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| Preface | |
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| Prologue | |
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| Where to Start | |
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| Instructions | |
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| What Do I Need to Know? | |
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| Instructions for Use | |
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| Studying and Exams | |
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| Trivia Sorter | |
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| Protein Structure | |
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| Amino Acid Structure | |
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| Interactions | |
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| Water | |
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| Hydrophobic Interaction | |
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| van der Waals Interactions and London Dispersion Forces | |
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| Hydrogen Bonds | |
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| Secondary Structure | |
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| Protein Stability | |
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| Favorable (Good) Interactions | |
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| Unfavorable (Bad) Interactions | |
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| Temperature-Sensitive Mutations | |
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| Ligand-Binding Specificity | |
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| Global Conclusion | |
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| Membranes and Membrane Proteins | |
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| General Membrane Function | |
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| Membrane Composition | |
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| Phospholipid Bilayer | |
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| Membrane Structure | |
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| Posttranslational Modification | |
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| Membrane Fluidity | |
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| Diffusion in Membranes | |
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| Movement of Ions and Molecules Across Membranes | |
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| Transport Across Membranes | |
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| The Nernst Equation | |
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| DNA-RNA Structure | |
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| DNA Structure | |
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| DNA Stability | |
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| RNA Secondary Structure | |
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| Expression of Genetic Information | |
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| Information Metabolism | |
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| Directions and Conventions | |
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| DNA Replication | |
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| Types of DNA Polymerase | |
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| Recombination | |
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| Regulation of Information Metabolism | |
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| Transcription | |
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| Regulation of Transcription | |
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| Translation | |
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| Use of High-Energy Phosphate Bonds During Translation | |
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| Recombinant-DNA Methodology | |
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| Restriction Analysis | |
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| Gels and Electrophoresis | |
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| Blotting | |
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| Restriction Fragment-Length Polymorphism | |
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| Cloning | |
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| Sequencing | |
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| Mutagenesis | |
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| Polymerase Chain Reaction | |
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| Enzyme Mechanism | |
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| Active Site | |
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| Transition State | |
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| Catalysis | |
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| Lock and Key | |
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| Induced Fit | |
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| Nonproductive Binding | |
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| Entropy | |
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| Strain and Distortion | |
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| Transition-State Stabilization | |
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| Transition-State Analogs | |
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| Chemical Catalysis | |
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| Enzyme Kinetics | |
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| S, P, and E (Substrate, Product, Enzyme) | |
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| Amounts and Concentrations | |
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| Active Site | |
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| Assay | |
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| Velocity | |
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| Initial Velocity | |
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| Mechanism | |
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| Little k's | |
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| Michaelis-Menten Equation | |
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| V[subscript max] | |
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| K[subscript cat] | |
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| K[subscript m] | |
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| Special Points | |
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| k[subscript cat]/K[subscript m] | |
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| Rate Accelerations | |
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| Steady-State Approximation | |
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| Transformations and Graphs | |
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| Inhibition | |
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| Allosterism and Cooperativity | |
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| The Monod-Wyman-Changeaux Model | |
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| Signal Transduction Pathways | |
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| Signal Transduction Pathways | |
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| Organization | |
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| Signals | |
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| Receptors | |
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| Soluble Receptors | |
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| Transmembrane Receptors | |
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| Enzyme Coupled Receptors | |
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| G-Protein Coupled Receptors | |
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| Ion-Channel Coupled Receptors | |
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| Second Messengers | |
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| Amplifiers | |
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| Integrators | |
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| Inhibitors | |
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| Glycolysis and Gluconeogenesis | |
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| Glycolysis Function | |
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| Glycolysis Location | |
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| Glycolysis Connections | |
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| Glycolysis Regulation | |
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| Glycolysis ATP Yields | |
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| Glycolysis Equations | |
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| Effect of Arsenate | |
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| Lactate or Pyruvate | |
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| Gluconeogenesis Function | |
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| Gluconeogenesis Location | |
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| Gluconeogenesis Connections | |
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| Gluconeogenesis Regulation | |
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| Gluconeogenesis ATP Costs | |
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| Gluconeogenesis Equations | |
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| Glycogen Synthesis and Degradation | |
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| Function | |
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| Location | |
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| Connections | |
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| Regulation | |
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| ATP Yield | |
