Biochemistry. Trudy McKee. James R. McKee THE MOLECULAR BASIS OF LIFE FIFTH EDITION. Oxford. New York OXFORD UNIVERSITY PRESS

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1 THE MOLECULAR BASIS OF LIFE FIFTH EDITION Trudy McKee James R. McKee New York Oxford OXFORD UNIVERSITY PRESS

2 Contents Preface xxi 1 : An Introduction 1 Life: It Is a Mystery! What is Life? Biomolecules 7 Functional Groups of Organic Biomolecules 7 Major Classes of Small Biomolecules Is the Living Cell a Chemical Factory? 15 Biochemical Reactions 16 Energy 19 Overview of Metabolism 20 Biological Order Systems Biology 22 Emergence 23 Robustness 23 Modularity 24 An Introduction 25 Chapter Summary 25 Suggested Readings 26 Keywords 26 Review Questions 2? Thought Questions 29 2 Living Cells 31 Our Bodies, Our Selves Basic Themes 34 Water 34 Biological Membranes 35 Self-Assembly 35 Molecular Machines 36 Macromolecular Crowding 37 Signal Transduction Structure of Prokaryotic Celts 38 Cell Wall 38 Plasma Membrane 40 Cytoplasm 41 Pili and Flagella Structure of Eukaryotic Cells 42 Plasma Membrane 4Z Endoplasmic Reticulum 45 Golgi Apparatus 46 Nucleus 47 Vesicular Organelles 50 Mitochondria 53 Peroxisomes 55 Plastids 56 Cytoskeleton 57 Ribosomes 61 Primary Cilia and Human Disease 62 CeU Technology 63 Organelles and Human Disease Chapter Summary 65 Suggested Readings 66 KeyWords 66 Review Questions 66 Thought Questions 68 3 Water: The Matrix of Life 69 Water, Water, Everywhere Molecular Structure of Water Noncovalent Bonding 73 Ionic Interactions 74 Hydrogen Bonds 74 Van der Waals Forces Thermal Properties of Water Solvent Properties of Water 78 Hydrophilic Molecules, Cell Water Structuring, and Sol-Gel Transitions 78 Hydrophobic Molecules and the Hydrophobic Effect Amphipathic Molecules 81 Osmotic Pressure Ionization of Water 86 Acids, Bases, and ph 86 Buffers 88 Physiological Buffers 94 Cell Volume Regulation and Metabolism % Water, Abiotic Stress, and Compatible Solutes Dialysis XV

3 xvi Contents Chapter Summary 97 Suggested Readings 98 Keywords 98 Review Questions 98 Thought Questions Energy 101 Energy and Life's Deep, Dark Secrets Thermodynamics 104 First Law of Thermodynamics 105 Second Law of Thermodynamics Free Energy 109 Standard Free Energy Changes 110 Coupled Reactions 111 The Hydrophobic Effect Revisited The Role of ATP 115 Protein Technology 173 Protein Poisons Protein Folding and Human Disease Myosin: A Molecular Machine Protein Sequence Analysis: The Edman Degradation Chapter Summary 178 Suggested Readings 178 Keywords 179 Review Questions 179 Thought Questions 180 Nonequilibrium Thermodynamics and the Evolution of Life The Extremophiles: Organisms That Make a Living in Hostile Environments Chapter Summary 119 Suggested Readings 119 Keywords 119 Review Questions 120 Thought Questions 121 Amino Acids, Peptides, and Proteins 123 Spider Silk: A Biosteel Protein Amino Acids 125 Amino Acid Classes 127 Biologically Active Amino Acids 129 Modified Amino Acids in Proteins 130 Amino Acid Stereoisomers 130 Titration of Amino Acids 131 Amino Acid Reactions Peptides Proteins 141 Protein Structure 142 The Folding Problem 157 Fibrous Proteins 160 Globular Proteins Molecular Machines 168 Motor Proteins 169 in perspective Spider Silk and Biomimetics 170 1U 6 Enzymes 182 Humans and Enzymes: A Brief History Properties of Enzymes Classification of Enzymes Enzyme Kinetics 190 Michaelis-Menten Kinetics 192 Lineweaver-Burk Plots 194 Multisubstrate Reactions 195 Enzyme Inhibition 196 Enzyme Kinetics, Metabolism, and Macromolecular Crowding Catalysis 203 Organic Reactions and the Transition State 203 Catalytic Mechanisms 204 The Roles of Amino Acids in Enzyme Catalysis 207 The Role of Cofactors in Enzyme Catalysis 208 Effects of Temperature and ph on Enzyme-Catalyzed Reactions 210 Detailed Mechanisms of Enzyme Catalysis Enzyme Regulation 213 Genetic Control 215 Covalent Modification 215 Allosteric Regulation 216 Compartmentation 218 Alcohol Dehydrogenase: A Tale of Two Species 220 Enzymes and Clinical Medicine Quantum Tunneling and Catalysis

