Biochemistry, 4th Edition

Front Cover......Page 1
Title Page......Page 5
Copyright......Page 6
Preface......Page 9
Brief Contents......Page 14
Contents......Page 15
Guide to Media Resources......Page 18
PART I: INTRODUCTION AND BACKGROUND......Page 31
1. Prokaryotes......Page 33
2. Eukaryotes......Page 36
3. Biochemistry: A Prologue......Page 44
4. Genetics: A Review......Page 49
5. The Origin of Life......Page 58
6. The Biochemical Literature......Page 64
1. Properties of Water......Page 70
2. Acids, Bases, and Buffers......Page 75
1. First Law of Thermodynamics: Energy Is Conserved......Page 82
2. Second Law of Thermodynamics: The Universe Tends Toward Maximum Disorder......Page 84
3. Free Energy: The Indicator of Spontaneity......Page 87
4. Chemical Equilibria......Page 88
APPENDIX: Concentration Dependence of Free Energy......Page 91
PART II: BIOMOLECULES......Page 95
1. The Amino Acids of Proteins......Page 97
2. Optical Activity......Page 103
3. “Nonstandard” Amino Acids......Page 108
1. Nucleotides and Nucleic Acids......Page 112
2. DNA Is the Carrier of Genetic Information......Page 115
3. Double Helical DNA......Page 118
4. Gene Expression and Replication: An Overview......Page 125
5. Molecular Cloning......Page 134
1. Protein Isolation......Page 159
2. Solubilities of Proteins......Page 163
3. Chromatographic Separations......Page 165
4. Electrophoresis......Page 176
5. Ultracentrifugation......Page 182
6. Nucleic Acid Fractionation......Page 186
CHAPTER 7 Covalent Structures of Proteins and Nucleic Acids......Page 193
1. Primary Structure Determination of Proteins......Page 194
2. Nucleic Acid Sequencing......Page 206
3. Chemical Evolution......Page 215
4. Bioinformatics: An Introduction......Page 224
5. Chemical Synthesis of Polypeptides......Page 235
6. Chemical Synthesis of Oligonucleotides......Page 239
1. Secondary Structure......Page 251
2. Fibrous Proteins......Page 262
3. Globular Proteins......Page 271
4. Protein Stability......Page 289
5. Quaternary Structure......Page 296
APPENDIX: Viewing Stereo Pictures......Page 301
1. Protein Folding: Theory and Experiment......Page 308
2. Folding Accessory Proteins......Page 320
3. Protein Structure Prediction and Design......Page 332
4. Protein Dynamics......Page 336
5 CONFORMATIONAL DISEASES:AMYLOID AND PRIONS......Page 339
6. Structural Evolution......Page 346
1. Hemoglobin and Myoglobin Function......Page 353
2. Structure and Mechanism......Page 361
3. Abnormal Hemoglobins......Page 371
4. Allosteric Regulation......Page 377
APPENDIX: Derivations\n of Symmetry Model Equations......Page 384
1. Monosaccharides......Page 389
2. Polysaccharides......Page 395
3. Glycoproteins......Page 403
1. Lipid Classification......Page 416
2. Properties of Lipid Aggregates......Page 423
3. Biological Membranes......Page 429
4. Membrane Assembly and Protein Targeting......Page 448
5. Lipoproteins......Page 479
PART III: MECHANISMS OF ENZYME ACTION......Page 497
1. Historical Perspective......Page 499
2. Substrate Specificity......Page 500
3. Coenzymes......Page 503
4. Regulation of Enzymatic Activity......Page 504
5. A Primer of Enzyme Nomenclature......Page 509
1. Chemical Kinetics......Page 512
2. Enzyme Kinetics......Page 517
3. Inhibition......Page 522
4. Effects of pH......Page 526
5. Bisubstrate Reactions......Page 527
APPENDIX: Derivations of Michaelis–Menten Equation Variants......Page 531
1. Catalytic Mechanisms......Page 536
2. Lysozyme......Page 547
3. Serine Proteases......Page 555
4. Drug Design......Page 569
PART IV: METABOLISM......Page 587
1. Metabolic Pathways......Page 589
2. Organic Reaction Mechanisms......Page 592
3. Experimental Approaches to the Study of Metabolism......Page 599
4. Thermodynamics of Phosphate Compounds......Page 608
5. Oxidation–Reduction Reactions......Page 613
6. Thermodynamics of Life......Page 616
1. The Glycolytic Pathway......Page 623
2. The Reactions of Glycolysis......Page 625
3. Fermentation: The Anaerobic Fate of Pyruvate......Page 644
4. Metabolic Regulation and Control......Page 649
