Biochemistry

Cover......Page 1
Title Page......Page 3
Copyright......Page 4
Preface......Page 7
Brief Contents......Page 12
Contents......Page 13
Guide to Media Resources......Page 16
PART I: INTRODUCTION AND BACKGROUND......Page 29
1. Prokaryotes......Page 31
2. Eukaryotes......Page 34
3. Biochemistry: A Prologue......Page 42
4. Genetics: A Review......Page 47
5. The Origin of Life......Page 56
6. The Biochemical Literature......Page 62
1. Properties of Water......Page 68
2. Acids, Bases, and Buffers......Page 73
1. First Law of Thermodynamics: Energy Is Conserved......Page 80
2. Second Law of Thermodynamics: The Universe Tends Toward Maximum Disorder......Page 82
3. Free Energy: The Indicator of Spontaneity......Page 85
4. Chemical Equilibria......Page 86
APPENDIX: Concentration Dependence of Free Energy......Page 89
PART II: BIOMOLECULES......Page 93
1. The Amino Acids of Proteins......Page 95
2. Optical Activity......Page 101
3. “Nonstandard” Amino Acids......Page 106
1. Nucleotides and Nucleic Acids......Page 110
2. DNA Is the Carrier of Genetic Information......Page 113
3. Double Helical DNA......Page 116
4. Gene Expression and Replication: An Overview......Page 123
5. Molecular Cloning......Page 132
1. Protein Isolation......Page 157
2. Solubilities of Proteins......Page 161
3. Chromatographic Separations......Page 163
4. Electrophoresis......Page 174
5. Ultracentrifugation......Page 180
6. Nucleic Acid Fractionation......Page 184
CHAPTER 7 Covalent Structures of Proteins and Nucleic Acids......Page 191
1. Primary Structure Determination of Proteins......Page 192
2. Nucleic Acid Sequencing......Page 204
3. Chemical Evolution......Page 213
4. Bioinformatics: An Introduction......Page 222
5. Chemical Synthesis of Polypeptides......Page 233
6. Chemical Synthesis of Oligonucleotides......Page 237
1. Secondary Structure......Page 249
2. Fibrous Proteins......Page 260
3. Globular Proteins......Page 269
4. Protein Stability......Page 287
5. Quaternary Structure......Page 294
APPENDIX: Viewing Stereo Pictures......Page 299
1. Protein Folding: Theory and Experiment......Page 306
2. Folding Accessory Proteins......Page 318
3. Protein Structure Prediction and Design......Page 330
4. Protein Dynamics......Page 334
5 CONFORMATIONAL DISEASES:AMYLOID AND PRIONS......Page 337
6. Structural Evolution......Page 344
1. Hemoglobin and Myoglobin Function......Page 351
2. Structure and Mechanism......Page 359
3. Abnormal Hemoglobins......Page 369
4. Allosteric Regulation......Page 375
APPENDIX: Derivations
of Symmetry Model Equations......Page 382
1. Monosaccharides......Page 387
2. Polysaccharides......Page 393
3. Glycoproteins......Page 401
1. Lipid Classification......Page 414
2. Properties of Lipid Aggregates......Page 421
3. Biological Membranes......Page 427
4. Membrane Assembly and Protein Targeting......Page 446
5. Lipoproteins......Page 477
PART III: MECHANISMS OF ENZYME ACTION......Page 495
1. Historical Perspective......Page 497
2. Substrate Specificity......Page 498
3. Coenzymes......Page 501
4. Regulation of Enzymatic Activity......Page 502
5. A Primer of Enzyme Nomenclature......Page 507
1. Chemical Kinetics......Page 510
2. Enzyme Kinetics......Page 515
3. Inhibition......Page 520
4. Effects of pH......Page 524
5. Bisubstrate Reactions......Page 525
APPENDIX: Derivations of Michaelis–Menten Equation Variants......Page 529
1. Catalytic Mechanisms......Page 534
2. Lysozyme......Page 545
3. Serine Proteases......Page 553
4. Drug Design......Page 567
PART IV: METABOLISM......Page 585
1. Metabolic Pathways......Page 587
2. Organic Reaction Mechanisms......Page 590
3. Experimental Approaches to the Study of Metabolism......Page 597
4. Thermodynamics of Phosphate Compounds......Page 606
5. Oxidation–Reduction Reactions......Page 611
