after a fire has cleared away potential competitors. Other fire-adapted plants store resources in their roots and resprout quickly after a fire. Because fire affects different species in different ways, the frequency of fire influences competitive interactions. For example, when naturally occurring fires are suppressed, plants adapted to periodic burning lose their competitive edge. The fire-adapted plants can be overgrown by plants that devote all of their energy to growing and reproducing, rather than investing in fire-related adaptations. consumer  Organism that obtains energy and nutrients from organisms or their remains. decomposer  Consumer that breaks organic remains into their inorganic building blocks. detritivore  Consumer that feeds on small bits of organic material (detritus). ecosystem  A community and its environment. exotic species  A species that has been introduced to a new community and become established there. invasive species  Exotic species that disrupts the structure of its adopted community. keystone species  A species that has a disproportionately large effect on community structure. producer  Organism that captures light or chemical energy and makes its food from inorganic materials.

Species Losses or Additions  Keystone Species  A keystone species has a disproportionately large effect on

a community relative to its abundance. Robert Paine coined this term to describe the results of his studies of a sea star (Pisaster) common along rocky coastlines (Figure 18.15). When Paine experimentally removed this sea star from some plots, species richness within those plots declined. The sea star feeds mainly on mussels, and its presence prevents mussels from overgrowing other species. Keystone species need not be predators. For example, the large rodents called beavers can be a keystone species. Beavers cut down trees, then use the branches and logs to build a dam across a stream. Construction of a beaver dam creates a deep pool where none previously existed. By altering the physical conditions in a section of the stream, the beaver affects the types of fish and aquatic invertebrates that can live there.

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Communities and Ecosystems  Chapter 18  379  

Exotic and Invasive Species  The United States is now home to more than 4,500 exotic species. An exotic species is a species that was introduced to a new habitat

and became established there. Most exotic species do no harm, but some are invasive. An invasive species is an exotic species whose introduction disrupts the community structure in its new home. Red imported fire ants are one example. Kudzu is another (Figure 18.16A). Native to Asia, this vine was introduced to the American Southeast as a food for grazers and to control erosion. However, it has become a notorious weed, growing over and shading other plants. Nutrias, large semiaquatic rodents from South America, are another invasive species (Figure 18.16B). Descendants of nutrias imported for their fur in the 1940s now live in marshes where they threaten native plants, contribute to marsh erosion, and destroy levees that were built to control floods.

Take-Home Message 18.4 ●●

●● ●●

●●

In ecological succession, one array of species changes the habitat in a way that allows another array of species to take hold. Large and small disturbances shift community structure on an ongoing basis. A change in the presence or abundance of a keystone species has a disproportionate effect on other species in a habitat. An exotic species that leaves behind the predators, parasites, and competitors it evolved with can dramatically affect the structure of its adopted community.

A. Kudzu native to Asia is overgrowing trees across the southeastern United States.

B. Nutrias native to South America are now abundant in freshwater marshes and riversides of the Gulf states, the Chesapeake Bay region, and Oregon.

Figure 18.16  Exotic species that have become pests in the United States.

18.5  The Nature of Ecosystems

To learn about others, visit the National Invasive Species Information Center online at www.invasivespeciesinfo.gov.

Learning Objectives

(A) Angelina Lax/Science Source; (B) Greg Lasley Nature Photography, www.greglasley.net

●●

Give an example of a food chain with four trophic levels.

●●

Explain why an energy pyramid is always broadest at the bottom.

●●

Describe the process of biological magnification.

Organisms of a community interact with their environment as an ecosystem. In all ecosystems, there is a one-way flow of energy and a cycling of essential materials (Figure 18.17). An ecosystem’s producers capture energy and use it to make their own food from nonbiological (inorganic) materials in the environment. In most ecosystems, the producers are photosynthetic organisms that capture sunlight energy. An ecosystem’s consumers obtain energy and carbon by feeding on tissues, wastes, and remains of producers and one another. Herbivores, predators, and parasites are consumers that feed on living organisms. Detritivores such as crabs and earthworms eat tiny bits of organic matter (detritus). Bacterial, protistan, and fungal decomposers break down wastes and remains of organisms into inorganic building blocks. Light energy captured by producers is converted to bond energy in organic molecules. That bond energy is used in metabolic reactions that give off heat as a by-product. This is a one-way process because organisms cannot convert heat back into chemical bond energy. Unlike energy, with its one-way flow, nutrients cycle within an ecosystem. The cycle begins when producers take up hydrogen, oxygen, and carbon from inorganic sources such as the air and water. They also take up dissolved nitrogen, phosphorus,

light energy

Producers

plants, some protists and prokaryotes energy in chemical bonds

materials cycling Consumers

animals, fungi, some protists and prokaryotes heat energy

Figure 18.17  Generalized model for the one-way flow of energy (yellow arrows) and the cycling of materials (blue arrows) in an ecosystem.

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energy pyramid  Diagram that illustrates the energy flow in an ecosystem. food chain  Sequence of steps by which energy moves from one trophic level to the next. food web  System of cross-connecting food chains. primary production  The capture and storage of energy by an ecosystem’s producers. trophic level  Position an organism occupies in terms of feeding relationships within an ecosystem.

and other necessary minerals. Nutrients move from producers into the consumers who eat them. Decomposition returns nutrients to the environment, from which producers take them up again.

Food Chains and Webs  All organisms of an ecosystem take part in a hierarchy of feeding relationships. The position that an organism occupies in this hierarchy is referred to as its trophic levels (“troph” means nourishment). When one organism eats another, energy (in the form of chemical bonds) and nutrients are transferred from the eaten to the eater. All organisms at the same trophic level are the same number of transfers away from the source of energy for that system. A food chain is one sequence of steps by which energy captured by producers moves to higher trophic levels. Consider one food chain in a tallgrass prairie (Figure 18.18). The main producers in this ecosystem—grasses and other plants—are at the first trophic level. Energy flows from the plants to grasshoppers, to sparrows, and finally to hawks. Grasshoppers are primary consumers and are at the second trophic level. Sparrows that eat grasshoppers are second-level consumers and at the third trophic level. Hawks that eat sparrows are third-level consumers and at the fourth trophic level. Food chains cross-connect with one another as a food web. Figure 18.19 shows some participants in an Arctic food web. Nearly all food webs include two types of food chains. In grazing food chains, energy stored by producers flows next to herbivores, which tend to be relatively large animals. In a detrital food chain, energy in producers flows to detritivores, which tend to be smaller animals, and to decomposers. In most land ecosystems, detrital food chains predominate. For example, in an Arctic ecosystem, grazers such as voles, lemmings, and hares eat some plant parts. However, far more plant matter becomes detritus that sustains soil-dwelling insects and decomposers such as bacteria and fungi. Detrital food chains and grazing food chains interconnect as the ecosystem’s overall food web.

Energy Capture and Transfers The flow of energy through an ecosystem begins with primary production: the capture and storage of energy by producers. Primary production, which is measured in terms of the amount of carbon taken up per unit area, varies seasonally and among habitats. On average, primary production is higher on land than it is in the oceans (Figure 18.20). However, because the oceans cover

Figure 18.18  One food chain in a tallgrass prairie.

First Trophic Level

Second Trophic Level

Third Trophic Level

Fourth Trophic Level

Producer

Primary Consumer

Second-Level Consumer

Third-Level Consumer

Grass

Grasshopper

Sparrow

Hawk

Species at the first trophic level capture sunlight energy. Arrows represent the transfer of nutrients and energy from one trophic level to the next. From left, Van Vives; © D. A. Rintoul; © D. A. Rintoul; Lloyd Spitalnik/ lloydspitalnikphotos.com

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Communities and Ecosystems  Chapter 18  381  

human (Inuk)

arctic fox

arctic wolf

Higher Trophic Levels A sampling of carnivores that feed on herbivores and one another

gyrfalcon

snowy owl

ermine

Second Trophic Level mosquito

A sampling of primary consumers (herbivores) that eat plants

Parasitic consumers feed at more than one trophic level.

arctic hare

vole

lemming

First Trophic Level Examples of primary producers (plants)

flea

grasses, sedges

purple saxifrage

arctic willow

Detritivores and decomposers (nematodes, annelids, saprobic insects, protists, fungi, bacteria)

Figure 18.19  Some participants in an Arctic food web. Arrows point from eaten to eater.

about 70 percent of Earth’s surface, they contribute about half of Earth’s total primary production. An energy pyramid is a graphic representation of the proportion of the energy captured by producers that reaches higher trophic levels. Figure 18.21 shows an energy pyramid for a freshwater ecosystem in Florida. Energy pyramids always have a large energy base, representing producers, and taper up. Only about 10 percent of the energy in tissues of organisms at one trophic level ends up in tissues of those at the next trophic level. Several factors limit the efficiency of transfers. All organisms lose energy as metabolic heat, and this energy is not available to organisms at the

From left, top row, B. & C. Alexander/Science Source; Dave Mech; Tom & Pat Leeson, Ardea London Ltd.; 2nd row, © Tom Wakefield/www.bciusa.com; Paul Fusco/Science Source; E. R. Degginger/Science Source; 3rd row, Hugo Willocx/Minden Pictures; Dave Mech; Tom McHugh/Science Source, Photo by James Gathany, Centers for Disease Control; Edward S. Ross; 4th row, Jim Steinborn; Jim Riley; Matt Skalitzky; Peter Firus, flagstaffotos.com.au.

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382  Unit 4 ECOLOGY

Figure 18.20  Satellite data showing net primary production for land and oceans. Productivity is coded as red (highest) down through orange, yellow, green, blue, and purple (lowest). Source: NASA

21

top carnivores

383

carnivores

3,369

herbivores

20,810

producers

Figure 18.21  Energy pyramid for a freshwater ecosystem. Numbers are energy in kilocalories per square meter per year. Figure It Out: Approximately what percentage of the sunlight energy captured by producers was transferred to the herbivores that ate them?

next trophic level. Also, some energy gets stored in molecules that most consumers cannot break down. For example, most carnivores cannot access the energy tied up in bones, scales, hair, feathers, or fur. The inefficiency of energy transfers limits the possible length of food chains. When people promote a vegetarian or vegan diet by touting the benefits of “eating lower on the food chain,” they are referring to the inefficiency of energy transfers. Eating plant material involves only a single energy transfer. When plants are instead fed to livestock, the animal uses some of the energy it obtains from that food to sustain itself, loses some energy as heat, and invests some energy building inedible parts such as bones, hooves, and fur. Only a small percentage of the energy in the original plant material ends up as meat that a person can eat. Thus, feeding a population of meat-eaters requires far greater crop production than sustaining a population of vegetarians.

Answer: 3,369/20,810 × 100 = 16 percent

Biological Accumulation and Magnification

DDT Residues (In parts per million of wet weight of organism) Osprey Green heron Atlantic needlefish Summer flounder Sheepshead minnow Hard clam Marsh grass Flying insects (mostly flies) Mud snail Shrimps Green alga Water

13.8 3.57 2.07 1.28 0.94 0.48 0.33 0.30 0.26 0.16 0.083 0.00005

Figure 18.22  Biological magnification of DDT in an estuary. Gary Head

Like nutrients and energy, some toxic substances move through food webs. In animals, fat-soluble toxins that are ingested or absorbed across the skin can accumulate in fatty tissues. The concentration of fat-soluble toxins in an animal body increases over time, so long-lived species tend to accumulate a higher concentration of these substances than shorter-lived ones. Within a species, old individuals have a higher toxin load than younger ones. Over the course of a predator’s life, the predator consumes all the toxic substances previously taken up and accumulated by its many prey. Thus, by a process called biological magnification, a toxin becomes increasingly concentrated as it moves up a food chain. Figure 18.22 provides data documenting biological magnification of DDT (an insecticide) in a salt marsh ecosystem during the 1960s. Notice that the concentration of DDT in ospreys (a type of fish-eating bird), was 276,000 times higher than the concentration in the water. As a result of biological magnification, even very low environmental concentrations of toxic chemicals can have detrimental effects on a species. Concern about DDT’s effects on nontarget species led to a ban on its use in the United States. Biological magnification of mercury remains a problem worldwide. Mercury is a nervous system poison that coal-burning power plants emit. In the environment, mercury becomes incorporated into methyl mercury. This toxic compound is absorbed by aquatic plants and plankton, then moved up the food chain. Large-bodied predatory fishes such as swordfish, shark, and albacore tuna contain the most methyl mercury, but all seafood contains some. To learn more about the healthiest seafood choices, visit the Environmental Protection Agency’s website: www.EPA.gov/fishadvice.

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Communities and Ecosystems  Chapter 18  383  

Take-Home Message 18.5 ●●

●● ●●

●●

Materials cycle between organisms and their environment, but energy flow is oneway because energy is lost as heat during every transfer. Energy and raw materials taken up by producers flow to consumers. Food chains and food webs describe routes by which energy and nutrients move from one trophic level to another. Energy transfers between trophic levels are inefficient because energy is lost as metabolic heat, and some energy becomes tied up in materials that are not easily digested by consumers.

18.6  The Water, Nitrogen,

and Phosphorus Cycles Atmosphere

Learning Objectives ●●

Describe the main environmental reservoirs for phosphorus and nitrogen.

●●

Explain the roles of bacteria in the nitrogen cycle.

●●

Explain why addition of nitrogen or phosphorus to water can stimulate algal blooms.

In a biogeochemical cycle, an essential element moves from one or more environmental reservoirs, through the living components of an ecosystem, and then back to the reservoirs (Figure 18.23). Depending on the element, environmental reservoirs may include Earth’s rocks and sediments, waters, and atmosphere. Chemical and geologic processes move elements to, from, and among environmental reservoirs. Some elements locked in rocks become part of the atmosphere as a result of volcanic activity. Movement of Earth’s tectonic plates (Section 12.5) can uplift rocks, so an area that was once seafloor becomes part of a landmass. On land, erosion breaks down rocks, allowing the elements in them to enter rivers and flow to seas. Compared to the movement of elements within a community, movement of elements among nonbiological reservoirs is far slower. Processes such as erosion and uplifting operate over thousands or millions of years. We focus on four biogeochemical cycles that move important elements: the water cycle, phosphorus cycle, nitrogen cycle, and carbon cycle.

The Water Cycle  The water cycle moves water from oceans to the atmosphere, onto land and into freshwater ecosystems, and back to the oceans (Figure 18.24A). Solar energy drives evaporation of water from the oceans and from freshwater reservoirs. Water that enters the lower atmosphere spends some time aloft as vapor, clouds, and ice crystals. By the process of precipitation, water falls from the atmosphere mainly as rain and snow. Oceans cover about 70 percent of Earth’s surface, so most water evaporates from oceans and most precipitation falls on oceans. Most precipitation that falls on land runs into streams or seeps into the ground. Plant roots take up soil water (the water between soil particles). Transpiration, the evaporation of water from the aboveground parts of plants, returns most of this water to the atmosphere.

Living organisms

Rocks and sediments

Seawater and freshwater

Nonliving environmental reservoirs

Figure 18.23  Generalized biogeochemical cycle. I love photo/Shutterstock.com

biogeochemical cycle  Cycle in which a nutrient moves among environmental reservoirs and into and out of food webs. biological magnification  A chemical pollutant becomes increasingly concentrated as it moves through a food chain. transpiration  Evaporation of water from a plant’s aboveground parts. water cycle  Water moves from its main reservoir— the ocean—into the atmosphere, falls as rain and snow, and flows back to the ocean.

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384  Unit 4 ECOLOGY

Atmosphere Windborne water vapor

Evaporation from ocean

Precipitation into ocean

Transpiration (evaporation from plants)

Precipitation onto land

Surface and groundwater flow Land

Ocean

A. Water moves from the ocean into the atmosphere, onto land, and then back.

Reservoir Ocean Polar ice, glaciers Groundwater Lakes, rivers Atmosphere (water vapor)

Volume (103 km3) 1,370,000 29,000 4,000 230 14

B. The volume of water in the various environmental reservoirs. Figure 18.24  The water cycle. Bottom, Triff/Shutterstock.com

Our planet has a lot of water, but 97 percent of it is saltwater (Figure 18.24B). Of the 3 percent that is freshwater, most is frozen in glaciers and polar ice sheets. Groundwater, another freshwater reservoir, includes water in the soil and water stored in porous rock layers called aquifers. About half of the population of the United States relies on aquifers for drinking water. Surface water (water in streams, rivers, lakes, and freshwater marshes) constitutes less than 1 percent of Earth’s freshwater. Movement of water results in the movement of soluble nutrients. Carbon, nitrogen, and phosphorus all have soluble forms that can be moved from place to place by flowing water. As water trickles through soil, it carries soluble nutrients from upper soil layers deeper into the soil. As a stream flows over limestone, water slowly dissolves the rock and carries carbonates to the seas. Flowing water can transport pollutants too; runoff from heavily fertilized lawns and agricultural fields carries dissolved phosphates and nitrates into streams and lakes.

The Phosphorus Cycle  Atoms of phosphorus are highly reactive, so phosphorus does not occur naturally in its elemental form. Most of Earth’s phosphorus is bonded to oxygen as phosphate (PO43–), an ion abundant in rocks and sediments. There is no commonly occurring gaseous form of phosphorus, so the atmosphere is not one of its reservoirs. In the phosphorus cycle, phosphate moves among Earth’s rocks, soil, and water, and into and out of food webs (Figure 18.25). In the environmental portion of the cycle, weathering and erosion move phosphate ions from rocks into soil, lakes, and rivers 1. Rivers deliver phosphate ions to the ocean 2, where most of the phosphorus comes out of solution and settles as deposits on the seafloor 3. Over millions of years, these deposits become rock. Movements of Earth’s crust can later uplift phosphate-rich rocks onto land 4, where the environmental portion of the phosphorus cycle starts over again. All organisms require phosphorus to build ATP, nucleic acids, and phospholipids. The biological portion of the phosphorus cycle begins with the

Land food webs

Rocks on land

Figure 18.25  The phosphorus cycle. In this cycle, most of the phosphorus moves in the form of phosphate ions. Earth’s main phosphorus reservoir is rocks and sediments.

1

weathering, 5 uptake erosion by producers

excretion, death, decomposition

6

Phosphates in soil, lakes, rivers

2 leaching, runoff

7 Phosphates in seawater

Marine food web

8 3 4 uplifting over geologic time

Marine sediments

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Communities and Ecosystems  Chapter 18  385  

CLOSER LOOK Figure 18.26  The nitrogen cycle.

Atmospheric nitrogen (mainly N2)

Figure It Out: What are the two forms of nitrogen that plants can take up?

Answer: Ammonium and nitrate

1 nitrogen fixation

6 denitrification by bacteria

Waste and remains

by bacteria

2 uptake

by producers Soil ammonium (NH4+)

3 decomposition by bacteria and fungi 4 nitrification by bacteria

5 uptake by producers Soil nitrates (NO3–)

Figure Summary The main reservoir for nitrogen is the atmosphere. Activity of nitrogen-fixing bacteria converts gaseous nitrogen to forms that producers can use.

uptake of phosphate by producers. Roots of land plants take up dissolved phosphate from soil water 5. Land animals get phosphate by eating plants or one another. Phosphorus returns to the soil in wastes and remains 6. In the seas, phosphorus enters food webs when producers take up dissolved phosphate from seawater 7. As on land, wastes and remains replenish the supply 8. Lack of phosphorus often limits plant growth, so most fertilizers include phosphate. Phosphorus-rich droppings from seabird or bat colonies can be harvested as a natural fertilizer. However, most commercial fertilizer contains phosphorus derived from rock that has been mined and then chemically treated.

The Nitrogen Cycle  Earth’s atmosphere, which is about 80 percent gaseous nitrogen (N2), is the largest nitrogen reservoir. In the nitrogen cycle, nitrogen moves among the atmosphere, reservoirs in soil and water, and food webs (Figure 18.26). Plants cannot use gaseous nitrogen because they do not have an enzyme that can break the triple covalent bond between its two nitrogen atoms. Some bacteria have such an enzyme that breaks apart nitrogen gas and produces ammonia, a process called nitrogen fixation 1. Ammonia dissolves in water to form ammonium, which plants take up from the soil as their main source of nitrogen 2. Consumers obtain nitrogen by eating plants or one another. When bacterial and fungal decomposers break down organic wastes and remains, they release ammonium back into the soil 3. Bacteria play additional roles in the nitrogen cycle. Some bacteria that live in soil and water can convert ammonium to nitrate (NO3–) by a process called nitrification 4. Like ammonium, nitrate can be taken up from the soil and used by producers 5. Ecosystems lose nitrogen when still another group of bacteria converts nitrate to gaseous forms that escape into the atmosphere 6.

aquifer  Porous rock layer that holds some groundwater. groundwater  Water between soil particles and in aquifers. nitrogen cycle  Movement of nitrogen among the atmosphere, soil, and water, and food webs. nitrogen fixation  Conversion of nitrogen gas to ammonia. phosphorus cycle  Movement of phosphorus among rocks, water, soil, and living organisms.

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386  Unit 4 ECOLOGY

In the early 1900s, German scientists discovered a method of fixing atmospheric nitrogen and producing ammonium on an industrial scale. This process allowed the manufacture of synthetic nitrogen fertilizers that have boosted crop yields, helping to feed the rapidly increasing human population. However, use of fertilizers, along with other human activities, has added large amounts of nitrogen-containing compounds to our water and air. Nitrates commonly pollute drinking water in agricultural areas, raising the risk of thyroid cancer. Nitrous oxide, a gas released by bacteria in overfertilized soil and by the burning of fossil fuel, contributes to destruction of the ozone layer (the layer that filters out dangerous ultraviolet radiation from the sun).

Nutrient Pollution and Algal Blooms

Figure 18.27  Algal bloom. An ecologist samples water in Florida canal during a bloom of cyanobacteria. The canal receives nutrientenriched water from Lake Okeechobee. Miami Herald/Tribune News Service/Getty Images

Industrially produced fertilizers are a relatively inexpensive way to enhance crop yield and maintain lush lawns. However, nutrients from these fertilizers can run off and contaminate aquatic habitats. Similarly, sewage from cities and animal wastes from farms can cause nutrient pollution. Lack of phosphorus and nitrogen limits the growth of cyanobacteria and photosynthetic protists, so addition of these nutrients to a body of water can cause a population explosion of these microbes—an algal bloom. In Florida, heavy rains sometimes wash large amounts of nutrients from land into Lake Okeechobee, the state’s largest lake. The resulting population explosion of cyanobacteria can be hazardous as well as unsightly (Figure 18.27). Some species of cyanobacteria produce toxins that can harm humans and wildlife. Rivers and canals deliver nutrient-rich water from Lake Okeechobee to Florida’s Gulf Coast, where the influx of nutrients may contribute to another type of algal bloom. Algal blooms of the dinoflagellate Karenia brevis are known as “red tides” because high concentrations of this protist color seawater reddish brown. A nerve toxin produced by K. brevis kills fishes, sea turtles, dolphins, and manatees. Eating shellfish that have accumulated this toxin can cause neurotoxic shellfish poisoning. Symptoms include gastrointestinal distress, dizziness, and loss of motor control.

Take-Home Message 18.6 ●●

●●

●●

Water moves on a global scale from the ocean (its main reservoir), through the atmosphere, onto land, then back to the ocean. Phosphorus cycles between its main reservoir—rocks and sediments—and soils and water. Phosphorus enters food webs when producers take up dissolved phosphates. The atmosphere does not play a significant role in this cycle. Nitrogen moves from its main reservoir—the atmosphere—into soils and water, and into and out of food webs. Bacteria play a pivotal role in the nitrogen cycle by producing forms of nitrogen that producers can take up and use.

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18.7  The Carbon Cycle

carbon cycle  Movement of carbon among rocks, water, the atmosphere, and living organisms.

and Climate Change Learning Objectives ●● ●●

●●

Describe the main environmental reservoirs for carbon. Describe the evidence that atmospheric carbon dioxide is increasing, and the human actions responsible for that increase. Explain the greenhouse effect and how it relates to global climate change.

Figure 18.28  The carbon cycle. Earth’s crust is the largest carbon reservoir.

The Carbon Cycle Carbon occurs abundantly in the atmosphere, combined with oxygen as carbon dioxide (CO2). All molecules of life (carbohydrates, fats, lipids, and proteins) have a carbon backbone. In the carbon cycle, carbon moves among rocks, water, and the atmosphere, and into and out of food webs (Figure 18.28). On land, plants take up and use carbon dioxide in photosynthesis 1. Plants and most other land organisms release carbon dioxide back to the atmosphere when they carry out aerobic respiration 2. Bicarbonate ions (HCO3–) form when carbon dioxide dissolves in water 3. Bicarbonate ions taken up by aquatic producers can be converted to CO2 and used in photosynthesis 4. As on land, most aquatic organisms carry out aerobic respiration and release carbon dioxide. Soil contains more than twice as much as carbon as the atmosphere. Soil carbon consists of organic wastes and remains along with living soil organisms. Over time, bacteria and fungi in the soil decompose organic material and release carbon dioxide into the atmosphere. The rate of decomposition and the carbon content of the soil vary with the regional climate. In the tropics, decomposition happens fast, so

1 Carbon enters land food webs when plants take up carbon dioxide from the air and carry out photosynthesis. 2 Carbon returns to the atmosphere as carbon dioxide when plants and other land organisms carry out aerobic respiration. 3 Carbon diffuses between the atmosphere and the ocean. Carbon dioxide becomes bicarbonate when it dissolves in ocean water. 4 Marine producers take up bicarbonate for use in photosynthesis, and marine organisms release carbon dioxide produced by aerobic respiration. 5 Many marine organisms incorporate carbon into their shells. After they die, these shells become part of the sediments. Over time, these sediments become carbonrich rocks such as limestone and chalk in Earth’s crust. 6 Burning fossil fuels derived from the ancient remains of plants adds additional carbon dioxide into the atmosphere.

Atmospheric CO2

1 photosynthesis

6 burning fossil fuels

2 aerobic respiration

3 diffusion between atmosphere and ocean

Land food webs

Dissolved carbon in ocean Fossil fuels

death, burial, compaction over millions of years

4 Earth’s crust

5 sedimentation

Marine organisms

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388  Unit 4 ECOLOGY

Digging Into Data Changes in Atmospheric Carbon Dioxide

350

300

250

Industrial revolution

1. What was the highest CO2 level between 400,000 b.c. and a.d. 0? 2. During this period, how many times did the CO2 level exceed the CO2 level observed in 1980? 3. The industrial revolution began around 1800. How did the CO2 level change in the 800 years prior to this event? What about in the 185 years after it? 4. Which was greater, the rise in CO2 level between 1800 and 1975 or the rise between 1980 and 2013?

400 Atmospheric carbon dioxide (ppm)

To assess the impact of human activity on the carbon dioxide level in Earth’s atmosphere, it helps to take a long view. One useful data set comes from deep core samples of Antarctic ice. The oldest ice core that has been fully analyzed dates back a bit more than 400,000 years. Air bubbles trapped in the ice are tiny samples of Earth’s atmosphere at the time the ice formed, and scientists can analyze their carbon dioxide content. Combining this type of ice core data with more recent direct measurements of atmospheric carbon dioxide—as in Figure 18.29—allows scientists to put the current amount of atmospheric carbon dioxide level into historical perspective.

200

150

400,000 B.C.

0 A.D. 1000 Time interval

1975 1980

2013

Figure 18.29  Changes in atmospheric carbon dioxide (in parts per million). Data from 1980 on are direct measurements. Earlier data are based on ice cores.

most carbon is stored in living plants, rather than in soil. By contrast, in temperate zone forests and grasslands, soil holds more carbon than the living plants. Soils hold the most carbon in the Arctic, where low temperature hampers decomposition, and in peat bogs, where acidic, anaerobic conditions do the same. Sedimentary rocks such as limestone constitute Earth’s largest carbon reservoir. These rocks formed over millions of years by the compaction of the carbon-rich shells of marine organisms 5. Plants do not take up dissolved carbon from the soil, so carbon in these rocks is not readily accessible to organisms in land ecosystems. Deposits of fossil fuels formed over hundreds of millions of years from carbonrich remains 6. High pressure and temperature transformed the remains of ancient land plants to coal. A similar process transformed the remains of marine diatoms to deposits of oil and natural gas. Until we began burning these fossil fuels, the carbon in them, like the carbon in rocks, had little impact on ecosystems. Today, burning this fuel releases billions of tons of CO2 into the atmosphere every year.

Increasing Atmospheric Carbon Dioxide greenhouse effect  Warming of Earth’s lower atmosphere and surface as a result of heat trapped by greenhouse gases. greenhouse gas  Atmospheric gas that helps keep heat from escaping into space and thus warms the Earth.

In 1960, scientists began taking air samples at Mauna Loa Observatory in Hawaii. These samples show that between 1960 and the present, the concentration of carbon dioxide rose from about 315 parts per million to more than 415 parts per million. Analysis of air trapped in arctic ice and the composition of the shells of ancient marine organisms provide information about even earlier times. These data show that the carbon dioxide content of Earth’s atmosphere has not been this high for at least 3 million years.

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Communities and Ecosystems  Chapter 18  389  

Natural processes can cause a rise in atmospheric carbon dioxide, but there is no evidence that they are causing the current increase. For example, volcanoes emit carbon dioxide, but the number of volcanic eruptions has not increased during the past century. Two changes in the composition of the atmosphere indicate that the rise in carbon dioxide is caused mainly by our use of fossil fuels. The first change is a decrease in atmospheric oxygen (O2). When fossil fuels burn, their carbon binds with oxygen in the air to form carbon dioxide, so the atmospheric oxygen concentration decreases. The second change is in the ratio of carbon isotopes in the atmosphere. As Section 2.2 explained, isotopes of an element have different numbers of protons and so have different mass numbers. One isotope of carbon (12C) is stable, and another (14C) is a radioisotope that decays over time. Fossil fuels contain carbon that was taken up by photosynthetic organisms millions of years ago, so they contain mainly 12 C. Burning these fuels increases the ratio of 12C to 14C in the atmosphere, an effect that scientists have been documenting since the 1990s.

Ocean Acidification As the concentration of carbon dioxide in the atmosphere increases, more carbon dioxide dissolves in the oceans. When dissolved carbon dioxide reacts with water to form bicarbonate, hydrogen ions are released, making the ocean more acidic. Increased acidity interferes with calcium carbonate formation, so ocean acidification poses a threat to animals that have a calcium carbonate shell (such as bivalves) or skeleton (such as corals). In a more acidic ocean, these animals must expend extra energy to build hard parts, and the parts that they do make are thinner and weaker than normal.

The Greenhouse Effect Carbon dioxide, methane (natural gas), and nitrogen oxides are greenhouse gases—atmospheric gases that keep Earth warm by absorbing and reradiating heat. The mechanism by which this warming occurs is called the greenhouse effect (Figure 18.30). When energy from the sun reaches Earth’s atmosphere, some of it is reflected back into space 1. However, more of the energy passes through the atmosphere and warms Earth’s surface 2. When the warmed surface radiates heat energy, greenhouse gases absorb some of that heat, then emit a portion of it back toward Earth 3. If greenhouse gases did not exist, heat energy emitted by Earth’s surface would escape into space, leaving the planet cold and entirely lifeless.

Figure 18.30  The greenhouse effect.

light energy

3 1

heat energy

1 Light energy from the sun is reflected by Earth’s atmosphere or surface.

2 More light energy reaches and warms Earth’s surface. 3 Earth’s warmed surface emits heat energy. Some of this energy 2

escapes into space, and some is absorbed and then emitted in all directions by greenhouse gases. The emitted heat warms Earth’s surface and lower atmosphere.

Source: NASA

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390  Unit 4 ECOLOGY 1.5 1.2

lower than average temperature

0.9

1.5

2018

2010

2000

1990

-0.6 1980

-1.0 1970

-0.3

1960

-0.5

1950

0.0

1940

0.0

1930

0.3

1920

0.5

1910

0.6

1900

1.0

1880

Source: Data from http://www.climate.gov/news-features/understanding-climate/climate-change-global-temperature.

higher than average temperature

1890

Variations in the annual average global temperature on land. The y axes (vertical axes) are the difference in degrees from the average temperature between 1901 and 2000. Blue bars indicate years that were cooler than this average. Red bars indicate years that were warmer than this average.

2.0

Temperature anomaly (°C)

Figure 18.31  Global warming.

Temperature anomaly (°F)

2.5

Year

Global Climate Change

global climate change  Wide-ranging changes in rainfall patterns, average temperature, and other climate factors that result from a change in average global temperature.

