On Fri, 13 Feb 2004 06:04:47 +0000 (UTC), 
TomHendricks474  wrote:

> This is one of those IF...THEN questions.
> 
> IF we have a strand of RNA that has a loose end,
> the 3' end that goes many bases beyond any base pairing,
> 
> AND IF this loose end is made up of only G and A bases
> or purine bases.
> 
> AND IF the carboxyl end of a peptide, is h-bonded to
> any one of these purines - (let's use for example either
> GGG or GAG bases, with the h-bond to the middle G or A)

In an aqueous solution (i.e., lots of water) you can NOT form stable
hydrogen bond between a free amino acid and a single-stranded
polynucleotide. Such hydrogen bonds would have to compete with
equivalent hydrogen bonds to water molecules. Since the concentration
of water molecules is a million times greater than the concentration
of amino acids or bases, there won't be any of the "bonding" that
your "theory" requires.

Furthermore, even if such hydrogen bonds were stable there is still
the problem of specificity. Each amino acid has a number of different
hydrogen bond donors and acceptors and each base has several different
potential hydrogen bonding sites. Take adenylate as an example. If
we look only at the base part (and not the sugar or phosphate groups)
then there are three potential hydrogen bond acceptors at N1, N3, and
N7 and two potential hydrogen bond donors on the amino group. (Not 
counting alternatate tautomers of adenine.) The total number of possible 
different hydrogen bonds between an amio acid and an adenylate residue 
is at least a dozen and could be a lot more depending on the amino acid 
side  chain. None of these bonds will have a significant half-life in 
aqueous solution.

Your crazy "theory" is inconsistent with known chemistry and biochemistry.
You need to learn about reaction rates and basic thermodynamics.
(I haven't even mentioned the fact that the -COOH group doesn't exist 
on free amino acids in solution.)
 
In order to get specific hydrogen bonding of the sort you require, you
have to create a hydrophobic environmment and binding sites that
position the molecules in the proper relationship. In the case of free
amino acids interacting with a polynucleotide this would require a 
large protein with a complex binding site for polynucleotide and 
amino acids. In that case, it's the binding protein that confers the
specificity and not the polynucleotide.

Forget about hydrogen bonds. It's much easier to envisage a primitive
enzyme that creates a covalent bond between a free amino acid and the
end of a polynucleotide chain. This primitive enzyme would be the
ancestor of all amino acid snthetases. The enzyme can be specific 
because it has binding sites that will only bind certain amino 
acids and certain polynucleotides. The covalent bond it creates is
stable in agueous solution. As an added bonus, it could "activate"
the amino acid for subsequent peptide bond formation.




Larry Moran
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