Contents
PART 1 The Realm of Biochemistry
CHAPTER 1The Scope of Biochemistry //3
Biochemistry and the Biological Revolution//3
The Roots of Biochemistry //4
Biochemistry as a Chemical Science//7
Biochemistry as a Biological Science //10
Biochemistry and the Information Explosion //13
PART 2Molecular Architecture of Living Matter
CHAPTER 2Nucleic Acids//17
The Nature of Nucleic Acids //17
Primary Structure of Nucleic Acids//22
Secondary and Tertiary Structure of Nucleic Acids //24
The Biological Functions of Nucleic Acids: A Preview of Molecular Biology35
Plasticity of Secondary and Tertiary DNA Structure //40
Stability of Secondary and Tertiary Structure//43
CHAPTER 3Introduction to Proteins: The Primary Level of Protein Structure 46
Amino Acids //46
Peptides and the Peptide Bond //55
Proteins: Polypeptides of Defined Sequence//58
From Gene to Protein//60
Protein Sequence Homology //61
CHAPTER 4The Three-Dimensional Structure of Proteins//64
Secondary Structure: Regular Ways to Fold the Polypeptide Chain//64
Fibrous Proteins: Structural Materials of Cells and Tissues //71
Globular Proteins: Tertiary Structure and Functional Diversity//76
Factors Determining Secondary and Tertiary Structure //79
Prediction of Secondary and Tertiary Protein Structure//88
Quaternary Structure of Proteins//88
CHAPTER 5Protein Function and Evolution//93
Oxygen Transport: The Roles of Hemoglobin and Myoglobin//94
The Mechanism of Oxygen Binding by Heme Proteins //95
Oxygen Transport: Hemoglobin//100
Allosteric Effectors of Hemoglobin //110
Protein Evolution: Myoglobin and Hemoglobin as Examples//114
Hemoglobin Variants: Evolution in Progress //118
PART 3 Dynamics of Life: Catalysis and Metabolism
CHAPTER 6Enzymes: Biological Catalysts //127
The Role of Enzymes //127
Chemical Reaction Rates and the Effects of Catalysts: A Review //127
How Enzymes Act as Catalysts: Principles and Examples//131
Enzyme Inhibition//142
Cofactors, Vitamins, and Essential Metals //146
The Diversity of Enzymatic Function//148
Nonprotein Biocatalysts: Catalytic Nucleic Acids //148
The Regulation of Enzyme Activity: Allosteric Enzymes //151
Covalent Modifications Used to Regulate Enzyme Activity //154
CHAPTER 7Chemical Logic of Metabolism//159
A First Look at Metabolism //159
Freeways on the Metabolic Road Map//161
Biochemical Reaction Types //165
Some Bioenergetic Considerations //165
Major Metabolic Control Mechanisms//171
CHAPTER 8Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway //176
Glycolysis: An Overview //176
Reactions of Glycolysis//178
Metabolic Fates of Pyruvate //185
Energy and Electron Balance Sheets//186
Gluconeogenesis//188
Coordinated Regulation of Glycolysis and Gluconeogenesis //192
Entry of Other Sugars into the Glycolytic Pathway//197
Polysaccharide Metabolism//200
Glycogen Metabolism in Muscle and Liver //200
Coordinated Regulation of Glycogen Metabolism//203
Biosynthesis of Other Polysaccharides //208
A Biosynthetic Pathway That Oxidizes Glucose: The Pentose Phosphate Pathway208
CHAPTER 9Citric Acid Cycle//216
Overview of Pyruvate Oxidation and the Citric Acid Cycle//216
Pyruvate Oxidation: A Major Entry Route for Carbon into the Citric Acid Cycle219
Coenzymes Involved in Pyruvate Oxidation and the Citric Acid Cycle //221
Action of the Pyruvate Dehydrogenase Complex//223
The Citric Acid Cycle//225
Stoichiometry and Energetics of the Citric Acid Cycle //229
Regulation of Pyruvate Dehydrogenase and the Citric Acid Cycle //230
CHAPTER 10Electron Transport and Oxidative Phosphorylation//234
Electron Transport //236
Oxidative Phosphorylation//247
CHAPTER 11Lipid MetabolismⅠ: Fatty Acids, Triacylglycerols, and Lipoproteins263
Utilization and Transport of Fat and Cholesterol //263
Fatty Acid Oxidation //277
Fatty Acid Biosynthesis//287
CHAPTER 12Interorgan and Intracellular Coordination of
Energy Metabolism in Vertebrates //301
Interdependence of the Major Organs in Vertebrate Fuel Metabolism //301
Hormonal Regulation of Fuel Metabolism//305
