Biochemistry [2 ed.] 0367465531, 9780367465537

Biochemistry Second Edition, is a single-semester text designed for undergraduate non-biochemistry majors. Accessible, e

184 96 44MB

English Pages 512 [513] Year 2021

Table of contents :
Cover
Half Title
Title Page
Copyright Page
Dedication
Table of Contents
Preface to the First Edition
Preface to the Second Edition
Acknowledgments
Author
Glossary
Chapter 1 Foundations
1.1 Origins of Biochemistry
1.2 Some Chemical Ideas
1.2.1 Reactions and Their Kinetic Description
1.2.1.1 Equilibrium
1.2.2 The Steady-State
1.3 Acid–Base Reactions
1.4 Redox
1.5 Energy
1.6 Cell Theory
1.7 Species Hierarchy and Evolution
1.8 Biological Systems
Key Terms
Bibliography
Chapter 2 Water
2.1 Structure of Water
2.1.1 Gas Phase Water
2.1.2 Partial Charges and Electronegativity
2.1.3 Condensed Phase Water: Hydrogen Bonding
2.1.4 Hydrogen Bonding in Condensed Phase Water
2.2 The Hydrophobic Effect
2.3 Molecules Soluble in Water
2.4 High Heat Retention: The Unusual Specific Heat of Liquid Water
2.5 Ionization of Water
2.6 Some Definitions for the Study of Acids and Bases
2.7 The pH Scale
2.8 The Henderson–Hasselbalch Equation
2.9 Titration and Buffering
Summary
Review Questions
Chapter 2 Addendum: The Dielectric
Key Terms
Bibliography
Chapter 3 Lipids
3.1 Significance
3.2 Fatty Acids
3.3 Triacylglycerols
3.4 Phospholipids
3.5 Cholesterol
3.6 Lipid–Water Interactions of Amphipathic Molecules
3.7 Phospholipid Monolayers
3.8 Lipid Composition of Membranes
3.9 Water Permeability of Membranes and Osmosis
Summary
Review Questions
Chapter 3 Addendum: Inverted Micelles
Key Terms
Bibliography
Chapter 4 Carbohydrates
4.1 Monosaccharides
4.2 Ring Formation in Sugars
4.3 Disaccharides
4.4 Polysaccharides
4.4.1 Linear Polysaccharides
4.4.2 Branched Polysaccharides
4.5 Carbohydrate Derivatives
4.5.1 Simple Modifications
4.5.2 Substituted Carbohydrates
Summary
Review Questions
Chapter 4 Addendum: The Discovery of Stereoisomerism
Key Terms
Bibliography
Chapter 5 Amino Acids and Proteins
5.1 Common Structure of the Amino Acids
5.2 Biology of the Amino Acids
5.3 Amino Acid Individuality: The R Groups
5.3.1 Polarities
5.3.2 Functional Groups
5.4 Acid–Base Properties and Charge
5.4.1 Titration and Net Charge
5.4.2 Interactions between the α-Carboxylate and α-Amine Groups
5.4.2.1 Inductive Effect
5.4.2.2 Electric Field Effect
5.4.3 Multiple Dissociable Groups
5.5 The Peptide Bond
5.6 Peptides and Proteins
5.7 Levels of Protein Structure
5.7.1 Primary Structure
5.7.2 Secondary Structure
5.7.2.1 α-Helix
5.7.2.2 β-Sheet
5.7.3 Domains
5.7.4 Tertiary Structure
5.7.5 Quaternary Structure
5.8 Protein Folding
5.9 Oxygen Binding in Myoglobin and Hemoglobin
5.10 Other Binding Reactions Involving Proteins
5.10.1 Extracellular Binding Proteins
5.10.2 Cell Surface Binding Proteins
5.10.3 Intracellular Binding Proteins
5.11 Protein Purification and Analysis
5.11.1 Purification
5.11.2 Analysis
Summary
Review Questions
Chapter 5 Addendum: Atomic Charged Forms
Key Terms
Bibliography
Chapter 6 Enzymes
6.1 Energetics of Enzyme-Catalyzed Reactions
6.2 The Enzyme Assay and Initial Velocity
6.3 A Simple Kinetic Mechanism
6.3.1 Assumptions
6.3.2 The Michaelis–Menten Equation
6.4 How the Michaelis–Menten Equation Describes Enzyme Behavior
6.5 The Meaning of Km
6.6 Reversible Inhibition
6.6.1 Competitive Inhibition
6.6.2 Anticompetitive Inhibition (Uncompetitive)
6.6.3 Mixed Inhibition (Noncompetitive)
6.7 Double-Reciprocal or Lineweaver–Burk Plot
6.8 Allosteric Enzymes
6.9 Irreversible Inhibition
6.10 Enzyme Mechanisms
6.10.1 Nucleophilic Substitution
6.10.2 Acid–Base Catalysis
6.11 Enzyme Categories
6.12 Enzyme-Like Qualities of Membrane Transport Proteins
Summary
Review Questions
Chapter 6 Addendum: The Haldane Relationship
Key Terms
Bibliography
Chapter 7 Coenzymes
7.1 Coenzymes: Bound and Mobile
7.2 Coenzymes and Vitamins
7.3 Redox Coenzymes
7.3.1 Nicotinamides
7.3.2 Ubiquinone
7.3.3 Flavin Coenzymes
7.4 Acyl Transfers
7.4.1 CoA
7.4.2 Carnitine
7.4.3 Lipoic Acid
7.5 Carboxylation
7.5.1 Biotin
7.5.2 Vitamin K
7.6 Exchange Coenzymes
7.6.1 Thiamine Pyrophosphate
7.6.2 Pyridoxal Phosphate
7.7 Metal Ion Cofactors
7.7.1 Mg2+
7.7.2 Iron
7.7.3 Copper
7.7.4 Co2+
7.7.5 Mn2+and Zn2+
7.7.6 Selenium
7.7.7 Dietary Essentials
Review Questions
Chapter 7 Addendum: The Vitamin K Cycle
Key Terms
Bibliography
Chapter 8 Metabolism and Energy
8.1 Origins of Thermodynamics
8.2 First Law of Thermodynamics
8.2.1 Heat and Work
8.2.2 Enthalpy
8.3 Entropy and the Second Law of Thermodynamics
8.3.1 Entropy as a Ratio of Heat to Temperature
8.3.2 Entropy as a Statistical Distribution of States
8.4 Free Energy
8.5 Standard Free Energy
8.6 Nonstandard Free Energy Changes
8.7 Near-Equilibrium and Metabolically Irreversible Reactions
8.8 ATP
8.9 Energy Coupling with ATP
8.9.1 Creatine Phosphokinase
8.9.2 NDP Kinase
8.9.3 Adenylate Kinase
8.10 Energy of Redox Reactions
8.10.1 Electricity Fundamentals
8.10.2 The Electrochemical Cell
8.10.3 Standard Reduction Potentials
8.10.4 Reduction Potentials and Free Energy
8.10.5 Reduction Potentials
8.11 Mobile Cofactors and the Pathway View
Summary
Review Questions
Chapter 8 Addendum: Free Energy Derivation
Key Terms
Bibliography
Chapter 9 Glycolysis
9.1 Glucose Transport
9.2 From Glucose to Pyruvate
9.2.1 Hexokinase
9.2.2 Glucose Phosphate Isomerase
9.2.3 Phosphofructokinase
9.2.4 Aldolase
9.2.5 Triose Phosphate Isomerase
9.2.6 Glyceraldehyde Phosphate Dehydrogenase
9.2.7 Phosphoglycerate Kinase
9.2.8 Phosphoglycerate Mutase
9.2.9 Enolase
9.2.10 Pyruvate Kinase
9.3 Completing the Pathway
9.3.1 Lactate Formation
9.3.2 Ethanol Formation
9.4 Energetics of Glycolysis
9.4.1 Pathway Thermodynamics
9.4.2 Red Blood Cell Shunt Pathway
9.4.3 Arsenate Poisoning
9.4.4 Fructose Metabolism
9.4.5 Energy Balance and Glycolytic Connections
9.5 Metabolic Connections to Glycolysis
9.5.1 Alternative Entry Points
9.5.2 Glycolytic Intermediates as Intersection Points
9.5.3 Alternative Endpoints of Glycolysis
Summary
Review Questions
Chapter 9 Addendum: Alternatives to Glycolysis
Key Terms
Bibliography
Chapter 10 The Krebs Cycle
10.1 A Cyclic Pathway
10.2 Acetyl-CoA: Substrate of the Krebs Cycle
10.3 Overview of Carbon Flow
10.4 Steps of the Pathway
10.4.1 Citrate Synthase
10.4.2 Aconitase
10.4.3 Cis-Aconitate as a Krebs Cycle Intermediate
10.4.4 Prochirality
10.4.5 The R/S System of Nomenclature
10.4.6 Fluoroacetate Poisoning
10.4.7 Isocitrate DH
10.4.8 α-Ketoglutarate DH Complex
10.4.9 Succinyl-CoA Synthetase
10.4.10 Succinate DH
10.4.11 Fumarase
10.4.12 Malate DH
10.5 Energy Balance
10.6 Regulation
10.7 Krebs Cycle as a Second Crossroad of Metabolic Pathways
Summary
Review Questions
Chapter 10 Addendum: Cyclic Pathways Connected to the Krebs Cycle
1. Glyoxylate Cycle
2. Itaconate Pathway
Key Terms
Bibliography
Chapter 11 Oxidative Phosphorylation
11.1 The Phenomenon
11.2 Mitochondrial Inner Membrane
11.3 Carriers of Electrons, Protons, or Both
11.3.1 Carriers of Electrons
11.3.2 Carriers of Protons
11.3.3 Carriers of Both Electrons and Protons
11.4 Membrane-Bound Complexes
11.5 The Electrochemical Cell and the Mitochondria
11.6 Electron Pathways
11.6.1 Sequence of Electron Flow
11.6.2 Energetics of Electron Flow
11.7 Mechanisms of the Mitochondrial Membrane Protein Complexes
11.7.1 Complex I: Proton Pump
11.7.2 Complex II: Succinate Dehydrogenase
11.7.3 Complex III: Loop Mechanism
11.7.4 Complex IV: Pump and Annihilation
11.7.5 Complex V: ATP Synthesis
11.7.5.1 The Stator
11.7.5.2 The Rotor
11.8 Proton-Motive Force
11.8.1 Electric Circuit Analogy to the Proton Gradient
11.8.2 Utilization of Δp beyond ATP Synthesis
11.9 Mitochondrial Membrane Transport
11.9.1 Adenine Nucleotide Translocase
11.9.2 Phosphate Exchange
11.9.3 Other Transport Proteins
11.9.4 Coupling of Oxidation and Phosphorylation
11.10 Uncoupling
11.10.1 Physiological Uncoupling: Brown Fat
11.11 Superoxide Formation by Mitochondria
11.12 Control of Mitochondria
11.13 How Mitochondria Can Utilize Cytosolic NADH
11.13.1 Glycerol Phosphate Shuttle
11.13.2 Malate/Aspartate Shuttle
Summary
Review Questions
Chapter 11 Addendum: Supercomplexes
Key Terms
Bibliography
Chapter 12 Photosynthesis
12.1 Light and Carbon Reactions
12.2 Chloroplasts
12.2.1 Orientations: N and P Sides of the Membrane
12.2.2 Light Reactions of Photosynthesis as a Reversed Oxidative Phosphorylation
12.2.3 Carbon Reactions of Photosynthesis: CO2 Fixation
12.3 Harnessing Light Energy
12.3.1 Light Absorption and the Antennae
12.3.2 Electron Transfer at Reaction Centers
12.4 Proton and Electron Flow for the Light Reactions
12.5 Cyclic Electron Transfer and Other Variations
12.6 The Calvin Cycle
12.6.1 Ribulose Bisphosphate Carboxylase
12.6.2 Reaction Steps Following Carbon Fixation to Glyceraldehyde-P: Energy Consuming Portion
12.6.3 From GAP to the RuBP: Overview
12.6.4 From GAP to the RuBisCo Step: Reactions
12.7 Variations in CO2 Handling: C3, C4, and CAM Plants
12.8 Pathway Endpoints: Sucrose and Starch
Summary
Review Questions
Chapter 12 Addendum: Dark vs Carbon Reactions
Key Terms
Bibliography
Chapter 13 Carbohydrate Pathways Related to Glycolysis
13.1 Glycogen Metabolism
13.1.1 Glycogen Synthesis
13.1.2 Glycogenolysis
13.1.3 Physiological Context of Glycogen Metabolism
13.1.4 Regulation of Glycogen Metabolism by Glucagon
13.1.5 Regulation of Glycogen Metabolism by Epinephrine
13.1.6 Regulation of Glycogen Metabolism by Insulin
13.1.7 Regulation of Glycogen Metabolism by AMP Kinase
13.2 Gluconeogenesis
13.2.1 Lactate Dehydrogenase as a Gluconeogenic Enzyme
13.2.2 Pyruvate to PEP
13.2.3 Indirect Transport of Oxaloacetate from Mitochondria to Cytosol
13.2.4 Fructose-1,6-P2 to Fructose-6-P
13.2.5 Glucose-6-P to Glucose
13.2.6 Pathway Integration: Glycolysis, Glycogen Metabolism, and Gluconeogenesis
13.2.6.1 The Feeding–Fasting Transition
13.2.6.2 The Resting–Exercise Transition
13.3 The Pentose Phosphate Shunt
13.3.1 Oxidative Stage
13.3.2 Nonoxidative Stage
13.3.2.1 Reactions of the Nonoxidative Stage
13.3.2.2 A Pseudo Three-Dimensional View and Comparison to the Calvin Cycle
13.3.3 Distribution Between NADPH Production and Ribose-5-P
13.4 Galactose Utilization
Summary
Review Questions
Chapter 13 Addendum: Phosphorylation of Glycogen
Key Terms
Bibliography
Chapter 14 Lipid Metabolism
14.1 Absorption of Dietary Lipids
14.2 Fatty Acid Oxidation
14.2.1 Activation
14.2.2 Transport
14.2.3 β-Oxidation
14.2.3.1 Unsaturated Fatty Acids
14.2.3.2 Odd Carbon-Numbered Fatty Acids
14.2.3.3 Shorter and Longer Fatty Acids
14.3 Ketone Body Metabolism
14.4 Fatty Acid Biosynthesis
14.4.1 Export of Acetyl-CoA to the Cytosol
14.4.2 Carboxylation of Acetyl-CoA to Malonyl-CoA
14.4.3 Sequential Addition of Two-Carbon Fragments to Form Palmitate
14.4.3.1 Loading
14.4.3.2 Condensation
14.4.3.3 Reduction
14.4.3.4 Dehydration
14.4.3.5 Second Reduction
14.5 Triacylglycerol Formation
14.6 Phospholipid Metabolism
14.7 Cholesterol Metabolism
14.8 Other Lipids
14.8.1 Eicosanoids
14.8.2 Sphingolipids
14.8.3 Unusual Bacterial Fatty Acids
14.9 Overview of Lipid Metabolism in the Fed and Fasted States
14.10 Integration of Lipid and Carbohydrate Metabolism
14.10.1 Lipid and Carbohydrate Intersections in the Feeding–Fasting Transition
14.10.2 Lipid and Carbohydrate Intersections in the Resting–Exercise Transition
14.10.3 Lipid and Carbohydrate Intersections in Diabetes Mellitus
Summary
Review Questions
Chapter 14 Addendum: The Isoprenes
Key Terms
Bibliography
Chapter 15 Nitrogen Metabolism
15.1 The Nitrogen Cycle
15.2 Reaction Types in NH3 Assimilation
15.2.1 Redox-Neutral
15.2.2 Redox-Active
15.2.3 Redox-Balanced
15.3 Metabolically Irreversible Nitrogen Exchange Reactions
15.4 Near-Equilibrium Nitrogen Exchange Reactions
15.4.1 Glutamate DH
15.4.2 Transaminases
15.5 The Urea Cycle
15.5.1 [NH3] Exceeds [Aspartate]
15.5.2 [Aspartate] Exceeds [NH3]
15.5.3 Steps from NH3 to Citrulline
15.5.4 Cytosolic Steps of the Urea Cycle
15.5.5 Overall Urea Cycle
15.6 Amino Acid Metabolism: Catabolism
15.6.1 Branched-Chain Amino Acid Breakdown
15.6.2 Threonine
15.6.3 Lysine
15.6.4 Tryptophan
15.6.5 Phenylalanine and Tyrosine Degradation
15.6.6 Amino Acids Directly Connected to Major Metabolic Pathways
15.6.7 Arginine, Proline, and Histidine Are All Converted to Glutamate
15.6.8 One-Carbon (1C) Metabolism and Serine, Glycine, and Methionine Breakdown
15.7 Amino Acids: Anabolism
15.7.1 Nonessential Amino Acids
15.7.2 Essential Amino Acids
15.7.3 Aromatic Amino Acid Biosynthesis
15.8 Nucleotide Metabolism
15.8.1 Pyrimidine Synthesis
15.8.2 Pyrimidine Degradation
15.8.3 Purine Synthesis
15.8.4 Purine Degradation
15.8.5 Salvage Reactions
15.8.6 Purine Nucleotide Regulation
15.8.7 Purine Nucleotide Cycle
15.8.8 Deoxynucleotide Formation
15.8.9 A Unique Methylation to Form dTMP
15.9 Other Nitrogen Pathways
Summary
Review Questions
Chapter 15 Addendum: Nitrogen Disposal
The Tilapia of Lake Magadi
The Alligator and the Crocodile
Low Creatinine and Liver Failure
Key Terms
References
Chapter 16 Nucleic Acids
16.1 Strand Structures of the Nucleic Acids
16.2 Structure of the Double Helix
16.3 Supercoiling
16.4 Histones
16.5 Replication
16.5.1 Initiation
16.5.2 Replication Fork and the Replisome
16.5.3 Primer Formation
16.5.4 Creating the Double Helix
16.5.5 Distinctive Features of Eukaryotic Replication
16.6 DNA Repair
16.6.1 Mismatch Repair
16.6.2 Excision Repair
16.6.3 PARP
16.7 Transcription
16.7.1 RNA Polymerase Binding to DNA
16.7.2 Transcription Events in E. coli
16.7.3 Eukaryotic Transcription
Summary
Review Questions
Chapter 16 Addendum: Restriction Enzymes and PCR
Restriction Enzymes
PCR
Key Terms
Bibliography
Chapter 17 Protein Synthesis and Degradation
17.1 Three Forms of RNA Employed in Protein Synthesis
17.1.1 tRNA
17.1.2 rRNA and the Ribosomes
17.2 The Genetic Code
17.3 Steps in Protein Synthesis
17.3.1 Initiation
17.3.2 Elongation
17.3.3 Termination
17.3.4 Distinctive Features of Eukaryotic Translation
17.3.5 Regulation of Eukaryotic Translation
17.4 Co-Translational and Post-Translational Modifications of Proteins
17.4.1 Co-Translational Modifications
17.4.2 Post-Translational Modifications
17.5 Protein Degradation
17.5.1 Extracellular Proteases
17.5.2 Intracellular Proteases
17.6 The mTOR Pathway in the Control of Protein Synthesis
Summary
Review Questions
Chapter 17 Addendum: Skeletal Muscle and Exercise
Key Terms
Bibliography
Appendix
Index

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Biochemistry [2 ed.]
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Biochemistry

Biochemistry Second Edition

Raymond S. Ochs

Second edition published 2022 by CRC Press 6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487-2742 and by CRC Press 2 Park Square, Milton Park, Abingdon, Oxon, OX14 4RN © 2022 Raymond S. Ochs First edition published by Jones and Bartlett Publishers, Inc 2012 CRC Press is an imprint of Taylor & Francis Group, LLC Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, access www.copyright.com or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. For works that are not available on CCC please contact mpkbookspermissions@tandf.co.uk Trademark notice: Product or corporate names may be trademarks or registered trademarks and are used only for identification and explanation without intent to infringe. ISBN: 978-0-367-46553-7 (hbk) ISBN: 978-0-367-46187-4 (pbk) ISBN: 978-1-003-02964-9 (ebk) Typeset in Warnock Pro by Deanta Global Publishing Services, Chennai, India

To my wife, Jessica, for her continued support.

