Biochemical Reaction Networks
1 2 1
Figure 5.1 A general representation o f reactions considered in a m etabolic netw ork.
the cell and are converted into
m etabolic products via a total o f
in tracellular m etabolites. The
conversions occur via
in tracellular reactions for w hich the rates are given by v ,.
. ,vj. R ates o f substrate
form ation (rsb .
..,r sN) and product form ation
. .,rpM) are also show n.
Whereas the NADH requirement of a given pathway reaction can be calculated as discussed in
Section 3.4 this is not the case for the “energy equivalents” which are often represented solely by
ATP. There is really no way of telling if the conversion of one metabolite to another with less
free energy is accompanied by release of ATP or the difference in Gibbs free energy is dissipated
as heat. Thus, the hydrolysis of glycerol-3-phosphate (G3P) to glycerol is not accompanied with
formation of ATP whereas the corresponding reaction from acetyl-phosphate to acetate does lead
to formation of ATP (see Fig. 2.6). In order to identify the involvement of ATP in specific
reactions it is therefore necessary to consult the biochemistry literature (or reaction databases on
the internet, e.g., www.g en o m e.ad.jp). For the main pathways such as the EMP pathway leading
from glucose to pyruvate the release of ATP is the same (2 moles of ATP per mole glucose) for
all organisms using this pathway.
Balance for A
Balance for B
Balance for C
V5 j \
Metabolite 2 Metabolite 3
Figure 5.2 A schem atic illustration o f the concept of m etabolite balancing. For the sim ple m etabolic
pathw ays the fluxes through the different enzym atic reactions are related through the three algebraic
equations that represent balances for the three in tracellular m etabolites A , B and C.