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| Brief Contents | |
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| Preface | |
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| Acknowledgement | |
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| Biochemistry: Subject Overview | |
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| Central Themes | |
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| Central Dogma of Molecular Biology | |
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| Cell Biology Review | |
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| The Animal Cell | |
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| The Plant Cell | |
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| Selected Organelles | |
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| The Cell Cycle: Mitotic Cell Division | |
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| Viruses | |
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| Chemistry Review | |
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| Organic Compounds | |
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| Chirality | |
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| Chemical Reactions | |
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| Physical Chemistry Concepts | |
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| Buffering of Blood: The Bicarbonate System | |
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| Amino Acids | |
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| Basic Structures | |
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| Amino acid 'R Groups' | |
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| Ionization Properties | |
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| Drawing Peptide Titration Plots | |
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| Factors That Influence the pKa of Protonatable/Deprotonatable Groups in Proteins | |
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| Proteins | |
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| Peptide Bonds | |
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| Purification and Characterization of Proteins | |
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| Protein Structure | |
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| Conformation | |
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| Classification of Substructure | |
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| Alpha (?) Helices | |
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| Beta Sheets | |
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| U-Turns | |
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| Ramachandran Plot | |
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| Stabilizing Factors | |
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| Thermodynamics of Protein Folding: The Hydrophobic Effect | |
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| Temperature-Dependant Denaturation | |
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| Chaotropes and The Hofmeister Series | |
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| Sodium Dodecyl Sulfate (SDS): Chaotrope Action | |
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| Visualizing the Energy Landscape | |
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| Protein Maturation | |
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| Ligand Binding and Functional Control | |
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| Oxygen Transport in Blood | |
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| Hemoglobin Oxygen Binding: Cooperativity | |
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| Antibodies: Immunological Recognition | |
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| Enzymes | |
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| Enzymes are Biological Catalysts | |
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| Enzyme Function: Activity Assays and Enzyme Kinetics | |
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| Requirements for Catalysis | |
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| Comparing Enzymes and Relative Efficiency of Use of Substrates | |
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| Drug Design | |
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| Enzyme Inhibitors | |
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| Allosterism | |
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| Phosphorylation and Dephosphorylation | |
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| Metabolic Enzyme Action | |
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| Enzyme Mechanisms | |
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| Modes of Catalysis | |
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| The Reaction Coordinate | |
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| Induced Fit Revisited | |
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| Acid-Base Catalysis | |
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| Covalent Group Transfer | |
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| The Serine Protease Catalytic Triad Mechanism | |
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| The Active Site of Tyrosyl-t | |
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| RNA Synthetase | |
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| Coenzymes | |
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| Classification | |
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| Survey of the Coenzymes | |
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| 3 Metals | |
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| Carbohydrates-Based Cofactors | |
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| Fat Soluble Vitamins | |
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| Carbohydrates and Glycoconjugates | |
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| Carbohydrates: Definition | |
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| Monosaccharides: Aldoses | |
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| Monosaccharides: Ketoses | |
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| Structural Features | |
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| Intramolecular Cyclization | |
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| Conformations: Sugar Puckers | |
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| Sugar Derivatives | |
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| Disaccharides | |
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| Polysaccharides | |
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| Carbohydrate-Protein Conjugates | |
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| Synthesis and Structural Characterization | |
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| Lipids | |
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| Structural Overview | |
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| Saturated and Unsaturated Fatty Acids | |
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| Functions | |
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| Diacylglycerol Lipid Derivatives | |
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| Structural Motifs | |
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| Assembly | |
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| Structural and Dynamic Characterization | |
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| Eicosanoids | |
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| Phospholipases | |
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| Phosphoinositides | |
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| Steroids | |
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| A Potpourri of Lipids | |
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| Membranes | |
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| The Fluid Mosaic Model | |
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| Detergents | |
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| Distribution of Lipids in Biological Membranes | |
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| The Hydropathicity Scale | |
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| Lipid-Anchored Membrane Proteins | |
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| The Erythrocyte Cytoskeleton | |
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| Transport Through Membranes | |
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| The Transmembrane Potential | |
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| Active Transport | |
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| Ionophores | |
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| The Acetylcholine Receptor Ion Channel | |
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| Lactose Permease and Secondary Active Transport | |
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| Mechanism of Transport by Na+, K+ ATPase | |
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| Ion Channel Blockers | |
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| Signal Transduction | |
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| Signaling Pathways: Hormones, GTPases, Second Messengers and Intracellular Regulation | |
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| The Adenylate Cyclase Signaling Pathway | |
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| The Inositol-Phospholipid Signaling Pathway | |
