On Tue, 17 Feb 2004 18:05:03 +0000 (UTC), 
TomHendricks474  wrote:
> 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.
> 
> Accepting the above, then this type of bonding could
> only happen in the dry phase of a heat cycle, or in
> water if and only if it somehow was protected from the water.

Hydrogen bonds won't form in any kind of "dry phase" that I could
imagine. The second part of your statement is correct.

>> 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.
> 
> This presents problems for sure. 

That's a mild way of putting it.

> At first I would think that any h-bonding in a dry phase would help in 
> thermal stability, and allow those molecules to last another day.
> IF my scenario has any truth, then there must have been a selective 
> advantage for the h-bonding to be in the way I suggested.

Why not just admit that your "theory" is ridiculous?

> Another thing this suggests is that, in a heat cycle we have a dry 
> phase where there are numerous h-bonded variants, and a wet phase
> where all these  h-bonds are severed. Thus each day in the cycle we 
> have numerous variants or hybrids for selection. This makes more sense 
> than a single fluke event like most scenarios have.

Nothing about your "theory" makes sense.

>>  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" 
> 
> I consider it an hypothesis.

You could call it wild uniformed speculation. 

>> 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.
> 
> I think if the conditions above are correct, then my scenario is indeed 
> wrong. Yet I think in the earliest times of the origin, I don't think 
> the above applies.

That's the nature of crazy theories. They don't have to agree with facts.

>> 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.
> 
> But this just presents more problems than answers for many reasons. 
> Perhaps the most important is this
> Why would a polynucleotide chain need connections to an amino acid, 
> or vice versa?

To activate the amino acid for peptide bond formation, for one thing.

> If you respond with 'it was a fluke' then we have yet another fluke 
> moment in the OOL. That kind of 'many random fluke events' scenario, 
> just does not make any sense to me at all.

I understand. You prefer the perfectly sensible idea that the 
temperature of the ocean (or a small puddle) could fluctuate between 
100C and 60C every day for thousands of years.



Larry Moran
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