Information Technology Reference
In-Depth Information
In doing so, the enzyme switches the state of the substrate from one to another.
Before this process can occur, a recognition process must take place, where the
enzyme distinguishes the substrate from other, possibly similar molecules. This
is achieved by virtue of what Conrad refers to as the “lock-key” mechanism,
whereby the complementary structures of the enzyme and substrate fit together
and the two molecules bind strongly (Figure 1.1b). This process may, in turn, be
affected by the presence or absence of ligands. Allosteric enzymes can exist in
more than one conformation (or “state”), depending on the presence or absence
of a ligand. Therefore, in addition to the active site of an allosteric enzyme
(the site where the substrate reaction takes place), there is a ligand binding
site, which, when occupied, changes the conformation and hence the properties
of the enzyme. This gives an additional degree of control over the switching
behavior of the entire molecular complex.
In 1991, Hjelmfelt et al. [14] highlighted the computational capabilities of
certain biochemical systems, as did Arkin and Ross in 1994 [4]. In 1995, Bray
[7] discussed how the primary function of many proteins in the living cell
appears to be the transfer and processing of information rather than metabolic
processing or cellular construction. Bray observed that these proteins are linked
into circuits that perform computational tasks such as amplification, integration,
and intermediate storage.
GENETIC REGULATORY NETWORKS
In this section we develop the notion of circuits being encoded in genetic regu-
latory networks rather than simply being used as a useful metaphor. The central
dogma of molecular biology is that DNA produces RNA, which in turn produces
proteins. The basic building blocks of genetic information are known as
genes
.
Each gene codes for a specific protein, and these genes may (simplistically)
be turned on (
expressed
)oroff(
repressed
). For the DNA sequence to be con-
verted into a protein molecule, it must be read (
transcribed
) and the transcript
converted (
translated
) into a protein (Figure 1.2).
Transcription of a gene produces a messenger RNA (mRNA) copy, which
can then be translated into a protein. This results in the DNA containing the
information for a vast range of proteins (
effector molecules
), but only those that
are being expressed are present as mRNA copies. Each step of the conversion,
from stored information (DNA) through mRNA (messenger) to protein synthe-
sis (effector), is catalyzed by effector molecules. These effector molecules may
be enzymes or other factors that are required for a process to continue. Conse-
quently, a loop is formed, where products of one gene are required to produce
further gene products, which may even influence that gene's own expression.
Genes are composed of a number of distinct regions that control and encode
the desired product. These regions are generally of the form promoter-gene-