Contents Preface to the First Edition�� xvii Preface to the Second Edition��xix Acknowledgments��xxi Author�� xxiii Glossary��xxv Chapter 1 Foundations��1 1.1 Origins of Biochemistry��1 1.2 Some Chemical Ideas��1 1.2.1 Reactions and Their Kinetic Description��2 1.2.1.1 Equilibrium��3 1.2.2 The Steady-State��5 1.3 Acid–Base Reactions��6 1.4 Redox��7 1.5 Energy��8 1.6 Cell Theory��9 1.7 Species Hierarchy and Evolution��11 1.8 Biological Systems��12 Key Terms�� 13 Bibliography�� 14 Chapter 2 Water��15 2.1 Structure of Water��15 2.1.1 Gas Phase Water��15 2.1.2 Partial Charges and Electronegativity��16 2.1.3 Condensed Phase Water: Hydrogen Bonding��18 2.1.4 Hydrogen Bonding in Condensed Phase Water�� 20 2.2 The Hydrophobic Effect��21 2.3 Molecules Soluble in Water�� 23 2.4 High Heat Retention: The Unusual Specific Heat of Liquid Water��24 2.5 Ionization of Water�� 25 2.6 Some Definitions for the Study of Acids and Bases�� 26 2.7 The pH Scale�� 27 2.8 The Henderson–Hasselbalch Equation�� 28 2.9 Titration and Buffering�� 30 Summary�� 31 Review Questions�� 31 Chapter 2 Addendum: The Dielectric�� 32 Key Terms�� 34 Bibliography�� 34 Chapter 3 Lipids�� 35 3.1 Significance�� 35 3.2 Fatty Acids�� 35 3.3 Triacylglycerols�� 39 3.4 Phospholipids��41 vii

viii Contents

3.5 Cholesterol�� 42 3.6 Lipid–Water Interactions of Amphipathic Molecules��44 3.7 Phospholipid Monolayers��47 3.8 Lipid Composition of Membranes�� 49 3.9 Water Permeability of Membranes and Osmosis�� 49 Summary�� 51 Review Questions�� 51 Chapter 3 Addendum: Inverted Micelles�� 52 Key Terms�� 53 Bibliography�� 54 Chapter 4 Carbohydrates�� 55 4.1 Monosaccharides�� 55 4.2 Ring Formation in Sugars��59 4.3 Disaccharides�� 62 4.4 Polysaccharides�� 64 4.4.1 Linear Polysaccharides�� 66 4.4.2 Branched Polysaccharides�� 68 4.5 Carbohydrate Derivatives�� 68 4.5.1 Simple Modifications�� 68 4.5.2 Substituted Carbohydrates�� 70 Summary�� 75 Review Questions�� 76 Chapter 4 Addendum: The Discovery of Stereoisomerism�� 76 Key Terms�� 77 Bibliography�� 78 Chapter 5 Amino Acids and Proteins�� 79 5.1 Common Structure of the Amino Acids�� 79 5.2 Biology of the Amino Acids�� 79 5.3 Amino Acid Individuality: The R Groups�� 80 5.3.1 Polarities�� 80 5.3.2 Functional Groups��81 5.4 Acid–Base Properties and Charge�� 85 5.4.1 Titration and Net Charge�� 85 5.4.2 Interactions between the α-Carboxylate and α-Amine Groups�� 87 5.4.2.1 Inductive Effect�� 87 5.4.2.2 Electric Field Effect�� 88 5.4.3 Multiple Dissociable Groups�� 90 5.5 The Peptide Bond�� 90 5.6 Peptides and Proteins�� 92 5.7 Levels of Protein Structure�� 93 5.7.1 Primary Structure�� 93 5.7.2 Secondary Structure�� 93 5.7.2.1 α-Helix�� 94 5.7.2.2 β-Sheet�� 94 5.7.3 Domains�� 94 5.7.4 Tertiary Structure�� 97 5.7.5 Quaternary Structure�� 98 5.8 Protein Folding�� 99 5.9 Oxygen Binding in Myoglobin and Hemoglobin��100 5.10 Other Binding Reactions Involving Proteins��103 5.10.1 Extracellular Binding Proteins��104 5.10.2 Cell Surface Binding Proteins��104 5.10.3 Intracellular Binding Proteins��104

Contents ix

5.11 Protein Purification and Analysis��105 5.11.1 Purification��105 5.11.2 Analysis��107 Summary�� 107 Review Questions�� 108 Chapter 5 Addendum: Atomic Charged Forms�� 108 Key Terms�� 109 Bibliography�� 110 Chapter 6 Enzymes��111 6.1 Energetics of Enzyme-Catalyzed Reactions��111 6.2 The Enzyme Assay and Initial Velocity��113 6.3 A Simple Kinetic Mechanism�� 114 6.3.1 Assumptions��115 6.3.2 The Michaelis–Menten Equation��115 6.4 How the Michaelis–Menten Equation Describes Enzyme Behavior��117 6.5 The Meaning of Km��119 6.6 Reversible Inhibition��120 6.6.1 Competitive Inhibition�� 121 6.6.2 Anticompetitive Inhibition (Uncompetitive)��122 6.6.3 Mixed Inhibition (Noncompetitive)�� 124 6.7 Double-Reciprocal or Lineweaver–Burk Plot��125 6.8 Allosteric Enzymes��126 6.9 Irreversible Inhibition��128 6.10 Enzyme Mechanisms��129 6.10.1 Nucleophilic Substitution��129 6.10.2 Acid–Base Catalysis�� 131 6.11 Enzyme Categories�� 132 6.12 Enzyme-Like Qualities of Membrane Transport Proteins�� 132 Summary�� 133 Review Questions�� 134 Chapter 6 Addendum: The Haldane Relationship�� 135 Key Terms�� 137 Bibliography�� 137 Chapter 7 Coenzymes��139 7.1 Coenzymes: Bound and Mobile��139 7.2 Coenzymes and Vitamins��140 7.3 Redox Coenzymes ��140 7.3.1 Nicotinamides��140 7.3.2 Ubiquinone ��144 7.3.3 Flavin Coenzymes��144 7.4 Acyl Transfers ��146 7.4.1 CoA��146 7.4.2 Carnitine��147 7.4.3 Lipoic Acid��148 7.5 Carboxylation��148 7.5.1 Biotin��149 7.5.2 Vitamin K��150 7.6 Exchange Coenzymes�� 151 7.6.1 Thiamine Pyrophosphate�� 151 7.6.2 Pyridoxal Phosphate ��152 7.7 Metal Ion Cofactors��154 7.7.1 Mg2+�� 155 7.7.2 Iron��155

x Contents

7.7.3 Copper��155 7.7.4 Co2+�� 155 7.7.5 Mn2+and Zn2+��156 7.7.6 Selenium��156 7.7.7 Dietary Essentials��156 Review Questions�� 156 Chapter 7 Addendum: The Vitamin K Cycle�� 157 Key Terms�� 158 Bibliography�� 159 Chapter 8 Metabolism and Energy�� 161 8.1 Origins of Thermodynamics�� 161 8.2 First Law of Thermodynamics�� 161 8.2.1 Heat and Work�� 161 8.2.2 Enthalpy��163 8.3 Entropy and the Second Law of Thermodynamics��164 8.3.1 Entropy as a Ratio of Heat to Temperature��165 8.3.2 Entropy as a Statistical Distribution of States��165 8.4 Free Energy��165 8.5 Standard Free Energy��167 8.6 Nonstandard Free Energy Changes��168 8.7 Near-Equilibrium and Metabolically Irreversible Reactions��169 8.8 ATP��170 8.9 Energy Coupling with ATP�� 171 8.9.1 Creatine Phosphokinase��173 8.9.2 NDP Kinase��173 8.9.3 Adenylate Kinase�� 174 8.10 Energy of Redox Reactions�� 174 8.10.1 Electricity Fundamentals�� 175 8.10.2 The Electrochemical Cell�� 176 8.10.3 Standard Reduction Potentials��177 8.10.4 Reduction Potentials and Free Energy��178 8.10.5 Reduction Potentials ��179 8.11 Mobile Cofactors and the Pathway View ��180 Summary�� 181 Review Questions�� 182 Chapter 8 Addendum: Free Energy Derivation�� 182 Key Terms�� 183 Bibliography�� 184 Chapter 9 Glycolysis��185 9.1 Glucose Transport��185 9.2 From Glucose to Pyruvate��186 9.2.1 Hexokinase��186 9.2.2 Glucose Phosphate Isomerase��189 9.2.3 Phosphofructokinase��190 9.2.4 Aldolase��193 9.2.5 Triose Phosphate Isomerase��194 9.2.6 Glyceraldehyde Phosphate Dehydrogenase��194 9.2.7 Phosphoglycerate Kinase��195 9.2.8 Phosphoglycerate Mutase��195 9.2.9 Enolase��196 9.2.10 Pyruvate Kinase��197

Contents xi

9.3

Completing the Pathway��199 9.3.1 Lactate Formation�� 200 9.3.2 Ethanol Formation�� 200 9.4 Energetics of Glycolysis��201 9.4.1 Pathway Thermodynamics��201 9.4.2 Red Blood Cell Shunt Pathway��203 9.4.3 Arsenate Poisoning��203 9.4.4 Fructose Metabolism��205 9.4.5 Energy Balance and Glycolytic Connections��206 9.5 Metabolic Connections to Glycolysis��207 9.5.1 Alternative Entry Points��207 9.5.2 Glycolytic Intermediates as Intersection Points��207 9.5.3 Alternative Endpoints of Glycolysis��208 Summary�� 208 Review Questions�� 208 Chapter 9 Addendum: Alternatives to Glycolysis�� 209 Key Terms�� 209 Bibliography�� 210 Chapter 10 The Krebs Cycle�� 211 10.1 A Cyclic Pathway�� 211 10.2 Acetyl-CoA: Substrate of the Krebs Cycle�� 212 10.3 Overview of Carbon Flow��216 10.4 Steps of the Pathway�� 217 10.4.1 Citrate Synthase�� 217 10.4.2 Aconitase��218 10.4.3 Cis-Aconitate as a Krebs Cycle Intermediate��220 10.4.4 Prochirality��220 10.4.5 The R/S System of Nomenclature��221 10.4.6 Fluoroacetate Poisoning��223 10.4.7 Isocitrate DH��223 10.4.8 α-Ketoglutarate DH Complex��224 10.4.9 Succinyl-CoA Synthetase��224 10.4.10 Succinate DH��225 10.4.11 Fumarase��226 10.4.12 Malate DH��226 10.5 Energy Balance��227 10.6 Regulation��228 10.7 Krebs Cycle as a Second Crossroad of Metabolic Pathways��229 Summary�� 230 Review Questions�� 230 Chapter 10 Addendum: Cyclic Pathways Connected to the Krebs Cycle�� 230 1. Glyoxylate Cycle��231 2. Itaconate Pathway��231 Key Terms�� 232 Bibliography�� 233 Chapter 11 Oxidative Phosphorylation��235 11.1 The Phenomenon��235 11.2 Mitochondrial Inner Membrane��236 11.3 Carriers of Electrons, Protons, or Both��237 11.3.1 Carriers of Electrons��237 11.3.2 Carriers of Protons��237 11.3.3 Carriers of Both Electrons and Protons��238

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11.4 Membrane-Bound Complexes��238 11.5 The Electrochemical Cell and the Mitochondria��239 11.6 Electron Pathways��240 11.6.1 Sequence of Electron Flow��240 11.6.2 Energetics of Electron Flow�� 241 11.7 Mechanisms of the Mitochondrial Membrane Protein Complexes��243 11.7.1 Complex I: Proton Pump��244 11.7.2 Complex II: Succinate Dehydrogenase��245 11.7.3 Complex III: Loop Mechanism��245 11.7.4 Complex IV: Pump and Annihilation��247 11.7.5 Complex V: ATP Synthesis��247 11.7.5.1 The Stator��250 11.7.5.2 The Rotor��250 11.8 Proton-Motive Force��250 11.8.1 Electric Circuit Analogy to the Proton Gradient��250 11.8.2 Utilization of Δp beyond ATP Synthesis��251 11.9 Mitochondrial Membrane Transport��252 11.9.1 Adenine Nucleotide Translocase��252 11.9.2 Phosphate Exchange��252 11.9.3 Other Transport Proteins��252 11.9.4 Coupling of Oxidation and Phosphorylation��253 11.10 Uncoupling�� 254 11.10.1 Physiological Uncoupling: Brown Fat��256 11.11 Superoxide Formation by Mitochondria��256 11.12 Control of Mitochondria��257 11.13 How Mitochondria Can Utilize Cytosolic NADH��258 11.13.1 Glycerol Phosphate Shuttle��258 11.13.2 Malate/Aspartate Shuttle��258 Summary�� 260 Review Questions�� 261 Chapter 11 Addendum: Supercomplexes�� 261 Key Terms�� 262 Bibliography�� 263 Chapter 12 Photosynthesis��265 12.1 Light and Carbon Reactions��265 12.2 Chloroplasts��266 12.2.1 Orientations: N and P Sides of the Membrane��266 12.2.2 Light Reactions of Photosynthesis as a Reversed Oxidative Phosphorylation��267 12.2.3 Carbon Reactions of Photosynthesis: CO2 Fixation��268 12.3 Harnessing Light Energy��269 12.3.1 Light Absorption and the Antennae��270 12.3.2 Electron Transfer at Reaction Centers��270 12.4 Proton and Electron Flow for the Light Reactions��272 12.5 Cyclic Electron Transfer and Other Variations��274 12.6 The Calvin Cycle��274 12.6.1 Ribulose Bisphosphate Carboxylase��275 12.6.2 Reaction Steps Following Carbon Fixation to Glyceraldehyde-P: Energy Consuming Portion��277 12.6.3 From GAP to the RuBP: Overview��277 12.6.4 From GAP to the RuBisCo Step: Reactions��278 12.7 Variations in CO2 Handling: C3, C4, and CAM Plants��282 12.8 Pathway Endpoints: Sucrose and Starch�� 284 Summary�� 285 Review Questions�� 285

Contents xiii

Chapter 12 Addendum: Dark vs Carbon Reactions�� 286 Key Terms�� 286 Bibliography�� 287 Chapter 13 Carbohydrate Pathways Related to Glycolysis��289 13.1 Glycogen Metabolism��289 13.1.1 Glycogen Synthesis��289 13.1.2 Glycogenolysis��291 13.1.3 Physiological Context of Glycogen Metabolism��296 13.1.4 Regulation of Glycogen Metabolism by Glucagon��296 13.1.5 Regulation of Glycogen Metabolism by Epinephrine��299 13.1.6 Regulation of Glycogen Metabolism by Insulin�� 300 13.1.7 Regulation of Glycogen Metabolism by AMP Kinase��303 13.2 Gluconeogenesis�� 304 13.2.1 Lactate Dehydrogenase as a Gluconeogenic Enzyme�� 304 13.2.2 Pyruvate to PEP��305 13.2.3 Indirect Transport of Oxaloacetate from Mitochondria to Cytosol�� 306 13.2.4 Fructose-1,6-P2 to Fructose-6-P��309 13.2.5 Glucose-6-P to Glucose�� 310 13.2.6 Pathway Integration: Glycolysis, Glycogen Metabolism, and Gluconeogenesis�� 311 13.2.6.1 The Feeding–Fasting Transition�� 311 13.2.6.2 The Resting–Exercise Transition�� 312 13.3 The Pentose Phosphate Shunt�� 313 13.3.1 Oxidative Stage�� 314 13.3.2 Nonoxidative Stage�� 314 13.3.2.1 Reactions of the Nonoxidative Stage�� 315 13.3.2.2 A Pseudo Three-Dimensional View and Comparison to the Calvin Cycle�� 316 13.3.3 Distribution Between NADPH Production and Ribose-5-P�� 318 13.4 Galactose Utilization�� 318 Summary�� 320 Review Questions�� 321 Chapter 13 Addendum: Phosphorylation of Glycogen�� 321 Key Terms�� 322 Bibliography�� 323 Chapter 14 Lipid Metabolism��325 14.1 Absorption of Dietary Lipids��325 14.2 Fatty Acid Oxidation��326 14.2.1 Activation��327 14.2.2 Transport��328 14.2.3 β-Oxidation��330 14.2.3.1 Unsaturated Fatty Acids��331 14.2.3.2 Odd Carbon-Numbered Fatty Acids��331 14.2.3.3 Shorter and Longer Fatty Acids��334 14.3 Ketone Body Metabolism��334 14.4 Fatty Acid Biosynthesis��335 14.4.1 Export of Acetyl-CoA to the Cytosol��336 14.4.2 Carboxylation of Acetyl-CoA to Malonyl-CoA��339 14.4.3 Sequential Addition of Two-Carbon Fragments to Form Palmitate�� 340 14.4.3.1 Loading��341 14.4.3.2 Condensation��341 14.4.3.3 Reduction��342 14.4.3.4 Dehydration��343 14.4.3.5 Second Reduction��343

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14.5 14.6 14.7 14.8

Triacylglycerol Formation��343 Phospholipid Metabolism��343 Cholesterol Metabolism�� 346 Other Lipids��351 14.8.1 Eicosanoids��351 14.8.2 Sphingolipids��353 14.8.3 Unusual Bacterial Fatty Acids��353 14.9 Overview of Lipid Metabolism in the Fed and Fasted States��353 14.10 Integration of Lipid and Carbohydrate Metabolism��355 14.10.1 Lipid and Carbohydrate Intersections in the Feeding–Fasting Transition��357 14.10.2 Lipid and Carbohydrate Intersections in the Resting–Exercise Transition��357 14.10.3 Lipid and Carbohydrate Intersections in Diabetes Mellitus��357 Summary�� 358 Review Questions�� 359 Chapter 14 Addendum: The Isoprenes�� 359 Key Terms�� 360 Bibliography�� 361 Chapter 15 Nitrogen Metabolism��363 15.1 The Nitrogen Cycle��363 15.2 Reaction Types in NH3 Assimilation�� 364 15.2.1 Redox-Neutral�� 364 15.2.2 Redox-Active�� 364 15.2.3 Redox-Balanced��365 15.3 Metabolically Irreversible Nitrogen Exchange Reactions��365 15.4 Near-Equilibrium Nitrogen Exchange Reactions�� 366 15.4.1 Glutamate DH�� 366 15.4.2 Transaminases�� 366 15.5 The Urea Cycle�� 368 15.5.1 [NH3] Exceeds [Aspartate]�� 368 15.5.2 [Aspartate] Exceeds [NH3]��369 15.5.3 Steps from NH3 to Citrulline��369 15.5.4 Cytosolic Steps of the Urea Cycle��369 15.5.5 Overall Urea Cycle��371 15.6 Amino Acid Metabolism: Catabolism��372 15.6.1 Branched-Chain Amino Acid Breakdown��372 15.6.2 Threonine��372 15.6.3 Lysine��372 15.6.4 Tryptophan��374 15.6.5 Phenylalanine and Tyrosine Degradation��374 15.6.6 Amino Acids Directly Connected to Major Metabolic Pathways��376 15.6.7 Arginine, Proline, and Histidine Are All Converted to Glutamate��377 15.6.8 One-Carbon (1C) Metabolism and Serine, Glycine, and Methionine Breakdown��378 15.7 Amino Acids: Anabolism��380 15.7.1 Nonessential Amino Acids��382 15.7.2 Essential Amino Acids��382 15.7.3 Aromatic Amino Acid Biosynthesis��382 15.8 Nucleotide Metabolism��383 15.8.1 Pyrimidine Synthesis�� 384 15.8.2 Pyrimidine Degradation��386 15.8.3 Purine Synthesis��386 15.8.4 Purine Degradation��391 15.8.5 Salvage Reactions��393 15.8.6 Purine Nucleotide Regulation��393

Contents xv

15.8.7 Purine Nucleotide Cycle��394 15.8.8 Deoxynucleotide Formation��394 15.8.9 A Unique Methylation to Form dTMP��395 15.9 Other Nitrogen Pathways��398 Summary�� 399 Review Questions�� 400 Chapter 15 Addendum: Nitrogen Disposal�� 400 The Tilapia of Lake Magadi�� 401 The Alligator and the Crocodile�� 401 Low Creatinine and Liver Failure�� 401 Key Terms�� 402 References�� 403 Chapter 16 Nucleic Acids�� 405 16.1 Strand Structures of the Nucleic Acids�� 405 16.2 Structure of the Double Helix��407 16.3 Supercoiling�� 410 16.4 Histones��411 16.5 Replication�� 412 16.5.1 Initiation�� 412 16.5.2 Replication Fork and the Replisome�� 413 16.5.3 Primer Formation�� 414 16.5.4 Creating the Double Helix�� 414 16.5.5 Distinctive Features of Eukaryotic Replication�� 415 16.6 DNA Repair�� 415 16.6.1 Mismatch Repair�� 415 16.6.2 Excision Repair�� 416 16.6.3 PARP�� 416 16.7 Transcription�� 416 16.7.1 RNA Polymerase Binding to DNA�� 418 16.7.2 Transcription Events in E. coli�� 419 16.7.3 Eukaryotic Transcription�� 419 Summary�� 423 Review Questions�� 424 Chapter 16 Addendum: Restriction Enzymes and PCR �� 425 Restriction Enzymes�� 425 PCR�� 425 Key Terms�� 426 Bibliography�� 427 Chapter 17 Protein Synthesis and Degradation��429 17.1 Three Forms of RNA Employed in Protein Synthesis��429 17.1.1 tRNA��429 17.1.2 rRNA and the Ribosomes��431 17.2 The Genetic Code��432 17.3 Steps in Protein Synthesis��433 17.3.1 Initiation��433 17.3.2 Elongation��433 17.3.3 Termination��436 17.3.4 Distinctive Features of Eukaryotic Translation��437 17.3.5 Regulation of Eukaryotic Translation��437 17.4 Co-Translational and Post-Translational Modifications of Proteins��437 17.4.1 Co-Translational Modifications��437 17.4.2 Post-Translational Modifications�� 440

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17.5 Protein Degradation�� 440 17.5.1 Extracellular Proteases�� 440 17.5.2 Intracellular Proteases��442 17.6 The mTOR Pathway in the Control of Protein Synthesis��443 Summary�� 445 Review Questions�� 445 Chapter 17 Addendum: Skeletal Muscle and Exercise�� 446 Key Terms�� 446 Bibliography�� 447 Appendix�� 449 Index��461

Preface to the First Edition

CONSIDERING METABOLISM

ORGANIZATION

Metabolic diseases, such as diabetes and others associated with the current obesity crisis, have thrust metabolism into the forefront of popular thinking. In many ways, metabolism is the central science of biochemistry. This is the view I have adopted as the core concept of this textbook. Having a research background in metabolism, a long-standing interest in the fundamental topics of biochemistry – including kinetics and thermodynamics – and having taught a one-semester biochemistry course for over 25 years, I have long wanted to write a book that reflects the whole of the subject with the unifying theme of metabolism.

The presentation of biochemistry topics is mostly a classical one, with a slight divergence: the introduction to lipids directly follows the chemistry of water. This is in keeping with presenting molecular classes in the order of increasing chemical complexity: water, lipids, carbohydrates, nitrogen compounds. It also has the virtue of contrasting water solubility with water insolubility in the case of lipids. When using this book for medically oriented courses, the chapter on photosynthesis may be omitted. In that case, however, the photosynthetic “dark reactions” should at least be referenced, as they are similar to those in the pentose cycle; this analogy is made explicit in the chapter on carbohydrate pathways.

BREVITY A key consideration when writing this text was to keep the book short enough and approachable enough that a student can read it in one semester. The alternative approach – having a book far too long for continuous reading and having the instructor suggest which portions to omit – is already well represented. In my experience, for students who are not biochemistry majors, the fragmentation resulting from parsing longer texts leads to less reading and, therefore, less understanding. The areas of special interest to the instructor can be readily augmented with primary sources, while the textbook provides continuity and context. I have emphasized recurring ideas such as commonalities in chemical reaction mechanisms and pathway construction as much as possible. The decision of whether the book is for teaching or reference is decidedly in favor of teaching; for example, only a few protein domains are presented. The wealth of information available on the Web (notably ncbi.nlm.nih.gov) can substitute for a more extensive collection. The present text will provide students with an introduction to the foundations of biochemistry.