Given that the greenhouse effect warm’s Earth’s surface, it stands to reason that an increase in greenhouse gases, would raise the planet’s temperature. The first scientist to predict such warming was Svante Arrhenius, a Nobel Prize-winning chemist from Sweden. In 1896, Arrhenius calculated that burning coal would, over about 3,000 years, increase the atmospheric level of carbon dioxide by 50 percent. Arrhenius was not concerned by this prospect; he expected the resulting increase in temperature to make Sweden’s climate more pleasant. Since the time of Arrhenius, scientists have documented ongoing increases in both greenhouse gas concentrations and average global temperature (Figure 18.31). Arrhenius underestimated how quickly the concentration of atmospheric carbon dioxide would rise. In the past 100 years, the atmospheric concentration has gone up more than 30 percent and Earth’s average temperature has risen by about 0.74°C (1.3°F). A rise of a degree or two in average temperature may not seem like a big deal, but it is enough to increase the rate of glacial melting and raise sea level. Sea level is currently rising at a rate of about one-eighth of an inch (3.2 millimeters) per year, increasing the risk of catastrophic flooding in low-lying areas. Scientists expect the global mean sea level to rise at least 8 inches (0.2 meter) and perhaps as much as 6.6 feet (2.0 meters) by 2100. As you will learn in Chapter 19, the temperature of the land and seas affects evaporation, winds, and currents, which in turn affect weather. Thus, rising global temperatures trigger changes in many weather patterns. For example, warmer temperatures are correlated with extremes in rainfall patterns: periods of drought interrupted by unusually heavy rains. An increase in sea temperature also makes strong hurricanes stronger. Scientists refer to the many climate-related effects of a change in average global temperature as global climate change. We return to the ecological effects of these changes in Chapter 19. Climate refers to the average weather conditions in a region over a long period. Earth’s climate has varied greatly over its history. During ice ages, much of the planet was covered by glaciers. Other periods were warmer than the present, and tropical plants and coral reefs thrived at what are now cool latitudes. Scientists can correlate some historical large-scale temperature changes with shifts in Earth’s orbit, which varies in a regular fashion over 100,000 years, and Earth’s tilt, which varies over 40,000 years. Changes in solar output, the arrangement of landmasses and the

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Communities and Ecosystems  Chapter 18  391  

frequency of volcanic eruptions also influence Earth’s temperature. However, the overwhelming majority of scientists agree that these factors cannot explain the current climate change. There is broad scientific consensus that this climate change is the result of the ongoing rise in greenhouse gases. Looking forward, the rise in greenhouse gas emissions is likely to continue as China and India become increasingly industrialized. Minimizing this increase will require using fossil fuels more efficiently and shifting toward energy sources that do not release carbon. Renewable energy sources (solar power, wind power) and nuclear energy do not emit greenhouse gases. Researchers are also investigating innovative ways to remove carbon dioxide from the atmosphere and store it.

Take-Home Message 18.7 ●●

●●

●●

Carbon’s main reservoir is rocks, but most carbon enters food webs when producers take up carbon dioxide from the air or water. Carbon dioxide is one of the greenhouse gases. The presence of these gases in the atmosphere keeps Earth warm enough to support life. Burning fossil fuels adds excess carbon dioxide to the air. The resulting increase in temperature is affecting global climate.

Summary Section 18.1  All species in a defined area are a community. Interactions among members of a community affect species distribution and population size. A species introduced to a new community without any natural enemies can increase in number and become a pest.

parasites lay eggs in another’s nest. Parasitoids are insects whose larvae develop inside and feed on a host, which they eventually kill. In a commensalism, one species benefits and neither helps nor harms the other. In a mutualism, two species exploit one another to their mutual benefit.

Section 18.2  Each species occupies a certain habitat and has a unique niche. The species diversity of a community is determined by nonbiological factors such as climate, as well as biological ones such as how species interact.

Section 18.4  Ecological succession is the sequential replacement of arrays of species within a community. Primary succession occurs in habitats without soil. Secondary succession takes place in disturbed habitats. The first species in a community are pioneer species. Their presence may help other potential colonists. Community structure is affected by physical factors, but also by random events and disturbances such as fires. The presence of a keystone species has a large effect on community structure. Arrival of an exotic species that is an invasive species can drastically alter a community.

Section 18.3  Species interactions affect community structure. Interspecific competition harms both participants. The principle of competitive exclusion states that species with identical resource needs cannot share a habitat indefinitely. Resource partitioning allows similar species to coexist. Predation occurs when a predator captures, kills, and eats its prey. In one type of mimicry, well-defended prey species have similar warning coloration. Less well-defended species also mimic well-defended ones. Camouflage can hide both predators and prey. Herbivory may or may not kill a plant. A long-term interspecific association in which individuals are physically close is a symbiosis. With parasitism, a parasite withdraws nutrients from a host, usually without killing it. Brood

Section 18.5  Producers in most ecosystems convert sunlight energy to chemical bond energy. The ecosystem’s consumers obtain energy and nutrients by feeding on other organisms. A food chain is a path by which energy flows from one trophic level to another. By the process of biological magnification, a toxic chemical becomes increasingly concentrated as it moves up a food chain. Food chains intersect as food webs. In a typical land

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392  Unit 4 ECOLOGY

Summary (Continued) ecosystem, most energy in producers flows directly to detritivores and decomposers. Energy transfers are inefficient (energy is lost as heat and tied up in inedible parts), so most ecosystems support no more than a few trophic levels. The rate of primary production—the capture and storage of energy by producers—varies with climate, season, and other factors. Energy pyramids show how available energy decreases as it is transferred from one trophic level to the next. Section 18.6  In a biogeochemical cycle, water or a nutrient moves through the environment, then through organisms, then back to an environmental reservoir. In the water cycle, water moves from the ocean into the atmosphere, falls on land, and flows back to the ocean, its main reservoir. Transpiration from plants releases water into the atmosphere. Aquifers and soil store groundwater, but most of Earth’s freshwater is in the form of glacial ice. In the phosphorus cycle, living things take up dissolved forms of phosphorus released by Earth’s rocks and sediments. No gaseous form of phosphorus plays a role in this cycle. The atmosphere is the main reservoir in the nitrogen cycle. Bacteria and the fertilizer industry carry out nitrogen fixation (convert atmospheric nitrogen to ammonium that plants can take up). Bacteria and fungi that act as decomposers also release ammonium. Addition of phosphorus and nitrogen to an aquatic environment can result in an algal bloom that threatens other aquatic organisms. Section 18.7  The global carbon cycle moves carbon from its reservoirs in rocks and seawater, through its gaseous form in the atmosphere, and through living organisms. By burning fossil fuels, we are adding excess carbon dioxide to Earth’s atmosphere and waters. Carbon dioxide that dissolves in seawater makes the ocean more acidic, a change that threatens organisms with a calcium carbonate shell or skeleton. Carbon dioxide is one of the greenhouse gases. Through the greenhouse effect, these gases trap heat in Earth’s atmosphere and make life possible. The increase in atmospheric carbon dioxide from burning fossil fuels is causing global climate change.

Self-Quiz Answers in Appendix I 1. A community consists of species __________ . a. that share a habitat c. that share a gene pool b. that do not compete d. with the same niche

2. Which of the following can be a symbiosis? a. Interspecific competition b. Predation c. Commensalism d. All of the above 3. Match the species interaction with a suitable description. a. A snake kills and eats a mouse. mutualism b. A bee pollinates a flower while competition sipping floral nectar. predation c. An owl and a wood duck both need parasitism a tree cavity to nest. herbivory d. A mosquito sucks your blood. e. A goat grazes on grass. 4. With interspecific competition, individuals of both species who are most __________ the competing species have a selective advantage. a. similar to b. different from 5. Parasitoids are __________ that lay eggs in their hosts. a. birds c. insects b. reptiles d. fish 6. The establishment of a biological community on a newly formed volcanic island is an example of __________ . a. primary succession b. secondary succession c. competitive exclusion d. resource partitioning 7. Match the terms with suitable descriptions. a. steals parental care producer b. feeds on small bits of brood parasite organic matter decomposer c. degrades organic wastes and detritivore remains to inorganic forms exotic species d. captures sunlight energy e. new to a community 8. Match each substance with its largest environmental reservoir. One reservoir choice will be used more than once. a. seawater carbon b. rocks and sediments water c. the atmosphere phosphorus nitrogen

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Communities and Ecosystems  Chapter 18  393  

9. Earth’s largest reservoir of freshwater is __________ . a. lakes c. ice in glaciers and ice sheets d. water in the bodies of living organisms b. soil water 10. __________ that fix nitrogen convert nitrogen gas to ammonia. c. Mammals a. Fungi b. Bacteria d. Mosses 11. Land plants take up the __________ they require for photosynthesis from the air. a. carbon dioxide c. ammonium ions b. phosphate ions d. nitrogen gas 12. Addition of __________ to water encourages algal blooms. a. carbon dioxide c. salt b. phosphate ions d. bicarbonate ions 13. A biological control agent is __________ a pest species. a. the prey of c. mutualistic with d. a natural enemy of b. a descendant of 14. Carbon dioxide __________ . a. is a greenhouse gas b. is released by burning fossil fuels c. has increased in the atmosphere since 1800 d. all of the above 15. A(n) __________ species is one that arrives early in succession. a. keystone c. commensal b. pioneer d. exotic

CRITICAL THinking 1. With antibiotic resistance on the rise, researchers are looking for ways to reduce use of these drugs. Instead of antibioticlaced food, some cattle are now fed food containing beneficial bacteria. Explain why the presence of these bacteria make it more difficult for harmful bacteria with similar resource needs to thrive. 2. Figure 18.6 shows a stingless fly that mimics a stinging wasp. Researchers have found that in such mimicry systems, mimics benefit most when they are rare relatives to the well-protected species they mimic. Can you explain why? 3. Ectotherms (cold-blooded animals) such as invertebrates, fish, and amphibians convert more of the energy in the food they eat into body tissues than do endotherms (warm-blooded animals) such as birds and mammals. What allows ectotherms to make more efficient use of food energy? 4. Scientists study bubbles trapped in ancient glacial ice to determine how concentrations of nitrogen and carbon dioxide gas have changed over time. However, bubbles in glacial ice cannot provide information about changes in phosphorus. Explain why air samples are not useful for this purpose and propose an alternative method to study how the amount of phosphorus in a region has changed over time. 5. Two marine mammals that live in the same Arctic waters differ in the level of pollutants in their bodies. Bowhead whales have a lower pollutant load than ringed seals. What are some factors that might explain this difference?

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19 The Biosphere and Human Effects

19.1

Decline of the Monarchs  395

19.2

Climate and the Distribution of Biomes  396

19.3

Forest Biomes  399

19.4

Grasslands, Chaparral, Deserts, and Tundra  402

19.5

Aquatic Ecosystems  405

19.6

Global Effects of Pollution  407

19.7

Conservation Biology  411

A hyena in Nairobi National Park in Kenya. Human development is increasingly encroaching on natural areas worldwide.

Concept Connections Buena Vista Images/The Image Bank/Getty Images

All living species are descended from a single-celled organism that lived billions of years ago (Section 14.2). Through the evolutionary processes described in Chapter 13, new lineages arose and became adapted to Earth’s diverse environments. Complex webs of interactions now connect these organisms with one another (Chapter 18). In this chapter, you will learn about the physical factors that influence the distribution of life, and how the ever-increasing human population (Section 17.5) threatens other species. We will draw upon what you learned about the pH scale (Section 2.5), the mutation-causing effects of ultraviolet radiation (Section 7.6), and the climate-altering effects of greenhouse gases (Section 18.7).

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The Biosphere and Human Effects  Chapter 19  395  

Application 19.1  Decline of the Monarchs High in the mountains of central Mexico is a conifer forest so special that the United Nations has designated it a World Heritage site. The majority of North America’s monarch butterflies (Danaus plexippus) spend the winter here, at the Monarch Butterfly Biosphere Reserve. The large orange and black butterflies cluster on fir trees, where the densely packed evergreens keep the local humidity high and provide protection against strong winds (Figure 19.1). A monarch butterfly that spends the winter in Mexico is a long-distance migrant whose reproductive system is on temporary hold. The butterfly’s life began a few months earlier, somewhere in the United States or southern Canada. After hatching from an egg as a caterpillar, the monarch fed for a few weeks on milkweed, then underwent metamorphosis to become a butterfly. Over the next month or so, it flew south to Mexico, sustaining itself along the way by sipping nectar from flowers. If this butterfly survives until spring, it will activate its reproductive system and head north, once again feeding on flower nectar as it travels. The butterfly will not fly as far north as its birthplace. Rather, it will travel partway, find a patch of milkweed, reproduce, and die. Successive generations will travel still farther north, mate, and die—until a sexually dormant generation arises in the late summer. This generation (the great-grandchildren or great-great-grandchildren of the previous long-distance migrants) will fly back to Mexico for the winter. The extraordinary, long-distance, multigenerational migration of the monarch butterfly makes this species vulnerable to environmental changes in a variety of ecosystems. Logging of conifer forests in Mexico threatens the butterflies’ winter home. Conversion of prairies to agricultural fields or housing developments reduces the availability of the monarch caterpillars’ sole food source—native milkweeds. It also reduces the number of nectar-producing “weeds” available to feed the adults as they travel. On farms, increased use Figure 19.1  Monarch butterflies in Mexico’s Monarch of herbicide-resistant crop plants further decreases the availability of nectar Butterfly Biosphere Reserve. The inset photo shows a plants and milkweed. monarch on milkweed. Not surprisingly, the North American population of the monarch butterfly is Photos, (top) USGS; (inset) Catherine Avilez/Shutterstock.com in decline. At one monitoring site in central Florida, the number of both caterpillars and adults declined 80 percent between 2005 and 2017. In Mexico, the estimated number of adult butterflies in the winter of 2018–19 was less than one-third of Discussion Questions the number in 1997–98. 1. Monarch butterflies are beautiful, but their decline does not threaten humans directly. As this chapter explains, physical facWhat types of organisms might be threatened if monarch butterflies disappeared? tors such rainfall and temperature deter2. As with monarch butterflies, the range of many species extends across national mine the distribution of ecosystems—where borders. What challenges does this extended range pose for conservation? desert, prairie, and forests are located. The 3. Protecting the forests where the monarch butterflies overwinter required the Mexigeographic distribution of plants affects can government to prohibit logging of those forests. What factors would you use the distribution of animals. In each of Earth’s to decide whether land that could be put to an economically profitable use should ecosystems, organisms take part in a cominstead be set aside to sustain nonhuman species? plex web of biological interactions. By altering 4. Suggest ways to increase monarch-friendly areas—that is, areas that are pesticideor destroying natural areas, humans disrupt free and that support native wildflowers, including native milkweeds. these webs, thus decreasing Earth’s carrying capacity for other species.

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396  Unit 4 ECOLOGY

Figure 19.2  Variation in intensity of solar radiation with latitude. For simplicity, we depict two equal parcels of incoming radiation on an equinox, a day when incoming rays are perpendicular to Earth’s axis, but the same principles apply on other days.

A

Rays that fall on high latitudes A pass through more atmosphere (blue) than those that fall near the equator B. Compare the length of the green lines. Depth of the atmosphere is not to scale.

B

Also, energy in the rays that fall at the high latitude is spread over a greater area than energy that falls on the equator. Compare the length of the red lines.

19.2  Climate and the Distribution

of Biomes Learning Objectives Figure 19.3  Air circulation patterns that result from latitudinal differences in the amount of solar radiation reaching Earth.

4

3

608N

●●

Describe how latitudinal differences in incoming sunlight give rise to air circulation patterns that affect climate.

●●

Explain the forces that drive ocean currents, and how these currents affect climate.

●●

Explain why organisms in geographically distant portions of a biome often show similar traits.

The biosphere includes all regions of Earth where life can exist. What lives where in the biosphere depends largely on differences in regional climate. Climate refers to the average weather conditions in a region over a long period of time, usually decades. When scientists talk about “climate change,” they are pointing out a longterm change in the weather pattern, rather than one unusual week, winter, or year.

2

Solar Energy and Latitude

2 30 degrees north: Cool, dry air sinks.

Energy from the sun is not evenly dispersed across Earth’s surface. On any given day, regions near the equator receive more sunlight energy than higher latitudes. (Latitude, the distance from the equator, is measured in degrees (°), with the equator being a latitude of 0° and the poles being 90°.) Two factors give rise to the latitudinal difference in solar energy input. The first factor is the amount of atmosphere that sunlight travels through. Some components of the atmosphere reflect or absorb solar energy, so the more atmosphere the sunlight travels through, the less reaches the surface. As the green lines in Figure 19.2 show, sunlight travels through more atmosphere to reach Earth’s surface at the poles than at the equator. The second factor is the amount of surface over which any incoming parcel of sunlight is dispersed. As the red lines in Figure 19.2 show, sunlight is spread out over a smaller surface area at the equator than at the higher latitudes. As a result of these factors, average temperature is highest at the equator and decreases toward the poles. Note that elevation (distance above sea level) also affects temperature. At any given latitude, the average temperature decreases as elevation increases. This temperature decrease occurs because air at high altitudes is thinner and less able to retain heat than air at lower altitudes.

3 60 degrees north: Warm, moist air rises, loses

Air Circulation and Rainfall

4 North pole: Cold, dry air sinks.

Latitudinal differences in surface warming, and the resulting effects on air and water, give rise to global patterns of air circulation and rainfall (Figure 19.3). At the

308N

1 equator

308S

608S

1 Equator: Warm, moist air rises, loses moisture as rain as it flows north and south.

moisture as rain.

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The Biosphere and Human Effects  Chapter 19  397  

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South Equatorial

Equatorial Counter

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N. Equator

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Au stralian

Benguela

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Hum Antarctic Circu mpolar

South Equatorial

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Equatorial Counter Sou

South Pac ific

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uatorial North Eq

uatorial

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North Equatorial Equatorial Counter

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So uth Atlantic

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Alaska

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Antarctic Circump olar

Antarctic

Tropical

Dry

Temperate

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Figure 19.4  Global ocean circulation.

equator, intense sunlight warms the air and causes evaporation of water from the ocean. When the moist air heats up, it expands and rises 1. As the equatorial air mass rises, it flows north and south and begins to cool. Cool air can hold less moisture than warm air, so moisture leaves the air as rain. The heavy equatorial rainfall supports tropical rain forests. When the air reaches about 30° north and south latitude, it has cooled and dried out. Being cool, the air sinks downward 2. Where it descends, it draws moisture from the soil. As a result, deserts form at around 30° north and south latitude. Air that continues flowing along Earth’s surface toward the poles once again picks up heat and moisture. At a latitude of about 60° it has become warm and moist, and it rises, giving up moisture as rain 3. In polar regions, cold air with little moisture descends 4. Precipitation is sparse, so polar regions are cold deserts.

Warm surface currents start moving from the equator toward the poles, but prevailing winds, Earth’s rotation, gravity, the shape of ocean basins, and landforms influence the direction of flow. Water temperatures, which differ with latitude and depth, contribute to the regional differences in air temperature and rainfall. NASA.

Ocean Currents  The waters of Earth’s oceans circulate on a global scale. At the equator, seawater warms and expands, making the sea level about 3 inches (8 centimeters) higher than it is at the poles. This difference in sea level sets the pattern of ocean circulation in motion. Winds, Earth’s rotation, and the shape and location of landmasses also influence the movement of ocean water. Collectively, these factors produce the pattern of surface currents (Figure 19.4). Surface currents circulate clockwise in the northern hemisphere and counterclockwise in the southern hemisphere. Ocean currents affect climate by distributing heat energy. Heat given off by water flowing from the equator toward the poles warms the eastern coast of continents. For example, the east coast of the North America is warmed by the northward flowing Gulf Stream. Conversely, western coasts are cooled by loss of heat to currents of cold water flowing from the poles to the equator. Water’s ability to stabilize temperature (Section 2.4) keeps coastal areas from experiencing the dramatic shifts in temperature that occur farther inland. For

biosphere  The collective term for all regions of Earth where life can exist. climate  Average weather conditions in a region over a long time period.

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398  Unit 4 ECOLOGY

Figure 19.5  Major land biomes. Most biomes include areas on more than one continent. From Russell/Wolfe/Hertz/Starr. Biology, 2e. © 2011 Brooks/Cole, a part of Cengage Learning®.

Tropical forest

Savanna

Temperate deciduous forest

Chaparral

Boreal forest

Desert

Temperate grassland

Tundra

Equator

Tropical forest

Savanna

Temperate deciduous forest

Chaparral

Boreal forest

Desert

example, Seattle, Washington, has milder winters than Minneapolis, Minnesota, even Tundra Temperate grassland though Seattle is farther north. Being a coastal city, Seattle draws heat from the adjacent Pacific Ocean, whereas landlocked Minneapolis has no similar source of heat.

Distribution of Biomes Climate—especially rainfall and temperature—is the major factor in determining the distribution of biomes, which are categories of ecosystems. Each biome is a large-scale area in which specific physical conditions support a distinctive biological community adapted to those conditions. Most biomes are geographically discontinuous, meaning they consist of widely separated regions on different continents. The term “biome” was originally coined to describe areas on land, and land biomes are characterized primarily by main type of plants, such as trees versus grasses. Unrelated species that live in widely separated parts of a biome often have similar traits because they face similar conditions. For example, plants with a water-storing stem and a spiny exterior are common in both North American and African deserts. These geographically separated plants do not share an ancestor that had these features. Rather, their spines and stems are analogous traits: traits that evolved independently in the two groups as a result of similar selection pressures (Section 12.6). Figure 19.5 shows the distribution of seven major land biomes. Sections 19.3 and 19.4 look more closely at their characteristic features.

Take-Home Message 19.2 ●●

●●

●●

Latitudinal differences in the amount of solar radiation reaching Earth give rise to difference in annual temperature and produce global air circulation patterns. Water warmed at the equator expands and flows “downhill” toward the poles. Winds, Earth’s rotation, and the shape of continents affect the water’s movement, establishing ocean currents that carry heat from the equator to higher latitudes. The distribution of biomes is determined mainly by climate.

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The Biosphere and Human Effects  Chapter 19  399  

B. Temperate deciduous forest.

A. Tropical rain forest.

Figure 19.6  Examples of forest biomes. (A) Antonio Jorge Nunes/Shutterstock.com; (B) Dean Pennala/Shutterstock.com; (C) Serg Zastavkin/Shutterstock.com

C. Boreal forest.

19.3  Forest Biomes Learning Objectives ●● ●●

●●

Describe the dominant vegetation and geographic locations of three types of forest biome. Explain why tropical rain forest is especially rich in species, and why it plays an important role in the global carbon cycle. Describe the negative effects of deforestation.

Trees dominate the forest biomes, which receive more rainfall than deserts or grasslands. Depending on the forest, the dominant trees may be broad-leaved trees (which are angiosperms) or conifers (which are gymnosperms). Collectively, the forest biomes cover about one-third of Earth’s land.

Tropical Forests Tropical Rain Forests  Evergreen broad-leaved trees dominate tropical rain forests

of equatorial Asia, Africa, and South America (Figure 19.6A). These trees shed and replace their leaves a few at a time, rather than all at once. The forest has a multilayered structure, with vines climbing on the trees, and orchids and ferns growing on tree branches. Abundant rain, warm temperatures, and consistent day length allow plants of the tropical rain forest to grow year-round. Of all land biomes, these forests have the greatest primary production; they carry out the most photosynthesis and remove the most carbon dioxide from the atmosphere. Tropical rain forests are home to an enormous variety of species. Compared to other land biomes, tropical rain forest has a greater variety of plants, insects, birds, and primates. Tropical rain forest is the oldest biome, as well as the most

biome  A region (often discontinuous) in which specific physical conditions support a distinctive biological community adapted to those conditions. tropical rain forest  Multilayered forest that occurs where warm temperatures and continual rains allow plant growth year-round. Most productive and species-rich land biome.

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400  Unit 4 ECOLOGY

species-rich. The biome’s age may contribute to the number of species. Some tropical rain forests have existed for more than 50 million years, a long interval in which many opportunities for speciation could have arisen. Decomposition and mineral cycling happen fast in tropical rain forest. Rapid decay of leaf litter provides the nutrients that sustain the forests’ high primary production. The soil itself is highly weathered and heavily leached. Being a poor nutrient reservoir, this soil is not well suited to agriculture if the forest is removed. Tropical Dry Forests  Tropical regions where rainfall is seasonal support tropical dry forests. Broad-leaved trees that dominate such forests are smaller than rain forest trees, and most lose their leaves and become dormant in the dry season.

Temperate Deciduous Forests Temperate deciduous forests are dominated by broad-leaved trees that shed all

their leaves at once in the fall (Figure 19.6B). Winters are cold, and trees remain dormant while water is locked in snow and ice. In spring, the trees flower and put out new leaves. At the same time, leaves that were shed the prior autumn decay to form a rich soil. During the growing season, a somewhat open canopy allows sunlight to reach the ground, where short understory plants flourish.

Coniferous Forests Conifers are the main plants in coniferous forests. As a group, these trees tolerate drought, cold, and nutrient-poor soils better than broad-leaved trees. Coniferous forests occur mainly in the northern hemisphere. Boreal forest, a high-latitude coniferous forest, is the most extensive land biome (Figure 19.6C). It covers broad bands of land in northern Asia, Europe, and North America. Russians call this forest the taiga or “swamp forest,” because rain that falls during the cool summers keep the soil soggy. Winters in boreal forests are dry and cold. Spruce, fir, and pine trees are the main plants. Their conical shape helps them shed snow, and their needlelike leaves help minimize evaporative water loss during the winter, when they cannot take up water from the frozen ground. Other types of coniferous forest exist in more temperate regions. Conifers are the dominant trees on North America’s mountain ranges. For example, highelevation forests of oyamel fir shelter monarch butterflies that spend their winter in Mexico. Conifers also dominate temperate lowlands along the Pacific coast from Alaska into northern California. The coniferous forests of the Pacific Northwest hold some of the world’s tallest trees—Sitka spruce and coast redwoods.

Deforestation boreal forest  At high northern latitudes, a biome dominated by conifers that can withstand the long, cold winters. deforestation  Removal of all trees from a forested area. temperate deciduous forest  Biome dominated by broad-leaved trees that flower and grow in warm seasons, then drop their leaves and become dormant during cold winters.

The amount of forested land is currently stable or increasing in North America, Europe, and China, but tropical forests continue to disappear at an alarming rate. Most tropical forests are located in developing countries with a rapidly growing human population that looks to the forest as a source of lumber, fuel, and potential cropland. Effects of Deforestation  Deforestation, the removal of all trees from a forested

area, has detrimental effects that extend beyond the immediate destruction of forest organisms. Deforestation encourages flooding, because water that otherwise would have been taken up by tree roots instead runs off into streams. The runoff removes

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The Biosphere and Human Effects  Chapter 19  401  

mineral ions from the soil, leaving the soil nutrient poor. In hilly areas, deforestation raises the risk of landslides. Without living tree roots to hold soil in place, waterlogged soil is more likely to slide. Loss of trees can even alter the local weather. When a forest is cut down, lack of shade and reduced transpiration cause daytime temperatures to rise. The reduction in transpiration also decreases rainfall, because when less water is released into the air by transpiration, less is available to fall as rain. In the case of tropical forests, the nutrient losses and drier, hotter conditions can make it impossible for tree seeds to germinate or for seedlings to survive. Thus, tropical deforestation is especially difficult to reverse. Deforestation contributes to global climate change in two ways. First, trees that are cut to clear land for other uses are often burned, releasing carbon into the atmosphere. Second, conversion of forest to cropland or pasture decreases the rate at which carbon is taken up by plants. Deforestation of Brazil’s Rain Forest  The largest existing expanse of tropical rain forest biome is in South America’s Amazon River Basin. This forest extends through several developing countries, but most of it (about 60 percent) is in Brazil. Thus, political and economic factors in Brazil have a major effect on this forest (Figure 19.7). In 2004, nearly 11,000 square miles (28,000 square kilometers) of Brazil’s tropical rain forest were deforested. That’s an area about the size of Massachusetts. Most of this land was illegally cleared for cattle ranches or soybean farms. This enormous loss of species-rich, highly productive forest inspired an international outcry. In response, the Brazilian government increased its efforts to protect the forest. A few years later, publicity about the link between rain forest destruction and Brazilian beef and soybean production led to calls for a global boycott of these products. Faced with a possible boycott, Brazil’s food processors and exporters pledged to work only with farmers and ranchers who did not use deforested land. As a result of these governmental and private efforts, Brazil’s yearly loss of rain forest declined about 70 percent between 2004 and 2014. Sadly, that trend has since reversed. In 2018, deforestation of Brazil’s Amazon rain forest hit a 10-year high. A trade war between the United States and China has raised the value of Brazilian beef and soybeans in the global market, making

Figure 19.7  Deforestation. In Brazil, a tractor plows a field that once was forest. Frontpage/Shutterstock.com.

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402  Unit 4 ECOLOGY

conversion of forests into farms and ranches increasingly profitable. At the same time, the Brazilian government has weakened enforcement of environmental regulations that protect the forest.

Take-Home Message 19.3 ●●

●●

●●

●●

A. North American prairie, a temperate grassland where bison are among the native grazers.

Near the equator, abundant rainfall and continual warmth support tropical rain forests dominated by evergreen, broad-leaved (angiosperm) trees. Tropical rain forest is the oldest, most productive, and most species-rich land biome. Temperate deciduous forests dominate regions where summers are long, rainfall is plentiful, and winters are cold. Trees become dormant in winter. Conifers, which are tolerant of cold and drought, dominate boreal forest, which is the northernmost forest and the most extensive land biome. Deforestation increases the risk of flooding and nutrient runoff, alters local weather, and contributes to global climate change.

19.4  Grasslands, Chaparral, Deserts,

and Tundra Learning Objectives ●●

B. African savanna, a tropical grassland with scattered shrubs. It supports huge herds of grazing wildebeest.

Compare the climate conditions and dominant vegetation in grasslands, savanna, and chaparral.

●●

Explain the role of fire in maintaining grassland and chaparral.

●●

Using an appropriate example, describe an example of desertification.

●●

Describe permafrost and explain why permafrost melting is a concern.

Fire-Adapted Biomes Lightning-ignited fires and native grazers play an important role in maintaining grasslands and chaparral. Plants native to these biomes store energy and nutrients in their extensive root system, which allows them to recover after being burned or grazed. When fires are suppressed or native grazers removed, faster-growing plant species that are not adapted to fires and grazing may move in and outcompete the natives. Grasslands  About 25 percent of Earth’s surface is covered by grassland, a

C. Chaparral in California. Shrubby drought-resistant plants with small, leathery leaves predominate. Figure 19.8  Biomes dominated by plants adapted to occasional fire. (A) U.S. Fish & Wildlife Service; (B) Jonathan Scott/Planet Earth Pictures; (C) Tim Gray/Shutterstock.com

biome dominated by perennial grasses and other nonwoody plants. Grasslands typically occur in the middle of continents and are bordered by shrublands or desert.

Prairies  The North American grasslands called prairies once covered much of the

continent’s interior, where summers are hot, and winters are cold and snowy. The prairies supported herds of elk, pronghorn antelope, and bison (Figure 19.8A) that were prey to wolves. Today, these predators and prey are largely absent from most of their former range.

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The Biosphere and Human Effects  Chapter 19  403  

Prairie soils are highly fertile, with a deep layer of topsoil that has been enriched by the decay of countless grass roots. The rich soil of prairies makes these regions attractive for conversion to agricultural uses. Most areas of the United States that were once prairie are now used to grow wheat and other crops. Savannas  Savannas are tropical grasslands that include a few scattered shrubs and trees. They lie between the tropical forests and hot deserts of Africa, India, and Australia. Temperatures are warm year-round, and there is a distinct rainy season. Africa’s savannas are famous for their abundant wildlife. Herbivores include giraffes, zebras, elephants, a variety of antelopes, and immense herds of wildebeests (Figure 19.8B). Lions and hyenas eat the grazers. Chaparral  Drought-resistant, fire-adapted shrubs with small, leathery leaves are the main plants in chaparral. This biome occurs along the western coast of continents,

between 30 and 40 degrees north or south latitude. Mild winters bring a moderate amount of rain, and the summers are hot and dry. Chaparral is California’s most extensive ecosystem (Figure 19.8C). It also occurs in regions bordering the Mediterranean, as well as in Chile, Australia, and South Africa.

Desert  Low annual precipitation defines desert, a biome that covers about one-fifth of Earth’s land surface. Many deserts are located around 30° north and south latitude, where global air circulation causes dry air to sink. The Sonoran Desert, which encompasses parts of the southwestern United States and northwestern Mexico, is located at about 30° north latitude, as are Africa’s Sahara desert, and the deserts of the Middle East. Mountain ranges also influence the location of deserts. Their presence can result in a rain shadow, an area where mountains act as a barrier to prevailing winds that would otherwise bring rain. On the side of a mountain facing the wind, the presence of the mountain forces air to move upward. As the air rises, it cools and releases the moisture as rain or snow. By the time the air descends on the downwind side of a mountain (the side facing away from the wind), the air is dry. In this way, the Himalayas prevent rain from falling in China’s Gobi desert, and the Andes prevent rain from falling in Chile’s Atacama Desert. Lack of rainfall keeps the humidity in a desert low. With little water vapor to block rays, intense sunlight reaches and heats the ground. At night, the lack of insulating water vapor in the air allows the temperature to fall fast. As a result, deserts tend to have larger daily temperature shifts than other biomes. Despite their harsh conditions, many deserts support a variety of plant life (Figure 19.9). These plants are adapted to utilize the little water that forms during the sporadic rains. Desert annuals sprout after a rain and complete their life cycle quickly, before the soil dries out. Some desert perennials, such as cacti, take up water and store it in their spongy tissues for later use. Leaves modified as spines help cacti fend off animals that would like to tap this source of water. Many woody shrubs are drought deciduous—when water is scarce, they reduce their evaporative water loss by dropping some or all leaves.

Desertification Deserts naturally expand and contract over long periods as a result of fluctuations in climate. However, poor agricultural practices that encourage soil erosion sometimes

Figure 19.9  Sonoran Desert after a rain. Perennial cacti and drought-resistant shrubs grow beside annual wildflowers. Anton Foltin/Shutterstock.com

chaparral  Biome with cool, wet winters and hot, dry summers; dominant plants are shrubs with small, leathery leaves. desert  Biome with little precipitation; supports perennial plants adapted to withstand drought and annuals that complete their life cycle quickly after a rain. prairie  Temperate grassland of North America; dominated by perennial grasses and nonwoody plants. rain shadow  Region that receives little rainfall because it is downwind from a mountain range. savanna  Tropical grassland with a scattering of shrubs.

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404  Unit 4 ECOLOGY

result in desertification, a rapid shift from grassland or woodland to desert. Consider what happened in the United States in the mid-1930s. During this time, large areas of prairie on the southern Great Plains were plowed, exposing the soil to the force of the region’s constant winds. Coupled with a drought, the result was an economic and ecological disaster. The extensive roots of grasses had held the prairie soil in place. Once those grasses were gone, winds carried more than a billion tons of topsoil aloft, turning the region into what came to be known as the Dust Bowl. Today, a similar process is occurring in China, where the Gobi desert is expanding into what was once grassland.

