BIOCHEMISTRY

Table of Contents

Part I: Molecular Components of Cells

Chapter 1: Chemistry is the Logic of Biological Phenomena

• 1.1 Distinctive Properties of Living Systems
• 1.2 Biomolecules: The Molecules of Life
• 1.3 A Biomolecular Hierarchy: Simple Molecules Are the Units of Complex Structures
• 1.4 Properties of Biomolecules Reflect Their Fitness to the Living Condition
• 1.5 Organization and Structure of Cells
• 1.6 Viruses Are Supramolecular Assemblies Acting as Cell Parasites

Chapter 2: Water, pH and Ionic Equilibria

• 2.1 Properties of Water
• 2.2 pH
• 2.3 Buffers
• 2.4 Water's Unique Role in the Fitness of the Environment

Chapter 3: Amino Acids

• 3.1 Amino Acids: Building Blocks of Proteins
• 3.2 Acid-Base Chemistry of Amino Acids
• 3.3 Reactions of Amino Acids
• 3.4 Optical Activity and Stereochemistry of Amino Acids
• 3.5 Spectroscopic Properties of Amino Acids
• 3.6 Separation and Analysis of Amino Acid Mixtures

Chapter 4: Proteins: Their Biological Functions and Primary Structure

• 4.1 Proteins Are Linear Polymers of Amino Acids
• 4.2 Architecture of Protein Molecules
• 4.3 The Many Biological Functions of Proteins
• 4.4 Some Proteins Have Chemical Groups Other Than Amino Acids
• 4.5 Reactions of Peptides and Proteins
• 4.6 The Purification of Protein Mixtures
• 4.7 The Primary Structure of a Protein: Determining the Amino Acid Sequence
• 4.8 The Nature of Amino Acid Sequences
• 4.9 Synthesis of Polypeptides in the Laboratory
• Appendix: Protein Techniques

Chapter 5: Proteins: Secondary, Tertiary and Quaternary Structure

• 5.1 Forces Influencing Protein Structure
• 5.2 Role of the Amino Acid Sequence in Protein Structure
• 5.3 Secondary Structure in Proteins
• 5.4 Protein Folding and Tertiary Structure
• 5.5 Subunit Interactions and Quaternary Structure

Chapter 6: Nucleotides and Nucleic Acids

• 6.1 Nitrogenous Bases
• 6.2 The Pentoses of Nucleotides and Nucleic Acids
• 6.3 Nucleosides Are Formed by Joining a Nitrogenous Base to a Sugar
• 6.4 Nucleotides Are Nucleoside Phosphates
• 6.5 Nucleic Acids Are Polynucleotides
• 6.6 Classes of Nucleic Acids
• 6.7 Hydrolysis of Nucleic Acids

Chapter 7: Structure of Nucleic Acids

• 7.1 The Primary Structure of Nucleic Acids
• 7.2 The ABZs of DNA Secondary Structure
• 7.3 Supercoils and Cruciforms: Tertiary Structure in DNA
• 7.4 Denaturation and Renaturation of DNA
• 7.5 Chromosome Structure
• 7.6 Chemical Synthesis of Nucleic Acids
• 7.7 Secondary and Tertiary Structure of RNA

Chapter 8: Recombinant DNA: Cloning and Creation of Chimeric Genes

• 8.1 Cloning
• 8.2 DNA Libraries
• 8.3 Polymerase Chain Reaction (PCR)
• 8.4 Recombinant DNA Technology: An Exciting Scientific Frontier

Chapter 9: Lipids and Membranes

• 9.1 Classes of Lipids
• 9.2 Membranes
• 9.3 Structure of Membrane Proteins

Chapter 10: Carbohydrates and Cell Surfaces

• 10.1 Carbohydrates Nomenclature
• 10.2 Monosaccharides
• 10.3 Oligosaccharides
• 10.4 Polysaccharides
• 10.5 Glycoproteins
• 10.6 Proteoglycans

Part II: Enzymes and Energetics

Chapter 11: Enzyme Kinetics

• 11.1 Enzymes - Catalytic Power, Specificity, and Regulation
• 11.2 Introduction to Enzyme Kinetics
• 11.3 Kinetics of Enzyme-Catalyzed Reactions
• 11.4 Enzyme Inhibition
• 11.5 Kinetics of Enzyme-Catalyzed Reactions Involving Two or More Substrates
• 11.6 RNA and Antibody Molecules as Enzymes: Ribozymes and Abzymes