KEY FEATURES ◾◾ Dual diagrams of enzymatic reactions. A unique method of presenting electron flow for reaction mechanisms was devised for this book. For each mechanism, the substrate, intermediates, and product are presented on the top line. Below a separator (dotted line), the molecules are redrawn with their electron flows, using the traditional curved arrows. This separation allows the student to visualize the result of the electron flow, which is commonly obscured by the need to show the electron arrows for the next transformation. ◾◾ Word Origins feature box. Included in most chapters is a box that provides a short history of certain words that are rich in meaning, without which it is often more difficult to understand the underlying concept. Providing an explanation of their origins helps students become familiar with these important terms and achieve a better understanding of what is being described. ◾◾ Thermodynamics treatment. The development of thermodynamics for metabolic purposes leads to

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xviii Preface to the First Edition

the distinction between two classes of enzymes: near-equilibrium and metabolically irreversible. This allows a simplification, as near-equilibrium reactions are not sites of cellular regulation. The roles of standard, actual, and near-equilibrium states for free energy are distinct and consistently presented to aid student understanding. ◾◾ Chemical mechanisms. A study of biochemistry should impart a viewpoint enriched by understanding the underlying chemistry of events in living systems. This extended view of biology is best achieved by understanding how enzymatic reactions function. All of the background chemistry needed for this text should be covered by prerequisite courses of chemistry. Some further information is presented in the appendix; a review of organic chemistry reaction mechanisms (most critically, nucleophilic reactions) may be necessary for those who are less comfortable with the material. ◾◾ Enzyme kinetics treatment. The text emphasizes direct plots of substrate concentration against initial velocity, introducing double-reciprocals only after a complete development of the subject. While in widespread use, the double-reciprocal form is difficult to visualize and leads to the false impression that memorizing patterns of lines for enzyme inhibition provides insight into how inhibitors work. Instead, direct plots, with an emphasis on the behavior of reaction velocity at different substrate concentrations, deliver the message clearly. Coupled with everyday descriptions of the different types of inhibition, these critical ideas are easily grasped. A further distinct notion is the use of the kinetic term Vmax /K M rather than K M in developing kinetics. Too

often, "K M " becomes a focal point and is treated as an equilibrium constant rather than a steadystate constant. This common misuse of K M versus Vmax/K M is part of the reason that many students have difficulty understanding enzyme kinetics, and it is a problem this text carefully avoids. ◾◾ Minimalist molecular biology treatment. The essence of molecular biology is included in the final two chapters. The emphasis is on providing an overview with a chemical perspective. For example, stacking interactions in DNA, the basis for forming the double helix, are explained in simple, chemical terms. ◾◾ The pathway view. The distinction between a reaction view and a pathway view is clearly emphasized to facilitate student comprehension. For example, the distinction between a bound cofactor like FADH2 from a free cofactor like NADH becomes obvious: only NADH can transfer electrons between metabolic reactions. ◾◾ Appendix. The appendix of this text contains both entries for students needing a little extra help and more advanced material that, while perhaps not appropriate for the level of this particular text, is nonetheless important to the field of biochemistry as a whole. For remediation, basic ideas of mathematics and chemistry with which students traditionally have difficulty can be found in the appendix, as can certain extended pathways like amino acid and cholesterol routes. The advanced material includes the mechanism of aconitase and the role of fluoroacetate, which represent milestone achievements in biochemistry. These may be of interest to the more inquisitive student wishing to go beyond the fundamentals.

Preface to the Second Edition Metabolism remains the focal point of the textbook, as does the goal of maintaining a one-semester book. The organization is the same, although a new chapter on coenzymes follows enzymes. This chapter can either be read in sequence to expand the chemistry of enzymes or skimmed to consult when specific coenzymes are encountered later. Some expansion of chemistry is provided, such as a more detailed treatment of acid–base and redox reactions and a fuller explanation of prochirality, as my own understanding of that concept has evolved. Each chapter has a new addendum, providing an optional reading topic, usually of a more advanced nature than the book narrative. The organizing principles of near-equilibrium and metabolically irreversible enzymes are carried over from the first edition. In this edition, I have added two more. The first is an idea taken from the advertising industry, applied to perplexing pathway routes that are not quite

linear or cyclic: repetition-variation. This description fits several pathways and provides a new way of thinking about them. The second, introduced in the final chapter, is pathway-reversible versus pathway-irreversible as a means to discriminate between regulation that can be reverted by opposing reactions (reversible) or incorporated into proteins for their entire existence (irreversible). I have tried to make more explicit in this edition the underpinnings of chemistry in biological sciences. In the present climate, there is a tendency for students to believe that they can look up whatever they need rather than examine the roots of the subject. This view is unfortunate; it means that every new fact or idea is searched anew and committed to memory in isolation. A few principles of biochemistry can be instead the foundation of a deeper understanding.

xix

Acknowledgments The invaluable feedback from reviewers is gratefully acknowledged: Sergio Abreu, Fordham University Lois Bartsch, Graceland University Sajid Bashir, Texas A&M University - Kingsville Mrinal Bhartacharjee, Long Island University Debra Boyd-Kimball, University of Mount Union Barbara Bowman, University of California - Berkeley Jeanne Buccigross, College of Mount St. Joseph Mickael Cariveau, Mount Olive College John Brian Chapman, Federation University Australia James Cheetham, Carleton University Zhe-Sheng Chen, St. John’s University David Eldridge, Baylor University Susan Evans, Ohio University John Fain, University of Tennessee Health Science Center Sue Ford, St. John’s University Matthew Gage, Northern Arizona University Eric Gauthier, Laurentian University Neil Haave, University of Alberta - Augustana Campus

David Hilmey, St. Bonaventure University Blaine Legaree, Keyano College Lisa Lindert, California State University - Sacramento Meagan Mann, Austin Peay State University Nick Menhart, Illinois Institute of Technology Abdel Omri, Laurentian University Gordon Rule, Carnegie Mellon University Mary Railing, Wheeling Jesuit University Gerald Reeck, Kansas State University Abbey Rosen, Marian College of Fond du Lac Frank Schmidt, University of Missouri Michael Sehorn, Clemson University Kavita Shah, Purdue University Andrew Shiemke, West Virginia University Amrurhesh Shivachar, Texas Southern University Todd Silverstein, Willamette University Madhavan Soundararajan, University of Nebraska - Lincoln Salvarore Sparace, Clemson University Vicky Valancius-Mangel, Governors State University David Watt, University of Kentucky Wu Xu, University of Louisiana - Lafayette Mali Yin, Sarah Lawrence College

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Author Raymond S. Ochs is a biochemist with a career-long specialty in metabolism spanning 30 years. Previously, he has written the textbook Biochemistry, the monograph Metabolic Structure and Regulation, contributed the metabolism chapters to another text, Principles of Biochemistry, and co-edited a collection of articles published as Metabolic Regulation. His research interests

concern major pathways of liver and muscle, including glycolysis, gluconeogenesis, ureogenesis, fatty acid metabolism, glycogen metabolism, and control by cAMP, Ca 2+, diacylglycerol, and AMPK. He is currently professor of pharmacy at St. John’s University in New York, teaching biochemistry, physiology, and medicinal chemistry.

xxiii

Glossary

A α-carbon – Carbon adjacent to a carboxyl group; often referred to as the carbon bearing a carboxyl group and an amino group in an amino acid. α-hydrogen – The hydrogen attached to the α-carbon of an amino acid. ACP-SH – See acyl carrier protein. acceptor site – During protein synthesis, the location of the ribosomal binding site for aminoacyl-transfer RNA (also termed A site). acceptor stem – Located at the opposite end of the anticodon on a transfer RNA, the 3' end with a CCA sequence, where the appropriate amino acid bonds with the terminal end adenine (A) residue. activation energy – Energy beyond the difference in energies between substrates and products necessary to bring about reaction. active site – Specific region of an enzyme where substrates bind and reaction catalysis takes place. acyl carrier protein – A small protein containing a free –SH from a cysteine residue that forms thioester intermediates in fatty acid biosynthesis. adipocyte – Fat cell. adrenergic receptors – Hormone receptors for epinephrine or norepinephrine (also known as adrenaline and noradrenaline, respectively). affinity – Binding ability, characterized by an equilibrium constant. affinity chromatography – A form of chromatography in which the stationary phase contains molecules that selectively combine with components of the mobile phase. agar – A mixture of agarose and agaropectin with a gelatinous consistency that can support growth of microorganisms for in vitro analysis. agaropectin – A polysaccharide similar to agarose, except that it has branched sugars and sulfuric acid esters to some of its hydroxyl groups. agarose – A polysaccharide found in certain seaweeds, it has alternating galactosyl and anhydro-L-glucosyl subunits. aldoses – Sugars containing an aldehyde (at carbon 1). alkaloids – A class of naturally occurring nitrogenous organic compounds found in plants, some fungi, and animals. Examples: caffeine, morphine, nicotine, quinine, and strychnine.

allopurinol – A synthetic drug (a hypoxanthine analog) used to treat gout through its inhibition of xanthine oxidase and thus uric acid formation. allosteric – Literally “other site”, a binding site for a protein apart from the active site for binding or catalysis, involved in regulation. alpha (form) – The hydroxyl group of an anomeric carbon that is on the same side of the ring as the hydroxyl group that determines the d-form of most monosaccharides. amide – A bond formed (formally by dehydration) between an amine and a carboxyl group. amino acids – The building blocks of proteins and intermediates in metabolism, all contain an amine group and a carboxyl group attached to the α-carbon. amino-acyl-tRNA synthetases – Enzymes that selectively recognize and bind an amino acid to a matching transfer RNA. amino end – The end of a protein or peptide that terminates in a free α-amine (also, the N end). ampere – A unit of measure for electrical current. amphipathic – Having both polar and nonpolar parts within a single molecule. Example: fatty acids. ammoniotelic – Organisms that produce ammonia as their major nitrogen excretion product. anabolic steroid – A synthetic hormone that promotes protein synthesis and cell growth, sometimes used by athletes to increase muscle size and strength. anapleurotic – Filling reaction for a cyclic pathway. For example, pyruvate carboxylase catalyzes oxalacetate formation, an intermediate of the Krebs cycle. annihilation – A mechanism of formation of the mitochondrial proton gradient in which proteins are removed from the matrix space through their reaction with oxygen to form water. anomeric carbon – In a sugar ring, the carbon bearing the hydroxyl group that was a carbonyl in the open chain form. antennae – In photosynthesis, a large pool of chlorophyll molecules that absorb light. anticodon – Located on one end of transfer RNA, a sequence of three adjacent nucleotides. Functions during the translation phase of protein synthesis to bind to the complementary coding triplet of nucleotides in messenger RNA (see codon). xxv

xxvi Glossary

anticompetitive inhibition – Occurs when an enzyme inhibitor only binds to an enzyme substrate (ES) complex (see uncompetitive inhibition). antiparallel – In β-sheet of an amino acid sequence, when the strands run in opposite directions. aquaporins – Protein channels selective for water transport. apoprotein – The protein portion of a larger complex, formed with a prosthetic group. apoptosis – Programmed cell death. This process prevents release of cellular components as a cell is extinguished either during development or in response to some disease states. Arrhenius definition – A classification of acid–base reactions, for which an acid increases the proton concentration in water, and a base decreases the proton concentration in water. assay – Quantitative or qualitative procedure to analyze a substance. assimilation – The incorporation of nutrients into living tissue. Also used specifically as a term for bacterial conversion of nitrate and nitrite into ammonia. autophagy – Lysosomal digestion of a cell's own cytoplasmic material. auxotrophic – Organisms requiring carbon sources other than CO2.

B :B – Enzyme-bound base. β-barrel – Portion of a protein domain formed from multiple β-sheets. beta (form) – The hydroxyl group of an anomeric carbon that is on the opposite side of the ring from the hydroxyl group that determines the d-form of most monosaccharides. β-oxidation – The process of oxidative degradation of fatty acids, where two-carbon units are sequentially removed from the carboxyl end of the polymer. bile – A mixture of bile salts, phospholipids, and cholesterol that is secreted by the liver, stored in the gallbladder, and released into the duodenum, where it forms mixed micelles with dietary lipids to facilitate their hydrolysis. bile salts – Modified cholesterol derivatives that are amphipathic and can form mixed micelles with dietary lipids, such as cholate. binding change – A mechanism for complex V (F1FoATPase), proposed by Paul Boyer, that a protein segment of the complex moves among the three adenine nucleotide binding sites, driven by proton entry.

biopterin – A pterine (heterocycle) redox cofactor that can transfer single electrons as well as electron pairs. biotin – A carboxylation cofactor in which an intermediate CO2 is transiently attached to a nitrogen atom of this molecule. bisphosphonate – A drug containing a phosphorous atom with a P–C bond used in the treatment of osteoporosis, as it inhibits osteoclasts which dissolve bone. Bohr effect – The diminished binding of oxygen to hemoglobin in response to an increased concentration of protons. branch points – Location on a polymer chain in which a chain diverges to form a new polymer end. This usually refers to polysaccharides, which have multiple hydroxyl groups, in which the branch points are often αl→6 linkages. Bronsted definition – An acid–base definition, in which an acid is a proton donor, and a base is a proton acceptor. brown adipose – A type of fat cell with numerous small lipid droplets rather than just one, many mitochondria, and an uncoupling protein that can initiate uncoupled respiration to generate heat. buffering region – The region of a titration curve in which addition of acid or base has minimal effects on the pH; visually, a flat region in the the curve. bundle sheath – Inner plant cells that converts the fourcarbon malate to pyruvate and CO2.

C C3 plants – Plants that directly incorporate CO2 into P-glycerate (the C3) rather than intermediate conversion to a C4 for the purpose of localizing CO2. C4 plants – Plants with specialized pathways to protect against RuBisCo using O2 as an alternative substrate to CO2. The C4 refers to a four-carbon intermediate that is synthesized from PEP, carrying CO2 as the fourth carbon and releasing it in a separate inner cell. calmodulin – A small calcium-binding protein attached to some proteins noncovalently to confer calcium sensitivity. Calvin cycle – Cyclic pathway in photosynthetic organisms that serves to convert three CO2 molecules to 3-P-glycerate. CAM plants – Crassulacean acid metabolism. These plants have a physical barrier modification to prevent O2 from reaction at RuBisCo. Pores open at night to admit CO2

Glossary xxvii

cap – A 7-methylguanosine in 5'–5' triphosphate linkage to the first nucleotide of the mRNA; this is added post transcriptionally and is not encoded in the DNA. capping – At the terminal point of a chromosome (see telomere), structures protecting the ends from degradation and fusion, a requirement for linear DNA. carbon cycle – Global reactions of CO2 between auxotrophs (such as animals) and photosynthetic organisms (such as plants). carbon fixation – Net incorporation of CO2 into sugars and ultimately other carbon compounds in cells. carbon reaction – Reactions in photosynthetic organisms that convert CO2 into sugars. Formerly known as dark reactions. carboxyl end – The end of a protein or peptide that terminates in a free α-carboxyl group (also, the C end). carnitine shuttle – A pathway for transport of fatty acylCoA molecules into mitochondria that involves intermediate conversion of the thioester into a carnitine ester. catalytic rate constant – Rate constant for the species directly leading to product in an enzyme mechanism. In our simple enzyme mechanism, that species is ES and the catalytic rate constant is kcat. catalytic triad – Three proximal amino acid residues in an enzyme active site that are involved in catalysis, connected by a relay system that uses acid–base catalysis to enhance a nucleophile, commonly a serine residue. cell theory – A concept that cells are the fundamental unit of living systems, arising from other cells. cellulose – A linear polymer of glucose that has β1→4 linkages and a very regular three-dimensional solution structure; an insoluble polysaccharide that comprises plant cell walls, vegetable tissue fibers (e.g., cotton), and wood. Cellulose is the most abundant macromolecule on earth. ceramide – A structure that is an analog of diacylglycerol, except with no acyl groups; an intermediate in the biosynthesis of sphingolipids. change in state – Thermodynamic variables that are defined by the difference between one condition and another undergo a change in state if the change is independent of the path taken between the two, and leads to a difference in state variables, such as entropy. chaperones – A protein that assists folding of another protein into its active conformation, either during the synthesis of the protein or afterwards. charge – An electrical primitive term having no deeper definition that is an entity considered either

positive or negative, in which opposite charges attract and like charges repel. charged tRNA – A tRNA with an amino acid attached (tRNAamino acid). chemiosmotic hypothesis – The theory that protons are the essential intermediate between oxidation of substances (with attendant electron transfer) and the phosphorylation of ADP to form ATP. chelate – See dative bond. chiral – An asymmetric carbon center in a molecule; Latin for handedness. A carbon atom to which four distinct groups are attached is a chiral center. chloroplast – Plant cellular organelle in which photosynthesis occurs. chorismate – An intermediate in the biosynthesis of aromatic amino acids. The common pathway to aromatic amino acids bifurcates at chorismate: one leads to phenylalanine and tyrosine; the other leads to tryptophan. chromatography – A group of analytic techniques for purification of materials that works by different molecular affinities within the mixture for a mobile phase and a stationary phase. chylomicron – A lipoprotein particle carrying dietary lipid synthesized in intestinal epithelial of the small intestine that is transported by the lymphatic system to the blood and subsequently various tissues in the body. chyme – Liquefied digest following physical processing in the stomach that exits through the pylorus to the duodenum for digestion. citric acid cycle – A cyclic series of reactions that catalyzes the complete oxidation of acetyl-CoA to CO2 (see Krebs cycle, tricarboxylic acid cycle). classical thermodynamics – Thermodynamic principles developed in the 19th century based upon postulates (called “laws of thermodynamics”) that have never been contradicted. The first law is energy conservation; the second postulates an increase in entropy (roughly, disorder) in the universe. CMC – see critical micelle concentration. cobalamin – see Vitamin B12 . CoA – Coenzyme of acetylation. Its sulfhydryl group participates in exchange of acyl groups in metabolic reactions. codon – A triplet of bases in the messenger RNA that, when bound to the ribosome, bind to the three bases of the anticodon region in transfer RNA (see anticodon). coenzyme – Molecules associating with enzymes that participate in the chemistry of the catalytic reaction. colloids – Early name for macromolecules.

xxviii Glossary

collision theory – A concept of reaction kinetics that the rate of a reaction is proportional to the number of collisions. Coulombs – Units of charge, based on current (rate of charge) and time (seconds); the units are amp-sec. competitive inhibition – A form of reversible inhibition in which the inhibitor binds exclusively to the free enzyme form. complementarity – The selective binding of nucleotides within a DNA or RNA chain to another nucleic acid that follows the rule that A binds T (or U, if the nucleic acid is RNA), and G binds C. complete pathway – A metabolic pathway that is balanced, so that all mobile cofactors are regenerated. concerted – Electron movements within a chemical mechanism that occur at the same time; a singlestep reaction. condensed phase – A form of matter in which the molecules (or atoms) are incompressible, such as a solid or liquid. conjugated – Electron clouds of π-bonds of at least two unsaturated centers are able to interact, enabling delocalization and stabilization. Commonly applies to double bonds separated by a single methylene moiety. conjugate acid – A positively-charged proton donor formed by protonating a neutral Bronsted base. conjugate base – A negatively-charged proton acceptor formed by dissociating a proton from a neutral Bronsted acid. consensus (sequences) – Similar sequences between strands of DNA in different species that have a common function. The term can also be applied to RNA or protein sequences. coordinate covalent bond – See dative bond. cooperativity – A model to explain deviations from the normal Michaelis–Menten curve for enzyme activity, or the S-shaped curve for binding oxygen to hemoglobin. The concept usually involves conformational changes of individual subunits in a multi-subunit protein that subsequently alter the affinity of other subunits for substrate or ligand. coordination number – The number of directed molecular bonds from electron-rich atoms to a metal like Fe2+. core – After RNA is synthesized in transcription, the σ subunit of the holoenzyme dissociates, thereby producing the core complex, α2ββ’. coproduct – A product of an enzymatic reaction that is not part of the pathway view and connects with other reactions in the cell; it is a mobile cofactor. corrosive – A gas that is reactive; the term refers to the ability to oxidize metal. Oxygen is an example of a corrosive gas.

cosubstrate – A substrate of an enzymatic reaction that is not part of the pathway view and connects with other reactions in the cell; it is a mobile cofactor. Cori cycle – An inter-organ metabolic pathway in which glucose forms lactate in the muscle (glycolysis), and the lactate is converted to glucose in the liver (gluconeogenesis). coupled – In oxidative phosphorylation, it refers to the oxidation of substrates, usually through the intermediacy of NADH, to O2, tied to the production of ATP. coupling – see coupled. critical micelle concentration – The concentration of fatty acids (or other lipid molecules) added to a water solution that enables them to form a micelle, so that further addition will not increase the free concentration. The concept is also applied to molecules that form non-micelle aggregates such as certain phospholipids. current – Rate of movement of charge, measured in amps. CRISPR – A technique for incorporating DNA segments into organisms, derived from a defense system formed by bacteria against bacteriophages. The full name is “Clustered Regularly Interspaced Short Palindromic Repeats”. cyclooxygenase – An enzyme converting arachidonate to a cyclic lipid that is the first step in the synthesis of prostaglandins and prostacyclins. The enzyme is the target of aspirin inhibition. cyclosporine – A cyclic peptide (1200 Da) that causes inactivation of the protein phosphatase calcineurin and suppresses formation of the cytokine IL-2 from T cells, leading to immunosuppression. The drug known as an immunophilin, used to prevent organ rejection in transplant patients. cytochrome P450 – Any of a group of enzymes catalyzing mixed-function oxidation, leading to hydroxylation of xenobiotics, including drugs, which renders them more water soluble and facilitates their excretion from the body. cytosol – The major water space within a cell.

D dark reactions – Earlier term for reactions of photosynthesis that do not require light, now replaced by carbon reactions. dative bond – A coordinate-covalent, or chelate bond, where electrons are not shared, and yet there is directionality to the bond. dehydrogenases – A category of enzymes that catalyzes the exchange of hydrides between substrates and nicotinamide nucleotides (NAD+ and NADP+).