Tundra  Figure 19.10  Arctic tundra. Permafrost underlies the upper layer of defrosted soil that supports low-growing plants. Darrell Gulin/Encyclopedia/Corbis

Tundra, the biome with the coldest temperature, lies between the polar ice cap and

the belts of boreal forests in the northern hemisphere. Most tundra is in northern Russia and Canada. Tundra is Earth’s youngest biome, having appeared about 10,000 years ago when glaciers retreated at the end of the last ice age. Emergence of land from beneath these glaciers opened the way to a process of primary succession that has produced the current communities. Snow blankets the Arctic tundra for up to nine months of the year. Seasonal differences in day length are greatest at high latitudes, so winters are dark, as well as cold. During the brief growing season, nearly continuous sunlight fuels the growth of shallow-rooted low-growing plants and lichens (Figure 19.10). These producers are the base for food webs that include voles, arctic hares, caribou, arctic foxes, wolves, and brown bears. Many migratory birds nest in the tundra during the summer, when the air is thick with insects. Even in midsummer, only the surface layer of tundra soil thaws. Below that, a layer of permanently frozen soil called permafrost can be as thick as 1,600 feet (500 meters). Permafrost acts as a barrier that prevents drainage, so the soil above it remains perpetually waterlogged. Cool, anaerobic conditions slow decay, so organic remains accumulate, making the permafrost one of Earth’s greatest stores of carbon. As global temperatures rise, the amount of frozen soil that melts each summer is increasing. As a result, more and more of the organic material previously frozen in the permafrost is thawing out. When soil microbes break down the defrosted organic material, they release carbon dioxide and methane into the atmosphere. These compounds are greenhouse gases, so their release encourages further warming and thawing of the permafrost.

Take-Home Message 19.4 ●●

desertification  Conversion of grassland or woodlands to desertlike conditions. estuary  A highly productive ecosystem where nutrient-rich water from a river mixes with seawater. permafrost  Layer of soil that remains frozen year-round. tundra  Coldest biome; dominated by low plants that grow over a layer of permafrost.

●●

●● ●●

Plants in temperate grasslands, tropical savannas, and chaparral are adapted to grazing and periodic fire. Deserts receive little rain, so perennial desert plants have traits that reduce their water loss or allow them to store water. Annual desert plants complete their life cycle in a brief period after a rain. Drought and poor land use practices can convert grasslands to desert. The most northerly, coldest, and youngest biome is Arctic tundra, where low plants are adapted to a short growing season and a layer of permafrost underlies the soil.

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The Biosphere and Human Effects  Chapter 19  405  

19.5  Aquatic Ecosystems Learning Objectives ●●

Describe the physical factors that affect the distribution of life in freshwater ecosystems.

●●

Compare the characteristics of ecosystems on rocky shores, sandy shores, and estuaries.

●●

Describe the coral reef ecosystem and why these ecosystems are in decline.

●●

Give examples of ecosystems in the open ocean and on the seafloor.

The term “biome” was coined to describe land areas. However, we can also recognize distinct types of aquatic ecosystems on the basis of their physical characteristics and the communities of species they support. Temperature, salinity, rate of water movement, and depth influence the composition of aquatic communities.

Streams and Rivers Streams typically originate from runoff or melting snow or ice. As they flow downhill, they grow and merge to form rivers. Properties of a stream or river vary along its length. The type of rocks a stream flows over can affect its solute concentration, as when limestone rocks dissolve and add calcium to the water. Shallow water that flows rapidly over rocks mixes with air and so holds more oxygen than slower-moving, deeper water. Also, cold water holds more oxygen than warm water. As a result, different parts of a stream or river support species with different oxygen needs. When humans alter the speed of water flow, as with a dam, they also alter the array of species that live in the river.

Lakes A lake is a body of standing freshwater. All but the shallowest lakes have zones that differ in their physical characteristics and species composition. Near shore, where sunlight penetrates all the way to the lake bottom, rooted aquatic plants and algae that attach to the bottom are primary producers. A lake’s open waters include an upper well-lit zone and, if the lake is deep or cloudy, a zone where light does not penetrate. Producers in the well-lit water include photosynthetic protists and bacteria. In the deeper dark zone, consumers feed on organic debris that drifts down from above. A lake undergoes succession, which means that the community of lake organisms changes over time. A newly formed lake is deep. It is also clear and has low primary productivity, because it contains few nutrients (Figure 19.11). As sediments accumulate, the lake becomes shallower. Nutrients accumulate and encourage growth of photosynthetic bacteria, diatoms, and other producers that cloud the water. These producers serve as food for tiny consumers such as crustaceans, which are then eaten by larger consumers such as fish.

Nearshore Marine Ecosystems  Many organisms live along the Earth’s coastlines, which collectively extend for about 370,000 miles (620,000 kilometers).

Figure 19.11  Low-nutrient lake.

Estuaries  An estuary is a mostly enclosed coastal region where seawater mixes with

Crater Lake in Oregon formed when a collapsed volcano began to fill with snowmelt about 7,700 years ago. From a geologic standpoint, it is a young lake, and its clear water is a sign of its low primary productivity.

nutrient-rich freshwater from a river or rivers. In an estuary, the influx of water from upstream continually replenishes nutrients that support a high level of productivity.

Lindsay Douglas/Shutterstock.com

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406  Unit 4 ECOLOGY

Incoming freshwater also carries silt. Where the speed of water flow slows, the silt falls to the bottom, forming mudflats. Photosynthetic bacteria and protists in biofilms on mudflats often account for a large portion of an estuary’s primary production. Plants adapted to withstand high salinity and changes in water level also serve as producers. For example, cordgrass (Spartina) is the dominant plant in the salt marshes of many estuaries along the Atlantic coast (Figure 19.12A). Estuaries and tidal flats of tropical and subtropical latitudes often support nutrient-rich mangrove wetlands (Figure 19.12B). “Mangrove” is the common term for certain salt-tolerant woody plants. A. South Carolina estuary dominated by cordgrass.

Rocky and Sandy Shores  Organisms that live along rocky and sandy shores are

adapted to the mechanical force of the waves and to tidal changes. Many species are underwater during high tide, then exposed to the air when the tide is low. Along rocky shores, where waves prevent detritus from piling up, algae that cling to rocks are the producers in grazing food chains. In contrast, waves continually rearrange loose sediments along sandy shores, and make it difficult for algae to take hold. Here, some animals such as clams filter plankton from the water during high tides. Other animals such as crabs feed on organic debris from land or offshore.

Coral Reefs B. Florida wetland dominated by red mangroves. Figure 19.12  Examples of coastal ecosystems. (A) Kevin M. Kerfoot/Shutterstock.com; (B) iStock.com/Amnajtandee

Warm, shallow, well-lit tropical seas hold coral reefs, formations made primarily of calcium carbonate secreted by generations of corals, which are invertebrate animals (Section 16.3). Like tropical rain forests, tropical coral reefs are home to an extraordinary assortment of species (Figure 19.13). The main producers in a coral reef community are photosynthetic dinoflagellates (Section 14.6) that live inside the reef-building corals. In this mutually beneficial arrangement, the protists receive shelter and nutrients while providing their coral host with sugars. A coral stressed by environmental change such as a shift in temperature expels its protist symbionts in a response called coral bleaching. If conditions improve quickly, the symbiont population in the coral can recover. If adverse conditions persist, the population of symbionts will not be restored, so the coral will starve and die. The incidence of coral bleaching events has been increasing, most likely as a result of warming sea temperature.

The Open Ocean and Seafloor

Figure 19.13  Coral reef near Fiji. John Easley, www.johneasley.com

coral reef  In tropical sunlit seas, a formation composed of secretions of coral polyps; serves as home to many other species. hydrothermal vent  Place where hot, mineral-rich water streams out from an underwater opening in Earth’s crust. pollutant  A natural or man-made substance that is released into the environment in greater than natural amounts and that damages the health of organisms. seamount  An undersea mountain.

In the brightly lit waters of the open ocean, photosynthetic protists and bacteria are the primary producers, and grazing food chains predominate. Under most conditions, light penetrates only about 650 feet (200 meters) beneath the sea surface. Below that, organisms live in darkness, sustained by organic material that drifts down from above. On the seafloor, most species live along the edges of continents. There are also some largely unexplored communities at hydrothermal vents and on seamounts. In places where tectonic plates are moving apart, hot, mineral-rich water spews out of hydrothermal vents on the seafloor. When this water mixes with cold seawater, the minerals settle out as extensive deposits. Bacteria and archaea that can extract energy from these deposits serve as primary producers for food webs that include invertebrates such as tube worms and crabs (Figure 19.14). Seamounts are underwater mountains that stand 1,000 yards or more above the ocean floor, but remain below the surface of the sea. Seamounts attract large numbers of fishes and are home to many marine invertebrates. Like islands, they

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The Biosphere and Human Effects  Chapter 19  407  

harbor many species that evolved there and live nowhere else. Scientists estimate that there are more than 30,000 seamounts, and they have only recently begun to investigate these little-known ecosystems.

Take-Home Message 19.5 ●●

●●

●●

●●

●●

●●

Water’s temperature and speed of flow affect its oxygen content, which in turn affects where aquatic organisms can live. In lakes, the main producers are aquatic plants and photosynthetic microbes. New lakes have fewer nutrients and lower primary production than older ones. Salt-tolerant plants and biofilms of photosynthetic microbes are the main producers in estuaries. Algae are the main producers on rocky shores. On sandy shores, food webs begin with plankton or detritus. On coral reefs, the main producers are photosynthetic protists that live in the coral’s tissues. Reefs are home to a vast array of species. Photosynthetic microbes are the main producers in sunlit ocean waters. Seamounts and hydrothermal vents are ecosystems on the seafloor.

19.6  Global Effects of Pollution

Figure 19.14  Hydrothermal vent community. Bacteria and archaea that extract energy from minerals are the producers here. Consumers include crabs and giant tube worms (close-up in inset photo) that grow meters long without ever eating. The worms rely on bacteria that live in their tissues to produce their food. Photos, (main) NOAA/Photo courtesy of Cindy Van Dover, Duke University Marine Lab; (inset) Image Quest Marine

Learning Objectives ●●

Explain why discarded plastic poses a threat to wildlife.

●●

Describe the causes and effects of acid rain.

●●

Explain what is meant by the “ozone hole” and the steps that have been taken to address it.

●●

Using appropriate examples, describe ways in which global climate change harms species.

The rising size of the human population and its increasing industrialization have far-reaching effects on the biosphere. We discussed desertification and deforestation earlier in this chapter. Here we consider the wide-ranging impacts of pollution. A pollutant is a natural or man-made substance that is released into soil, air, or water in greater than natural amounts. It disrupts the physiological processes of organisms that evolved in its absence, or that are adapted to lower levels of it. Pesticides, herbicides, and fertilizers that run off from farms pollute water, as do sewage from cities and oil spilled by tankers. Most air pollution arises from burning fuels or leaked industrial chemicals.

Talking Trash  Historically, humans buried unwanted material in the ground or dumped it out at sea. The United States no longer dumps its trash at sea, but plastic and other garbage still enter coastal waters worldwide. Waste plastic that enters the ocean poses a threat to marine life. Many marine animals mistake pieces of plastic for food, sometimes with deadly results (Figure 19.15). Marine species that filter food from the water take in microscopic bits of plastic along with plankton. This microplastic can then pass up the food chain. If you eat shellfish such as clams, oysters, and mussels, you have probably eaten plastic. Ocean currents can carry plastic for thousands of miles, and they cause plastic to accumulate in some areas of the open ocean. Consider the Great Pacific Garbage

Figure 19.15  Death by plastic. When scientists dissected this recently deceased Laysan albatross chick, they found more than 300 pieces of plastic. The chick died after one piece punctured its gut wall. Clair Fackler/ NOAA.

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408  Unit 4 ECOLOGY

Digging Into Data Plastic Pollution in the Pacific In 2018, a team headed by ocean scientist Laurent Lebreton published results of a survey of the Great Pacific Garbage Patch (GPGP). The size of the GPGP and the composition of the plastic within it was determined by trawling (pulling a net along the surface to collect trash), taking aerial photos of floating material, and analyzing water samples. One unexpected finding was that about half of the plastic was fishing gear, typically netting. Figure 19.16 shows the estimated concentration of microplastic debris from this most recent survey, as well as data from earlier assessments. 1. How does the most recently measured concentration of plastic within the GPGP differ from that in the area around it? What does this indicate about the researcher’s ability to determine the borders of the GPGP? 2. How did the difference between the GPGP and the nearby area change in the interval shown? 3. Describe the overall trend in the concentration of plastic within the GPGP. 4. During the interval shown, was concentration of plastic in the GPGP ever as low as it currently is in the surrounding area?

1.4

Measured concentration (kg km22)

1.2

1.0

0.8

0.6

0.4

0.2

0

1965–1974 n 5 20 n 5 58

1975–1984 n50 n 5 19

1985–1994 n54 n52

Within GPGP

1995–2004 n52 n 5 252

2005–2014 n 5 195 n 5 861

2015 n 5 288 n 5 213

Around GPGP

Figure 19.16  Changes in the concentration of microplastics detected by trawling in or around the Great Pacific Garbage Patch. Bars indicate standard error. Source date: https://www.nature.com/articles/s41598-018-22939-w#Fig6

Patch in the subtropical waters between California and Hawaii. There, floating plastic debris swirls slowly around an area twice as large as the state of Texas. Plastic has also made its way to the ocean’s greatest depths. Video taken at the bottom of the ocean’s deepest trench showed a plastic grocery bag.

Acid Rain

acid rain  Unusually acidic rain that forms when pollutants released by burning fossil fuels mix with water vapor in the atmosphere. ozone layer  Region of upper atmosphere with a high ozone concentration; acts as a sunscreen against UV radiation.

When air pollutants released by burning coal and other fossil fuels combine with atmospheric water vapor, the resulting acid rain can be 10 times more acidic than normal rain. Pollutants are distributed by the winds, so acid rain can affect regions hundreds of miles from the source of the pollutions. Acid rain that falls onto or drains into waterways, ponds, and lakes harms aquatic organisms from diatoms to fish. Acid rain that falls on forests burns tree leaves and encourages loss of nutrient ions from the soil. As a result, trees become malnourished and more susceptible to disease. In the United States, the incidence of acid rain peaked during the 1970s. Since then, a decline in the use of coal and federal regulations that reduce sulfur dioxide

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The Biosphere and Human Effects  Chapter 19  409  

1989–1991

2014–2016

Figure 19.17  Controlling acid rain in the United States. Green indicates normal pH, with yellow and red indicating increasing acidity.

emissions have greatly reduced the acidity of precipitation (Figure 19.17). The world’s greatest sulfur dioxide emitters are now China and India, where industrialization and coal use continue to increase. These countries cover a vast expanse of land (China is a bit larger than the United States), so their increased production of acid rain threatens a huge array of species.

Destruction of the Ozone Layer  Between 10.5 and 17 miles (17 and 27 kilometers) above sea level, the concentration of ozone gas (O3) is so great that scientists refer to this region as the ozone layer. The ozone layer benefits land organisms by absorbing most of the ultraviolet (UV) radiation in incoming sunlight. UV radiation damages DNA, so it causes mutations. In the mid-1970s, scientists noticed that the ozone layer was thinning. Its thickness had always varied a bit with the season, but now there was steady decline from year to year. By the mid-1980s, spring ozone thinning over Antarctica was so pronounced that people referred to the low-ozone region as an “ozone hole” (Figure 19.18). In response to the potential threat posed by ozone thinning, countries worldwide agreed in 1987 to phase out the use of chlorofluorocarbons (CFCs). At that time, these ozone-destroying gases were widely used as propellants in aerosol cans, as coolants, and to make plastic foam. As a result of that agreement (the Montreal Protocol), the rise in atmospheric concentrations of CFCs has slowed. However, the ozone layer has not yet recovered. One factor is illegal use of banned CFCs, especially in China. In addition, CFCs are highly stable, so once in the atmosphere, they break down very slowly. If the current illegal usage of CFCs can be halted, the ozone layer may recover by about 2060.

Antarctica

Global Climate Change 

Figure 19.18  Ozone hole.

As Section 18.7 explained, greenhouse gases keep Earth warm by trapping and then reemitting heat energy. By burning fossil fuels, we are increasing atmospheric concentrations of these gases. The result is global climate change.

This graphic shows the September 2006 ozone hole, which was the largest ever recorded. Purple indicates the least ozone, with blue, green, and yellow indicating increasingly higher levels.

Melting Ice, Rising Seas, Extreme Weather  An increase in average annual tem-

Check the current status of the ozone hole at NASA’s website (http://ozonewatch.gsfc.nasa.gov).

perature elevates sea level by two mechanisms. First, it causes the volume of the

NASA Ozone Watch.

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410  Unit 4 ECOLOGY

MuirGlacier Glacier1941 1941 Muir

Muir MuirGlacier Glacier 2004 Glacier2004 2004

Figure 19.19  Melting glaciers, evidence of climate change. National Snow and Ice Data Center

ocean to increase directly, because water expands as it absorbs heat. Second, heating melts glaciers (Figure 19.19), so water that has been locked on land enters the ocean. Together, the processes have caused the sea level to rise about 8 inches (20 centimeters) in the past century. As a result, some coastal wetlands have already disappeared underwater. Until recently, ice sheets covered the Arctic Ocean year-round, but those ice sheets are shrinking. At the same time, ice on the Arctic landmass is disappearing. Loss of ice accelerates warming because ice reflects sunlight, whereas water and soil absorb it, then reemit the energy as heat. Thus, melting of ice from water or land causes increased warming, which in turn causes more melting. As a result of this feedback process, temperature is rising faster in the Arctic than at lower latitudes. The temperature of the land and seas affects evaporation, winds, and currents. As a result, weather patterns change as temperature rises. For example, warmer temperatures are correlated with extremes in rainfall patterns, with periods of drought interrupted by unusually heavy rains. Warmer seas also increase the intensity of hurricanes. Ecological Effects  Climate change is already having widespread effects on biologi-

cal systems. In the Arctic, animals such as polar bears and walruses that normally spend most of their time on ice are being forced onto land. In the tropics, warming ocean waters are increasing the frequency of coral bleaching events. For many temperate zone species, seasonal temperature changes trigger physiological and behavioral changes. As a result, warmer-than-normal springs cause deciduous trees to leaf out earlier, and spring-blooming flowers to blossom earlier. Animal breeding seasons and migration patterns are also shifting. Consider how temperature change could affect monarch butterflies. During the summer, successive generations of monarchs fly north until decreasing day length cues them to turn around. During winter, day length changes have no effect. Butterflies that spend the winter in Mexico will not fly north unless an interval of cold resets their navigation system. If the forest where the butterflies spend their winter continues to warm, their northward migration may cease. Some species benefit from the warming, expanding their range to higher latitudes or elevations that were previously too cool to sustain them. For example,

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The Biosphere and Human Effects  Chapter 19  411  

mosquito species that cannot survive cold are extending their range to higher elevations and latitudes. Expansion of mosquito ranges worries public health officials because mosquitos transmit a variety of human diseases.

Take-Home Message 19.6 ●●

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Plastic trash is now distributed throughout the ocean. Currents cause it to accumulate to high concentrations in some regions. Pollutants emitted by burning fossil fuels can combine with water in the atmosphere and fall as harmful acid rain. Emission of industrial chemicals called CFCs threatens the protective ozone layer. A global agreement to halt use of CFCs has somewhat reduced the threat. Global climate change resulting from emissions of greenhouse gases is melting glaciers and causing sea level to rise. Climate change displaces some species from their native habitats, encourages the spread of other species, alters weather patterns, and disrupts long-standing seasonal migrations.

19.7  Conservation Biology Learning Objectives ●●

Distinguish between threatened and endangered species.

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Using appropriate examples, describe some factors that raise the risk of species extinctions.

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Present the arguments for conserving biodiversity.

Biodiversity refers to the degree of variation within a level of biological organiza-

tion. It includes the number of different genotypes in a population, the number of different species in a biological community, or the number of different ecosystems in some geographical area. Human activities are causing declines in biodiversity at every level. Conservation biology addresses these declines. The goals of this relatively new field of biology are to survey the range of biodiversity, and to find ways to maintain it. The aim is to conserve as much biodiversity as possible by encouraging people to value it and use it in ways that do not destroy it.

The Extinction Crisis Like speciation, extinction is a natural process. Species arise and become extinct on an ongoing basis. The rate of extinction picks up dramatically during a mass extinction, in which many kinds of organisms become extinct in a relatively short interval. We are currently in the midst of such an event. Unlike previous extinction events, this one is caused by human actions. The World Conservation Union has compiled a list of more than 800 documented extinctions that occurred since 1500. The passenger pigeon is one of them. When European settlers first arrived in North America, they found between 3 and 5 billion passenger pigeons. The last wild passenger pigeon was shot in 1900, and the last captive member of the species died in 1914.

biodiversity  Biological diversity; for example, the genetic variation within species, the variety of species, or the variety of ecosystems.

Extinct, Endangered, and Threatened Species  For purposes of conservation,

mass extinction  Event in which many species in many habitats become extinct in the same relatively short interval.

a species is considered extinct if repeated, extensive surveys of its known range repeatedly fail to turn up signs of any individuals. It is “extinct in the wild” if the only known members of the species are in captivity.

conservation biology  Field of applied biology that surveys biodiversity and seeks ways to maintain it. endangered species  A species that faces extinction in all or part of its range.

threatened species  A species likely to become endangered in the near future.

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412  Unit 4 ECOLOGY

Figure 19.20  Endangered species.

An endangered species is currently at a high risk of extinction in the wild. A threatened species is likely to become endangered in the near future. Note that not all rare species are threatened or endangered. Some species have always been uncommon. In the United States, species are listed as endangered or threatened by the Fish and Wildlife Service (USFWS). The International Union for Conservation of Nature and Natural Resources (IUCN) monitors threats to species worldwide. The IUCN has assessed almost 49,000 species for vulnerability to extinction, and more than one-third of them are threatened or endangered. We know of about 1.8 million other species but have yet to determine their vulnerability. Some types of species are more affected by human activities than others. Indicator species are particularly sensitive to environmental change and can be monitored as indicators of environmental health. For example, a decline in lichens tells us that air quality is likely deteriorating. The loss of mayflies from a stream tells us that the quality of water in a stream is probably declining. An endemic species, one that remains confined to the area where it evolved, is more likely to go extinct than a species with a more widespread distribution. Also, a species with highly specific needs is more likely to go extinct than one that thrives under a wider range of conditions. Consider giant pandas (Figure 19.20A), which are endemic to China’s bamboo forests and subsist almost entirely on bamboo. As humans cut bamboo forests down, pandas declined. Their population, which may once have been as high as 100,000 animals, is now reduced to about 1,600 animals in the wild. As the plight of pandas illustrates, humans often increase the risk of extinctions by their effect on habitats. Each species requires a specific type of environment, and any loss, degradation, or fragmentation of its habitat can pose a threat. Deforestation and desertification destroy forests and grasslands. Warming of ocean waters kills corals and endangers the multitude of species that live on coral reefs. Deliberate or accidental introduction of exotic species can also pose a threat, as when arrival of red imported fire ants to the United States degraded the habitat for a variety of native species. Our buildings, fences, walls, and roads can be problematic too. These structures fragment habitats, dividing large ranges into many smaller habitat islands. In the eastern United States, spotted turtles are threatened by development that prevents them from moving between the wetlands where they feed and the areas where they breed. Both feeding and breeding sites remain intact, but the turtles can no longer travel between them.

C. Black Black rhinos have been hunted to near A. Pandas Pandas areendangered endangered destruction ofofbamboo White abalones have been hunted totonear C. Black C. rhinos rhinos have have been been hunted to near to near A. Pandas A.are Pandas are endangered are endangered by destruction by destruction bamboo of bamboo B. White B. White abalones abalones have been been hunted to near nearC. Black rhinos have been hunted tohunted near byby destruction of bamboo B. White abalones have have been hunted tohunted near extinction for their horns. extinction for forests. forests. extinction for use as human food. extinction for use asashuman food. extinction for their horns. extinction for use human food. forests. extinction fortheir theirhorns. horns. forests. extinction foras use human food. Hung Chung Chih/Shutterstock.com

John Butler, NOAA

George Sanker/Nature Picture Library

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The Biosphere and Human Effects  Chapter 19  413  

Hunting reduces a species’ numbers more directly. Consider what happened to the white abalone (Figure 19.20B). This fist-sized gastropod mollusk is native to kelp forests along the coast of California. During the 1970s, it became so popular in restaurants that its numbers were reduced by about 99 percent. In 2001, the white abalone became the first invertebrate listed as endangered by the U.S. Fish and Wildlife Service. Some white abalones remain in the wild, but not enough for effective reproduction. Abalones release their eggs and sperm into the water, a strategy that works only when many individuals live close to one another. In an attempt to save the white abalone, scientists are now breeding it in captivity. Species are overharvested not only as food, but also for use in traditional medicine, for the pet trade, and for use as ornaments. Some orchids prized by collectors have become nearly extinct in the wild. Elephants are killed for their ivory tusks, and black rhinos (Figure 19.20C) for their horns.

The Value of Biodiversity Why should we care if wild species disappear? From a purely selfish standpoint, doing so is an investment in our future. Healthy ecosystems are essential to the survival of our own species. Other organisms produce the oxygen we breathe and the food we eat. They also remove waste carbon dioxide from the air and decompose and detoxify other wastes. Plants take up rain and hold soil in place, preventing erosion and reducing the risk of flooding. Compounds discovered in wild species often serve as medicines. For example, two widely used chemotherapy drugs, vincristine and vinblastine, were extracted from the rosy periwinkle, a low-growing plant native to Madagascar’s rain forests. Many antibiotics are compounds that were first discovered in fungi (Section 15.9), and animal venoms were the initial source of a variety of drugs (Chapter 16). Wild relatives of crop plants serve as reservoirs of genetic diversity that plant breeders can draw upon to protect and improve crops. Wild plants often have genes that make them more resistant to disease or adverse conditions than their domesticated relatives. Plant breeders use traditional crossbreeding methods or biotechnology to introduce genes from wild species into domesticated ones, thus creating improved varieties. There are also ethical reasons to preserve biodiversity. As you know, the current array of living species is the result of an ongoing evolutionary process that stretches back billions of years. Each species has a unique combination of traits. The extinction of a species removes its unique collection of traits from the world of life forever.

Setting Priorities Protecting biological diversity can pose a challenge. People often oppose environmental protections because they fear that such measures will have adverse economic consequences. Conservation biologists help us make difficult choices about how to most efficiently protect biodiversity. They identify biodiversity hot spots, areas of high biodiversity that are under the greatest threat. As you might expect, many hot spots are in tropical regions of developing countries. However, there are two biodiversity hot spots in the United States. The California Floristic Province on the West Coast is home to a diverse array of endemic conifers, including the giant sequoia. The Coastal Plain hot spot in the Southeast extends along the Gulf and Atlantic coasts. The red-cockaded woodpecker, which nests only in old-growth pines, is among the endangered species in this region.

biodiversity hot spot  Area where a great variety of species are under threat of extinction. endemic species  A species that evolved in one place and is found nowhere else. indicator species  A species that is particularly sensitive to environmental changes and can be monitored to assess whether an ecosystem is threatened.

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414  Unit 4 ECOLOGY

Figure 19.21  Biodiversity hot spots. These areas were designated as hot spots by the Critical Ecosystems Partnership Fund (www.cepf.net) because they are home to a large number of endemic species and have lost much of their native vegetation.

Figure 19.21 shows the location of 36 global biodiversity hot spots. Each of these areas has more than 1,500 species of endemic vascular plants (plants found only in that region) and has lost more than 70 percent of its vegetation as a result of human activities. Although the combined area of these biodiversity hot spots constitutes about 2 percent of the world’s landmass, they collectively contain more than half of the world’s endemic plant species and 40 percent of its endemic vertebrates.

Protection and Restoration Worldwide, about 15 percent of Earth’s land has now been designated as protected, meaning it is managed with the goal of conserving biodiversity. Mexico’s Monarch Butterfly Biosphere Reserve is one such area. Prohibition of logging in the reserve has helped protect the fir trees essential to the butterfly’s survival. In the ocean, protected areas comprise about 7 percent of the total area. Marine protected areas are usually coastal waters, rather than open sea areas. For example, the coastal waters around Florida’s Keys are a marine protected area. Sometimes, an ecosystem is so damaged, or there is so little of it left, that protection alone is not enough to sustain biodiversity. Ecological restoration is work designed to bring about the renewal of a natural ecosystem that has been degraded or destroyed, fully or in part. Many ecological restoration projects are supervised by trained biologists but carried out primarily through the efforts of volunteers. For example, restoration of Idaho’s Little Salmon River is an ongoing project that aims to improve the habitat for endangered salmon and trout that breed in the river (Figure 19.22).

Reducing Human Impacts  ecological restoration  Actively altering an area in an effort to restore or create a functional ecosystem.

Ultimately, the health of our planet depends on our ability to recognize that the principles of energy flow and of resource limitation that govern the survival of all systems of life do not change. As our population continues to expand, we must find

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The Biosphere and Human Effects  Chapter 19  415  

Figure 19.22  Ecological restoration. These volunteers are restoring the Little Salmon River in Idaho so that salmon can migrate upstream to their breeding grounds. You can learn more about this project at www.rivermenders.net. Mountain Visions/NOAA.

a way to live within our limits. Keep in mind that unthinking actions of billions of individuals are the greatest threat to biodiversity. Each of us may have little impact on our own, but our collective behavior, for good or for bad, will determine the future of life on this planet.

Take-Home Message 19.7 ●●

●●

●●

Biodiversity refers to the genetic diversity of individuals of a species, the variety of species, and the variety of ecosystems. Worldwide, biodiversity is declining at all of these levels. Conservation biologists are working to identify threatened regions with high biodiversity and prioritize which receive protection. Ecological restoration is the process of re-creating or renewing a diverse natural ecosystem that has been destroyed or degraded.

Summary Section 19.1  Monarch butterflies native to North America are in decline. They are threatened by loss of milkweed and native nectar plants, as well as loss of forest at the site where they overwinter. Remaining overwintering habitat has now been set aside as a protected area. Section 19.2  The biosphere includes all areas of Earth that support life. Distribution of life across the biosphere is influenced by climate. Variations in climate depend largely upon differences in the amount of solar energy reaching different parts of Earth. The closer a region is to the equator, the more solar energy it receives. Warming of air and water at the equator sets in motion global patterns of air circulation and ocean currents. Circulating air and water distribute heat and moisture.

Biomes are categories of major ecosystems on land. Their distribution is determined by regional variations in climate and described in terms of their dominant plant life. Section 19.3  Near the equator, high rainfall and mild temperatures support tropical rain forests, which are dominated by trees that remain leafy and productive all year. This is Earth’s most productive and oldest biome. Many tropical rain forests are currently threatened by deforestation. In temperate deciduous forests, trees grow during warm summers, then lose their leaves and become dormant in winter. Boreal forest, dominated by conifers, is the most extensive biome. It is found only in the northern hemisphere where winters are cold and dry, and summers are cool and rainy.

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416  Unit 4 ECOLOGY

Summary (Continued) Section 19.4  Grasslands form at mid-latitudes in the interior of continents and are dominated by plants adapted to grazing. Prairie is a North American grassland biome; savanna is an African grassland that also includes scattered shrubs. Chaparral, a biome dominated by shrubby plants with tough leaves, occurs in regions with cool, wet winters and hot, dry summers. Both grasses and chaparral plants are adapted to withstand periodic fires. Deserts occur at latitudes about 30° north and south latitude, where dry air descends, and annual rainfall is sparse. They also occur where mountains cause a rain shadow. Perennial desert plants are adapted to withstand drought; desert annuals complete their life cycle fast after a rain. Poor agricultural practices can cause desertification, a transformation of grassland or woodland to desert. Tundra forms at high latitudes in the northern hemisphere. It is the youngest biome and has an underlying layer of permafrost. Section 19.5  The distribution of ecosystems in aquatic environments is determined by gradients of sunlight penetration, water temperature, salinity, and dissolved gases. Lakes are standing bodies of water. Different communities of organisms live at different depths and distances from the shore. Physical characteristics of a stream or river that vary along its length influence the types of organisms that live in it. A semi-enclosed area where nutrient-rich water from a river mixes with seawater is an estuary, a highly productive environment. Seashores may be rocky or sandy. Grazing food chains based on algae form on rocky shores. Detrital food chains dominate sandy shores. Coral reefs are species-rich ecosystems found in well-lit tropical waters. Photosynthetic protists that live inside corals are the main producers in this ecosystem. The open ocean’s upper waters hold photosynthetic organisms that form the basis for grazing food chains. Most deeper water communities subsist on material that drifts down from above. However, bacteria and archaea that can obtain energy from minerals serve as the producers at hydrothermal vent ecosystems. Seamounts are undersea mountains that have a high species richness. Section 19.6  Pollutants affect life throughout the biosphere. Plastic trash floats on the ocean surface and lies in its deepest depths. Pollutants released into the air by burning fossil fuels cause acid rain. CFCs are pollutants that cause depletion of the ozone layer, thus increasing the amount of UV radiation that reaches Earth’s surface. Global climate change is causing glaciers and sea ice to melt and making sea level rise. It is also

having ecological effects, as by increasing the frequency of coral bleaching events and altering the range of some species. Section 19.7  Biodiversity includes the variation within species, the variety of species, and the variety of ecosystems. All three levels of biodiversity are declining. Humans are causing a mass extinction. We are overharvesting species, degrading and destroying habitats, and introducing exotic species. Endangered species are currently at risk of extinction; threatened species are likely to become endangered. Endemic species are more vulnerable to extinction than widely dispersed ones. Scientists who study conservation biology document the extent of biodiversity and look for ways to preserve it, while benefiting humans. A decrease in biodiversity can harm humans. We rely on ecosystems to produce oxygen and decompose waste. We also benefit from many compounds produced by wild species, and by tapping their genetic diversity to enhance our crops. Loss of indicator species warns us that a habitat is being degraded. Conservation biologists identify biodiversity hot spots, areas with high biodiversity that are most threatened. Ecological restoration is the work of actively renewing an ecosystem that has been damaged or destroyed.