6. Thermodynamics of Life......Page 614
1. The Glycolytic Pathway......Page 621
2. The Reactions of Glycolysis......Page 623
3. Fermentation: The Anaerobic Fate of Pyruvate......Page 642
4. Metabolic Regulation and Control......Page 647
5. Metabolism of Hexoses Other than Glucose......Page 658
1. Glycogen Breakdown......Page 666
2. Glycogen Synthesis......Page 672
3. Control of Glycogen Metabolism......Page 675
4. Glycogen Storage Diseases......Page 694
1. Hormones......Page 699
2. Heterotrimeric G Proteins......Page 716
3 Tyrosine Kinase–Based Signaling
......Page 727
4. The Phosphoinositide Cascade......Page 753
1. Thermodynamics of Transport......Page 772
2. Kinetics and Mechanisms of Transport......Page 773
3. ATP-Driven Active Transport......Page 786
4. Ion Gradient–Driven Active Transport......Page 796
5. Neurotransmission......Page 799
1. Cycle Overview......Page 817
2. Metabolic Sources of Acetyl-Coenzyme A......Page 820
3. Enzymes of the Citric Acid Cycle......Page 834
4. Regulation of the Citric Acid Cycle......Page 843
5. The Amphibolic Nature of the Citric Acid Cycle......Page 845
1. The Mitochondrion......Page 851
2. Electron Transport......Page 856
3. Oxidative Phosphorylation......Page 873
4. Control of ATP Production......Page 890
1. Gluconeogenesis......Page 899
3. Biosynthesis of Oligosaccharides and Glycoproteins......Page 908
4. The Pentose Phosphate Pathway......Page 920
1. Chloroplasts......Page 929
2. Light Reactions......Page 931
3. Dark Reactions......Page 954
1. Lipid Digestion, Absorption, and Transport......Page 968
2. Fatty Acid Oxidation......Page 973
3. Ketone Bodies......Page 987
4. Fatty Acid Biosynthesis......Page 989
5. Regulation of Fatty Acid Metabolism......Page 1001
6. Cholesterol Metabolism......Page 1003
7. Eicosanoid Metabolism: Prostaglandins, Prostacyclins, Thromboxanes, Leukotrienes, and Lipoxins......Page 1021
8. Phospholipid and Glycolipid Metabolism......Page 1032
1. Amino Acid Deamination......Page 1047
2. The Urea Cycle......Page 1053
3. Metabolic Breakdown of Individual Amino Acids......Page 1057
4. Amino Acids as Biosynthetic Precursors......Page 1075
5. Amino Acid Biosynthesis......Page 1092
6. Nitrogen Fixation......Page 1106
1. Major Pathways and Strategies of Energy Metabolism: A Summary......Page 1116
2. Organ Specialization......Page 1118
3. Metabolic Homeostasis: Regulation of Appetite, Energy Expenditure, and Body Weight......Page 1123
4. Metabolic Adaptation......Page 1129
1. Synthesis of Purine Ribonucleotides......Page 1135
2. Synthesis of Pyrimidine Ribonucleotides......Page 1142
3. Formation of Deoxyribonucleotides......Page 1147
4. Nucleotide Degradation......Page 1158
5. Biosynthesis of Nucleotide Coenzymes......Page 1164
PART V: EXPRESSION AND TRANSMISSION OF GENETIC INFORMATION......Page 1171
1. Double Helical Structures......Page 1173
2. Forces Stabilizing Nucleic Acid Structures......Page 1179
3. Supercoiled DNA......Page 1186
1. DNA Replication: An Overview......Page 1201
2. Enzymes of Replication......Page 1204
3. Prokaryotic Replication......Page 1218
4. Eukaryotic Replication......Page 1229
5. Repair of DNA......Page 1241
6. Recombination and Mobile Genetic Elements......Page 1253
7. DNA Methylation and Trinucleotide Repeat Expansions......Page 1274
1. The Role of RNA in Protein Synthesis......Page 1288
2. RNA Polymerase......Page 1293
3. Control of Transcription in Prokaryotes......Page 1311
4. Post-Transcriptional Processing......Page 1329
1. The Genetic Code......Page 1366
2. Transfer RNA and Its Aminoacylation......Page 1373
3 Ribosomes And Polypeptide Synthesis
......Page 1390
4. Control of Eukaryotic Translation......Page 1426
5. Post-Translational Modification......Page 1431
6. Protein Degradation......Page 1436
INDEX......Page 1457