Kinetic model of the TCA cycle

The tricarboxylic acid (TCA) cycle (also known as the citric acid cycle and the Krebs cycle) is a collection of biochemical reactions that oxidize certain organic molecules, generating CO2 and reducing the cofactors NAD and FAD to NADH and FADH2 [147], In turn, NADH and FADH2 donate electrons in the electron transport chain, an important component of oxidative ATP synthesis. The TCA cycle also serves to feed precursors to a number of important biosynthetic pathways, making it a critical hub in metabolism [147] for aerobic organisms. Its ubiquity and importance make it a useful example for the development of a kinetic network model. 

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The Power-Law Formalism possesses a number of advantages that recommend it for the analysis of integrated biochemical systems. As discussed above, we saw that estimation of the kinetic parameters that characterize the molecular elements of a system in this representation reduces to the straightforward task of linear regression. Furthermore, the experimental data necessary for this estimation increase only as the number of interactions, not as an exponential function of the number of interactions, as is the case in other formalisms. The mathematical tractability of the local S-system representation is evident in the characterization of the intact system and in the ease with which the systemic behavior can be related to the underlying molecular determinants of the system (see above). Indeed, the mathematical tractability of this representation is the very feature that allowed proof of its consistency with experimentally observed growth laws and allometric relationships. It also allowed the diagnoses of deficiencies in the current model of the TCA cycle in Dictostelium and the prediction of modifications that led to an improved model (see above). 

This chapter will present a general methodology for incorporating these elements into a simulation of a biochemical system and illustrate the concepts based on the specific example of a kinetic model of the tricarboxylic acid (TCA) cycle. 

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