12
Chapter 2
The conversion of substrates to biomass is dearly the result of a very large number of chemical
reactions and events like gene expression, translation of mRNA into functional proteins, further
processing of proteins into functional enzymes or structural proteins, and long sequences of
biochemical reactions leading to building blocks needed for synthesis of cellular components.
The many reactions and processes have traditionally been categorized into four types (see Fig.
2.1): 1) fueling reactions; 2) biosynthesis reactions; 3) polymerization reactions; and 4) assembly
reactions (Neidhardt
et a i,
1990). Reactions involved in transport of compounds across the
cytoplasmic membrane do, however, also play a very important role, and in our discussion of
processes underlying cellular growth we therefore consider five categories of reactions:
Transport reactions,
which are involved in the uptake of substrates and export of
metabolites. Transport reactions may also ensure secretion of macromolecules needed outside
the cells, e.g., enzymes that are involved in degradation of complex carbohydrates to
monomers that can serve as carbon and energy sources for the cells.
Fueling reactions,
which convert the substrates into 12 so-called
precursor metabolites
(see
Table 2.4) which forms the basis for biosynthesis of cell mass. Additionally, the fueling
reactions generate Gibbs free energy in the form of ATP that is used for biosynthesis,
polymerization, and assembling reactions (see below). Finally, the fueling reactions produce
reducing power needed for biosynthesis. The fueling reactions include all biochemical
pathways generally referred to as the
catabolism
that are involved in degrading and oxidizing
substrates. As indicated in Fig. 2.1 some of the precursor metabolites may be secreted as
metabolic products or they may be converted via a few reaction steps to other metabolites
that are secreted. The reactions leading to these metabolic products, e.g., ethanol, lactic acid
or acetic acid, are included in the group of fueling reactions.
Biosynthetic reactions, which convert the precursor metabolites into so-called
building
blocks
used in the synthesis of macromolecules (in the polymerization reactions, see below).
These reactions also produce co-enzymes and related metabolic factors, including signal
molecules. There is a large number of biosynthetic reactions, which occur in functional units
called biosynthetic pathways, each consisting of one to a dozen sequential reactions leading
to the synthesis of one or more building blocks. Pathways are easily recognized and are often
controlled
en bloc.
In bacteria and other prokaryotes their reactions are often catalyzed by
enzymes made from a single piece of mRNA transcribed from a set of contiguous genes
forming an operon, whereas in eukaryotes genes encoding enzymes of a given pathway are
often collected in so-called gene clusters where the genes are expressed from similar
promoters. All biosynthetic pathways begin with one of 12 precursor metabolites. Some
pathways begin directly with such a precursor metabolite, others indirectly by branching
from an intermediate or an end product of a related pathway. As indicated in Fig. 2.1 some of
the building blocks may be secreted as metabolic products, e.g. amino acids, or they may
serve as precursors for more complex metabolites - often referred to as secondary
metabolites (see Section 2.1.5).
Polymerization reactions,
which represent directed, sequential linkage of the building
blocks into long (branched or unbranched) polymeric chains. The macromolecules formed by
these reactions makes up almost the whole cell mass. The sum of the biosynthetic reactions
and the polymerization reactions is generally referred to as the
anabolism.
The last group of reactions is the
assembly reactions,
which include chemical modifications
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