2022

THE GENETIC CODE

Nature
The genetic code is the way in which the nucleotide sequence in nucleic
acids specifies the amino acid sequence in proteins. It is a triplet code,
where the codons (groups of three nucleotides) are adjacent
(nonoverlapping) and are not separated by punctuation (comma-less).
Because many of the 64 codons specify the same amino acid, the genetic
code is degenerate (has redundancy). ie. More than one codon code for
one amino acid

Features

Eighteen of the 20 amino acids are specified by multiple (or synonymous)

codons which are grouped together in the genetic code table (table 1).
Usually they differ only in the third codon position. If this is a pyrimidine,
then the codons always specify the same amino acid. If a purine, then this
is usually also true
1 Dr. Mohammed Al-Bayati
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THE GENETIC CODE

Effect of mutation

The grouping of synonymous codons means that the effects of mutations

are minimized. Transitions in the third position often have no effect, as do
transversions more than half the time. Mutations in the first and second
position often result in a chemically similar type of amino acid being used.

Universality

Until recent time, the standard genetic code was considered universal:
however, some deviations are now known to occur in mitochondria and
some unicellular organisms.

ORFs

Inspection of DNA sequences, by eye or by computer will identify

continuous groups of adjacent codons that start with ATG and end with
TGA, TAA or TAG. These are referred to as open reading frames, or ORFs,
when there is no known protein product. When a particular ORF is known
to encode a certain protein, the ORF is usually referred to as a coding
region. Hence, an ORF is a suspected coding region.

Overlapping genes

These occur when the coding region of one gene partially or completely
overlaps that of another. Thus one reading frame encodes one protein, and
one of the other possible frames encodes part or all of a second protein.
Some small viral genomes use this strategy to increase the coding capacity
of their genomes.

2 Dr. Mohammed Al-Bayati

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THE GENETIC CODE

Aminoacylation reaction of tRNAs

The general aminoacylation reaction is a two-step reaction driven by ATP.
1. In the first step, AMP is linked to the carboxyl group of the amino
acid giving a high-energy intermediate called an aminoacyl
adenylate. The hydrolysis of the pyrophosphate released (to two
molecules of inorganic phosphate) drives the reaction forward.
2. In the second step, the aminoacyl adenylate reacts with the
appropriate uncharged tRNA to give the aminoacyl-tRNA and AMP.
The formation of an aminoacyl-tRNA helps to drive protein synthesis as the
aminoacyl-tRNA bond is of a higher energy than a peptide bond and thus
peptide bond formation is a favorable reaction once this energy-consuming
step has been performed.

Aminoacyl-tRNA synthetases
All the synthetases carry out the same reaction of joining an amino acid to
a tRNA. They have to be able to distinguish between about 40 similarly
shaped, but different, tRNA molecules in cells, and they use particular parts
of the tRNA molecules, called identity elements, to be able to do this
(Fig.2). These are not always the anticodon sequence (which does differ
between tRNA molecules). They often include base pairs in the acceptor
stem, and if these are swapped between tRNAs then the synthetase
enzymes will start to add the amino acid to the wrong tRNA.

3 Dr. Mohammed Al-Bayati

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THE GENETIC CODE

Figure 2 Identity elements in various tRNA molecules

Figure 1 the L-shaped tertiary
structure of yeast tRNATyr.

Proofreading

Some synthetase enzymes that have to distinguish between two

chemically similar amino acids can carry out a proofreading step. If they
accidentally carry out step 1 of the aminoacylation reaction with the wrong
amino acid, then they will not carry out step 2. Instead they will hydrolyze

the amino acid adenylate.

4 Dr. Mohammed Al-Bayati