Self-Quiz Answers in Appendix I 1. The amount of solar radiation reaching the ground is greatest at __________ . a. the equator c. mid-latitudes b. the north pole d. the south pole 2. When air is heated, it __________ and can hold __________ water. c. rises; less a. sinks; less b. sinks; more d. rises; more 3. Most North American __________ has been converted to cropland. a. tundra c. desert b. prairie d. boreal forest 4. Plants in __________ are adapted to grazing and periodic fires. a. deserts c. tropical rain forests b. boreal forests d. grasslands

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The Biosphere and Human Effects  Chapter 19  417  

5. Permafrost underlies __________ . a. savanna c. desert d. prairie b. tundra 6. The oldest and most productive biome is __________ . c. tropical rain forest a. boreal forest b. tundra d. desert 7. Bacteria and archaea that can obtain energy from minerals are the main producers at __________ . a. hydrothermal vents b. estuaries c. coral reefs d. seamounts 8. Which would hold more oxygen? a. A fast-moving, cool stream b. A warm pond 9. Match the ecosystem with the most suitable description. a. freshwater and seawater mix tundra b. low humidity, and little rainfall chaparral c. North American grassland desert d. fire-adapted shrubs with tough leaves prairie e. coldest biome estuary f. most extensive biome boreal forest g. main producers are protists coral reef h. broad-leaved trees are active tropical rain all year forest 10. An __________ species is one whose population level has become so low that it is at great risk of extinction in the near future. a. endemic c. indicator b. endangered d. exotic 11. An __________ species can be monitored to gauge the health of its environment. a. endemic c. indicator b. endangered d. exotic 12. The 1930s environmental disaster known as the Dust Bowl is an example of __________ . a. deforestation c. ecological restoration b. desertification d. species extinction

13. The ozone layer __________ . a. is getting thicker b. helps keep Earth warm c. is a layer in the deep ocean d. screens out UV radiation 14. __________contributes to formation of acid rain. a. Use of CFCs b. Habitat fragmentation c. Burning fossil fuels d. Discarding plastic waste 15. Some mosquito species are expanding their range as a result of __________ . a. acid rain b. global climate change c. ozone depletion d. plastic pollution

CRITICAL THinking 1. Scientists in Mexico have been transplanting oyamel fir seedlings in the Monarch Butterfly Biosphere Reserve to an elevation about a half mile above where they now grow. The goal is to ensure that mature trees are available for overwintering monarch butterflies in the future. Why is the change in elevation necessary? 2. In one seaside community in New Jersey, the U.S. Fish and Wildlife Service suggested trapping and removing feral cats (domestic cats that live in the wild). The goal was to protect some endangered wild birds (plovers) that nested on the town’s beaches. Many residents were angered by the proposal, arguing that the cats have as much right to be there as the birds. Do you agree? Why or why not? 3. The Antarctic Ocean now receives an increased amount of ultraviolet radiation during winter and early spring, when it is under the ozone hole. During this time, the primary production of phytoplankton declines. What causes this decrease and what effects will it have on other organisms in this ecosystem? 4. With the rate of deforestation once again increasing in Brazil, scientists predict rainfall in Brazil and neighboring countries will decrease. Explain the reasoning behind this prediction.

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Appendix I Answers to Self-Quizzes Chapter 1 1. a 2. a 3. c 4. c 5. d 6. a 7. c 8. b 9. a, d, e 10. a, b 11. a 12. b 13. b 14. b 15. c e b g d a f

Chapter 3 1.1 1.2 1.2 1.3 1.3 1.3 1.3 1.4 1.2, 1.4 1.4 1.4 1.5 1.6 1.7 1.2 1.6 1.1 1.5 1.5 1.5 1.3

3.2 3.2 3.4 3.2 3.4 3.3 3.5 3.3 3.5 3.5 3.5 3.6 3.6 3.5 3.5 3.5 3.2 3.5 3.6 3.6 3.6

Chapter 4

Chapter 2 1. c 2. a 3. a 4. b 5. c 6. a 7. c 8. a 9. double bonds 10. e 11. d 12. d 13. c b d a e f i h g 14. c e d g a b f 15. g a b c d e f h

1. c 2. c 3. c 4. c 5. False 6. b 7. b 8. c 9. a 10. b 11. c, b, d, a 12. d 13. b 14. b 15. c f e d a g b

2.2 2.2 2.3 2.4 2.4 2.5 2.6 2.7 2.8 2.8 2.9, 2.10 2.9 2.4 2.2 2.4 2.2 2.2 2.4 2.5 2.3 2.2 2.8 2.7 2.8 2.10 2.9 2.10 2.7 2.9 2.8 2.9 2.8 2.10 2.7 2.10 2.7

1. c 4.2 2. b 4.2 4.3 3. a 4. c 4.3 4.3, 4.4 5. c 6. Temperature, pH, or salt concentration 4.4 7. d 4.4 4.5 8. b 9. a 4.5 10. c 4.5 11. a 4.5 12. b 4.5 13. b 4.6 14. d 4.6 15. c 4.3 e 4.6 f 4.2 b 4.3 a 4.4 g 4.5 h 4.6 i 4.4 d 4.4

Chapter 5

Chapter 7

1. Autotroph: weed. Heterotrophs: caterpillar, 5.2 bird, cat. 5.1, 5.2 2. a 3. b 5.1, 5.2 5.2 4. a 5. a 5.2 5.3 6. d 7. c 5.3 8. b 5.4 5.4 9. c 10. c 5.4 11. b 5.4 12. a 5.5 13. b 5.5 14. c 5.5 15. c 5.5 a 5.2 d 5.2 f 5.3 g 5.1 e 5.5 b 5.4 i 5.3 h 5.4

1. a 2. c 3. c 4. c 5. b 6. b 7. a 8. b 9. b 10. a 11. d 12. a 13. b 14. d 15. d c b a f e g

Chapter 6 1. b 2. False 3. d 4. c 5. d 6. b 7. c 8. c 9. d, b, c, a 10. d 11. f 12. b 13. c 14. d 15. b d a c e f i g h

6.1 6.2 6.2 6.2 6.3 6.3 6.3 6.3 6.3 6.4 6.4 6.4 6.4 6.4 6.3 6.2 6.4 6.4 6.2 6.5 6.1 6.3 6.5

7.2 7.2 7.3 7.3 7.3 7.3 7.4 7.4 7.4 7.5 7.5 7.4 7.3 7.6 7.3 7.1 7.4 7.5 7.6 7.2 7.5

Chapter 8 1. c 2. c 3. a 4. a 5. b 6. c 7. c 8. d 9. d 10. d 11. b 12. c 13. c, a, d, b 14. c 15. c f g e a b d

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8.2 8.2 8.2 8.2 8.2 8.3 8.4 8.5 8.6 8.7 8.7 8.7 8.2–8.4, 8.7 8.7 8.7 8.6 8.3 8.4 8.7 8.3 8.4

Appendix I  419  Chapter 9

Chapter 11

1. b 2. a 3. a 4. Two 5. c 6. a 7. b 8. c 9. b 10. b 11. d 12. b 13. b 14. b, e, a, c, d 15. e d g f a b c

9.2 9.2 9.2 9.2 9.2 9.2 9.5 9.5 9.6 9.6 9.6 9.6 9.6 9.3 9.3 9.4 9.3 9.6 9.4 9.6 9.6

Chapter 14

1. c 2. a 3. b 4. b 5. a 6. b 7. a 8. b 9. d 10. e, a, d, b, c 11. c 12. True 13. b 14. True 15. c f d b a e

11.2 11.2 11.2 11.2 11.3 11.3 11.2 11.3 11.3 11.2–11.3 11.4 11.4, 11.5 11.5 11.5 11.3 11.3 11.5 11.1 11.4 11.4

Chapter 12 Chapter 10 1. b 10.2 2. a 10.2 10.3 3. c 4. c 10.3 10.3, 10.7 5. a 6. False; nonMendelian patterns are more common. 10.4 7. c 10.4 10.5 8. d 9. b 10.6 10. A male child inherits an X chromosome from his mother, and a Y chromosome 10.7 from his father. 11. b 10.8 10.8 12. True 13. c 10.8 10.3 14. b d 10.3 a 10.2 c 10.2 15. b 10.8 a 10.6 d 10.8 e 10.3 f 10.2 c 10.7

1. b 12.2 2. a 12.2 3. b 12.3 4. c 12.3 12.3 5. a 6. b 12.4 7. True 12.4 8. d 12.4 9. a, c, d, e, f 12.1, 12.4–12.5 12.5 10. Gondwana 11. 66 12.1 12.6 12. d 13. e 12.6–12.7 14. b 12.7 15. b 12.2 g 12.4 d 12.3 a 12.7 e 12.4 c 12.6 f 12.6

Chapter 13 1. a 2. d 3. a, b 4. d 5. b 6. b 7. f 8. a 9. c 10. a 11. c 12. d 13. d 14. b 15. c e i g b a h f d

13.2 13.5 13.3 13.4 13.4 13.5 13.2, 13.3, 13.5 13.6 13.5 13.6 13.4 13.8 13.7 13.8 13.5 13.4 13.8 13.7 13.5 13.7 13.8 13.7 13.8

1. d 2. b 3. c 4. b 5. c 6. b 7. a 8. d 9. b 10. c 11. d 12. c 13. c 14. a 15. g d j e i f a c b h

Chapter 16 14.3 14.2 14.2 14.5 14.6 14.6 14.6 14.6 14.6 14.4 14.7 14.7 14.4 14.4 14.6 14.7 14.4 14.6 14.6 14.6 14.3 14.6 14.6 14.3

Chapter 15 1. d 2. c 3. b 4. c 5. b 6. d 7. b 8. c d f e a b g 9. c 10. a 11. c 12. d 13. b 14. d 15. g f b c a d e

15.6, 15.7 15.5 15.3 15.4 15.6 15.5 15.5 15.6 15.2 15.4 15.3 15.2 15.2 15.7 15.8 15.9 15.8 15.9 15.9 15.8 15.9 15.8 15.8 15.8 15.8 15.8 15.8

1. c 2. b 3. d 4. b 5. c 6. c 7. Dorsal nerve cord, notochord, pharynx with gill slits, and a tail that extends beyond the anus. Adult tunicates retain only the pharynx with gill slits. 8. d 9. b 10. a 11. a 12. False 13. d 14. b g m j e c d f k a h i l 15. b a f c d e

Chapter 18 16.2 16.2 16.3 16.2 16.4 16.5

16.6 16.7 16.6 16.8 16.8 16.9 16.9 16.3 16.3 16.4 16.5 16.4 16.5 16.4 16.6 16.7 16.7 16.8 16.8 16.9 16.2 16.2 16.7 16.7 16.8 16.9

Chapter 17 1. a 2. c 3. b 4. b 5. a 6. a 7. b 8. a 9. a 10. d 11. c 12. b 13. c 14. d 15. d c e a f b

17.2 17.2 17.3 17.3 17.4 17.3 17.4 17.3 17.5 17.5 17.3 17.5 17.3 17.5 17.3 17.3 17.3 17.5 17.3 17.4

1. a 2. c 3. b, c, a, d, e 4. b 5. c 6. a 7. d a c b e 8. b a b c 9. c 10. b 11. a 12. b 13. d 14. d 15. b

18.2 18.3 18.3 18.3 18.3 18.4 18.5 18.3 18.5 18.5 18.4 18.7 18.6 18.6 18.6 18.6 18.6 18.7 18.6 18.3 18.7 18.4

Chapter 19 1. a 2. c 3. b 4. d 5. b 6. c 7. a 8. a 9. e d b c a f g h 10. b 11. c 12. b 13. d 14. c 15. b

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19.2 19.4 19.2 19.4 19.4 19.3 19.5 19.5 19.4 19.4 19.4 19.4 19.5 19.3 19.5 19.3 19.5 19.7 19.4 19.6 19.6 19.6

APPENDIX II Periodic Table of the Elements 1

1

2

Period

3

4

5

6

7

18

1

H

1.008

2

3

4

Li

9.0122

11

12

Mg

22.99

13

14

15

16

17

5

6

7

8

9

B

C

N

O

F

10.81

12.011

14.007

15.999

18.998

13

14

15

16

17

Al

Si

P

S

Cl

22.990

24.305

3

4

5

6

7

8

9

10

11

12

26.982

28.085

30.974

32.06

35.45

19

20

21

22

23

24

25

26

27

28

29

30

31

32

33

34

35

K

Ca

Sc

Ti

V

Cr

Mn

Fe

Co

Ni

Cu

Zn

Ga

Ge

As

Se

Br

39.098

40.078

44.956

47.867

50.942

51.996

54.938

55.845

58.933

58.693

63.546

65.38

69.723

72.63

74.922

78.96

79.904

37

38

39

40

41

42

43

44

45

46

47

48

49

50

51

52

53

85.468

87.62

88.906

91.224

92.906

95.96

(97.91)

101.07

102.91

106.42

107.87

112.41

114.82

118.71

121.76

127.60

126.90

55

56

71

72

73

74

75

76

77

78

79

80

81

82

83

84

85

132.91

137.33

174.97

178.49

180.95

183.84

186.21

190.23

192.22

195.08

196.97

200.59

204.38

207.2

87

88

103

104

105

106

107

108

109

110

111

112

113

114

Rb Cs Fr

Sr

Y

Ba * Lu Ra ** Lr

(223.02) (226.03)

*Lanthanoids

**Actinoids

Zr

Hf Rf

57

La

89

Ac

58

Ce

Ta

Db

W

H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr

59

Pr

60

61

144.24

91

92

25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48

231.04

(270)

Ru

Os Hs 62

U

(144.91) 150.36

93

Np

Rh Ir

Mt

Pd Pt

Ds

Ag Au

Rg

Cd Hg Cn

In

Tl

Nh

Sn

Pb Fl

Sb

Te

94

Pu

63

Eu

64

Gd

65

Tb

66

Dy

67

Ho

68

Er

Po

At

115

116

117

(293)

(294)

Mc 69

Tm

Lv

10

Ne

20.180

18

Ar

39.948

36

Kr

83.798

54

Xe

131.29

86

Rn

Ts

118

Og (294)

70

157.25

158.93

162.50

164.93

167.26

168.93

173.05

96

97

98

99

100

101

102

Es

4.0026

Yb

95

Cf

He

208.98 (208.98) (209.99) (222.02)

151.96

Am Cm Bk

I

B

(277.15) (276.15) (281.16) (280.16) (285.17) (284.18) (289.19) (288.19)

Nd Pm Sm

140.91

Pa

Re

Bh

90

Th

Tc

Sg

140.12

(227.03) 232.04

Hydrogen Helium Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon Potassium Calcium Scandium Titanium Vanadium Chromium

Nb Mo

(262.11) (265.12) (268.13) (271.13)

138.91

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24

2

11

Na

(Atomic weight is a ratio: the mass of an atom relative to 1/12 the mass of a carbon 12 atom. Atomic weights given in parentheses are those of the most stable or best known isotopes of radioactive elements.)

Be

6.94

Na

Atomic number Symbol Atomic weight

Fm Md No

238.03 (237.05) (244.06) (243.06) (247.07) (247.07) (251.08) (252.08) (257.10) (258.10) (259.10)

Manganese Iron Cobalt Nickel Copper Zinc Gallium Germanium Arsenic Selenium Bromine Krypton Rubidium Strontium Yttrium Zirconium Niobium Molybdenum Technetium Ruthenium Rhodium Palladium Silver Cadmium

Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd

49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72

Indium Tin Antimony Tellurium Iodine Xenon Cesium Barium Lanthanum Cerium Praseodymium Neodymium Promethium Samarium Europium Gadolinium Terbium Dysprosium Holmium Erbium Thulium Ytterbium Lutetium Hafnium

In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Hf

73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96

Tantalum Tungsten Rhenium Osmium Iridium Platinum Gold Mercury Thallium Lead Bismuth Polonium Astatine Radon Francium Radium Actinium Thorium Protactinium Uranium Neptunium Plutonium Americium Curium

Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U Np Pu Am Cm

97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118

Berkelium Californium Einsteinium Fermium Mendelevium Nobelium Lawrencium Rutherfordium Dubnium Seaborgium Bohrium Hassium Meitnerium Darmstadtium Roentgenium Copernicium Nihonium Flerovium Moscovium Livermorium Tennessine Oganesson

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Bk Cf Es Fm Md No Lr Rf Db Sg Bh Hs Mt Ds Rg Cn Nh Fl Mc Lv Ts Og

APPENDIX Iii A Plain English Map of the Human Chromosomes

1

chymotrypsin Rh blood group antigen cannabinoid receptor (peripheral) tRNAs (gly, glu) endorphin receptor δ T cell leukemia virus receptor glucose transporter leptin receptor: obesity amylase thyroid stimulating hormone (TSH) beta chain receptor for IgG tRNA (asn) receptor for IgG peptidoglycan (PAMP) receptor interleukin-6 receptor lamin A: HutchinsonGilford progeria receptors for IgE, IgG receptors for IgA, IgM feline leukemia virus receptor flagellin (PAMP) receptor presenilin 2: Alzheimer’s disease 2 actin (cytoplasmic) interleukin-6 cytochrome c

7

EGF receptor elastin calcitonin receptor collagen I alpha-2: osteogenesis imperfecta CFTR: cystic fibrosis leptin: obesity blue cone opsin: bluedeficient colorblindness trypsin: pancreatitis

anthrax toxin receptor antibody light chain gene clusters interleukin-1 lactase

male pattern baldness tRNA (val) somatostatin 3

Burkitt lymphoma thyroid hormones 8

estrogen receptor 2

14

prolactin receptor

aldosterone receptor fibrinogen

interleukins 3, 4, 5, 9, and 13

double-stranded RNA (PAMP) receptor

tRNAs: val, pro, thr, and lys 5

TYRP1 interferons

vitamin B12 receptor

galactosemia alcohol dehydrogenase, cytoplasmic: alcohol flushing reaction Friedreich ataxia fructose intolerance

mannose (PAMP) receptor

10

15

GH releasing hormone: acromegaly 21

11 hemoglobin alpha chain gene cluster: thalassemias DNAse I VKORC1: Warfarin resistance MC1R

16

rRNA gene repeats 4 amyloid beta precursor protein: Alzheimer’s disease interferon receptors superoxide dismutase: amyotrophic lateral sclerosis (ALS)

estrogen receptor endorphin receptor, μ 6

insulin: diabetes beta globin parathyroid hormone calcitonin follicle stimulating hormone (FSH) beta chain PAX6: aniridia thrombin catalase pepsinogen folate receptor tyrosinase: albinism Tourette syndrome APOA5

perforin

rRNA gene repeats 3 Prader-Willi/ Angelman syndrome antibody heavy chain variable region gene cluster fibrillin: Marfan syndrome Tay-Sachs disease

antidiuretic hormone oxytocin prion protein: CreutzfeldtJakob disease

20

anthrax toxin receptor 2

prolactin histone proteins hemochromatosis tRNAs: val, arg tRNAs: val, ser, thr, met tumor necrosis factor MHC markers alpha chain of FSH, LH, TSH, and HCG cannabinoid receptor, brain

growth hormone receptor: dwarfism

ABO blood group

presenilin 1: Alzheimer’s TSH receptor: hypoand hyperthyroidism antibody heavy chain gene cluster

dopamine transporter telomerase

4

9

BRCA2: breast cancer

Huntington disease achondroplasia Ellis-van Creveld syndrome lipoprotein (PAMP) receptor casein alcohol dehydrogenase albinism interleukin-2: SCID

rhodopsin TSH releasing hormone

fibronectin

rRNA gene repeats 2

leutinizing hormone (LH) tRNAs: gly, val LDL receptor insulin receptor: diabetes receptor for IgE Cushing syndrome interferons APOE receptor for IgG human chorionic gonadotropin (HCG) beta chain receptor for IgA

camptodactyly

Cowden syndrome, macrocephaly, cancer synesthesia glucagon

rRNA gene repeats 1

13

ghrelin oxytocin receptor TRH receptor tRNA (arg) bacterial DNA (PAMP) receptor

gonadotropin-releasing hormone (GnRH) Werner syndrome tissue plasminogen activator endorphin receptor, κ corticotropin-releasing hormone (CRH) hypertrichosis

severe gastroesophageal reflux

19

follicle-stimulating hormone (FSH) receptor luteinizing hormone (LH) receptor

17

Canavan disease capsaicin receptor p53: cancer tRNA: gly, arg, leu, gln aurora B kinase neurofibromatosis serotonin transporter: OCD, anxiety thyroid hormone receptor keratins BRCA1: cancer collagen I alpha-1: osteogenesis imperfecta growth hormone (GH) glucagon receptor

rRNA gene repeats 5 antibody light chain variable region gene cluster RAD53: cancer myoglobin 22

12

18

Y

More than 45,000 genes code for RNA or protein products; some of the genes and gene products discussed in this book are indicated. Genetic disorders and other phenotypes associated with single-gene mutations are in red. Annotations per NCBI Homo sapiens release 107, genome assemblies GRCh38.p2 and CHM1_1.1.

ACTH receptor laminin alpha-1 carpel tunnel syndrome, familial obesity, autosomal dominant cytochrome b5: methemoglobinemia dystrophin: Duchenne muscular dystrophy MAO-B testosterone receptor: androgen insensitivity neuroligin 3: autism IL2RG: SCID, X-linked XIST

SRY

Genes on human chromosomes. Characteristic bands appear after treatment with a stain called Giemsa.

GABA transporter CD4 helper T cell antigen KRAS: leukemia, other cancers keratins collagen II vitamin D receptor: rickets Hoxc6 lysozyme gamma interferon phenylketonuria cryptochrome I alcohol dehydrogenase, mitochondria: alcohol flushing reaction

X

factor IX: hemophilia B fragile X syndrome red cone opsin: reddeficient colorblindness green cone opsin: greendeficient colorblindness incontinentia pigmenti factor VIII: hemophilia A

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GLOSSARY acid  Substance that releases hydrogen ions in water. 37 acid rain  Unusually acidic rain that forms when pollutants released by burning fossil fuels mix with water vapor in the atmosphere. 408 activation energy  Minimum amount of energy required to start a chemical reaction. 78 active site  Pocket in an enzyme where substrates bind and a reaction occurs. 81 active transport  Energy-requiring mechanism in which a transport protein pumps a solute across a cell membrane against the so-lute’s concentration gradient. 87 adaptation  Adaptive trait. 224 adaptive radiation  Macroevolutionary pattern in which a lineage undergoes a rapid burst of genetic divergences that gives rise to many species. 259 adaptive trait A form of a heritable trait that enhances an individual’s fitness; an evolutionary adaptation. 224 adhesion protein  Plasma membrane protein that helps cells stick together in animal tissues. Some types form adhering junctions and tight junctions. 59 aerobic  Involving or requiring the presence of oxygen. 107 aerobic respiration  Oxygen-requiring cellular respiration. Includes glycolysis, the citric acid cycle, and electron transfer phosphoryla-tion. 107 age structure  Of a population, the distribution of individuals among various age groups. 354 alcoholic fermentation  Fermentation pathway that produces ATP, ethanol, and CO2. 114 allele frequency  Abundance of a particular allele in a gene pool, expressed as the fraction of chromosomes that have the allele. 244 alleles  Forms of a gene with slightly different DNA sequences; may encode slightly different versions of the gene’s product. 168 allopatric speciation  Speciation pattern in which a physical barrier arises and ends gene flow between populations. 255 alternation of generations  As in plants, a life cycle that alternates between a diploid sporeproducing body and a haploid, gamete-producing one. 295 amino acid  Small organic compound that is a monomer of proteins. Consists of a carboxyl group, an amine group, and one of 20 R groups, all bonded to the same carbon atom. 44 amniote  Member of the vertebrate group that produces amniote eggs (eggs in which the embryo develops surrounded by fluid and enclosed within extraembryonic membranes); a reptile (including birds) or a mammal. 339 amoeba  Single-celled, unwalled, heterotrophic protist that feeds and moves by extending lobes of cytoplasm (pseudopods). 281 amphibian  Tetrapod with a three-chambered heart and scaleless skin. Larva are aquatic and have gills, but most are air-breathing as adults. 336

anaerobic  Occurring in (or requiring) the absence of oxygen. 108 analogous structures  Similar body parts that evolved independently in different lineages (by convergent evolution). 234 anaphase  Stage of mitosis during which sister chromatids separate and move toward opposite spindle poles. 163 aneuploidy  Condition of having too many or two few copies of a particular chromosome. 196 angiosperm  Seed plant that produces flowers and fruits. 302 animal  A multicelled eukaryotic consumer that is made up of unwalled cells and develops through a series of stages. Most ingest food, reproduce sexually, and can move from place to place. 8, 319 annelid  Segmented worm with a coelom, complete digestive system, and closed circulatory system. For example, an earthworm. 325 antenna  Of some arthropods, sensory structure on the head that detects touch and odors. 328 anther  Of a flower, the part of the stamen that produces pollen grains. 305 anthropoids  Primate subgroup that includes monkeys, apes, and humans. 342 anticodon  In a tRNA, set of three nucleotides that base-pairs with an mRNA codon. 147 apicomplexan  Single-celled, parasitic protist that enters and lives inside the cells of its host. For example, the parasite that causes malaria. 283 aquifer  Porous rock layer that holds some groundwater. 385 arachnids  Arthropods with four pairs of walking legs and no antennae; most live on land (for example, spiders, scorpions, or ticks). 328 archaea  Singular, archaeon. Group of prokaryotes that are more closely related to eukaryotes than to bacteria. 8 arthropod  Invertebrate with jointed legs and a hardened exoskeleton that is periodically molted.

326

asexual reproduction  Reproductive mode by which offspring arise from a single parent only. 161 atom  Smallest unit of matter. Consists of varying numbers of protons, neutrons, and electrons. 4 atomic number  Number of protons in the atomic nucleus; defines the element. 28 ATP  Adenosine triphosphate. Nucleotide that consists of an adenine base, a ribose sugar, and three phosphate groups. Nucleotide monomer of RNA and a coenzyme in many reactions. Important energy carrier in cells. 49 australopiths  Informal name for chimpanzeesized hominins that lived in Africa between 4 million and 1.2 million years ago. Some are considered likely ancestors of modern humans. 344 autosome  A chromosome of a pair that is the same in males and females; a chromosome that is not a sex chromosome. 132

autotroph  Producer. Organism that makes its own food using energy from the environment and carbon from CO2. 95 B lymphocyte  See B cell. bacteria  Singular, bacterium. The largest, most diverse and well-known group of prokaryotes (organisms that lack a nucleus); branched off from the lineage leading to archaea and eukaryotes early in the history of life. 8, 270 bacteriophage  Virus that infects bacteria. 287 Barr body  Condensed, inactivated X chromosome in a body cell of a female mammal (the other X chromosome is active). 155 base  Substance that accepts hydrogen ions in water. 37 base-pair substitution  Type of mutation in which a single base pair changes. 150 bell curve  Bell-shaped curve; typically results from graphing frequency versus distribution for a trait that varies continuously. 190 bilateral symmetry  Having right and left halves with similar parts, and a front and back that differ. 319 binary fission  Method of asexual reproduction in which a prokaryote divides into two identical descendant cells. 274 biodiversity  Scope of variation among living organisms. Of a region, the genetic diversity within its species, variety of species, and variety of ecosystems. 411 biodiversity hot spot  Area where a great variety of species found nowhere else are under threat of extinction. 413 biofilm  Community of microorganisms living within a shared mass of secreted slime. 61 biogeochemical cycle  Cycle in which a nutrient moves among environmental reservoirs and into and out of food webs. 383 biogeography  Study of patterns in the geographic distribution of species and communities. 221 biological magnification  A chemical pollutant becomes increasingly concentrated as it moves through a food chain. 383 biology  The scientific study of life. 3 bioluminescence  Light produced by a living organism. 281 biome  Any of Earth’s major land ecosystems, characterized by climate and main vegetation and found in several regions. 399 biosphere  All regions of Earth where organisms live. 4 biotic potential  Maximum possible population growth under optimal conditions. 358 bipedalism  Habitually walking upright. 342 birds  Common name for the lineage of feathered amniotes that descended from one group of dinosaurs. 341 bivalve  Mollusk with a hinged two-part shell. 325 bony fish  Common name for a jawed fish with a skeleton composed mainly of bone. 336

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GLOSSARY  423  boreal forest  At high northern latitudes, a biome dominated by conifers that withstand cold winters. 400 bottleneck  See population bottleneck. brood parasite  An animal that manipulates another species into raising its young, for example a cowbird.

374

brown alga  Multicelled, photosynthetic protist with brown accessory pigments; for example a kelp. 281 bryophytes  See nonvascular plants. buffer  Set of chemicals that can keep the pH of a solution stable by alternately donating and accepting ions that contribute to pH. 37 CalvinÐBenson cycle  Cyclic carbon-fixing pathway that forms sugars from CO2; light-independent reactions of photo-synthesis. 103 camouflage  Evolved body shape, color pattern, or behavior that helps an organism blend into its surroundings. 374 cancer  Group of diseases characterized by malignant cells (abnormally dividing cells that can migrate to other body tissues). 167 carbohydrate  Saccharide. Molecule that consists primarily of carbon, hydrogen, and oxygen atoms in a ratio of approximately 1:2:1. Complex types (polysaccharides such as cellulose, starch, and glycogen) are polymers of monosaccharides. 39 carbon cycle  Movement of carbon among rocks, water, the atmosphere, and living organisms. 387 carbon fixation  Process in which carbon from an inorganic source such as carbon dioxide becomes incorporated (fixed) into an or-ganic molecule. 103 carpel  Floral reproductive organ that produces the female gametophyte; consists of an ovary, stigma, and (usually) a style. 305 carrying capacity  Maximum number of individuals of a species that a specific environment can sustain. 357 cartilaginous fish  Jawed fish that has paired fins and a skeleton made of cartilage; for example, a shark. 334 cell  Smallest unit of life. All start out life with a plasma membrane, cytosol, and DNA. 4 cell cycle  The collective series of intervals and events of a eukaryotic cell’s life, from the time it forms until it divides. 161 cell junction  Molecular assembly that connects a cell to another cell or to extracellular matrix; e.g., tight junction, adhering junction, or gap junction (of animals). 68 cell theory  Theory that all organisms consist of one or more cells; the cell is the basic unit of life; all cells come from division of preexisting cells; and all cells pass hereditary material (DNA) to offspring. 57 cell wall  Rigid, permeable layer of extracellular matrix that surrounds the plasma membrane of some cells. 61 cellular respiration  Any of several pathways that break down organic molecules (typically glucose) to form ATP and include an electron transfer chain. 107 cellular slime mold  Heterotrophic protist that usually lives as a single-celled, amoeba-like predator. With unfavorable conditions, cells aggregate into a cohesive group that can form a spore-producing fruiting body.

284

cellulose  Tough, insoluble polysaccharide that is the major structural material in plants. 41 centromere  Of a duplicated eukaryotic chromosome, constricted region where sister chromatids attach to each other. 130

cephalopod  Mollusk that has a foot modified to form arms or tentacles and moves by jet propulsion; for example, an octopus or squid. 325 chaparral  Biome with cool, wet winters and hot, dry summers; dominant plants are shrubs with small, leathery leaves. 403 chemical bond  A strong attractive force between two atoms; links atoms in molecules. See covalent bond, ionic bond. 33 chlorophyll a  Main photosynthetic pigment in eukaryotes and cyanobacteria. 99 chloroplast  Organelle of photosynthesis in the cells of plants and photosynthetic protists. Outer membranes enclose stroma and a highly folded thylakoid membrane. 63 choanoflagellates  Heterotrophic protists with a collared flagellum; protist group most closely related to animals. 284 chordates  Animal phylum in which embryos have a notochord, dorsal nerve cord, pharyngeal gill slits, and a tail that extends beyond the anus. Includes invertebrate and vertebrate groups. 332 chromosome  Structure that consists of DNA together with associated proteins; carries part or all of a cell’s genetic information. 130 chromosome number  The total number of chromosomes in a cell of a given species. 132 chytrid fungus  Fungus that produces flagellated spores. 309 cilia  Singular, cilium. Short, hairlike motile structures that project from the plasma membrane of some eukaryotic cells. 66 ciliate  Unwalled, single-celled protist with many cilia.

281

citric acid cycle  Also called the Krebs cycle. Cyclic pathway that dismantles acetyl–CoA to produce CO2, NADH, FADH2, and ATP. 111 clade  A group that includes a species in which a derived trait evolved, together with all of its descendants. 260 cladistics  Method of making hypotheses about evolutionary relationships. Involves grouping species into clades based on derived traits. 260 cladogram  Evolutionary tree diagram that shows how a group of clades are related. 260 cleavage furrow  In a dividing animal cell, the indentation where cytoplasmic division will occur. 165 climate  Average weather conditions in a region over a long time period. 397 cloaca  Of some vertebrates, a body opening that releases urinary and digestive waste, and also functions in reproduction. 336 clone  Genetically identical copy of an organism. 123 cloning vector  See vector. closed circulatory system  System in which blood flows through a continuous network of vessels, and all exchanges with cells take place across vessel walls. 325 club fungus  Fungus that produces spores by meiosis in club-shaped cells. 309 cnidarian  Radially symmetrical invertebrate with two tissue layers; uses tentacles with stinging cells to capture food. 322 coal  Fossil fuel consisting primarily of the carbon-rich remains of seedless vascular plants. 300

codominance  Inheritance pattern in which the full and separate phenotypic effects of two alleles are apparent in heterozygous individuals. 186 codon  Three-nucleotide unit of information in an mRNA; the order of the three bases determines the instruction. Most specify par-ticular amino acids. 147 coelom  A body cavity completely lined by tissue derived from mesoderm. 321 coenzyme  An organic cofactor; e.g., NAD. 81 coevolution  The joint evolution of two closely interacting species; macroevolutionary pattern in which each species is a selective agent for traits of the other. 259 cofactor  A metal ion or small non-protein organic molecule that associates with an enzyme and is necessary for its function. 81 cohesion  Property in which the molecules of a substance resist separating from one another. 35 cohort  Group of individuals born during the same interval. 358 colonial organism  Organism composed of many integrated cells, each capable of surviving and reproducing on its own. 278 colonial theory of animal origins Well-accepted hypothesis that animals evolved from a colonial protist.