4 Contents xvii Chapter Summary 221 Suggested Readings 222 Keywords 222 Review Questions 222 Thought Questions 224 $$M3 7 Carbohydrates 226 Sweet and Bitter Taste-. The Roles of Sugar Molecules Monosaccharides 228 Monosaccharide Stereoisomers 229 Cyclic Structure of Monosaccharides 229 Reactions of Monosaccharides 232 Important Monosaccharides 238 Monosaccharide Derivatives 7.2 Disaccharides Polysaccharides 242 Homoglycans 242 Heteroglycans Glycoconjugates 248 Proteoglycans 248 Glycoproteins The Sugar Code D Lectins: Translators of the Sugar Code 252 TheGlycome 253 Glycomics 254 Scurvy and Ascorbic Acid Sweet Medicine Conversion of Fischer Structures into Haworth Structures Chapter Summary 255 Suggested Readings 255 Keywords 256 Review Questions 256 Thought Questions Gluconeogenesis 277 Gluconeogenesis Reactions 277 Gluconeogenesis Substrates 282 Gluconeogenesis Regulation The Pentose Phosphate Pathway Metabolism of Other Important Sugars 289 Fructose Metabolism Glycogen Metabolism 291 Glycogenesis 291 Glycogenolysis 294 Regulation of Glycogen Metabolism 295 Saccharomyces cerevisiaemi the Crabtree Effect Turbo Design Can Be Dangerous 279 Fermentation: An Ancient Heritage Chapter Summary 299 Suggested Readings 299 Keywords 299 Review Questions 300 Thought Questions 301 Aerobic Metabolism I: Acid Cycle The Citric Oxygen and Evolution: Chance and Necessity Oxidation-Reduction Reactions 305 Redox Coenzymes 308 Aerobic Metabolism Citric Acid Cycle 312 Conversion of Pyruvate to Acetyl-CoA 314 Reactions of the Citric Acid Cycle 317 Fate of Carbon Atoms in the Citric Acid Cycle 321 The Amphibolic Citric Acid Cycle 321 Citric Acid Cycle Regulation 323 The Citric Acid Cycle and Human Disease 326 The Glyoxylate Cycle 327 The Evolutionary History of the Citric Acid Cycle Carbohydrate Metabolism 259 Metabolism and Jet Engines Glycolysis 261 The Reactions of the Glycolytic Pathway 264 The Fates of Pyruvate 270 The Energetics of Glycolysis 272 Regulation of Glycolysis 274 Hans Krebs and the CitricAcid Cycle Chapter Summary 330 Suggested Readings 331 Keywords 331 Review Questions 331 Thought Questions 332

5 xviii Contents 10 Aerobic Metabolism II: Electron 12 Transport Phosphorylation 334 and Oxidative Oxygen: A Molecular Paradox Electron Transport 336 Electron Transport and Its Components 336 Electron Transport: The Fluid-State and Solid-State Models 343 Electron Transport Inhibitors Oxidative Phosphorylation 344 The Chemiosmotic Theory 344 ATP Synthesis 347 Control of Oxidative Phosphorylation 348 The Complete Oxidation of Glucose 349 Uncoupled Electron Transport Oxygen, Cell Function, and Oxidative Stress 353 Reactive Oxygen Species 354 Antioxidant Enzyme Systems 359 Antioxidant Molecules 361 Myocardial Infarct: Ischemia and Reperfusion 364 Glucose-6-Phosphate Dehydrogenase Deficiency Chapter Summary 365 Suggested Readings 365 Keywords 365 Review Questions 366 Thought Questions JLo 11 Lipids and Membranes 369 The Low-Fat Diet Lipid Classes 371 Fatty Acids 371 The Eicosanoids 374 Triacylglycerols 377 Wax Esters 378 Phospholipids 378 Phospholipases 382 Sphingolipids 382 Sphingolipid Storage Diseases Isoprenoids 385 Lipoproteins Membranes 391 Membrane Structure 392 Membrane Function 398 Botulism and Membrane Fusion 405 Chapter Summary 406 Suggested Readings 407 Keywords 407 Review Questions 407 Thought Questions 409 Lipid Metabolism 410 Abetalipoproteinemia Fatty Acids, Triacylglycerols, and the Lipoprotein Pathways Glyceroneogenesis and the TG Cycle 414 Fatty Acid Degradation 418 The Complete Oxidation of a Fatty Acid 422 Fatty Acid Oxidation: Double Bonds and Odd Chains 424 Fatty Acid Biosynthesis 427 Regulation of Fatty Acid Metabolism in Mammals 435 Lipoprotein Metabolism: The Endogenous Pathway Membrane Lipid Metabolism 439 Phospholipid Metabolism 439 Sphingolipid Metabolism Isoprenoid Metabolism 442 Cholesterol Metabolism 442 The Cholesterol Biosynthetic Pathway and Drug Therapy 453 Atherosclerosis 440 Biotransformation 454 Chapter Summary 456 Suggested Readings 456 Keywords 457 Review Questions 457 Thought Questions 459 Photosynthesis 460 Climate Change, Renewable Energy, and Photosynthesis Chlorophyll and Chloroplasts Light Light Reactions 472 Photosystem II and Water Oxidation 474 Photosystem I and NADPH Synthesis 476 Photophosphorylation The Light-Independent Reactions 479 The Calvin Cycle 479 Photorespiration 483 Alternatives to C3 Metabolism Regulation of Photosynthesis 486 Light Control of Photosynthesis 487 Control of Ribulose-1,5-Bisphosphate Carboxylase 488 Photosynthesis in the Deep 490 Starch and Sucrose Metabolism Photosynthetic Studies