Glossary xxix

denitrification – Process of removing nitrogen or nitrogen groups from a compound or reducing nitrites and nitrates to N2. dielectric constant – A number assigned to a molecule that measures how well it separate ions in solution. Values are based on a vacuum, set at 1.0; water has a value of about 80. diester – A double ester; for example, a phosphate group esterified both to choline and to glycerol in phosphatidyl choline. diffusion – Random motion of molecules that results in their redistribution from regions of high to low concentration. dihydrobiopterin – A redox cofactor with electron transfer properties similar to flavins. dinuclear copper center – Redox transferring copper metal ion complex found in cytochrome oxidase. dipole moment – A measure of bond polarity, it determines electron distribution across a bond. The value is greater if the atoms across the bond have greater differences in electronegativity. disaccharide – Two sugars linked by a glycosidic bond. DNA gyrase – A topoisomerase, involved in unwinding coiled DNA. DNA ligase – An enzyme that catalyzes diester formation between adjacent nucleotides in doublestranded DNA. DNA polymerase – Enzymes active in the replication and repair of DNA that catalyze the synthesis of a new DNA strand from an existing DNA template. domain – A protein structure that may have separate secondary structural elements that have a specific function (e.g., NADH binding). double helix – The two strands of DNA polymers linked together by hydrogen bonds. double-reciprocal plot – see Lineweaver–Burk plot. down regulation – A mechanism that decreases the number of receptors on a cell surface target, making the cell less sensitive to excess hormones or other ligands by degrading or internalizing them. downstream – Direction of a nucleic acid polymer that is further away from a given point (often the start site) for transcription.

E EF hand – A 40-amino-acid-residue domain containing a helix-loop-helix design that binds Ca2+ ions with high affinity. eicosanoids – A group of endogenous lipid-signaling molecules synthesized from arachidonic acid. electric field effect – A through-space effect within a molecule due to electrically charged groups.

electrochemical cell – A device to measure redox potentials by separating oxidation from reduction in separate half-cells. electrical potential – A difference in charge between two points; also known as a voltage. electrode – A metal that serves to enable a redox reaction on its surface and carry electrons to or from a wire in an electrochemical cell. electrogenic – An exchange process for molecules across a biological membrane that is not charge balanced. electron-releasing – A through-bond effect of donating electrons due to a difference in the electronegativity between atoms across a bond. electron-withdrawing – A through-bond effect of accepting electrons due to a difference in the electronegativity between atoms across a bond. electron paramagnetic resonance – A type of spectroscopy in which there is resonant absorption of radiation from chemical substances with unpaired electrons. A spectrographic technique that identifies and measures free radicals. electron sink – An electron deficient portion of a molecule that attracts electrons in the course of a reaction mechanism. electron transport chain – A connected series of redox reactions that exist in the mitochondrial membrane that accept electrons from NADH and donate them to O2. A similar structure exists in the thylakoid membrane of the chloroplast. electronegativity – A concept derived from the relative attraction of atoms across a bond. Atoms with high values of electronegativity have a greater ability to attract bonding electrons. electrophoresis – A form of chromatography in which the mobile phase is driven by an electric field imposed by electrodes; the stationary phase may be a gel composed of a polymer, such as polyacrylamide (see chromatography). elongation – The process of extending a polymer, such as an RNA chain or a protein. emulsification – The dispersion of insoluble lipids (e.g., triglycerides) into water solutions. enantiomers – Molecules whose structures are nonsuperimposable mirror images. endergonic – A positive change in free energy. An endergonic reaction will only proceed in the reverse direction to the one written. endoplasmic reticulum – A membrane network of tubules forming an enclosed space within the cell that is active in lipid transport, vesicular transport, protein export, and Ca2+ release to the cytosol. endothermic – A change in enthalpy for a reaction that is positive (ΔH>0).

xxx Glossary

energy – A nonmaterial driving force for reactions, classified as potential (stored) or kinetic (expressed). Different forms of energy include electrical, gravitational, heat, and mechanical. energy coupling – The use of high energy molecules within a reaction to ensure that it can proceed with a negative free energy. As a formal procedure, reactions that do not actually take place can be summed using their standard free energies to arrive at an overall favorable free energy change. This formalism should not be confused with an actual mechanism, however. enthalpy – A heat change for a system at constant pressure; a defined energy change for thermodynamic systems. The enthalpy change results largely from bond energies in reactions. enthalpy driven – A chemical reaction in which the free energy change is dominated by the enthalpy term (ΔH). entropy – An expenditure of energy that is unavailable to apply to work. The increased entropy is due to an increased dispersion of a system. For example, when two bonded atoms are split apart, the reaction entropy increases. entropy driven – A chemical change in which the free energy change is dominated by the entropy term (ΔS). enzyme – A biological catalyst that lowers the activation energy for a reaction without affecting the equilibrium position, enabling a reaction to proceed with minimal changes in temperature. enzyme activity – Measure of an enzyme function in units of moles of substrate converted to product per unit time. enzyme complex – A group of enzymes that catalyzes a metabolic sequence without releasing intermediates. enzyme conservation – A statement that the total amount of enzyme (Etot) is constant for the course of a reaction and can be expressed as the sum of all enzyme forms. epimerase – A type of enzyme that catalyzes the stereochemical rearrangement of hydroxyl groups in a sugar. epimers – Sugars that differ at chiral centers other than the D or L positions. epinephrine – A catecholamine hormone released by the adrenal glands and some neurotransmitters of the central nervous system in response to stress. equilibrium – A state that exists when the forward and reverse rates of a reaction are equal. In chemistry, it is when the products and reactants are in a constant ratio. ES – Intermediate enzyme–substrate complex. essential amino acids – Any of the amino acids not synthesized by the body and so must come from the

diet. These amino acids are required for the formation of proteins. essential fatty acids – A group of unsaturated fatty acids essential to human health that cannot be manufactured in the body, so they come from oils and fats found in plants and animals. Examples: omega-3 and omega-6 fatty acids. evolution – The fundamental thesis of biology explaining how species arise: from previous species. The principle applies also to macromolecules, such as DNA and protein, which can be mapped from their earliest origins and indicate their relationship to other, similar forms. excision repair – A process to correct DNA damaged after replication by removing the faulty segment and, through DNA synthesis, replacing it with the correct segment replicated from a template of an undamaged DNA strand. exciton transfer – A form of resonance energy transfer that occurs between chlorophyll molecules in photosynthesis. exergonic – A reaction for which ΔG < 0, where G is free energy. Every reaction in a functional metabolic pathway is exergonic. exothermic – A change in enthalpy for a reaction that is negative (ΔH < 0). exome sequencing – A laboratory technique for separating the exons from the remainder of the DNA and then sequencing just those nucleotides. exons – A segment of a gene that contains information used in coding for protein synthesis. Genetic information within genes is discontinuous, split among the exons that encode for messenger RNA and absent from the DNA sequences in between (see introns). Genetic splicing, catalyzed by enzymes, results in the final version of mRNA, which contains only genetic information from the exons. exonuclease – An enzyme capable of detaching the terminal nucleotide from a nucleic acid chain; any of a group of enzymes that catalyze the hydrolysis of single nucleotides from the end of a DNA or RNA chain. extremophiles – Organisms that thrive in extreme external environments, such as high temperature, pressure, or salinity.

F fatty acids – Molecules with two parts: a long hydrocarbon segment (the tail), and a smaller region that typically consists of a carboxyl group (head). The hydrocarbon tail consists mostly of chemically unreactive methylene groups with a variable number of double bonds.

Glossary xxxi

Faraday – An electrical conversion constant converting numbers of electrons to mols. feed-forward activation – A modulator (stimulation or inhibition) of an enzyme that arises from a reaction that occurs earlier in the same metabolic pathway. fermentation – An early name for yeast glycolysis, which produces ethanol and CO2. ferredoxin – A mobile protein electron carrier in photosynthesis that slides along the stromal surface of the thylakoid membrane of the chloroplast, accepting electrons from PSI, and donating to NADP+ (linear photosynthesis) or cyt. b6f (cyclic photosynthesis). Fischer projection – A two-dimensional representation of the three-dimensional structure of an organic molecule. 5' end – One end of a linear polynucleotide strand at which the 5'-hydroxyl group of the terminal nucleoside residue is not joined to another nucleotide (i.e., the free end). flavonoids – A large group of water-soluble plant pigments that are polyphenols that have reputed antiviral, antioxidant, and anti-inflammatory health benefits. fluid phases – Forms of matter that assume the shape of their container. These include both gases and liquids. folic acid – A water-soluble vitamin (classified as a B vitamin) that is a precursor to tetrahydrofolate (THF) and dihydrofolate (DHF), cofactors in one-carbon metabolism. fractional saturation – Proportion of binding of a ligand to a macromolecule, such as oxygen binding to myoglobin or hemoglobin. free energy – A thermodynamic term that describes the overall directional change of a reaction, combining the first law (energy changes as enthalpy) and the second law (entropy). fructose bisphosphatase – Hydrolase enzyme converting the bisphosphate of fructose into fructose-6-P.

G galactose – A sugar that is the 4-epimer of glucose. galactose catabolism – Breakdown of galactose, converging with the glycolytic pathway at glucose-6-P. gas liquid chromatography – An analytical technique where the sample and carrier fluid are converted into the gas phase (the mobile phase); the stationary phase is packed into a long, thin column. genetic code – The rules for matching of codons to their amino acids. In the polynucleotide chain, the pattern of nucleotides governing the sequence of

amino acids that make up each protein synthesized in the cell. glucagon – Hormone secreted by the α-cells of the pancreas during fasting conditions, as blood glucose concentrations are decreased. Glucagon acts on the liver to increase glucose release into the bloodstream. glucogenic – Giving rise to or producing glucose. glucokinase – Isozyme of hexokinase with a very high Km (20 mM) for glucose. gluconeogenesis – A process by which glucose is made in the liver from noncarbohydrate precursors (e.g., lactate, amino acids, and glycerol). glucose-6-phosphatase – An enzyme that catalyzes the hydrolytic dephosphorylation of glucose-6-phosphate, which is the principal route for hepatic gluconeogenesis, thus allowing glucose stored in the liver to enter the blood. glutathione – A peptide composed of glycine, cysteine, and glutamic acid. Reduced glutathione (due to the cysteinyl –SH group) reacts with intracellular proteins in order to maintain their sulfhydryl groups in the reduced form, part of the antioxidant system in cells. glycerol phosphate shuttle – A mechanism for the transport of electrons from cytosolic NADH to mitochondrial carriers of the oxidative phosphorylation pathway. glyceroneogenesis – Metabolic pathway occurring in adipose tissues and liver in mammals that can convert pyruvate to the glycerol of triacylglycerol (the major storage form of fat). glycogen – A branched polysaccharide that is the major form of carbohydrate storage in animal cells. glycogen branching enzyme – In glycogen synthesis, the enzyme that catalyzes the transfer of a linear (αl→4) segment of the molecule to a hydroxyl group at the 6 position to create a branch. glycogen phosphorylase – In glycogenolysis, the major enzyme leading to a release of glucose-1-phosphate from glycogen. glycogen phosphorylase kinase – An enzyme that catalyzes the conversion of phosphorylase b to phosphorylase a (the phosphorylated, active form); activated by Ca2+ and cyclic AMP dependent protein kinase. glycogen storage diseases – A set of inborn genetic errors of metabolism deleterious to glycogen metabolism. glycogen synthase – An enzyme that catalyzes the transfer of a glucosyl unit from uridine diphosphate glucose (UDP-glucose) to glycogen. glycogen synthase kinase (GSK) – A cytosolic protein kinase that catalyzes the phosphorylation

xxxii Glossary

of serine residues in glycogen synthase and inactivates it. glycogen synthesis – Pathway of formation of glycogen from individual glucosyl subunits. glycogenin – A protein at the core of the glycogen particle, linked to the glucose subunit through a tyrosine residue. glycogenolysis – Degradative pathway converting glycogen to glucosyl subunits (glucose-1-P). glycosidic bond – The molecular link between sugars, chemically an acetal or a ketal. gout – A metabolic arthritis resulting from over-production of uric acid (see allopurinol). G protein – Signaling proteins that are either bound to GTP (active form) or GDP (inactive form). On the inner surface of plasma membranes, trimeric G proteins transmit some hormone signals to their effectors such as in the production of cyclic AMP. Within cells, small G proteins act as intermediate control systems, such as those regulating protein synthesis. grana – Overlapping stacks of membranes within the chloroplast organelle.

H hairpin turn – In RNA transcripts that have a palindromic sequence, the formation of a doublestranded segment functions as a control signal for protein-nucleic acid interactions. half-cell – One of two solutions of electrolytes with an electrode enabling separate oxidation and reduction in a galvanic cell. half-reaction – The oxidation or reduction portion of a redox reaction, either a formal representation, or a physical one within a half-cell. Haldane – An equilibrium constant for an enzyme expressed in terms of kinetic constants rather than rate constants. Haworth projection – A perspective representation of the molecular ring structure of sugars, using pentagons, hexagons, and shading to depict bonds in three dimensions. heat – A form of energy that transfers among molecular particles through the kinetic force of those particles, always in the direction of high temperature to low temperature. helix breakers – Amino acids that disturb the ability of a protein segment to form an alpha helix, either through restricted bonding (like proline), too much rotational freedom (glycine), or neighboring charge interactions (like multiple proximal glutamate residues). heme – An iron binding cofactor made up of linked imidazoles. The iron may be redox active, as in

cytochromes, or at fixed oxidation state, as in hemoglobin. heme regulated inhibitor – A protein kinase that suppresses protein translation in reticulocytes when heme or iron concentration is low. hemiacetals – The condensation product of an alcohol and an aldehyde. The hydroxyl group of the hemiacetal is used to form glycosides in sugars. hemiketals – The condensation product of an alcohol and a ketone. The hydroxyl group of the hemiketal is used to form glycosides in sugars. hemimethylated – A DNA chain that has a methyl group on one strand but not the other. high-energy electrons – The electrons carried in redox transfer cofactors such as NADH that ultimately lead to energy generation. high-energy molecules – Molecules containing localized electrons that can be redistributed and used as an energy source in a further reaction, such as NADH and ATP. high-energy phosphate – A phosphoryl group that is exchanged between molecules, usually involving at some point the mobile cofactor intermediate, ATP. high pressure liquid chromatography (HPLC) – An analytical technique using many small beads and a correspondingly large surface area for the stationary phase. High pressure is needed to drive flow of the mobile phase (see chromatography). histones – Small basic proteins that bind the negatively charged backbone of DNA and contribute to the condensation and packing of DNA. holistic – A view that focuses on system properties rather than its parts. hydrated – Attached to water molecules. hydride ion – The anion of hydrogen (H:-). hydrogen bond – An interaction involving a hydrogen atom attached to a N or O atom and another N or O atom. The bond strength is intermediate between van der Waals forces and covalent bonds. hydrolases – A category of enzymes that are actually a type of transferase (itself a separate category of enzymes) in which water is a substrate. hydrophobic effect – A clustering of nonpolar molecules driven by more favorable water–water interactions.

I immunophilins – Drugs that form a complex with prolyl isomerase and then inhibit specific targets, such as calcineurin, a protein phosphatase essential to T-cell proliferation in the immune system.

Glossary xxxiii

inhibitor – A substance that decreases the rate of an enzymatic reaction. insulin – A hormone secreted from the cells of the pancreas into the bloodstream in response to an increase in blood glucose. Insulin leads to a decrease in blood glucose concentrations by stimulating glucose uptake and metabolism in cells. insulin receptor substrate 1 (IRS-1) – A cytosolic regulatory protein that is phosphorylated by the insulin receptor and serves as a binding site for other regulators in the cell. insulin-resistant – A condition in which cells respond poorly to the presence of insulin, found almost universally in obese individuals, and a precursor state to diabetes. initial velocity – The first (linear) portion of a reaction progress curve, either disappearance of substrate, or appearance of product. In theory, the slope of this curve as time approaches zero is defined as the initial velocity; in practice, the first 5% to 10% of the progress curve is approximately a straight line. inner mitochondrial membrane – One of two membranes in the mitochondrion, this membrane is infolded, providing a greater membrane area for the components of oxidative phosphorylation and transport proteins (see outer mitochondrial membrane, matrix space). inorganic phosphate – An isolated phosphate group that is a weak acid and can combine with an alcohol to form an ester. intermediary metabolism – Connected reaction sequences in cells that represent the major pathways, common to cells in many biological organisms. internal energy – The energy of the system under study, combining the amount of heat put into a system with the amount of work delivered by the system. intrinsic factor – A protein found in cells of the stomach lining (epithelia), secreted into the stomach, and used later in the small intestine in the uptake of dietary vitamin B12. introns – A segment of a gene situated between exons that does not function in coding for protein synthesis. After transcription of a gene to messenger RNA, the introns are removed, and the exons are spliced together by enzymes before translation and assembly of amino acids into proteins (see exons). ionization of water – The dissociation of water into hydrogen ions (H+) and hydroxide ions (OH−). ionophore – A molecule that binds an ion and transports it across a membrane. irreversible inhibition – Inhibition that is not characterized by an equilibrium constant, but is instead

produced by covalent incorporation of the molecule into the enzyme. isolated double bond – A type of double bond in which the π orbitals do not overlap with those of other double bonds (alternatively, nonconjugated). isoelectric point – The pH at which a molecule has a net zero charge. isoforms – Distinct proteins that function identically; isomeric form of the same protein, with different amino acid sequences but with the same activity. isomerases – A class of enzymes that catalyze rearrangement reactions, such as the interconversion of ketoses and aldoses. isozymes – Enzymes with different structures that catalyze the same reaction.

K ketogenic – Amino acids that are catabolized to acetylCoA and thus potentially to ketone bodies. ketone bodies – Products of partial lipid oxidation between liver and target tissues such as brain, heart, and skeletal muscle. Acetoacetate and β-hydroxybutyrate are the major ketone bodies. ketoses – Sugars in which the carbonyl group is a ketone, located at carbon two. kinetic constant – A collection of rate constants that characterizes enzymatic rate equations. Km – A kinetic constant that is a substrate concentration occurring at half of the maximum velocity of an enzyme. Krebs cycle – One of the major metabolic pathways in cellular metabolism. A cyclic pathway that converts acetyl CoA to CO2 and extracts energy intermediate molecules NADH, UQH2, and GTP (see citric acid cycle, tricarboxylic acid cycle).

L lac operon – A grouping of genes and regulatory products in bacteria that controls the synthesis of three enzymes that enable utilization of lactose as a carbon source. lactose intolerance – A common genetic deficiency of lactase (an enzyme that catalyzes conversion of lactose to galactose and glucose) that impairs the digestion of dairy products. The partial bacterial oxidation of lactose in the large intestine is responsible for the symptoms of bloating and gas production. laforin – A phosphatase active on glycogen polymer, defective in Lafora disease. Lafora disease – A rare disorder of glycogen metabolism in which large and hyper-phosphorylated

xxxiv Glossary

glycogen particles appear in brain and other tissues. lagging strand – In DNA replication, the strand in which the nascent strand is synthesized in discontinuous segments because all transcription must be in the 5' to 3' direction and both DNA strands (oppositely arranged) must be replicated (see Okazaki fragments, leading strand). leading strand – In DNA replication, the strand that is synthesized continuously during replication (see lagging strand). Le Chatlier principle – A postulate that reactions proceed in the direction of greater to lesser concentrations, compared with equilibrium concentrations. lecithin – A common name for phosphatidylcholine. leghemoglobin – A monomeric heme containing protein structurally similar to myoglobin, found in the root nodules of leguminous plants (such as soybeans) that are host to nitrogen-fixing bacteria. Oxygen inhibits nitrogenase; leghemoglobin sequesters oxygen, keeping its concentration low, but still able to supply bacterial respiration. Lewis acid or base – Acids defined as electron pair acceptors; bases defined as electron pair donors. leukotrienes – A group of biologically active compounds derived from arachidonic acid that are responsible for allergic and inflammatory reactions. light reactions – Steps in photosynthesis in which light energy is utilized to produce the high energy intermediate compounds ATP and NADPH. lipid droplet – An intracellular organelle in which the interior is largely triacylglycerols and other lipid molecules, with a monolayer phospholipid membrane. Lineweaver–Burk plot – Double reciprocal transform plot of the Michaelis–Menten equation, which linearizes the resulting graph (also termed double-reciprocal plot ). lipids – Relatively unreactive hydrocarbons such as oils and fats; they are entirely or mostly water insoluble. Functions include energy storage and membrane formation. liposomes – A spherical particle formed by a lipid bilayer enclosing an aqueous compartment; used to convey viruses, drugs, and other substances. loop – Describes the shape of a type of secondary structure of protein formed with the backbone atoms and their hydrogen bonds that link other secondary structures together (also termed random coil). loop mechanism – A mechanism for creating the proton gradient in the Q cycle, involving the movement of oxidized and reduced ubiquinone moving

between the faces of the mitochondrial membrane (see Q cycle). lovastatin – Inhibitor of hydroxymethylglutaryl CoA reductase and thus cholesterol synthesis; it is a natural product isolated from a fungus used to treat hypercholesterolemia. lumen – Most interior water space of the chloroplast, bounded by the thylakoid membrane. Also, a general anatomical term for an extracellular space interior to the body, such as the lumen of the intestines. lyase – A category of enzymes that catalyze the splitting of a substrate into pieces; lyase reactions do not involve water as a substrate.

M macromolecules – A large molecular polymer such as a protein that exhibits new properties that distinguish it from small molecules. major groove – One of two grooves along the DNA double helix, this has the larger gap between the sugar base structures when viewed from the top of the helix structure (see minor groove, double helix). malate/aspartate shuttle – A pathway for importing NADH from the cytosol to the mitochondria, using reduction of oxalacetate to malate in the cytosol, malate to oxalacetate in the mitochondrial matrix, and interconversion between oxalacetate and aspartate; neither NADH nor oxalacetate can cross the mitochondrial membrane. malin – A part of the ubiquitin system (a ligase attaching the protein ubiquitin) defective in Lafora disease. maple syrup urine disease – A genetic disease caused by the accumulation of three amino acids – leucine, isoleucine, and valine – due to their inability to be oxidized through the branched chain ketoacid dehydrogenase complex. Named for the distinct burned sugar odor of urine (also termed branched chain ketoaciduria ). mass action ratio – The ratio of the reaction products multiplied together to the substrates multiplied together for a reaction at any given point. When the forward and reverse reaction rates are the same, the mass action ratio is equal to the equilibrium constant. mass spectrometry – A system for identifying molecules by fragmenting them into ions in the gas phase and then separating them in an electric field by mass. matrix space – The water space enclosed by the mitochondrial inner membrane.

