Guide to Biochemistry

PrefaceAcknowledgments1 Biological Molecules 1.1 Cell Theory 1.2 The Role of Carbon 1.3 Stereochemistry 1.4 The Nature of Macromolecules 1.5 Hybrid Molecules 1.6 The Functions of Macromolecules 1.7 Other Functions of Monomeric Units2 The Physical Chemistry of Aqueous Systems 2.1 Ionization and Macromolecules 2.2 Hydrogen Bonding in Water 2.3 Ionization of Water 2.4 pH Scale 2.5 Theories of Acids and Bases 2.6 The Relative Strengths of Acids and Bases 2.7 The Interaction of Aqueous Solutions of Monoprotic Acids and Bases 2.8 The Interaction of Polyprotic Weak Acids and Strong Bases 2.9 Buffer Systems 2.10 Summary of Useful Equations in pH Calculations 2.11 Example Calculations3 Carbohydrates 3.1 The Definition of Carbohydrate 3.2 The Monosaccharides 3.3 The Ring Structures of Monosaccharides 3.4 Derivatives of Monosaccharides 3.5 Oligosaccharides 3.6 Polysaccharides: Homoglycans 3.7 Polysaccharides: Heteroglycans4 Amino Acids and Proteins 4.1 The Classification of Amino Acids 4.2 Ionic Properties of Amino Acids 4.3 The Major Bonds between Amino Acids in Polypeptide Chains 4.4 The Primary Structure of Proteins 4.5 The Secondary Structure of Proteins 4.6 The Tertiary Structure of Proteins 4.7 The Quaternary Structure of Proteins5 Enzymes 5.1 Comparison of Chemical and Enzymic Reactions 5.2 Enzyme Architecture 5.3 Enzyme Classification 5.4 Enzyme Catalysis 6 Enzyme Kinetics 6.1 Factors Influencing the Rate of an Enzyme-Catalysed Reaction 6.2 Steady-State Enzyme Kinetics 6.3 Enzyme Inhibition 6.4 Allostery 6.5 Isoenzymes7 Nucleic Acids 7.1 The Structure of Nucleotides 7.2 Polynucleotide Chains 7.3 The Structure of DNA 7.4 The Structure of RNA 7.5 Some Properties of Nucleic Acids8 Lipids 8.1 The Classes of Lipids 8.2 Fatty Acids 8.3 Waxes 8.4 Acylglycerols 8.5 Phosphoacylglycerols 8.6 Plasmalogens 8.7 Sphingolipids 8.8 Eicosanoids 8.9 Terpenes 8.10 Steroids 8.11 Circulatory Lipid Complexes 9 Eukaryotic Cellular Organization 9.1 Prokaryotic and Eukaryotic Cells 9.2 The Plasma Membrane: Structure 9.3 The Plasma Membrane: Transport Mechanisms 9.4 Nuclear Structures 9.5 Electron-Transporting Organelles 9.6 Organelles Associated with Protein Synthesis 9.7 Lysosomes and Microbodies 9.8 The Cytoskeleton 10 Principles of Cellular Metabolism 10.1 Biological Energetics 10.2 Equilibrium Thermodynamics 10.3 Coupled Reactions 10.4 The Role of ATP 10.5 Metabolic Pathways 10.6 Intracellular Control of Metabolism 10.7 Extracellular Control of Metabolism11 Carbohydrate Metabolism 11.1 The Pathways of Carbohydrate Metabolism 11.2 The Reactions of Glycolysis 11.3 NAD+ and Glycolysis 11.4 The Role of Glycogen 11.5 Glycogenesis and Glycogenolysis 11.6 The Role of Gluconeogenesis 11.7 The Reactions of Gluconeogenesis 11.8 The Role of the Pentose Phosphate Pathway 11.9 The Reactions of the Pentose Phosphate Pathway 11.10 The Energetics of Carbohydrate Metabolism 11.11 The Regulation of Carbohydrate Metabolism12 The Tricarboxylate Cycle 12.1 Role in Metabolism 12.2 Entry of Pyruvate into the Mitochondrion 12.3 The Oxidative Decarboxylation of Pyruvate 12.4 The Reactions of the Tricarboxylate Cycle 12.5 The Energetics of the Cycle 12.6 Anaplerosis 12.7 The Regulation of the Cycle 12.8 The Glyoxylate Cycle13 Mitochondrial Oxidative Phosphorylation 13.1 The Role of Oxidative Phosphorylation 13.2 The Structure of Electron-Transport Assemblies 13.3 Oxidation-Reduction Reactions 13.4 The Sequence of Electron-Transport Carriers 13.5 The Synthesis of ATP 13.6 Mechanisms of Coupling Electron Transport to ATP Synthesis 13.7 Inhibitors of Oxidative Phosphorylation14 Photosynthesis 14.1 The Role of Photosynthesis 14.2 The Thylakoid Photosystems 14.3 The Light Reactions: Electronic Excitation 14.4 The Light Reactions: Electron Transport 14.5 The Dark Reactions: The Calvin Cycle 14.6 The Dark Reactions: Carbohydrate Synthesis15 The Metabolism of Lipids 15.1 Fatty Acids as Energy Sources 15.2 The β-Oxidation Pathway 15.3 Ketone Body Metabolism 15.4 The Synthesis of Fatty Acids 15.5 The Synthesis of Triacylglycerols 15.6 The Synthesis of Eicosanoids 15.7 The Synthesis of Cholesterol 15.8 The Metabolism of Steroid Hormones16 Nitrogen Metabolism 16.1 The Biosynthesis of Amino Acids in Plants and Microorganisms 16.2 The Biosynthesis of Amino Acids in Mammals and Humans 16.3 The Degradation of Amino Acids 16.4 The Disposal of Amino Nitrogen in the Animal Kingdom 16.5 The Urea Cycle 16.6 The Biosynthesis of Heterocyclic Compounds 16.7 The Hybridoma Technique 16.8 The Degradation of Heterocyclic Compounds17 Gene Expression 17.1 The Central Dogma 17.2 Transcription: Initiation and Elongation 17.3 Transcription: Termination 17.4 Translation: The Role of Amino-Acid-TRNA Ligases 17.5 Translation: The Genetic Code 17.6 Translation: The Mechanism of Protein Biosynthesis 17.7 Mutation 17.8 Control of Gene Expression18 The Replication of Deoxyribonucleic Acid 18.1 Semiconservative Replication 18.2 An Overview of DNA Replication 18.3 The Enzymology of DNA Replication in Prokaryotes 18.4 DNA Repair19 Gene Cloning 19.1 Applications of Gene Cloning 19.2 Outline of Gene Cloning Methodology 19.3 Vectors Employed in E. Coli 19.4 Restriction Endonucleases 19.5 The Transport of Recombinant DNA Molecules into a Host Bacterium 19.6 Selection of Recombinant DNA 19.7 DNA-Sequencing TechniquesIndex