Biochemistry: The Molecular Basis of Life

Transcription

1 Biochemistry: The Molecular Basis of Life McKee, Trudy ISBN-13: Table of Contents * New to this edition Preface 1. WHAT IS LIFE? 1.1 The Living World Bacteria Archaea Eukarya 1.3 Biomolecules Functional Groups of Organic Biomolecules Major Classes of Small Biomolecules 1.4 Is the Living Cell a Chemical Factory? Biochemical Reactions Energy Overview of Metabolism Biological Order * 1.5 Systems Biology Emergence Robustness Modularity Biochemistry in the Lab: An Introduction 2. LIVING CELLS 2.1 Basic Themes Water Biological Membranes Self-Assembly Molecular Machines * Macromolecular Crowding Signal Transduction 2.2 Structure of Prokaryotic Cells Cell Wall Plasma Membrane Cytoplasm Pili and Flagella 2.3 Structure of Eukaryotic Cells Plasma Membrane * Endoplasmic Reticulum Golgi Apparatus Nucleus Vesicular Organelles Mitochondria Peroxisomes Biochemistry in Perspective: Organelles in Human Disease Plastids Cytoskeleton Ribosomes Biochemistry in the Lab: Cell Technology 3. WATER: THE MATRIX OF LIFE 3.1 Molecular Structure of Water 3.2 Noncovalent Bonding

2 Ionic Interactions Hydrogen Bonds Van der Waals Forces 3.3 Thermal Properties of Water 3.4 Solvent Properties of Water * Hydrophilic Molecules Hydrophobic Molecules and the Hydrophobic Effect Amphipathic Molecules Osmotic Pressure 3.5 Ionization of Water Acids, Bases, and ph Buffers Physiological Buffers * Biochemistry in Perspective: Water, Abiotic Stress, and Compatible Solutes Biochemistry in the Lab: Dialysis Biochemistry in Perspective: Cell Volume Regulation and Metabolism 4. ENERGY 4.1 Thermodynamics The First Law of Thermodynamics Second Law of Thermodynamics 4.2 Free Energy Standard Free Energy Changes Coupled Reactions The Hydrophobic Effect Revisited * Biochemistry in Perspective: Non-Equilibrium Thermodynamics 4.4 The Role of ATP * Biochemistry in Perspective: The Extremophiles: Organisms that Make a Living in Hostile Environments 5. AMINO ACIDS, PEPTIDES, AND PROTEINS 5.1 Amino Acids Amino Acid Classes Biologically Active Amino Acids Modified Amino Acids in Proteins Amino Acid Stereoisomers Titration of Amino Acids Amino Acid Reactions 5.2 Peptides * 5.3 Proteins Protein Structure * Biochemistry in Perspective: Molecular Machines The Folding Problem Biochemistry in Perspective: Protein Folding and Human Disease Fibrous Proteins Globular Proteins Biochemistry in the Lab: Protein Technology 6. ENZYMES 6.1 Properties of Enzymes 6.2 Classification of Enzymes 6.3 Enzyme Kinetics Michaelis-Menten Kinetics Lineweaver-Burk Plots Enzyme Inhibition Enzyme Kinetics, Metabolism and Macromolecular Crowding 6.4 Catalysis Organic Reactions and the Transition State Catalytic Mechanisms

