C O N T E N T S: Preface Xiii Prologue XV

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Preface Prologue xiii xv CHAPTER 1 WHERE TO START Instructions What Do I Need to Know? Instructions for Use Studying and Exams Trivia Sorter 1 1 2 2 2 4 CHAPTER 2 PROTEIN STRUCTURE Amino Acid Structure Interactions Water Hydrophobic Interaction van der Waals Interactions and London Dispersion Forces Hydrogen Bonds Secondary Structure Protein Stability Favorable (Good) Interactions Unfavorable (Bad) Interactions Temperature-Sensitive Mutations Ligand-Binding Specificity Global Conclusion CHAPTER 3 MEMBRANES AND MEMBRANE PROTEINS General Membrane Function Membrane Composition Phospholipid Bilayer Membrane Structure Posttranslational Modification Membrane Fluidity Diffusion in Membranes Movement of Ions and Molecules Across Membranes
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Copyright 2000 by The McGraw-Hill Companies Retrieved from: www.knovel.com
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Transport Across Membranes The Nernst Equation

CHAPTER 4 DNA-RNA STRUCTURE DNA Structure DNA Stability RNA Secondary Structure
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CHAPTER 5 EXPRESSION OF GENETIC INFORMATION Information Metabolism Directions and Conventions DNA Replication Types of DNA Polymerase Recombination Regulation of Information Metabolism Transcription Regulation of Transcription Translation Use of High-Energy Phosphate Bonds During Translation CHAPTER 6 RECOMBINANT-DNA METHODOLOGY Restriction Analysis Gels and Electrophoresis Blotting Restriction Fragment-Length Polymorphism Cloning Sequencing Mutagenesis Polymerase Chain Reaction CHAPTER 7 ENZYME MECHANISM Active Site Transition State Catalysis Lock and Key Induced Fit Nonproductive Binding Entropy Strain and Distortion 40 40 41 42 45 47 49 53 55 57 60 61 61 65 67 69 70 73 75 76 80 81 81 83 83 83 85 87 88
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Transition-State Stabilization Transition-State Analogs Chemical Catalysis

CHAPTER 8 ENZYME KINETICS S, P, and E (Substrate, Product, Enzyme) Amounts and Concentrations Active Site Assay Velocity Initial Velocity Mechanism Little ks Michaelis-Menten Equation Vmax kcat Km Special Points kcat/Km Rate Accelerations Steady-State Approximation Transformations and Graphs Inhibition Allosterism and Cooperativity The Monod-Wyman-Changeaux Model
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CHAPTER 9 SIGNAL TRANSDUCTION PATHWAYS Signal Transduction Pathways Organization Signals Receptors Soluble Receptors Transmembrane Receptors Enzyme Coupled Receptors G-Protein Coupled Receptors Ion-Channel Coupled Receptors Second Messengers Amplifiers Integrators Inhibitors
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CHAPTER 11 GLYCOGEN SYNTHESIS AND DEGRADATION Function Location Connections Regulation ATP Yield ATP Cost Molecular Features CHAPTER 12 TCA Cycle TCA CYCLE 147 147 147 148 148 150 150 150 153 153 CHAPTER 13 FAT SYNTHESIS AND DEGRADATION Fatty Acid Synthesis Function Fatty Acid Synthesis Location Fatty Acid Synthesis Connections Fatty Acid Synthesis Regulation Fatty Acid Synthesis ATP Costs (for C16) Fatty Acid Synthesis Equation Elongation and Desaturation Triglyceride and Phospholipid Synthesis 155 156 156 157 157 157 159 160 162
CHAPTER 10 GLYCOLYSIS AND GLUCONEOGENESIS Glycolysis Function Glycolysis Location Glycolysis Connections Glycolysis Regulation Glycolysis ATP Yields Glycolysis Equations Effect of Arsenate Lactate or Pyruvate Gluconeogenesis Function Gluconeogenesis Location Gluconeogenesis Connections Gluconeogenesis Regulation Gluconeogenesis ATP Costs Gluconeogenesis Equations
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CHAPTER 14 ELECTRON TRANSPORT AND OXIDATIVE PHOSPHORYLATION Oxidation and Reduction The Electron Transport Chain Connections Regulation P/O Ratios Uncouplers Inhibitors CHAPTER 15 PENTOSE PHOSPHATE PATHWAY Pentose Phosphate Pathway 173 173 174 176 178 178 179 180 183 183 CHAPTER 16 AMINO ACID METABOLISM Nonessential Amino Acid Synthesis Essential Amino Acids Amino Acid Degradation Generalities of Amino Acid Catabolism Products of Amino Acid Degradation CHAPTER 17 INTEGRATION OF ENERGY METABOLISM Integrating Metabolic Pathways ATP Glucose Storage Molecules Metabolic States and Signals Insulin 186 186 187 187 187 188 190 191 192 192 193 194 195
-Oxidation Function -Oxidation Location Carnitine Shuttle -Oxidation Connections -Oxidation Regulation -Oxidation ATP Yield -Oxidation Equation -Oxidation of Unsaturated Fatty Acids -Oxidation of Odd-Chain-Length Fatty Acids
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CHAPTER 18 UREA CYCLE Urea Cycle 225 225 CHAPTER 19 PURINE METABOLISM Purine Synthesis Purine Salvage Deoxynucleotides Purine Degradation 227 227 228 228 229 CHAPTER 20 PYRIMIDINE METABOLISM Pyrimidine Synthesis Pyrimidine Salvage Pyrimidine Degradation 230 230 231 232
Glucagon Epinephrine Secondary Signals Generalities of Metabolism Phosphorylation Glycogen Metabolic Movements of Glycogen Fat Metabolic Movements of Fat Protein Metabolic Movements of Protein Tissue Cooperation Liver Muscle Adipose Brain Connection of Storage Pools Feeding Fasting Starvation Excitement Interorgan Cycles Cori Cycle Alanine Cycle Ketone Bodies
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CHAPTER 21 ONE-CARBON METABOLISM One-Carbon Metabolism Oxidation States of Carbon CHAPTER 22 TRACKING CARBONS Glucose to Pyruvate TCA Cycle
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CHAPTER 23 ph, pKA, pROBLEMS Proton: H or H3O Acid Base Not All Acids and Bases Are Created Equal log (Ka) pKa Weak Acids Make Strong Bases (and Vice Versa) Who Gets the Proton? Dont Forget Stoichiometry The Sadistic Little p Taking log10(x) Taking log10(x) pH log10 [H ] log10 (Ka) pKa Buffers Henderson-Hasselbalch Equation Titration Curves pIIsoelectric Point The Bicarbonate Buffer Imbalance in Blood pH Acidosis and Alkalosis CHAPTER 24 THERMODYNAMICS AND KINETICS Thermodynamics Free Energy Adding Free-Energy Changes Coupling Free Energies Thermodynamic Cycles G H T S Driving Force 241 242 242 242 243 244 244 245 245 246 247 247 248 248 248 249 250 254 255 257 258 261 261 263 268 268 269 272 273
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Appendix Glossary Index 284 287 319
Kinetics Velocity Transition State Theory Rate Constants Rate Constants and Mechanism
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C O N T E N T S: Preface Xiii Prologue XV

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Transport Across Membranes The Nernst Equation

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Transition-State Stabilization Transition-State Analogs Chemical Catalysis

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