On Tue, 17 Feb 2004 18:05:03 +0000 (UTC),
TomHendricks474 <
[email protected]> wrote:
<Larry Moran 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
