Initial Rate Enzyme Kinetics

I Nomenclature, Definitions, and Evolution of the Kinetic Mechanism.- A. Nomenclature.- B. Evolution of Initial Rate Kinetics.- References.- II Derivation of Initial Velocity Rate Equations.- A. Definitions and Derivations.- 1. Steady-State.- 2. Initial Velocity.- 3. The Maximal Velocity and Michaelis Constant.- 4. Reverse Reaction Parameters and Rate Constants.- B. The Equilibrium Assumption.- C. Derivation of Complex Steady-State Rate Equations.- D. Derivation of the Rate Equation Using the Rapid Equilibrium Assumption.- 1. The Random Bi Bi Mechanism.- 2. The Ordered Bi Bi Mechanism.- E. Derivation of Initial Rate Equations Using a Combination of Equilibrium and Steady-State Assumptions.- F. Derivation of Steady-State Rate Equations by Using the Digital Computer.- References.- III Experimental Protocol and Plotting of Kinetic Data.- A. General Considerations.- B. Analysis of Radioactive Substrates and Determination of Radiopurity.- C. pH Effects.- D. Substrate Concentration.- E. Studies of Forward and Reverse Reactions.- F. Studies of Nucleotide Dependent Enzymic Reactions.- G. The Kinetic Assay.- 1. The Continuous Assay.- 2. The Stop-Time Assay.- H. Plotting Methods.- I. Graphical Procedures.- J. The Point of Convergence of Sequential Double Reciprocal Plots as a Criterion of Kinetic Mechanism.- K. Protocol and Data Plotting for Three Substrate Systems.- L. Graphical Methods for Differentiating between Steady-State and Equilibrium Ordered Bi Bi Mechanisms.- References.- IV Use of Competitive Substrate Analogs and Alternative Substrates for Studying Kinetic Mechanisms.- A. Competitive Inhibition.- B. Partial Competitive Inhibition.- C. Noncompetitive Inhibition.- D. Ucompetitive Inhibition.- E. Nonlinear Enzyme Inhibition.- F. The Use of Substrate Analogs for Studying Kinetic Mechanisms.- 1. Bireactant Enzymic Systems.- 2. Terreactant Systems.- 3. Kinetic Studies of Adenylosuccinate Synthetase Using Dead End Inhibitors.- G. Cleland’s Rules for Dead End Inhibition.- H. The Stereochemical Nature of Enzyme and Substrate Interaction.- I. Kinetics of Enzyme Specificity.- J. The Kinetics of Transition State Analogs.- References.- V Product, Substrate, and Alternative Substrate Inhibition.- A. Product Inhibition Experiments.- 1. Experimental Protocol.- 2. One Substrate Systems.- 3. Two Substrate Systems.- 4. Abortive Ternary Complex Formation.- 5. Calculation of Rate Constants from Product Inhibition Experiments.- 6. Noncompetitive Product Effects.- B. Substrate Inhibition.- 1. A Simple Model for Substrate Inhibition.- 2. Two Substrate Systems.- C. Alternative Substrate Inhibition.- 1. Alternative Substrates Acting as Inhibitors Only.- 2. Bireactant Systems.- 3. Terreactant Systems.- D. Alternative Product Inhibition.- E. Multisite Ping Pong Mechanisms.- F. Enzymes with Identical Substrate-Product Pairs.- References.- VI Isotope Exchange.- A. Abortive Complex Formation.- B. Derivation of Rate Equations.- 1. The Equilibrium Case: Ping Pong Bi Bi.- 2. The Steady-State Case: Ordered Bi Bi (Theorell-Chance).- 3. Random Bi Bi.- 4. Theorell-Chance Mechanism.- C. Substrate Synergism.- D. Calculation of Kinetic Parameters.- 1. The Ping Pong Bi Bi Mechanism.- 2. The Random Bi Bi Mechanism (Rapid Equilibrium).- E. Experimental Protocol.- F. Isotope-Trapping.- References.- VII Isomerization Mechanisms and the ? and Haldane Relationships.- A. The ? Relationships.- B. The Haldane Relationships.- 1. Ordered Bi Bi.- 2. Rapid Equilibrium Random Bi Bi.- 3. Steady-State Random Bi Bi.- C. Isomerization Mechanisms.- References.- VIII The Effect of Temperature and pH on Enzyme Activity.- A. Effect of pH on Enzyme Kinetics.- 1. pH Functions.- 2. The Effect of pH on Unireactant Models.- 3. Evaluation of Ionization Constants.- 4. Bisubstrate Systems.- 5. Cooperative Proton Binding.- 6. Identification of Amino Acid Residues from Studies of pH Kinetics.- 7. Some Limitations in the Study of pH Kinetics.- 8. Choosing a Buffer for Kinetic Experiments.- 9. The pH Kinetics of the Fumarase Reaction.- B. The Effect of Temperature on Enzyme Catalyzed Reactions.- 1. Collision Theory and the Arrhenius Equation.- 2. Transition-State Theory.- 3. Significance of Activation Enthalpy and Activation Entropy.- 4. Application of Transition-State Theory to the ?-Chymotrypsin Reaction.- References.- IX Cooperativity and Allostery.- A. Cooperativity.- 1. The Hill Equation.- 2. The Adair Equation.- 3. The Scatchard Plot.- B. Molecular Models.- 1. The Monod Model.- 2. The Adair-Koshland Model.- 3. Subunit-Subunit Polymerization.- 4. Protein Isomerization.- C. Kinetic Models.- 1. Kinetic Models Involving Subunit-Subunit Interaction.- 2. Kinetic Models Involving Alternative Pathways of Substrate Addition and Enzyme Isomerization.- D. Allostery.- 1. Nonsigmoidal Systems.- 2. The Monod Model.- 3. The Adair-Koshland Model.- 4. Enzyme Isomerization Mechanisms.- 5. Kinetic Models.- E. Product Effects.- References.- Appendix I Rate Equations, Determinants, and Haldane Expressions for Some Common Kinetic Mechanisms.- Appendix II A Computer Program for Deriving Enzyme Rate Equations.- Appendix III Plotting and Statistical Analysis of Kinetic Data Using the OMNITAB Program.