Glossary xxxv

melanosomes – Lysosome organelles that contain the pigment melanin. melting curve – A plot of strand separation of DNA with increasing temperature. melting temperature – The midpoint of the DNA melting curve. membrane fluidity – The relative ability of individual molecules to move within the bilayer of a cell. mesophyll cells – Cells of C4 plants found in an outer ring that capture CO2 for RuBisCo by carboxylation of PEP, and transporting subsequently formed malate into the inner ring cells (bundle sheath) which is where RuBisCo is located. metabolically irreversible – Metabolic reactions within cells that are greatly displaced from their equilibrium positions and never run in the reverse direction under cellular conditions. These reactions are the sites of metabolic control, through allosteric or covalent modification. methionine cycle – Metabolic pathway of one carbon metabolism in which methionine is converted to S-adenosyl methionine and a methyl group is donated to an acceptor. methylcelluloses – A biologically inert polymer formed in the laboratory by creating methyl esters to some of the hydroxyl groups of cellulose; their partial solubility in water can be controlled by the extent of methylation. micelles – A form taken by lipid amphiphiles in water solution in which the polar portions of the molecules face the aqueous exterior and the nonpolar portion forms an interior core excluded from water. midpoint potential – The redox potential for a reaction under (biological) standard conditions. minor groove – One of two spacings along the DNA double helix, this has the smaller gap between the sugar base structures when viewed from the top of the helix structure (see major groove, double helix). mismatch repair – A system within the cell during replication that corrects errors in DNA by detecting and replacing bases in the DNA that are wrongly paired; an enzyme catalyzes removal of the mismatched segments, and then DNA polymerases fills the gaps in the strands with the appropriate bases. mitochondria – Organelle evolutionarily derived from bacteria, responsible for most of the energy generation of the cell through oxidative phosphorylation. Mitochondria contain portions of several metabolic pathways, such as urea synthesis and gluconeogenesis. mixed inhibition – A type of reversible enzyme inhibition in which the inhibitor binds both the free

enzyme and the enzyme-substrate complex (also called noncompetitive inhibition). mobile cofactors – Part of an enzymatic reaction that can dissociate from the enzyme at the conclusion of the reaction and participate in a reaction in a separate pathway in the cell. Examples are NADH, UQH2, and cytochrome c. By contrast, bound cofactors never leave the enzyme during the catalytic cycles. molecular biology – A broad term encompassing genetics, biochemistry, and growth processes of the cell. monomers – Individual protein chains (subunits). motif – Here used as a synonym for domain. Some investigators consider a motif as a specific portion of a domain. mTOR – A protein kinase (positively) regulating protein synthesis by catalyzing phosphorylation of control proteins such as S6K. Originally named as “mammalian target of rapamycin”, it is also named “mechanistic target of rapamycin”. muscle hypertrophy – Increase in the size of muscle tissue.

N N-acetylglutamate – A compound produced from acetyl coenzyme A and glutamate; an allosteric activator of carbamoyl phosphate synthetase in the urea cycle. NAD binding domain – The site of binding of this mobile cofactor, common to a large number of enzymes. near-equilibrium – A reaction in cells that has a mass action ratio close to the equilibrium constant, and can run in the reverse direction in a separate pathway. Such reactions are controlled by substrate and product concentrations and are not regulated by external means (i.e., by allosterism or covalent modification). negative cooperativity – Cooperativity in which successive ligand molecules appear to bind with decreasing affinity. negative supercoil – Occurs when the double helix strand of DNA is twisted in a counterclockwise direction (the opposite direction to turns in the helix), which either unwinds or twists the entire structure (see supercoils, double helix). Nernst equation – Expression of the reaction potential derived from the free energy equation; this equation relates the redox potential to the reaction concentrations. nitrification – A process where the oxidation of ammonia (NH3) to nitrites and nitrates is accomplished by bacteria in a series of reactions.

xxxvi Glossary

nitrogen cycle – A global nitrogen cycle by which atmospheric nitrogen gas (N2) is fixed into nitrogen oxides and ammonia, which can be incorporated into biological systems, and then converted back to N2. nitrogen fixation – The incorporation of atmospheric nitrogen, catalyzed by nitrogenase into ammonia by various bacteria; the process whereby certain microorganisms, such as rhizobia, convert atmospheric nitrogen into compounds that plants and other organisms can assimilate. nitrogenase – An enzyme complex converting N2 to NH3. non-cooperative – A binding process in which ligands bind independently to monomers of a multimeric protein. nonessential amino acids – Amino acids that can be synthesized by the organism and, thus, do not need to be present in the diet (see essential amino acids). nonpolar lipids – Lipids that are not amphiphiles. Example: triacylglycerols. nonreducing end – The sugar residue at the end of a polysaccharide that has no free anomeric hydroxyl group. nonreducing sugars – Any saccharide that has no free anomeric carbon atoms. Examples: sucrose and trehalose. N side – Negatively charged side of an energy producing vesicle (chloroplast, bacteria, or mitochondria) produced when hydrogen ions leave this space. nuclear magnetic resonance (NMR) spectroscopy – A method for the study of molecular structure in which a magnetic field is imposed and the absorption of electromagnetic radiation at specific frequencies is measured. nuclear membrane – The double-layered membrane surrounding the nucleus of a cell. nucleotides – Modified sugar molecules that contain a nitrogenous base and at least one phosphate ester; the most common are AMP, ADP, and ATP, key energy transfer molecules widely used in metabolic reactions in cells. Additionally, nucleotides form the polymers DNA and RNA.

O oil – The liquid form of lipids. Okazaki fragments – During DNA replication, the relatively short fragments of DNA synthesized on the lagging strand; later these fragments will be covalently connected into a continuous strand. oligosaccharides – A carbohydrate whose molecules are composed of a relatively small number of monosaccharides linked via glycosidic bonds.

operon – A group of genes or a segment of DNA that functions as a single transcription unit, comprised of an operator, promoter, and one or more structural genes that are transcribed into one polycistronic mRNA. osmosis – The ability of water to move across a semipermeable membrane due to differences in solute concentrations across the membrane. osmotic pressure – The applied pressure needed to equalize the fluid levels across a semipermeable membrane that exhibits osmotic imbalance. outer mitochondrial membrane – One of two membranes in the mitochondrion; porous to molecules with a molecular weight up to about 10,000 (e.g., ions, ATP, ADP, and nutrient molecules) (see inner mitochondrial membrane). oxidation number – An assignment to an atom indicating what its charge would be if it were not engaged in a covalent bond. Useful in determining redox states of organic molecules. oxidative phosphorylation – The oxidation of reduced substances tied to the production of ATP by mitochondria. oxidoreductases – A category of enzymes in which the substrate changes the oxidation state during the process of going to product; there must be a mobile cofactor that removes or adds those electrons, often NAD+.

P P – Phosphoryl group, often referred to as a phosphate group, such as in the carbohydrate derivative glucose-6-phosphate (glucose-6-P). palindrome – A self-complementary nucleic acid sequence. In general, any sequence of letters that reads the same in the forward direction as in the reverse. parallel – In a β-sheet of a protein, when the strands run in the same direction. PARP – see poly ADP-ribose polymerase. partially ionic bond – A description of a covalent bond that emphasizes its partial ionic character due to electronegativity differences of the atoms on either side of the bond. Pasteur effect – A 19th-century observation by Louis Pasteur that glucose utilization is decreased in the presence of oxygen in yeast metabolism. path-dependent – A change in a system that varies depending on how it is accomplished. For example, the amount of work accomplished in a process depends on the route taken. path-independent – A change from one state to the next that is independent of the route that is taken. This describes several changes in thermodynamics

Glossary xxxvii

such as the change in internal energy, enthalpy, and free energy. pathway completion – In a metabolic pathway, all mobile cofactors must be balanced so that the route can be traversed again by further pathway substrates. pathway flux – The overall rate of a pathway that is also the rate of every individual reaction in the pathway under a given steady-state condition (see pathway substrate, pathway product). pathway-irreversible – A modification of an enzyme that cannot be reverted by a separate reaction(s) in a cell, and is thus a permanent change until the enzyme is degraded by proteolysis. pathway product – The final product of a series of reactions that defines a pathway in cells. pathway substrate – The initial product of a series of reactions that defines a pathway in cells. pathway-reversible – A modification of an enzyme that can be reverted by a separate cellular reaction without requiring proteolysis. The most common example is protein phosphorylation, reverted by a protein phosphatase. PCR – see polymerase chain reaction. pentose phosphate shunt – Pathway branching from glycolysis at glucose-6-P that produces ribose carbon for nucleotides and NADPH. peptides – Short chains (roughly 25) of amino acids that have sufficient flexibility in solution so that a fixed higher order structure does not exist. peptide bond – An amide linkage found between the amino acids of proteins. phenylketonuria – A genetic disorder in humans caused by an inability of the body to metabolize phenylalanine to tyrosine. pheophytins – Part of the reaction center in the light reactions of photosynthesis, these molecules are structurally similar to chlorophyll molecules except that the chelate ring has no metal inside it ( see reaction center). phosphatidic acid – A phospholipid with a single fatty acyl chain attached to a glycerol phosphate backbone. phosphatidylinositol phosphate 3-kinase – An enzyme that catalyzes the incorporation of a phosphoryl group into the 3-position of the inositol ring. phosphodiesterase – An enzyme that cleaves phosphodiesters into a free hydroxyl group and a phosphomonoester. phosphoenolpyruvate carboxykinase (PEPCK) – The rate-limiting step of gluconeogenesis under most conditions, this enzyme converts oxaloacetate to carbon dioxide and phosphoenolpyruvate. phospholipid-dependent kinase – A regulatory enzyme that phosphorylates serine and threonine residues in response to protein kinase B and membrane phospholipids.

phosphonate – Phosphate in which one of the P–O bonds is substituted by a P–C bond. phosphoribosylpyrophosphate (PRPP) – This multiply phosphorylated ribose is a precursor in the synthesis of nucleotides. phosphotyrosine binding domain – Domains of 100– 150 residue modules that commonly bind the Asn-Pro-X-Tyr motifs where the tyrosine residue is phosphorylated. Found in proteins involved in regulatory cascades. photosynthesis – Pathway for utilization of light energy to form high energy intermediates (the light reactions); usually also refers to the ultimate synthesis of carbon compounds such as carbohydrates (see carbon reactions). photosynthetic – Type of organism that can utilize light to synthesize carbon compounds. photosystem (PS) – Complex of proteins involved in photosynthetic energy transfer that accept light input and boost electron energy of other molecules. photosystem I (PS I) – In green plant photosynthesis, contains iron-sulfur proteins and transfers electrons from plastoquinone to ferredoxin. photosystem II (PS II) – In green plant photosynthesis, contains an iron center and transfers electrons from water to plastoquinone. photon – Minimal unit of light energy defined from the equation E = hν where E is energy, h is the Planck constant, and ν is the frequency of light. phylloquinone – A form of Vitamin K. ping-pong (mechanism) – An enzyme mechanism in which one substrate binds and the product is released before a second substrate binds. This mechanism occurs in transaminase reactions. PKC – see protein kinase C. PKU – see phenylketonuria. plasmodesmata – A bridge of cytoplasm that spans adjacent plant cells to permit communication and transport between individual cells. Gap junctions are the functional equivalents in animal cells. polar bond – A bond between two atoms that have large differences in electronegativity. polarimeter – A device that detects chiral molecules and differentiates the two forms by determining the rotation of the plane of polarized light as it passes through a solution. polar lipids – Lipid molecules that are amphipathic, with one portion of the molecule interacting with water. These include cell membrane lipids. polar molecule – Describes a molecule with a net polarity due to the overall vector sum of its bonds. polyamines – Molecules with multiple amines, bearing a net positive charge and interacting with DNA through electrostatic attraction. The polyamines are: putresciene, spermidine, and spermine.

xxxviii Glossary

poly-A tail – A structure of up to 250 adenylate residues located on the 3' end of eukaryotic mRNAs used in translation and protecting the mRNA against nuclease action. poly A polymerase – An enzyme catalyzing the incorporation of a string of adenosine residue on the 3’ end of mRNA. poly ADP-ribose polymerase – An enzyme catalyzing the incorporation of multiple copies of the ADPribose portion of NAD+ into proteins involved in DNA repair. The poly-ADP tail is a binding site for other repair proteins. polycistronic – Bacterial mRNA that contains sequences for several different proteins in the same messenger RNA strand. polymerase chain reaction – A technique for amplifying small quantities of DNA by multiple rounds of synthesis of complementary chains, heating to release the finished chains, and cooling to synthesize chains. The polymerase enzyme is isolated from a thermophile (an extremophile). polymers – Large molecules composed of many repeating subunits. polyprotic acid – An acid that can donate more than one proton, such as phosphoric acid. polysaccharides – A carbohydrate polymer composed of monosaccharide residues bound together via glycosidic bonds. polyunsaturated – Fatty acids with more than one double bond. porins – Protein molecules lining the outer membrane of the mitochondria, which enable passage of molecules up to 10,000 Da. (see also VDAC) positive cooperativity – Cooperativity in which successive ligand molecules appear to bind with increasing affinity. positive supercoil – Occurs when the double helix strand of DNA is twisted in a clockwise direction (the same direction as the turns in the helix), which tightly coils the structure (see supercoils, double helix). postprandial state – A period immediately after the ingestion of a meal. post-translational modification – A covalent modification to a protein apart from its ribosomal synthesis. prenylation – The incorporation of branched chain lipids (isoprene derivatives) into proteins that commonly enables interaction with membranes. Pribnow box – A highly conserved sequence element located upstream from the start site of transcription, to which the sigma subunit of RNA polymerase binds; found in prokaryotes, such as E. coli and bacteriophage genes. primary structure – The sequence of amino acids in a linear protein chain.

primitive – A concept that has no deeper understanding and is accepted on faith as there have been no contradictions. For example, the concept of charge is a primitive, as we understand its qualities but nothing further. primase – An RNA polymerase that catalyzes complementary ribonucleotide base additions to singlestranded DNA in the first biochemical reactions to add bases to the strand. primosome – During DNA replication, the protein complex containing primase and helicase that initiates the RNA primers on the lagging DNA strand. probenecid – A drug used to treat gout by increasing urate excretion by the kidneys (see gout). processivity – The movement and catalysis of a molecule on a substrate surface without dissociation between catalytic cycles. prochiral – An achiral molecule that can be enzymatically converted to a chiral one. Prochiral molecules all have double bonds at positions that become chiral centers. promoters – A site in a DNA molecule at which RNA polymerase and transcription factors bind to initiate transcription of messenger RNA. prosthetic group – A small molecule that is bound to a protein to assist its function. These molecules remain bound to the protein surface as it functions, and may be considered an extension of the protein itself. protease – An enzyme that hydrolyzes peptide bonds in proteins. proteasome – A cytosolic protein complex in which proteins enter and are degraded to small peptides. protein – Linear chains of amino acids that form a specific three-dimensional structure (thus distinguishing them from smaller peptides that are usually on the order of 25 amino acids or less). Proteins are the most diverse biomolecules, including virtually all of the enzymes, the biological catalysts. protein kinase C – A protein kinase that catalyzes the phosphorylation of serine or threonine amino acid residues. The “C” in the name derives from an early finding that a calcium-stimulated protease activated the enzyme; however, this proteolysis is not the mechanism for its rapid activation in cells. An increase in the lipid mediator diacylglycerol is the activator of PKC. proton motive force – The driving force for oxidative phosphorylation, composed of a chemical (pH) gradient and an electrical gradient, both due to a difference of hydrogen ions across the inner mitochondrial membrane. PS I – Photosystem I of chloroplasts (see photosystem). PS II – Photosystem II of chloroplasts (see photosystem).

Glossary xxxix

P side – Positively charged side of an energy producing vesicle (chloroplast, bacteria, or mitochondria) established when hydrogen ions enter this space. purine nucleotide cycle – A metabolic cycle between AMP and IMP that serves to convert aspartate into fumarate as an anapleurotic (refilling) reaction for the Krebs cycle. pyridoxal phosphate – A cofactor derived from vitamin B6 that is the prosthetic group of glycogen phosphorylase and amino acid transaminases. pyrrole – A five-member heterocycle containing one nitrogen atom and four carbon atoms. pyruvate carboxylase – An enzyme that catalyzes the carboxylation of pyruvate to oxalacetate, important in lactate gluconeogenesis, fatty acid synthesis, and as an anapleurotic reaction for the Krebs cycle. pyruvate dehydrogenase complex – A noncovalent association of enzymes that converts pyruvate to acetyl CoA. pyruvate transporter – In the inner mitochondrial membrane, transports pyruvate into the mitochondrial matrix space.

Q Q cycle – The mechanism for complex III production of the proton gradient across mitochondria in which oxidized and reduced forms of ubiquone (UQ, UQH2) move between the membrane faces and ferry protons across the membrane. quaternary structure – A structural level for proteins that have more than one protein chain.

R racemase – An enzyme that catalyzes the inversion around an asymmetric carbon atom. racemic mixture – A mixture of two optical isomers in solution that shows no net optical activity. radical anion – A molecule containing both a free radical and a negatively charged ion. raffinose – A sugar found in foods such as cabbage and beans that is poorly digested due to the presence of the galactose (α1→ 6) glucose bond in the first two sugar moieties of the trisaccharide; its bacterial degradation in the large intestine causes gas. random coil – A protein segment with no recognizable structure of its own linking secondary structures in proteins. ras oncogene – A G-protein gene having an inactive GTPase, which leads to a state of constant activation and hyperactive cell growth, and is a cause of cancer.

rate constant (k) – The proportionality between velocity and substrate concentration for a reaction. reaction center – In photosynthesis, a special pair of chlorophyll molecules that accept energy transferred from other chlorophyll molecules. reactive oxygen species – Molecules formed ultimately from oxygen (a diradical) that contain unpaired electrons and can cause cellular damage. receptor tyrosine kinases – A class of membrane receptors that have intrinsic kinase activity selective for tyrosine residues. redox – Oxidation-reduction reactions involving an electron transfer. reducing end – The sugar residue at the end of a polysaccharide that has an equilibrium form with an open-chain aldose or ketose. reducing equivalents – Energy-rich electrons that can be transferred from cofactors and utilized for energy extraction or reduction of compounds, such as in the hydride NADH. reducing sugar – Any saccharide that has at least one free anomeric carbon (i.e., an anomeric carbon not involved in a glycosidic bond). A small amount of this open-chain form exists in solution, so its carbonyl group can reduce certain metal ions in diagnostic tests. reductases – Enzymes that catalyze the reduction of their substrate. reductionist – A “bottom up” perspective; in biochemical terms, focusing on specific reactions or chemical species or decomposing a more complex system into its elements in order to study finer detail. reduction potential – A measure of the capacity of a redox half-reaction to donate electrons. repetition-variation – A process that is repeated with a slight variant, as the Krebs cycle and other metabolic reactions. replication – The process by which DNA can be used as a template to form daughter DNA molecules for cell division. replication fork – The section of a DNA molecule at which the two strands are just separated; here, both daughter molecules are being synthesized. replisome – In DNA replication, a protein complex containing two DNA polymerase molecules for synthesizing the leading and lagging ends of the DNA strands. resistance training – Exercise that leads to increased protein synthesis in muscle, involving fast (glycolytic) muscle. restriction enzyme – Bacterial DNA hydrolysis enzymes derived from a bacterial defense from bacteriophage. The enzymes recognize specific sequences in DNA and are invaluable for virtually all phases of molecular biology.

xl Glossary

rho protein factor – A protein involved in prokaryotic transcription termination, which binds and disassembles the RNA transcript with concomitant ATPase activity. resonance – In conjugated double bonds, where electrons can spread out over more than two nuclei. respiration – Energy linked process in cells that utilizes oxygen to enable electron flow that ultimately leads to the formation of ATP. rhodopsin – Molecule formed from the covalent linking of retinal with the protein opsin, responsible for light absorption in the visual cycle of animals. ribosome – A cytosolic complex of proteins and ribosomal RNA (rRNA) that binds mRNA and tRNA and functions in the synthesis of proteins. ribozymes – An RNA segment able to catalyze the cleavage and formation of covalent bonds in specific sites of RNA strands; ribosomes are a nonprotein type of enzyme. rotor – The moving (spinning) part of a motor mechanism such as that in F1FoATP synthase.

S S-adenosylmethionine (SAM) – A condensation product of ATP and methionine that functions as a one-carbon donor. saccharide – Sugar (Latin). saturated – Fatty acids containing no double bonds. saturation – A high and unchanging enzyme velocity achieved at high substrate concentration. Schiff base – An adduct formed between an aldehyde and an amine. secondary metabolism – Pathways that produce specialized metabolic products (secondary metabolites) that are not essential for the physiologic function of the organism. secondary metabolites – Molecules that are end products of pathways specific to one or a few organisms and, thus, are less universal than primary metabolic routes. Secondary metabolites protect the organisms from being consumed by predators. secondary structure – A regular, repeating structural element of an amino acid that is formed when a segment of the molecular chain folds in three dimensions. semialdehyde – A molecule containing a dicarboxylic acidand an aldehyde. semipermeable – A membrane that permits the transport of molecules but acts as a barrier to others; partially permeable.

sequential mechanism – An enzyme mechanism with multiple substrates in which all must bind to the enzyme in turn before any product is released. SH2 – see src homology 2. Shine–Dalgarno sequence – Located on a prokaryotic mRNA molecule upstream of the translational start site, the short (3–10), purine-rich sequence of nucleotides that binds ribosomal RNA, thereby aligning the ribosome on the initiation codon on the messenger RNA. Proposed by John Shine and Lynn Dalgarno in 1975. shunt pathway – A pathway that branches from another pathway and terminates at some other point in that pathway. Example: the 2,3-bisphosphoglycerate shunt of glycolysis. shuttles – A pathway for transferring portions of a compound across membranes. Examples: the malate/ aspartate shuttle for reducing equivalents; the citrate shuttle for acetyl-CoA. signal sequence – During protein translation, several amino acid residues at the amino terminus are recognized by the signal recognition particle, which permits transport of the nascent protein to its new destination in an organelle. Once it enters into the new location, this set of amino acids is removed by proteolysis. single-strand binding protein – Protein binding to separated DNA strands, such as at the replication fork of DNA, that enables replication (see replication fork). soft nucleophile – An electron-rich center that is less localized and more easily polarized. species hierarchies – The classification of plants and animals into classes, orders, families, etc. splice variants – RNA products that differ despite arising from the same transcription event due to differences in how the exons are joined together. spontaneous – A term that has diffuse meanings in thermodynamics; often a substitute for exergonic, but at other times used to mean nonenzymatic. It is not a well-defined thermodynamic term. spontaneous generation – The erroneous hypothesis that living organisms arise from nothingness. src – Sarcoma virus protein (src is the sarcoma virus gene), it is the parent of a family of protein kinases that lead to phosphorylation of tyrosine residues, called src kinases. src homology 2 – A protein-building domain in the src (sarcoma virus like) family of cytoplasmic tyrosine kinases, which can bind phosphotyrosinecontaining proteins. S6K (S6 Kinase) – A protein target of the small subunit of the ribosomal assembly that is a substrate of mTOR.

