From Cellular Function to Industrial Products
13
of macromolecules, their transport to pre-specified locations in the cell, and, finally their
association to form cellular structures like cell wall, membranes, the nucleus, etc. Thus, the
assembly reaction results
in the formation of a functional
cell
from the
individual
macromolecules synthesized by the polymerization reactions.
Besides the above listed categories of reactions there are other processes that play a very important
role. In particular expression of genes determines the overall function of the cell, and by an altered
gene expression the cell can vary its active metabolic network (or its catabolic and anabolic
activity). As gene expression to a large extent determines which enzymes are active within the cell,
one can argue that gene expression represents an overall control of cell function. However, there is
a close interaction between metabolism and gene expression, and it is therefore not possible to
divide the control into different levels that are separated from each other.
The distinction made here between substrates and metabolic products is in most cases obvious, but
in a few cases the cells may reuse a metabolic product, i.e., the product may serve as a second
substrate, and here it is more difficult to categorize the compound as either a substrate or a product.
An example is the diauxic growth of
Saccharomyces cerevisiae
at aerobic conditions. Here ethanol
is formed together with biomass when the yeast grows on glucose present in excess, and when the
glucose is exhausted, the growth continues with ethanol as a substrate. Due to glucose repression on
the genes encoding enzymes involved in ethanol metabolism there is a lag-phase between
exhaustion of glucose and initiation of ethanol consumption. Throughout this text we will only
consider substances originally present in the medium as substrates, i.e. in the example stated above,
glucose is a substrate and ethanol is a metabolic product. Depending on the process to be described,
a given compound may therefore appear both as a substrate and as a metabolic product.
In the following we give a separate treatment of the key processes involved in cellular growth and
product formation:
1
) gene transcription and translation;
2
) transport processes (substrate uptake
and product excretion);
3)
catabolism
(fueling
reactions);
4) anabolism
(biosynthetic
and
polymerization reactions); and 5) secondary metabolism. Only those aspects of metabolic processes
that appear to be important to a biochemical engineer who wishes to understand how fermentation
processes work under various operating conditions will be discussed. In a text of reasonable length
and with the above-mentioned aim, it will be impossible to give even a reasonably correct summary
of the vast repository of knowledge concerning the biochemistry of cellular function, and we
therefore refer to standard textbooks in microbiology and biochemistry. One may also consult the
many different reaction databases available on-line, e.g., www.genome.ad.jp.
2.1.1 From Genotype to Phenotype
The genes in living cells are located in the chromosome(s). In prokaryotes (bacteria) there is
normally only one chromosome whereas in eukaryotes (fungi, plants, animals, human) there may
be several chromosomes of varying size. The number of genes in the chromosome(s) depends
significantly on the complexity of the cell. A few bacteria have only a few hundred genes, e.g.
Mycoplasma genitalium
has only about 500 genes, other bacteria have thousands of genes, e.g.,
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