Principles of biochemistry


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Principles of biochemistry

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  2. 2. Principles of Biochemistry
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  4. 4. Principles of Biochemistry Fifth Edition Laurence A. Moran University of Toronto H. Robert Horton North Carolina State University K. Gray Scrimgeour University of Toronto Marc D. Perry University of Toronto Boston Columbus Indianapolis New York San Francisco Upper Saddle River Amsterdam Cape Town Dubai London Madrid Milan Munich Paris Montreál Toronto Delhi Mexico City Sao Pauló Sydney Hong Kong Seoul Singapore Taipei Tokyo
  5. 5. Editor in Chief: Adam Jaworski Executive Editor: Jeanne Zalesky Marketing Manager: Erin Gardner Project Editor: Jennifer Hart Associate Editor: Jessica Neumann Editorial Assistant: Lisa Tarabokjia Marketing Assistant: Nicola Houston Vice President, Executive Director of Development: Carol Truehart Developmental Editor: Michael Sypes Managing Editor, Chemistry and Geosciences: Gina M. Cheselka Project Manager, Science: Wendy Perez Senior Technical Art Specialist: Connie Long Art Studios: Mark Landis Illustrations /Jonathan Parrish /2064 Design—Greg Gambino Image Resource Manager: Maya Melenchuk Photo Researcher: Eric Schrader Art Manager: Marilyn Perry Interior/Cover Designer: Tamara Newnam Media Project Manager: Shannon Kong Senior Manufacturing and Operations Manager: Nick Sklitsis Operations Specialist: Maura Zaldivar Composition/Full Service: Nesbitt Graphics, Inc. Cover Illustration: Quade Paul, Echo Medical Media Cover Image Credit: Monkey adapted from Simone van den Berg/Shutterstock Credits and acknowledgments borrowed from other sources and reproduced, with permission, in this textbook appear on page 767. Copyright ©2012, 2006, 2002, 1996 Pearson Education, Inc., All rights reserved. Manufactured in the United States of America. This publication is protected by Copyright and permission should be obtained from the publisher prior to any prohibited reproduction, storage in a retrieval system, or transmission in any form or by any means, electronic, mechanical, photocopying, recording, or likewise. To obtain permission(s) to use material from this work, please submit a written request to Pearson Education, Inc., Permissions Department, 1900 E. Lake Ave., Glenview, IL 60025. For information regarding permissions, call (847) 486-2635. Many of the designations used by manufacturers and sellers to distinguish their products are claimed as trademarks. Where those designations appear in this book, and the publisher was aware of a trademark claim, the designations have been printed in initial caps or all caps. Library of Congress Cataloging-in-Publication Data Principles of biochemistry / H. Robert Horton ... [et al]. — 5th ed. p. cm. ISBN 0-321-70733-8 1. Biochemistry. I. Horton, H. Robert, 1935- QP514.2.P745 2012 612'.015—dc23 2011019987 ISBN 10: 0-321-70733-8 ISBN 13: 978-0-321-70733-8 1 2 3 4 5 6 7 8 9 10—DOW—16 15 14 13 12
  6. 6. Science should be as simple as possible, but not simpler. – Albert Einstein
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  8. 8. vii Brief Contents Part One Introduction 1 Introduction to Biochemistry 1 2 Water 28 Part Two Structure and Function 3 Amino Acids and the Primary Structures of Proteins 55 4 Proteins: Three-Dimensional Structure and Function 85 5 Properties of Enzymes 134 6 Mechanisms of Enzymes 162 7 Coenzymes and Vitamins 196 8 Carbohydrates 227 9 Lipids and Membranes 256 Part Three Metabolism and Bioenergetics 10 Introduction to Metabolism 294 11 Glycolysis 325 12 Gluconeogenesis, the Pentose Phosphate Pathway, and Glycogen Metabolism 355 13 The Citric Acid Cycle 385 14 Electron Transport and ATP Synthesis 417 15 Photosynthesis 443 16 Lipid Metabolism 475 17 Amino Acid Metabolism 514 18 Nucleotide Metabolism 550 Part Four Biological Information Flow 19 Nucleic Acids 573 20 DNA Replication, Repair, and Recombination 601 21 Transcription and RNA Processing 634 22 Protein Synthesis 666
  9. 9. Contents To the Student xxiii Preface xxv About the Authors xxxiii Part One Introduction 1 Introduction to Biochemistry 1 1.1 Biochemistry Is a Modern Science 2 1.2 The Chemical Elements of Life 3 1.3 Many Important Macromolecules Are Polymers 4 A. Proteins 6 B. Polysaccharides 6 C. Nucleic Acids 7 D. Lipids and Membranes 9 1.4 The Energetics of Life 10 A. Reaction Rates and Equilibria 11 B. Thermodynamics 12 C. Equilibrium Constants and Standard Gibbs Free Energy Changes 13 D. Gibbs Free Energy and Reaction Rates 14 1.5 Biochemistry and Evolution 15 1.6 The Cell Is the Basic Unit of Life 17 1.7 Prokaryotic Cells: Structural Features 17 1.8 Eukaryotic Cells: Structural Features 18 A. The Nucleus 20 B. The Endoplasmic Reticulum and Golgi Apparatus 20 C. Mitochondria and Chloroplasts 21 D. Specialized Vesicles 22 E. The Cytoskeleton 23 1.9 A Picture of the Living Cell 23 1.10 Biochemistry Is Multidisciplinary 26 Appendix: The Special Terminology of Biochemistry 26 Selected Readings 27 2 Water 28 2.1 The Water Molecule Is Polar 29 2.2 Hydrogen Bonding in Water 30 Box 2.1 Extreme Thermophiles 32 2.3 Water Is an Excellent Solvent 32 A. Ionic and Polar Substances Dissolve in Water 32 Box 2.2 Blood Plasma and Seawater 33 B. Cellular Concentrations and Diffusion 34 C. Osmotic Pressure 34 2.4 Nonpolar Substances Are Insoluble in Water 35viii
  10. 10. CONTENTS ix 2.5 Noncovalent Interactions 37 A. Charge–Charge Interactions 37 B. Hydrogen Bonds 37 C. Van der Waals Forces 38 D. Hydrophobic Interactions 39 2.6 Water Is Nucleophilic 39 Box 2.3 The Concentration of Water 41 2.7 Ionization of Water 41 2.8 The pH Scale 43 Box 2.4 The Little “p” in pH 44 2.9 Acid Dissociation Constants of Weak Acids 44 Sample Calculation 2.1 Calculating the pH of Weak Acid Solutions 49 2.10 Buffered Solutions Resist Changes in pH 50 Sample Calculation 2.2 Buffer Preparation 50 Summary 52 Problems 52 Selected Readings 54 PART TWO Structure and Function 3 Amino Acids and the Primary Structures of Proteins 55 3.1 General Structure of Amino Acids 56 3.2 Structures of the 20 Common Amino Acids 58 Box 3.1 Fossil Dating by Amino Acid Racemization 58 A. Aliphatic R Groups 59 B. Aromatic R Groups 59 C. R Groups Containing Sulfur 60 D. Side Chains with Alcohol Groups 60 Box 3.2 An Alternative Nomenclature 61 E. Positively Charged R Groups 61 F. Negatively Charged R Groups and Their Amide Derivatives 62 G. The Hydrophobicity of Amino Acid Side Chains 62 3.3 Other Amino Acids and Amino Acid Derivatives 62 3.4 Ionization of Amino Acids 63 Box 3.3 Common Names of Amino Acids 64 3.5 Peptide Bonds Link Amino Acids in Proteins 67 3.6 Protein Purification Techniques 68 3.7 Analytical Techniques 70 3.8 Amino Acid Composition of Proteins 73 3.9 Determining the Sequence of Amino Acid Residues 74 3.10 Protein Sequencing Strategies 76 3.11 Comparisons of the Primary Structures of Proteins Reveal Evolutionary Relationships 79 Summary 82 Problems 82 Selected Readings 84 4 Proteins: Three-Dimensional Structure and Function 85 4.1 There Are Four Levels of Protein Structure 87 4.2 Methods for Determining Protein Structure 88
  11. 11. x CONTENTS 4.3 The Conformation of the Peptide Group 91 Box 4.1 Flowering Is Controlled by Cis/Trans Switches 93 4.4 The a Helix 94 4.5 b Strands and b Sheets 97 4.6 Loops and Turns 98 4.7 Tertiary Structure of Proteins 99 A. Supersecondary Structures 100 B. Domains 101 C. Domain Structure, Function, and Evolution 102 D. Intrinsically Disordered Proteins 102 4.8 Quaternary Structure 103 4.9 Protein–Protein Interactions 109 4.10 Protein Denaturation and Renaturation 110 4.11 Protein Folding and Stability 114 A. The Hydrophobic Effect 114 B. Hydrogen Bonding 115 Box 4.2 CASP: The Protein Folding Game 116 C. Van der Waals Interactions and Charge–Charge Interactions 117 D. Protein Folding Is Assisted by Molecular Chaperones 117 4.12 Collagen, a Fibrous Protein 119 Box 4.3 Stronger Than Steel 121 4.13 Structure of Myoglobin and Hemoglobin 122 4.14 Oxygen Binding to Myoglobin and Hemoglobin 123 A. Oxygen Binds Reversibly to Heme 123 B. Oxygen-Binding Curves of Myoglobin and Hemoglobin 124 Box 4.4 Embryonic and Fetal Hemoglobins 126 C. Hemoglobin Is an Allosteric Protein 127 4.15 Antibodies Bind Specific Antigens 129 Summary 130 Problems 131 Selected Readings 133 5 Properties of Enzymes 134 5.1 The Six Classes of Enzymes 136 Box 5.1 Enzyme Classification Numbers 137 5.2 Kinetic Experiments Reveal Enzyme Properties 138 A. Chemical Kinetics 138 B. Enzyme Kinetics 139 5.3 The Michaelis-Menten Equation 140 A. Derivation of the Michaelis-Menten Equation 141 B. The Calalytic Constant Kcat 143 C. The Meanings of Km 144 5.4 Kinetic Constants Indicate Enzyme Activity and Catalytic Proficiency 144 5.5 Measurement of Km and Vmax 145 Box 5.2 Hyperbolas Versus Straight Lines 146 5.6 Kinetics of Multisubstrate Reactions 147 5.7 Reversible Enzyme Inhibition 148 A. Competitive Inhibition 149 B. Uncompetitive Inhibition 150
  12. 12. CONTENTS xi C. Noncompetitive Inhibition 150 D. Uses of Enzyme Inhibition 151 5.8 Irreversible Enzyme Inhibition 152 5.9 Regulation of Enzyme Activity 153 A. Phosphofructokinase Is an Allosteric Enzyme 154 B. General Properties of Allosteric Enzymes 155 C. Two Theories of Allosteric Regulation 156 D. Regulation by Covalent Modification 158 5.10 Multienzyme Complexes and Multifunctional Enzymes 158 Summary 159 Problems 159 Selected Readings 161 6 Mechanisms of Enzymes 162 6.1 The Terminology of Mechanistic Chemistry 162 A. Nucleophilic Substitutions 163 B. Cleavage Reactions 163 C. Oxidation–Reduction Reactions 164 6.2 Catalysts Stabilize Transition States 164 6.3 Chemical Modes of Enzymatic Catalysis 166 A. Polar Amino Acids Residues in Active Sites 166 Box 6.1 Site-Directed Mutagenesis Modifies Enzymes 167 B. Acid–Base Catalysis 168 C. Covalent Catalysis 169 D. pH Affects Enzymatic Rates 170 6.4 Diffusion-Controlled Reactions 171 A. Triose Phosphate Isomerase 172 Box 6.2 The “Perfect Enzyme”? 174 B. Superoxide Dismutase 175 6.5 Modes of Enzymatic Catalysis 175 A. The Proximity Effect 176 B. Weak Binding of Substrates to Enzymes 178 C. Induced Fit 179 D. Transition State Stabilization 180 6.6 Serine Proteases 183 A. Zymogens Are Inactive Enzyme Precursors 183 Box 6.3 Kornberg’s Ten Commandments 183 B. Substrate Specificity of Serine Proteases 184 C. Serine Proteases Use Both the Chemical and the Binding Modes of Catalysis 185 Box 6.4 Clean Clothes 186 Box 6.5 Convergent Evolution 187 6.7 Lysozyme 187 6.8 Arginine Kinase 190 Summary 192 Problems 193 Selected Readings 194 2 OC C OH H CH2OPO3 H His-95 Glu-165 1 2 3 C O CH2 H2C O H CH2 N N
  13. 13. xii CONTENTS 7 Coenzymes and Vitamins 196 7.1 Many Enzymes Require Inorganic Cations 197 7.2 Coenzyme Classification 197 7.3 ATP and Other Nucleotide Cosubstrates 198 Box 7.1 Missing Vitamins 200 7.4 NAD and NADP 200 Box 7.2 NAD Binding to Dehydrogenases 203 7.5 FAD and FMN 204 7.6 Coenzyme A and Acyl Carrier Protein 204 7.7 Thiamine Diphosphate 206 7.8 Pyridoxal Phosphate 207 7.9 Vitamin C 209 7.10 Biotin 211 Box 7.3 One Gene: One Enzyme 212 7.11 Tetrahydrofolate 213 7.12 Cobalamin 215 7.13 Lipoamide 216 7.14 Lipid Vitamins 217 A. Vitamin A 217 B. Vitamin D 218 C. Vitamin E 218 D. Vitamin K 218 7.15 Ubiquinone 219 Box 7.4 Rat Poison 220 7.16 Protein Coenzymes 221 7.17 Cytochromes 221 Box 7.5 Noble Prizes for Vitamins and Coenzymes 223 Summary 223 Problems 224 Selected Readings 226 8 Carbohydrates 227 8.1 Most Monosaccharides Are Chiral Compounds 228 8.2 Cyclization of Aldoses and Ketoses 230 8.3 Conformations of Monosaccharides 234 8.4 Derivatives of Monosaccharides 235 A. Sugar Phosphates 235 B. Deoxy Sugars 235 C. Amino Sugars 235 D. Sugar Alcohols 236 E. Sugar Acids 236 8.5 Disaccharides and Other Glycosides 236 A. Structures of Disaccharides 237 B. Reducing and Nonreducing Sugars 238 C. Nucleosides and Other Glycosides 239 Box 8.1 The Problem with Cats 240 8.6 Polysaccharides 240 A. Starch and Glycogen 240 B. Cellulose 243 ᮍᮍ
