Cell Metabolism - Bioprocess Engineering: Kinetics, Biosystems, Sustainability and Reactor Design - page 477

When these words are put into a sequence, they can make a “sentence” (i.e. a gene), which
when properly transcribed and translated is a protein. Other combinations of words regulate
when the gene is expressed. Carrying the analogy to the extreme, we may look at the
complete set of information in an organism's DNA (i.e. the genome) as a topic. (For the human
genome, it would be more than 1000 topics the size of this one.)
This simple language of 64 words is all that is necessary to summarize the total physical
make up of all living organisms at birth and all natural capabilities of a living organism. It is
essentially universal, the same for Escherichia coli and Homo sapiens (humans). This univer-
sality has helped us to make great strides in understanding life and is a practical tool in
genetic engineering and biotechnology.
Each of the steps in information storage and transfer ( Figs 10.1 and 10.2 ) requires a macro-
molecular template. Let us next examine how these templates are made and how this genetic-
level language is preserved and expressed.
10.2. DNA REPLICATION: PRESERVING AND PROPAGATING
THE CELLULAR MESSAGE
The double-helix structure of DNA discussed in Chapter 2 is extremely well suited to its
role of preserving genetic information. Information resides simply in the linear arrangement
of the four nucleotide letters (A, T, G, and C). Because G can hydrogen-bind only to C and A only
to T, the strands must be complementary if an undistorted double helix is to result. Replication is
semiconservative (see Fig. 2.31); each daughter chromosome contains one parental strand and
one newly generated strand.
To illustrate the replication process (see Figs 2.34, 10.3 ,and 10.4 ), let us briefly consider DNA
replication in E. coli. The enzyme responsible for covalently linking themonomers is DNApoly-
merase. Escherichia coli has three DNA polymerases (named Pol I, Pol II, and Pol III). A DNA
polymerase is an enzyme that will link deoxynucleotides together to form a DNA polymer.
Pol III enzymatically mediates the addition of nucleotides to an RNA primer. Pol I can hydro-
lyze an RNA primer and duplicates single-stranded regions of DNA; it is also active in the
repair of DNAmolecules. Pol II enzyme is 90 kDa in size and is coded by the pol B gene. Strains
lacking the gene show no defect in growth or replication. Synthesis of Pol II is induced during
the stationary phase of cell growth. This is a phase in which little growth and DNA synthesis
occurs. It is also a phase in which the DNA can accumulate damage such as short gaps, which
act as a block to DNA Pol III. Under these circumstances, Pol II helps to overcome the problem
because it can reinitiate DNA synthesis downstream of gaps. Pol II has a low error rate but it is
much too slow to be of any use in normal DNA synthesis. Pol II differs from Pol I in that it lacks
a C5-to-C3 exonuclease activity and cannot use a nicked duplex template.
In addition to the enzyme, the enzymatic reaction requires activated monomer and the
template. The activated monomers are the nucleoside triphosphates. The formation of the
C5 e C3 phosphodiester bond to link a nucleotide with the growing DNA molecule results in
the release of a pyrophosphate, which provides the energy for such a biosynthetic reaction.
The resulting nucleoside monophosphates are the constituent monomers of the DNAmolecule.
Replication of the chromosome normally begins at a predetermined site, the origin of repli-
cation, which in E. coli is attached to the plasma membrane at the start of replication. Initiator