Chapter 12: Enzyme Specificity and Allosteric Regulation

• 12.1 Specificity Is the Result of Molecular Recognition
• 12.2 Controls Over Enzymatic Activity - General Considerations
• 12.3 The Allosteric Regulation of Enzymatic Acitivity
• 12.4 Hemoglobin and Myoglobin
• 12.5 Eschericia coli Aspartate Transcarbamoylase - An Allosteric Enzyme
• 12.6 Allosteric Models
• Appendix: The Oxygen-Binding Curves of Myoglobin and Hemoglobin

Chapter 13: Mechanisms of Enzyme Action

• 13.1 The Basic Principle - Stabilization of the Transition State
• 13.2 Enzymes Provide Enormous Rate Accelerations
• 13.3 The Binding Energy of ES is Crucial to Catalysis
• 13.4 Entropy Loss and Destabilization of the ES Complex
• 13.5 Transition-State Analogs Bind Very Tightly to the Active Site
• 13.6 Covalent Catalysis
• 13.7 General Acid-Base Catalysis
• 13.8 Metal Ion Catalysis
• 13.9 Proximity
• 13.10 Typical Enzyme Mechanisms
• 13.11 Serine Proteases
• 13.12 The Aspartic Proteases
• 13.13 Lysozyme
• 13.14 Carboxypeptidase A
• 13.15 Liver Alcohol Dehydrogenase

Chapter 14: Coenzymes and Vitamins

• 14.1 Vitamin B1: Thiamine and Thiamine Pyrophosphate
• 14.2 Vitamins Containing Adenine Nucleotides
• 14.3 Nicotinic Acid and the Nicotinamide Coenzymes
• 14.4 Riboflavin and the Flavin Coenzymes
• 14.5 Pantothenic acid and Coenzyme A
• 14.6 Vitamin B6: Pyridoxine and Pyridoxal Phosphate
• 14.7 Vitamin B12: Cyanocobalamin
• 14.8 Vitamin C: Ascorbic Acid
• 14.9 Biotin
• 14.10 Lipoic Acid
• 14.11 Folic Acid
• 14.12 The Vitamin A Group
• 14.13 The Vitamin D Group
• 14.14 Vitamin E: Tocopherol
• 14.15 Vitamin K: Naphthoquinone

Chapter 15: Thermodynamics of Biological Systems

• 15.1 Basic Thermodynamic Concepts
• 15.2 The First Law: Heat, Work, and Other Forms of Energy
• 15.3 Enthalpy: A More Useful Function for Biological Systems
• 15.4 The Second Law and Entropy: An Orderly Way of Thinking About Disorder
• 15.5 The Third Law: Why is "Absolute Zero" So Important?
• 15.6 A Hypothetical But Useful Device
• 15.7 The Physical Significance of Thermodynamic Properties
• 15.8 The Effect of pH on Standard-State Free Energies
• 15.9 The Important Effect of Concentration on Net Free Energy Changes
• 15.10 Irreversible Thermodynamics - Life in the Nonequilibrium Lane
• 15.11 The Importance of Coupled Processes in Living Things

Chapter 16: ATP and Energy-Rich Compounds

• 16.1 The High-Energy Biomolecules
• 16.2 Classes of High-Energy Compounds
• 16.3 Complex Equilibria Involved in ATP Hydrolysis
• 16.4 The Effect of Concentration on the Free Energy of Hydrolysis of ATP
• 16.5 The Daily Human Reguirement for ATP

Part III: Metabolism and Its Regulation

Chapter 17: Metabolism - An Overview

• 17.1 Virtually All Organisms Have the Same Basic Set of Metabolic Pathways
• 17.2 Metabolism Consists of Catabolism and Anabolism
• 17.3 Intermediary Metabolism Is a Tightly Regulated, Integrated Process
• 17.4 Experimental Methods To Reveal Metabolic Pathways

Chapter 18: Glycolysis

• 18.1 Overview of Glycolysis
• 18.2 The Importance of Coupled Reactions in Glycolysis
• 18.3 The First Phase of Glycolysis
• 18.4 The Second Phase of Glycolysis
• 18.5 The Metabolic Fates of NADH and Pyruvate - The Products of Glycolysis
• 18.6 Anaerobic Pathways for Pyruvate
• 18.7 The Energetic Elegance of Glycolysis
• 18.8 Utilization of Other Substrates in Glycolysis