Glossary xli

stacking interaction – An attractive force between each hydrogen-bonded base pair (AT and GC, the “rungs” of the double helix “ladder”) above and below them along the long axis of the DNA double helix (see double helix). state – A thermodynamic condition in which certain variables, such as temperature, pressure, volume, and number of moles, are fixed. state variables – Variables that determine the state of a system, including temperature (T), pressure (P), volume ( V), and number of moles (n). statins – Inhibitors of hydroxyl-methyl-CoA reductase, the rate-limiting step of cholesterol biosynthesis, these drugs are used to lower blood cholesterol concentration particularly in low density lipoproteins (LDLs). statistical thermodynamics – A derivation of the thermodynamic principles that uses the laws of large numbers, calculating the behavior of atoms and molecules on the basis of statistical laws. stator – The stationary part of a motor mechanism (see rotor). steady-state – A condition in which the intermediates of a process, such as a metabolic pathway, are constant with time, while the pathway substrate decreases and pathway product increases. steady-state assumption – In enzyme kinetics, the assumption that the intermediates of a reaction mechanism are constant with time (see steady-state). steady-state constant (Km) – A ratio of rate constants for an enzymatic reaction, the constant is also the concentration of substrate corresponding to the half-maximal initial velocity for an enzyme. stereochemistry – The arrangement of atoms of a molecule in space. stroma – Water space in the chloroplast between the membrane of the chloroplast organelle and the thylakoid membrane. strong acid – An acid that completely dissociates in water, forming H+ and an anion. strong base – A base that dissociates completely in water, forming OH- ion (lowering H+ ion concentration) and a cation. subcutaneous fat – Less saturated lipid-containing adipocytes found just under the skin. substrate – Reactants for enzyme reactions or pathways. substrate cycle – Reactions that involve the same pathway substrates and products, but in opposing directions. Together, the reactions catalyze a net hydrolysis of a high energy phosphate intermediate such as ATP. These cycles enable more precise metabolic control (also termed futile cycle). substrate-level phosphorylation – Reaction(s) that form a high energy phosphate intermediate such as

ATP by direct chemical means, such as phosphoglycerate kinase or succinyl CoA thiokinase. sugar acid – A monosaccharide derivative in which the carbonyl group is oxidized to an acid, such as glyceric acid. suicide substrate – An inhibitor that is converted by the enzyme into a molecule that either binds tightly or covalently and impedes further enzymatic reaction with true substrates. supercoils – Circular or closed loops of DNA that occur when DNA is twisted around its own axis, which changes the number of turns in the double axis (see double helix). supersecondary structure – In protein molecules, the combinations of α-helices and β-sheets connected through loops that form folding patterns stabilized through the same types of linkages as in the tertiary level. surfactant – An amphiphile acting at an air–water interface. surroundings – Everything in the universe apart from the system under study. Svedberg – A unit of measure equal to 10 −13 seconds used as a measure of size of large macromolecules and particles. The term refers to the material’s sedimentation during ultracentrifugation. symmetrical intermediate – Within some enzyme mechanisms that are rearrangement reactions, such as isomerases, addition of protons and/or electrons lead to an intermediate that displays symmetry. The second half of the mechanism will then be a mirror image of the first. synthase – Enzymes that catalyze joining reactions that do not involve a high energy intermediate molecule like ATP. Synonym: lyase (named for the reverse direction). synthetases – See ligases. system – That portion of the universe under study.

T TATA – Located in the promoter region of most eukaryotic genes, a consensus sequence (5'-TATAAAA-3') at −25 nucleotides upstream of the site of the initiation of transcription. telomerase – An enzyme that forms, maintains, and repairs the ends of chromosomes (see telomeres). telomeres – The repetitive nucleotide segments located at the ending segments of chromosomes; these protect the chromosome from deterioration. temperature – The energy measure of a system that shows the average kinetic energy of its molecules. termination – Occurs when the RNA reaches a specific sequence (terminator) and the transcription

xlii Glossary

complex dissociates from the DNA, thereby releasing the RNA polymerase to begin a new initiation event (see transcription, termination sequence). termination sequence – In RNA transcription, a polymerase-specific DNA binding protein found close to the end of a coding sequence; rho-independent sequences are inverted and form a hairpin back onto the sequence; rho-dependent terminators rapidly unwind the DNA–RNA hybrid formed during transcription, thereby freeing the newly synthesized RNA (see transcription). tertiary structure – The entire three-dimensional arrangement, or conformation, of a protein chain in three dimensions. tetrahydrobiopterin – Redox cofactor involved in the hydroxylation of phenylalanine to tyrosine. tetrahydrofolate – Cofactor involved in one-carbon metabolism. thermodynamics – A field of study of energy changes of processes useful in understanding chemical reactions. thermophiles – Organisms that thrive at very high temperatures. They are part of a larger group of extremophiles. thioredoxin reductase – Enzyme catalyzing the reduction of thioredoxin, which is involved in forming deoxynucleotides. The mechanism of thioredoxin reductase is the same as that of glutathione reductase. through-space effect – An electrostatic interaction within a molecule that involves interaction between attached groups, such as the carboxyl and amine groups of an amino acid. thylakoid membrane – Most interior membrane of the chloroplast; separates the inner (lumen) space from the stroma. titration curve – A plot of pH versus the equivalents of a strong base (or strong acid) in a solution of a weak acid (or weak base). topoisomerases – A class of enzymes that catalyze changes in double-stranded DNA by transiently cutting one or both strands of the helix; in supercoiling the twisting results in a shortened molecule (see supercoils, double helix). transaldolase – Transferase enzyme that exchanges carbon fragments between substrates using the same mechanism as aldolase. transaminase – Enzyme catalyzing exchange between an amino acid and a ketoacid. transcription – The synthesis of ribonucleic acid (RNA) from a deoxyribonucleic acid (DNA) template. transferases – A category of enzymes that catalyze reactions that move a piece of one substrate on to another.

transhydrogenase – Enzyme that catalyzes movement of electrons between NADH and NADPH. transketolase – Transferase enzyme that uses thiamine as a bound cofactor to exchange carbon fragments between substrates, converting one ketone into another. transfer RNA – Form of RNA that binds a triplet codon in mRNA and carries an amino acid to incorporate the next unit in a protein chain. translation – A cellular process in which messenger RNA (mRNA) provides a template for protein synthesis to form new protein. translocase – An enzyme catalyzing membrane transport, i.e., a transport protein. transporter – A protein enabling membrane transport; synonymous with translocase. trehalose – The disaccharide glucose (α1→α1) glucose found in bacteria, fungi, plants, and insects. tricarboxylic acid cycle – see Krebs cycle, citric acid cycle. triose – A three-carbon monosaccharide that is the smallest sugar. triosephosphate isomerase (TIM) domain – A domain that is donut-shaped, with an inner portion composed of a β-sheet and an outer portion of α-helices (see domain). triosephosphate isomerase – A glycolytic enzyme that catalyzes the interconversion of two isomeric three-carbon phosphorylated sugars. type I diabetes – A disease in which blood glucose concentrations are above normal due to little or no insulin production by the pancreas (formerly known as juvenile or insulin-dependent diabetes). type II diabetes – A disease in which blood glucose concentrations are above normal due to tissue insensitivity to insulin (formerly known as adult-onset or noninsulin-dependent diabetes).

U ubiquitin – A small protein that can become attached to cytosolic proteins and serve as a signal for degradation in the proteasome (see proteasome, ubiquitination). ubiquitination – The process of attachment of ubiquitin to a protein (see ubiquitin). umami receptor – Taste receptor responsive to glutamate, responsible for the savory sensation. uncompetitive inhibition – A reversible inhibitor that binds exclusively to the enzyme-substrate complex (also termed anticompetitive inhibition). uncoupling – The dissociation of ATP formation (phosphorylation) from mitochondrial electron

Glossary xliii

transfer. Uncouplers accelerate electron transport but diminish ATP formation (see coupling). universe – All that exists; in thermodynamics, the sum of the system and surroundings. unsaturated – Fatty acids containing double bonds. Examples: arachidonic acid, oleic acid. upstream – In transcription, the sequence before the start site (see downstream). ureido – The NH2 CO–NH– group, present in citrulline and urea. uricotelic – Organisms using uric acid as their major nitrogen excretion product. ureotelic – Organisms synthesizing urea as their major nitrogen excretion product.

V vectorial – A process that involves both a quantity and a direction, such as the movement of protons across the mitochondrial membrane during oxidative phosphorylation. vibrational – A form of elementary energy arising from the relative motion of two bonded atoms. To a first approximation, this energy arises from simple periodic motion. visceral fat – Adipose deposits located in the organs, especially of the abdomen (also termed organ fat, intra-abdominal fat). VDAC – Voltage dependent anion channel. Named for an in vitro activity, this is an opening of the outer mitochondrial membrane that allows small molecules up to 10,000 D to cross this membrane. Only proteins are blocked (see porin). vitalism – The principle (erroneous) that living systems do not obey the same chemical principles as inert materials. vitalist – One who believes (erroneously) that living systems do not obey the same chemical principles as inert materials. vitamins – Precursors to enzyme cofactors, classified as fat or water soluble molecules needed in small amounts. vitamin B12 – Vitamin involved in methyl transfer reactions, having a central cobalt ion (also known as cobalamin). Vitamin K – Vitamin used in enzyme post-translational modification to incorporate carboxyl groups that serve as extracellular calcium binding sites. voltage – See potential difference. The term is also used for the units of potential difference. Vmax – A kinetic constant that is the rate of an enzymatic reaction at saturating substrate concentration.

Vmax/Km – The first order rate constant for an enzymatic reaction as substrate concentration approaches zero.

W warfarin – Synthetic analog of coumarin, an inhibitor of Vitamin K-dependent carboxylation. The drug is used to diminish blood clotting, popularly known as a “blood thinner”. weak acid – An acid that only partially dissociates in water. Examples: acetic acid, oleic acid. weak base – A base that only partially dissociates in water. Examples: ammonia, diethylamine. wobble hypothesis – A proposal explaining how a specific transfer RNA molecule can use different codons in a messenger RNA template, but carry the same amino acid. The third base of the transfer RNA anticodon does not have strict base pairing rules. work – An energy of motion (displacement), the product of force and distance.

X X-ray crystallography – A method for determining the structure of a crystal (including proteins and nucleic acids) by subjecting them to x-ray radiation, measuring the scattering pattern that results, and mathematically constructing a three-dimensional image from that data. xenobiotic – Any substance (often, a drug) introduced into an organism that is foreign (xeno) to that organism.

Y ylid – A resonance-stabilized carbanion involved in nucleophilic addition leading to subsequent decarboxylation, as in pyruvate decarboxylase and the pyruvate dehydrogenase complex.

Z zwitterions – Molecule having no overall charge containing balanced negatively charged and positively charged parts (German word zwitter, meaning a hybrid of two forms).

Foundations

1

Biochemistry is the study of the chemical nature of biology. Biochemists use chemical ideas and tools to elucidate living systems. We begin with a review of some chemical concepts: reactions, kinetics, equilibrium, steady-state, and energy. Next, we introduce acid–base and redox reactions. Some foundational ideas of biology complete the chapter: cell theory, evolution, and species hierarchies.

1.1 ORIGINS OF BIOCHEMISTRY Compared to its component sciences, biochemistry itself is a young discipline. Hoppe-Seyler coined the word Biochimie in 1877. He also edited the first biochemistry journal, Biological Chemistry, still in existence today. In this period – the later part of the 19th century – both the notions of spontaneous generation and vitalism were dispelled, clearing the way for a discipline that required new thinking. According to the hypothesis of spontaneous generation, living systems arose from nothingness, as bacteria seem to do in a nutrient-rich broth. In the 1860s, however, Louis Pasteur demonstrated that bacteria exist in the air; no bacteria appear in the broth if the container is isolated from the atmosphere. This discovery led to the cell theory, which holds that cells are the fundamental unit of living systems and arise from other cells. Despite this advance, Pasteur himself was a vitalist, believing that living systems do not obey the same chemical principles as inert objects. Two challenges to vitalism bracketed the work of Pasteur. In 1828, Wohler discovered that urea could be synthesized in a laboratory from ammonia cyanate. The strictly in vitro synthesis of an organic compound did not need the “aid of a kidney” as Wohler put it (see Box 1.1). In 1897, the German chemists (and brothers) Eduard and Hans Buchner showed that fermentation occurs in extracts from ruptured cells, thus dispelling the notion that cellular organization is required for processes that occur in living systems. In the 20th century, biochemistry was dominated first by organic chemistry, as metabolic pathways were discovered, then by enzymology, then bioenergetics, and later by molecular biologists as the study of DNA intensified. As biochemistry plays an increasingly large role in physical and chemical sciences today, these disciplines overlap considerably. What remains distinctive about biochemistry is the chemical perspective of biological phenomena. Biochemical principles are presented in the following chapters. In the present one, we consider some fundamental concepts of chemistry and biology.

1.2 SOME CHEMICAL IDEAS To determine if you might need a review or can instead skip to the next section, take the following self-test: ◾◾ Without specifying a value, what is the meaning of Avogadro’s number? ◾◾ Distinguish between atoms, electrons, molecules, and moles. ◾◾ When is it appropriate to use mole units as opposed to grams? 1

2 1.2 Some Chemical Ideas

Box 1.1 Word Origins: Organic Among its rich meanings, the word organic also implies a sense of the whole, as in organism, which also implies animate, living, or vital. The root word stems from the Greek ergon, meaning work in the sense that an organism is a collection of working entities. Vitalists identified substances believed to be produced only by a living organism. After vitalism was discounted, organic was redefined rather than cast aside. Today, organic chemistry is defined as a branch of chemistry that focuses on compounds of carbon. Strictly speaking, inorganic chemistry refers to molecules containing other elements. In recent times, another meaning for organic has emerged that is closer to its historical roots. In this context, organic is a label for farming methods that do not use synthesized chemicals (e.g., fertilizers and pesticides for plants, antibiotics and hormones for animals). Thus, growing plants and raising animals in this way is said to produce organic food. Whether this is a definite health benefit is debatable. For example, the absence of pesticides can lead to greater bacterial content in food. Moreover, there is no settled agreement on exactly what organic farming is, so products vary. Despite the various uses of the word, we are concerned with only the definition of organic chemistry as the chemistry of carbon compounds. ◾◾ Why is the equilibrium constant for a reaction expressed as the equilibrium concentrations of the products multiplied together, divided by the equilibrium concentrations of the substrates multiplied together? ◾◾ How does equilibrium relate to kinetics? The ideas of the mole, Avogadro’s number, atoms, and molecules are presented in Appendix A.1. Here, we consider here the notions of kinetics and thermodynamics and other chemical principles with the assumption that those ideas are well in hand. 1.2.1 REACTIONS AND THEIR KINETIC DESCRIPTION Suppose substances A and B react to form substances C and D. This is a generic reaction, which can be written in the form: (1.1)

A + B C + D

A and B are called substrates; C and D are products. Each represents a chemical species and can also be called a compound or a metabolite. To visualize what is happening, let us relax our molecular thinking and describe the molecules pictorially as Figure 1.1. In this representation, the reaction involves removing a piece of molecule A and affixing it to B, thus creating C and D. This is a mechanistic view. To more fully characterize the reaction, we consider each direction separately. Fixing a direction allows us to define the rate of a reaction, a characterization known as kinetics. Consider first the forward direction, which proceeds from left to right. This reaction is written: (1.2)

FIGURE 1.1 A generic reaction.

A + B ® C + D

Chapter 1 – Foundations 3

FIGURE 1.2 Collision theory of reaction rates. Suppose there are 3 A molecules and 4 B molecules, as shown in Figure 1.2. Each A can combine with any of 4 Bs. This procedure follows Equation (1.2), which excludes the reaction of A with itself or B with itself. There are 12 possible collisions (3 × 4). Another way of expressing the situation is that the reaction is proportional to 3 × 4. This analysis is formally known as collision theory: the rate of a reaction is proportional to the number of collisions. Since the number of molecules of a substrate is represented by its concentration in solution, the rate of our reaction is proportional to [A]×[B]. The rate in the forward direction we write as ratef. It can be expressed as an equality rather than a proportionality by introducing a constant, known as the rate constant (see Box 1.2). The equation that results is: (1.3)

ratef = k f [A][B]

where k f is the rate constant for the reaction in the forward direction. The overall rate is measured as a change in concentration per unit time (typically in seconds). For the reverse reaction, C + D → A + B, following a similar line of reasoning, we arrive at a similar expression: (1.4)

rater = k r[C][D]

The terms in this expression are rater, representing the rate in the reverse direction of our original equilibrium of Equation (1.1), and kr, the rate constant in this direction. The expressions for reaction rates shown in Equations (1.3) and (1.4) can be generalized to any reaction. While independent of changes in concentration, the rate constant can vary with environmental conditions, such as temperature or ionic strength. A rate, by definition, has only one direction. Yet chemical reactions are commonly written with double arrows between substrates and products as in Equation (1.1). This notation indicates that both forward and reverse reactions can occur and is commonly used when a reaction has reached a position of equilibrium. 1.2.1.1 EQUILIBRIUM Perhaps the most fundamental idea in chemistry is that of equilibrium. A state of equilibrium exists when the forward and reverse rates of a reaction are equal. Once reactions reach equilibrium, no further observable change occurs in substrate or product concentrations

4 1.2 Some Chemical Ideas

Box 1.2 Rate Constants A rate constant is neither a rate nor a concentration. Rather, it is merely a constant of proportionality between the rate of a reaction and the concentrations. The constancy refers to its independence of concentration. Rate constants are symbolized by a lower case k, and have units that vary with the reaction itself. Since the rate is in units of concentration per time, say mol/l/sec, and concentrations are in units of mol/l, then the rate constants must have units that balance. Thus, in the example used in the text, the rate depends on two compounds, so that the rate constant is second-order, and has units of M−1sec−1 included in the table below: Reaction Aconst → products A→ products A + B → products A + B + C → products

Order

Rate Constant Units

0th or zero-order 1st 2nd 3rd

M sec−1 sec−1 M−1sec−1 M−2sec−1

The first entry in the table represents a situation in which the reaction is entirely independent of substrate concentration. First-order reactions are common when the reactant is in very high concentration and thus does not appreciably change with time over the reaction course. It is more common in enzymatic reactions, which we consider in a later chapter. Notice the pattern of the rate constant units, which shows how they are sequentially divided by the concentration as the order increases. It is important to recognize this variation to firmly identify the rate constant term that represents a proportionality that is independent of concentrations.

unless there is a change in external conditions. Reactions that have not yet achieved equilibrium have a driving force toward the equilibrium situation, just as a rolling ball eventually comes to rest as the forces acting on it balance. To become familiar with the state of equilibrium, we examine the origins of the equilibrium expression and the equilibrium constant. As a definition of the equilibrium condition, the rate of the forward reaction equals the rate of the reverse reaction, that is: (1.5)

ratef = rater

Since the forward and reverse rates were expressed by Equations 1.3 and 1.4, we can make these substitutions to arrive at: (1.6)

k f [A][B] = k r[C][D]

Sometimes, to emphasize the fact that we are describing an equilibrium situation, subscripts are added to the concentration terms (e.g., they appear as [A]eq, [B]eq, etc.). We will assume the concentrations expressed are those at equilibrium under our conditions. Rearranging: (1.7)

k f /k r = [C][D]/[A][B] = K eq

where Keq is the equilibrium constant. This equation defines this constant in terms of equilibrium concentrations and shows its relationship to the rate constants. It is apparent from our derivation that the reaction components at equilibrium represent a balanced state of the collisions in each direction.

Chapter 1 – Foundations 5

Another statement of this type of balance is known as the Le Chatelier principle. For a reaction at equilibrium, this principle states that concentrations will shift to counter changes in the concentration of any component. While this principle is simply a restatement of the relationship between concentrations and the equilibrium constant (Equation 1.7), it has an intuitive value. Suppose in our reaction that [A] is increased; we might imagine an experimenter adding in more A. This increase will push the reaction from left to right until the original Keq value is obtained. The idea of an increase in the concentration on one side pushing the reaction to the other side is apparent from the mathematical requirements for rates and equilibrium as developed here. However, the Le Chatelier principle can intuitively predict how the reaction components change to re-establish an equilibrium. Equilibrium can also exist in the case of multiple connected reactions, such as: (1.8)

A B C D E

Under biological conditions, though, multiply connected reactions require a different model: the steady-state. 1.2.2 THE STEADY-STATE One problem with applying the equilibrium model to living cells is that biological systems never reach equilibrium. Thus, a more elaborate system must be used to model metabolism: the steady-state. A sequence of connected reactions can be said to achieve a steady-state when the concentrations of all reaction intermediates are constant. Nonetheless, the first substrate may be depleted with time, and the final product accumulates. To understand this concept, we can compare it to an equilibrium, which requires a minimum of two components, as in this example: (1.9)

S P

and we can characterize it with the equilibrium constant: (1.10)

K eq = [P]eq /[S]eq

To describe a steady-state, we need a minimum of 3 components, for example, a substrate (S), an intermediate (I), and a product (P): S ® I ® P

(1.11) Equation (1.11) represents two reactions: (1.12)

S ® I

(1.13)

I ® P

just as an equilibrium has two reactions, a forward and reverse reaction. The similarity also extends to the rates of the reactions in both models. In our steady-state example, the rates of these reactions are also equal. The distinction is that the steady-state produces a net flow. Over time, [S] decreases, [I] is constant, and [P] increases. In biological systems, there are usually multiple intermediate species between S and P. In Equation (1.14), for example: (1.14)

S ® I ® J ® K ® L ® P

all of the intermediate rates (e.g., S I, I J, etc.) are equal. Not only that, the overall rate, S P is the same too. The result is that the intermediate concentrations (I, J, K, and L above) do not

6 1.3 Acid–Base Reactions

FIGURE 1.3 The steady-state window. People are moving through a building at a constant rate. As long as the entry and exit rates are equal, the number of people visible in the large window will be constant (eight). At any instant in time, the eight people in this intermediate state will be different. vary with time: they are the ones forming the steady-state. The intermediates are constant because each one is formed at the same rate at which it is removed. The concentrations of S and P need not be constant, however. To achieve a constant rate of S → I – a necessity for the steady-state – there are two possibilities. First, another reaction may supply S at the same rate as it is converted to I. Alternatively, [S] may be saturating for the first reaction, meaning that its concentration is so high that its depletion is negligible. The product P cannot revert to L, so its accumulation does not affect the rate of L → P. Suppose the metabolic pathway of Equation (1.14) achieves a steady-state. We can form an analogy by considering a line of people forced to move single file through a gate. Figure 1.3 shows people flowing through a building without backup. The number of people entering represents the [S]; the number of those leaving represents the [P]. At any time we glance at the window in this building, we always see eight people. Of course, if we look at another time, the people will be different, but their number is the same. This situation is the essence of the steady-state. While the steady-state is distinct from an equilibrium, equating the two is a common scientific error. An equilibrium is often used for situations where there is an element of balance, not recognizing that this is inappropriate when a series of chemical reactions produce a net flow. In that situation, only the steady-state model is appropriate. Finally, it is important to stress that both equilibrium and steady-state are models. Thus, while they are usually appropriate for the situations we will encounter, they are always approximations. In some instances, they are wildly inaccurate ones. For example, before an enzymatic reaction or series of reactions can form constant intermediate concentrations, neither model applies. This condition is the pre-steady-state, which requires a different model entirely.