  14. 14. CONTENTS xiii C. Chitin 244 8.7 Glycoconjugates 244 A. Proteoglycans 244 Box 8.2 Nodulation Factors Are Lipo-Oligosaccharides 246 B. Peptidoglycans 246 C. Glycoproteins 248 Box 8.3 ABO Blood Group 250 Summary 252 Problems 253 Selected Readings 254 9 Lipids and Membranes 256 9.1 Structural and Functional Diversity of Lipids 256 9.2 Fatty Acids 256 Box 9.1 Common Names of Fatty Acids 258 Box 9.2 Trans Fatty Acids and Margarine 259 9.3 Triacylglycerols 261 9.4 Glycerophospholipids 262 9.5 Sphingolipids 263 9.6 Steroids 266 9.7 Other Biologically Important Lipids 268 9.8 Biological Membranes 269 A. Lipid Bilayers 269 Box 9.3 Gregor Mendel and Gibberellins 270 B. Three Classes of Membrane Proteins 270 Box 9.4 New Lipid Vesicles, or Liposomes 272 Box 9.5 Some Species Have Unusual Lipids in Their Membranes 274 C. The Fluid Mosaic Model of Biological Membranes 274 9.9 Membranes Are Dynamic Structures 275 9.10 Membrane Transport 277 A. Thermodynamics of Membrane Transport 278 B. Pores and Channels 279 C. Passive Transport and Facilitated Diffusion 280 D. Active Transport 282 E. Endocytosis and Exocytosis 283 9.11 Transduction of Extracellular Signals 283 A. Receptors 283 Box 9.6 The Hot Spice of Chili Peppers 284 B. Signal Transducers 285 C. The Adenylyl Cyclase Signaling Pathway 287 D. The Inositol–Phospholipid Signaling Pathway 287 Box 9.7 Bacterial Toxins and G Proteins 290 E. Receptor Tyrosine Kinases 290 Summary 291 Problems 292 Selected Readings 293
  15. 15. xiv CONTENTS PART THREE Metabolism and Bioenergetics 10 Introduction to Metabolism 294 10.1 Metabolism Is a Network of Reactions 294 10.2 Metabolic Pathways 297 A. Pathways Are Sequences of Reactions 297 B. Metabolism Proceeds by Discrete Steps 297 C. Metabolic Pathways Are Regulated 297 D. Evolution of Metabolic Pathways 301 10.3 Major Pathways in Cells 302 10.4 Compartmentation and Interorgan Metabolism 304 10.5 Actual Gibbs Free Energy Change, Not Standard Free Energy Change, Determines the Direction of Metabolic Reactions 306 Sample Calculation 10.1 Calculating Standard Gibbs Free Energy Change from Energies of Formation 308 10.6 The Free Energy of ATP Hydrolysis 308 10.7 The Metabolic Roles of ATP 311 A. Phosphoryl Group Transfer 311 Sample Calculation 10.2 Gibbs Free Energy Change 312 Box 10.1 The Squiggle 312 B. Production of ATP by Phosphoryl Group Transfer 314 C. Nucleotidyl Group Transfer 315 10.8 Thioesters Have High Free Energies of Hydrolysis 316 10.9 Reduced Coenzymes Conserve Energy from Biological Oxidations 316 A. Gibbs Free Energy Change Is Related to Reduction Potential 317 B. Electron Transfer from NADH Provides Free Energy 319 Box 10.2 NAD and NADH Differ in Their Ultraviolet Absorption Spectra 321 10.10 Experimental Methods for Studying Metabolism 321 Summary 322 Problems 323 Selected Readings 324 11 Glycolysis 325 11.1 The Enzymatic Reactions of Glycolysis 326 11.2 The Ten Steps of Glycolysis 326 1. Hexokinase 326 2. Glucose 6-Phosphate Isomerase 327 3. Phosphofructokinase-1 330 4. Aldolase 330 Box 11.1 A Brief History of the Glycolysis Pathway 331 5. Triose Phosphate Isomerase 332 6. Glyceraldehyde 3-Phosphate Dehydrogenase 333 7. Phosphoglycerate Kinase 335 Box 11.2 Formation of 2,3-Bisphosphoglycerate in Red Blood Cells 335 Box 11.3 Arsenate Poisoning 336 8.Phosphoglycerate Mutase 336 9.Enolase 338 10.Pryuvate Kinase 338 ᮍ
  16. 16. CONTENTS xv 11.3 The Fate of Pryuvate 338 A. Metabolism of Pryuvate to Ethanol 339 B. Reduction of Pyruvate to Lactate 340 Box 11.4 The Lactate of the Long-Distance Runner 341 11.4 Free Energy Changes in Glycolysis 341 11.5 Regulation of Glycolysis 343 A. Regulation of Hexose Transporters 344 B. Regulation of Hexokinase 344 Box 11.5 Glucose 6-Phosphate Has a Pivotal Metabolic Role in the Liver 345 C. Regulation of Phosphofructokinase-1 345 D. Regulation of Pyruvate Kinase 346 E. The Pasteur Effect 347 11.6 Other Sugars Can Enter Glycolysis 347 A. Sucrose Is Cleaved to Monosaccharides 348 B. Fructose Is Converted to Glyceraldehyde 3-Phosphate 348 C. Galactose Is Converted to Glucose 1-Phosphate 349 Box 11.6 A Secret Ingredient 349 D. Mannose Is Converted to Fructose 6-Phosphate 351 11.7 The Entner–Doudoroff Pathway in Bacteria 351 Summary 352 Problems 353 Selected Readings 354 12 Gluconeogenesis, the Pentose Phosphate Pathway, and Glycogen Metabolism 355 12.1 Gluconeogenesis 356 A. Pyruvate Carboxylase 357 B. Phosphoenolpyruvate Carboxykinase 358 C. Fructose 1,6-bisphosphatase 358 Box 12.1 Supermouse 359 D. Glucose 6-Phosphatase 359 12.2 Precursors for Gluconeogenesis 360 A. Lactate 360 B. Amino Acids 360 C. Glycerol 361 D. Propionate and Lactate 361 E. Acetate 362 Box 12.2 Glucose Is Sometimes Converted to Sorbitol 362 12.3 Regulation of Gluconeogenesis 363 Box 12.3 The Evolution of a Complex Enzyme 364 12.4 The Pentose Phosphate Pathway 364 A. Oxidative Stage 366 B. Nonoxidative Stage 364 Box 12.4 Glucose 6-Phosphate Dehydrogenase Deficiency in Humans 367 C. Interconversions Catalyzed by Transketolase and Transaldolase 368 12.5 Glycogen Metabolism 368 A. Glycogen Synthesis 369 B. Glycogen Degradation 370 12.6 Regulation of Glycogen Metabolism in Mammals 372
  17. 17. xvi CONTENTS A. Regulation of Glycogen Phosphorylase 372 Box 12.5 Head Growth and Tail Growth 373 B. Hormones Regulate Glycogen Metabolism 375 C. Hormones Regulate Gluconeogenesis and Glycolysis 376 12.7 Maintenance of Glucose Levels in Mammals 378 12.8 Glycogen Storage Diseases 381 Summary 382 Problems 382 Selected Readings 383 13 The Citric Acid Cycle 385 Box 13.1 An Egregious Error 386 13.1 Conversion of Pyruvate to Acetyl CoA 387 Sample Calculation 13.1 390 13.2 The Citric Acid Cycle Oxidizes Acetyl CoA 391 Box 13.2 Where Do the Electrons Come From? 392 13.3 The Citric Acid Cycle Enzymes 394 1. Citrate Synthase 394 Box 13.3 Citric Acid 396 2. Aconitase 396 Box 13.4 Three-Point Attachment of Prochiral Substrates to Enzymes 397 3. Isocitrate Dehydrogenase 397 4. The ␣-Ketoglutarate Dehydrogenase Complex 398 5. Succinyl CoA Synthetase 398 6. Succinate Dehydrogenase Complex 399 Box 13.5 What’s in a Name? 399 Box 13.6 On the Accuracy of the World Wide Web 401 7. Fumarase 401 8. Malate Deydrogenase 401 Box 13.7 Converting One Enzyme into Another 402 13.4 Entry of Pyruvate Into Mitochondria 402 13.5 Reduced Coenzymes Can Fuel the Production of ATP 405 13.6 Regulation of the Citric Acid Cycle 406 13.7 The Citric Acid Cycle Isn’t Always a “Cycle” 407 Box 13.8 A Cheap Cancer Drug? 408 13.8 The Glyoxylate Pathway 409 13.9 Evolution of the Citric Acid Cycle 412 Summary 414 Problems 414 Selected Readings 416 14 Electron Transport and ATP Synthesis 417 14.1 Overview of Membrane-associated Electron Transport and ATP Synthesis 418 14.2 The Mitochondrion 418 Box 14.1 An Exception to Every Rule 420 14.3 The Chemiosmotic Theory and the Protonmotive Force 420 A. Historical Background: The Chemiosmotic Theory 420 B. The Protonmotive Force 421
  18. 18. CONTENTS xvii 14.4 Electron Transport 423 A. Complexes I Through IV 423 B. Cofactors in Electron Transport 425 14.5 Complex I 426 14.6 Complex II 427 14.7 Complex III 428 14.8 Complex IV 431 14.9 Complex V: ATP Synthase 433 Box 14.2 Proton Leaks and Heat Production 435 14.10 Active Transport of ATP, ADP, and Pi Across the Mitochondrial Membrane 435 14.11 The P/O Ratio 436 14.12 NADH Shuttle Mechanisms in Eukaryotes 436 Box 14.3 The High Cost of Living 439 14.13 Other Terminal Electron Acceptors and Donors 439 14.14 Superoxide Anions 440 Summary 441 Problems 441 Selected Readings 442 15 Photosynthesis 443 15.1 Light-Gathering Pigments 444 A. The Structures of Chlorophylls 444 B. Light Energy 445 C. The Special Pair and Antenna Chlorophylls 446 Box 15.1 Mendel’s Seed Color Mutant 447 D. Accessory Pigments 447 15.2 Bacterial Photosystems 448 A. Photosystem II 448 B. Photosystem I 450 C. Coupled Photosystems and Cytochrome bf 453 D. Reduction Potentials and Gibbs Free Energy in Photosynthesis 455 E. Photosynthesis Takes Place Within Internal Membranes 457 Box 15.2 Oxygen “Pollution” of Earth’s Atmosphere 457 15.3 Plant Photosynthesis 458 A. Chloroplasts 458 B. Plant Photosystems 459 C. Organization of Cloroplast Photosystems 459 Box 15.3 Bacteriorhodopsin 461 15.4 Fixation of CO2: The Calvin Cycle 461 A. The Calvin Cycle 462 B. Rubisco: Ribulose 1,5-bisphosphate Carboxylase-oxygenase 462 C. Oxygenation of Ribulose 1,5-bisphosphate 465 Box 15.4 Building a Better Rubisco 466 D. Calvin Cycle: Reduction and Regeneration Stages 466 15.5 Sucrose and Starch Metabolism in Plants 467 Box 15.5 Gregor Mendel’s Wrinkled Peas 469 15.6 Additional Carbon Fixation Pathways 469 A. Compartmentalization in Bacteria 469
  19. 19. xviii CONTENTS B. The C4 Pathway 469 C. Crassulacean Acid Metabolism (CAM) 471 Summary 472 Problems 473 Selected Readings 474 16 Lipid Metabolism 475 16.1 Fatty Acid Synthesis 475 A. Synthesis of Malonyl ACP and Acetyl ACP 476 B. The Initiation Reaction of Fatty Acid Synthesis 477 C. The Elongation Reactions of Fatty Acid Synthesis 477 D. Activation of Fatty Acids 479 E. Fatty Acid Extension and Desaturation 479 16.2 Synthesis of Triacylglycerols and Glycerophospholipids 481 16.3 Synthesis of Eicosanoids 483 Box 16.1 sn-Glycerol 3-Phosphate 484 Box 16.2 The Search for a Replacement for Asprin 486 16.4 Synthesis of Ether Lipids 487 16.5 Synthesis of Sphingolipids 488 16.6 Synthesis of Cholesterol 488 A. Stage 1: Acetyl CoA to Isopentenyl Diphosphate 488 B. Stage 2: Isopentenyl Diphosphate to Squalene 488 C. Stage 3: Squalene to Cholesterol 490 D. Other Products of Isoprenoid Metabolism 490 Box 16.3 Lysosomal Storage Diseases 492 Box 16.4 Regulating Cholesterol Levels 493 16.7 Fatty Acid Oxidation 494 A. Activation of Fatty Acids 494 B. The Reactions of ␤-Oxidation 494 C. Fatty Acid Synthesis and ␤-Oxidation 497 D. Transport of Fatty Acyl CoA into Mitochondria 497 Box 16.5 A Trifunctional Enzyme for ␤-Oxidation 498 E. ATP Generation from Fatty Acid Oxidation 498 F. ␤-Oxidation of Odd-Chain and Unsaturated Fatty Acids 499 16.8 Eukaryotic Lipids Are Made at a Variety of Sites 501 16.9 Lipid Metabolism Is Regulated by Hormones in Mammals 502 16.10 Absorption and Mobilization of Fuel Lipids in Mammals 505 A. Absorption of Dietary Lipids 505 B. Lipoproteins 505 Box 16.6 Extra Virgin Olive Oil 506 Box 16.7 Lipoprotein Lipase and Coronary Heart Disease 507 C. Serum Albumin 508 16.11 Ketone Bodies Are Fuel Molecules 508 A. Ketone Bodies Are Synthesized in the Liver 509 B. Ketone Bodies Are Oxidized in Mitochondria 510 Box 16.8 Lipid Metabolism in Diabetes 511 Summary 511 Problems 511 Selected Readings 513
  20. 20. CONTENTS xix 17 Amino Acid Metabolism 514 17.1 The Nitrogen Cycle and Nitrogen Fixation 515 17.2 Assimilation of Ammonia 518 A. Ammonia Is Incorporated into Glutamate and Glutamine 518 B. Transamination Reactions 518 17.3 Synthesis of Amino Acids 520 A. Aspartate and Asparagine 520 B. Lysine, Methionine, Threonine 520 C. Alanine, Valine, Leucine, and Isoleucine 521 Box 17.1 Childhood Acute Lymphoblastic Leukemia Can Be Treated with Asparaginase 522 D. Glutamate, Glutamine, Arginine, and Proline 523 E. Serine, Glycine, and Cysteine 523 F. Phenylalanine, Tyrosine, and Tryptophan 523 G. Histidine 527 Box 17.2 Genetically Modified Food 528 Box 17.3 Essential and Nonessential Amino Acids in Animals 529 17.4 Amino Acids as Metabolic Precursors 529 A. Products Derived from Glutamate, Glutamine, and Aspartate 529 B. Products Derived from Serine and Glycine 529 C. Synthesis of Nitric Oxide from Arginine 530 D. Synthesis of Lignin from Phenylalanine 531 E. Melanin Is Made from Tyrosine 531 17.5 Protein Turnover 531 Box 17.4 Apoptosis–Programmed Cell Death 534 17.6 Amino Acid Catabolism 534 A. Alanine, Asparagine, Aspartate, Glutamate, and Glutamine 535 B. Arginine, Histidine, and Proline 535 C. Glycine and Serine 536 D. Threonine 537 E. The Branched Chain Amino Acids 537 F. Methionine 539 Box 17.5 Phenylketonuria, a Defect in Tyrosine Formation 540 G. Cysteine 540 H. Phenylalanine, Tryptophane, and Tyrosine 541 I. Lysine 542 17.7 The Urea Cycle Converts Ammonia into Urea 542 A. Synthesis of Carbamoyl Phosphate 543 B. The Reactions of the Urea Cycle 543 Box 17.6 Diseases of Amino Acid Metabolism 544 C. Ancillary Reactions of the Urea Cycle 547 17.8 Renal Glutamine Metabolism Produces Bicarbonate 547 Summary 548 Problems 548 Selected Readings 549 18 Nucleotide Metabolism 550 18.1 Synthesis of Purine Nucleotides 550 Box 18.1 Common Names of the Bases 552 18.2 Other Purine Nucleotides Are Synthesized from IMP 554 18.3 Synthesis of Pyrimidine Nucleotides 555