319

commensalism  Species interaction that benefits one species and has no effect on the other. 374 community  All populations of all species living in a defined area. 4, 370 comparative morphology  The scientific study of similarities and differences in body plans. 221 complete digestive tract  Tubular digestive tract with two openings. 325 compound  Molecule that has atoms of more than one element. 33 compound eye  Eye that consists of many individual units, each with its own lens. 328 concentration  Amount of solute per unit volume of solution. 35 conifer  Woody gymnosperm with needlelike leaves.

302

conjugation  Mechanism of gene transfer in which one prokaryotic cell directly transfers a plasmid to another.

274

conservation biology  Field of applied biology that surveys biodiversity and seeks ways to maintain and use it. 411 consumer  Heterotroph. Organism that acquires carbon by feeding on the tissues, wastes, or remains of other organisms; most also acquire energy the same way. 7, 378 continuous variation  A range of small differences in forms of a trait. 189 contractile vacuole  In freshwater protists, an organelle that collects and expels excess water. 278 control group  In an experiment, a group of individuals identical to an experimental group except for the variable under investigation. 15 convergent evolution  Evolutionary pattern in which similar body parts evolve separately in different lineages. 234 coral reef  In tropical sunlit seas, a formation composed of the mineral secretions of coral polyps; serves as home to many other species. 406 covalent bond  Type of chemical bond in which two atoms share electrons. 33

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

424  GLOSSARY critical thinking  The act of evaluating information before accepting it. 12 crossing over  Process in which homologous chromosomes exchange corresponding segments during prophase I of meiosis. 175 crustaceans  Lineage of mostly marine arthropods with two pairs of antennae and at least five pairs of legs; for example, a shrimp, crab, lobster, or barnacle. 331 cuticle  Secreted covering at a body surface. 68, 295 cyanobacteria  Bacteria that carry out photosynthesis by the oxygen-producing noncyclic pathway. 273 cytoplasm  In a eukaryotic cell, collective term for everything between the cell’s plasma membrane and its nucleus. In a prokaryotic cell, everything enclosed by the plasma membrane. 54 cytoskeleton  Network of protein filaments that support, organize, and move eukaryotic cells and their internal structures. See microtubule, microfilament, intermediate filament. 66 cytosol  Jellylike mixture of water and solutes enclosed by a cell’s plasma membrane. 54 data  Factual information collected from experiments or observations of the natural world. 12 deciduous plant  Plant that sheds all its leaves in preparation for a seasonal dormancy. 302 decomposer  Organism that breaks down organic material into its inorganic subunits. 274, 378 deforestation  Removal of all trees from a forested area. 400 deletion  Type of mutation in which one or more nucleotides are lost from DNA. 153 demographic transition model  Model describing how human birth and death rates change as a region becomes industrialized. 364 denaturation  Loss of a protein’s three-dimensional shape. 47 density-dependent limiting factor  Factor whose negative effect on population growth is felt most in dense populations; for example, in-fectious disease or intraspecific competition. 357 density-independent limiting factor  Factor that limits growth in populations regardless of their density; for example, a natural disaster or harsh weather. 357 deoxyribonucleic acid  See DNA. desert  Biome with little precipitation; dominant plants are perennials adapted to withstand drought and annuals that complete their life cycle quickly after a rain. 403 desertification  Conversion of grassland or woodlands to desertlike conditions. 404 detritivore  Consumer that feeds on small bits of organic material (detritus). 378 deuterostomes  Animal lineage with a three-layer embryo in which the mouth is the second opening to form; includes echinoderms and chordates. 319 development  In multicelled species, the process by which the first cell of a new individual gives rise to an adult. 7 diatom  Single-celled nonmotile photosynthetic protist with brown accessory pigments and a two-part silica shell. 281 differentiation  Process in which cells become specialized during development; occurs as different cell lineages begin to use different subsets of their DNA. 127 diffusion  The spontaneous spreading of molecules or atoms through a fluid or gas. 85

dihybrid cross  Cross between two individuals identically heterozygous for alleles of two genes; e.g., AaBb × AaBb. 184 dinoflagellates  Single-celled, aquatic protists typically with cellulose plates and two flagella; may be heterotrophic or photosynthetic. 281 diploid  Having two of each type of chromosome characteristic of the species (2n). 132 directional selection  Pattern of natural selection in which a form of a trait at one end of a range of variation is adaptive. 244 disruptive selection  Pattern of natural selection in which forms of a trait at both ends of a range of variation are adaptive, and interme-diate forms are not. 244 divergent evolution  Evolutionary pattern in which lineages descended from a common ancestor diverge.

234

DNA  Deoxyribonucleic acid. Double-stranded nucleic acid that consists of deoxyribose-containing nucleotides. Carries hereditary information. 7, 49 DNA cloning  Set of methods that uses living cells to mass-produce targeted DNA fragments. 205 DNA fingerprinting  See DNA profiling. DNA library  Collection of cells that host different fragments of foreign DNA, often representing an organism’s entire genome. 207 DNA polymerase  Enzyme that carries out DNA synthesis during DNA replication; uses a DNA template to assemble a complementary strand of DNA. 132 DNA profiling  Identifying an individual by the unique parts of his or her DNA. 208 DNA replication  Process by which a cell duplicates its DNA before it divides. 132 DNA sequence  Order of nucleotides bases in a strand of DNA. 130 DNA sequencing  Method of determining DNA sequence. 207 dominant  Refers to an allele that masks the effect of a recessive allele on the homologous chromosome. Also used to describe a trait associated with a dominant allele. 183 double fertilization  Fertilization as it occurs in flowering plants. One sperm cell fuses with the egg to form the zygote; a second sperm cell fuses with the central cell, forming a triploid cell that gives rise to endosperm.

305

echinoderms  Invertebrates with a water-vascular system and an endoskeleton made of calcium carbonate plates and spines. 332 ECM  See extracellular matrix. ecological footprint  Area of Earth’s surface required to sustainably support a particular level of development and consumption. 364 ecological restoration  Actively altering an area in an effort to restore or create a functional ecosystem. 414 ecological succession  A gradual change in a community in which one array of species replaces another.

377

ecology  The study of interactions among organisms, and between organisms and their environment. 352 ecosystem  A community interacting with its environment. 4, 378 ectotherm  Animal that gains heat from the environment and adjusts its internal temperature by altering its behavior; commonly called “old-blooded. “339 electron  Negatively charged subatomic particle. 28

electron transfer chain  Array of membrane-bound enzymes and other molecules that accept and give up electrons in sequence, thus releasing the energy of the electrons in small, usable amounts. 82 electron transfer phosphorylation  Process by which electron flow through electron transfer chains sets up a hydrogen ion gradient that drives ATP formation. 100 electrophoresis  Laboratory technique that separates DNA fragments by size. 207 element  A pure substance that consists only of atoms with the same number of protons. 28 endangered species  A species that faces extinction in all or part of its range. 411 endemic species  A species that evolved in one place and is found nowhere else. 413 endocytosis  Process by which a cell takes in a small amount of extracellular fluid (and its contents) by the ballooning inward of the plasma membrane. 88 endoplasmic reticulum (ER) Membrane-enclosed organelle that consists of a continuous system of sacs and tubes extending from the nuclear envelope. Rough ER makes and modifies proteins; smooth ER makes phospholipids, stores calcium, and has additional functions in some cells. 65 endoskeleton  Internal skeleton; hard internal parts that muscles attach to and move. 332 endosperm  Nutritive tissue in the seeds of angiosperms (flowering plants). 305 endospore  Spore (resting structure) formed by some soil bacteria; contains a dormant cell and is highly resistant to adverse conditions. 276 endosymbiont hypothesis  Mitochondria and chloroplasts evolved from free-living bacteria that entered and lived inside another cell. 278 endotherm  Animal that maintains its body temperature by varying its production of metabolic heat; commonly called “arm-blooded.” 339 energy  The capacity to do work. 76 energy pyramid  Diagram that illustrates the energy flow in an ecosystem. 380 environmentalism  Advocacy for protection of the natural environment. 352 enzyme  Organic molecule (protein or RNA) that speeds up a reaction without being changed by it. 39 epigenetic  Refers to potentially heritable modifications to DNA that affect gene expression without changing the DNA sequence. 155 epiphyte  Plant that grows on the trunk or branches of another plant but does not withdraw nutrients from it. 298 equilibrial life history  Life history favored in stable environments; individuals grow large, then invest heavily in each of their few offspring; typical of K-selected species. 361 ER  See Endoplasmic reticulum. estuary  Highly productive, aquatic ecosystem where nutrient-rich water from a river mixes with seawater.

404

eudicots  Most diverse angiosperm lineage; characterized by two seed leaves; includes herbaceous plants, woody trees, and cacti. 307 eukaryotes  Organisms whose cells characteristically have a nucleus (protists, fungi, plants, and animals). 8 evaporation  Transition of a liquid to a vapor. 37

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GLOSSARY  425  evergreen plant  Plant that has leaves throughout the year. 302 evolution  Change in a line of descent. 222 exocytosis  Process by which a cell expels a vesicle’s contents to extracellular fluid. 88 exon  Gene segment that remains in an RNA after post-transcriptional modification. 145 exoskeleton  External skeleton; hard external parts that muscles attach to and move. 326 exotic species  A species that has been introduced to a new community and become established there. 378 experiment  Procedure designed to evaluate a prediction; typically yields data. 12 experimental group  In an experiment, a group of individuals who have a certain characteristic or receive a certain treatment. Tested side by side with a control group. 15 exponential model of population growth Model for population growth when resources are unlimited. The per capita growth rate remains constant as population size increases. 357 extinct  Refers to a species that no longer has living members. 259 extracellular matrix (ECM)  Complex mixture of substances secreted by a cell onto its surface; composition and function vary by cell type. 68 extreme halophile  Organism that lives in a highly salty habitat. 276 extreme thermophile  Organism that lives in a high temperature habitat. 276 facilitated diffusion  Passive transport mechanism in which a solute follows its concentration gradient across a membrane by moving through a transport protein. 87 fat  A triglyceride. See saturated fat, unsaturated fat. 42 fatty acid  Lipid that consists of a (hydrophilic) carboxyl group “ead”and a (hydrophobic) “ail. “See saturated fatty acid, unsaturated fatty acid. 41 feedback inhibition  Of a metabolic pathway, regulatory mechanism in which a reaction product slows or stops a pathway that produces it. 82 fermentation  Any of several anaerobic pathways that break down organic molecules (typically glucose) to produce ATP without the use of an electron transfer chain. 108 ferns  Most diverse lineage of seedless vascular plants.

298

first law of thermodynamics  Energy cannot be created or destroyed. 76 fitness  Degree of adaptation to an environment, as measured by an individual’s relative genetic contribution to future generations. 224 fixed  Refers to an allele for which all members of a population are homozygous. 250 flagellum  Plural, flagella. Long, slender cellular structure used for movement. 61 flatworm  Soft-bodied, bilaterally symmetrical invertebrate with organs but no coelom; for example, a planarian or tapeworm. 322 flower  Reproductive structure of a flowering plant.

302

fluid mosaic  Model of a cell membrane as a twodimensional fluid of mixed composition. 57 food chain  Sequence of steps by which energy moves from one trophic level to the next. 380 food web  System of cross-connecting food chains.

380

foraminiferan  Plural, foraminifera. Heterotrophic single-celled protist that secretes a calcium carbonate shell. 278 fossil  Physical evidence of an organism that lived in the ancient past. 224 founder effect  After a small group of individuals found a new population, allele frequencies in the new population differ from those in the original population.

250

free radical  Atom with an unpaired electron. Most are highly reactive and can damage biological molecules. 31 fruit  Mature ovary of a flowering plant, often with tissues derived from other parts of the flower; encloses a seed or seeds. 305 fungus  Plural, fungi. Single-celled or multicelled eukaryotic consumer that breaks down material outside itself, then absorbs nutrients released from the breakdown. 8, 307 gamete  Mature, haploid reproductive cell; e.g., an egg or a sperm. 175 gametophyte  Haploid gamete-forming body; the haploid generation in a plant life cycle. 295 gastropod  Mollusk that moves about on an enlarged “oot”at its lower surface; for example a snail. 325 gastrovascular cavity  In cnidarians and flatworms, a saclike cavity that functions in digestion and respiration. 322 gene  Unit of information encoded in the sequence of nucleotide basis in DNA; encodes an RNA or protein product. 142 gene expression  Multistep process of converting information in a gene into an RNA or protein product. See tran-scription, translation. 142 gene flow  The movement of alleles between populations. 252 gene pool  All alleles of all genes in a population; a pool of genetic resources. 244 gene therapy  Treating a genetic defect or disorder by transferring a gene into the affected individual. 215 genetic code  Complete set of sixty-four codons. 147 genetic drift  Change in allele frequency due to chance alone. 250 genetic engineering  Laboratory process by which deliberate changes are introduced into a genome, with the intent of modifying phe-notype. 210 genetically modified organism (GMO) Organism whose genome has been modified by genetic engineering. 210 genome  An organism’s complete set of genetic material. 205 genomics  The study of genome structure and function. 208 genotype  The particular set of alleles that occurs in an individual’s chromosomes. 183 genus  Plural, genera. A group of species that share a unique set of traits. First part of a species name. 10 geologic time scale  Chronology of Earth’s history; correlates rock layers with time. 230 germ layer  Embryonic tissue layer; endoderm, mesoderm, or ectoderm. 319 gland  See endocrine gland, exocrine gland. global climate change  Wide-ranging changes in rainfall patterns, average temperature, and other climate factors that result from rising concentrations of greenhouse gases. 390

glycolysis  Set of reactions that collectively convert one molecule of glucose to two molecules of pyruvate, two ATP, and two NADH. First part of fermentation and aerobic respiration. 108 GMO  See genetically modified organism. Golgi body  Organelle that modifies polypeptides and lipids, then sorts and packages the finished products into vesicles. Also called Golgi apparatus. 65 Gondwana  Supercontinent that existed before Pangaea, more than 500 million years ago. 230 green algae  Single-celled, colonial, or multicelled photosynthetic protists belonging to the group most closely related to land plants. 283 greenhouse effect  Warming of Earth’s lower atmosphere and surface as a result of heat trapped by greenhouse gases. 388 greenhouse gas  Atmospheric gas that helps keep heat from escaping into space and thus warms the Earth. 388 groundwater  Water between soil particles and in aquifers. 385 growth  Increases in the number, size, and volume of cells. 7 gymnosperm  Seed plant that produces “aked”seeds (seeds that are not encased within a fruit). 302 habitat  The type of place in which a species lives. 370 half-life  Characteristic time it takes for half of a quantity of a radioisotope to decay. 226 haploid  Having one of each type of chromosome characteristic of the species. 171 herbivory  An animal feeds on a plant, which may or may not die as a result. 374 hermaphrodite  Individual animal that makes both eggs and sperm. 322 heterotroph  Consumer. Organism that obtains carbon from organic compounds assembled by other organisms. 95 heterozygous  Describes a genotype in which homologous chromosomes have different alleles of a gene. 183 histone  Type of protein that associates with the DNA double helix; one of many proteins that structurally organize eukaryotic chro-mosomes. 130 HIV (human immunodeficiency virus) Enveloped RNA virus that causes AIDS. 287 homeostasis  Process in which cells and multicelled organisms keeps their internal conditions within tolerable ranges by sensing and responding appropriately to change. 7 hominins  Lineage of bipedal primates; includes humans and extinct humanlike species. 342 Homo erectus  Extinct human species with body proportions similar to modern humans; arose in and dispersed out of Africa; likely ancestor of Homo sapiens.

344

Homo habilis  Earliest named human species; had australopith-like proportions and is known only from Africa. 344 Homo neanderthalensis  Neanderthals. Closest extinct relatives of modern humans; had large brain, stocky body. 344 Homo sapiens  Modern humans; evolved in Africa by about 200,0 years ago, then expanded their range worldwide. 344

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

426  GLOSSARY homologous chromosomes  In a cell nucleus, chromosomes that have the same length, shape, and set of genes. 161 homologous structures  Body structures that may appear different in different lineages, but are derived from a common ancestral form. 234 homozygous  Describes a genotype in which homologous chromosomes have the same allele of a gene. 183 humans  Members of the genus Homo. 344 hydrogen bond  Attraction between a covalently bonded hydrogen atom and another atom taking part in a separate covalent bond. 35 hydrophilic  Describes a substance that dissolves easily in water. 35 hydrophobic  Describes a substance that resists dissolving in water. 35 hydrothermal vent  Underwater opening from which mineral-rich water heated by geothermal energy streams out. 268, 406 hypertonic  Describes a fluid that has a high overall solute concentration relative to another fluid. 85 hypha  A single filament in a fungal mycelium; consists of a chain of cells. 309 hypothesis  Testable explanation for a natural phenomenon. 12 hypotonic  Describes a fluid that has a low overall solute concentration relative to another fluid. 85 inbreeding  Mating among close relatives. 252 incomplete dominance  Inheritance pattern in which one allele is not fully dominant over another, so the heterozygous phenotype is an intermediate blend between the two homozygous phenotypes. 184 indicator species  A species that is particularly sensitive to environmental changes and can be monitored to assess the state of an eco-system. 413 inheritance  Transmission of DNA to offspring. 7 insects  Land-dwelling arthropods with a pair of antennae, three pairs of legs, and—in the most diverse groups—wings. 331 insertion  Type of mutation in which one or more nucleotides are inserted into DNA. 153 intermediate filament  Stable cytoskeletal element that structurally supports cells and tissues of animals and some protists. Different types are assembled from different fibrous proteins. 66 interphase  In a eukaryotic cell cycle, the interval between divisions during which the cell grows, roughly doubles the number of its cytoplasmic components, and replicates its DNA. 161 interspecific competition  Two species compete for a resource in an interaction harmful to both. 370 intraspecific competition  Competition among members of the same species. 357 intron  Gene segment that intervenes between exons and is removed from a new RNA during post-transcriptional modification. 145 invasive species  Exotic species that disrupts the structure of its adopted community. 378 invertebrate  Animal without a backbone. 317 ion  An atom or molecule that carries a net charge. 31 ionic bond  Type of chemical bond in which a strong mutual attraction links ions of opposite charge. 33 isotonic  Describes two fluids that have the same overall solute concentration. 85 isotopes  Forms of an element that differ in the number of neutrons. 28

jawless fish  Fish that has a skeleton of cartilage, but no jaws or paired fins; for example, a lamprey. 334 karyotype  Image of an individual’s complement of chromosomes arranged by size, length, shape, and centromere location. 132 key innovation  An evolutionary adaptation that gives its bearer the opportunity to exploit a particular environment more efficiently or in a new way. 259 keystone species  A species that has a disproportionately large effect on community structure. 378 kidney  Organ of the vertebrate urinary system; filters blood, adjusts its composition, and forms urine. 334 knockout  Technique of introducing a mutation that disables expression of a gene in an organism. 155 Krebs cycle  See citric acid cycle. lactate fermentation  Fermentation pathway that produces ATP and lactate. 114 lancelets  Invertebrate chordates that have a fishlike shape and retain their defining chordate traits into adulthood. 332 larva  In some animals, a sexually immature individual that has a different body form than the adult. 322 law of nature  Generalization describing a consistent natural phenomenon that has an incomplete scientific explanation. 21 lichen  Composite organism consisting of a fungus and a green alga or cyanobacterium. 313 life history traits  Characteristics related to growth, survival, and reproduction such as life span, age-specific mortality, age at first reproduction, and number of breeding events. 358 lignin  Compound that stiffens walls of some cells (including xylem) in vascular plants. 295 lineage  Line of descent. 222 lipid  Fatty, oily, or waxy organic compound; e.g., a triglyceride, steroid, or wax. 41 lipid bilayer  Double layer of phospholipids arranged tail-to-tail; structural foundation of all cell membranes.

42

lobe-finned fish  Bony fish that has bony supports inside its fins. 336 logistic model of population growth  Model for growth of a population limited by density-dependent factors; numbers increase exponentially at first, then the growth rate slows and population size levels off at carrying capacity. 357 lungs  Internal saclike organs inside which blood exchanges gases with the air; the respiratory organs in most land vertebrates and some fish. 334 lysosome  Enzyme-filled vesicle that breaks down particles such as cellular debris. 65 macroevolution  Patterns of evolutionary change in taxa above the species level; e.g., adaptive radiation, coevolution. 257 mammal  Vertebrate that nourishes its young with milk from mammary glands. 341 mantle  Skirtlike extension of tissue in mollusks; covers the mantle cavity and secretes the shell if one is present.

325

marsupial  Mammal in which offspring complete development in a pouch on the mother’s body. 341 mass extinction  Event in which many species in many habitats become extinct in the same interval. 411 mass number  Of an isotope, the total number of protons and neutrons in the atomic nucleus. 28

master regulator  Gene whose expression triggers a gene expression cascade that ultimately changes cells in a lineage from one type to other, more differentiated types. 153 medusa  Bell-shaped, free-swimming cnidarian body form. 322 megaspore  In seed plants, a haploid cell that gives rise to a female gametophyte. 300 meiosis  Nuclear division process that halves the chromosome number for forthcoming gametes. Basis of sexual reproduction. 171 messenger RNA (mRNA)  RNA that carries proteinbuilding instructions. 142 metabolic pathway  Series of enzyme-mediated reactions by which cells build, remodel, or break down an organic molecule. 82 metabolism  Collective term for all of the enzymemediated chemical reactions in a cell. 39 metamorphosis  Dramatic remodeling of body form during the transition from larva to adult. 328 metaphase  Stage of mitosis at which all chromosomes are aligned midway between spindle poles. 163 metastasis  The process in which cells of a malignant tumor spread from one part of the body to another. 167 methanogen  Organism that produces methane gas as a metabolic by-product. 276 microbiota  Collection of microorganisms that can live in a specific environment. 267 microevolution  Change in allele frequency. 244 microfilament  Cytoskeletal element of eukaryotes that reinforces cell membranes and functions in cell movement. Fiber of actin subunits. 66 microspore  In seed plants, a haploid cell that gives rise to a male gametophyte (pollen grain). 300 microtubule  Cytoskeletal element of eukaryotes that forms a dynamic scaffolding for many cellular processes involving movement. Hollow filament of tubulin subunits. 66 mimicry  Evolutionary process whereby two or more species come to resemble one another. 373 mitochondrion  Double-membraned organelle that produces ATP by aerobic respiration in eukaryotes. 63 mitosis  Nuclear division mechanism that maintains the chromosome number. Basis of body growth and tissue repair in multicelled eukaryotes; also asexual reproduction in some eukaryotes. Occurs in four stages: prophase, metaphase, anaphase, and telophase. 161 model  Analogous system in an experiment; tested in place of another subject. 12 molecule  Two or more atoms joined by chemical bonds. 4 mollusk  Invertebrate with a reduced coelom complete digestive system, and a mantle that, in some groups, secretes a shell. 325 monocots  Lineage of angiosperms that includes grasses, orchids, and palms. 307 monohybrid cross  Cross between two individuals identically heterozygous for alleles of one gene; for example Aa × Aa. 184 monomer  Molecule that is a subunit of polymers. 39 monotreme  Egg-laying mammal. 341 morphological convergence  See convergent evolution. morphological divergence  See divergent evolution.

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GLOSSARY  427  motor protein  Type of energy-using protein that interacts with cytoskeletal elements to move the cell’s parts or the whole cell. 66 mRNA  See messenger RNA. multicellular organism  Organism composed of a variety of specialized cells, each unable to survive and reproduce on its own. 278 mutation  Permanent change in the DNA sequence of a chromosome. See base-pair substitution, deletion, insertion. 135 mutualism  Species interaction that benefits both species. 311, 377 mycelium  Plural, mycelia. Mass of threadlike filaments (hyphae) that compose the body of a multicelled fungus. 311 mycorrhiza  Plural, mycorrhizae. Fungus”lant root partnership. 311 natural selection  Differential survival and reproduction of individuals of a population based on differences in shared, heritable traits. Driven by environmental pressures. 224 neutron  Uncharged subatomic particle that occurs in the atomic nucleus. 28 niche  The role of a species in its community; the conditions it requires and the interactions it takes part in. 370 nitrogen cycle  Movement of nitrogen among the atmosphere, soil, and water, and into and out of food webs. 385 nitrogen fixation  Process of combining nitrogen gas with hydrogen to form ammonia. 274, 385 nondisjunction  Failure of chromosomes to separate properly during mitosis or meiosis. 196 nonvascular plants  Plant lineages that lack xylem and phloem; for example, the mosses. All have flagellated sperm and disperse by releasing spores. 296 notochord  Stiff rod of connective tissue that runs the length of the body in chordate larvae or embryos. 332 nuclear envelope  A double membrane that constitutes the outer boundary of the nucleus. Nuclear pores in the membrane control the entry and exit of large molecules. 63 nucleic acid  Molecule that consists of one or more strands of nucleotides; DNA or RNA. 49 nucleotide  Small organic molecule with a deoxyribose or ribose sugar, a nitrogen-containing base, and one, two, or three phosphate groups; e.g., adenine, guanine, cytosine, thymine, uracil. 49 nucleus  Of an atom; core area occupied by protons and (in most atoms) neutrons. Of a eukaryotic cell; organelle with a double membrane that holds, protects, and controls access to the cell’s DNA. 28, 54 nutrient  A substance that an organism must acquire from the environment to support growth and survival. 7 oncogene  Gene that can transform a normal cell into a tumor cell. Carries a mutation that results in the inappropriate stimulation of mitosis. 165 open circulatory system  Circulatory system in which the circulatory fluid leaves open-ended vessels and flows among tissues before returning to the heart.

325

opportunistic life history  Life history favored in unpredictable environments; individuals reproduce while young and invest a small amount in each of many offspring; typical of r-selected species. 361

organ  In multicelled organisms, a structure that consists of tissues engaged in a collective task. 4 organ system  In multicelled organisms, a set of interacting organs and tissues that carry out one or more body functions. 4 organelle  Structure that carries out a specialized function inside a cell; e.g., a nucleus, mitochondrion, or ribosome. 54 organic  Describes a compound that consists mainly of carbon and hydrogen atoms. 39 organism  Individual that consists of one or more cells. 4 osmosis  Diffusion of water across a selectively permeable membrane; occurs when there is a difference in solute concentration between the fluids on either side of the membrane. 85 ovary  In flowering plants, the enlarged base of a carpel, inside which one or more ovules form. In animals, the egg-producing female gonad. 305 ovule  In a seed-bearing plant, structure in an ovary that gives rise to an egg-containing gametophyte. Develops into a seed after fer-tilization. 300 ozone layer  Atmospheric layer with a high concentration of ozone that prevents much UV radiation from reaching Earth’s surface. 273, 408 Pangaea  Supercontinent that began to form about 300 million years ago and broke up 100 million years later.

229

parasitism  A species withdraws nutrients from another species (its host), usually without killing it. 374 parasitoid  An insect that lays eggs in or on another insect, and whose young devour their host from the inside. 374 passive transport  Membrane-crossing mechanism that requires no energy input. 87 pathogen  Disease-causing agent. 267 PCR  Polymerase chain reaction. Technique that rapidly amplifies (generates many copies of) a specific section of DNA. 207 pedigree  Chart that marks the appearance of a phenotype through generations of a family tree. 190 peptide bond  A covalent bond between the amine group of one amino acid and the carboxyl group of another. Joins amino acids in peptide and polypeptide chains. 44 per capita growth rate  The number of individuals added during some interval divided by the initial population size. 354 permafrost  Layer of permanently frozen soil in the Arctic. 404 pH  Measure of the amount of hydrogen ions in a fluid.

37

phagocytosis  “ell eating” an endocytic pathway by which a cell engulfs a large particle such as another cell.

88

phenotype  An individual’s observable traits. 183 phloem  Complex vascular tissue of plants; its living sieve elements compose sieve tubes that distribute sugars through the plant. Con-sists of sieve-tube members and companion cells. 295 phospholipid  Lipid with two (hydrophobic) fatty acid tails and a (hydrophilic) head that contains a phosphate group. Main constituent of eukaryotic cell membranes.

42

phosphorus cycle  Movement of phosphorus among rocks, water, soil, and living organisms. 385

phosphorylation  Chemical reaction in which an enzyme attaches a phosphate group to an organic molecule. 82 photosynthesis  Metabolic pathway by which most autotrophs use light energy to make sugars from carbon dioxide and water. 7, 95 phylogeny  Evolutionary history of a species or group of species. 260 pigment  Organic molecule that can absorb light of certain wavelengths. Wavelengths that are not absorbed impart a characteristic color. 97 pilus  Plural, pili. Protein filament that projects from the surface of some prokaryotic cells. 61 pioneer species  Species that can colonize a new habitat. 377 placental mammal  Mammal in which developing offspring are nourished within the mother’s body by way of a placenta. 341 plankton  Community of mostly microscopic drifting or swimming organisms. 278 plant  A multicelled eukaryotic producer; most are photosynthetic and live on land. Develops from an embryo that forms on the parent and is nourished by it. 8, 295 plasma membrane  Membrane that encloses a cell and separates it from the external environment. 54 plasmid  Of many prokaryotes, a small ring of nonchromosomal DNA. 274 plasmodial slime mold  Heterotrophic protist that moves and feeds as a multinucleated mass; forms a spore-producing fruiting body when conditions are unfavorable. 284 plate tectonics theory  Theory that Earth’s outermost layer of rock is cracked into plates, the slow movement of which conveys continents to new locations over geologic time. 229 pleiotropy  Inheritance pattern in which a single gene affects multiple traits. 186 polarity  Separation of charge into positive and negative regions. 33 pollen grain  Immature male gametophyte of a seed plant. 295 pollen sac  Of seed plants, chamber in which microspores form and develop into male gametophytes (pollen grains). 300 pollination  Delivery of a pollen grain to the egg-bearing part of a seed plant. 300 pollinator  Animal pollination vector. Facilitates pollination by moving pollen from one plant to another.

305

pollutant  A natural or man-made substance that is released into the environment in greater than natural amounts and that damages the health of organisms. 406 polygenic inheritance  Pattern of inheritance in which multiple genes affect one trait. 186 polymer  Molecule that consists of multiple monomers. 39 polymerase chain reaction  See PCR. polyp  In cnidarians, a tubular, typically sessile, body form. 322 polyploidy  Condition of having three or more of each type of chromosome characteristic of the species. 196 population  A group of organisms of the same species who live in a specific location and breed with one another more often than they breed with members of other populations. 4, 351

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

428  GLOSSARY population bottleneck  Reduction in population size so severe that it reduces genetic diversity. 250 population density  Number of members of a population in a given area. 352 population distribution  The way in which members of a population are dispersed in their environment. 352 population size  Number of individuals in a population. 352 potential energy  Energy stored in the arrangement of objects in a system. 76 prairie  Temperate grassland biome of North America. Its grasses and other plants are adapted to recover after grazing and the occa-sional fire. 403 predation  One species (the predator) captures, kills, and feeds on another (its prey). 373 prediction  Statement, based on a hypothesis, about a condition that should reasonably occur if the hypothesis is correct. 12 primary production  The energy captured by an ecosystem’s producers. 380 primary succession  Ecological succession that occurs in an area where there was previously no soil.

377

primate  Mammalian group with grasping hands; includes lemurs, tarsiers, monkeys, apes, and humans.

342

primer  Short, single strand of DNA or RNA that serves as an attachment point for DNA polymerase. 132 principle of competitive exclusion  Species that require the same limited resources and access them in the same way cannot coexist indefi-nitely in an environment. 373 prion  Infectious protein. 47 probability  Out of all possible outcomes of an event, the chance that a particular outcome will occur. 18 probe  Short fragment of DNA labeled with a tracer; designed to hybridize with a nucleotide sequence of interest. 207 producer  Autotroph. Organism that makes its own food using energy and nonbiological raw materials from the environment. 7, 378 product  A molecule that is produced by a chemical reaction. 76 prokaryotes  Informal name for single-celled organisms with no nucleus (bacteria and archaea). 8 promoter  In DNA, special sequence of nucleotide bases that functions as a binding site for RNA polymerase; site where transcription begins. 145 prophase  Stage of mitosis during which chromosomes condense and become attached to a newly forming spindle. 163 protein  Organic molecule that consists of one or more amino acid chains folded into a specific shape. 44 protist  General term for eukaryote that is not a fungus, plant, or animal. 8, 278 protocell  Membranous sac that contains interacting organic molecules; hypothesized to have formed prior to the earliest cells. 270 proton  Positively charged subatomic particle that occurs in the nucleus of all atoms. 28 protostomes  Animal lineage with a three-layer embryo in which the first opening to form is the mouth; includes flatworms, annelids, mollusks, roundworms, and arthropods. 319

pseudopod  A temporary protrusion from a eukaryotic cell that helps it move or engulf prey. 68 pseudoscience  Claims, arguments, or methods that are presented as science, but do not follow scientific principles. 21 Punnett square  Diagram used to predict the genotypic and phenotypic outcomes of a cross. 183 radial symmetry  Having parts arranged around a central axis, like spokes around a wheel. 319 radioactive decay  Process in which atoms of a radioisotope emit energy and subatomic particles when their nucleus spontaneously breaks up. 28 radioisotope  An isotope with an unstable nucleus. 28 radiometric dating  Method of estimating the age of a rock or fossil by measuring the content and proportions of a radioisotope and its daughter elements. 229 radula  Tonguelike organ of many mollusks. 325 rain shadow  Dry region on the downwind side of a coastal mountain range. 403 range  Of a species, the total geographic area where its members live. 352 ray-finned fish  Bony fish with fins supported by thin rays derived from skin. 336 reactant  A molecule that enters a reaction and is changed by participating in it. 76 reaction  Process of molecular change. 39 receptor protein  Membrane protein that triggers a change in cell activity in response to a stimulus such as a hormone binding to it. 59 recessive  Refers to an allele with an effect that is masked by a dominant allele on the homologous chromosome. Also used to describe a trait associated with a recessive allele. 183 recombinant DNA  A hybrid DNA molecule; contains genetic material from more than one organism.

