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In-Depth Information
BIOLOGICAL REPRESENTATIONS
An organism's genome, the sum of all the DNA from all its chromosomes,
encodes the organism's proteome, the set of all protein species capable of be-
ing created by the organism through the processes of DNA transcription and
translation. Each protein is specified by a gene, a sequence of codons stating the
order and nature of the components from which the protein is to be assembled,
concluded by a termination codon, marking the end of the gene. Proteins have
four layers of structure. Unfolded, they form a string of amino acids. Amino
acids are chemicals unified by a common structure and differentiated by the
chemical properties of their side chains. However, proteins do not remain un-
folded. Secondary structure, the emergence of physical members and chemical
surfaces, is caused by chemical attractions between the amino acids within
the chain. This effect is compounded by the aqueous environment of the cell
which, through interactions between the protein and water molecules, forces the
structure into a distinct folded form known as the tertiary structure. The final
layer of structure, quaternary, emerges from single-chain molecules bonding
together to form macromolecular complexes.
The overall behavior of an organism does not emerge from isolated proper-
ties of individual proteins, but rather from the interactions between proteins and
between proteins and other chemicals. These interactions lead to the formation
of structures called biochemical pathways; sequences of protein-mediated reac-
tions and interactions that carry out functional tasks within the organism. There
are three broad categories of biochemical pathway, illustrated conceptually in
Figure 3.3. Metabolic pathways exist within cells and emerge from the inter-
actions of locally transcribed proteins. Signaling pathways comprise cellular
responses to intercellular signals. Gene expression networks describe regulatory
gene
expression
pathway
transcription
blocked by
enzyme
DNA
gene
<<transcription>>
metabolite
enzyme
activation
untranscribed
gene product
signalling
pathway
metabolic
pathway
Figure 3.3
Biochemical pathways.