Chapter 19: The Tricarboxylic Acid Cycle

• 19.1 Hans Krebs and the Discovery of the TCA Cycle
• 19.2 The TCA Cycle - A Brief Summary
• 19.3 The Bridging Step: Oxidative Decarboxylation of Pyruvate
• 19.4 Entry into the Cycle: The Citrate Synthase Reaction
• 19.5 The Isomerization of Citrate by Aconitase
• 19.6 Isocitrate Dehydrogenase - The First Oxidation in the Cycle
• 19.7 Alpha-Ketoglutarate Dehydrogenase - A Second Decarboxylation
• 19.8 Succinyl-CoA Synthetase - A Substrate-Level Phosphorylation
• 19.9 Succinate Dehydrogenase - An Oxidation Involving FAD
• 19.10 Fumarase Catalyzes Trans-Hydration of Fumarate
• 19.11 Malate Dehydrogenase - Completing the Cycle
• 19.12 A Summary of the Cycle
• 19.13 The TCA Cycle Provides Intermediates for Biosynthetic Pathways
• 19.14 The Anaplerotic, or "Filling Up", Reactions
• 19.15 Regulation of the TCA Cycle
• 19.16 The Glyoxylate Cycle of Plants and Bacteria

Chapter 20: Electron Transport and Oxidative Phosphorylation

• 20.1 Electron Transport and Oxidative Phosphorylation Are Membrane-Associated Processes
• 20.2 Reduction Potentials - An Accounting Device for Free Energy Changes in Redox Reactions
• 20.3 The Electron Transport Chain - An Overview
• 20.4 Complex I: NADH-Coenzyme Q Reductase
• 20.5 Complex II: Succinate-Coenzyme Q Reductase
• 20.6 Complex III: Coenzyme Q - Cytochrome c Reductase
• 20.7 Complex IV: Cytochrome c Oxidase
• 20.8 The Thermodynamic View of Chemiosmotic Coupling
• 20.9 ATP Synthase
• 20.10 Inhibitors of Oxidative Phosphorylation
• 20.11 Uncouplers Disrupt the Coupling of Electron Transport and ATP Synthase
• 20.12 Shuttle Systems Feed the Electrons of Cytosolic NADH into Electron Trasnport
• 20.13 ATP Exits the Mitochondria via an ATP-ADP Translocase
• 20.14 What is the P/O Ratio for Mitochondrial Electron Trasnport and Oxidative Phosphorylation?

Chapter 21: Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

• 21.1 Gluconeogenesis
• 21.2 Regulation of Gluconeogenesis
• 21.3 Glycogen Catabolism
• 21.4 Glycogen Synthesis
• 21.5 Control of Glycogen Metabolism
• 21.6 The Pentose Phosphate Pathway

Chapter 22: Photosynthesis

• 22.1 General Aspects of Photosynthesis
• 22.2 Photosynthesis Depends on the Photoreactivity of Chlorophyll
• 22.3 Eukaryotic Phototrophs Posess Two Distinct Photosystems
• 22.4 The Z Scheme of Photosynthesis
• 22.5 The Molecular Architecture of Photosynthetic Reaction Centers
• 22.6 The Quantum Yield of Photosynthesis
• 22.7 Light-Driven ATP Synthesis - Photophosphorylation
• 22.8 Carbon Dioxide Fixation
• 22.9 The Ribulose Bisphosphate Oxygenase Reaction: Photorespiration
• 22.10 The Calvin-Benson Cycle
• 22.11 Regulation of Carbon Dioxide Fixation
• 22.12 The C-4 Pathway of CO2 Fixation
• 22.13 Crassulacean Acid Metabolism

Chapter 23: Fatty Acid Metabolism

• 23.1 Mobilization of Fats from Dietary Intake and Adipose Tissue
• 23.2 Beta-Oxidation of Fatty Acids
• 23.3 Beta-Oxidation of Odd-Carbon Fatty Acids
• 23.4 Beta-Oxidation of Unsaturated Fatty Acids
• 23.5 Other Aspects of Fatty Acid Oxidation
• 23.6 Ketone Bodies