205

red alga  Single-celled or multicelled photosynthetic protist with a red accessory pigment. 281 reproduction  Processes by which organisms produce offspring. See sexual reproduction, asexual reproduction. 7 reproductive isolation  The end of gene flow between populations. 252 reptile  Amniote clade that includes modern lizards, snakes, turtles, crocodilians, and birds, as well as some extinct groups such as dinosaurs. 339 resource partitioning  Evolutionary process whereby traits of competing species come to differ as a result of the selective pressure imposed by the competition between them. 373 restriction enzyme  Type of enzyme that cuts DNA at a specific nucleotide sequence. 205 rhizoids  Threadlike structures that hold a moss gametophyte in place. 296 rhizome  Stem that grows horizontally along or just below the ground. 298 ribonucleic acid  See RNA. ribosomal RNA (rRNA)  RNA component of ribosomes. 142 ribosome  Organelle of protein synthesis. An intact ribosome has two subunits, each composed of rRNA and proteins. 54 RNA  Ribonucleic acid. Nucleic acid that consists of ribose-containing nucleotides; most types are singlestranded. See messenger RNA, transfer RNA, ribosomal RNA. 49

RNA polymerase  Enzyme that carries out transcription (RNA synthesis). 145 RNA world hypothesis  Hypothesis that RNA served as the first material of inheritance. 270 roundworm  Unsegmented worm with a pseudocoelom and a cuticle that is molted as the animal grows.

326

rRNA  See ribosomal RNA. rubisco  Carbon-fixing enzyme of the Calvin–Benson cycle. 103 sac fungus  Fungus that produces spores by meiosis in saclike cells. 309 salt  Ionic compound that releases ions other than H+ and OH– when it dissolves in water. 35 sampling error  Difference between results obtained from a subset, and results obtained from the whole. 18 saturated fat  Triglyceride with three saturated fatty acid tails. 42 saturated fatty acid  Fatty acid with only single bonds linking the carbons in its tail. 42 savanna  Tropical biome dominated by grasses and other plants adapted to grazing, as well as a scattering of shrubs. 403 scales  Hard, flattened elements that cover the skin of reptiles and some fishes. 334 science  Systematic study of the observable world. 12 scientific method  Making hypotheses, evaluating predictions that flow from them, and forming conclusions based on the resulting data. 15 scientific theory  A hypothesis that stands after many years of systematic testing, is consistent with existing evidence, and is useful for making predictions about a wide range of phenomena. 21 SCNT  See somatic cell nuclear transfer. seamount  An undersea mountain. 406 second law of thermodynamics  Energy tends to disperse spontaneously. 76 secondary succession  Ecological succession occurs in an area where a community previously existed and soil remains. 377 seed  Mature ovule of a seed-bearing plant. Embryo sporophyte packaged with nutritive tissue inside a protective coat. 295 seed plant  Vascular plant that produces seeds; an angiosperm or gymnosperm. 295 sequencing  See DNA sequencing. sex chromosome  Chromosome involved in determining anatomical sex; member of a pair of chromosomes that differs between males and females. 132 sexual reproduction  Reproductive mode by which offspring arise from two parents and inherit genes from both. 171 sexual selection  Type of natural selection in which some individuals in a population outreproduce others because they are better at securing mates. 248 shell model  Conceptual diagram of electron distribution in an atom. 31 short tandem repeat  In chromosomal DNA, region in which a sequence of a few nucleotides is repeated multiple times in a row. 189 single-nucleotide polymorphism  See SNP. sister chromatids  Of a duplicated eukaryotic chromosome, the two identical DNA molecules attached to one another at the centromere. 130

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GLOSSARY  429  SNP  Single-nucleotide polymorphism. A one-nucleotide DNA sequence variation carried by a measurable percentage of a population. 203 solute  A dissolved substance. 35 solution  Uniform mixture of solute completely dissolved in a solvent. 35 solvent  Liquid in which other substances dissolve. 35 somatic cell nuclear transfer (SCNT)  Reproduc­tive cloning method in which the nucleus of an unfertilized egg is replaced with the DNA of a donor’s body cell.

127

sorus  Plural, sori. Cluster of spore-forming chambers on a fern frond. 298 speciation  Emergence of a new species. See allopatric speciation, sympatric speciation. 252 species  Unique type of organism. Of sexual reproducers, often defined as one or more groups of individuals that can potentially interbreed, produce fertile offspring, and do not interbreed with other groups. Designated by genus name and specific epithet. 3 species diversity  The number of species and their relative abundance within a community. 370 spindle  Temporary structure that moves chromosomes during nuclear division; consists of microtubules that elongate from two spin-dle poles. 163 sponge  Aquatic invertebrate that has no tissues or organs and filters food from the water. 321 sporophyte  Diploid spore-forming body that forms in a plant life cycle. 295 stabilizing selection  Pattern of natural selection in which an intermediate form of a trait is adaptive, and extreme forms are not. 244 stamen  Floral reproductive organ that consists of an anther and filament. 305 statistically significant  Refers to a result that is statistically very unlikely to have occurred by chance alone. 18 steroid  A type of lipid with four carbon rings and no fatty acid tails. 42 stigma  Of a flower, upper part of a carpel; specialized for receiving pollen. 305 stomata  Singular, stoma. Closable gaps formed by pairs of guard cells on aboveground plant surfaces. When open, they allow the plant to exchange gases with air. When closed, they limit water loss. 97, 295 stroma  Cytosol-like fluid between the thylakoid membrane and the two outer membranes of a chloroplast. 97 stromatolites  Dome-shaped structures composed of layers of prokaryotic cells and sediments; form in shallow seas. 273 style  Elongated portion of a carpel that elevates the stigma above the ovary. 305 substrate  Of an enzyme, specific molecule that can bind to the enzyme’s active site and be converted to a product. A reactant in an enzyme-mediated reaction. 81 surface-to-volume ratio  A relationship in which the volume of an object increases with the cube of the diameter, and the surface area in-creases with the square. Limits cell size. 54 survivorship curve  Graph showing the decline in numbers of a cohort over time. 358 symbiosis  Interspecific interaction in which two species have a permanent or long-lasting, physically close association. 374

sympatric speciation  Speciation pattern in which genetic divergence within a population leads to reproductive isolation; occurs in the absence of a physical barrier to gene flow. 257 T lymphocyte  See T cell. taiga  See boreal forest. taxon  Plural, taxa. A rank in the classification of life; consists of a group of organisms that share a unique set of traits. E.g., domain, kingdom, phylum, class, order, family, genus, species. 10 taxonomy  Practice of naming, describing, and classifying species. 10 telophase  Stage of mitosis during which chromosomes arrive at the spindle poles and become enclosed by a new nuclear envelope. 163 temperate deciduous forest  Biome dominated by broad-leaved trees that flower and grow in warm summers, then drop their leaves and become dormant during cold winters. 400 temperature  Measure of molecular motion. 35 tetrapod  Vertebrate that has four limbs or is descended from a four-limbed ancestor. 334 theory  See scientific theory. threatened species  A species likely to become endangered in the near future. 411 thylakoid membrane  Inner membrane system of chloroplasts and cyanobacteria; site of light-dependent reactions of photosynthesis. 95 tissue  In multicelled organisms, collection of specialized cells organized in a way that allows them to perform a collective function. 4 total fertility rate  Average number of children born to females of a population over the course of their lifetimes. 364 tracer  A substance that can be traced via its detectable component. 28 trait  An inherited characteristic of an organism or species. 10 transcription  RNA synthesis; process in which a gene is copied into RNA form. 142 transcription factor  Regulatory protein that influences transcription by binding directly to DNA. 153 transduction  Mechanism of gene transfer in which a virus moves genes from one host cell to another. 274 transfer RNA (tRNA)  RNA that delivers amino acids to a ribosome during translation. 142 transformation  Mechanism of gene transfer in which a prokaryotic cell takes up and uses DNA from its environment. 274 transgenic  Refers to a genetically modified organism that carries a gene from a different species. 210 translation  Process by which a polypeptide chain is assembled according to the protein-building information in an mRNA. 142 transpiration  Evaporation of water from a plant’s aboveground parts. 383 transport protein  Membrane protein that passively or actively helps specific ions or molecules move across the membrane. 59 triglyceride  A lipid with three fatty acid tails bonded to a glycerol; a fat. 42 tRNA  See transfer RNA. trophic level  Position an organism occupies in terms of feeding relationships within an ecosystem. 380

tropical rain forest  Multilayered forest biome that occurs where warm temperatures and continual rains allow plant growth year-round. Most productive and species-rich biome. 399 tumor  A mass of abnormally dividing cells in a tissue. 165 tundra  Northernmost biome, dominated by low plants that grow over a layer of permafrost. 404 tunicates  Invertebrate chordates that lose their defining chordate traits during the transition to adulthood; adults have a secreted “unic. “332 turgor pressure  Pressure that a fluid exerts against a cell wall, membrane, or other structure that contains it. 87 unsaturated fat  Triglyceride molecule with one or more unsaturated fatty acid tails. 42 unsaturated fatty acid  Fatty acid that has at least one double bond between carbons making up its tail. 42 variable  In an experiment, a characteristic or event that differs among individuals or over time. 12 vascular plant  A plant that has xylem and phloem.

295

vector  In DNA cloning, a virus or molecule that can accept foreign DNA and be replicated inside a host cell. 205 vertebral column Backbone. 334 vertebrate  Animal with a backbone. 317, 334 vesicle  Saclike organelle that stores, transports, or breaks down its contents. 65 viral envelope  Outermost layer of an enveloped virus; consists of cell membrane from the host cell in which the virus was produced. 287 viral reassortment  Two viruses of the same type infect an individual at the same time and swap genes.

289

virus  A noncellular infectious particle with a protein coat and a genome of RNA or DNA; replicates only in living cells. 287 warning coloration  Distinctive color or pattern that makes a well-defended prey species easy to recognize.

373

water cycle  Water moves from the ocean into the air, falls as rain and snow, and flows back to the ocean. 383 water-vascular system  Of echinoderms, a system of fluid-filled tubes and tube feet that function in locomotion. 332 wavelength  Distance between the crests of two successive waves. 97 wax  Firm, water-repellent substance that is a complex, varying mixture of lipids. 44 wood  Lignin-stiffened accumulated secondary xylem of some seed plants. 300 xylem  Complex vascular tissue of plants; its dead tracheids and vessel elements form tubes that distribute water and dissolved nu-trients from roots to shoots. 295 zygote  Diploid cell that forms when two gametes fuse; the first cell of a new individual. 175 zygote fungus  Fungus that usually grows as a mold; sexual reproduction yields a thick-walled zygospore.

309

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INDEX The letter f designates figure; t designates table; bold designates key terms; n indicates human health applications; n indicates environmental topics.

A ABA. See Abscisic acid Abdomen, insect, 327f, 327, 329, 329f, 330f ABO gene, 186, 186f, 243 Accessory pigments, 98, 98f, 99 Acetyl-CoA, 108f, 108, 110f, 111, 112f, 116–118, 117f, 120f n Achondroplasia, 192–193, 192t, 192f Acid(s), 36f, 37 n Acid rain, 408–409, 409f Actin, 66, 67f Activation energy, 78, 79f and enzymes, 80, 81f Active sites, 80, 80f, 81f Active transport, 87, 88f n Acute lymphocytic leukemia, 214f Adaptation(s), evolutionary, 224. for flight, 235, 340 to dry climate, 235, 302, 403 to fire, 378 to life as parasite, 374–375 to life in trees, by primates, 342, 342f to life on land, 295f, 327, 336 to marine ecosystems, 406 to periodic disturbance, 378 phenotypic plasticity and, 188–189, 188f to predation, 373 selection pressure and, 241, 243, 246–248 to upright walking, 344, 448 Adaptive radiation, 258–259, 258f during Cambrian, 320–321 of dinosaurs, 339 of jawed vertebrates, 334 Adaptive trait, 238. See Adaptation, evolutionary Adenine (A), 128, 130, 128f, 142–144, 145, 150, 151f Adenosine diphosphate. See ADP. Adenosine triphosphate. See ATP ADH (alcohol dehydrogenase), 75, 75f Adhering junctions, 68 Adhesion proteins, 58, 58f, 285 ADP (adenosine diphosphate), 82, 82f, 88f, 100, 101f, 102f, 104f, 109, 109f Aerobic, 107 Aerobic respiration, 107, 108, 108f and ATP production, 116, 117f and carbon cycle, 387, 387f energy release in, 79 equation for, 113–114 evolution of, 273 African milk barrel plant, 221f, 235f n African sleeping sickness, 283 Age structure, of population, 354, 364, 364f n Aging and telomeres, 168 Agriculture. See also Food crops

and antibiotic use on animals, 241–242, 241f and population growth, 363 n AIDS (acquired immune deficiency syndrome), 214, 286–287, 311, 317. See also HIV Air circulation patterns, 396, 396f n Air pollution and acid rain, 408–409, 409f fossil fuels and, 93, 408, 409 and selection pressure, 246–247 n Albinism, 193t, 194 Albumin, 86 n Alcoholic drinks, 75, 188 Alcoholic fermentation, 114f, 114 beer and wine production, 114, 114f bread production, 114 ALDH, 82–83 n Algal blooms, 386, 386f Allantois, 340f Allele(s), 169–171, 169f, 180–182, 182f dominant, 182, 182f fixed, 250 meiosis and, 174, 174f, 183, 183f, 184–185 multiple, maintaining, 249–250, 250f mutations and, 243, 243t in populations, 242–244 recessive, 182, 182f Allele frequency, 244 Alligators, 339 Allopatric speciation, 255, 255f Alpha globin, 151, 151f Alternation of generations, 294, 294f Alternative splicing, 145, 145f, 152, 152f n Alzheimer’s disease, 196, 203 American diet, 27 Amino acid(s), 44, 45f digestion of, 117f, 117–118 and genetic code, 146, 146f sequence, in protein comparisons, 236, 236f in translation, 146–148, 147f, 148f n Amish communities, 252, 252f n Amniocentesis, 199, 199f Amniotes, 334, 334f, 338–341 Amniotic egg, 334, 334f, 338, 338f, 340, 340f Amoeba, 68, 279f, 281, 281f Amoeba proteus, 281, 281f Amphibians, 336–337, 337f n declining populations, 337–338 n Amyloid fibrils, 47f, 48, 196 Anaerobic, 108 Analogous structures, 235, 235f Anaphase, 160f, 162f, 163, 164 Anaphase I, 172, 172f Anaphase II, 173, 173f n Androgen insensitivity syndrome, 194t n Anemias

mutations and, 151–152, 152f Anemonefish, 376f, 376 n Aneuploidy, 196, 198 Angiosperms, 294f, 296, 303–306 evolutionary success of, 305 flower structure and function, 303–304, 304f n human uses, 306 life cycle, 304–305, 304f major groups, 305 Animal(s), 8, 9f, 318 cells, cytoplasmic division in, 164, 164f evolution of, 318–320, 319f vs. fungi, 307t fur color in, 186, 186f, 188f, 189f n genetically modified, 212–213, 212f, 213f life cycle, 172f major groups, 318–320, 319f meiosis in, 174 mitosis in, 162f origin of, 318 vs. plants, 307t as pollinators, 305, 305f seasonal behavior in, 189 Annelids, 319f, 320, 320f, 324, 324f Ant(s) coevolution in, 259, 259f n red imported fire ants, 369, 369f, 379, 412 Antarctic ice, atmospheric record trapped in, 93, 93f Antennae, 327f, 328, 329, 330f, 330 Antennapedia, 237 Anther, 180, 181f, 304, 304f n Anthrax, 276 Anthropoids, 342f, 343 Antibiotic-resistant bacteria evolution of, 241 n Antibiotics and human population growth, 364 resistance to, 241–242, 241f uses of, 241–242, 241f Anticodon(s), 147–148, 148f n Antiviral drugs, 287 Apes, 343, 343f Apicomplexans, 279f, 283 Apolipoproteins, 46, 46f, 203 AquAdvantage Salmon, 212 Aquatic ecosystems, 405–407, 405f, 406f coral reefs, 406, 406f lakes, 405, 405f nearshore marine ecosystems, 405–406, 406f open ocean and seafloor, 406–407 streams and rivers, 405 n Aquifers, 384 Arachnids, 328–330, 329f Arber, Werner, 204

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INDEX  431  Archaea, 8, 8f, 61f, 271, 276–277 cell membrane of, 58 in extreme habitats, 61f, 84, 84f gene exchange in, 274, 274f genetic code and, 146 metabolism, 277, 277f origin of, 277–278 reproduction, 274, 274f structure, general, 59–61, 60f, 273–274, 273f Arctic tundra, 398f, 404, 404f Areolar connective tissue, 424, 425f Aristotle, 221, 221f Armadillo, 223–224, 223f Armillaria, 310 Arthropod(s), 68, 319f, 327, 328f, 326–331 Artificial embryo splitting, 126 Asexual reproduction, 161, 170, 170f in bryophytes, 296 and population distribution, 352 in seedless vascular plants, 298 vs. sexual reproduction, 170–171, 170f, 170t n Aspirin, 306 Asteroid impacts, 219, 219f, 226, 226f, 340 n Atherosclerosis, 27 n Athlete’s foot, 311 Atmosphere. See also Greenhouse effect n carbon dioxide levels in, 93, 93f, 388, 388f early, 269, 269f, 273 Atom(s), 4, 28–31, 28f electrons in, 29–31, 30f, 31f Atomic apartment building, 30 Atomic number, 28, 28f Atomic theory, 20, 20t ATP (adenosine triphosphate), 48, 48f, 82, 82f in active transport, 67, 87, 88f in aerobic respiration, 108, 109–113, 110f, 112f,  116 in fermentation, 113–115 muscle production of, 115, 115f in photosynthesis, 95, 100, 101f, 102f as special coenzyme, 82, 82f Australopiths, 344, 344f n Autism, 107, 191, 213, 213f n Autosomal dominant disorders, 192–193, 192f, 192t n Autosomal recessive disorders, 193–194, 193f, 193t Autosome, 132 Autotroph, 95, 95f Avery, Oswald, 124 AZT, 317

B Baboons, 343, 343f Bacillus, 274 Bacteria, 8, 8f, 271, 273–277 n antibiotic resistance in, 241–242, 241f, 276 ecology and diversity, 275 n as food contaminant, 53, 241 gene exchange in, 274, 274f genetically modified, 211, 211f genetic code and, 146 and human health, 275–276 intestinal, 41, 53, 61f, 267f, 375

lactate-fermenting, 115, 115f, 275, 275f nitrogen-fixing, 275, 376, 385, 385f and nutrient cycling, 275 n as pathogens, 53, 187, 187f, 241–242, 241f, 276, 276t as producers, 275 reproduction, 274, 274f research and industrial uses, 211, 275, 275f structure, general, 59–61, 60f, 273–274, 273f Bacteriophage, 125, 125f, 126, 287–288, 288f Balanced polymorphism, 249, 249f Ball and stick models, 38, 38f Barnacles, 330, 330f Barr body, 154, 154f Basement membrane, 68, 68f, 69f Base, 37 in nucleotides, 48, 48f, 128, 128f Base-pairing, 130, 130f codons and anticodons, 147–148 in DNA replication, 130, 133, 143, 143f RNA and DNA, 143, 144, 144f mismatches, and mutations, 134, 134f Base pair substitution, 151–152, 151f, 152f. See also Mutation(s) Bats, 235, 235f, 305, 311, 311f, 341 Bayliss, Julian, 3 Beagle (ship), 223–224, 223f Beak bird, 340 turtle, 340 n Bedbugs, 331, 331f Beer, 114, 114f Bees honey and, 44 as pollinators, 254, 254f, 331f Varroa mites and, 611–612, 611f warning coloration, 373, 373f Beetles, 251f, 331, 331f Behavioral isolation, 254, 254f Bell curve, 190, 190f Betacarotene (β-carotene), 98, 98f, 211 Beta globin, 151, 151f, 152, 152f n Beta thalassemia, 151f, 152, 170 Bias, 19, 197 Bicarbonate, 37, 387 Bicarbonate buffer system, 37 Big bang theory, 20t Bilateral symmetry, 319, 319f Bilophila wadsworthia, 267f Binary fission, 274, 274f n Binge drinking, 75 n Biodiversity, 8, 261–262, 411–415 hot spots, 414, 414f n medicine and, 413 Biofilm, 61, 61f, 84f, 477 n Biofuels, 282 Biogeochemical cycles, 383, 383f Biogeography, 221 n Biological magnification, 382, 382f n Biological pest control, 375, 375f Biological species concept, 12 Biology, 3 research specializations, 14t, 15 Bioluminescence, 74f, 82f, 280 Biome(s) desert, 403, 403f

fire-adapted, 402–403, 402f forest, 399–402, 399f, 401f tundra, 404, 404f Biosphere, 5, 396 n human impact on, 5, 93 n Biotic potential, 359 Bipedalism, 343 Bird(s), 340, 340f chromosomes, 132 circulatory system, 453, 453f evolution of, 234f, 235, 235f as pollinators, 305 as reptiles, 261, 338, 339 Bird flu. See H5N1 flu n Birth defects, 289 n Bisphenol A (BPA), 175, 175f Bivalves, 325, 325f Black-bellied seedcrackers, 248, 248f Blair, Tony, 208 Blood n cholesterol levels, 27, 46, 46f clotting of, 195, 245 n disorders of, 151–152, 152f, 195, 249–250, 283, 283f glucose levels, regulation of, 116 pH of, 37 Blood flukes, 324 Blood type, 186, 186f, 243 B lymphocytes. See B cells Body cavities, 320, 320f Body plans, animal, 320–321, 320f Boivin, André, 126 Bond(s), 32–33. See also Chemical bond; Covalent bond; Hydrogen bond; Ionic bond polarity, comparing, 33, 33f Boneless lean beef trimmings, 53 Bonobos, 343 Bony fishes, 335f, 336, 336f Boreal forest, 399f, 400 Bottleneck. See Population bottleneck Botulism, 276t n Bovine spongiform encephalitis (BSE), 47 n BPA (Bisphenol A), 175, 175f Brain earthworm, 324, 324f primate, 342 Brazil, deforestation in, 401 n BRCA genes, 166 BRCA1, 166, 191 Bread, fermentation and, 114 Bread molds, 312f n Breast cancer, 165f gene, discovering, 191 Bromadiolone, 246, 246f Brood parasites, 375, 375f Brown algae, 279f, 281, 281f Bryophytes, 296 n BSE. See Bovine spongiform encephalitis Buffer, 37 Burning (combustion), 78, 79f, 83 Butterfly coevolution in, 259, 259f defenses of, 16, 16f metamorphosis, 330, 331f

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432  INDEX

C Cacti, 221f, 235, 235f, 306, 403, 403f Caenorhabditis elegans, 326 Caiman, 339 Calcium pump, 87–88, 88f Calvin–Benson cycle, 102, 102f, 103 Cambrian period, 232f–233f, 320 Camouflage, 374 Canada geese, managing, 351–352, 351f n Cancer, 167 anal, 288 breast, 165f cells, 159, 159f, 166–169, 166f, 168f cervical, 288 gene therapy and, 214 genetic factors, 136, 167, 191 liver, 288 nitrate pollution and, 386 ovarian, 136 research, 312–313 risk factors, 167 skin, 135, 135f telomeres and, 167 thyroid, 386 treatment, 141–142, 203, 212, 214, 317 viral infection and, 288 Capsaicin, 374 Capsule, of bacteria, 60f, 60 Carbohydrates, 39–41, 40f breakdown pathways, 108–109 digestion of, 116–117, 117f Carbon, 28, 28f, 29f, 38, 38f, 93 isotopes of, 29f, 166–169, 166f, 168f rings, 38, 38f Carbon cycle, 93, 280, 387–388, 387f Carbon dating (CO2), 227–228, 228f Carbon dioxide in aerobic respiration, 108, 110f, 111 in atmosphere, 93–94, 93f, 94f, 103, 103f, 280, 388, 388f atmospheric, rise in, 93–94, 93f, 94f, 103, 103f 388–389 and carbon cycle, 93, 387–388, 387f and global climate change, 93–94, 93f, 94f in fermentation, 114, 114f, 115 n as greenhouse gas, 389, 389f in photosynthesis, 93, 95, 95f, 102, 102f Carbon fixation, 102 Carbonic acid, 37 Carboniferous period, 232f–233f, 300, 300f, 301, 338 Carboxysomes, 60f n Cardiovascular disease, 47 Carpel, 180, 181f, 304, 304f, 305 n Carrying capacity, 356–357, 363 human effects on, 358 increased, 363 Cartilaginous fishes, 334f, 335–336, 335f Castor, 141, 141f Cat, hairless, 140f, 152 Catastrophism, 222 Celera Genomics, 208 Cell(s), 5 basic components of, 54–55, 54f energy storage in, 77–78, 78f, 79, 79f

eukaryotic, features of, 62–69, 62t, 62f, 63f, 64f, 67f, 68f, 69f, 71f evolution of, 268–271, 271f, 319, 319f malignant, 166, 167 membrane structure, 57–59, 57f, 58f, 59f origin of, 268–271 prokaryotic, features of, 59–61, 60f, 61f reproduction. See Mitosis, Meiosis size, 54f, 55, 55f somatic, 127 Cell cycle, 160, 160f, 165, 166, 168 Cell differentiation. See Differentiation Cell division, DNA packaging, 132 Cell division limit, 168 Cell junction(s), 68. See also Tight junction; Adhering junction; Gap junction; Plasmodesmata in animal tissues, 69f Cell lines, 159 Cell membrane(s). See also Lipid bilayer origin, 270 structure, 57–59, 58f–59f Cell plate, 164, 164f Cell theory, 20t, 57, 57t Cell wall, 60, 60f, 68 Cellular respiration, 107. See also Aerobic respiration Cellular slime molds, 284 Cellulose, 40–41, 40f, 78 Cenozoic era, 232f Centipede, 330, 330f Centromere, 131, 133, 161, 162f Century plants, 361 Cephalopods, 325–326, 325f, 537 Cephalothorax, 328, 329, 329f, 330f Cetaceans, evolution of, 227, 227f n CF. See Cystic fibrosis n CFCs (chlorofluorocarbons), 409 Chalky-shelled foraminifera, 279–280, 280f Chaparral, 398f, 402f, 403 Chargaff ’s rules, 128, 130 Charge, 28, 85 Charophyte algae, 294 Chase, Martha, 125, 125f, 126f Checkpoints, in cell cycle, 165, 166f, 168, 312 Chemical bond(s), 32–33, 32f, 33f, 33t carbon–carbon, 38 energy storage in, 76f, 77–78, 78f, 79f, 95 Chemical reaction(s), 39, 39f, 44f, 77–78, 78f n Chemical weapons, 141 Chemicals, mutation-causing, 136–137 in tobacco smoke, 136 Chemoautotroph, 275 Cheung, Melissa, 150 n Chicken pox, 288 n Chiggers, 330 Chimpanzee, 342f, 343, 343f China n ecological footprint, 365, 365f population, 365 Chinook salmon, 212 Chitin, 68, 308, 325, 327 n Chlamydia, 276t Chlorella, 282, 282f n Chlorofluorocarbons (CFCs), 409

Chlorophyll a, 98, 98f, 99, 101 Chloroplasts, 63, 63f, 95–96, 96f, 102, 102f, 296 in algae, 281 evolution of, 278 genetic code and, 146–147 origin of, 278, 278f in protists, 279, 279f, 280f, 281 Choanoflagellates, 279f, 284, 285, 285f n Cholera, 276, 276t, 364 Cholesterol, 43, 43f. See also HDL, LDL n blood levels, 27, 46, 46f n good and bad forms of, 46–47 Chordates, 319f, 333–334, 333f, 334f Chorion, 199, 199f, 340f n Chorionic villus sampling, 199, 199f Chromatids, 131, 133, 161, 161f, 162f, 171–173, 173f Chromosome number, 132, 132f changes in, 196–197, 197f, 197t, 256 in malignant cells, 166, 168, 168f meiosis and, 171–174 mitosis and, 161, 161f, 166 Chromosomes, 131, 131f DNA packing in, 130–132, 131f genes on, 180–182, 182f homologous, 161, 161f, 169, 169f in malignant cells, 166, 167 in meiosis, 171–175, 172f–173f in mitosis, 160–164, 161f, 162f telomeres, 168–169 Chymosin, 211 Chytrids, 308, 311 Cicadas, 253 Cichlid fishes, 256–257, 256f Cilia, 67, 179f, 280, 281f Ciliated protozoans, 279f Ciliates, 280, 281f Circulatory system. See also Cardiovascular system annelids, 324, 324f arthropods, 327 cephalopods, 325–326 closed, 324 open, 324 vertebrates, 334 n Cirrhosis, 75, 86 Citric acid cycle, 110f, 111, 112f, 116, 117, 117f, 120f and ketogenic diet, 118 Clade, 261, 261f Cladistics, 260–261, 261f Cladogram, 261, 261f Cleavage furrow, 164, 164f Climate, 396–397 Climate change in Cambrian period, 320 n current global, 20t, 94, 94f, 280, 390–391, 390f, 409–411, 410f increasing CO2 level and, 94, 94f Clinton, Bill, 208 Cloaca, 336, 340 Clones. See Cloning Cloning, 127 n animals, 127, 127f DNA, 204–206, 205f

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INDEX  433  Cloning vector, 204–205, 205f, 214, 215 Closed circulatory system, 324, 325 Clotting, 245 n disorders, 195 Club fungi, 309, 309f, 310, 310f, 311, 312 Club mosses, 294f, 299, 299f, 300, 300f Cnidarians, 319, 319f, 322, 322f Coal, 300, 300f n Coastal waters, restoration of, 414 Coast redwoods, 302f, 400 Coca plant, 306 Coccyx, 221f n Codfish, and life history evolution, 362, 362f Codominance, 186 Codons, 146–147, 146f, 148–150 Coelacanths, 257, 257f, 336 Coelom, 320, 320f, 324, 324f Coenzymes, 81–82 ATP as, 82, 82f Coevolution, 259–260, 259f, 376 predation and, 321, 371t, 373, 373f Cofactors, 81–82 Cohesion, of liquid water, 35–36 in water molecules, 35–36 Cohort, 359 n Colds, 288 n Cold sores, 288, 288f n CO . See Carbon dioxide 2 Collagen, 244 Colonial choanoflagellate, 285, 285f Colonial organism, 279 Colonial theory of animal origins, 318 n Color blindness, 194t, 195, 195f Commensalism, 371t, 375, 375f n Community, 5, 370 disturbance, role of, 378 ecological succession in, 377–378, 377f, 338f factors shaping, 370–371 species interaction in, 371–377 Comparative embryology, 237, 237f Comparative morphology, 221, 221f Competition, interspecific, 371t, 371–372, 372f, 373f Competitive exclusion, 372, 373f Complete digestive tract, 324, 325 Complex carbohydrates, 40, 40f digestion of, 116–117 Compound, 32 Compound eyes, 327f, 328 Concentration, 35 Concentration gradient, 85 Conclusion, 19 Condensation reaction, 39, 39f Cone snails, 317, 317f Conifers, 294f, 302, 302f, 303f Conjugation, prokaryotic, 274, 274f n Conservation biology, 411–415 biodiversity, value of, 413 biodiversity hot spots, 413–414, 414f cladistic analysis and, 261–262 extinction crisis, 411–413 human impacts, reducing of, 414–415 protection and restoration, 414 Consumer(s), 6, 6f, 77, 77f, 379, 379f Continental drift, 229, 231f Continuous variation, 178f, 189–190, 189f

Contractile ring, 164, 164f Contractile vacuole, 279, 279f Control group, 14 Convergent evolution, 235 Copernicus, Nicolaus, 22 Coprolites, 225f Coral, 280, 322 bleaching, 406 reefs, 322, 406, 406f Corn, 306 n genetically modified, 211–212, 211f Cornea, 68f n Coronary artery disease. See Atherosclerosis Cotton, 306, 306f Cotyledon(s), 306 Covalent bond(s), 32, 32f, 33t polarity of, 33, 33f Covas, Rita, 247 Cow, 127f Crabs, 328f, 328, 329, 329f, 330 Cretaceous period, 232f, 339–340 n Creutzfeldt–Jakob disease, 47–48, 47f Crick, Francis, 128, 129 CRISPR gene editing, 214–215, 215f Critical thinking, 12–13, 19 pseudoscience and, 21, 21t Crocodilians, 339, 340 Crops (food). See Food crops Crosses, 180. See also Dihybrid cross; Monohybrid cross Crossing over, chromosomal, 174, 174f, 184, 243t Crustaceans, 328, 330, 330f Cuticle animal, 68, 326, 327, 330 plant, 68, 68f, 295, 295f Cuttlefish, 325 Cuvier, Georges, 222, 222f Cyanobacteria, 60f, 272–273, 275, 275f, 281, 312 Pseudanabaena, 60f Cycad, 294f, 303, 303f Cyst, prokaryotic, 282 n Cystic fibrosis (CF), 66, 66f, 179, 179f, 186, 187, 187f, 193t, 198, 212, 213 Cytoplasm, 55, 60, 60f. See also, Cytosol Cytoplasmic division, 160f, 161, 161f, 164, 164f, 172f–173f Cytosine (C), 128, 128f, 130, 142, 143 Cytoskeleton, 62t, 66, 67f, 71f, 164, 166 Cytosol, 54–55, 54f

