Chapter 7
Note 7.4. What should be positioned in the active compartment in a simple structured model?
When the cell is divided into an active and an inactive part, it is necessary to define which biomass
components should be considered active and which should be considered inactive. Most of the biomass
components are involved in the overall growth process, and the only truly inactive components are
structural material such as membranes or the cell wall. Thus for most microorganisms the inactive part of
the cell is small. There are, however, a larger number of components that do not participate directly in the
growth process, and furthermore the concentration of a number of components does not influence the
overall growth kinetics. An example is DNA, which is of course essential for growth, but it is not an active
component since it does not synthesize new material by itself. It is rather the polymerases that synthesize
new DNA and mRNA which are active components, but these are present in very low concentrations and do
not play a key role in regulation of DNA transcription and gene expression. The compartment model
concept is based on an assumption of a constant composition of the individual macromolecules within each
compartment. With only two compartments, i.e., an active and an inactive one, one has to make a very
rough division of the components, and this partition can therefore not be expected to hold under all
operating conditions. However, one should attempt to group the various macromolecules so that all
components that decrease or increase with, e.g., dilution rate in approximately the same fashion are grouped
in the same compartment.
A conceptual problem with the division of the cell into two parts is that many active components are placed
in the inactive compartment. The tRNA is found to have a constant ratio to DNA at different specific
growth rates and should therefore be included in the same compartment as the “inactive” DNA. However,
tRNAs are strongly involved in protein synthesis and they are therefore active compounds. Similarly, many
non-PSS proteins that are involved in the primary metabolism, e.g. enzymes involved in the EMP pathway
and TCA cycle, are obviously active even though they are positioned in the inactive compartment. The
should therefore not be interpreted in a strict sense, but rather according to the
following: the size of the active compartment increases with and is linearly correlated with the specific
growth rate, whereas the size of the inactive compartment decreases with the specific growth rate.________
et al.
(1967) presented one of the first structured models. In their model biomass was
divided into two compartments: a G compartment composed of nucleic acids and a D compartment
with enzymatic proteins. Hence the whole biomass is considered to be active since both genetic
material and proteins are involved in the growth process. Both G and D compartments can be
degraded to inactive material by the action of a non-specified
These degradation
processes are especially important for description of cell death at the end o f batch fermentations,
but since this is only of small relevance for normal operating conditions we shall leave these
empirical degradation reactions out of our discussion. The stoichiometry of the processes by which
G and D compartment are synthesized is
X 0 + 2 X q
a x,s
X c
K.qq s
K sG
2 X D + X G~ a 2ls ~ X D - X c = 0
= k 2
X ,
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