Brief ContentsPrefaceAcknowledgement1. Biochemistry: Subject Overview1.1 Central Themes1.2 Central Dogma of Molecular Biology2. Cell Biology Review2.1 The Animal Cell2.2 The Plant Cell2.3 Selected Organelles2.
4 The Cell Cycle: Mitotic Cell Division2.5 Viruses3. Chemistry Review3.1 Organic Compounds3.2 Chirality3.3 Chemical Reactions3.4 Physical Chemistry Concepts3.5 Buffering of Blood: The Bicarbonate System4.
Amino Acids4.1 Basic Structures4.2 Amino acid ''R Groups''4.3 Ionization Properties4.4 Drawing Peptide Titration Plots4.5 Factors That Influence the pKa of Protonatable/Deprotonatable Groups in Proteins5. Proteins5.1 Peptide Bonds5.
2 Purification and Characterization of Proteins6. Protein Structure6.1 Conformation6.2 Classification of Substructure6.3 Alpha (?) Helices6.4 Beta Sheets6.5 U-Turns6.6 Ramachandran Plot6.
7 Stabilizing Factors6.8 Thermodynamics of Protein Folding: The Hydrophobic Effect6.8.1 Temperature-Dependant Denaturation6.9 Chaotropes and The Hofmeister Series6.10 Sodium Dodecyl Sulfate (SDS): Chaotrope Action6.11 Visualizing the Energy Landscape6.12 Protein Maturation7.
Ligand Binding and Functional Control7.1 Oxygen Transport in Blood7.2 Hemoglobin Oxygen Binding: Cooperativity7.3 Antibodies: Immunological Recognition8. Enzymes8.1 Enzymes are Biological Catalysts8.2 Enzyme Function: Activity Assays and Enzyme Kinetics8.3 Requirements for Catalysis8.
4 Comparing Enzymes and Relative Efficiency of Use of Substrates8.5 Drug Design8.6 Enzyme Inhibitors8.7 Allosterism8.8 Phosphorylation and Dephosphorylation9. Metabolic Enzyme Action9.1 Enzyme Mechanisms9.2 Modes of Catalysis9.
3 The Reaction Coordinate9.4 Induced Fit Revisited9.5 Acid-Base Catalysis9.6 Covalent Group Transfer9.7 The Serine Protease Catalytic Triad Mechanism9.8 The Active Site of Tyrosyl-tRNA Synthetase10. Coenzymes10.1 Classification10.
2 Survey of the Coenzymes10. 3 Metals10.4. Carbohydrates-Based Cofactors10.5 Fat Soluble Vitamins11. Carbohydrates and Glycoconjugates11.1 Carbohydrates: Definition11.2 Monosaccharides: Aldoses11.
3 Monosaccharides: Ketoses11.4 Structural Features11.5 Intramolecular Cyclization11.6 Conformations: Sugar Puckers11.7 Sugar Derivatives11.8 Disaccharides11.9 Polysaccharides11.10 Carbohydrate-Protein Conjugates11.
11 Synthesis and Structural Characterization12. Lipids12.1 Structural Overview12.2 Saturated and Unsaturated Fatty Acids12.3 Functions12.4 Diacylglycerol Lipid Derivatives12.5 Structural Motifs12.6 Assembly12.
7 Structural and Dynamic Characterization12.8 Eicosanoids12.9 Phospholipases12.10 Phosphoinositides12.11 Steroids12.12 A Potpourri of Lipids13. Membranes13.1 The Fluid Mosaic Model13.
2 Detergents13.3 Distribution of Lipids in Biological Membranes13.4 The Hydropathicity Scale13.5 Lipid-Anchored Membrane Proteins13.6 The Erythrocyte Cytoskeleton14. Transport Through Membranes14.1 The Transmembrane Potential14.2 Active Transport14.
3 Ionophores14.4 The Acetylcholine Receptor Ion Channel14.5 Lactose Permease and Secondary Active Transport14.6 Mechanism of Transport by Na+, K+ ATPase14.7 Ion Channel Blockers15. Signal Transduction15.1 Signaling Pathways: Hormones, GTPases, Second Messengers and Intracellular Regulation15.2 The Adenylate Cyclase Signaling Pathway15.
3 The Inositol-Phospholipid Signaling Pathway15.4 Phorbol Myristyl Acetate15.5 The Insulin Receptor15.6 Glucagon15.7 G-Proteins16. Nucleic Acids: DNA16.1 DNA and RNA16.2 Physical Properties16.
