Chapter 5. Metabolism

Summary

This chapter contains sections titled:

• Enzyme Kinetics and Thermodynamics

  • The Law of Mass Action

  • Reaction Kinetics and Thermodynamics

  • Michaelis-Menten Kinetics

    • How to Derive a Rate Equation

    • Parameter Estimation and Linearization of the Michaelis-Menten Equation

    • The Michaelis-Menten Equation for Reversible Reactions

  • Regulation of Enzyme Activity by Protein Interaction

  • Inhibition by Irreversible Binding of Inhibitor to Enzyme

  • Substrate Inhibition

  • Inhibition by Binding of Inhibitor to Substrate

  • Binding of Ligands to Proteins

  • Positive Homotropic Cooperativity and the Hill Equation

  • The Monod-Wyman-Changeux Rate Expression for Enzymes with Sigmoid Kinetics

• Metabolic Networks

  • Systems Equations

  • Information Contained in the Stoichiometric Matrix N

  • Elementary Flux Modes and Extreme Pathways

  • Flux Balance Analysis

  • Conservation Relations: Null Space of N^T

  • Compartments and Transport across Membranes

  • Characteristic Times

  • Approximations Based on Timescale Separation

    • The Quasi-steady-state Approximation

    • Quasi-equilibrium Approximation

• Metabolic Control Analysis

  • The Coefficients of Control Analysis

    • The Elasticity Coefficients

    • Control Coefficients

    • Response Coefficients

    • Matrix Representation of the Coefficients

  • The Theorems of Metabolic Control Theory

    • The Summation Theorems

    • The Connectivity Theorems

    • Derivation of Matrix Expressions for Control Coefficients

  • Extensions of Metabolic Control Analysis

    • Control Analysis for Variables other than Fluxes and Concentrations

    • Time-dependent Control Coefficients

    • Spatially Heterogeneous and Time-varying Cellular Reaction Networks