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| ATP Cost | |
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| Molecular Features | |
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| TCA Cycle | |
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| TCA Cycle | |
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| Fat Synthesis and Degradation | |
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| Fatty Acid Synthesis Function | |
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| Fatty Acid Synthesis Location | |
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| Fatty Acid Synthesis Connections | |
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| Fatty Acid Synthesis Regulation | |
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| Fatty Acid Synthesis ATP Costs (for C[subscript 16]) | |
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| Fatty Acid Synthesis Equation | |
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| Elongation and Desaturation | |
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| Triglyceride and Phospholipid Synthesis | |
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| [beta]-Oxidation Function | |
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| [beta]-Oxidation Location | |
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| Carnitine Shuttle | |
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| [beta]-Oxidation Connections | |
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| [beta]-Oxidation Regulation | |
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| [beta]-Oxidation ATP Yield | |
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| [beta]-Oxidation Equation | |
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| [beta]-Oxidation of Unsaturated Fatty Acids | |
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| [beta]-Oxidation of Odd-Chain-Length Fatty Acids | |
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| Electron Transport and Oxidative Phosphorylation | |
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| Oxidation and Reduction | |
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| The Electron Transport Chain | |
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| Connections | |
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| Regulation | |
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| P/O Ratios | |
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| Uncouplers | |
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| Inhibitors | |
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| Pentose Phosphate Pathway | |
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| Pentose Phosphate Pathway | |
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| Amino Acid Metabolism | |
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| Nonessential Amino Acid Synthesis | |
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| Essential Amino Acids | |
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| Amino Acid Degradation | |
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| Generalities of Amino Acid Catabolism | |
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| Products of Amino Acid Degradation | |
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| Integration of Energy Metabolism | |
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| Integrating Metabolic Pathways | |
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| ATP | |
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| Glucose | |
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| Storage Molecules | |
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| Metabolic States and Signals | |
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| Insulin | |
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| Glucagon | |
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| Epinephrine | |
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| Secondary Signals | |
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| Generalities of Metabolism | |
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| Phosphorylation | |
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| Glycogen | |
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| Metabolic Movements of Glycogen | |
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| Fat | |
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| Metabolic Movements of Fat | |
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| Protein | |
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| Metabolic Movements of Protein | |
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| Tissue Cooperation | |
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| Liver | |
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| Muscle | |
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| Adipose | |
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| Brain | |
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| Connection of Storage Pools | |
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| Feeding | |
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| Fasting | |
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| Starvation | |
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| Excitement | |
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| Interorgan Cycles | |
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| Cori Cycle | |
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| Alanine Cycle | |
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| Ketone Bodies | |
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| Urea Cycle | |
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| Urea Cycle | |
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| Purine Metabolism | |
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| Purine Synthesis | |
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| Purine Salvage | |
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| Deoxynucleotides | |
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| Purine Degradation | |
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| Pyrimidine Metabolism | |
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| Pyrimidine Synthesis | |
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| Pyrimidine Salvage | |
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| Pyrimidine Degradation | |
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| One-Carbon Metabolism | |
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| One-Carbon Metabolism | |
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| Oxidation States of Carbon | |
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| Tracking Carbons | |
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| Glucose to Pyruvate | |
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| TCA Cycle | |
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| ph, pK[subscript A], Problems | |
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| Proton: H[superscript +] or H[subscript 3]O[superscript +] | |
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| Acid | |
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| Base | |
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| Not All Acids and Bases Are Created Equal | |
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| pK[subscript a] = -log (K[subscript a]) | |
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| Weak Acids Make Strong Bases (and Vice Versa) | |
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| Who Gets the Proton? | |
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| Don't Forget Stoichiometry | |
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| The Sadistic Little p | |
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| Taking log[subscript 10](x) | |
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| Taking -log[subscript 10](x) | |
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| pH = -log[subscript 10] [H[superscript +]] | |
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| pK[subscript a] = - log[subscript 10] (K[subscript a]) | |
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| Buffers | |
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| Henderson-Hasselbalch Equation | |
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| Titration Curves | |
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| plIsoelectric Point | |
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| The Bicarbonate Buffer | |
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| Imbalance in Blood pH | |
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| Acidosis and Alkalosis | |
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| Thermodynamics and Kinetics | |
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| Thermodynamics | |
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| Free Energy | |
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| Adding Free-Energy Changes | |
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| Coupling Free Energies | |
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| Thermodynamic Cycles | |
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| [Delta]G = [Delta]H - T[Delta]S | |
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| Driving Force | |
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| Kinetics | |
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| Velocity | |
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| Transition State Theory | |
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| Rate Constants | |
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| Rate Constants and Mechanism | |
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| Appendix | |
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| Glossary | |
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| Index | |