1.3 ACID–BASE REACTIONS The idea of acid–base chemistry is at once familiar and poorly grasped. As it permeates our study of biochemistry, it is worth detailed study. We will introduce reactions involving acids and bases in the next chapter (Water) as we are most interested in their behavior in water, the cell’s solvent. Here we explore the origins of acids and bases and why a seemingly simple concept can be elusive. Acids (meaning sour) and bases (meaning bitter) are each represented among the five taste receptors on the tongue. Citrus fruits are everyday examples of acids; what is literally called citric acid is a specific molecule, an intermediate of the Krebs cycle (Chapter 10). A classical base is formed by mixing ash from burned wood with water (“potash” or potassium hydroxide). The problem of the scientific classification of acids and bases is not a simple one.

Chapter 1 – Foundations 7

In fact, there are three separate views of acid–base chemistry. The first is the Arrhenius definition, which defines an acid as a substance that increases the proton concentration of a water solution. A base is a substance that decreases the proton concentration of a water solution. Apart from the restriction that this requires water as the solvent, it is also not easy to distinguish features within the molecule that contribute to acid or base properties. Still, it allows us to classify molecules with no protons, such as carbon dioxide, as an acid. The second view is the most prominent in this book: the Bronsted definition. A Bronsted acid is a proton donor, and a Bronsted base a proton acceptor. Often, this definition is stated without the Bronsted adjective. A proton must be a part of the acid, in this view, with the ability to release the proton into solution. A third acid–base description is the Lewis definition. This view is the most general but more subtle. Here, the focus is on electron pairs rather than protons. An acid is defined as an electron pair acceptor. A base is defined as an electron pair donor, arising from lone pair (that is, nonbonding) electrons. This is the broadest definition; for example, we can consider metal-ligand chelates as acid–base pairs. While this brief introduction to acids and bases is long on definitions and short on details and examples, we will expand this notion throughout our study of biochemistry. We will encounter numerous acid–base reactions. While most of our focus will be on the Bronsted definition, the expansion to the others will pay dividends in our ability to understand all types of acid–base reactions.

1.4 REDOX Apart from acid–base chemistry, the other pillar of biochemistry involves redox reactions. Redox is a contraction of reduction-oxidation. There are many parallels between acid–base and redox reactions. There are multiple views of redox, and once again, we need to consider different viewpoints to become familiar with the notion. The first definition of redox is an oxidation model that considers that a molecule becomes more oxidized as it literally incorporates oxygen atoms. The other partner of the reaction then becomes more reduced. This model is somewhat limiting, as it requires that oxygen be a part of the molecule. Still, it remains widely used in the field of pyrotechnics (fireworks). More practically, for our purposes, it allows us to easily rank oxygen-containing organic molecules as increasingly oxidized as they contain more bonds to oxygen, as in the series illustrated in Table 1.1. However, it provides no insight into the process and ignores the fact that redox reactions – like acid–base reactions – must occur in pairs. One partner is oxidized, the other is reduced. The second definition of redox is useful when ions can exchange electrons with other ions. This is the basis of redox chemistry first discovered by Alessandro Volta in 1800, who

TABLE 1.1 Increasing Incorporation of Oxygen Progressively Increases Oxidation State of Molecules Molecule

Oxidation state of C

Structure

Alkane

−3 R

Alcohol

CH3

R

CH2OH

R

C H

Aldehyde

Acid CO2

O

R O

COOH C

O

−1 +1

+3 +4

8 1.5 Energy

discovered the battery (and is honored in the unit volts). The Volta battery is a redox reaction that exchanges electrons in an overall reaction that is represented by the oxidation half: (1.15)

Zn ® Zn 2 + + 2e-

and the reduction half: (1.16)

Cu 2 + + 2e- ® Cu

By definition, oxidation is a loss of electrons, and a reduction is a gain of electrons. The two are coupled; combining both halves produces the overall reaction: (1.17)

Zn + Cu 2 + ® Zn 2 + + Cu

A third definition is necessary because the organic molecules of biochemistry are not generally redox-active ions and are not always readily discerned by their oxygen atom content. Thus, a more general redox definition is needed: an artificial assignment of an oxidation number to each atom in a molecule. We will consider this model in more detail in later chapters, but the essence of the assignment is to consider which atom across a bond attracts electrons more strongly (i.e., is more electronegative) and assign a number as if that atom was a pure ion. These numbers are the same in actual ions: in Equation 1.15, for example, the Zn species has an oxidation number of zero, and the Zn2+ has an oxidation number of 2. The assigned oxidation numbers of the carbon atom explicitly shown in the middle column are given in the last column of Table 1.1. The method for calculation will be presented in Chapter 8.

1.5 ENERGY Energy is a notion that is at once simple and complex. It is simple because it is part of everyday vocabulary: a child knows about “having a lot of energy,” the relative difficulty of walking uphill, and the existence of friction. It is also complicated. Energy exists in multiple forms: electrical, gravitational, pressure-volume work, and heat flow, each having specific conditions and equations. An important observation from the early 19th century was that all forms of energy are interconvertible. Further advances in that century led to a formal science of energy changes known as thermodynamics, which can elucidate the energy of a waterfall, a galloping horse, a chemical reaction, or that contained within a single molecule. There are two faces of thermodynamics: the classical and the statistical. The classical approach uses a few postulates and definitions but makes no assumptions about the exact nature of the systems under investigation – even the existence of molecules is unnecessary. The statistical approach considers the collective behavior of large numbers of molecules. Both approaches lead to accurate descriptions of energy changes. To begin our study of thermodynamics, we need to consider three of its fundamental ideas: internal energy, enthalpy, and entropy. Internal energy is the energy of a system, the sum of the work and heat transferred to that system. Work is an energy of motion, such as the product of force and distance. Heat is an energy transfer due to a difference in temperature between a system and its surroundings. Enthalpy (derived from the Greek enthalpos, meaning “putting heat in”) is the heat absorbed or released by a system at constant pressure. As this situation is common in laboratory experiments – and in living cells – tables of enthalpy changes for reactions are widely used in chemistry and biochemistry. Entropy is best understood using the statistical approach to thermodynamics. It is related to the number of ways that energy can be distributed as a result of a process (usually a reaction). For example, if we suddenly apply brakes in a speeding car, the energy of motion is

Chapter 1 – Foundations 9

FIGURE 1.4 The global CO2 cycle. Radiation from the Sun is used to energize electrons in the chloroplasts of plants, forming the high-energy molecule NADPH. These electrons drive the synthesis of sugar from atmospheric CO2 in plants; this overall process is photosynthesis. Subsequently, the plants are eaten by animals, and the sugars (and other molecules) break down to release CO2 in to the atmosphere, completing the cycle. In the breakdown process, energy is trapped as electrons in NADH and used to produce ATP for cell processes. redistributed into particles of tire rubber on the street, as well as frictional heat. Entropy increases with an increase in energy dispersion. When we discuss energy in a biochemical context, we are invariably referring to a combination of enthalpy and entropy changes, called free energy. The free energy change for a reaction determines whether it can proceed in the direction written. A more expansive treatment of thermodynamics, free energy, and the relationship between free energy and equilibrium are discussed elsewhere in this book. Here, we will just assume that energy is equivalent to free energy. We commonly speak of both molecules and portions of molecules as having high energy. Two high energy molecules of particular importance in biochemistry are nicotinamide adenine dinucleotide (NADH) and adenosine triphosphate (ATP). Both of these molecules are mobile cofactors that allow communication between hundreds of different reactions within the cell. NADH transfers electrons; we consider it a donor of high energy electrons. ATP transfers a terminal phosphoryl group; we consider this molecule to be a high energy phosphate compound. The connection between electron flow and ATP formation is a profound one in biochemistry. In the global energy cycle (Figure 1.4), radiation from the sun induces the formation of high energy electrons by driving the formation of nicotinamide adenine dinucleotide phosphate (NADPH), a close analog of NADH. NADPH then donates electrons to convert atmospheric CO2 to sugars and other molecules. Subsequently, animals consume those sugars, moving their electrons to NADH, and using this to form ATP. In the process, sugars and other molecules form CO2, which is once again utilized by plants.

1.6 CELL THEORY The cell – the smallest unit of life – is a key organizing principle in biology. Single-cell organisms, such as bacteria, yeasts, and protozoans (e.g., the paramecium), comprise the largest number of species. Our primary focus, however, is on multicellular organisms, primarily humans.

10 1.6 Cell Theory

The features of a representative mammalian cell are illustrated in Figure 1.5, which shows internal organelles and their arrangement within a cell. There are many variations on this theme, which we can illustrate by a few examples. At one extreme, the mammalian red blood cell or erythrocyte in humans contains no intracellular inclusions (organelles), retaining only the plasma membrane and cytosol. Another extreme is the fat cell or adipocyte, which has many typical organelles, but also an exaggerated lipid droplet that comprises virtually the entire cell volume, appearing as a featureless blob with a thin film of cytosol between the fat droplet and the plasma membrane. While not shown in the representative cell of Figure 1.5, lipid droplets are found in many cells as multiple small spherical organelles rather than the single large one of the adipocyte. As another variation, melanosomes are modified lysosomes that contain the dark brown colored compound melanin, present in the epidermal cells of the skin’s outer layer. Melanin absorbs ultraviolet light, protecting the underlying tissue from radiation damage. Finally, Figure 1.6 shows a section of a skeletal muscle cell. The regular appearance of stripes (striations) represent protein components responsible

FIGURE 1.5 The mammalian cell. A representative drawing of the cell shows the compartments that are created by membranes. The cell itself is separated from its exterior by a plasma membrane; several interior membranes, such as the mitochondria, the lysosome, and the endoplasmic reticulum, define separate reaction spaces within the cell.

FIGURE 1.6 A skeletal muscle cell. A transverse section of a stained skeletal muscle cell is illustrated, demonstrating the large number of protein fibers filling the cytosol. The various organelles fit between groups of the protein fibers. Source: https://commons.wikimedia.org/w/index .php?curid=29092851

Chapter 1 – Foundations 11

FIGURE 1.7 The cell as a concept. The cell is represented as separate chemical reaction spaces, separated by semipermeable membranes. Specific exchanges across the membranes are indicated by the arrows drawn across the membranes in both directions. for contraction (actin and myosin fibers). Some organelles are visible such as mitochondria, stained as dark purple spheres between fiber groups. Despite wide variation in the arrangements of cells, there is a functional unity to their behavior in terms of biochemistry. As represented in Figure 1.7, we can conceptually draw a few key compartments that are responsible for most metabolic activities in cells. An outer plasma membrane encloses the cell, serving as its boundary with the outside. This membrane, like all cell membranes, is semi-permeable. Some molecules readily cross the membrane, such as O2, H2O, and CO2. Others can traverse the membrane only if there is a specific carrier protein they can pass through. From a chemical viewpoint, the membranes create separate water spaces to isolate chemical reactions. Only those molecules that can communicate across these spaces – those that can diffuse or those with a specific transporter – can participate in the reactions. The major water space within the cell is called the cytosol. Other membrane-delimited organelles that define separate water spaces for reactions are the endoplasmic reticulum, the mitochondria, and the nucleus. In addition to defining reactive spaces, membranes are sites of lipid biosynthesis.

1.7 SPECIES HIERARCHY AND EVOLUTION Evolution is a fundamental principle of biology. It is also commonly misunderstood, perhaps due to the popularization of the phrase “survival of the fittest”. It is ironic that this phrase has survived in the popular lexicon but did not find itself in the landmark work on evolution, Charles Darwin’s On the Origin of the Species. Darwin formulated the theory of evolution based on the extremes of plant and animal species found in the isolated Galapagos Islands, 1000 km off the coast of Ecuador. The idea was that species arose from other species, and those that could adapt to their environment survived and reproduced. Eventually, adaptive characteristics emerged. It is now commonplace to apply evolutionary principles to biochemistry, mapping the formation of numerous enzymes and DNA sequences from early origins to divergent present forms. To catalog the complexity of the immense number of known species, currently believed to number in the tens of millions, scientists have long turned to another important biological organizing principle: the classification hierarchy. At the top of the currently accepted hierarchy are three domains: Archaea, Bacteria, and Eukarya (see Box 1.3: Archaea). There are several lower levels of organization: Kingdom, Phylum, Class, Order, Family, Genus, Species. Our focus is on mammalian, mostly human, biochemistry; although plant, bacterial, and, occasionally, yeast examples will be considered. Most discoveries in biochemistry are based on only a very small sampling of the biological universe, largely due to practical considerations. Still, there are many indications of similarity of pathways and mechanisms between

12 1.8 Biological Systems

Box 1.3 Archaea It was the archaea that forced a revision of the previous standard taxonomy of organisms. Archaea – like bacteria – are single-celled and have no nucleus but constitute a separate domain from bacteria (now also called true bacteria or eubacteria). They do have other organelles, like mitochondria. The categories of Archaea, Bacteria, and Eukaryota are domains, classifications above the kingdom. The more intriguing aspect of the archaea is that it includes the extremophiles, organisms that can survive what we would consider harsh conditions. For example, extreme temperatures, such as hot springs, harbor archaea species as do ocean depths (extreme pressure) and areas of extremes of acid or base. There are also the radiophiles, organisms that survive intense radiation (both ultraviolet and ionizing radiation). Adaptations include modifications to lipids for the membranes of the organisms, unusual repair enzymes for their DNA, and even specialized “antifreeze proteins” to survive extreme cold. As a practical and perhaps most famous example, one enzyme isolated from a species of the hot springs Archaea, a DNA polymerase, is the basis of method of amplification of DNA, which uses cycles of heating and cooling to greatly amplify the amount of DNA present and has moved beyond the research laboratory to become a standard forensic tool to detect extremely low DNA concentrations. different organisms. Some differences between organisms will be considered to get a sense of how biological variation is expressed.

1.8 BIOLOGICAL SYSTEMS There is another hierarchy that identifies the viewpoint of the investigator of biological systems. Figure 1.8 shows a ranking with organism at the top level and subatomic particles at the bottom. There are even higher levels than the organism, such as a population, which have medical and scientific importance (as in the transmission of infection between organisms). However, levels beyond the organism are usually of interest to other fields, such as the social sciences. The rankings in Figure 1.8 can also be used to exemplify two extremes in the analysis of biochemistry: a view close to the top, taking in as wide a swath as possible, is called holistic. Those who favor the holistic view argue that it leads to physiologically relevant observations. And a view close to the bottom, examining specific interactions at a molecular or submolecular level, is called reductionist. Those who favor the reductionist view argue that it alone allows firm conclusions to be drawn because the number of variables studied is much smaller and better defined than in the holistic approach. Both are essential, and we will move between them in the text. We begin with a reductionist approach, examining the chemical properties of water, the molecule most essential for life.

Chapter 1 – Foundations 13

FIGURE 1.8 Hierarchies of biological study. Different levels of investigation are possible in the experimental study of biology. Physiologists usually study higher levels, such as organisms, organ systems, and organs. Physicists typically study atoms and subatomic particles. Biochemists usually examine the intermediate levels. If the study is closer to the top of the hierarchy, it is considered physiologically relevant, and the approach is holistic. However, there is greater uncertainty about the data. If the study is closer to the bottom, it is considered more exact, and the approach is reductionist. However, the relevance to biology is less certain. Both approaches, while in conflict, are essential for a full understanding of biology.

KEY TERMS adipocyte Arrhenius definition Bronsted definition cell theory collision theory cytosol electronegative endoplasmic reticulum energy enthalpy entropy epidermal equilibrium

extremophiles free energy heat high energy electrons high energy molecules high energy phosphate holistic internal energy kinetics Le Chatelier principle Lewis definition melanosomes mitochondria

14 Bibliography

nucleus oxidation number rate constant reductionist saturation semipermeable

spontaneous generation steady-state thermodynamics vitalism vitalist work

BIBLIOGRAPHY M.G. Ord, L.A. Stocken, Eds. Foundations of Modern Biochemistry, Vol. 1, Early Adventures In Biochemistry. JAI Press, Greenwich, CT, 1995. P.S. Cohen, S.M. Cohen. Part of a multi-volume history of biochemistry; the information in the present chapter is found mostly in the first two chapters. Wohler's Synthesis of Urea: How do the Textbooks Report It?, J. Chem. Educ., 73 (1996) 883–886. H.J. Morowitz. Discussion of the details of the Wohler synthesis and the slow rejection of vitalism despite the finding. Entropy for Biologists. An Introduction to Thermodynamics. Academic Press, New York, 1970. Kotz, J.C., P.M. Treichel, J.R. Townsend, and D.A. Treichel. A gentle introduction to thermodynamics with biological examples. Acids and Bases: The Arrhenius Definition. In Chemistry and Chemical Reactivity, Instructor's Edition, Vol. 116. 9th ed. Cengage Learning, Stanford, CT. 2015. I. Yajima, L. Larue, The Location of Heart Melanocytes Is Specified and the Level of Pigmentation in the Heart May Correlate with Coat Color, Pigment Cell Melanoma Res. 21 (2008) 471–476. G. Raposo, M.S. Marks, Melanosomes: Dark Organelles Enlighten Endosomal Membrane Transport, Nat. Rev. Mol. Cell Biol., 8 (2007) 786. B. Lewin, L. Cassimeris, V.R. Lingappa, G. Plopper, eds. Melanosomes are considered a lysosome related particle. Cell. Jones and Bartlett Publishers, Boston, 2007. L. Marulis, K.V. Schwartz, A cell biology textbook providing broad introductions to life at the cellular level. Five Kingdoms. An Illustrated Guide to the Phyla of Life on Earth. 2nd ed. W.H. Freeman and Co., New York, 1988. J.A. Coker, In addition to a catalog displaying drawings and photographs of examples of the major life forms, the work contains an introduction to the science of taxonomy, the hierarchies of life. Recent Advances in Understanding Extremophiles, F1000Res, 8 (2019). F.C. Fang, A. Casadevall, Reductionistic and Holistic Science, Infect. Immun., 79 (2011) 1401–1404. Smith, M.B. Organic Chemistry: An Acid-Base Approach. CRC Press, Boca Raton. 2011.

Water

2

We are mostly water. Our daily weight fluctuations are mainly due to the gain or loss of water from our bodies. At a philosophical level, most feel an almost mystical connection to water. Thus, Ishmael’s claim in Moby Dick that we all yearn for the sea stirs a sentiment in readers well over 150 years after it was written. In most cells, the relative number of water molecules is even more impressive than its preponderance by weight. The number-dominance of water molecules is a consequence of its low molecular mass (18 daltons). In fact, for every single protein molecule, there are 75 lipid molecules, 100 Na+ ions, and 20,000 water molecules. Although we generally refer to the molecule itself as water, each physical phase has its own name: water for the liquid, steam for the gas, and ice for the solid. While abundant, water is curiously distinct from other liquids. One unique property of water is its ability to dissolve most other substances. While it falls short of being a “universal solvent”, the number and type of substances that dissolve in water are important biological considerations. Water also has unusually strong heat retention compared to other liquids. Finally, water has unusual phase transitions, such as a very high boiling point, and unusual behavior at low temperatures. For example, the solid form of water is less dense than the liquid form. All of these properties can be traced to the molecular structure of the water molecule.

2.1 STRUCTURE OF WATER To begin our examination of water, we consider the isolated molecule as it exists in water vapor. The phases of water are illustrated in Figure 2.1, which also indicates two separate groupings. The gas and liquid are called fluid phases. Molecules in these phases are mobile and distribute evenly throughout space. Liquid and solid phases are called condensed phases. Molecules in these phases are considered incompressible: molecules cannot be brought appreciably closer together by increasing pressure, for example. The overlapping of characteristics demonstrates that phase properties depend upon context. A study of each phase, and the transitions between them, provides insight into both the behavior of water and its interaction with other molecules. 2.1.1 GAS PHASE WATER The essential feature of the gas phase is that there is virtually no interaction with other molecules. Physiologically, gas phase water is important for both animals and plants. For example, the transition of surface water to water vapor is a cooling mechanism called evaporative heat loss. The properties of biochemical consequence arise from the arrangement of electrons and nuclei within this molecule. It is evident from the formula H2O that two atoms of hydrogen are attached to a single atom of oxygen, and that the molecule is electrically neutral. When the atoms are drawn on paper as they are known to be arranged geometrically into the twodimensional structure of Figure 2.2. The H–O–H bond angle is 104.5°. The underlying reason for this structure becomes apparent when we consider the three-dimensional representation of Figure 2.3. The oxygen atom contains eight electrons: two inner electrons (which are not 15

16 2.1 Structure of Water Phases Gas Fluid Liquid Condensed Solid

FIGURE 2.1 Liquid water is a condensed fluid. The three phases of matter can be characterized as fluid or condensed (incompressible). The liquid state of water (as with other substances) shares the properties of being both fluid and condensed. O H

104.5°

H

FIGURE 2.2 Two-dimensional structure of water. The three atoms of water can be drawn in a plane; the two bonded hydrogens make an obtuse angle, the value of which can only be explained by a consideration of its three-dimensional structure.

