Biochemistry

Preface Acknowledgement

Chapter 1. Biochemistry: Subject Overview 1.1 Central Themes 1.2 Central Dogma of Molecular Biology

Chapter 2. Cell Biology Review 2.1 The Animal Cell 2.2 The Plant Cell 2.3 Selected Organelles 2.4 The Cell Cycle: Mitotic Cell Division 2.5 Viruses

Chapter 3. Chemistry Review 3.1 Organic Compounds 3.2 Chirality 3.3 Chemical Reactions 3.4 Physical Chemistry Concepts 3.5 Buffering of Blood: The Bicarbonate System

Chapter 4. Amino Acids 4.1 Basic Structures 4.2 Amino Acid 'R Groups' 4.3 Ionization Properties 4.4 Drawing Peptide Titration Plots 4.5 Factors That Influence the pKa of Protonatable/Deprotonatable Groups in Proteins

Chapter 5. Proteins 5.1 Peptide Bonds 5.2 Purification and Characterization of Proteins

Chapter 6. Protein Structure 6.1 Conformation 6.2 Classification of Substructure 6.3 Alpha Helices 6.4 Beta Sheets 6.5 U-Turns 6.6 Ramachandran Plot 6.7 Stabilizing Factors 6.8 Thermodynamics of Protein Folding: The Hydrophobic Effect 6.8.1 Temperature-Dependent Denaturation 6.9 Chaotropes and the Hofmeister Series 6.10 Sodium Dodecyl Sulfate (SDS): Chaotrope Action 6.11 Visualizing the Energy Landscape 6.12 Protein Maturation

Chapter 7. Ligand Binding and Functional Control 7.1 Oxygen Transport in Blood 7.2 Hemoglobin Oxygen Binding: Cooperativity 7.3 Antibodies: Immunological Recognition

Chapter 8. Enzymes 8.1 Enzymes Are Biological Catalysts 8.2 Enzyme Function: Activity Assays and Enzyme Kinetics 8.3 Requirements for Catalysis 8.4 Comparing Enzymes and Relative Efficiency of Use of Substrates 8.5 Drug Design 8.6 Enzyme Inhibitors 8.7 Allosterism 8.8 Phosphorylation and Dephosphorylation

Chapter 9. Metabolic Enzyme Action 9.1 Enzyme Mechanisms 9.2 Modes of Catalysis 9.3 The Reaction Coordinate 9.4 Induced Fit Revisited 9.5 Acid-Base Catalysis 9.6 Covalent Group Transfer 9.7 The Serine Protease Catalytic Triad Mechanism 9.8 The Active Site of Tyrosyl-tRNA Synthetase

Chapter 10. Coenzymes 10.1 Classification 10.2 Survey of the Coenzymes 10.3 Metals 10.4. Carbohydrates-Based Cofactors 10.5 Fat Soluble Vitamins

Chapter 11. Carbohydrates and Glycoconjugates 11.1 Carbohydrates: Definition 11.2 Monosaccharides: Aldoses 11.3 Monosaccharides: Ketoses 11.4 Structural Features 11.5 Intramolecular Cyclization 11.6 Conformations: Sugar Puckers 11.7 Sugar Derivatives 11.8 Disaccharides 11.9 Polysaccharides 11.10 Carbohydrate-Protein Conjugates 11.11 Synthesis and Structural Characterization

Chapter 12. Lipids 12.1 Structural Overview 12.2 Saturated and Unsaturated Fatty Acids 12.3 Functions 12.4 Diacylglycerol Lipid Derivatives 12.5 Structural Motifs 12.6 Assembly 12.7 Structural and Dynamic Characterization 12.8 Eicosanoids 12.9 Phospholipases 12.10 Phosphoinositides 12.11 Steroids 12.12 A Potpourri of Lipids

Chapter 13. Membranes 13.1 The Fluid Mosaic Model 13.2 Detergents 13.3 Distribution of Lipids in Biological Membranes 13.4 The Hydropathicity Scale 13.5 Lipid-Anchored Membrane Proteins 13.6 The Erythrocyte Cytoskeleton

Chapter 14. Transport Through Membranes 14.1 The Transmembrane Potential 14.2 Active Transport 14.3 Ionophores 14.4 The Acetylcholine Receptor Ion Channel 14.5 Lactose Permease and Secondary Active Transport 14.6 Mechanism of Transport by Na+, K+ ATPase 14.7 Ion Channel Blockers