6 Contents xix Chapter Summary 490 Suggested Readings 491 Keywords 491 Review Questions 491 Thought Questions Amino Acid Catabolism 544 Deamination 544 Urea Synthesis 545 Control of the Urea Cycle 548 Catabolism of Amino Acid Carbon Skeletons Neurotransmitter Degradation 559 Nitrogen Metabolism I: Synthesis 494 Nitrogen and the Gulf of Mexico Dead Zone 495 H.I Nitrogen Fixation 497 The Nitrogen Fixation Reaction 497 Nitrogen Assimilation Amino Acid Biosynthesis 500 Amino Acid Metabolism Overview 500 Reactions of Amino Groups 502 Synthesis of the Amino Acids Biosynthetic Reactions Involving Amino Acids 512 One-Carbon Metabolism 513 Glutathione 518 Neurotransmitters 519 Nucleotides 524 Heme 533 Gasotransmitters 522 The Amine Neurotransmitters Parkinson's Disease and Dopamine Heme and Chlorophyll Biosynthesis The Essential Amino Acids The Nucleotides: IMP Biosynthesis Lead Poisoning Chapter Summary 534 Suggested Readings 534 Keywords 534 Review Questions 535 Thought Questions 536 Nitrogen Metabolism II: Degradation 538 Degradative Pathways and Human Disorders Protein Turnover 540 Ubiquitin Proteasomal System 541 Autophagy-Lysosomal System Nucleotide Degradation 559 Purine Catabolism 560 Pyrimidine Catabolism 562 in perspective Disorders of Amino Acid Catabolism 558 Hyperammonemia Gout Heme Biotransformation Chapter Summary 564 Suggested Readings 564 Keywords 564 Review Questions 565 Thought Questions Integration of Metabolism 568 Hypertension and Uric Acid: A Diet Connection? Overview of Metabolism Hormones and Intercellular Communication 572 Peptide Hormones 572 Growth Factors 580 Steroid and Thyroid Hormone Mechanisms Metabolism in the Mammalian Body: Division of Labor 584 Gastrointestinal Tract 535 Liver 585 Muscle 586 Adipose Tissue 586 Brain 586 Kidney The Feeding-Fasting Cycle 587 The Feeding Phase 587 The Fasting Phase 590 Feeding Behavior 591 Diabetes MeUitus 581 Obesity and the Metabolic Syndrome 594 Mammalian Hormones and the Hormone Cascade System Chapter Summary 595 Suggested Readings 596

7 xx Contents Keywords 596 Review Questions 596 Thought Questions Nucleic Acids 599 What Makes Us Human? DNA 604 DNA Structure: The Nature of Mutation 607 DNA Structure: The Genetic Material 611 DNA Structure: Variations on a Theme 613 DNA Supercoiling 616 Chromosomes and Chromatin 617 Genome Structure RNA 626 Transfer RNA 629 Ribosomal RNA 636 Messenger RNA 637 Noncoding RNA Viruses 639 Bacteriophage T4: A Viral Lifestyle 640 Epigenetics and the Epigename: Genetic Inheritance beyond DNABase Sequences 62? Nucleic Acid Methods 630 Forensic Investigations 635 HIV Infection 642 A Short History of DNA Research: The Early Years Chapter Summary 615 Suggested Readings 646 Keywords 646 Review Questions 646 Thought Questions Genetic Information 649 DNA and Chimeras: A Biological and Legal Mystery Genetic Information: Replication, Repair, and Recombination 652 DNA Replication 653 DNA Repair 662 Direct Repairs 664 DNA Recombination Transcription 683 Transcription in Prokaryotes 683 RNAP and the Prokaryotic Transcription Process 684 Transcription in Eukaryotes Gene Expression 693 Gene Expression in Prokaryotes 695 Gene Expression in Eukaryotes 697 Genomics 676 in the lab Carcinogenesis 705 Chapter Summary 707 Suggested Readings 708 Keywords 708 Review Questions 709 Thought Questions Protein Synthesis 712 MRSA: The Superbug The Genetic Code 715 Codon Usage Bias 716 Codon-Anticodon Interactions 717 The Aminoacyl-tRNA Synthetase Reaction Protein Synthesis 720 Prokaryotic Protein Synthesis 723 Eukaryotic Protein Synthesis 729 Trapped RibDsomes: RNA to the Rescue! 730 Context-Dependent Coding Reassignment 737 Proteomics 748 in the lab EF-Tu: A Motor Protein Chapter Summary 749 Suggested Readings 750 Keywords 750 Review Questions 750 Thought Questions 752 in perspective Appendix: Solutions A-1 Glossary G-1 Credits C-1 Index 1-1

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