Chapter 24: Lipid Biosynthesis

• 24.1 The Fatty Acid Biosynthesis and Degradation Pathways Are Different
• 24.2 Biosynthesis of Complex Lipids
• 24.3 Eicosanoid Biosynthesis and Function
• 24.4 Cholesterol Biosynthesis
• 24.5 Transport of Many Lipids Occurs via Lipoprotein Complexes
• 24.6 Biosynthesis of Bile Acids
• 24.7 Synthesis and Metabolism of Steroid Hormones

Chapter 25: Metabolic Integration and the Unidirectionality of Pathways

• 25.1 A systems Analysis of Metabolism
• 25.2 Metabolic Stoichiometry and ATP Coupling
• 25.3 Unidirectionality
• 25.4 Metabolism in a Multicellular Organism

Chapter 26: Nitrogen Acquisition and Amino Acid Metabolism

• 26.1 The Two Major Pathways of Biological N Acquisition
• 26.2 The Fate of Ammonium
• 26.3 Escherichia coli Glutamine Synthetase: A Case Study in Enzyme Regulation
• 26.4 Amino Acid Biosynthesis
• 26.5 Metabolic Degradation of Amino Acids

Chapter 27: The Synthesis and Degradation of Nucleotides

• 27.1 Nucleotide Biosynthesis
• 27.2 The Biosynthesis of Purines
• 27.3 Purine Salvage
• 27.4 Purine Degradation
• 27.5 The Biosynthesis of Pyrimidines
• 27.6 Pyrimidine Degradation
• 27.7 Deoxyribonucleotide Biosynthesis
• 27.8 Synthesis of Thymine Nucleotides

Part IV: Genetic Information

Chapter 28: DNA: Genetic Information, Recombination and Mutation

• 28.1 Genetic Information: The One-Gene, One-Enzyme Hypothesis
• 28.2 The Discovery That DNA Carries Genetic Information
• 28.3 Genetic Information in Bacteria: Its Organization, Transfer, and Rearrangement
• 28.4 The Molecular Mechanism of Recombination
• 28.5 The Immunoglobulin Genes: Generating Protein Diversity Using Genetic Recombination
• 28.6 The Molecular Nature of Mutation
• 28.7 RNA as Genetic Material
• 28.8 Transgenic Animals

Chapter 29: DNA Replication and Repair

• 29.1 DNA Replication is Semiconservative
• 29.2 The Enzymology of DNA Replication
• 29.3 General Features of DNA Replication
• 29.4 The Mechanism of DNA Replication in E. coli
• 29.5 Eukeryotic DNA Replication
• 29.6 Reverse Transcriptase: An RNA-Directed DNA Polymerase
• 29.7 DNA Repair

Chapter 30: Transcription and the Regulation of Gene Expression

• 30.1 Transcription in Prokaryotes
• 30.2 Transcription in Eukaryotes
• 30.3 The Regulation of Transcription in Prokaryotes
• 30.4 Transcription Regulation in Eukaryotes
• 30.5 Structural Motifs in DNA-Binding Regulatory Proteins
• 30.6 Post-Transcriptional Processing of mRNA
• Appendix: DNA:Protein Interactions

Chapter 31: The Genetic Code

• 31.1 The Collinearity of Gene Structure and Protein Structure
• 31.2 Elucidating the Genetic Code
• 31.3 The Nature of the Genetic Code
• 31.4 Amino Acid Activation for Protein Synthesis: Aminoacyl-tRNA Synthetases
• 31.5 Codon-Anticodon Pairing, Third-Base Degeneracy, and the Wobble Hypothesis
• 31.6 Codon Usage
• 31.7 Nonsense Suppression

Chapter 32: Protein Synthesis and Degradation

• 32.1 Ribosome Structure and Assembly
• 32.2 The Mechanics of Protein Synthesis
• 32.3 Protein Synthesis in Eukaryotic Cells
• 32.4 Inhibitors of Protein Synthesis
• 32.5 Protein Folding
• 32.6 Post-Translational Processing of Proteins
• 32.7 Protein Degradation

Chapter 33: Molecular Evolution

• 33.1 An Overview of Evolution
• 33.2 Evolutionary Change in Nucleotide Sequences
• 33.3 Molecular Clocks
• 33.4 Nonrandom Codon Usage
• 33.5 Evolution by Gene Duplication and Exon Shuffling
• 33.6 Gene Sharing
• 33.7 Proton-Translocating ATPases: Clues to Early Evolution

Part V: Molecular Aspects of Cell Biology

Part V: Molecular Aspects of Cell Biology is published separately in a paperback edition by Saunders College Publishing.