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Enzymes and Catalytic Mechanisms | |
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Catalysis and the Active Site | |
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Rate Enhancement in Enzymatic Catalysis | |
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Conformational Mobility in Catalysis | |
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Substrate-Induced Conformational Changes | |
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Catalysis of Multistep Reactions | |
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Structural Mobility in Enzymes | |
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Acid-Base Catalysis | |
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Acids and Bases | |
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Acid- and Base-Catalyzed Reactions | |
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Nucleophilic Catalysis | |
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Electrophilic Catalysis | |
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Catalysis of Enolization | |
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Imine Formation by Lysine | |
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Catalysis by Metal Ions | |
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Hydrogen Bonding | |
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Strong and Weak Hydrogen Bonds | |
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Hydrogen Bonding in Catalysis | |
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Binding Energy in Catalysis | |
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Binding and Activation Energy | |
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The Active Site as an Entropy Trap | |
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Dissecting the Binding Effect in Enzymatic Action | |
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Stabilization of the Transition State | |
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Binding the Near Attack Conformation | |
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Destabilization of Ground States | |
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Rate Enhancement through Binding of Remote Groups | |
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Characterization of Active Sites | |
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Competitive Inhibitors: Analogs of Substrates | |
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Group-Selective Chemical Modification | |
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Site-Directed Mutagenesis | |
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Affinity Labeling | |
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Why Are Enzymes Large Molecules? | |
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Sizes of Enzymatic Binding Domains | |
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Catalytic Antibodies | |
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Kinetics of Enzymatic Reactions | |
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Steady-State Kinetics | |
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One-Substrate Reactions | |
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Two-Substrate Reactions | |
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Three-Substrate Reactions | |
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Isotope Effects | |
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Classes of Isotope Effects | |
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Measurement of Isotope Effects | |
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Transient-Phase Kinetics | |
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Reaction Characteristics | |
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Transient Methods | |
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pH-Rate Profiles | |
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Profile Interpretation | |
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Measurements of pH-Rate Profiles | |
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Allosteric Regulation | |
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Theory | |
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Binding Equations for Cooperative Systems | |
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Aspartate Transcarbamoylase | |
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Coenzymes I: Organic Coenzymes | |
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Nicotinamide Coenzymes | |
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Structures and Functions of Nicotinamide Coenzymes | |
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Stereospecificity of Hydride Transfer | |
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NAD[superscript +] as a Coenzyme | |
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Thiamine Pyrophosphate | |
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Structure | |
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Reaction Mechanism | |
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[alpha]-Lipoamide | |
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Pyridoxal-5[prime]-Phosphate | |
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Enzymatic Reactions Facilitated by Pyridoxal-5[prime]-Phosphate | |
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Pyridoxal-5[prime]-Phosphate-Stabilized Amino Acid Carbanions | |
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Mechanisms of Pyridoxal-5[prime]-Phosphate-Dependent Reactions | |
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Flavin Coenzymes | |
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Structures of Flavin Coenzymes | |
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Mechanisms of Flavin Catalysis | |
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Biotin | |
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Structure and Role as a Carboxyl Carrier | |
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Chemistry of Biotin and N[superscript 1]-Carboxybiotin | |
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Mechanism of Biotin-Dependent Carboxylation | |
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Phosphopantetheine Coenzymes | |
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Structures of Phosphopantetheine Coenzymes | |
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Mechanism of Phosphopantetheine Action | |
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Folate Compounds | |
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Folate Compounds of One-Carbon Metabolism | |
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Enzymes in Tetrahydrofolate Metabolism | |
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Biological Importance of Folate | |
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Amino Acid-Based Coenzymes | |
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Pyruvoyl Decarboxylases | |
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Methylidene Imidazolinone-Dependent Deaminases | |
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Quinoproteins | |
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Coenzymes II: Metallic Coenzymes | |
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Vitamin B[subscript 12] Coenzymes | |
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Chemistry of B[subscript 12] Coenzymes | |
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Adenosylcobalamin-Dependent Enzymes | |
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Methylcobalamin-Dependent Enzymes | |
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Heme Coenzymes | |
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Chemistry of Oxygen and Heme | |
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Heme Enzymes | |
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Oxygen Binding and Electron Transfer | |
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Mononuclear Nonheme Iron | |
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Monooxygenases | |
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Dioxygenases | |
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Oxo-Fe[subscript 2] Complexes | |
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Structures | |
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Reactions of Di-iron Enzymes | |
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Metallopterin Enzymes | |
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Molybdopterin and Tungstopterin | |
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Iron-Sulfur Centers | |
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Structures | |
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Catalytic Functions | |
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S-Adenosylmethionine and Iron-Sulfur Centers | |