Chapter 15. Signal Transduction 15.1 Signaling Pathways: Hormones, GTPases, Second Messengers, and Intracellular Regulation 15.2 The Adenylate Cyclase Signaling Pathway 15.3 The Inositol-Phospholipid Signaling Pathway 15.4 Phorbol Myristyl Acetate 15.5 The Insulin Receptor 15.6 Glucagon 15.7 G-Proteins

Chapter 16. Nucleic Acids: DNA 16.1 DNA and RNA 16.2 Physical Properties 16.3 Secondary Structure 16.4 Backbone Structure 16.5 Counterions 16.6 Chemical Synthesis 16.7 Watson-Crick Base Pairs 16.8 Structural Modifications 16.9 Three-Dimensional Structures 16.10 Recognition of Sequences 16.11 Genetic Mutations and Antisense Nucleic Acids 16.12 Unusual DNA 16.13 Stabilization of Nucleic Acids 16.14 Secondary Structure Predictions 16.15 Chromosomes 16.16 Some Protein Nucleic Acid Binding Motifs 16.17 Recombination

Chapter 17. RNA 17.1 Cells Contain a Variety of Types of RNA 17.2 RNAs Have Stable Secondary Structure 17.3 Tertiary Structure: Transfer RNA 17.4 Messenger RNA (mRNA) 17.5 Eukaryotic Messenger RNA 17.6 Alkaline Hydrolysis of RNA 17.7 Small Interfering RNA

Chapter 18. Biotechnology 18.1 Restriction Endonucleases 18.2 Cloning in a Nutshell 18.3 DNA Preparation: Phenol-Chloroform Extraction 18.4 Polymerase Chain Reaction 18.5 Probe DNA

Chapter 19. Metabolism 19.1 Overview 19.2 Metabolic Pathway Types 19.3 Energy Conservation 19.4 Key Pathways/Reactions

Chapter 20. Bioenergetics 20.1 Reaction Equilibria: Standard and Actual Free Energies 20.2 Metabolically Irreversible and Near Equilibrium Reactions 20.3 Energies and Regulation of Glycolysis

Chapter 21. Bioelectrochemistry 21.1 Redox Reaction Principles 21.2 Redox Energetics: The Nernst Equation 21.3 Electron Transport Chains

Chapter 22. Glycolysis 22.1 Reactions 1 through 10 22.2 Regulation: Activation and Inhibition 22.3 Four Fates of Pyruvate

Chapter 23. The Krebs Cycle 23.1 Pathway 23.2 Reactions 23.3 Yields 23.4 Cellular Redox Potential 23.5 Regulation

Chapter 24. Gluconeogenesis 24.1 Reactions 24.2 Regulation 24.3 Sources Used to Produce Glucose

Chapter 25. Electron Transport and Oxidative Phosphorylation 25.1 Mitochondria in Red and White Muscle 25.2 Overall Process 25.3 Chemical and Potential Energies That Drive Proton Transport 25.4 Mitochondrial Electron Transport 25.5 Electron Transfer and Proton Flow in Complexes I through IV 25.6 Oxidative Phosphorylation

Chapter 26. The Malate-Aspartate Shuttle and Proteomics 26.1 Getting NADH into the Mitochondrion: Isozymes 26.2 Isozymes and Proteomics 26.3 Characterization by Two-dimensional Gel Electrophoresis 26.4 Mass Spectrometry and Proteomics

Chapter 27. Degradation and Synthesis of Lipids 27.1 Beta Oxidation of Saturated Fatty Acids 27.2 Biosynthesis of Fatty Acids 27.3 Length Determination of Fatty Acids 27.4 Synthesis of Acidic Phospholipids 27.5 Cholesterol Biosynthesis 27.6 Regulating Cholesterol Levels

Chapter 28. Photosynthesis 28.1 Light and Dark Reactions 28.2 Photo-Gathering Pigments 28.3 Photosynthetic Electron Transport Pathway (Z Scheme)

Chapter 29. The Calvin Cycle 29.1 The Dark Reactions: Carbon Fixation 29.2 Biosynthesis of Ribose-5-phosphate 29.3 RuBisCO Mechanism 29.4 The C4 and CAM Pathways

Chapter 30. The Urea Cycle 30.1 Purpose and Reactions 30.2 Regulation 30.3 Comparative Nitrogen Excretion 30.4 Protein Degradation and Programmed Cell Death

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