  21. 21. xx CONTENTS A. The Pathway for Pyrimidine Synthesis 556 Box 18.2 How Some Enzymes Transfer Ammonia from Glutamate 558 B. Regulation of Pyrimidine Synthesis 559 18.4 CTP Is Synthesized from UMP 559 18.5 Reduction of Ribonucleotides to Deoxyribonucleotides 560 18.6 Methylation of dUMP Produces dTMP 560 Box 18.3 Free Radicals in the Reduction of Ribonucleotides 562 Box 18.4 Cancer Drugs Inhibit dTTP Synthesis 564 18.7 Modified Nucleotides 564 18.8 Salvage of Purines and Pyrimidines 564 18.9 Purine Catabolism 565 18.10 Pyrimidine Catabolism 568 Box 18.5 Lesch–Nyhan Syndrome and Gout 569 Summary 571 Problems 571 Selected Readings 572 PART FOUR Biological Information Flow 19 Nucleic Acids 573 19.1 Nucleotides Are the Building Blocks of Nucleic Acids 574 A. Ribose and Deoxyribose 574 B. Purines and Pyrimidines 574 C. Nucleosides 575 D. Nucleotides 577 19.2 DNA Is Double-Stranded 579 A. Nucleotides Are Joined by 3Ј–5Ј Phosphodiester Linkages 580 B. Two Antiparallel Strands Form a Double Helix 581 C. Weak Forces Stabilize the Double Helix 583 D. Conformations of Double-Stranded DNA 585 19.3 DNA Can Be Supercoiled 586 19.4 Cells Contain Several Kinds of RNA 587 Box 19.1 Pulling DNA 588 19.5 Nucleosomes and Chromatin 588 A. Nucleosomes 588 B. Higher Levels of Chromatin Structure 590 C. Bacterial DNA Packaging 590 19.6 Nucleases and Hydrolysis of Nucleic Acids 591 A. Alkaline Hydrolysis of RNA 591 B. Hydrolysis of RNA by Ribonuclease A 592 C. Restriction Endonucleases 593 D. EcoRI Binds Tightly to DNA 595 19.7 Uses of Restriction Endocucleases 596 A. Restriction Maps 596 B. DNA Fingerprints 596 C. Recombinant DNA 597 Summary 598 Problems 599 Selected Readings 599
  22. 22. 20 DNA Replication, Repair, and Recombination 601 20.1 Chromosomal DNA Replication Is Bidirectional 602 20.2 DNA Polymerase 603 A. Chain Elongation Is a Nucleotidyl-Group–Transfer Reaction 604 B. DNA Polymerase III Remains Bound to the Replication Fork 606 C. Proofreading Corrects Polymerization Errors 607 20.3 DNA Polymerase Synthesizes Two Strands Simultaneously 607 A. Lagging Strand Synthesis Is Discontinuous 608 B. Each Okazaki Fragment Begins with an RNA Primer 608 C. Okazaki Fragments Are Joined by the Action of DNA Polymerase I and DNA Ligase 609 20.4 Model of the Replisome 610 20.5 Initiation and Termination of DNA Replication 615 20.6 DNA Replication in Eukaryotes 615 A. The Polymerase Chain Reaction Uses DNA Polymerase to Amplify Selected DNA Sequences 615 B. Sequencing DNA Using Dideoxynucleotides 616 C. Massively Parallel DNA Sequencing by Synthesis 618 20.7 DNA Replication in Eukaryotes 619 20.8 Repair of Damaged DNA 622 A. Repair after Photodimerization: An Example of Direct Repair 622 B. Excision Repair 624 BOX 20.1 The Problem with Methylcytosine 626 20.9 Homologous Recombination 626 A. The Holliday Model of General Recombination 626 B. Recombination in E. coli 627 BOX 20.2 Molecular Links Between DNA Repair and Breast Cancer 630 C. Recombination Can Be a Form of Repair 631 Summary 631 Problems 632 Selected Readings 632 21 Transcription and RNA Processing 633 21.1 Types of RNA 634 21.2 RNA Polymerase 635 A. RNA Polymerase Is an Oligomeric Protein 635 B. The Chain Elongation Reaction 636 21.3 Transcription Initiation 638 A. Genes Have a 5Ј 3Ј Orientation 638 B. The Transcription Complex Assembles at a Promoter 639 C. The s sigma Subunit Recognizes the Promoter 640 D. RNA Polymerase Changes Conformation 641 21.4 Transcription Termination 643 21.5 Transcription in Eukaryotes 645 A. Eukaryotic RNA Polymerases 645 B. Eukaryotic Transcription Factors 647 C. The Role of Chromatin in Eukaryotic Transcription 648 21.6 Transcription of Genes Is Regulated 648 21.7 The lac Operon, an Example of Negative and Positive Regulation 650 A. lac Repressor Blocks Transcription 650 B. The Structure of lac Repressor 651 : CONTENTS xxi
  23. 23. xxii CONTENTS C. cAMP Regulatory Protein Activates Transcription 652 21.8 Post-transcriptional Modification of RNA 654 A. Transfer RNA Processing 654 B. Ribosomal RNA Processing 655 21.9 Eukaryotic mRNA Processing 655 A. Eukaryotic mRNA Molecules Have Modified Ends 657 B. Some Eukaryotic mRNA Precursors Are Spliced 657 Summary 663 Problems 663 Selected Readings 664 22 Protein Synthesis 665 22.1 The Genetic Code 665 22.2 Transfer RNA 668 A. The Three-Dimensional Structure of tRNA 668 B. tRNA Anticodons Base-Pair with mRNA Codons 669 22.3 Aminoacyl-tRNA Synthetases 670 A. The Aminoacyl-tRNA Synthetase Reaction 671 B. Specificity of Aminoacyl-tRNA Synthetases 671 C. Proofreading Activity of Aminoacyl-tRNA Synthetases 673 22.4 Ribosomes 673 A. Ribosomes Are Composed of Both Ribosomal RNA and Protein 674 B. Ribosomes Contain Two Aminoacyl-tRNA Binding Sites 675 22.5 Initiation of Translation 675 A. Initiator tRNA 675 B. Initiation Complexes Assemble Only at Initiation Codons 676 C. Initiation Factors Help Form the Initiation Complex 677 D. Translation Initiation in Eukaryotes 679 22.6 Chain Elongation During Protein Synthesis Is a Three-Step Microcycle 679 A. Elongation Factors Dock an Aminoacyl-tRNA in the A Site 680 B. Peptidyl Transferase Catalyzes Peptide Bond Formation 681 C. Translocation Moves the Ribosome by One Codon 682 22.7 Termination of Translation 684 22.8 Protein Synthesis Is Energetically Expensive 684 22.9 Regulation of Protein Synthesis 685 A. Ribosomal Protein Synthesis Is Coupled to Ribosome Assembly in E. coli 685 Box 22.1 Some Antibiotics Inhibit Protein Synthesis 686 B. Globin Synthesis Depends on Heme Availability 687 C. The E. coli trp Operon Is Regulated by Repression and Attenuation 687 22.10 Post-translational Processing 689 A. The Signal Hypothesis 691 B. Glycosylation of Proteins 694 Summary 694 Problems 695 Selected Readings 696 Solutions 697 Glossary 751 Illustration Credits 767 Index 769
  24. 24. xxiii Welcome to biochemistry—the study of life at the molecular level. As you venture into this exciting and dynamic discipline, you’ll discover many new and wonderful things. You’ll learn how some enzymes can catalyze chemical reactions at speeds close to theo- retical limits—reactions that would otherwise occur only at imperceptibly low rates. You’ll learn about the forces that maintain biomolecular structure and how even some of the weakest of those forces make life possible. You’ll also learn how biochemistry has thousands of applications in day-to-day life—in medicine, drug design, nutrition, forensic science, agriculture, and manufacturing. In short, you’ll begin a journey of dis- covery about how biochemistry makes life both possible and better. Before we begin, we would like to offer a few words of advice: Don’t just memorize facts; instead, understand principles In this book, we have tried to identify the most important principles of biochemistry. Because the knowledge base of biochemistry is continuously expanding, we must grasp the underlying themes of this science in order to understand it. This textbook is de- signed to expand on the foundation you have acquired in your chemistry and biology courses and to provide you with a biochemical framework that will allow you to under- stand new phenomena as you meet them. Be prepared to learn a new vocabulary An understanding of biochemical facts requires that you learn a biochemical vocabu- lary. This vocabulary includes the chemical structures of a number of key molecules. These molecules are grouped into families based on their structures and functions. You will also learn how to distinguish among members of each family and how small mole- cules combine to form macromolecules such as proteins and nucleic acids. Test your understanding True mastery of biochemistry lies with learning how to apply your knowledge and how to solve problems. Each chapter concludes with a set of carefully crafted problems that test your understanding of core principles. Many of these problems are mini case stud- ies that present the problem within the context of a real biochemical puzzle. For more practice, we are pleased to refer you to The Study Guide for Principles of Biochemistry by Scott Lefler and Allen Scism which presents a variety of supplementary questions that you may find helpful. You will also find additional problems on TheChemistryPlace® for Principles of Biochemistry ( Learn to visualize in 3-D Biochemicals are three-dimensional objects. Understanding what happens in a bio- chemical reaction at the molecular level requires that you be able to “see” what happens in three dimensions. We present the structures of simple molecules in several different ways in order to illustrate their three-dimensional conformation. In addition to the art in the book, you will find many animations and interactive molecular models on the website. We strongly suggest you look at these movies and do the exercises that accom- pany them as well as participate in the molecular visualization tutorials. Feedback Finally, please let us know of any errors or omissions you encounter as you use this text. Tell us what you would like to see in the next edition. With your help we will continue to evolve this work into an even more useful tool. Our e-mail addresses are at the end of the Preface. Good luck, and enjoy! To the Student
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  26. 26. xxv Given the breadth of coverage and diversity of ways to present topics in biochemistry, we have tried to make the text as modular as possible to allow for greater flexibility and organization. Each large topic resides in its own section. Reaction mechanisms are often separated from the main thread of the text and can be passed over by those who prefer not to cover this level of detail. The text is extensively cross-referenced to make it easier for you to reorganize the chapters and for students to see the interrelationships among various topics and to drill down to deeper levels of understanding. We built the book explicitly for the beginning student taking a first course in bio- chemistry with the aim of encouraging students to think critically and to appreciate scientific knowledge for its own sake. Parts One and Two lay a solid foundation of chemical knowledge that will help students understand, rather than merely memo- rize, the dynamics of metabolic and genetic processes. These sections assume that stu- dents have taken prerequisite courses in general and organic chemistry and have ac- quired a rudimentary knowledge of the organic chemistry of carboxylic acids, amines, alcohols, and aldehydes. Even so, key functional groups and chemical proper- ties of each type of biomolecule are carefully explained as their structures and func- tions are presented. We also assume that students have previously taken a course in biology where they have learned about evolution, cell biology, genetics, and the diversity of life on this planet. We offer brief refreshers on these topics wherever possible. New to this Edition We are grateful for all the input we received on the first four editions of this text. You’ll notice the following improvements in this fifth edition: • Key Concept margin notes are provided throughout to highlight key concepts and principles that students must know. • Interest Boxes have been updated and expanded, with 45% new to the fifth edition. We use interest boxes to explain some topics in more detail, to illustrate certain prin- ciples with specific examples, to stimulate students curiosity about science, to show applications of biochemistry, and to explain clinical relevance. We have also added a few interests boxes that warn students about misunderstanding and misapplications of biochemistry. Examples include Blood Plasma and Sea Water; Fossil Dating by Amino Acid Racemization; Embryonic and Fetal Hemoglobins; Clean Clothes; The Perfect Enzyme; Supermouse; The Evolution of a Complex Enzyme; An Egregious Error; Mendels Seed Color Mutant; Oxygen Pollution of Earth’s Atmosphere; Extra Virgin Olive Oil; Missing Vitamins; Pulling DNA; and much more. • New Material has been added throughout, including an improved explanation of early evolution (the Web of Life), more emphasis on protein protein interactions, a new section on intrinsically disordered proteins, and a better description of the dis- tinction between Gibbs free energy changes and reaction rates. We have removed the final chapter on Recombinant DNA Technology and integrated much of that material into earlier chapters. We have added descriptions of a number of new pro- tein structures and integrated them into two major themes: structure-function and multienzyme complexes. The best example is the fatty acid synthase complex in Chapter 16. In some cases new material was necessary because recent discoveries have changed our view of some reactions and processes. We now know, for example, that older versions of uric acid catabolism were incorrect, the correct pathway is shown in Figure 18.23. Preface