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| Phorbol Myristyl Acetate | |
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| The Insulin Receptor | |
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| Glucagon | |
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| G-Proteins | |
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| Nucleic Acids: DNA | |
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| DNA and RNA | |
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| Physical Properties | |
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| Secondary Structure | |
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| Backbone Structure | |
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| Counterions | |
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| Chemical Synthesis | |
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| Watson-Crick Base Pairs | |
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| Structural Modifications | |
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| Three-Dimensional Structures | |
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| Recognition of Sequences | |
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| Genetic Mutations and Antisense Nucleic Acids | |
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| Unusual DNA | |
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| Stabilization of Nucleic Acids | |
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| Secondary Structure Predictions | |
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| Chromosomes | |
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| Some Protein Nucleic Acid Binding Motifs | |
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| Recombination | |
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| RNA | |
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| Cells Contain a Variety of Types of RNA | |
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| RNAs Have Stable Secondary Structure | |
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| Tertiary Structure: Transfer RNA | |
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| Messenger RNA (mRNA) | |
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| Eukaryotic Messenger RNA | |
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| Alkaline Hydrolysis of RNA | |
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| Small Interfering RNA | |
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| Biotechnology | |
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| Restriction Endonucleases | |
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| Cloning in a Nutshell | |
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| DNA Preparation: Phenol-Chloroform Extraction | |
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| Polymerase Chain Reaction | |
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| Probe DNA | |
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| Metabolism | |
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| Overview | |
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| Metabolic Pathway Types | |
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| Energy Conservation | |
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| Key Pathways/Reactions | |
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| Bioenergetics | |
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| Reaction Equilibria: Standard and Actual Free Energies | |
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| Metabolically Irreversible and Near Equilibrium Reactions | |
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| Energies and Regulation of Glycolysis | |
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| Bioelectrochemistry | |
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| Redox Reaction Principles | |
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| Redox Energetics: The Nernst Equation | |
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| Electron Transport Chains | |
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| Glycolysis | |
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| Reactions 1 Through | |
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| Regulation: Activation and Inhibition | |
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| Four Fates of Pyruvate | |
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| The Krebs Cycle | |
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| Pathway | |
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| Reactions | |
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| Yields | |
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| Cellular Redox Potential | |
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| Regulation | |
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| Gluconeogenesis | |
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| Reactions | |
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| Regulation | |
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| Sources Used to Produce Glucose | |
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| Electron Transport and Oxidative Phosphorylation | |
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| Mitochondria in Red and White Muscle | |
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| Overall Process | |
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| Chemical and Potential Energies That Drive Proton Transport | |
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| Mitochondrial Electron Transport | |
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| Electron Transfer and Proton Flow in Complexes I through IV | |
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| Oxidative Phosphorylation | |
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| The Malate-Aspartate Shuttle and Proteomics | |
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| Getting NADH Into the Mitochondrion: Isozymes | |
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| Isozymes and Proteomics | |
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| Characterization by Two-dimensional Gel Electrophoresis | |
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| Mass Spectrometry and Proteomics | |
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| Degradation and Synthesis of Lipids | |
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| Beta Oxidation of Saturated Fatty Acids | |
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| Biosynthesis of Fatty Acids | |
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| Length Determination of Fatty Acids | |
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| Synthesis of Acidic Phospholipids | |
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| Cholesterol Biosynthesis | |
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| Regulating Cholesterol Levels | |
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| Photosynthesis | |
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| Light and Dark Reactions | |
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| Photo-Gathering Pigments | |
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| Photosynthetic Electron Transport Pathway (Z scheme) | |
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| The Calvin Cycle | |
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| The Dark Reactions: Carbon Fixation | |
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| Biosynthesis of Ribose-5-phosphate | |
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| RuBis CO Mechanism | |
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| The C4 and CAM Pathways | |
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| The Urea Cycle | |
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| Purpose and Reactions | |
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| Regulation | |
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| Comparative Nitrogen Excretion | |
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| Protein Degradation and Programmed Cell Death | |
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| Study Guide | |
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| Review Session for Chapters 1 � 3 | |
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| Review Session for Chapter 4 | |
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| Review Session for Chapters 5 and 6 | |
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| Review Session for Chapters 7 - 8.6 | |
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| Review Sessions for Chapters 8.7 - 8.8 | |
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| Review Session for Chapter 9 | |
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| Review Session for Chapters 10 - 11.4 | |
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| Review Session for Chapters 10 - 11.4: Key | |
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| Review Session for Chapters 11.5 - 12.5 | |
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| Review Session for Chapters 11.5 - 12.5: Key | |
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| Review Session for Chapters 13 - 14.7 | |
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| Review Session for Chapters 13 - 14.7: Key | |
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| Review Session for Chapters 16.2 - 17.6 | |
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| Review Session for Chapters 16.2 - 17.6: Key | |
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| Review Session for Chapters 19 � 20 | |