3 Quantum Tunneling and Enzyme Catalysis * The Role of Amino Acids in Enzyme Catalysis The Role of Cofactors in Enzyme Catalyses Effects of Temperature and ph on Enzyme-Catalyzed Reactions Detailed Mechanisms of Enzyme Catalysis 6.5 Enzyme Regulation Genetic Control Covalent Modification Allosteric Regulation Compartmentation Biochemistry in Perspective: Enzymes and Clinical Medicine 7. CARBOHYDRATES 7.1 Monosaccharides Monosaccharide Stereoisomers Cyclic Structure of Monosaccharides Reactions of Monosaccharides Important Monosaccharides Monosaccharide Derivatives 7.2 Disaccharides 7.3 Polysaccharides Homopolysaccharides Heteropolysaccharides 7.4 Glycoconjugates Proteoglycans Glycoproteins 7.5 The Sugar Code Lectins: Translators of the Sugar Code The Glycome * Biochemistry in Perspective Biochemistry in Perspective: Scurvy and Ascorbic Acid 8. CARBOHYDRATE METABOLISM 8.1 Glycolysis The Reactions of the Glycolytic Pathway The Fates of Pyruvate The Energetics of Glycolysis * Regulation of Glycolysis * Biochemistry in Perspective: Glycolysis and Jet Engines 8.2 Gluconeogenesis Gluconeogenesis Reactions Gluconeogenesis Substrates Gluconeogenesis Regulation 8.3 The Pentose Phosphate Pathway 8.4 Metabolism of Other Important Sugars Fructose Metabolism 8.5 Glycogen Metabolism Glycogenesis Glycogenolysis Regulation of Glycogen Metabolism Biochemistry in Perspective: Fermentation: An Ancient Heritage 9. AEROBIC METABOLISM I: THE CITRIC ACID CYCLE 9.1 Oxidation-Reduction Reactions Redox Coenzymes Aerobic Metabolism 9.2 Citric Acid Cycle

4 Conversion of Pyruvate to Acetyl-CoA Reactions of the Citric Acid Cycle Fate of Carbon Atoms in the Citric Acid Cycle The Amphibolic Citric Acid Cycle Citric Acid Cycle Regulation The Glyoxylate Cycle * Biochemistry in Perspective: The Evolutionary History of the Citric Acid Cycle Biochemistry in Perspective: Hans Krebs and the Citric Acid Cycle 10. AEROBIC METABOLISM II: ELECTRON TRANSPORT AND OXIDATIVE PHOSPHORYLATION 10.1 Electron Transport Electron Transport and Its Components Electron Transport Inhibitors 10.2 Oxidative Phosphorylation The Chemiosmotic Theory ATP Synthesis Control of Oxidative Phosphorylation The Complete Oxidation of Glucose Uncoupled Electron Transport * 10.3 Oxidative Stress Reactive Oxygen Species Antioxidant Enzyme Systems Antioxidant Molecules Biochemistry in Perspective: Ischemia and Reperfusion Biochemistry in Perspective: Glucose-6-Phosphate Dehydrogenase Deficiency 11. LIPIDS AND MEMBRANES * 11.1 Lipid Classes Fatty Acids and Their Derivatives The Eicosanoids Triacylglycerols Wax Esters Phospholipids Sphingolipids Sphingolipids Storage Diseases Isoprenoids Lipoproteins 11.2 Membranes Membrane Structure * Membrane Function Biochemistry in Perspective: The Aquaporins * Biochemistry in Perspective: Membrane Fusion and Botulism 12. LIPID METABOLISM 12.1 Fatty Acids and Triacylglycerols Fatty Acid Degradation The Complete Oxidation of a Fatty Acid Fatty Acid Oxidation: Double Bonds and Odd Chains Fatty Acid Biosynthesis Eicosanoid Metabolism * Regulation of Fatty Acid Metabolism in Mammals * Biochemistry in Perspective: Atherosclerosis 12.2 Membrane Lipid Metabolism Phospholipid Metabolism Sphingolipid Metabolism 12.3 Isoprenoid Metabolism Cholesterol Metabolism