D da Conceição Miranda, Ana Gledis, 3f Dandelions, 360, 360f Darwin, Charles, 223–226, 223f Data, 13, 14t Deciduous forests, temperate, 399f, 400 Deciduous plants, 303 Decomposers, 6, 310, 379, 380, 381f bacteria as, 275 fungi as, 8, 307, 308, 310, 310f roundworms as, 326 n Deforestation, 400–401, 401f Delaware Bay, 358 Deletion mutations, 151f, 152

Demographics, 365 Demographic transition model, 365 Denaturing of proteins, 47, 80 Denisovans, 346–347, 346f Density-dependent limiting factors, 356, 357–358, 357f, 358f Density-independent limiting factors, 357 n Dental plaque, 61 Derived trait, 260 Desert(s), 397, 398f, 403, 403f n Desertification, 403–404 Detritivores, 379, 380, 381f Deuterostomes, 319, 319f Development, 7 similarities across species, 237, 237f Devonian period, 232f n Diabetes mellitus, 191, 211, 212 Diatomaceous earth, 280 Diatoms, 279f, 280, 280f silica-shelled, 280, 280f Dickonsonia, 320, 320f Dictyostelium discoideum, 284, 285f n Diet. See Nutrition, human Differentiation, 127, 153–154, 155 Diffusion, 84–85, 85f facilitated, 87, 88f Digestion of carbohydrates, 116–117, 117f of fats, 116, 117f microbiome and, 267–268 of proteins, 117f, 117–118 Digestive system arthropod, 327 cnidarian, 322 earthworm, 324, 324f flatworm, 323–324 invertebrate, 333 roundworm, 326 sea star, 332 sponge, 321 vertebrate, 334 Digestive tract, complete, 324 Digitalis, 306 Dihybrid cross, 184–185, 185f Dikaryotic cell, 309, 309f Dimorphisms, 243, 248 Dinoflagellates, 279f, 280, 280f, 322 Dinosaurs, 219, 225f, 259, 340, 343 Diploid, 132 Directional selection, 245–247, 245f Disaccharide, 40 n Disease(s) bacterial, 179, 187, 187f, 191, 241–242, 241f, 275, 276, 276t ciliate, 280 fungal, 293, 293f, 311, 311f, 312f and human population, 364 of plants, 293, 293f, 311 and population growth, 356 roundworms and, 326–327, 327f, 331 vectors, 261–262, 329 viral, 166, 262, 288–289 Disruptive selection, 245, 245f, 248, 248f Distribution, population, 352–353, 353f Divergent evolution, 234 DNA, 7, 48–49, 124f n

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434  INDEX bacterial, 273–274, 273f base-pairing in, 130, 133, 133f, 143t base pair substitutions, 151–152, 151f, 152f as cell component, 54f, 55 chloroplast, 63 in chromosomes, 130–131, 131f, 132, 132f cloning, 204–206, 205f n damage to, 135 deletion mutations, 151f, 152 discovery of structure, 128–129, 128f eukaryotic, 62, 62f function, discovery of, 124–127 gene exchanges, prokaryotic, 274, 274f as hereditary material, 7, 126–127 insertion mutations, 151f, 152 methylation of, 154–155, 155f, 188 n mutations in, 134–137, 137f, 151–152, 151f origins of, 270 prokaryotic, 60, 60f recombinant, 204, 204f, 205f repair mechanisms, 134–135, 134f, 261 replication, 133–134, 133f sequence comparisons, 11, 236–237 sequencing, 207–208, 208f sticky ends, 204, 204f, 205f structure, 48, 48f, 128–130, 130f, 131f, 143, 143f viral, 286, 288f vs. RNA, 142–143, 143f DNA fingerprinting, 210. See also DNA profiling DNA library, 206 DNA ligase, 133, 133f, 204, 204f, 205f DNA polymerase, 133–134, 133f, 206–207, 206f, 209, 209f n DNA profiling, 209–210, 209f, 210f DNA replication, 133–134, 133f vs. transcription, 144 DNA sequence, 130 comparisons, 11, 209f, 236–237 human, 208, 208f n DNA testing, personal, 203, 203f Dodder, 374f Dog(s), 123, 123f, 186–187, 186f, 189, 189f Domain(s) taxonomic, 10f, 11 of protein, 44–45, 44f–45f Dominant allele, 182, 182f Dorudon atrox, 227, 227f Double fertilization, 304f, 305 Double helix structure of DNA, 128–130, 130f, 131f n Down syndrome, 196, 197f Drinking alcohol, 75, 82–83 Drosophila (fruit flies), 249 n Duchenne muscular dystrophy, 194–195 n Dust Bowl (North American plains), 404 n Dwarfism, 192, 192t, 193t Dynein, 67

E n

E. coli, 60f, 81f, 211, 211f, 263, 263f as food contaminant, 53, 53f, 141 ST131, 263, 263f Earth. See also Atmosphere early, 268, 269, 269f, 271 orbit, and climate, 409

Ear, 244f Earthworms body plan, 320, 324, 324f digestive system, 324 n Ebola, 289 Echinoderms, 319f, 332–333, 332f ECM. See Extracellular matrix n Ecological footprint, 365, 365f Ecological isolation, 253–254 n Ecological restoration, 414, 415f Ecological succession, 377–378, 377f Ecology, 352 EcoRI enzyme, 204, 204f n Ecosystems, 5, 379 aquatic, 405–407, 405f, 406f, 407f energy flow in, 6, 6f, 379–382, 379f, 382f food chains and webs in, 380, 380f, 381f nutrient cycling in, 379–382, 379f–382f Ectoderm, 319, 320f Ectotherms, 338–339 Ediacarans, 320, 320f Egg (ovum), 174 amniotic, 334, 334f, 338, 340, 340f animal, 322, 325, 334, 336 in plants, 296, 297f, 298, 299f, 301, 301f, 304, 304f, 305 Electromagnetic spectrum, 97, 97f Electron(s), 28, 28f, 29–31, 30f Electron microscopes, 56–57, 56f Electron transfer chain, 83, 83f, 99–100, 101f, 110f, 111–113, 112f Electron transfer phosphorylation, 100, 108f, 110f, 111–113, 112f, 116, 117f Electrophoresis, 207–208, 208f, 210 Element(s), 28, 28f n Elephantiasis, 327, 327f Elephant seals, northern, 249f, 251 n Ellis–van Creveld syndrome, 193t, 252, 252f Embryo bird, 340, 340f plant, 304f, 305 similarities across species, 237, 237f n splitting, in reproductive cloning, 126–127 Embryophytes, 294 n Endangered species, 261–262, 262f, 412, 412f n Endemic species, 412 Endler, John, 361 Endocytosis, 88, 89f, 179, 483, 483f Endoderm, 319, 320f Endomembrane system, 63–65, 64f evolution of, 278, 278f Endoplasmic reticulum (ER), 64f, 65, 279, 279f Endoskeleton, 332 Endosperm, 304f, 305 Endospores, 276 Endosymbiont hypothesis, 278 Endotherms, 338–339 Energy, 76–77 activation, 78, 79f n flow in ecosystem, 6–7, 6f, 77, 77f, 379–382, 379f–382f food as source of, 116–118, 117f and laws of thermodynamics, 76 dispersal, 76–77, 76f in molecules of life, 77–79, 78f, 79f reducing use of, 414–415 n renewable, negative impacts of, 414–415

solar radiation, variation with latitude, 396, 396f storage in chemical bonds, 77–79, 78f, 79f, 95 sunlight as source of, 6f, 77f, 379, 380f, 396, 396f, 397 Energy capture and transfer, in ecosystem, 380–382, 382f Energy pyramid, 381, 382f n Environmental protection, public resistance to, 413 Enzyme(s), 39, 79–81, 80f activity, 80–81, 80f, 81f active site, 80, 80f and activation energy, 80, 81f in cell membrane, 59f, 59 coenzymes, 81–82 cofactors, 81–82 DNA repair, 134f, 135 in metabolic pathways, 82–83, 83f and regulatory molecules, 81, 81f pH and, 80, 81f, 84, 84f restriction, 204, 204f, 205f salts and, 80–81 temperature and, 80, 81f Epigenetic modifications of DNA, 155, 188, 190 Epiphyte, 299 Epithelium. See Epithelial tissues Equilibrial life history, 360f, 361 Equisetum, 299 ER. See Endoplasmic reticulum Eribulin (Halaven), 317 Erythrocytes. See Red blood cells Escherichia coli. See E. coli Estrogens, 43f Estuary, 382f, 405–406, 406f Ethanol, 75. See also Alcoholic drinks alcoholic fermentation and, 114f, 114 n Ethical issues genetic engineering, 212–213, 215 patenting of human genome, 208 Eudicots, 294f, 305–306 Eukaryote(s), 8, 9f cell cycle, 160, 160f cell structure, 62–69, 62t, 62f, 63f, 64f, 67f, 68f, 69f, 71f DNA packaging, 130–132, 131f evolutionary tree, 279f fossil, 277 mixed heritage, 277–278 origins, 277–278, 278f transcription in, 145 translation in, 148–150, 149f Euphorbias, 221f Evaporation, 36 and water cycle, 383, 384f Evolution, 222. See also Adaptation of amniotes, 338 of angiosperms, 304f, 305 of animals, 318–320, 319f of cells, 268–273, 271f, 318–319 of chloroplasts, 63 convergent, 235 defined, 222 divergent, 234 early evidence and theories, 220–221 fossil evidence, 225–227, 225f, 226f, 227f mutations and, 236–237, 243–244

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INDEX  435  of humans, 341–347, 342f key innovations, 259 of life history patterns, 361–362 macroevolution, 257–260 of mammals, 340 microevolution, 244 missing links, 227, 227f of mitochondria, 63 of plants, 294–295, 294f of primates, 341–347 and resource partitioning, 372 natural selection and, 224, 224t, 2 45–250, 245f nonselective, 250–252, 251f seed plants, 301–302 speciation, 253–257 as theory, 21, 225 vertebrates, 334, 334f Exclusion, competitive, 372, 373f Exocytosis, 89, 89f Exon(s), 145, 145f Exoskeleton, 327 n Exotic species, 379, 379f Experiment(s), 13–17, 15f–16f, 15f knockouts, 154, 154f, 209, 212 Experimental group, 14, 15 Exponential model of population growth, 356, 356f Extinct, 259 n Extinction(s), 219, 232f, 259, 261–262, 262f, 411 mass, 219, 232f, 259, 411 n Extinction crisis, 411–413 Extracellular matrix (ECM), 68, 68f, 321 Extreme halophiles, 276–277, 277f Extreme thermophiles, 276–277, 277f Eye amphibian, 336 arthropod, 328, 330 compound, 327f, 328 n disorders, 154, 154f, 194, 194f flatworm, 330 insect, 328 primate, 342–343, 342f Eyeless gene, 154, 154f Eyespot, 279, 279f, 323, 332, 332f, 333, 333f

F Facilitated diffusion, 87, 88f Fall colors, 98–99, 98f Fallopian tubes. See Oviduct Fat(s), 42 digestion of, 116, 117f and nutrition, 27, 46, 46f saturated, 42, 46, 46f unsaturated, 43, 46, 46f Fatty acid(s), 41–42, 42f saturated, 42, 42f unsaturated, 42, 42f n Fatty liver, due to drinking, 82–83 Faults, geological, 230f, 230 Feathers, 259 Feedback inhibition, 82, 83f

Feed conversion ratio, 77f Fermentation, 113–115, 114f, 115f, 312 Ferns, 294f, 298–299, 299f Ferroglobus placidus, 61f Fertility rate, 364 Fertilization in amniotes, 338 animals, 322, 336 plants, 174–175, 296, 297f, 298, 299f, 301, 301f, 304f, 305 n Fertilizers, synthetic and crop yields, 363 and water pollution, 383, 384, 385 n Fetoscopy, 198, 198f Fetus n prenatal diagnosis, 198–199 n Fiber, dietary, 41 Fire, adaptations to, 378, 378f n Fire-adapted biomes, 402–403 Fire ants, 369, 369f, 378 First law of thermodynamics, 76 Fishes, 335–336 chromosomes, 132 Fitness, 224 Fixed allele, 250 Flagellated protozoans, 279f Flagellum (flagella), 60f, 61, 67, 279, 279f, 280, 280f, 284–285, 285f Flatworms, 319, 319f, 320f, 323–324, 323f Fleas, 331 Flower(s), 303–304, 304f Flowering plants. See Angiosperms Fluid balance, in body, 86 Fluid mosaic, cell membrane as, 57–58 Flukes, 324 Fluorescence microscopy, 56, 56f Fluorescent dyes, 56 n Food bacterial contamination, 53, 53f, 241 as energy source, 116–118, 117f fermentation and, 114–115, 114f, 312 Food-borne diseases, 53 Food chains, 380, 380f, 381f, 382 Food crops, 306, 312 angiosperms as, 306, 306f, 611 n diseases of, 293, 293f, 310 n fertilizers and, 363 n genetic modification of, 211–212, 211f, 212f insects as competitors for, 330–331 and roundworm parasites, 327, 327f n Food poisoning, 241 n Food safety, and human population growth, 364 Food webs, 380, 381f Foraminiferans, 226f, 279–280, 280f Forensic phylogenetics, 262 Forest(s) ancient, as coal source, 300, 300f biomes, 399–402, 399f n deforestation, 400–401, 401f tropical rain forests, 370–371, 399–400, 399f, 400 Forest biomes, 399–402, 399f coniferous forests, 399f, 400 deforestation, 400–402, 401f temperate deciduous forests, 399f, 400 tropical forests, 399–400

Formaldehyde, 137 Fossil(s), 225–227, 225f, 226f, 227f cells, earliest, 271–272, 272f dating of, 227–229, 228f early animals, 320, 320f fossilization process, 225–226 fossil record, 226–227, 230–231 fungal, 308 human, 344–345, 345f lineages, missing links in, 227, 227f Neanderthal, 345–346, 346f Fossil evidence, prokaryotes, 271–272, 272f n Fossil fuels and air pollution, 408–409 and carbon cycle, 93, 387f, 388 coal as, 300 emissions, 103, 103f and population growth, 363 use and rising atmospheric CO2 levels, 93–94, 103, 388–389 Founder effect, 251, 251f Frameshift mutations, 151f, 152 Franklin, Rosalind, 128–129, 136 Free-living roundworms, 326–327, 326f n Free radicals, 31, 98, 136, 195 Freshwater ecosystems, 381, 382f n Fried foods, 27 n Friedreich’s ataxia, 193t Frog, 337, 337f Fructose, 40 Fruit, 304, 304f, 305, 376 Fruit flies (Drosophila), 154f, 249 Fruit flies, Mediterranean, 331, 331f Fruiting bodies, 284, 285f, 308f, 309, 309f, 310f FSH. See Follicle-stimulating hormone Fungi vs. animals, 307t vs. plants, 307t Fungus, 8, 9f, 307–309 as decomposers, 307, 310, 310f diversity of, 307–309 ecology of, 310–313 evolution of, 279f, 307–308 as heterotrophs, 307 human uses of, 312–313 life cycle of, 308–309, 309f mutualisms, 311, 311f n as pathogen, 293, 293f, 310, 310f, 311f

G Galactose, 40 Galápagos islands, 224, 355, 355f Galileo, 22 Gametes, 174 animal, 174 incompatibility, 253f, 254 plant, 174, 294f, 295 Gametophytes, plant, 294f, 295, 296, 297f, 297, 298, 299f, 301, 301f, 304f, 305 Gamma rays, 97f, 136 Gap junctions, 69, 69f Gastropods, 325, 325f Gastrovascular cavity, 322, 322f cnidarians, 322 Gause, G. F., 372

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436  INDEX Geese, 351, 351f Gene(s), 142, 142f breast cancer, 191 checkpoint, 165, 168, 312 effects of mutations in, 151–152, 151f, 152f master regulators, 153–154 homeotic, 154–155, 154f location on chromosomes, 180–181, 182f transcription of, 144, 144f Gene expression, 142 control of, 153–155, 153f, 165–166 environment and, 188–190, 188f Gene flow, 252, 255, 255f Gene pool, 244 Genealogy databases, 210 Generations, alternation of, 294, 294f n Gene therapy, 214 Genetic abnormality, 190–191 n Genetically modified organisms (GMOs), 211–213, 211f, 212f animals, 212–213, 212f, 213f plants, 211–212, 211f, 212f Genetic analysis of humans, 190–191, 191f, 198–199, 199f Genetic code, 146–147, 146f, 151 n Genetic disorder, 186, 192 testing for, 198–199, 199f treatment of, 214, 214f Genetic diversity, 413. See also Biodiversity factors affecting, 248–252 Genetic drift, 250–251, 251f n Genetic engineering, 211–213 n Genetic testing, 198–199, 198f, 199f Genome, 205–206, 237 Genome, human n sequencing of, 208, 208f vs. other species, 209, 209f Genomics, 208–209 Genotype, 182, 182f Genus, 10, 10f Geologic evidence, 230, 230f Geologic time scale, 231, 232f–233f Germ cells, 174 Germ layers, 319 Gey, George and Margaret, 159 n Giardiasis, 282 Gibbons, 342f, 343 Gill(s) of amphibians, 336 of fish, 335, 335f Gill slits, 333, 333f, 335, 336f Gingerich, Philip, 227 Ginkgos, 294f, 303, 303f n Glaciers, global warming and, 410, 410f n Global climate change, 20t, 94, 94f, 280, 390–391, 390f, 409–411, 410f Global temperature, increasing CO2 level and, 94, 94f Globin(s), 44f–45f 151–152, 151f, 170 Glomeromycete fungus, 308, 311, 311f Glossopteris, 225f, 231 Gluconeogenesis, 118 Glucose, 40 in aerobic respiration, 111, 114

blood levels, regulation of, 116 energy storage in, 79, 109 storage of, 41 structure of, 40 Gluten, 114 Glycerol, 118 Glycogen, 40, 40f, 41, 116 Glycolysis, 108f, 109, 109f, 111, 112, 112f, 113 energy-harvesting steps, 109 energy-requiring steps, 109 yield, 109 Glycoproteins, 46 n Glyphosate, 212 Glyptodon, 223–224, 223f Gnetophytes, 294f Golden Clone Giveaway, 123 Golgi bodies, 62t, 64f, 65, 279, 279f Gonads, 326f Gondwana, 231, 231f, 321 n Gonorrhea, 276, 276t Google Earth, 3 Gorilla, 342f, 343, 343f Grain crops, 306, 306f Grand Canyon, 232f–233f Grasshopper, 327f, 330, 380f Grasslands, 398f, 402, 402f Great chain of being, 220–221 n Great Pacific Garbage Patch (GPGP), 408 Great Wall of China, 255 Green algae, 279f, 281–282, 282f, 294 n Greenhouse effect, 389, 389f n Greenhouse gases, 389, 389f Griffith, Frederick, 124 n Groundwater, 384, 384f Growth as characteristic of life, 7 n Growth factor receptors, 165, 165f n Growth factors, 165 n Growth hormone (GH), 192 Growth rate, population, 362–364, 363f GTP, 150 Guanine (G), 128, 130, 128f, 142, 143, 143t, 144 n Gum disease, 277 Guppies, life history evolution in, 361, 361f Gymnosperms, 294f, 296, 301f, 302–303, 302f, 303f n

H H22, 263 H30, 263 n H5N1 flu, 262 Habitat(s), 371 n degradation of, 412 Hair, as mammalian trait, 340 Half-life, 29, 227, 228f n Hallucinogens, 313 Halophiles, 276–277 n Hangovers, 75, 516 Haploid, 171 Hawaiian honeycreepers, 258, 258f, 261–262, 262f HbA allele, 249–250 HbS allele, 249–250, 250f

HDL (high-density lipoproteins), 46, 46f Heart amphibian, 336 bird, 340 crocodilian, 339 earthworm, 324, 324f fish, 335f, 336 vertebrate, 334 n Heart attack, 214 n Heart disease, 191 Heartworms, 327 n HeLa cells, 159, 159f, 168, 168f, 169 Helgen, Kris, 18f Helicobacter pylori, 60f Heme, 151, 151f Heme group, 45f Hemoglobin, 45f, 188f, 189 mutations, 151, 151f, 152f, 249 Hemoglobin C, 152 n Hemophilia, 194t, 195, 198 Hepatitis C virus, 262 Herbivores, 374 n Hereditary methemoglobinemia, 193t Hermaphrodites, 322, 324, 325 Hershey, Alfred, 125, 125f, 126, 287 Heterotrophs, 95, 95f, 275 Heterozygous individuals, 182–184, 182f–184f Hibernation, 115, 115f High-density lipoproteins (HDL), 46, 46f High-fat diet, effect on brown fat, 119f Hip. See Pelvic girdle Histones, 131, 131f, 155 n HIV (human immunodeficiency virus), 286–287, 287f n Homeostasis, 7 of body fluids, 87 pH, 37 temperature, 35 Homeotic genes, 154, 237 Hominids. See Hominins Hominins, 342f, 343 Homo erectus, 344, 345f Homo habilis, 344 Homo neanderthalensis, 345, 345f, 347 Homo sapiens, 344–345 Homologous chromosomes, 161, 161f, 169, 169f Homologous structures, 234–235, 234f Homozygous individuals, 182, 183f Hornworts, 294f, 296, 297–298 Horseshoe crabs, 328, 328f, 329, 329f Horsetails, 294f, 298, 299–300, 299f, 300f Household products, as mutation-causing, 137 Hoxc6 gene, 237, 237f n HPV (human papillomavirus), 166, 288 Human(s), 344 cloning of, 127 early, 344–345, 344f evolution of, 341–347, 342f genetic analysis of, 190–191, 191f, 198–199, 199f n impact on biosphere, 3, 93, 93f, 414–415, 415f microbiota of, 267–268, 267f

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INDEX  437  population growth, 362–365, 363f potential allele combinations in, 242–243 skin color variation, 187–188, 187f Human Genome Project, 208 Human genome statistics, 208, 209t n Human health, bacteria and, 275–276 Human Microbiome Project, 267 n Human papillomavirus (HPV), 166, 288 Human(s) carrying capacity and, 358 intestinal bacteria, 267f n Huntington’s disease, 192f, 192t, 193 n Hutchinson-Gilford progeria, 192f, 193 Hybrid inviability, 254–255 Hybrid sterility, 255 Hybridization, in DNA replication, 133 n Hydrogenated vegetable oil, 27, 27f, 43 Hydrogen bonds, 34, 34f, 35f Hydrogen ion gradient forms, electron transfer phosphorylation, 112 Hydrogen ion gradient forms, noncyclic pathway, photosynthesis, 100 Hydrogen ions and pH, 36 in photosynthesis, 100, 101f Hydrolysis, 39, 39f Hydrophilic substance, 34 Hydrophobic substance, 35 Hydrothermal vents, 269, 269f, 406, 407f Hydroxyl ions, and pH, 38 Hypertonic solution, 85, 86f Hyphae, fungal, 308, 308f, 309, 309f, 310, 310f, 311f Hypotheses, 13, 14, 14t, 16, 16f Hypotonic solution, 85–86, 86f

I Ichthyosaur, 225f Identical DNA clones with, 127, 127f identical twins with, 126 Identical twins, with identical DNA, 126 Immune system blood type and, 186, 186f microbiome and, 267 parasites and, 375 n Impetigo, 276t n Inbreeding, 252 Incompatibility, gamete, 254 Incomplete dominance, 185 n India ecological footprint, 365, 365f population, 364, 364f n Indicator species, 412 Industrial products, as mutation-causing, 137 n Influenza, mutations in, 289, 289f Inheritance, 7. See also Genetic disorders codominance, 185 complex variation, 188–190, 188f–190f crossing over and, 184 dihybrid crosses, 184–185, 185f incomplete dominance, 185 Mendel’s experiments in, 180, 181f monohybrid crosses, 184, 184f pleiotropy, 186

Inheritance patterns, in humans, 192–195 Injury, immune response to, 476 Insect(s), 328, 330–331, 331f diseases, 311 n as disease vector, 261–262, 288, 276, 276t, 283, 283f, 331 as pollinators, 254f, 305, 305f, 330, 331f wings, 235, 235f Insertion mutations, 151f, 152 Insulin, 211 Intermediate filaments, 67, 67f Interphase, 160, 160f, 162f, 163 Interspecific competition, 356, 357, 371t, 371–372, 372f Intestines. See Large intestine; Small intestine Introns, 145, 145f n Invasive species, 379 Invertebrate(s), 317 chordates, 333, 333f human uses of, 317 sex determination in, 132 n In vitro fertilization (IVF), 199 Ionic bonds, 32, 32f, 33, 33f n Ionizing radiation breakage and cross-links, 136, 136f dose-dependent damage, 136, 137f and genetic damage, 136, 136f mutation due to, 136, 136f, 137f Ions, 31, 31f Iridium, 219, 219f, 226, 226f Isolation behavioral, 254, 254f ecological, 253–254 mechanical, 254, 254f reproductive, 253–255, 253f, 254f temporal, 253 Isopods, 330 Isotonic solution, 85, 86f Isotopes, 29 of carbon, 29f Isthmus of Panama, 255, 255f n IVF (in vitro fertilization), 199

J Jaw, 334, 334f Jawed fishes, 335–336, 335f Jawless fishes, 334f, 335, 335f Jellies (Jellyfish), 322, 322f Jolie, Angelina, and personal genetic testing, 203f Joyce, Gerald, 70 Junctions, cellular, 68–69, 69f Jurassic period, 232f, 339, 340 Juvenile-onset diabetes. See Type I diabetes

K Karenia brevis, 386 Karyotype, 132, 132f, 168, 168f, 198 Katan, Martijn, 46 n Ketogenic diet, 118 Kelp, 281, 281f, 413 Keratin, 46, 67, 152, 152f, 335, 338, 339 Key innovation, 259 Keystone species, 378, 378f Kidney, 334, 338 Killer’s DNA, investigation, 210

King, Mary-Claire, 191 Kingdom, 10f, 11 Klein, David, 358 n Klinefelter syndrome, 197, 197t Knee joint, 439, 440f, 441, 442f Knockout experiments, 154, 154f, 209, 212 Komodo dragon, 338f, 339 K-Pg boundary layer, 219, 219f, 226, 226f Krebs cycle. See Citric acid cycle Krill, 330, 330f K-selected species, 361 Kudzu, 379, 379f

L Lacks, Henrietta, 159, 159f Lactate, 114, 118 Lactate fermentation, 114–115, 115f hibernation, 115, 115f in muscle cells, 115, 115f yogurt, 115, 115f Lactate-fermenting bacteria, 275f Lactobacillus bulgaricus, 115, 115f Lactose, 40 n Lactose intolerance, 510 Lake ecosystems, 405, 405f Lake Victoria, 256, 256f Lamarck, Jean-Baptiste, 222, 222f Lamarckian inheritance, 222 Lambda bacteriophage, 287 Lamins, 67 Lampreys, 335, 335f Lancelets, 333, 333f Land advantages of living on, 336 evolutionary adaptations to life on, 294, 295, 295f, 327, 336 Language, human, 363 Larva, 322, 323f, 328f, 328, 330, 331, 336, 337f Law of nature, 21 LDL (low-density lipoproteins), 46–47 Leaf, 295f Lean finely textured beef, 53 Leeches, 324, 324f Legumes, 306 Lemurs, 342f, 343, 343f n Lethal mutations, 244 Lettuce leaf, E. coli on, 53, 53f n Leukemia, 214, 214f Leukocytes. See White blood cells Lice, 331 Lichens, 282, 312f, 312, 376f, 377, 412 n air pollution and, 246–247 as pioneer species, 377 Life characteristics of, 6–7, 70 defining, 4, 70 diversity of, 8–12 energy and, 6, 70, 76–79, 77f last common ancestor of, 271 levels of organization, 4, 5 shared ancestry, 11f Life cycle angiosperms, 304–305, 304f apicomplexans, 283, 283f conifers, 302

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438  INDEX Life cycle (continued ) ferns, 298–299, 299f fungi, 308–309, 309f plants, 294–295, 294f seedless vascular plants, 298–300, 299f slime molds, 284, 285f tapeworms, 323, 323f Life history traits, 359 Life table, 359, 359t Light characteristics of, 97–99, 97f Light-dependent reactions, of photosynthesis, 95, 99–101, 101f noncyclic pathway, 99–100, 101f photosynthesis in dark, 101 photosystems, 99 Light energy, 97–99 fall colors, 98–99, 98f photosynthetic pigments, 97–98 visible light, 97, 97f Light-independent reactions of photosynthesis, 102–103, 102f Calvin–Benson cycle, 102, 102f sugar production efficiency, 102–103 Light microscopes, 55, 56, 55f–56f Lignin, 295 Limbs evolution of, 234f, 235 Limestone, origin of, 280 Limiting factors on population, 357–358, 357f, 358f Lineage, 222 Linnaean system, 10 Linnaeus, Carolus, 10, 12 Linoleic acid, 42f Linolenic acid, 42f Lipid(s), 41–44, 43f Lipid bilayer, 43, 43f, 54, 57, 58f–59f, 62, 64f membrane transport mechanisms, 87–89 selective permeability of, 85, 85f Lipoprotein, 203. See also HDL; LDL Liver n disorders, 75 functions, 75, 116 Liverworts, 294f, 296, 297 Living system properties, 70t Lizards, 339, 339f Lobe-finned fishes, 334f, 336, 336f Lobster, 330, 330f Logistic model of population growth, 357 Loris, 342f Low-density lipoproteins (LDL), 46–47 n LSD, 313 Lucy (fossil Australopithicus), 344, 344f Lung(s), 334, 334f evolution of, 259 Lungfish, 336, 336f Lyell, Charles, 222, 222f n Lyme disease, 276, 276t, 329 Lysis, 288f Lysogenic pathway, 288, 288f Lysosomes, 62t, 64 Lystrosaurus, 231 Lytic pathway, 287–288, 288f

M Macroevolution, 257–260 Mad cow disease, 47–48 Maeso, Juan, 262 n Malaria, 249, 250f, 283, 283f, 331 n Malignant neoplasms, 166f, 167, 167f. See also Cancer Malthus, Thomas, 224, 224f Mammals, 340–341, 341f cloning of, 123, 123f–127f evolution of, 234–235, 259 Mammary glands, 340 Mange, 330 Mantle, 324, 325, 325f Manzanita, 253 n Marfan syndrome, 186, 192t Marine ecosystems, 405–406, 406f, 407f Markov, Georgi, 141, 141f Mark-recapture sampling, 354–355 Marsupials, 340, 341f n Mass extinction, 219, 232f, 259, 340, 411 Mass number, 28f, 29 Mating, and sexual selection, 249–250, 249f Mayr, Ernst, 12 Mazia, Daniel, 126 McCarty, Maclyn, 124 Measurement, length, common units of, 55t Mechanical isolation, 254, 254f Mediterranean fruit flies, 331, 331f Medusa, 322, 322f Megafauna, extinction of, 360 Megaspores, 301, 301f, 304f, 306 Meiosis, 171–174, 172f–173f abnormalities in, 175, 175f allele mixing in, 174, 174f, 182, 183f, 184–185, 243t nondisjunction during, 196, 196f Melanin, 187, 194, 195 Melanosomes, 187 Membrane, semipermeable, 85–86, 85f Membrane-enclosed organelles, 62, 62t Membrane proteins, 58f–59f, 58, 62 Membrane transport mechanisms, 87–89, 88f Memory n autism and, 213 Mendel, Gregor, 180, 181f, 188, 243 Mensink, Ronald, 46 Mesentery, 320, 320f Mesoderm, 320, 320f Mesozoic era, 232f–233f Messenger RNA (mRNA), 143, 145f, 146, 148–150, 149f, 154 Metabolic pathways, 82, 95 Metabolism, 38–39, 39f control of, 81–82, 82f in eukaryotes, 274, 274t origins of, 269 Metamorphosis, 328 insect, 331, 331f tunicate, 333 Metaphase, 160f, 163, 164f Metaphase I, 172, 172f–173f Metaphase II, 173, 173f Metastasis, 166f, 167 Methanogens, 277, 277f n