Responses to Metabolic Stress: Starvation, Diabetes //310
CHAPTER 13Lipid Metabolism Ⅱ: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids315
Metabolism of Glycerophospholipids//315
Metabolism of Sphingolipids //322
Steroid Metabolism//323
Other Isoprenoid Compounds //328
Eicosanoids: Prostaglandins, Thromboxanes, and Leukotrienes//330
CHAPTER 14 Metabolism of Nitrogenous CompoundsⅠ: Principles of Biosynthesis, Utilization, and Turnover//336
Utilization of Ammonia: Biogenesis of Organic Nitrogen//336
The Nitrogen Economy: Aspects of Amino Acid Synthesis and Degradation //338
Protein Turnover//340
Amino Acid Degradation and Metabolism of Nitrogenous End Products//342
Coenzymes Involved in Nitrogen Metabolism//347
CHAPTER 15Metabolism of Nitrogenous Compounds Ⅱ: Amino Acids, Porphyrins, and
Neurotransmitters //355
Pathways of Amino Acid Degradation//355
Amino Acids as Biosynthetic Precursors//359
Porphyrin and Heme Metabolism //364
Amino Acids and Their Metabolites as Neurotransmitters and Biological Regulators 367
Amino Acid Biosynthesis//369
Methionine as the Source of Cysteine Sulfur in Animals//370
CHAPTER 16Nucleotide Metabolism//372
Outlines of Pathways in Nucleotide Metabolism//372
De Novo Biosynthesis of Purine Nucleotides//375
Purine Degradation and Clinical Disorders of Purine Metabolism//379
Pyrimidine Nucleotide Metabolism //383
Deoxyribonucleotide Biosynthesis and Metabolism//386
Thymidylate Synthase: A Target Enzyme for Chemotherapy //391
Biological and Medical Importance of Other Nucleotide Analogs//394
CHAPTER 17Mechanisms of Signal Transduction //398
An Overview of Hormone Action //398
Hierarchical Nature of Hormonal Control//400
Synthesis of Peptide Hormone Precursors//401
Signal Transduction: Receptors//402
Transducers: G Proteins //404
Effectors: Adenylate Cyclase//407
Second-Messenger Systems//408
Receptor Tyrosine Kinases//412
Steroid and Thyroid Hormones: Intracellular Receptors//415
Signal Transduction, Oncogenes, and Cancer //418
PART 4 Information CHAPTER 18Genes, Genomes, and Chromosomes //427
Prokaryotic and Eukaryotic Genomes //427
Restriction and Modification //430
Determining Genome Nucleotide Sequences //433
Physical Organization of Genes: The Nucleus, Chromosomes, and Chromatin435
CHAPTER 19 DNA Replication//442
Early Insights into DNA Replication//442
DNA Polymerases: Enzymes Catalyzing Polynucleotide Chain Elongation//443
Multiple DNA Polymerases //445
Other Proteins at the Replication Fork//445
Proteins in Eukaryotic DNA Replication//449
Replication of Chromatin//449
Initiation of DNA Replication //450
Replication of Linear Genomes//452
Fidelity of DNA Replication//453
RNA Viruses: The Replication of RNA Genomes //454
CHAPTER 20 DNA Restructuring: Repair, Recombination, Rearrangement, Amplification 457
DNA Repair //457
Mismatch Repair //464
Recombination//470
Gene Rearrangements //475
Gene Amplification//477
CHAPTER 21 Information Readout: Transcription and Post-transcriptional Processing479
DNA as the Template for RNA Synthesis //480
Enzymology of RNA Synthesis: RNA Polymerase//480
Mechanism of Transcription//483
Transcription and Its Control in Eukaryotic Cells //489
Post-transcriptional Processing//498
CHAPTER 22 Information Decoding: Translation and Post-translational Protein Processing 506
An Overview of Translation//506
The Genetic Code //506
The Major Participants in Translation: mRNA, tRNA, and Ribosomes//509
Mechanism of Translation //515
Inhibition of Translation by Antibiotics//520
Translation in Eukaryotes//522
Rates and Energetics of Translation //524
The Final Stages in Protein Synthesis: Folding and Covalent Modification 525
Protein Targeting in Eukaryotes //527
CHAPTER 23 Regulation of Gene Expression//533
Regulation of Transcription in Bacteria //533
Transcriptional Regulation in Eukaryotes//540
DNA Methylation, Gene Silencing, and Epigenetics//543
Regulation of Translation//546
RNA Interference //550
RNA Editing //552