  27. 27. xxvi PREFACE We have been careful not to add extra detail unless it supports and extends the basic concepts and principles that we have established over the past four editions. Similarly, we do not introduce new subjects unless they illustrate new concepts that were not covered in previous editions. The goal is to keep this textbook focused on the fundamentals that students need to know and prevent it from bloating up into an encyclopedia of mostly irrelevant information that detracts from the main pedagogical goals. • Selected Readings after each chapter reflect the most current literature and these have been updated and extended where necessary. We have added over 120 new references and deleted many that are no longer appropriate. Although we have al- ways included references to the pedagogical literature, you will note that we have added quite a few more references of this type. Students now have easy access to these papers and they are often more informative than advanced papers in the purely scientific literature. • Art is an important component of a good textbook. Our art program has been ex- tensively revised, with many new photos to illustrate concepts explained in the text; new and updated ribbon art, and improved versions of many figures. Many of the new photos are designed to attract and/or hold the students attention. They can be powerful memory aids and some of them are used to lighten up the subject in a way that is rarely seen in other textbooks (see page 204). We believe that the look and feel of the book has been much improved, making it more appealing to stu- dents without sacrificing any of the rigor and accuracy that has been a hallmark of previous editions. A focus on principles There are, in essence, two kinds of biochemistry textbooks: those for reference and those for teaching. It is difficult for one book to be both as it is those same thickets of detail sought by the professional that ensnare the struggling novice on his or her first trip through the forest. This text is unapologetically a text for teaching. It has been de- signed to foster student understanding and is not an encyclopedia of biochemistry. This book focuses unwaveringly on teaching basic principles and concepts, each principle supported by carefully chosen examples. We really do try to get students to see the forest and not the trees! Because of this focus, the material in this book can be covered in a two-semester course without having to tell students to skip certain chapters or certain sections. The book is also suitable for a one-semester course that concentrates on certain aspects of biochemistry where some subjects are not covered. Instructors can be confident that the core principles and concepts are explained thoroughly and correctly. A focus on chemistry When we first wrote this text, we decided to take the time to explain in chemical terms the principles that we want to emphasize. In fact, one of these principles is to show stu- dents that life obeys the fundamental laws of physics and chemistry. To that end, we offer chemical explanations of most biochemical reactions, including mechanisms that tell students how and why things happen. We are particularly proud of our explanations of oxidation-reduction reactions since these are extremely important in so many contexts. We describe electron move- ments in the early chapters, explain reduction potentials in Chapter 10 and use this un- derstanding to teach about chemiosmotic theory and protonmotive force in Chapter 14 (Electron Transport and ATP Synthesis). The concept is reinforced in the chapter on photosynthesis. A focus on biology While we emphasize chemistry, we also stress the bio in biochemistry. We point out that biochemical systems evolve and that the reactions that occur in some species are varia- tions on a larger theme. In this edition, we increase our emphasis on the similarities of
  28. 28. PREFACE xxvii prokaryotic and eukaryotic systems while we continue to avoid making generalizations about all organisms based on reactions that occur in a few. The evolutionary, or comparative, approach to teaching biochemistry focuses at- tention on fundamental concepts. The evolutionary approach differs in many ways from other pedagogical methods such as an emphasis on fuel metabolism. The evolu- tionary approach usually begins with a description of simple fundamental principles or pathways or processes. These are often the pathways found in bacteria. As the lesson proceeds, the increasing complexity seen in some other species is explained. At the end of a chapter we are ready to describe the unique features of the process found in com- plex multicellular species, such as humans. Our approach entails additional changes that distinguish us from other textbooks. When introducing a new chapter, such as lipid metabolism, amino acid metabolism, and nucleotide metabolism, most other textbooks begin by treating the molecules as potential food for humans. We start with the biosynthesis pathways since those are the ones fundamental to all organisms. Then we describe the degradation pathways and end with an explanation of how they realte to fuel metabolism. This biosynthesis first or- ganization applies to all the major components of a cell (proteins, nucleotides, nucleic acids, lipids, amino acids) except carbohydrates where we continue to describe glycoly- sis ahead of gluconeogenesis. We do, however, emphasize that gluconeogenesis is the original, primitive pathway and glycolysis evolved later. This has always been the way DNA replication, transcription, and translation have been taught. In this book we extend this successful strategy to all the other topics in bio- chemistry. The chapter on photosynthe sis is an excellent example of how it works in practice. In some cases the emphasis on evolution can lead to a profound appreciation of how complex systems came to exist. Take the citric acid cycle as an example. Students are often told that such a process cannot be the product of evolution because all the parts are needed before the cycle can function. We explain in Section 13.9 how such a pathway can evolve in a stepwise manner. A focus on accuracy We are proud of the fact that this is the most scientifically accurate biochemistry text- book.We have gone to great lengths to ensure that our facts are correct and our explana- tions of basic concepts reflect the modern consensus among active researchers. Our suc- cess is due, in large part, to the dedication of our many reviewers and editors. The emphasis on accuracy means that we check our reactions and our nomencla- ture against the IUPAC/IUBMB databases. The result is balanced reactions with correct products and substrates and correct chemical nomenclature. For example, we are one of the very few textbooks that show all of the citric acid cycle reactions correctly. Previous editions of this textbook have always scored highly on the Biochemical Howlers website [] and we feel confident that this edition will achieve a per- fect score! We take the time and effort to accurately describe some difficult concepts such as Gibbs free energy change in a steady-state situation where most reactions are near- equlibirium reactions (ΔG = 0). We present correct definitions of the Central Dogma of Molecular Biology. We don’t avoid genuine areas of scientific controversy such as the validity of the Three Domain Hypothesis or the mechanism of lysozyme. A focus on structure-function Biochemistry is a three-dimensional science. Our inclusion of the latest computer gen- erated images is intended to clarify the shape and function of molecules and to leave students with an appreciation for the relationship between the structure and function. Many of the protein images in this edition are new; they have been skillfully prepared by Jonathan Parrish of the University of Alberta. We offer a number of other opportunities. For those students with access to a com- puter, we have included Protein Data Bank (PDB) reference numbers for the coordinates
  29. 29. xxviii PREFACE from which all protein images were derived. This allows students to further explore the structures on their own. In addition, we have a gallery of prepared PDB files that stu- dents can view using Chime or any other molecular viewer; these are posted on the text’s TheChemistryPlace® website [] as are animations of key dynamic processes as well as visualization tutorials using Chime. The emphasis on protein/enzyme structure is a key part of the theme of structure- function that is one of the most important concepts in biochemistry. At various places in this new edition we have added material to emphasize this relationship and to develop it to a greater extent than we have in the past. Some of the most important reactions in the cell, such as the Q-cycle, cannot be properly understood without understanding the structure of the enzyme that catalyzes them. Similarly, understanding the properties of double-stranded DNA is essential to understanding how it serves as the storehouse of biological information. Walkthrough of features with some visuals Interests Biochemistry is at the root of a number of related sciences, including medicine, forensic science, biotechnology, and bioengineering; there are many interesting stories to tell. Throughout the text, you will find boxes that relate biochemistry to other topics. Some of them are intended to be humorous and help students relate to the material. BOX 8.1 THE PROBLEM WITH CATS One of the characteristics of sugars is that they taste sweet. You certainly know the taste of sucrose and you probably know that fructose and lactose also taste sweet. So do many of the other sugars and their derivatives, although we don’t recommend that you go into a biochemistry lab and start tasting all the carbohydrates in those white plastic bottles on the shelves. Sweetness is not a physical property of molecules. It’s a subjective interaction between a chemical and taste receptors in your mouth. There are five different kinds of taste recep- tors: sweet, sour, salty, bitter, and umami (umami is like the taste of glutamate in monosodium glutamate). In order to trigger the sweet taste, a molecule like sucrose has to bind to the receptor and initiate a response that eventually makes it to your brain. Sucrose elicits a moderately strong response that serves as the standard for sweetness. The response to fructose is almost twice as strong and the response to lactose is only about one-fifth as strong as that of sucrose. Artificial sweeteners such as saccharin (Sweet’N Low®), sucralose OO O N H Cl Cl Cl HO HO O OOHOH HO NH S O OO O NH2 CH2 CH2 HO CH2 CH2 CH2 CH2 CH2 OCH3 Sucralose Saccharin Aspartame Cats are carnivores. They probably can’t taste sweetness. (Splenda®), and aspartame (NutraSweet®) bind to the sweet- ness receptor and cause the sensation of sweetness. They are hundreds of times more sweet than sucrose. The sweetness receptor is encoded by two genes called Tas1r2 and Tas1r3. We don’t know how sucrose and the other ligands bind to this receptor even though this is a very active area of research. In the case of sucrose and the artifical sweet- eners, how can such different molecules elicit the taste of sweet? Cats, including lions, tigers and cheetahs, do not have a functional Tas1r2 gene. It has been converted to a pseudo- gene because of a 247 bp deletion in exon 3. It’s very likely that your pet cat has never experienced the taste of sweetness. That explains a lot about cats.