5 Steroid Hormone Synthesis Biochemistry in Perspective: Biotransformation 13. PHOTOSYNTHESIS 13.1 Chlorophyll and Chloroplasts 13.2 Light 13.3 Light Reactions Photosystem II and Oxygen Generation Photosystem I and NADPH Synthesis Photophosporylation 13.4 The Light-Independent Reactions The Calvin Cycle Photorespiration * Alternatives to C3 Metabolism Regulation of Photosynthesis Light Control of Photosynthesis Control of Ribulose-1,5-Bisphosphate Carboxylase * Biochemistry in Perspective: Photosynthesis in the Deep Biochemistry in Perspective: Starch and Sucrose metabolism Biochemistry in the Lab: Photosynthetic Studies 14. NITROGEN METABOLISM I: SYNTHESIS 14.1 Nitrogen Fixation The Nitrogen Fixation Reaction Nitrogen Assimilation 14.2 Amino Acid Biosynthesis Amino Acid Metabolism Overview Reactions of Amino Groups Synthesis of the Amino Acids 14.3 Biosynthetic Reactions of Amino Acids One-Carbon Metabolism Glutathione Neurotransmitters * Biochemistry in Perspective: Gaso Transmitters Alkaloids * Nucleotides Heme Biochemistry in Perspective: Parkinson's Disease and Dopamine Biochemistry in Perspective: Lead Poisoning 15. NITROGEN METABOLISM II: DEGRADATION * 15.1 Protein Turnover 15.2 Amino Acid Catabolism Deamination Urea Synthesis Control of the Urea Cycle Catabolism of Amino Acid Carbon Skeletons Biochemistry in Perspective: Disorders of Amino Acid Catabolism 15.3 Degradation of Selected Neurotransmitters 15.4 Nucleotide Degradation Purine Catabolism Pyrimidine Catabolism 15.5 Heme Biotransformation Biochemistry in Perspective: Hyperammonemia Biochemistry in Perspective: Gout

6 16. INTEGRATION OF METABOLISM 16.1 Overview of Metabolism 16.2 Hormones and Intercellular Communication Peptide Hormones Biochemistry in Perspective: Diabetes Mellitus Growth Factors Steroid and Thyroid Hormone Mechanisms 16.3 Metabolism in the Mammalian Body: Division of Labor Gastrointestinal Tract Liver Muscle Adipose tissue Brain Kidney 16.4 The Feeding-Fasting Cycle The Feeding Phase The Fasting Phase * Feeding Behavior * Biochemistry in Perspective: Obesity and the Metabolic Syndrome Biochemistry in the Lab: Hormone Methods 17. NUCLEIC ACIDS 17.1 DNA DNA Structure: The Nature of Mutation DNA Structure: From Mendel's Garden to Watson and Crick DNA Structure: Variations on a Theme DNA Supercoiling * Chromosomes and Chromatin * Genome Structure Biochemistry in the Lab: Nucleic Acid Methods Biochemistry in Perspective: Forensic Investigations 17.2 RNA Transfer RNA Ribosomal RNA Messenger RNA * Noncoding RNA 17.3 Viruses The Structure of Viruses Biochemistry in Perspective: Viral "Lifestyles" Available Online: Biochemistry in Perspective: Epigenetics and the Epigenome: Genetic Inheritance Beyond DNA Base Sequences 18. GENETIC INFORMATION 18.1 Genetic Information: Replication, Repair, and Recombination DNA Replication DNA Repair DNA Recombination Biochemistry in the Lab: Genomics 18.2 Transcription Transcription in Prokaryotes Transcription in Eukaryotes 18.3 Gene Expression * Gene Expression in Prokaryote * Gene Expression in Eukaryotes Biochemistry in Perspective: Carcinogenesis

7 Thought Question 19. PROTEIN SYNTHESIS 19.1 The Genetic Code Codon-Anticodon Interactions The Aminoacyl-tRNA Synthetase Reaction: The Second Genetic Code 19.2 Protein Synthesis Prokaryotic Protein Synthesis Eukaryotic Protein Synthesis Biochemistry in Perspective: EF-TU: A Motor Protein * Biochemistry in Perspective: Context-Dependent Coding Reassignment Biochemistry in the Lab: Proteomics Appendix A: Solutions Glossary Credits Index