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Catalytic Action of S-Adenosylmethionine and [4Fe-4S] Centers | |
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Stoichiometric Reactions of S-Adenosylmethionine and [4Fe-4S] Centers | |
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Divalent Metal Ions | |
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Electrostatic Activation of Coordinated Water | |
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Electrostatic Activation of Enolization | |
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Copper as a Cofactor | |
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Copper Proteins | |
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Other Copper Enzymes | |
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Nickel Coenzymes | |
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Nickel in Methanogenesis | |
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Other Nickel Coenzymes | |
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Long-Range Electron Transfer | |
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Biological Electron Transfer | |
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Marcus Theory | |
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Enzyme Inhibition | |
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Two-Substrate Analogs | |
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Inhibition and Binding | |
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PALA and Aspartate Transcarbamylase | |
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Suicide Inactivation | |
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Thymidylate Synthase | |
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[beta]-Hydroxydecanoyl Thioester Dehydratase | |
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[gamma]-Aminobutyrate Aminotransferase | |
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Kinetics of Slow-Binding and Tight-Binding Inhibition | |
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Slow Binding | |
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Tight Binding | |
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Slow-Binding Inhibition | |
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Dihydrofolate Reductase | |
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Prostaglandin H Synthase | |
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Tight-Binding Inhibition | |
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HMG-CoA Reductase | |
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Alanine Racemase | |
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5-Enolpyruvoylshikimate-3-Phosphate Synthase | |
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Acetylcholinesterase | |
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Acyl Group Transfer: Proteases and Esterases | |
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Chemistry of Acyl Transfer | |
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Serine Proteases | |
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Chymotrypsin | |
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Subtilisin | |
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Cysteine Proteases | |
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Papain | |
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Caspases | |
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Aspartic Proteases | |
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Molecular Properties | |
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Mechanism of Action | |
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Metalloproteases | |
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Carboxypeptidase A | |
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Thermolysin | |
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Esterases | |
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Structure and Function | |
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Phospholipase A[subscript 2] | |
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Isomerization | |
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Aldose and Ketose Isomerases | |
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Chemistry | |
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Phosphoglucose Isomerase | |
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Triosephosphate Isomerase | |
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Xylose Isomerase | |
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Phosphomutases | |
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[alpha]-Phosphoglucomutase | |
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[beta]-Phosphoglucomutase | |
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Phosphoglycerate Mutases | |
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Racemases and Epimerases | |
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Proline Racemase | |
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Glutamate Racemase | |
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Mandelate Racemase | |
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UDP-Galactose 4-Epimerase | |
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Ribulose-5-P 4-Epimerase | |
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UDP-N-Acetylglucosamine-2-Epimerase | |
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Chorismate Mutase | |
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[delta superscript 5]-3-Ketosteroid Isomerase | |
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Radical Isomerizations | |
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Glutamate Mutase | |
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Methylmalonyl CoA Mutase | |
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Lysine 2,3-Aminomutase | |
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Newer Isomerases | |
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UDP-Galactopyranose Mutase | |
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Pseudouridine Synthase | |
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Decarboxylation and Carboxylation | |
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Chemistry of Decarboxylation and Carboxylation | |
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Decarboxylases | |
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Pyruvate Decarboxylase | |
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Amino Acid Decarboxylases | |
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Acetoacetate Decarboxylase | |
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Mevalonate Pyrophosphate Decarboxylase | |
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Radical-Based Decarboxylases | |
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Orotidine Monophosphate Decarboxylase | |
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Carboxylases | |
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Ribulose-1,5-Bisphosphate Carboxylase | |
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Phosphoenolpyruvate Carboxylase | |
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Vitamin K-Dependent Carboxylase | |
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Addition and Elimination | |
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[alpha],[beta]-Elimination/Addition Reactions | |
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Cofactor-Independent [alpha],[beta]-Elimination/Addition Reactions | |
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Cofactor-Dependent [alpha],[beta]-Elimination/Addition Reactions | |
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[beta],[alpha]-Elimination/Addition Reactions | |
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Methylidene Imidazolone-Dependent Elimination and Addition | |
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Carbonic Anhydrase | |
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Isomerization and Elimination | |
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Catalytic Process | |
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Coenzyme B[subscript 12]-Dependent Elimination | |
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Phosphotransfer and Nucleotidyltransfer | |
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Chemistry of Phosphoryl Group Transfer | |
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Phosphomonoesters | |
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Phosphodiesters | |
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Phosphotriesters | |
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Five-Member Ring Phosphoesters | |
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Enzymatic Phosphoryl Group Transfer | |
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Single and Double Displacements | |
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Phosphotransferases | |