  30. 30. PREFACE xxix Key Concepts To help guide students to the information important in each concept, Key Concept notes have been provided in the margin highlighting this information. Complete Explanations of the Chemistry There are thousands of metabolic reactions in a typical organism. You might try to memorize them all but eventually you will run out of memory. What’s more, memo- rization will not help you if you encounter something you haven’t seen before. In this book, we show you some of the basic mechanisms of enzyme-catalyzed reactions—an extension of what you learned in organic chemistry. If you understand the mechanism, you’ll understand the chemistry. You’ll have less to memorize, and you’ll retain the in- formation more effectively. KEY CONCEPT The standard Gibbs free energy change ( G° ) tells us the direction of a reaction when the concentrations of all products and reactants are at 1 M concentration. These conditions will never occur in living cells. Biochemists are only interested in actual Gibbs free energy changes ( G), which are usually close to zero. The standard Gibbs free energy change ( G° ) tells us the relative concentrations of reactants and products when the reaction reaches equilibrium. ¿¢ ¢ ¿¢ His-57 Ser-195 Asp-102 Asp- 102 His-57 Ser-195 CH2 C O O H H O N N CH2 CH2 The distinction between the normal flow of information and the Central Dogma of Molecular Biology is explained in Section 1.1 and the intro- duction to Chapter 21. E site P site A site 5′ 3′ Activity site Catalytic site Specificity site Activity site Catalytic site Specificity site Margin Notes There is a great deal of detail in biochemistry but we want you to see both the forest and the trees. When we need to cross-reference something discussed earlier in the book, or something that we will come back to later, we put it in the margin. Backward references offer a review of concepts you may have forgotten. Forward references will help you see the big picture. Art Biochemistry is a three-dimensional science and we have placed a great emphasis on help- ing you visualize abstract concepts and molecules too small to see. We have tried to make illustrative figures both informative and beautiful. Cytochrome c or Plastocyanin P700 A-branch Ferredoxin or Flavodoxin Phylloquinone e e e e e FB FA Fx hν
  31. 31. xxx PREFACE Sample Calculations Sample Calculations are included throughout the text to provide a problem solving model and illustrate required calculations. SAMPLE CALCULATION 10.2 Gibbs Free Energy Change Q: In a rat hepatocyte, the concentrations of ATP, ADP, and Pi are 3.4 mM, 1.3 mM, and 4.8 mM, respectively. Calculate A: The actual Gibbs free energy change is calculated according to Equation 10.10. When known values and constants are substituted (with concentrations expressed as molar values), assuming pH7.0 and 25°C. The actual free energy change is about 11/2 times the standard free energy change. ¢G = -48000 J mol-1 = -48 kJ mol-1 ¢G = -32000 J mol-1 - 16000 J mol-1 ¢G = -32000 J mol-1 + (2480 J mol-1 )32.303 log(1.8 * 10-3 )4 c2.303 log (1.3 * 10-3 )(4.8 * 10-3 ) (3.4 * 10-3 ) d¢G = -32000 J mol-1 + (8.31 JK-1 mol-1 )(298 K) ¢Greaction = ¢G°¿reaction + RT ln 3ADP43Pi4 3ATP4 = ¢G°reaction + 2.303 RT log 3ADP43Pi4 3ATP4 the Gibbs free energy change for hydrolysis of ATP in this cell. How does this compare to the standard free energy change? The Organization We adopt the metabolism-first strategy of organizing the topics in this book. This means we begin with proteins and enzymes then describe carbohydrates and lipids. This is fol- lowed by a description of intermediary metabolism and bioenergetics. The structure of nucleic acids follows the chapter on nucleotide metabolism and the information flow chapters are at the back of the book. While we believe there are significant advantages to teaching the subjects in this order, we recognize that some instructors prefer to teach information flow earlier in the course. We have tried to make the last four chapters on nucleic acids, DNA replication, transcription, and translation less dependant on the earlier chapters but they do discuss aspects of enzymes that rely on Chapters 4, 5 and 6. Instructors may choose to intro- duce these last four chapters after a description of enzymes if they wish. This book has a chapter on coenzymes unlike most other biochemistry textbooks. We believe that it is important to put more emphasis on the role of coenzymes (and vitamins) and that’s why we have placed this chapter right after the two chapters on en- zymes. We know that most instructors prefer to teach the individual coenzymes when specific examples come up in other contexts. We do that as well. This organization al- lows instructors to refer back to chapter 7 at whatever point they wish. Student Supplements The Study Guide for Principles of Biochemistry by Scott Lefler (Arizona State University) and Allen J. Scism (Central Missouri State University) No student should be without this helpful resource. Contents include the following: • carefully constructed drill problems for each chapter, including short-answer, multiple- choice, and challenge problems • comprehensive, step-by-step solutions and explanations for all problems • a remedial chapter that reviews the general and organic chemistry that students re- quire for biochemistry—topics are ingeniously presented in the context of a metabolic pathway • tables of essential data
  32. 32. PREFACE xxxi Acknowledgments We are grateful to our many talented and thoughtful reviewers who have helped shape this book. Reviewers who helped in the Fifth Edition: Accuracy Reviewers Barry Ganong, Mansfield University Scott Lefler, Arizona State Kathleen Nolta, University of Michigan Content Reviewers Michelle Chang, University of California, Berkeley Kathleen Comely, Providence College Ricky Cox, Murray State University Michel Goldschmidt-Clermont, University of Geneva Phil Klebba, University of Oklahoma, Norman Kristi McQuade, Bradley University Liz Roberts-Kirchoff, University of Detroit, Mercy Ashley Spies, University of Illinois Dylan Taatjes, University of Colorado, Boulder David Tu, Pennsylvania State University Jeff Wilkinson, Mississippi State University Lauren Zapanta, University of Pittsburgh Reviewers who helped in the Fourth Edition: Accuracy Reviewers Neil Haave, University of Alberta David Watt, University of Kentucky Content Reviewers Consuelo Alvarez, Longwood University Marilee Benore Parsons, University of Michigan Gary J. Blomquist, University of Nevada, Reno Albert M. Bobst, University of Cincinnati Kelly Drew, University of Alaska, Fairbanks Andrew Feig, Indiana University Giovanni Gadda, Georgia State University Donna L. Gosnell, Valdosta State University Charles Hardin, North Carolina State University Jane E. Hobson, Kwantlen University College Ramji L. Khandelwal, University of Saskatchewan Scott Lefler, Arizona State Kathleen Nolta, University of Michigan Jeffrey Schineller, Humboldt State University Richard Shingles, Johns Hopkins University Michael A. Sypes, Pennsylvania State University Martin T. Tuck, Ohio University Julio F. Turrens, University of South Alabama David Watt, University of Kentucky James Zimmerman, Clemson University Thank you to J. David Rawn who’s work laid the foundation for this text. We would also like to thank our colleagues who have previously contributed material for particular chapters and whose careful work still inhabits this book: Roy Baker, University of Toronto Roger W. Brownsey, University of British Columbia Willy Kalt, Agriculture Canada Robert K. Murray, University of Toronto Ray Ochs, St. John’s University Morgan Ryan, American Scientist Frances Sharom, University of Guelph Malcolm Watford, Rutgers, The State University of New Jersey Putting this book together was a collaborative effort, and we would like to thank various members of the team who have helped give this project life: Jonathan Parrish, Jay McElroy, Lisa Shoemaker, and the artists of Prentice Hall; Lisa Tarabokjia, Editorial Assistant, Jessica Neumann, Associate Editor, Lisa Pierce, Assistant Editor in charge of supplements, Lauren Layn, Media Editor, Erin Gardner, Marketing Manager; and Wendy Perez, Production Editor. We would also like to thank Jeanne Zalesky, our Executive Editor at Prentice Hall. Finally, we close with an invitation for feedback. Despite our best efforts (and a terrific track record in the previous edi- tions), there are bound to be mistakes in a work of this size. We are committed to making this the best biochemistry text avail- able; please know that all comments are welcome. Laurence A. Moran Marc D. Perry Chemistry Place for Principles of Biochemistry An online student tool that includes 3-D modules to help visualize biochemistry and MediaLabs to investigate important issues related to its particular chapter. Please visit the site at
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  34. 34. xxxiii New problems and solutions for the fifth edition were created by Laurence A. Moran, University of Toronto. The remaining problems were created by Drs. Robert N. Lindquist, San Francisco State University, Marc Perry, and Diane M. De Abreu of the University of Toronto. About the Authors Laurence A. Moran After earning his Ph.D. from Princeton University in 1974, Professor Moran spent four years at the Université de Genève in Switzerland. He has been a member of the Department of Biochemistry at the University of Toronto since 1978, special- izing in molecular biology and molecular evolution. His re- search findings on heat-shock genes have been published in many scholarly journals. ( H. Robert Horton Dr. Horton, who received his Ph.D. from the University of Mis- souri in 1962, is William Neal Reynolds Professor Emeritus and Alumni Distinguished Professor Emeritus in the Department of Biochemistry at North Carolina State University, where he served on the faculty for over 30 years.Most of Professor Horton’s research was in protein and enzyme mechanisms. K. Gray Scrimgeour Professor Scrimgeour received his doctorate from the Univer- sity of Washington in 1961 and was a faculty member at the University of Toronto for over 30 years. He is the author of The Chemistry and Control of Enzymatic Reactions (1977, Aca- demic Press), and his work on enzymatic systems has been published in more than 50 professional journal articles during the past 40 years. From 1984 to 1992, he was editor of the journal Biochemistry and Cell Biology. ( Marc D. Perry After earning his Ph.D. from the University of Toronto in 1988, Dr. Perry trained at the University of Colorado, where he stud- ied sex determination in the nematode C. elegans. In 1994 he returned to the University of Toronto as a faculty member in the Department of Molecular and Medical Genetics. His re- search has focused on developmental genetics, meiosis, and bioinformatics. In 2008 he joined the Ontario Institute for Cancer Research. (