FIGURE 2.3 Three-dimensional structure of gas phase water. Four orbitals of the water molecule are shown; water has a tetrahedral structure. (a) Space-filling diagram shows bonded H orbitals coming out of the page, and nonbonded electron pairs behind the plane of the page. (b) Tetrahedral orientation depicts the oxygen in the center of the tetrahedron and the nonbonded orbitals and bonded hydrogen atoms at the vertices. involved in bonding) and six valence electrons. The number of valence electrons corresponds to the Period number or column heading in the Periodic Table (Figure 2.4). In the water molecule, 6 valence electrons of oxygen mix with two from the H atoms, recombining into four molecular orbitals, arranged as a tetrahedron, as in Figure 2.3. The tetrahedral structure is the result of the mutual repulsion of the electrons of these orbitals. Because they are all attached to a central oxygen, and thus in forced proximity, the orbitals assume a geometrical arrangement where they can be as far apart from one another as possible. The two lone-pair (unbounded) orbitals have a somewhat greater negative charge and repel each other more than the orbitals with bonded electrons. As a result, the H–O–H angle is somewhat less than the 109.5º of a perfect tetrahedron, as in methane (CH4). 2.1.2 PARTIAL CHARGES AND ELECTRONEGATIVITY A covalent bond is, by definition, a sharing of electrons between the nuclei of two atoms, but the sharing is usually unequal. In the case of the single bond between O and H in water,

Chapter 2 – Water 17

FIGURE 2.4 An abbreviated periodic table. The periods I through VIII are shown without the traditional intervening transition elements. Those elements towards the right and the top have the greatest electronegativity. Only the elements N, O, and F (shaded) participate in hydrogen bonding; in organic molecules, only N and O form significant hydrogen bonds. Elements of biological importance are highlighted in blue. the electrons are located closer to the oxygen atom. This uneven sharing results in partial charges that can be assigned to each atom involved in the bond. The O atom is partially negative and the H atom is partially positive. In general, atoms differ in their inherent ability to attract the electrons that are involved in bonding. The ability of an atomic nucleus to attract electrons in the bond to itself is called electronegativity. Values of electronegativity can be directly assigned to each atom, based upon measurements of bond energies involving different pairs of atoms. A normalized scale runs from zero (no electronegativity) to four (greatest electronegativity). A clear trend in electronegativity values is present in the arrangement of the elements in the Periodic Table. Those top right elements are the most electronegative; those in the bottom left are the least electronegative. These periodic trends indicate the different powers atoms have in attracting the bonding electrons. Elements on the right side are more stable when they attract electrons, completing their outer shell. Elements towards the top of the table have fewer electrons to shield the valence electrons from the charge of the nucleus. The electronegativity values of several elements are listed in Table 2.1. We are now in a position to examine the electronegativity values for the O–H bond in water. Since hydrogen has a value of 2.1 and oxygen a value of 3.5, the electronegativity difference is 1.4. It has been estimated that this makes the bond about 39% ionic. This merely adds quantification to the previous point that the electrons in this bond are more strongly attracted to the O than to the H. Thus, while the bond is in one view covalent, it is in fact a polar bond, or a partially ionic bond. TABLE 2.1 Electronegativity The polar bond is represented by a vector. This vector is shown as a directed line segment Values of Selected Elements drawn with the origin at the H and the arrowhead at the O. The vector may be further decoElectronegativity rated with a little plus sign at the origin to denote the relatively positive (electron deficient) Element part of the distribution. F 4 After assigning vectors for both of the bonds in water in three dimensions, it is possible O 3.5 to take a vector sum (Figure 2.5). Because the molecule has a nonzero net sum, it has a net N 3 polarity. The two orbitals of oxygen that are not bonded (containing electron pairs only) do C 2.5 not contribute to the overall polarity of the molecule. Not all molecules with polar bonds S 2.5 have a net polarity; for example, CO2 has polar bonds, but the vectors directly oppose each H 2.1 other, so the molecular polarity is zero (Figure 2.6). Cl 3 Because water has a net polarity, it is a polar molecule. We can assign partial charges Na 0.9 to the atoms within the molecule. By convention, polarity is indicated by the Greek letter

18 2.1 Structure of Water

O + H

+ H Net vector sum

FIGURE 2.5 Net polarity of water. The vectors resulting from electronegativity differences are indicated with plus annotations at their positive ends. The sum of these vectors is the overall polarity of the molecule. O

+

C

+

O

Net sum = 0

FIGURE 2.6 Lack of polarity in carbon dioxide. Despite having electronegativity differences within the molecule, the sum of the vectors in carbon monoxide is zero, so that it is a nonpolar molecule. d– O

d+

d+

H

H

FIGURE 2.7 Partial charges in gas phase water. The differences in electronegativity are indicated by partial positive and negative charges within the water. Thus, the bonding is only partly covalent. d–

d+ d– d+

d+

d+

FIGURE 2.8 The hydrogen bond. As a result of the partial charge interactions, two water molecules are shown interacting through a hydrogen bond. As indicated by the dotted circle, the bond requires one hydrogen atom attracted to two oxygen nuclei at once. The dotted portion of the bond is identified as the hydrogen bond. “delta”, superscripted with a negative or positive sign to symbolize the partial negative or positive charges as in Figure 2.7. These features of the water molecule in the gas phase give rise to the unusual interactions between molecules that occur in the condensed phases and provide an explanation for the distinct properties of water. 2.1.3 CONDENSED PHASE WATER: HYDROGEN BONDING Just as people change their behaviors in social settings, molecules in the condensed phases – liquid and solid – display new properties. Molecules in such close proximity are incompressible , which means that external pressure cannot cause them to move perceptively closer together. Most of our interest will be in the liquid state. Still, some consideration of the solid phase water, as well as the transitions between states (phase changes), will enhance our understanding of water. How neighboring water molecules are held together is illustrated for two water molecules in Figure 2.8. The hydrogen atom between the two oxygen nuclei in the figure has

Chapter 2 – Water 19

Box 2.1 Covalent and Ionic: Discreet or Continuous Distinction? In your first encounters with chemistry, a bond is defined as being either ionic or covalent. The division is important in distinguishing chemical behavior. For example, an ionic solid has a much higher melting point than a solid of a covalently bound compound, because of the strong adhesion of a large network of opposite charges. Yet ionic compounds dissolve readily in water and separate completely, losing the ordered structure they had as a crystal and becoming isolated ions surrounded by water. When organic compounds melt, only intermolecular bonds are disrupted, so they have far lower melting points and retain their identity in solution. It would seem that covalent and ionic bonds are therefore entirely distinct. Yet, we have noted that the electrons in a covalent bond involving different atoms are not equally shared and give rise to partial charges. An ionic bond is one extreme where the electrons are so skewed that one atom is essentially fully negative and the other fully positive; a covalent bond involving the same atom on each side of the bond is the other extreme. Between these extremes is a continuum from ionic to degrees of ionic bonding to covalent. Still, we must be cautious in thinking that all chemical situations can be considered as a continuum: the fundamental changes of quantum physics occur in discrete steps. However, bonding characteristics are a macroscopic quality that appears as a continuous process involving partial ionic bonds. We could consider water, for example, as a compound of O2− associated with two H+ ions such that the molecule has a preponderance of negative charge on one side and a preponderance of positive charge on the other. Because of the incomplete dissociation of water in its liquid state, we would conclude that water is not actually an ionic compound but rather a partially covalent one.

one bond indicated as a solid line and the other as a dotted line. The solid line represents a covalent bond, whereas the dotted line represents a hydrogen bond, one of the most important interactions in biochemistry. The bridged hydrogen atom has its only electron shared in the covalent linkage. Therefore, the hydrogen bond is essentially an electrostatic attraction of the hydrogen nucleus to one of the lone electron pairs of the oxygen atom of the other water molecule. Box 2.1 offers a further discussion of covalent and ionic bonding. Covalent bonds are much stronger than hydrogen bonds. The average bond energy for a covalent O–H bond is 467 kJ/mol, whereas a hydrogen bond is in the order of 10 kJ/mol. Despite the relative weakness of individual hydrogen bonds, they become a dominant force that explains the peculiar properties of water in the aggregate. The three-dimensional view of Figure 2.9 applies to both water and ice. The latter is the regular crystal from which the figure is taken. The liquid state is sometimes considered to be a “flickering crystal”; the distinguishing fluid property, adjusting to the shape of any vessel, is conferred by the greater motion of the liquid water molecules and their ability to exchange positions in the liquid crystal-like structure. Another way to view the liquid state is that the structure resembles the crystal but has an occasional defect that allows water molecules to rearrange themselves. Molecules in the solid state usually assume a denser structure than they do in the liquid state. For example, the density of liquid ethanol is 790 kg/m 3, while the solid form density is 950 kg/m 3. This difference is typical: molecules are usually closest together in a crystalline solid, and an increase in temperature (needed to convert a solid to a liquid) tends to cause the molecules to move further apart, decreasing the density. Liquid water, however, is already highly ordered, and the small amount of motion at temperatures close to the freezing point causes water molecules to move closer to one another on the average than in ice. As ice melts to water, its density increases, reaching a maximum at 4°C. At higher temperatures, the increased motion does reduce the density of liquid water (Figure 2.10). Thus, water has a maximum density at 4°C, which explains why ice floats on water.

20 2.1 Structure of Water

FIGURE 2.9 Condensed phase water. Two views of condensed phase water are shown. (a) The oxygen atoms are shown to bond to four positions throughout the structure. (b) A “side view” of condensed phase water showing a hexagonal structure that results from a plane of water molecules in regular array. In ice, these structures are representative. Liquid water approximates this structure but continuously breaks and re-forms bonds so that the structure overall is in constant change, even though most of it appears as an ordered structure.

FIGURE 2.10 How the density of water varies with temperature. The density of water has a maximum at 4oC. The variation of density with temperature is shown over a range of (a) zero to 30o C; (b) zero to 10oC. The change is modest but significant. There are two opposing effects as energy (temperature) is increased: a closer approach of more active molecules and increased separation as the temperature is increased further. TABLE 2.2 Boiling Points of Common Liquids Fluid Water Benzene Carbon Tetrachloride Chloroform Ethanol

BP °C 100 80 77 61 79

2.1.4 HYDROGEN BONDING IN CONDENSED PHASE WATER We have just seen that the unusual solid to liquid transition of water is a consequence of its hydrogen-bonded structure. The unusually high boiling point of water is also a consequence of hydrogen bonding (Table 2.2). The extensive hydrogen bonding in water produces cohesiveness that can resist the escape tendency of molecules into the gas as the temperature is increased. Thus, a higher temperature (and correspondingly greater energy) is needed to boil water. Another way of thinking about water is to view it as a hydride of oxygen. Other hydrides of closely related atoms are HF (hydrogen fluoride), H2S (hydrogen sulfide), and NH3 (ammonia).

Chapter 2 – Water 21

TABLE 2.3 Boiling Points of Hydrides Hydride H2O HF NH3 H2S

FIGURE 2.11 Comparing water to similar structures. Three-dimensional structures of HF, H2O, H2S, and NH3 indicates that NH3 and H2S are very similar to water, yet do not exhibit water’s extensive hydrogen bonding due to geometry differences (NH3) and lack of sufficient electronegativity differences (H2S). HF does not occur biologically; H2S occurs as a product of bacterial respiration. Ammonia is an intermediate in mammalian metabolism and is excreted as a final waste product of nitrogen metabolism in fish. The boiling points of these substances are listed in Table 2.3. Two factors – electronegativity and molecular geometry – explain the striking differences in boiling points between water and the other polar hydrides. The electronegativity of F is greater than the electronegativity of O (see Table 2.1). HF has a considerably lower boiling point than water due to a difference in spatial arrangement. Three-dimensional views of these molecules are shown in Figure 2.11. We have already seen how water interacts with other water molecules, creating an extensive network. It is not possible for either HF or NH3 to form extended hydrogen-bonding networks; they can only form limited intermolecular hydrogen bonds. Oxygen and sulfur are in the same column of the Periodic Table, so one might expect hydrogen sulfide to have properties very similar to those of water. However, the S–H bond is insufficiently polar; S and H have similar electronegativities. As a result, hydrogen sulfide (or any –SH-containing molecules) does not form hydrogen bonds. Accordingly, H2S has an extraordinarily low boiling point compared to H2O. Indeed, in our everyday experience, both H2S and NH3 occur only as gases. Thus, water’s uniqueness stems from its combination of electronegativity differences and the geometry of its hydrogen-bonded interactions. These features lead to a high degree of ordering and extensive lattice formation that is not shared by other very similar molecules. This combination of properties is the key to understanding how water interacts with other substances. At one extreme are molecules that strongly interact with water and tend to dissolve in water. At the other extreme are molecules with virtually no interactions with water. The hydrophobic effect explains this, a concept discussed in the next section.

2.2 THE HYDROPHOBIC EFFECT The aphorism “oil and water don’t mix” can be readily understood by considering the properties of the condensed state of water. Consider the molecule decane:

CH 3 - CH 2 - CH 2 - CH 2 - CH 2 - CH 2 - CH 2 - CH 2 - CH 2 - CH 3

It is composed entirely of C—C and C—H bonds. The electronegativity of the C–C bond is zero (2.5–2.5), which is always the case when the same element occurs across a bond. The electronegativity of the C–H bond is 0.4 (2.5–2.1). Even this small net polarity is offset by the geometry of the structure, as the polarity vectors (pointing to the carbon chain) largely cancel each other (see Figure 2.12). Hence decane and compounds with similar chemical composition are nonpolar and do not form hydrogen bonds with water. Another nonpolar substance is the oil in oil-and-vinegar salad dressing. It is a common experience that the dressing settles into separate layers even after they have been vigorously mixed.

BP °C 100 20 −33 −61

22 2.2 The Hydrophobic Effect

FIGURE 2.12 Polarity of methylene residues. Using the vector sum method, the polarity of the C–H bonds is low, as the small C–H electronegativity difference is further diminished as the vectors nearly cancel each other out spatially. The finding that nonpolar molecules separate from water is called the hydrophobic effect (Box 2.2). This term should be taken literally: an effect rather than an accurate description of the underlying chemistry. Although hydrophobic means “water-hating”, alkanes, such as decane, do not hate water at all. In fact, decane has a stronger affinity for water molecules than it has for other decane molecules! The water–alkane attraction results from water inducing a dipole in the electrons of the alkane. The induced dipole attraction, however, is a minor factor. Instead, our focus should be on water itself: water prefers to interact with other water molecules rather than with lipids. Hydrophobicity is sometimes described as water squeezing out nonpolar molecules so that the water can form its own phase. For a more thorough consideration of the forces underlying the hydrophobic effect, see Box 2.3. Box 2.2 Word Origins: Hydrophobic The word hydrophobic was used as a medical term for hundreds of years as a synonym for the disease rabies. A consequence of late-stage rabies infection is an inability to swallow, so those afflicted were said to have a “fear of water”, or hydrophobia. The use of “hydrophobic” for the exclusion of water from nonpolar substances is more recent, stemming from the early part of the 20th century. Even though the scientific usage is well-established and there is no debate about what it means, its strict translation implies that chemically water and lipid molecules display repulsive forces, which is not the case. The term only describes how water and nonpolar substances form separate phases as if they had some antipathy for each other. Ironically, as an archaic medical term for rabies, it is far removed from the underlying pathology. As an embedded term for water–nonpolar interactions, it is similarly a description of the phenomenon, far removed from the underlying chemistry.

Box 2.3 A Thermodynamic Look at the Hydrophobic Effect In our discussion of the hydrophobic effect, we considered the formation of two phases, colloquially an oil and a water phase, and suggested that the principal forces were water interactions with itself rather than with the oil. While this is true, the underlying reason for it is somewhat subtle and requires that we apply the ideas of thermodynamics. In particular, the free energy of a process is determined by two factors: the enthalpy and the entropy. To apply these notions, consider the process of moving from one state to the next. Suppose our process moves individual lipid molecules (substrate) into coalesced lipid molecules (product). Studies of nonpolar molecules in water have shown that hydrogen bonding of water molecules still occurs when lipid molecules are forced into a water solution; a representative drawing of two such molecules in a water solution is shown in Figure B2.3a. The binding energy (enthalpy) of water arranged around lipid molecules is similar to the binding energy of water molecules in a solution of pure water. Thus, enthalpy is not the driving force for the hydrophobic effect. The “product” represents the change modeled in Figure B2.3b, where the two lipid molecules have coalesced, and a cage of hydrogen-bonded waters surrounds both of them. The placement of water molecules around the lipids is believed to be far more ordered than in pure water; alternatively, we can say that water in this cage has less freedom of

Chapter 2 – Water 23

FIGURE B2.3 Hydrophobic Effect: Box Figure. (a) Two nonpolar molecules, introduced into water, become individually surrounded by hydrogen-bonded water molecules. The enthalpy of these water molecules is similar to that of the bulk water (not shown, but assumed as background in the figure). However, the entropy is less; these waters are more ordered than bulk water. (b) The same molecules are now shown, but now the lipid molecules are associated with each other. The number of surrounding water molecules is much less than that in (a), which means the unfavorable ordering of water molecules has been reduced. Compared to the situation in (a), the entropy is greater, and the situation in (b) is more favorable from a free energy standpoint. movement. This increase in order observed in Figure B2.3a translates into a decrease in the system entropy, which is an unfavorable free energy change. When the lipid molecules coalesce in Figure B2.3b, there is considerably less ordering of the water molecules. This result is evident in the figure, as fewer water molecules are required to corral the more extensive lipid combination shown in Figure B2.3b than the individual ones shown in Figure B2.3a. Thus, the relatively greater entropy of water drives the association of lipid molecules together.

2.3 MOLECULES SOLUBLE IN WATER The bonding between water molecules in pure solutions of water is extensive. The ability of another molecule to dissolve in water requires displacement of water–water indent hydrogen bonds by a stronger interaction. Imagine you are trying to dissolve table salt (NaCl) in water. In the solid form, NaCl is a crystal, a regular array of interspersed Na+ and Cl−. There is a considerable difference between Na (0.9) and Cl (3) electronegativities, so electrons are not shared equally between these ions. In the crystal, Na+ bears a full charge of +1, Cl− bears a full charge of −1, and the attraction is purely electrostatic. This attraction is ionic bonding. When solid NaCl is added to water, its identity disappears just as white table salt disappears as we stir it into water. Solubilization occurs as the Na+ becomes surrounded by the partially negative portion of water molecules and the Cl− becomes surrounded by the partially positive portion of water molecules, as illustrated in Figure 2.13. The dissociation can be represented as a reaction, in which solid NaCl is converted to isolated Na+ and Cl− ions that are surrounded by water (hydrated). It is customary to write the hydration as: (2.1)

NaCl ® Na + + Cl -

24 2.4 High Heat Retention: The Unusual Specific Heat of Liquid Water

FIGURE 2.13 Solubilizing NaCl. Entry into solution involves water molecules giving up their own hydrogen-bonded interactions in favor of an ionic interaction between the partial charge of the oxygen atom of water to the sodium ion and the partial charge of the hydrogen atom of water to the chloride ion. Thus, solubilized NaCl has a different and separate identity from the solid. Water is omitted from this chemical equation because it is not strictly a reactant or product in the formal sense. Still, the reaction is impossible without it. What is happening is that the energy of hydration – the strength of interaction of the ions for water – overcomes both the strength of interaction of water for other water molecules (hydrogen bonding), as well as the NaCl lattice interactions (ionic bonding), and the ions are brought into solution. We can assess the tendency for a solvent to bring crystals like NaCl into solution by exploring the dielectric constant. This constant is a measure of the ability of a solvent to separate charged species (detailed in the addendum to this chapter). There is a correlation between a high dielectric constant and the ability to dissolve ions; typical values are illustrated in Table 2.4. Common solvents are listed in order of their boiling points. The table also lists the net dipole (measured as a dipole moment, essentially the net vector of molecular polarity as illustrated in Figure 2.5), the value of the dielectric constant, and the solubility of NaCl in that solvent. It is apparent that water has one of the highest dielectric constants and is best at solubilizing NaCl. Most organic solvents have a dielectric constant an order of magnitude lower; hexane is typical. There is virtually no solubilization of NaCl in organic solvents. However, Table 2.4 also shows that other factors are responsible for solubilization. For example, formic acid and dimethyl formamide (DMF) have similar dielectric constants but differ markedly in their ability to dissolve polar molecules. It is also clear that while we have seen that water has a permanent dipole, reflected in a significant dipole moment, other molecules with higher dipole moments have poor solubilities for NaCl. It is the unique geometry of the water molecule that enables it to form strong polar bonds to salts and allows it to dissolve NaCl readily. This extends to polar molecules that do not form ions, such as alcohols and certain amines. For example, water forms solutions with ethanol in all proportions, which is also true of formamide. In all cases of dissolution, the dissolving molecules displace the hydrogen-bond network of water with stronger bonding interactions with the solute.

2.4 HIGH HEAT RETENTION: THE UNUSUAL SPECIFIC HEAT OF LIQUID WATER Another feature that results from hydrogen bonding is an exceptionally high specific heat for liquid water. The specific heat is the amount of energy needed to increase the temperature of 1 g of a substance by 1°C. Effectively, the high specific heat of water means that water acts as

Chapter 2 – Water 25

TABLE 2.4 Solvent Properties Name

Structure

Formamide

O HC

Dipole Moment (debyes)

Dielectric Constant (dimensionless ratio)

NaCl Solubility (g/100 ml)

210

3.7

109

9.4

153

3.82

47.2

0.04

100

1.85

80

36

100

1.41

58

5.2

81

3.92

36.6

0.003

NH2

DMF

O H 3C

BP (°C)

N

CH

CH3

Water

O

H

H

Formic Acid

H C HO

O

Acetonitrile H 3C

C

N

Hexane CH3OH

Methanol Acetone

O H 3C

69

0

2