Thursday, June 4, 2015

The invention of the genetic code

As is well known, the genetic code is the representation of the amino acid sequence of proteins by means of DNA strands. Now, the proteins of living beings are made of 20 different amino acids. However, there are only four different nucleotides in DNA. How can just four bases represent 20 amino acids?
With codons made of two nucleotides just 16 amino acids could be represented. As they are 20, two nucleotides are not enough: three must be used. Indeed, that is what life has done: each amino acid is represented by codons made of three nucleotides. The problem is, three nucleotides could represent 64 different amino acids, rather than 20 (21, considering that there codons mark the end of the string). What is the solution? Obviously, some amino acids must be represented by several codons (this is what is called degeneracy of the genetic code).
The four DNA nucleotides are made of a skeleton of sugar and phosphoric acid, combined with a nucleobase. In DNA there are four different bases:
  • Two purines (P): adenine (A) and guanine (G).
  • Two pyrimidines (Q): cytosine (C) y thymine (T).
The following table shows the genetic code:

Codón
Amin.
Codón
Amin.
Codón
Amin.
Codón
Amin.
AAP
Lysine
GAP
Glutamic ac.
CAP
Glutamine
TAP
Fin
AAQ
Asparagine
GAQ
Aspartic ac.
CAQ
Histidine
TAQ
Tyrosine
AGP
Arginine
GGP
Glycine
CGP
Arginine
TGP
End
Tryptophan
AGQ
Serine
GGQ
Glycine
CGQ
Arginine
TGQ
Cysteine
ACP
Threonine
GCP
Alanine
CCP
Proline
TCP
Serine
ACQ
Threonine
GCQ
Alanine
CCQ
Proline
TCQ
Serine
ATP
Isoleucine
Methionine
GTP
Valine
CTP
Leucine
TTP
Leucine
ATQ
Isoleucine
GTQ
Valine
CTQ
Leucine
TTQ
Phenylalanine

The table shows 32 boxes rather than 64, because the third base in each codon is specified by the group the base belongs to: purine (P) or pyrimidine (Q). Observe that in several cases the third base of the codon is completely ignored (the amino acid is defined by the first two), and that in almost all remaining cases, the only distinction is whether the third base is a purine or a pyrimidine. Just two boxes (TGP and ATP) take into account the concrete third base (adenine and guanine) in the codon. In both cases. it is a purine. Those cases are:
TGA: End codon
TGG: Tryptophan
ATA: Isoleucine
ATG: Methionine and start codon
The tree of life
Although the genetic code is nearly identical for all living beings, some variants have been discovered. For example, DNA in mitochondria (corpuscles of the eukaryotic cell) uses a slightly different code. There are also small changes in some species, such as Candida cylindracea, Acetabularia and Mycoplasma. But the fact that the code is almost identical for all living beings is taken as an indication that its origin was unique.
Some researchers think that the genetic code could be improved, that a better one could be designed. Others disagree. Some say that our code minimizes the deleterious effects of mutations, for a mutation in the third base will rarely have any effect on the protein represented by the gene.
The way the code originated is unknown. Current theories are divided into two groups:
a)      Top-down proposals, which start at the overall behavior and try to deduce the details by studying the chemical similarities of the amino acids representing the different codons; the complementarity of the codons; the possible effects of changes in the code; and the analysis of redundancy.
b)      Bottom-up proposals, which start at the properties of the constituent elements and try to deduce the properties of the global system by studying the origin of the associations between the codonsand the amino acids they represent; if those associations are accidental or must necessarily have arisen; and how this hypothesis is affected by the fact that RNA could have played at first both roles: encoder and enzyme (ribozyme).


 Manuel Alfonseca

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