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  36. 36. 1 Top: Adenovirus. Viruses consist of a nucleic acid molecule surrounded by a protein coat. Introduction to Biochemistry Biochemistry is the discipline that uses the principles and language of chemistry to explain biology. Over the past 100 years biochemists have discovered that the same chemical compounds and the same central metabolic processes are found in organisms as distantly related as bacteria, plants, and humans. It is now known that the basic principles of biochemistry are common to all living organisms. Although sci- entists usually concentrate their research efforts on particular organisms, their results can be applied to many other species. Anything found to be true of E. coli must also be true of elephants. —Jacques Monod This book is called Principles of Biochemistry because we will focus on the most im- portant and fundamental concepts of biochemistry—those that are common to most species. Where appropriate, we will point out features that distinguish particular groups of organisms. Many students and researchers are primarily interested in the biochemistry of humans. The causes of disease and the importance of proper nutrition, for example, are fascinating topics in biochemistry. We share these interests and that’s why we in- clude many references to human biochemistry in this textbook. However, we will also try to interest you in the biochemistry of other species. As it turns out, it is often eas- ier to understand basic principles of biochemistry by studying many different species in order to recognize common themes and patterns but a knowledge and appreciation of other species will do more than help you learn biochemistry. It will also help you recognize the fundamental nature of life at the molecular level and the ways in which species are related through evolution from a common ancestor. Perhaps future edi- tions of this book will include chapters on the biochemistry of life on other planets. Until then, we will have to be satisfied with learning about the diverse life on our own planet. We begin this introductory chapter with a few highlights of the history of biochem- istry, followed by short descriptions of the chemical groups and molecules you will en- counter throughout this book. The second half of the chapter is an overview of cell structure in preparation for your study of biochemistry.
  37. 37. 2 CHAPTER 1 Introduction to Biochemistry 1.1 Biochemistry Is a Modern Science Biochemistry has emerged as an independent science only within the past 100 years but the groundwork for the emergence of biochemistry as a modern science was prepared in earlier centuries. The period before 1900 saw rapid advances in the understanding of basic chemical principles such as reaction kinetics and the atomic composition of mol- ecules. Many chemicals produced in living organisms had been identified by the end of the 19th century. Since then, biochemistry has become an organized discipline and bio- chemists have elucidated many of the chemical processes of life. The growth of bio- chemistry and its influence on other disciplines will continue in the 21st century. In 1828, Friedrich Wöhler synthesized the organic compound urea by heating the inorganic compound ammonium cyanate. (1.1) This experiment showed for the first time that compounds found exclusively in living or- ganisms could be synthesized from common inorganic substances. Today we understand that the synthesis and degradation of biological substances obey the same chemical and physical laws as those that predominate outside of biology. No special or “vitalistic” processes are required to explain life at the molecular level. Many scientists date the begin- nings of biochemistry to Wöhler’s synthesis of urea, although it would be another 75 years before the first biochemistry departments were established at universities. Louis Pasteur (1822–1895) is best known as the founder of microbiology and an active promoter of germ theory. But Pasteur also made many contributions to biochem- istry including the discovery of stereoisomers. Two major breakthroughs in the history of biochemistry are especially notable—the discovery of the roles of enzymes as catalysts and the role of nucleic acids as informa- tion-carrying molecules. The very large size of proteins and nucleic acids made their ini- tial characterization difficult using the techniques available in the early part of the 20th century. With the development of modern technology we now know a great deal about how the structures of proteins and nucleic acids are related to their biological functions. The first breakthrough—identification of enzymes as the catalysts of biological re- actions—resulted in part from the research of Eduard Buchner. In 1897 Buchner showed that extracts of yeast cells could catalyze the fermentation of the sugar glucose to alcohol and carbon dioxide. Previously, scientists believed that only living cells could catalyze such complex biological reactions. The nature of biological catalysts was explored by Buchner’s contemporary, Emil Fischer. Fischer studied the catalytic effect of yeast enzymes on the hydrolysis (break- down by water) of sucrose (table sugar). He proposed that during catalysis an enzyme and its reactant, or substrate, combine to form an intermediate compound. He also pro- posed that only a molecule with a suitable structure can serve as a substrate for a given enzyme. Fischer described enzymes as rigid templates, or locks, and substrates as matching keys. Researchers soon realized that almost all the reactions of life are cat- alyzed by enzymes and a modified lock-and-key theory of enzyme action remains a central tenet of modern biochemistry. Another key property of enzyme catalysis is that biological reactions occur much faster than they would without a catalyst. In addition to speeding up the rates of reac- tions, enzyme catalysts produce very high yields with few, if any, by-products. In con- trast, many catalyzed reactions in organic chemistry are considered acceptable with yields of 50% to 60%. Biochemical reactions must be more efficient because by- products can be toxic to cells and their formation would waste precious energy. The mechanisms of catalysis are described in Chapter 5. The last half of the 20th century saw tremendous advances in the area of structural biology, especially the structure of proteins. The first protein structures were solved in the 1950s and 1960s by scientists at Cambridge University (United Kingdom) led by O ‘ NH4(OCN) Heat " H2N¬ C ¬NH2 ᭡ Friedrich Wöhler (1800–1882). Wöhler was one of the founders of biochemistry. By synthe- sizing urea, Wöhler showed that compounds found in living organisms could be made in the laboratory from inorganic substances. ᭡ Some of the apparatus used by Louis Pasteur in his Paris laboratory. ᭡ Eduard Buchner (1860–1917). Buchner was awarded the Nobel Prize in Chemistry in 1907 “for his biochemical researches and his discovery of cell-free fermentation.”
  38. 38. 1.2 The Chemical Elements of Life 3 John C. Kendrew and Max Perutz. Since then, the three-dimensional structures of several thousand different proteins have been determined and our understanding of the com- plex biochemistry of proteins has increased enormously. These rapid advances were made possible by the availability of larger and faster computers and new software that could carry out the many calculations that used to be done by hand using simple calcu- lators. Much of modern biochemistry relies on computers. The second major breakthrough in the history of biochemistry—identification of nucleic acids as information molecules—came a half-century after Buchner’s and Fis- cher’s experiments. In 1944 Oswald Avery, Colin MacLeod, and Maclyn McCarty ex- tracted deoxyribonucleic acid (DNA) from a pathogenic strain of the bacterium Streptococcus pneumoniae and mixed the DNA with a nonpathogenic strain of the same organism. The nonpathogenic strain was permanently transformed into a pathogenic strain. This experiment provided the first conclusive evidence that DNA is the genetic material. In 1953 James D. Watson and Francis H. C. Crick deduced the three-dimen- sional structure of DNA. The structure of DNA immediately suggested to Watson and Crick a method whereby DNA could reproduce itself, or replicate, and thus transmit bi- ological information to succeeding generations. Subsequent research showed that infor- mation encoded in DNA can be transcribed to ribonucleic acid (RNA) and then trans- lated into protein. The study of genetics at the level of nucleic acid molecules is part of the discipline of molecular biology and molecular biology is part of the discipline of biochemistry. In order to understand how nucleic acids store and transmit genetic information, you must understand the structure of nucleic acids and their role in information flow. You will find that much of your study of biochemistry is devoted to considering how en- zymes and nucleic acids are central to the chemistry of life. As Crick predicted in 1958, the normal flow of information from nucleic acid to protein is not reversible. He referred to this unidirectional information flow from nu- cleic acid to protein as the Central Dogma of Molecular Biology. The term “Central Dogma” is often misunderstood. Strictly speaking, it does not refer to the overall flow of information shown in the figure. Instead, it refers to the fact that once information in nucleic acids is transferred to protein it cannot flow backwards from protein to nucleic acids. 1.2 The Chemical Elements of Life Six nonmetallic elements—carbon, hydrogen, nitrogen, oxygen, phosphorus, and sul- fur—account for more than 97% of the weight of most organisms. All these elements can form stable covalent bonds. The relative amounts of these six elements vary among organisms. Water is a major component of cells and accounts for the high percentage (by weight) of oxygen. Carbon is much more abundant in living organisms than in the rest of the universe. On the other hand, some elements, such as silicon, aluminum, and iron, are very common in the Earth’s crust but are present only in trace amounts in cells. In addition to the standard six elements (CHNOPS), there are 23 other elements commonly found in living organisms (Figure 1.1). These include five ions that are essen- tial in all species: calcium potassium , sodium , magnesium and chloride Note that the additional 23 elements account for only 3% of the weight of living organisms. Most of the solid material of cells consists of carbon-containing compounds. The study of such compounds falls into the domain of organic chemistry. A course in or- ganic chemistry is helpful in understanding biochemistry because there is considerable overlap between the two disciplines. Organic chemists are more interested in reactions that take place in the laboratory, whereas biochemists would like to understand how re- actions occur in living cells. Figure 1.2a shows the basic types of organic compounds commonly encountered in biochemistry. Make sure you are familiar with these terms because we will be using them repeatedly in the rest of this book. (Clᮎ ) 1Mg~2+ 2,(Na{)(K{)1Ca~2+ 2, Translation RNA Protein Transcription Replication DNA ᭡ DNA encodes most of the information required in living cells. ᭡ Emil Fischer (1852–1919). Fischer made many contributions to our understanding of the structures and functions of biological molecules. He received the Nobel Prize in Chemistry in 1902 “in recognition of the extraordinary services he has rendered by his work on sugar and purine synthesis.” ᭡ Information flow in molecular biology. The flow of information is normally from DNA to RNA. Some RNAs (messenger RNAs) are translated. Some RNA can be reverse tran- scribed back to DNA but according Crick’s Central Dogma of Molecular Biology the transfer of information from nucleic acid (e.g., mRNA) to protein is irreversible.