3 Secondary Structure16.4 Backbone Structure16.5 Counterions16.6 Chemical Synthesis16.7 Watson-Crick Base Pairs16.8 Structural Modifications16.9 Three-Dimensional Structures16.10 Recognition of Sequences16.
11 Genetic Mutations and Antisense Nucleic Acids16.12 Unusual DNA16.13 Stabilization of Nucleic Acids16.14 Secondary Structure Predictions16.15 Chromosomes16.16 Some Protein Nucleic Acid Binding Motifs16.17 Recombination17. RNA17.
1 Cells Contain a Variety of Types of RNA17.2 RNAs Have Stable Secondary Structure17.3 Tertiary Structure: Transfer RNA17.4 Messenger RNA (mRNA)17.5 Eukaryotic Messenger RNA17.6 Alkaline Hydrolysis of RNA17.7 Small Interfering RNA18. Biotechnology18.
1 Restriction Endonucleases18.2 Cloning in a Nutshell18.3 DNA Preparation: Phenol-Chloroform Extraction18.4 Polymerase Chain Reaction18.5 Probe DNA19. Metabolism19.1 Overview19.2 Metabolic Pathway Types19.
3 Energy Conservation19.4 Key Pathways/Reactions20. Bioenergetics20.1 Reaction Equilibria: Standard and Actual Free Energies20.2 Metabolically Irreversible and Near Equilibrium Reactions20.3 Energies and Regulation of Glycolysis21. Bioelectrochemistry21.1 Redox Reaction Principles21.
2 Redox Energetics: The Nernst Equation21.3 Electron Transport Chains22. Glycolysis22.1 Reactions 1 Through 1022.2 Regulation: Activation and Inhibition22.3 Four Fates of Pyruvate23. The Krebs Cycle23.1 Pathway23.
2 Reactions23.3 Yields23.4 Cellular Redox Potential23.5 Regulation24. Gluconeogenesis24.1 Reactions24.2 Regulation24.3 Sources Used to Produce Glucose25.
Electron Transport and Oxidative Phosphorylation25.1 Mitochondria in Red and White Muscle25.2 Overall Process25.3 Chemical and Potential Energies That Drive Proton Transport25.4 Mitochondrial Electron Transport25.5 Electron Transfer and Proton Flow in Complexes I through IV25.6 Oxidative Phosphorylation26. The Malate-Aspartate Shuttle and Proteomics26.
1 Getting NADH Into the Mitochondrion: Isozymes26.2 Isozymes and Proteomics26.3 Characterization by Two-dimensional Gel Electrophoresis26.4 Mass Spectrometry and Proteomics27. Degradation and Synthesis of Lipids27.1 Beta Oxidation of Saturated Fatty Acids27.2 Biosynthesis of Fatty Acids27.3 Length Determination of Fatty Acids27.
4 Synthesis of Acidic Phospholipids27.5 Cholesterol Biosynthesis27.6 Regulating Cholesterol Levels28. Photosynthesis28.1 Light and Dark Reactions28.2 Photo-Gathering Pigments28.3 Photosynthetic Electron Transport Pathway (Z scheme)29. The Calvin Cycle29.
1 The Dark Reactions: Carbon Fixation29.2 Biosynthesis of Ribose-5-phosphate29.3 RuBisCO Mechanism29.4 The C4 and CAM Pathways30. The Urea Cycle30.1 Purpose and Reactions30.2 Regulation30.3 Comparative Nitrogen Excretion30.
4 Protein Degradation and Programmed Cell DeathStudy GuideReview Session for Chapters 1 - 3Review Session for Chapter 4Review Session for Chapters 5 and 6Review Session for Chapters 7 - 8.6Review Sessions for Chapters 8.7 - 8.8Review Session for Chapter 9Review Session for Chapters 10 - 11.4Review Session for Chapters 10 - 11.4: KeyReview Session for Chapters 11.5 - 12.5Review Session for Chapters 11.
5 - 12.5: KeyReview Session for Chapters 13 - 14.7Review Session for Chapters 13 - 14.7: KeyReview Session for Chapters 16.2 - 17.6Review Session for Chapters 16.2 - 17.6: KeyReview Session for Chapters 19 - 20Review Session for Chapters 19 - 20: KeyReview Session for Chapters 21 - 25Review Session for Chapters 21 - 25: KeyReview Session for Chapter 27Review Session for Chapter 27: KeyPractice Exam 1, KeyPractice Exam 2, KeyPractice Exam 3, KeyPractice Exam 4, KeyFinal Test ReviewFinal Test Review (with answers).