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Protein Phosphorylation: Protein Kinase A | |
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Phosphomonoesterases | |
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Enzymatic Nucleotidyl Group Transfer | |
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Nucleotidyltransferases | |
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Phosphodiesterases | |
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ATP-Dependent Synthetases and Ligases | |
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Ligation and the Energy of ATP | |
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Activation by Phosphorylation | |
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Glutamine Synthetase | |
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Carbamoyl Phosphate Synthetase | |
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Activation by Adenylylation | |
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DNA Ligase | |
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Aminoacyl-tRNA Synthetases | |
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Ubiquitin | |
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Glycosyl Group Transferases | |
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Chemical Mechanisms | |
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Chemistry of Glycoside Hydrolysis | |
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Enzymatic Glycosyl Transfer | |
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Glycosyltransferases | |
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Sucrose Phosphorylase | |
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Glycogen Phosphorylase | |
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Purine Nucleoside Phosphorylase | |
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Glycosidases | |
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Families and Structures | |
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Lysozyme | |
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T4 Lysozyme | |
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Nitrogen and Sulfur Transferases | |
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Nitrogen Transfer | |
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Aspartate Aminotransferase | |
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Tyrosine 2,3-Aminomutase | |
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Amidotransfer | |
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Glutamine:PRPP Amidotransferase | |
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Sulfur Transfer | |
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Biotin Synthase | |
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Lipoyl Synthase | |
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Carbon-Carbon Condensation and Cleavage | |
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Chemistry | |
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Enolization of Acetyl CoA | |
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Acetyl CoA in Ester Condensations | |
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Citrate Synthase | |
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Thiolases | |
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Carbanionic Mechanisms | |
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Transaldolase | |
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Transketolase | |
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Serine Hydroxymethyltransferase | |
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Carbocationic Mechanisms | |
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Farnesyl Pyrophosphate Synthase | |
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Squalene Synthase | |
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Alkyltransferases | |
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Chemistry of Alkylation | |
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Biological Alkylations | |
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Alkylation Mechanisms | |
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Enzymatic Alkylation | |
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Protein Farnesyltransferase | |
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Catechol O-Methyltransferase | |
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S-Adenosylmethionine Synthetase | |
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Methionine Synthases | |
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Oxidoreductases | |
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Pyridine Nucleotide-Dependent Dehydrogenases | |
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Alcohol Dehydrogenase | |
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Lactate Dehydrogenase | |
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Short-Chain Alcohol Dehydrogenases | |
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Glyceraldehyde-3-P Dehydrogenase | |
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Glutamate Dehydrogenase | |
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Disulfide Oxidoreductases | |
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Dihydrolipoyl Dehydrogenase | |
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Ribonucleotide Reductases | |
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Classes of Ribonucleotide Reductases | |
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Structural Relationships of Ribonucleotide Reductases | |
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Oxidases and Oxygenases | |
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Oxidases | |
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D-Amino Acid Oxidase | |
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Monoamine Oxidases | |
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Isopenicillin-N Synthase | |
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Urate Oxidase | |
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Monooxygenases | |
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Lactate Monooxygenase | |
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Cytochrome P450 Monooxygenases | |
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Iron-Methane Monooxygenase | |
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[alpha]-Ketoglutarate-Dependent Oxygenases | |
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Dopamine [beta]-Monooxygenase | |
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Copper-Methane Monooxygenase | |
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Nitric Oxide Synthase | |
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Dioxygenases | |
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Intradiol Dioxygenases | |
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Extradiol Dioxygenases | |
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Complex Enzymes | |
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Multienzyme Complexes | |
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[alpha]-Ketoacid Dehydrogenase Complexes | |
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Pyruvate Dehydrogenase Complex | |
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Fatty Acid Synthesis | |
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Acetyl CoA Carboxylase | |
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Fatty Acid Synthases | |
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Modular Enzymes | |
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Polyketide Synthases | |
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Nonribosomal Polypeptide Synthetases | |
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Ribosomal Protein Synthesis | |
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RNA Polymerase | |
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The Ribosome | |
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Energy-Coupling Enzymes | |
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Nitrogenase | |
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Cytochrome c Oxidase | |
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ATP Synthase | |
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Myosin and Muscle Contraction | |
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Appendices | |
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Haldane Relationships for Some Kinetic Mechanisms | |
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Inhibition Patterns for Three-Substrate Kinetic Mechanisms | |
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Equations for Number of Occupied Sites in the Binding of a Ligand to a Multisite Macromolecule | |
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Derivation of Steady-State Kinetic Equations by the King-Altman Method | |
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Index | |