Theoretical Systems Biology of Metabolism

04-Introduction.-Getting started: Balancing equations, enzyme kinetics and online databases; Stoichiometry; Balancing equations; Outline of enzyme kinetics; Generalized mass action kinetics; Michaelis-Menton kinetics; Cooperative kinetics; Inhibition kinetics; Approximative kinetics; Power laws; Linlog kinetics; Online metabolic and enzyme databases.-Network Analysis; Graph-theoretical approaches; Algebraic approaches; Conservation relations; Stationary states; Stability analysis; Bistability and multistability; Stoichiometric and kinetic considerations; Bifurcations of steady states; Examples of bistability; Metabolic Flux Analysis; Non-negative fluxes; Elementary modes; Definition and mathematical properties; Algorithms for computing elementary modes; Application in biochemistry; Extreme pathways; Structural robustness; Description by Petri nets.-Metabolic Control Analysis; Basic definitions; Simple example; Calculating control coefficients from elasticities; General properties of04 control coefficients; Extension to large changes; Outline of advanced techniques.-Kinetic Simulation of Metabolism; How is a dynamic model constructed?; Steady states and homeostasis; Model reduction; Quasi-equilibrium approximation; Quasi-steady-state approximation; Example: Erythrocyte metabolism; Another Example: Threonine synthesis; Relaxation to steady states; Partial steady states (Turbo effect); Metabolic oscillations; Limit cycles; Hopf bifurcation; When are average and steady-state values equal?;Isotopomer analysis; Pros and cons of whole-cell modeling.-Optimization and Game-Theoretical Approaches; Optimization of molar yields (Flux Balance Analysis); Theory; Example of application: Lysine synthesis; Maximizing pathway flux; Optimal allocation of ATP-producing steps; Minimizing intermediate concentrations; Optimal time course of gene expression; Applying evolutionary game theory; An example of the Prisoner s Dilemna in biochemistry; An example of the Hawk-Dove game in bi04ochemistry.