Biomedical Engineering Reference
In-Depth Information
chemistry, but there is a profound and transcen-
dental difference. The periodic table is almost
certainly valid and true all over the universe.
However, if there is life in other worlds, and if
this life is based on nucleic acids and proteins, of
which there is no guarantee, it is very likely that
the code there would be substantially different.
There are even small code variations in some ter-
restrial organisms. Genetic code, like life itself, is
not an aspect of the eternal nature of things, but,
at least partly, product of an accident.
The central lemma of genetic code is the rela-
tionship between the sequence of the bases of DNA
or of its transcribed m-RNA and the sequence of
protein amino acids. This means that the sequence
of bases of a gene is collinear with the sequence
of amino acids of its product polypeptide. What
makes this code, which is the same in all living
beings, so marvellous is its simplicity. A set of
three bases or codon specifies an amino acid. The
t-RNA molecules, which work as protein synthesis
adaptors, read the codons sequentially.
Crick et al.'s 1961 experiments (Crick et al.,
1961) established that genetic code had the fol-
lowing characteristics:
mosaic virus indicated that normally only
one amino acid altered, leading to the con-
clusion that genetic code does not overlap.
5. Codon reading sequentiality: The se-
quence of bases is read sequentially from a
fixed starting point. There are no commas,
i.e. genetic code does not require any punc-
tuation or signal whatsoever to indicate the
end of a codon or the start of the next one.
There is only an “initiation signal” in the
RNA, which indicates where the reading
should start. This signal is the AUG codon
that codes the amino acid methionine.
6. Code inefficiency or degeneracy: There
is more than one word or coding codon
for most amino acids. Mathematically, this
means that there is a superjective application
between the codons and the amino acids plus
the chain initiation and termination signals,
which is transcendental for the subject of
this paper. Table 2 shows genetic code. Only
tryptophan and methionine are encoded by a
single triplet. Two or more triplets encode the
other eighteen. Leucine, arginine and serine
are specified by six codons each. However,
under normal physiological conditions, the
code is not ambiguous: each codon desig-
nates a single amino acid. From this table,
the respective amino acid can be located,
given the position of the bases in a codon,
as follows. Suppose we have the m-RNA
codon 5'AUG 3', then we start at A in Table
2, then go to U and then to G and we find
methionine.
1.
The alphabet: A1 = {A,G,C,T}.
2.
Coding relationship: A group of three bases
codes an amino acid. This group of three
bases is called, as mentioned above, codon
or triplet.
3.
Non-optimality: The fact that there is a
code is such is likely to be due to structural,
electrochemical and physical criteria applied
to the molecules involved in the described
processes. The optimal base is actually 3
(Pazos, 2000).
Figure 1 shows a finite-state automaton that
recognises the DNA alphabet and translates the
codons into amino acids.
4.
Non-overlapping: In a code of non-overlap-
ping triplets, each codon specifies only one
amino acid, whereas in a code of overlap-
ping triplets, ABC specifies the first amino
acid, BCD the second, CDE the third and so
on. Studies of the amino acid sequence in
the protein cover of mutants of the tobacco
7.
Importance of the bases in the codon:
The codons that specify the same amino
acid are called synonyms, e.g. CAU and
CAC are synonyms for histidine. Note that
the synonyms are not distributed arbitrarily
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