  39. 39. 4 CHAPTER 1 Introduction to Biochemistry Biochemical reactions involve specific chemical bonds or parts of molecules called functional groups (Figure 1.2b). We will encounter several common linkages in bio- chemistry (Figure 1.2c). Note that all these linkages consist of several different atoms and individual bonds between atoms. We will learn more about these compounds, functional groups, and linkages throughout this book. Ester and ether linkages are com- mon in fatty acids and lipids. Amide linkages are found in proteins. Phosphate ester and phosphoanhydride linkages occur in nucleotides. An important theme of biochemistry is that the chemical reactions occurring in- side cells are the same kinds of reactions that take place in a chemistry laboratory. The most important difference is that almost all reactions in living cells are catalyzed by en- zymes and thus proceed at very high rates. One of the main goals of this textbook is to explain how enzymes speed up reactions without violating the fundamental reaction mechanisms of organic chemistry. The catalytic efficiency of enzymes can be observed even when the enzymes and re- actants are isolated in a test tube. Researchers often find it useful to distinguish between biochemical reactions that take place in an organism (in vivo) and those that occur under laboratory conditions (in vitro). 1.3 Many Important Macromolecules Are Polymers In addition to numerous small molecules, much of biochemistry deals with very large molecules that we refer to as macromolecules. Biological macromolecules are usually a form of polymer created by joining many smaller organic molecules, or monomers, via condensation (removal of the elements of water). In some cases, such as certain carbo- hydrates, a single monomer is repeated many times; in other cases, such as proteins and nucleic acids, a variety of different monomers is connected in a particular order. Each monomer of a given polymer is added by repeating the same enzyme-catalyzed reaction. (293) 118 (289) 116 (285) 114 117115113 (277) 112109 Mt (268) 108 Hs (265) 107 Bh (264) 104 Rf (261) (272) 111 (269) 110 VIIB VIIIB IB IIBIIIB IVB VB VIB IIA IA IIIA 0 IVA VA VIA VIIA 25 Mn 54.94 26 Fe 55.85 27 Co 58.93 43 Tc (98) 44 Ru 101.1 45 Rh 102.9 75 Re 186.2 76 Os 190.2 77 Ir 192.2 28 Ni 58.69 29 Cu 63.55 30 Zn 65.39 46 Pd 106.4 47 Ag 107.9 48 Cd 112.4 78 Pt 195.1 21 Sc 44.96 22 Ti 47.87 23 V 50.94 39 Y 88.91 40 Zr 91.22 41 Nb 92.91 57 La 138.9 72 Hf 178.5 73 Ta 180.9 24 Cr 52.00 89 Ac (227) 106 Sg (263) 105 Db (262) 20 Ca 40.08 38 Sr 87.62 4 Be 9.012 12 Mg 24.31 56 Ba 137.3 88 Ra (226) 19 K 39.10 37 Rb 85.47 3 Li 6.941 1 H 1.008 11 Na 22.99 55 Cs 132.9 87 Fr (223) 42 Mo 95.94 74 W 183.8 79 Au 197.0 80 Hg 200.6 13 Al 26.98 14 Si 28.09 15 P 30.97 31 Ga 69.72 32 Ge 72.61 33 As 74.92 49 In 114.8 50 Sn 118.7 51 Sb 121.8 81 Tl 204.4 82 Pb 207.2 83 Bi 209.0 16 S 32.07 17 Cl 35.45 18 Ar 39.95 5 B 10.81 2 He 4.003 6 C 12.01 7 N 14.01 8 O 16.00 9 F 19.00 10 Ne 20.18 34 Se 78.96 35 Br 79.90 36 Kr 83.80 52 Te 127.6 53 I 126.9 54 Xe 131.3 84 Po (209) 85 At (210) 86 Rn (222) 90 Th 232.0 58 Ce 140.1 92 U 238.0 91 Pa 231 94 Pu (244) 95 Am (243) 99 Es (252) 103 Lr (262) 101 Md (258) 102 No (259) 100 Fm (257) 98 Cf (251) 97 Bk (247) 96 Cm (247) 93 Np (237) 60 Nd 144.2 59 Pr 140.9 62 Sm 150.4 63 Eu 152.0 67 Ho 164.9 71 Lu 175.0 70 Yb 173.0 69 Tm 168.9 68 Er 167.3 66 Dy 162.5 65 Tb 158.9 64 Gd 157.3 61 Pm (145) ** ** * * ᭡ Figure 1.1 Periodic Table of the Elements. The important elements found in living cells are shown in color. The red elements (CHNOPS) are the six abundant elements. The five essential ions are purple. The trace elements are shown in dark blue (more common) and light blue (less common). KEY CONCEPT More than 97% of the weight of most organisms is made up of only six elements: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur (CHNOPS). KEY CONCEPT Living things obey the standard laws of physics and chemistry. No “vitalistic” force is required to explain life at the molecular level. The synthesis of RNA (transcription) and protein (translation) are described in Chapters 21 and 22, respectively.
  40. 40. 1.3 Many Important Macromolecules Are Polymers 5 Thus, all of the monomers, or residues, in a macromolecule are aligned in the same di- rection and the ends of the macromolecule are chemically distinct. Macromolecules have properties that are very different from those of their con- stituent monomers. For example, starch is a polymer of the sugar glucose but it is not soluble in water and does not taste sweet. Observations such as this have led to the gen- eral principle of the hierarchical organization of life. Each new level of organization re- sults in properties that cannot be predicted solely from those of the previous level. The levels of complexity, in increasing order, are: atoms, molecules, macromolecules, or- ganelles, cells, tissues, organs, and whole organisms. (Note that many species lack one or more of these levels of complexity. Single-celled organisms, for example, do not have tissues and organs.) The following sections briefly describe the principal types of macromolecules and how their sequences of residues or three-dimensional shapes grant them unique properties. (a) Organic compounds O CR OH Carboxylic acid1 Ketone O CR R1 O C HR Aldehyde R OH Alcohol Amines2 R NH Secondary R1 R Tertiary N R2 R1 R Primary NH2R SH Thiol (Sulfhydryl) (b) Functional groups Phosphate O PO O O Phosphoryl O P O O Hydroxyl OH Acyl O C R O C Carbonyl Carboxylate O C O NH2 NH3or AminoSulfhydryl (Thiol) SH (c) Linkages in biochemical compounds Ester O COC Ether COC Amide O CN Phosphoanhydride O PO O O P O OO 1 Under most biological conditions, carboxylic acids exist as carboxylate anions: 2 Under most biological conditions, amines exist as ammonium ions: ,R NH3 R NH R2 R1 R NH2 R1 O C OR Phosphate ester O POC O O and ᭣ Figure 1.2 General formulas of (a) organic compounds, (b) functional groups, and (c) linkages com- mon in biochemistry. R represents an alkyl group 1CH3 ¬1CH22n ¬2.
  41. 41. 6 CHAPTER 1 Introduction to Biochemistry In discussing molecules and macromolecules we will often refer to the molecular weight of a compound.A more precise term for molecular weight is relative molecular mass (abbreviated Mr). It is the mass of a molecule relative to one-twelfth (1/12) the mass of an atom of the carbon isotope 12 C. (The atomic weight of this isotope has been defined as ex- actly 12 atomic mass units. Note that the atomic weight of carbon shown in the Periodic Table represents the average of several different isotopes, including 13 C and 14 C.) Because Mr is a relative quantity, it is dimensionless and has no units associated with its value. The relative molecular mass of a typical protein, for example, is 38,000 The absolute molecular mass of a compound has the same magnitude as the molecular weight except that it is expressed in units called daltons ( mass unit). The molecular mass is also called the molar mass because it represents the mass (meas- ured in grams) of 1 mole, or molecules. The molecular mass of a typical protein is 38,000 daltons, which means that 1 mole weighs 38 kilograms. The main source of confusion is that the term“molecular weight”has become common jargon in biochem- istry although it refers to relative molecular mass and not to weight. It is a common error to give a molecular weight in daltons when it should be dimensionless. In most cases, this isn’t a very important mistake but you should know the correct terminology. A. Proteins Twenty common amino acids are incorporated into proteins in all cells. Each amino acid contains an amino group and a carboxylate group, as well as a side chain (R group) that is unique to each amino acid (Figure 1.3a). The amino group of one amino acid and the carboxylate group of another are condensed during protein synthesis to form an amide linkage, as shown in Figure 1.3b. The bond between the carbon atom of one amino acid residue and the nitrogen atom of the next residue is called a peptide bond. The end-to-end joining of many amino acids forms a linear polypeptide that may con- tain hundreds of amino acid residues. A functional protein can be a single polypeptide or it can consist of several distinct polypeptide chains that are tightly bound to form a more complex structure. Many proteins function as enzymes. Others are structural components of cells and organisms. Linear polypeptides fold into a distinct three-dimensional shape. This shape is determined largely by the sequence of its amino acid residues. This sequence infor- mation is encoded in the gene for the protein. The function of a protein depends on its three-dimensional structure, or conformation. The structures of many proteins have been determined and several principles gov- erning the relationship between structure and function have become clear. For example, many enzymes contain a cleft, or groove, that binds the substrates of a reaction. This cavity contains the active site of the enzyme—the region where the chemical reaction takes place. Figure 1.4a shows the structure of the enzyme lysozyme that catalyzes the hydrolysis of specific carbohydrate polymers. Figure 1.4b shows the structure of the en- zyme with the substrate bound in the cleft. We will discuss the relationship between protein structure and function in Chapters 4 and 6. There are many ways of representing the three-dimensional structures of biopoly- mers such as proteins. The lysozyme molecule in Figure 1.4 is shown as a cartoon where the conformation of the polypeptide chain is represented as a combination of wires, helical ribbons, and broad arrows. Other kinds of representations in the following chap- ters include images that show the position of every atom. Computer programs that cre- ate these images are freely available on the Internet and the structural data for proteins can be retrieved from a number of database sites. With a little practice, any student can view these molecules on a computer monitor. B. Polysaccharides Carbohydrates, or saccharides, are composed primarily of carbon, oxygen, and hydro- gen. This group of compounds includes simple sugars (monosaccharides) as well as their polymers (polysaccharides). All monosaccharides and all residues of polysaccha- rides contain several hydroxyl groups and are therefore polyalcohols. The most com- mon monosaccharides contain either five or six carbon atoms. 6.022 * 1023 1 dalton = 1 atomic (Mr = 38,000). The relative molecular mass (Mr) of a molecule is a dimensionless quantity referring to the mass of a molecule rel- ative to one-twelfth (1/12) the mass of an atom of the carbon isotope 12 C. Molecular weight (M.W.) is another term for relative molecular mass. (b) H3 N C COOCH O N CH H H3 N C H R R R COO(a) ᭡ Figure 1.3 Structure of an amino acid and a dipeptide. (a) Amino acids contain an amino group (blue) and a carboxylate group (red). Differ- ent amino acids contain different side chains (designated R). (b) A dipeptide is pro- duced when the amino group of one amino acid reacts with the carboxylate group of an- other to form a peptide bond (red). ¬ KEY CONCEPT Biochemical molecules are three-dimensional objects.
