Biochemical Reaction Networks

  • Jens Nielsen
  • John Villadsen
  • Gunnar Lidén

Abstract

Evolution has resulted in a complex metabolic network to ensure the proper function of living cells. In many biotech processes the metabolic networks of living cells are exploited for production of desired compounds. As discussed in Chapter 2 the metabolism can roughly be divided into catabolism and anabolism. The catabolism ensures supply of Gibbs free energy in the form of high-energy phosphate bonds in ATP, co-factors like NADH and NADPH, and a set of 12 precursor metabolites — everything that is needed for biosynthesis of cell mass. In Chapter 3 we lumped the myriad of reactions in the metabolic network into a single overall reaction — the black box model. This is very useful when the aim is to check the overall balances of carbon flowing in and out of the cell, but it does not supply any information about the processes occurring inside the cells. Clearly the complexity increases when intracellular reactions are considered in the analysis, but as will be discussed in this chapter there is a constant balancing of the formation and consumption of intracellular metabolites, and this imposes a large number of constraints on the fluxes through the different branches of the metabolic network. Thus, even though the complexity increases, the degrees of freedom do not necessarily increase, and expansion of the analysis to include intracellular reactions — in some cases lumped together into a few overall reactions — may in many cases be very useful. In this chapter we are going to look into the basic concepts of metabolic balancing (Section 5.1). In the rest of the chapter we will consider biochemical reaction models of increasing complexity — first simple models balanced only with respect to ATP, NADH and possibly NADPH (Section 5.2); thereafter simple metabolic networks where the metabolic network is lumped into a few overall pathway routes (Section 5.3), and finally more complete metabolic networks that permit a deeper analysis of the activities in the different branches of the metabolic network at varying growth conditions (Section 5.4).

Keywords

Glycerol Lactate Citrate Bacillus Cytosol 

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Copyright information

© Springer Science+Business Media New York 2003

Authors and Affiliations

  • Jens Nielsen
    • 1
  • John Villadsen
    • 1
  • Gunnar Lidén
    • 2
  1. 1.Technical University of DenmarkLyngbyDenmark
  2. 2.Lund UniversityLundSweden

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