5. Metabolism of Hexoses Other than Glucose......Page 660
1. Glycogen Breakdown......Page 668
2. Glycogen Synthesis......Page 674
3. Control of Glycogen Metabolism......Page 677
4. Glycogen Storage Diseases......Page 696
1. Hormones......Page 701
2. Heterotrimeric G Proteins......Page 718
3 Tyrosine Kinase–Based Signaling\n......Page 729
4. The Phosphoinositide Cascade......Page 755
1. Thermodynamics of Transport......Page 774
2. Kinetics and Mechanisms of Transport......Page 775
3. ATP-Driven Active Transport......Page 788
4. Ion Gradient–Driven Active Transport......Page 798
5. Neurotransmission......Page 801
1. Cycle Overview......Page 819
2. Metabolic Sources of Acetyl-Coenzyme A......Page 822
3. Enzymes of the Citric Acid Cycle......Page 836
4. Regulation of the Citric Acid Cycle......Page 845
5. The Amphibolic Nature of the Citric Acid Cycle......Page 847
1. The Mitochondrion......Page 853
2. Electron Transport......Page 858
3. Oxidative Phosphorylation......Page 875
4. Control of ATP Production......Page 892
1. Gluconeogenesis......Page 901
3. Biosynthesis of Oligosaccharides and Glycoproteins......Page 910
4. The Pentose Phosphate Pathway......Page 922
1. Chloroplasts......Page 931
2. Light Reactions......Page 933
3. Dark Reactions......Page 956
1. Lipid Digestion, Absorption, and Transport......Page 970
2. Fatty Acid Oxidation......Page 975
3. Ketone Bodies......Page 989
4. Fatty Acid Biosynthesis......Page 991
5. Regulation of Fatty Acid Metabolism......Page 1003
6. Cholesterol Metabolism......Page 1005
7. Eicosanoid Metabolism: Prostaglandins, Prostacyclins, Thromboxanes, Leukotrienes, and Lipoxins......Page 1023
8. Phospholipid and Glycolipid Metabolism......Page 1034
1. Amino Acid Deamination......Page 1049
2. The Urea Cycle......Page 1055
3. Metabolic Breakdown of Individual Amino Acids......Page 1059
4. Amino Acids as Biosynthetic Precursors......Page 1077
5. Amino Acid Biosynthesis......Page 1094
6. Nitrogen Fixation......Page 1108
1. Major Pathways and Strategies of Energy Metabolism: A Summary......Page 1118
2. Organ Specialization......Page 1120
3. Metabolic Homeostasis: Regulation of Appetite, Energy Expenditure, and Body Weight......Page 1125
4. Metabolic Adaptation......Page 1131
1. Synthesis of Purine Ribonucleotides......Page 1137
2. Synthesis of Pyrimidine Ribonucleotides......Page 1144
3. Formation of Deoxyribonucleotides......Page 1149
4. Nucleotide Degradation......Page 1160
5. Biosynthesis of Nucleotide Coenzymes......Page 1166
PART V: EXPRESSION AND TRANSMISSION OF GENETIC INFORMATION......Page 1173
1. Double Helical Structures......Page 1175
2. Forces Stabilizing Nucleic Acid Structures......Page 1181
3. Supercoiled DNA......Page 1188
1. DNA Replication: An Overview......Page 1203
2. Enzymes of Replication......Page 1206
3. Prokaryotic Replication......Page 1220
4. Eukaryotic Replication......Page 1231
5. Repair of DNA......Page 1243
6. Recombination and Mobile Genetic Elements......Page 1255
7. DNA Methylation and Trinucleotide Repeat Expansions......Page 1276
1. The Role of RNA in Protein Synthesis......Page 1290
2. RNA Polymerase......Page 1295
3. Control of Transcription in Prokaryotes......Page 1313
4. Post-Transcriptional Processing......Page 1331
1. The Genetic Code......Page 1368
2. Transfer RNA and Its Aminoacylation......Page 1375
3 Ribosomes And Polypeptide Synthesis\n......Page 1392
4. Control of Eukaryotic Translation......Page 1428
5. Post-Translational Modification......Page 1433
6. Protein Degradation......Page 1438
CHAPTER 33 Viruses: Paradigms for Cellular Functions......Page 1459
1. Tobacco Mosaic Virus......Page 1461
2. Icosahedral Viruses......Page 1466
3. Bacteriophage l......Page 1478
4. Influenza Virus......Page 1498
1. Chromosome Structure......Page 1511
2. Genomic Organization......Page 1526
3. Control of Expression......Page 1541
4. Cell Differentiation and Growth......Page 1579
1. Blood Clotting......Page 1623
2. Immunity......Page 1637
3. Motility: Muscles, Vesicle Transport, Cilia,\rand Flagella......Page 1669
INDEX......Page 1716