  42. 42. 1.3 Many Important Macromolecules Are Polymers 7 Sugar structures can be represented in several ways. For example, ribose (the most common five-carbon sugar) can be shown as a linear molecule containing four hydroxyl groups and one aldehyde group (Figure 1.5a). This linear representation is called a Fis- cher projection (after Emil Fischer). In its usual biochemical form, however, the struc- ture of ribose is a ring with a covalent bond between the carbon of the aldehyde group (C-1) and the oxygen of the C-4 hydroxyl group, as shown in Figure 1.5b. The ring form is most commonly shown as a Haworth projection (Figure 1.5c). This representation is a more accurate way of depicting the actual structure of ribose. The Haworth projection is rotated 90° with respect to the Fischer projection and portrays the carbohydrate ring as a plane with one edge projecting out of the page (represented by the thick lines). However, the ring is not actually planar. It can adopt numerous conformations in which certain ring atoms are out-of-plane. In Figure 1.5d, for example, the C-2 atom of ribose lies above the plane formed by the rest of the ring atoms. Some conformations are more stable than others so the majority of ribose mole- cules can be represented by one or two of the many possible conformations. Neverthe- less, it’s important to note that most biochemical molecules exist as a collection of structures with different conformations. The change from one conformation to another does not require the breaking of any covalent bonds. In contrast, the two basic forms of carbohydrate structures, linear and ring forms, do require the breaking and forming of covalent bonds. Glucose is the most abundant six-carbon sugar (Figure 1.6a on page 8). It is the monomeric unit of cellulose, a structural polysaccharide, and of glycogen and starch, which are storage polysaccharides. In these polysaccharides, each glucose residue is joined covalently to the next by a covalent bond between C-1 of one glucose molecule and one of the hydroxyl groups of another. This bond is called a glycosidic bond. In cel- lulose, C-1 of each glucose residue is joined to the C-4 hydroxyl group of the next residue (Figure 1.6b). The hydroxyl groups on adjacent chains of cellulose interact non- covalently creating strong, insoluble fibers. Cellulose is probably the most abundant biopolymer on Earth because it is a major component of flowering plant stems includ- ing tree trunks. We will discuss carbohydrates further in Chapter 8. C. Nucleic Acids Nucleic acids are large macromolecules composed of monomers called nucleotides. The term polynucleotide is a more accurate description of a single molecule of nucleic acid, just as polypeptide is a more accurate term than protein for single molecules composed of amino acid residues. The term nucleic acid refers to the fact that these polynu- cleotides were first detected as acidic molecules in the nucleus of eukaryotic cells. We (a) (b) ᭡ Figure 1.4 Chicken (Gallus gallus) eggwhite lysozyme. (a) Free lysozyme. Note the char- acteristic cleft that includes the active site of the enzyme. (b) Lysozyme with bound substrate. [PDB 1LZC]. The rules for drawing a molecule as a Fischer projection are described in Section 8.1. Conformations of monosaccharides are described in more detail in Section 8.3. OH CH2OH CH C O H C OHCH 1 2 3 4 5 OHH (a) HOCH2 OH H H H OH OHO H 1 3 4 5 2 (c)(b) Fischer projection (ring form) O HO OH CH2OH CH C H C CH 1 2 3 4 5 OHH Envelope conformation H H H HOH 1 2 3 4 OHHOCH2 5 HO O (d) Fischer projection (open-chain form) Haworth projection ᭡ Figure 1.5 Representations of the structure of ribose. (a) In the Fischer projection, ribose is drawn as a linear molecule. (b) In its usual biochemical form, the ribose molecule is in a ring, shown here as a Fischer projection. (c) In a Haworth projection, the ring is depicted as lying per- pendicular to the page (as indicated by the thick lines, which represent the bonds closest to the viewer). (d) The ring of ribose is not actually planar but can adopt 20 possible conformations in which certain ring atoms are out-of-plane. In the conformation shown, C-2 lies above the plane formed by the rest of the ring atoms.
  43. 43. 8 CHAPTER 1 Introduction to Biochemistry now know that nucleic acids are not confined to the eukaryotic nucleus but are abun- dant in the cytoplasm and in prokaryotes that don’t have a nucleus. Nucleotides consist of a five-carbon sugar, a heterocyclic nitrogenous base, and at least one phosphate group. In ribonucleotides, the sugar is ribose; in deoxyribonu- cleotides, it is the derivative deoxyribose (Figure 1.7). The nitrogenous bases of nu- cleotides belong to two families known as purines and pyrimidines. The major purines are adenine (A) and guanine (G); the major pyrimidines are cytosine (C), thymine (T), and uracil (U). In a nucleotide, the base is joined to C-1 of the sugar, and the phosphate group is attached to one of the other sugar carbons (usually C-5). The structure of the nucleotide adenosine triphosphate (ATP) is shown in Figure 1.8. ATP consists of an adenine moiety linked to ribose by a glycosidic bond. There are three phosphoryl groups (designated and ) esterified to the C-5 hydroxyl group of the ri- bose. The linkage between ribose and the group is a phosphoester linkage because it includes a carbon and a phosphorus atom, whereas the and -phosphoryl groups in ATP are connected by phosphoanhydride linkages that don’t involve carbon atoms (see Figure 1.2). All phosphoanhydrides possess considerable chemical potential energy and ATP is no exception. It is the central carrier of energy in living cells. The potential energy associated with the hydrolysis of ATP can be used directly in biochemical reactions or coupled to a reaction in a less obvious way. In polynucleotides, the phosphate group of one nucleotide is covalently linked to the C-3 oxygen atom of the sugar of another nucleotide creating a second phosphoester linkage. The entire linkage between the carbons of adjacent nucleotides is called a phos- phodiester linkage because it contains two phosphoester linkages (Figure 1.9). Nucleic acids contain many nucleotide residues and are characterized by a backbone consisting of alternating sugars and phosphates. In DNA, the bases of two different polynucleotide strands interact to form a helical structure. There are several ways of depicting nucleic acid structures depending on which fea- tures are being described. The ball-and-stick model shown in Figure 1.10 is ideal for show- ing the individual atoms and the ring structure of the sugars and the bases. In this case, the gb- a-phosphoryl ga, b, (a) OH 4 6 5 1 23 HO H H HOH H OH CH2OH H O (b) 23 5 6 H H HOH H H OH CH2OH 14 O H H OH H H OH H 6 CH2OH OO H H HOH H H OH CH2OH 4 23 5 6 1 O 14 23 5 O O O Figure 1.6 ᭤ Glucose and cellulose. (a) Haworth projection of glucose. (b) Cellulose, a linear polymer of glucose residues. Each residue is joined to the next by a glycosidic bond (red). The structures of nucleic acids are described in Chapter 19. HOCH2 OH H H H H OHO H 1 3 4 5 2 Figure 1.8 ᭤ Structure of adenosine triphosphate (ATP). The nitrogenous base adenine (blue) is attached to ribose (black). Three phosphoryl groups (red) are also bound to the ribose. ᭡ Figure 1.7 Deoxyribose, the sugar found in deoxyribonu- cleotides. Deoxyribose lacks a hydroxyl group at C-2. H H H H O CH2 OH O OH POPOP OOO O O O O NH2 N N N N γ β α The role of ATP in biochemical reac- tions is described in Section 10.7.
  44. 44. 1.3 Many Important Macromolecules are Polymers 9 two helices can be traced by following the sugar–phosphate backbone emphasized by the presence of the purple phosphorus atoms surrounded by four red oxygen atoms. The individual base pairs are viewed edge-on in the interior of the molecule. We will see several other DNA models in Chapter 19. RNA contains ribose rather than deoxyribose and it is usually a single-stranded polynucleotide. There are four different kinds of RNA molecules. Messenger RNA (mRNA) is involved directly in the transfer of information from DNA to protein. Transfer RNA (tRNA) is a smaller molecule required for protein synthesis. Ribosomal RNA (rRNA) is the major component of ribosomes. Cells also contain a heterogeneous class of small RNAs that carry out a variety of different functions. In Chapters 19 to 22, we will see how these RNA molecules differ and how their structures reflect their biological roles. D. Lipids and Membranes The term “lipid” refers to a diverse class of molecules that are rich in carbon and hydro- gen but contain relatively few oxygen atoms. Most lipids are not soluble in water but they do dissolve in some organic solvents. Lipids often have a polar, hydrophilic (water- loving) head and a nonpolar, hydrophobic (water-fearing) tail (Figure 1.11). In an aque- ous environment, the hydrophobic tails of such lipids associate while the hydrophobic heads are exposed to water, producing a sheet called a lipid bilayer. Lipid bilayers form the structural basis of all biological membranes. Membranes separate cells or compartments within cells from their environments by acting as barriers that are impermeable to most water-soluble compounds. Membranes are flexible because lipid bilayers are stabilized by noncovalent forces. The simplest lipids are fatty acids—these are long-chain hydrocarbons with a car- boxylate group at one end. Fatty acids are commonly found as part of larger molecules called glycerophospholipids consisting of glycerol 3-phosphate and two fatty acyl groups (Figure 1.12 on the next page). Glycerophospholipids are major components of biological membranes. Other kinds of lipids include steroids and waxes. Steroids are molecules like choles- terol and many sex hormones. Waxes are common in plants and animals but perhaps the most familiar examples are beeswax and the wax that forms in your ears. Membranes are among the largest and most complex cellular structures. Strictly speaking, membranes are aggregates, not polymers. However, the association of lipid molecules with each other creates structures that exhibit properties not shown by indi- vidual component molecules. Their insolubility in water and the flexibility of lipid ag- gregates give biological membranes many of their characteristics. Thymine (T) Adenine (A) 2 4 5 6 H3C O O 3NH 1 N 24 5 6 8 NH2 9 1 3 N N N N 7 5′CH2 O P O OPhosphodiester linkage O H H H H H O H H H H 1′ 2′3′ 4′ 5′ O CH2 O P O 1′ 2′3′ 4′ OH H O O ᭣ Figure 1.9 Structure of a dinucleotide. One deoxyribonu- cleotide residue contains the pyrimidine thymine (top), and the other contains the purine adenine (bottom). The residues are joined by a phosphodiester linkage between the two deoxyribose moieties. (The carbon atoms of deoxyribose are numbered with primes to distinguish them from the atoms of the bases thymine and adenine.) ᭡ Figure 1.10 Short segment of a DNA molecule. Two differ- ent polynucleotides associate to form a double helix. The sequence of base pairs on the inside of the helix carries genetic information. Hydrophobic interactions are discussed in Chapter 2. Polar head (hydrophilic) Nonpolar tail (hydrophobic) ᭡ Figure 1.11 Model of a membrane lipid. The molecule consists of a polar head (blue) and a nonpo- lar tail (yellow).
  45. 45. 10 CHAPTER 1 Introduction to Biochemistry Biological membranes also contain proteins as shown in Figure 1.13. Some of these membrane proteins serve as channels for the entry of nutrients and the exit of wastes. Other proteins catalyze reactions that occur specifically at the membrane surface. They are the sites of many important biochemical reactions. We will discuss lipids and bio- logical membranes in greater detail in Chapter 9. 1.4 The Energetics of Life The activities of living organisms do not depend solely on the biomolecules described in the preceding section and on the multitude of smaller molecules and ions found in cells. Life also requires the input of energy. Living organisms are constantly transform- ing energy into useful work to sustain themselves, to grow, and to reproduce. Almost all this energy is ultimately supplied by the sun. CO C O Fatty acyl groups Glycerophospholipid X 1 32 CH2 P O O O HO OH H2C O CH CH2 1 32 P O O O H2C O O O CH (a) Glycerol 3-phosphate (b) Figure 1.12 ᭤ Structures of glycerol 3-phosphate and a glyc- erophospholipid. (a) The phosphate group of glycerol 3-phosphate is polar. (b) In a glyc- erophospholipid, two nonpolar fatty acid chains are bound to glycerol 3-phosphate through ester linkages. X represents a sub- stituent of the phosphate group. Proteins Lipid bilayer ᭡ Figure 1.13 General structure of a biological membrane. Biological membranes consist of a lipid bilayer with as- sociated proteins. The hydrophobic tails of individual lipid molecules associate to form the core of the membrane. The hydrophilic heads are in contact with the aqueous medium on either side of the membrane. Most membrane proteins span the lipid bilayer; others are attached to the mem- brane surface in various ways. KEY CONCEPT Most of the energy required for life is supplied by light from the sun.