ABSTRACT

This chapter describes some of the basic and general concepts of biochemistry and metabolomics that are particularly pertinent for analyses in computational systems biology. It begins with the characterization of enzyme-catalyzed reactions, discusses means of controlling the rates of these reactions, establishes the foundation for mathematical methods that capture the dynamics of metabolic systems, and lists some of the methods of data generation and the comprehensive resources of information regarding metabolites that are presently available. Mass action formulations implicitly assume that many substrate molecules are available and that they are freely moving about in a homogeneous medium. In many cases, and especially in living cells, these assumptions are not really true, but they do provide good approximations to realistic metabolic systems. Most biochemical reactions in a metabolic system are catalyzed by enzymes. To yield valid snapshots of a metabolic system, any rapid-sampling method must instantaneously quench all metabolic activity.