Contents

Chapters 1 and 2 provide an introduction to biochemical enzyme kinetics, including basic definitions; the mathematical formulation of reaction schemes and the computer-based methods used in their analysis; and quantitative aspects of enzymology such as the analysis of kinetic data, the mechanistic basis of enzyme inhibitions, and models of enzyme regulation. Chapter 3 contains an introduction to the procedures used to simulate metabolic systems using symbolic computation; and a model of the urea cycle of the human liver is used to exemplify these. More advanced methods incorporating matrix algebra are introduced in Chapter 4, where we show that the differential rate equations describing complex metabolic reaction schemes can be represented in a simple and compact way. Our implementation of the key elements of metabolic control analysis (MCA) as presented by Heinrich and Schuster11 is described in Chapter 5. Parameter estimation is the subject of Chapter 6 and here we consider linear and nonlinear least-squares regression analysis for this purpose, and parameter estimation in large-scale metabolic networks where over-parameterization may be an issue. Chapter 7 applies the theory and methods developed in the previous chapters to the human erythrocyte to illustrate how a realistic model of metabolism can be built up. Finally, the concepts and methods described in Chapters 5 and 6 are used to perform MCA on the erythrocyte model presented in Chapter 7. The five appendices contain supplementary material and Mathematica code that is required to run the programs and worked examples contained in Chapters 1 - 8 from the interactive CD.

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