Methemoglobinemia, hereditary, 193t Methylation of nucleotides, 155–156, 155f, 188 n Methylmercury pollution, 382 Microbiota human, 267, 276, 277, 286 Microevolution, 244 Microfilaments, 66, 67f Microorganisms. See also Bacteria; Archaea; Protists, Viruses; Pathogens; Parasites; Fungi genetically modified, 211, 211f intestinal, 41, 53, 267, 277, 286, soil, 311 Microsatellite analysis, 209–210 Microscopy, 55–57 electron, 56–57, 56f fluorescence, 56, 56f light, 56, 56f Microspores, 301, 301f, 304f, 304 Microtubules, 66, 67, 67f spindle, 163–164, 163f, 164f, 172–173, 172f–173f, 175f Miescher, Johannes, 124 Migration, bird, 351 Mildews, 307, 307f, 310 Milk. See Lactation Miller, Stanley, 269, 269f Millipedes, 330, 330f Mimicry, 373, 373f n Miscarriage, 199 Mites, 329 Mitochondria, 62, 62t, 63, 63f, 107, 107f, 110f, 111, 112f, 119, 279, 279f in aerobic respiration, 108–109, 108f, 110f and Duchenne Muscular Dystrophy, 194 genetic code and, 146 inheritance of, 107, 255 origin of, 278, 278f n Mitochondrial disease, 107, 107f Mitochondrial DNA, 107, 255, similarities across species, 236 Mitosis, 161–164, 161f–164f controls, loss of, 165–168, 165f nondisjunction during, 196 pathological, 166–167, 166f Models, 13–14, 32, 33t Molds, 307, 307f Molecules, 4, 4f chemical bonds in, 32–33, 32f, 33f organic, 38–39, 38f Mollusks, 319f, 324–325, 325f Molting, 326, 327, 328f, 330 Monarch butterflies, decline of, 395, 395f Monocots, 294f, 305–306 Monohybrid cross, 184–185, 185f Monomers, 38–39 Monosaccharides, 39 Monotremes, 340, 341f n Montreal Protocol, 409 Morph(s), 242 Morphological traits, 11, 242, 242f Morphology, comparative, 221–222, 221f Mosses, 294f, 296, 297f Moth, 330 Motor proteins, 67, 67f Mount Lico, 3 Mount Saint Helens, eruption of, 378, 378f Mouse n

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INDEX  439  embryo, 237, 237f genome of, 209f use in research, 127, 175, 177–178, 209, 212, 212f Mozambique (Africa), 3 mRNA. See Messenger RNA Mules, 255 Multicellular organism, 279 n Multiple sclerosis (MS), 191 Muscle cells, lactate fermentation in, 115, 115f n Muscular dystrophies, 182f, 194, 194t, 195, 241 Mushrooms, 307–308, 307f, 308f, 312 Mutation(s), 134–135, 134f, 151–152, 151f, 152f, 165–167, 165f beneficial, 137, 151, 161, 243–244 chemicals and, 136–137 and evolution, 243–244 harmful, 244 ionizing radiation and, 136, 136f, 137f n lethal, 244 more mutations due to, 166, 166f neutral, 236, 244 persistence of, 186 rate in population, 242–243 as record of evolution, 236–237 in regulatory sites, 152, 152f replication errors, 134f, 135 sources of, 134, 243t UV light and, 135, 135f viral, 289 Mutualism, 311–312, 311f, 376–377, 376f, 376t Mycelium, 308, 308f, 309, 309f Mycorrhizae, 311, 311f, 312, 376

N NAD+/NADH (nicotinamide adenine dinucleotide), 82, 110f, 111, 112f, 114–115, 117f NADP+/NADPH, 102, 102f NADPH forms, noncyclic pathway, photosynthesis, 100 National Cancer Institute (NCI), 191 Native Americans, 251 Natural selection, 224, 224t and antibiotic-resistant bacteria, 242 and diversity, 248–249 mutations and, 244 modes of, 245f Nature vs. nurture, 188 Neanderthals, 345–347, 345f Nectar, floral, 376 Nematodes. See Roundworms Nerve cord, 333, 333f Nervous system earthworm, 324, 324f flatworm, 324 lancelet, 333, 333f roundworm, 326 sea star, 322 Neutral mutations, 236 Neutrons, 28, 28f New Guinea Foja Mountains, 3, 18f, 18 New World monkeys, 342f, 343, 343f Niche, 371 n Nitrate pollution, 384, 386

Nitrification, 385, 385f Nitrogen cycle, 385, 385f Nitrogen fixation, 275, 275f, 376, 385, 385f NK cells. See Natural killer cells Noncyclic pathway, 99–100, 101f ATP forms, 100 hydrogen ion gradient forms, 100 NADPH forms, 100 oxygen forms, 100 photosystem II in, 100 Nondisjunction, 196, 196f Nonpolar covalent bond, 33, 33f Nonvascular plants. See Bryophytes Normal flora. See Normal microbiota Normal microbiota, 276 Notochord, 257f, 333, 333f Nuclear envelope (membrane), 62, 62f Nuclear pores, 62, 62f Nucleic acid(s), 48, 48f Nucleic acid hybridization, 206 Nucleoid, 60, 60f Nucleotide dimers, 135, 135f Nucleotide repair, 135 Nucleotides, 48, 48f DNA, 128–129, 128f, 130f, 133, 135, 144, 114f in DNA sequencing, 207 and genetic code, 146–147, 146f methylation of, 154–155, 155f, 188 in PCR, 206 RNA, 143, 144, 144f Nucleus of atom, 28 origin of, 278, 278f Nucleus, of cell, 54, 54f in eukaryotic cells, 8, 62, evolution of, 278, 278f Nutrient, 6. See also Absorption cycling of, 6, 6f, 379, 379f, 383–388, 383f–388f as requirement for life, 6 n Nutrient pollution and algal blooms, 386, 386f n Nutrition, human dietary fat and, 41, 46, 46f genetically modified foods and, 212 microbiome and, 267 n

O Obesity genetic factors, 191 n Ocean acidification, 389 Ocean currents, 397–398, 397f Ocean ecosystems, 406, 406f Octopus, 325, 325f Oils, as hydrophobic, 35 Old Order Amish, 252, 252f Old World monkeys, 342f, 343, 343f n Olestra®, 15, 15f Oligochaetes, 324, 324f Oligosaccharides, 40 Oliver, Paul, 3f, 22f Oncogenes, 165, 165f One-way flow of energy, 6–7 Open circulatory system, 325 n Opium, 306 Opportunistic life history, 360, 360f Orangutan, 342f, 343 n

Organelles, 54, 54f, 62–64, 62f origin of, 277, 278f Organic compounds, origins of, 37–38, 269, 269f, 271f Organic molecules, 37–38, 38f Organisms, 5, 5f Organ transplantation. See Transplantation Organ, 4 Organ system, 4 Osmosis, 85–86, 85f Osmotic pressure, 86, 86f Ovary, human n cancer of, 136, 167 hormones, 154 Ovary, plant, 304, 304f, 305 n Overharvesting, of a species, 413 Ovule, 301, 301f, 303, 304, 304f, 305 Ovum. See Egg Oxaloacetate, 118 Oxygen in aerobic respiration, 110, 110f, 113 and early atmosphere, 268, 273 in photosynthesis, 98, 101f, 102, 102f, 102–103 Oxygen forms, noncyclic pathway, photosynthesis, 100 Ozone layer, 273, 409, 409f n destruction of, 386

P Packaged foods, PHO in, 27f Paine, Robert, 378 Paleozoic era, 232f–233f Palps, 329 PAMP. See Pathogen-associated molecular pattern Panda, 412, 412f Pangea, 229, 231, 231f Paramecium, 280, 281f, 372, 373f Parasites, 371t, 374–375, 374f, 375f. See also Brood parasites altering of host behavior, 284 arachnids as, 328 flatworms as, 323, 323f, 324 fungi as, 293, 310–311 n malaria-causing, 249, 250f plants as, 375, 375f protists as, 279, 281, 283, 283f roundworms as, 326–327, 327f, 331 Parasitism, 371t, 374–375, 374f Parasitoids, 375, 375f n Partially hydrogenated vegetable oil (PHO), 27, 43 in packaged foods, 27f Parturition. See Labor Passive immunization, 494 Passive transport, 87, 88f n Pasteurization, 364 n Pathogens. See also Disease in microbiome, diet and, 267 PAX6 gene, 154, 154f PCR (polymerase chain reaction), 206, 206f, 210 Peacock butterflies, 16–17, 16f, 19f Peat moss, 297 Pedigrees, 190, 191f, 198 Pellicle, 279f n Penicillin, 313, 364

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440  INDEX Peppered moths, 246–247, 246f Pepsin, 80, 81f Peptide, 45 Peptide bond, 45, 44f–45f Per capita growth rate, 355, 356f Permafrost, 404 Permian period, 232f–233f n Pertussis (whooping cough), 276, 276t n Pest control, biological, 375, 375f n Pesticides alternatives to, 211–212, 211f and crop yields, 363 PET (positron-emission tomography) scans, 29, 29f pH, 36, 36f of blood, 37 and enzyme function, 81, 81f Phagocytosis, 89, 89f Phenotype, 182, 182f environmental effects on, 188f, 189–190 gene interactions and, 189–191, 188f n Phenylketonuria (PKU), 193t, 198 Phloem, 295, 295f Phorid flies, 375f Phosphate, 384–385, 384f Phospholipids, 43, 43f, 57, 58f–59f Phosphorus cycle, 384–385, 384f Phosphorylation, 82, 82f, 87 electron transfer phosphorylation, 100, 110f, 111–112 Photosynthesis, 6 adaptations to climate, 102 and aerobic respiration, 109 and carbon cycle, 387, 387f in dark, 101 energy storage in, 79, 102 light-dependent reactions, 98, 99–102, 101f, 102f light-independent reactions, 98–99, 102f, 102–103 noncyclic pathway, 99–100, 101f overview, 98–99 photosynthetic pigments, 97–98, 98f, 99–100 Photosystem, 99, 101, 101f Photosystem I, 100 Photosystem II, noncyclic pathway, photosynthesis, 100 Phycobilins, 281 Phylogenetics, forensic, 262 Phylogeny, 260–261 Phylum, 10f, 11 Pigments, 97 in photosynthesis, 97–98, 98f, 99–100 retinal, 256 Pill bugs, 330 Pillus (pilli), 60f, 61, 273, 273f Pine trees, 302, 303f Pinocchio frog, 3f Pinworms, 327 Pioneer species, 377, 378f n PKU (phenylketonuria), 193t, 198 Placenta, 199 Placental mammals, 340, 341f Planarians, 323, 323f Plankton, 280 Plant(s), 8, 9f, 294

adaptations to climate, 96, 96f vs. animals, 307t asexual reproduction, 297, 298 bryophytes, 296–297, 297f carnivorous, 372, 372f cells, cytoplasmic division in, 164, 164f characteristics of, 294–295, 294f classification of, 11f diseases, 293, 293f, 310, 327, 327f evolution of, 281, 294–295, 294f flowering. See Angiosperms vs. fungi, 307t n genetically modified, 211–212, 211f glucose storage in, 41, 102 herbivory and, 374 immune system, 179 life cycle, 174, 294–295, 294f meiosis in, 173 mitosis in, 162f, 163, 164f mutualism in, 376–377, 376f osmotic pressure in, 86, 86f parasitic, 374, 374f phenotype plasticity in, 188f, 188 polyploidy in, 255, 256f seed, 295, 301, 301f seedless vascular, 294f, 298–300, 299f, 300f sexual reproduction, 294, 294f, 295 Plasma membrane, 54, 54f, 60, 60f, 164, 164f, 167 Plasmids, 60, 205, 205f, 205, 205f, 274 Plasmodesmata, 69 Plasmodial slime molds, 284–285, 285f Plastic pollution, in Pacific, 408 Plate tectonics theory, 20t, 229–230, 230f, 231f Platypus, 341f Pleiotropy, 186 Plot sampling, 354 Polar covalent bond, 33, 33f Polarity, 33, 32f, 34f n Polio vaccine, 159 Pollen grains, 295, 301, 301f, 304, 304f, 304, Pollen sac, 301, 301f, 304f, 304 Pollen tube, 301, 301f, 303, 304f, 305 Pollination, 301, 301f, 304f, 305 Pollinators, 305, 305f insects as, 254, 254f, 305, 305f, 330, 331f n Pollutant, 407 n Pollution. See also Air pollution; Water pollution and bioaccumulation, 382 and biological magnification, 382 n Pollution, global effects of, 407–411 acid rain, 408–409, 409f global climate change, 409–411, 410f ozone layer, destruction of, 409, 409f plastic in ocean, 407–408 Poly-A tail, 145 Polycheates, 324, 324f n Polydactyly, 191f, 192t, 252, 252f Polygenic inheritance (epistasis), 186–188, 186f, 187f, 189 Polymerase DNA, 133–134, 133f, 206, 206f, 207 RNA, 145, 153, 154 Polymerase chain reaction (PCR), 134, 206, 206f Polymers, 38–39 Polypeptide lengthens, 148, 150

Polypeptides, 45, 45f–46f Polyploidy, 196 Polyps, 322, 322f Polysaccharides, 40–41, 40f Poouli, 262f Population, 5, 5f, 351 age structures and, 354, 364, 364f biotic potential, 359 characteristics of, 352–354 density, 352 distribution, 352–353, 353f founding populations, 251 growth, 355–358 growth rate, 362–364, 363f human, 362–364 limiting factors, 356–357, 357f, 358f phenotype variation in, 242, 243f, 243t random distribution, 353, 353f sampling of, 354–355 size, 352, 362–364, 363f Population bottleneck, 251, 251f Positive feedback, 410 n Positron-emission tomography (PET) scans, 29, 29f Potential energy, 76, 76f Powdery mildew, 310 p53 protein, 166 Prairies, 402, 402f Precipitation n acid rain, 408–409, 409f global patterns of, 396, 396f n and pollution, 397 and water cycle, 383, 384f Predation in annelids, 324 in centipedes, 325 and coevolution, 318, 371t, 372–373, 373f evolution of, 319 and life history evolution, 361, 361f in mollusks, 324, 325 and natural selection, 246–247 in protists, 280, 280 in reptiles, 339, 340 Predictions, 13, 14t, 15, 15f n Prenatal diagnosis, 198–199, 198f, 199f Prey, defenses of, 16–17, 16f, 373–374, 374f Primary production, 380 Primary structure, of protein, 45, 45f–47f Primary succession, 377, 377f Primates, 342–343, 342f Primers, in DNA replication, 133, 133f, 206 Principle of competitive exclusion, 372 Prion, 47, 47f n Prion diseases, 46–48, 47f Probability, 18 Probes, DNA, 206 Procter & Gamble Co., 27 Producers, 6, 6f, 77, 77f, 379, 379f, 380, 382f Products, of reactions, 77 n Progeria, 192f, 192t, 193 Prokaryote(s), 8, 8f, 273–274. See also Archaea; Bacteria cell structure, 60–61, 60f–61f DNA, 59, 60f evolutionary tree, 271 external structures, 60–61

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INDEX  441  fossil evidence, 271–272, 272f gene transfers in, 274, 274f species diversity, 275–276 structural features, 60–61 structure and function, 273, 273f transcription in, 144 Promoter, 145 Prophase, 160f, 162f, 163 Prophase I, 171, 172f–173f, 174 Prophase II, 172f–173f, 173 Protein(s), 44–48 adhesion, 58f–59f, 58, 285 comparing, 236, 236f denaturing of, 47, 80 digestion of, 117f, 117 malfunctions of, 46f, 47–48 membrane, 58f–59f, 59, 62 receptor, 58f–59f, 58, 89 structure, 44–45, 44f–45f structure–function relationship, 46–48 synthesis of, 44–45, 44f–45f, 62f, 63, 144, 147f, 148–150. See also Translation transport, 58f–59f, 59, 66, 87–88, 88f, 179 Proterozoic era, 232f–233f Protists, 8, 9f, 279–289 classification of, 11f genetic code and, 147 as pathogens, 267, 276f, 586 reproduction, 279 structure of, 279 Protocells, 270f, 270, 271f Protons, 28, 28f Proto-oncogenes, 165 Protostomes, 319, 319f Protozoans ciliated, 279f flagellated, 279f, 280 PrP protein, 47–48, 47f Pseudanabaena, 60f Pseudocoelom, 320, 320f, 326, 326f Pseudopod, 68, 68f, 281, 281f, 285 Pseudoscience, 21, 21t Pterosaurs, 234f Punnett square, 183 Pupation, 329f, 330 Pyruvate,114–115, 117f, 118

Q Quaternary structure, of protein, 44f–45f, 45

R Radial symmetry, 319, 319f and genetic damage, 136, 136f Radioactive decay, 29 n Radioactive tracers, 29, 29f Radioisotope, 29, 29f Radiometric dating, 227–228, 228f Radula, 325, 325f n Rain forests, 399, 399f, 400, 401f Rain shadow, 403 Range, of species, 352 Rats diversity of, 341 n Hawaiian birds and, 258 rat poison resistance in, 245, 246, 246f

Ray-finned fishes, 336, 336f Reactants, 77 Reactions, chemical, 39 Ready-to-eat products, 53 Receptor proteins, 58f–59f, 58, 89 Recessive allele, 182, 182f Recombinant DNA, 204, 204f, 205f Recombination, viral, 289 Red algae, 279f, 281, 281f Red blood cells (erythrocytes), 86f n sickle cell anemia, 151, 152f n Red–green color blindness, 195 Red imported fire ants (RIFAs), 369, 369f, 379, 412 Reefs. See coral reefs Regulatory sites, mutations in, 152, 152f Replication errors, 134f, 135 mutations and, 134f, 135 proofreading and mismatch repair, 135 Reporting of results, 14, 14t, 15f Reproduction. See also Asexual reproduction; Sexual reproduction amniotes, 338 amphibians, 337 animals, 318 apicomplexans, 283, 283f archaea, 273, 274f asexual vs. sexual, 170t bacteria, 273, 274f barnacles, 330 birds, 339 bryophytes, 296–197, 297f of cells. See Meiosis; Mitosis as characteristic of life, 7 fungi, 308–309, 309f protists, 279 reptiles, 338 sea stars, 332 seedless vascular plants, 298–299, 299f and sexual selection, 249, 249f slime molds, 284, 285f sponges, 321 viruses, 286–287, 287f, 288f n Reproductive cloning, 127 Reproductive isolation, 253–254, 253f, 254f Reptiles, 235, 261, 339–340, 338f Resource partitioning, 372 Respiratory system. See also Gill(s); Lung(s) bird, 340 n Restoration, ecological, 414, 415f Restriction enzymes, 204–205, 205f Result, experimental, 14, 14t, 15f Reverse transcriptase, 287, 287f Reznick, David, 361, 361f n Rheumatoid arthritis, 267, 276 Rhizoid, 296 Rhizomes, 298, 299, 299f, 300 Ribosomal RNA (rRNA), 148, 148f Ribosome-inactivating proteins (RIPs), 141, 150 as cancer drugs, 150, 150f translation and, 150 Ribosomes, 60, 60f, 64f, 65 and ribosome-inactivating proteins (RIPs), 141, 150 structure and function, 148–150, 150f Ribozymes, 271

Rice, 211, 306 Ricin, 141 n Ringworm, 311 River ecosystems, 405 RNA base pairing in, 143 converge, 148 information flow, 143 messenger, 143, 145, 148–150, 153 post-transcription modifications, 145, 145f ribosomal, 147f, 148 structure and function, 48, 62, 143, 143f in transcription, 142, 144–145, 144f, 147f transfer, 148–150, 148f in translation, 148–150 types of, 143 viral, 286, 286, 286f vs. DNA, 143, 143f RNA polymerase, 144–145, 144f, 153, 160 RNA world hypothesis, 270 Rock, dating of, 227, 226f Rock pocket mice, 245 Rodhocetus kasrani, 227, 227f Rough ER, 64f, 65 Roundworms, 319f, 320, 320f, 326–327, 326f, 327f, 331 rRNA. See Ribosomal RNA r-selected species, 360–361, 360f Rubisco, 102, 102 RuBP, 102, 102f n

S Saccharides, 39–40, 40f Saccharomyces cerevisiae, 114f, 114 Sac fungi, 308, 309, 310, 311, 312 Saguaro cactus, 221f, 235f Sage, 254, 254f Sahara Desert, 403, 403f Salamanders, 337, 337f Salmonella, 187, 187f, 241 Salt, 34. See also Halophiles and enzyme action, 80 Sampling, of population, 354–355, 355f Sampling error, 17–18, 18f, 190, 191, 197, 355 San Andreas Fault, 230f Sandworms, 324, 324f n Sanitation, and human population, 364 Saturated fats, 42, 46, 46f Saturated fatty acids, 42, 42f Savannas, 398f, 402f, 403 n Scabies, 330 Scales, 335 Scallops, 325f Scanning electron microscopes, 56–57, 56f n Schistosomiasis, 324 n SCIDS (severe combined immunodeficiencies), 194t, 214–215 Science nature of, 13, 21 vs. pseudoscience, 21 Scientific method, 14, 14t Scientific theory, 20–21, 20t SCNT. See Somatic cell nuclear transfer Scorpion, 329, 329f Scrapie, 47–48

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442  INDEX Screening, genetic, 198–199, 199f Sea anemone, 319, 322, 322f, 376f, 376 Sea cucumber, 332, 332f Seafloor ecosystems, 406 Sea lettuce, 282f Sea levels, global warming and, 409 Seamounts, 407 Seasonal behavior in animals, 189–190 Sea stars, 332, 332f, 378, 378f Sea urchins, 332, 332f Sea whips, 317 Secondary growth, 301, 313 Secondary sexual traits, 197 Secondary structure, of protein, 44, 44f–45f Secondary succession, 377, 378f Second law of thermodynamics, 76–77 Sedimentary rock, 219f, 225, 226f, 231–232, 232f–233f Seed, 295 dispersal of, 305, 376 formation of, 308, 308f Seedless vascular plants, 294f, 298–300, 299f, 300f Seed plants, 295, 301, 301f Selective permeability, 85, 85f Semiconservative replication, 133 Semipermeable membranes, 84–86, 85f Senescence, 168 Sepals, 304, 304f Sequencing, DNA, 207–208, 208f n Severe combined immunodeficiencies (SCIDs), 214–215 Sex chromosomes, 132 gene expression controls, 154, 154f, 194 n number changes, 196–197, 197t Sex determination, 132, 154 Sexual reproduction, 170 vs. asexual reproduction, 170t and genetic variations, 169–170, 174–175, 189 meiosis and, 171, 174 in plants, 294, 294f, 295 Sexual selection, 249–250, 249f Shared traits, 169–170 Sharks, 335, 335f Shell models, of atoms, 30f, 30, 33t Shivering, 433, 480 Shock, 491 Short tandem repeats, 189, 189f, 209, 210f Shoulder. See Pectoral girdle (shoulder) Shrimp, 255f n Sickle-cell anemia, 151–152, 151f, 152f, 170, 186, 193t, 198, 214, 249, 250f Silica-shelled diatoms, 280, 280f Simple sugars. See Monosaccharides Single-nucleotide polymorphisms (SNPs), 203 Sister chromatids, 131, 133, 161, 161f, 162f, 171–172, 172f–173f Skin n cancer of, 193 color of, 187–188, 187f, 188–189 Skin cancer, due to UV light, 135 n Sleeping sickness, 283 Slime molds, 279f, 284–285, 285f Slugs, 325 Smith, Hamilton, 204 n

Smoking. See Tobacco use Smooth ER, 64f, 65 Snails, 317, 317f, 324, 325f Snakes, 338, 338f SNP chips, 209, 209f SNP genotyping, 209, 209f SNPs (single-nucleotide polymorphisms), 203 Soap, fatty acids in, 41 Sociable weaver birds, 247, 247f Sodium chloride, 32, 32f, 34 Sodium–potassium pumps, 88 Solar energy, and latitude, 396, 396f Solenopsis invicta. See Red imported fire ants Solutes, 34 Solution, 35 tonicity of, 85–86, 86f Solvent, 34 Somatic cell nuclear transfer (SCNT), 127, 127f Somites, 237, 237f n Sonography, obstetric, 198, 198f Sori, 298, 299f Speciation, 253–255 Species, 3, 10, 10f, 12 n evenness, 370 indicator, 412 interactions, 371–375 naming and classification of, 8–12, 10f, 11f new, discovery of, 3, 3f, 18f, 18 n richness, 370 n Species diversity, 370, 413 Sperm animal, 68, 174, 321, 325, 333, 336 plant, 295, 296, 297f, 297, 298, 299f, 301, 301f, 303–303, 304f, 305 Spiders, 329, 329f, 372, 372f Spike mosses, 294f Spindle, 163, 164f, 172–173, 172f–173f, 175f Spirillum, 274 Sponges, 319, 319f, 321, 321f Sporangium, 297f Spores, 295f, 294f, 296, 297f, 299, 299f, 300, 301, 301f, 308, 309, 309f Sporophytes, 294–295, 294f, 296, 297f, 299, 299f, 304f, 304 Sporozoans. See Apicomplexans Squids, 325 ST131, 263 Stabilizing selection, 245, 245f, 247, 247f Staining, in microscopy, 56 Stalk-eyed fly, 250f Stamens, 304, 304f Staphylococcus, 276 Starch, 40, 40, 40f Start codons, 146 Statistical significance, 19 n Stem cells, 168 Steroid(s), 43, 43f Sticky ends, of DNA, 204, 204f, 205f Stigma, 304, 304f, 305 Stomata, 295, 295f Stop codons, 146, 146f, 148, 149 Strain, 282 Stream ecosystems, 384 n Strep throat, 276t n

Streptococcus thermophilus, 115, 115f Stress response in animals, 189 Stroma, 96–97, 96f, 100, 101f, 102 Structural formula, 32, 33t, 38, 38f Structural model, 32, 33t Structure–function relationship, proteins, 46–48 Style (plant), 304, 304f Substrates, of enzyme, 80–81, 80f, 81f Succession, ecological, 405 Sucrose, 40 Sugars, 39. See also Monosaccharides Sully: Miracle on the Hudson, 351 Sunlight electromagnetic energy from, 97, 97f as energy source, 6f, 66, 66f, 97, 99, 379, 379f, 396, 396f, 397 Superbugs, 241 evolution of, 262–263, 263f Supercontinents, 231, 231f Surface-to-volume ratio, 55–56, 55f cell form, constraints on, 55 limits on cell size, 55, 55f, 55t Survivorship curves, 359, 359f n Sustainable living, 414–415 Swamp forests, of Carboniferous period, 300, 300f Sweating, 7f Swim bladder, 334, 334f, 335f, 336 Symbiosis, 374 Symington, James, 123, 123f Symmetry, bilateral, 319, 319f Sympatric speciation, 256–257, 256f n Syndrome, 191 n Syphilis, 276, 276t

T Tadpoles, 337, 337f Taiga. See Boreal forest Tapeworms, 323, 323f Tarsiers, 342f, 343, 343f n Tau protein, 63 Taxon, 10, 10f, 11 Taxonomy, 10, 10f, 11, 11f, 260 n Tay-Sachs disease, 193t, 194, 198 Teeth of mammals, 340 Tektites, 219 Telomerase, 168–169 Telomeres, 167f, 168–169 Telophase, 160f, 162f, 163–164 Telophase I, 172, 172f 196f Telophase II, 173–174, 173f, 196f Temperature, 35 and diffusion rate, 85 and enzyme action, 80, 81f n global, CO level rise and, 94, 94f 2 n homeostasis, 35 Temporal isolation, 253 Tertiary structure, of protein, 45–46, 45f Testicle n Test tube babies, 199 n Tetanus, 276, 276t n Tetracycline, 276 Tetrapods, 334, 334f, 336 Thermodynamics, laws of, 21, 76, 76f

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INDEX  443  Thermophiles, 276–277, 277f Theropods, 225f n Threatened species, 411, 412 Three-domain classification system, 271f Thylakoid membrane, 63, 63f, 95–96, 96f, 99 Thymine (T), 128, 128f, 143, 143f Thymine dimers, 135, 135f Ticks, 276, 329–330, 329f, 374–375, 374f Tight junctions, 68, 69f Tissue, 4 evolution of, 319, 319f layers (germ layers), 319, 320f T lymphocytes. See T cells Toads, 337 Tobacco mosaic virus, 286f Tobacco smoke as mutation-causing, 136 n Tobacco use health effects of, 188 Tonicity, 85, 86f Tortoises, 339 Total fertility rate, 364 Tracers, 29, 29f Trait(s), 11 and taxonomy, 11 derived, 260 shared, 169–170 Transcription, 142, 142f, 143, 143f, 144–146, 144f coding and noncoding strands, 144, 144f RNA modifications, 145–146, 145f RNA synthesis, 144f, 145 vs. DNA replication, 144 Transcription factors, 153 Transduction, prokaryotic, 246, 247f n Trans-fats, 27, 27f, 42, 42f, 43, 46f Transfer RNA (tRNA), 143, 148f Transformation, prokaryotic, 274, 274f n Transfusion, blood type and, 186 n Transgenic organisms, 211–213, 211f, 212f Translation, 143, 146–148, 147f RIPs interference with, 150 Transmission electron microscopes, 56, 56f Transpiration, 383 Transport active, 87–88, 88f passive, 87, 88f Transport proteins, 58f–59f, 59, 66, 87–88, 88f, 179 n Trash, environmental damage from, 407–408, 407f Tree kangaroo, golden-mantled, 18, 18f Triassic period, 232f n Trichinosis, 327 n Trichomoniasis, 282 Triglycerides, 42–43, 116 n Triple X syndrome, 197, 197t Triploid (3n) cell, 305 n Trisomy, 196 n Trisomy 21 (Down syndrome), 196, 197t n Trisomy X, 197, 197t tRNA. See Transfer RNA

Trophic levels, 380–382, 380f–382f Tropical dry forest, 400 n Tropical rain forests, 399–400, 399f, 401, 406 Truffles, 312 Trypanosomes, 283 Trypsin, 80, 81f n Tuberculosis, 276, 276t Tubulin, 66, 67f, 163 n Tumor, 165 Tumor suppressor genes, 166 Tundra, 404, 407f Tunicates, 333, 333f Turgor, 86, 86f Turgor pressure, 86, 86f, 87 n Turner syndrome, 197, 197t Turtles, 132, 339, 339f, 340 Twins, 127 n Typhoid fever, 187, 187f, 364

U Ultrasound imaging, 198, 198f Ultraviolet (UV) light mutations and, 135, 135f nucleotide dimers, 135, 135f nucleotide repair, 135 skin cancer, 135 Ultraviolet radiation, 97f n and skin, 193 Uniformitarianism, 222 United States n ecological footprint, 365, 365f population, 364, 364f n United States Department of Agriculture (USDA) dietary recommendations, 53 Unsaturated fats, 43, 46, 46f, 509 Unsaturated fatty acids, 42, 42f Uracil (U), 143, 143, 143f U.S. Food and Drug Administration (FDA), 27 n

V Vacancies, 30–31 Vaccines, 364 Vacuoles, 64–65 Vagina, 276 n Vaginitis, 311 Valves Variables, 13 n Variant Creutzfeldt–Jakob disease (vCJD), 47–48, 47f Variation, continuous, 189–190, 189f Vascular plants, 294f, 295 Vectors cloning, 204–205, 205f, 214, 215 n disease, 261–262, 276, 276t, 277, 331 n Vegan diet, 382 Vendrely, Roger, 126 Venoms, 339 Venter, Craig, 208 Vertebral column, 334 Vertebrates, 317 characteristics, 334 evolution of, 334f Vesicle-based transport, 88–89 endocytosis, 88, 89f n

exocytosis, 88, 89, 89f phagocytosis, 88, 89, 89f Vesicles, 62t, 64–65, 64f, 88–89, 89f, 164, 164f Vinyl chloride, 137 Viral envelope, 286–287, 286f Viral reassortment, 289, 289f Viral transmission, cladistic analysis and, 262 Virus(es), 286–289. See also HIV; HPV cladistics, 262 mutation and recombination, 289 mutations in, 289, 289f origins of, 286 n as pathogen, 288 replication, 286–288, 288f structure, 286, 286f, 287f Visible light, 97, 97f Vision. See also Eye n Vitamin(s) intestinal bacteria and, 375–376 vitamin A, 211 vitamin K, 245 VKOR enzyme, 245 Volvox, 282, 282f

W Wallace, Alfred, 221, 224–225, 225f Warfarin, 245, 246 Warning coloration, 373, 373f n Warts, 166 Wasps, 225f, 373, 373f Water in aerobic respiration, 108, 108f hydrogen bonding in, 34, 34f ice, 35, 35f molecule, 32, 32f, 33, 33f in plants, osmotic pressure of, 86, 86f properties of, 34–36, 34f, 35f Water fleas, 188f, 189 Water forms, electron transfer phosphorylation, 113 Water molds, 279f n Water pollution and amphibian population decline, 336 fertilizers and, 384, 385, 386 nitrates as, 384, 385 phosphates and, 383, 384 trash and, 407–408, 407f Water–vascular system, 332 Watson, James, 128, 129, 208 Wavelength, 97, 97f Waxes, 44 Weather patterns global, 396–397, 396f n global warming and, 410–411 Whales, 227, 227f, 361 Wheat, 256, 256f, 306, 306f Wheat stem rust, 293, 293f, 310 Whisk ferns, 294f White abalone, overharvest of, 412f, 413 White blood cells (leukocytes). See also Macrophage; Dendritic cell; B cell; T cell HIV and, 286, 286f phagocytosis by, 89, 89f n White nose syndrome, 311, 311f n Whooping cough (Pertussis), 276, 276t

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

444  INDEX Wikelski, Martin, 355 Wildebeests, 402f, 403 Wilkins, Maurice, 129 Wind, as pollination vector, 614 Wine, fermentation of, 312 Wine, production, 114, 114f Wings analogous structures, 235, 235f bird, 340 insect, 327, 331 Woese, Carl, 271 Womb. See Uterus Wood, 78, 79f, 300 Work, 76

X X chromosome, 132, 132f X-linked recessive disorders, 194–195, 194f, 194t, 195f n XO (Turner) syndrome, 197, 197t X-ray crystallography, 128–129 X rays, 97f, 136 n XXX syndrome, 197, 197t n XXY syndrome, 197 n XYY syndrome, 197, 197t

Yogurt, lactate fermentation, 115, 115f Yolk sac, 340f Yucca plants and moths, 376, 376f

n

Y Y chromosome, 132, 132f Yeast, 307, 307f, 312

Z n n

Ziconotide (Prialt), 316 Zika virus, 289 Zygospore, 307, 307f Zygote animal, 174, 282, 282f plant, 174, 294f, 295, 296, 297f, 297, 298, 299f, 301, 302, 305 Zygote fungi, 308, 308f

Copyright 2021 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.