A pleasant surprise

Just when you think that you understand the present state of science, a
new paper is brought to your attention. In this case

A mechanism for the association of amino acids with their codons and the
origin of the genetic code
Shelley D. Copley, Eric Smith, and Harold J. Morowitz 4442–4447
PNAS

March 22, 2005
vol. 102
no. 12

Which I did mention but I decided to re-read in light of the recent
discussion

<quote>
The genetic code has certain regularities that have resisted mechanistic
interpretation. These include strong correlations between the first base
of codons and the precursor from which the encoded amino acid is
synthesized and between the second base of codons and the hydrophobicity
of the encoded amino acid. These regularities are even more striking in
a projection of the modern code onto a simpler code consisting of
doublet codons encoding a set of simple amino acids. These regularities
can be explained if, before the emergence of macromolecules, simple
amino acids were synthesized in covalent complexes of dinucleotides with
alpha-keto acids originating from the reductive tricarboxylic acid cycle
or reductive acetate pathway. The bases and phosphates of the dinucleotide
are proposed to have enhanced the rates of synthetic reactions leading
to amino acids in a small-molecule reaction network that preceded the
RNA translation apparatus but created an association between amino acids
and the first two bases of their codons that was retained when
translation emerged later in evolution.
</quote>

In addition it provides (yet another) explanation of the homochirality

<quote>he reductive amination that converts a completed {alpha}-keto
acid into an amino acid is particularly important because it establishes
the stereochemical configuration (i.e., L or D) of the amino acid. A
mechanism for reductive amination involving G in the first position of
the dinucleotide was described above (see Fig. 4). For amino acids
encoded by codons beginning with A, C, or U, this reaction must occur
after some or all of the side-chain elaboration has taken place. In
particular, it is necessary to avoid generation of the amino group while
there are reactive groups present in the side chain, to avoid the
cyclization that occurs during synthesis of Pro (see Fig. 2). The final
reductive amination could be catalyzed by A, G, or C in the second
position, although probably not as effectively as by G in the first
position. U does not have an exocyclic amine, and whether U can catalyze
this reaction using the secondary amine in the ring is uncertain.
Because the reaction is postulated to occur in a chiral environment, it
would be expected to produce an excess of one stereoisomer. Thus, this
model provides a plausible and testable hypothesis for the dominance of
L-amino acids, a problem that has challenged prebiotic chemists for
decades.</quote>

The paper also reminded me that the stereochemical relationship between
coding triplets and amino acids can be dated back to Stereochemical
relationship between coding triplets and amino-acids. Pelc SR, Welton MG.
* *Nature. 1966 Feb 26;209(26):868-70.
Received on Sun Oct 2 20:47:43 2005