<< Tom, you will need to clarify here.
1. "h-bond to a nucleotide base pair on a single strand" - did you really mean to write "base
PAIR"? Or do you want to h-bond to the unpaired base. (The answer to your question is yes in
either case).
TH Unpaired base. My error.
2. "can it do it in both the COO- and COOH forms?" - did you really mean to write "the carboxyl
group of a peptide bond"? Or did you mean the carboxylic acid group of an amino acid? (The answer
is still yes in either case, but I must be misunderstanding the question because the answer seems
to me to be useless to you.
TH Again the carboxylic acid group of an amino acid is correct.
Any O or N with unpaired electrons can h-bond to any H that is weakly acidic - that is to any H that
is covalently bonded to an O or N. But a single h-bond buys you almost nothing. You need at least a
half dozen or so to have any kind of stability from h-bonding.)
Quoted message said:Quoted message said:
I see. But I still think this is the key to life's origin. Look at this scenario closely. We have
folded RNA strands so simple that they can easily be coded with ONLY G and A (purines that don't
have the problem of UV dimers) and any other zoo of bases around. Thus the structure has some
stability due to the folding and mismatched base pairing within the folds with two unpaired ends
sticking out. Imagine a ball of string with two ends sticking out unprotected.
The unprotected ends would be more thermally stable if they could latch on to anything - even with
an h-bond. That would be strong enough to protect it somewhat, but weak enough to set up variants. I
tend to think that the more prevalent aa's helped protect the more scarce nucleotide strands - so it
was a lopsided symbiosis.
All we need now is at least 3 unpaired bases sticking out at either end to h-bond to other
floating flotsam and jetsum in the primordial soup. I say three because you need the stability of
one in the center.
Let's say one end latches on to another bit of RNA (it evolves to the mRNA) and the other end
latches on to an amino acid. This end evolves to the acceptor stem. Our original ball of rna will
evolve to the tRNA. Thus we have a ball of proto tRNA attached to a proto mRNA at one end and an aa
on the other.
It is perhaps not necessary that they are stong h-bonds. What is key is that they are strongER bonds
than the competition. In my h-bond world, or purine world, the winners are those that can survive
denaturation due to the high heat that the sun cycle reaches on a daily basis. For instance all h-
bonded variants are less likely to be damaged by UV. That alone would select the h-bonders.
I also think that this would set up the genetic code - again all we need at the acceptor stem end is
3 unpaired bases of G and A with
GGwobble being enough for a center position that is a purine, and that is more protected due to its
h-bonding to the amino acid.
OR a
GAwobble being enough for a center position that is a purine, and that is more protected due to its
h-bonding to the amino acid.
In a sense the aa is a protective cap for the proto tRNA ball. At least at this primitive stage.
Notice wobble could be explained as that base that is the farthest out - or completely out on a limb
with only the middle base to base stack to.
Somehow this slight bonding of one end to other rna (the tRNA to mRNA we have today) and the other
end to amino acids (the acceptor stem to an aa) - set up similar h-bonding. That is important
because both ends will denature at the same temp due to similar h-bonding AND base stacking. And
they'll do this on a daily basis until the exact correlation or symbiosis between the two ends is
selected for.
Also if we can have both COO- and COOH forms on the carboxyl group of the aa - then perhaps GGwobble
favors one and GAwobble favors the other.
If so , wouldn't it be COO- + GGwobble COOH + GAwobble
That would lead to a two variation genetic code.
Also lead to these 3 amino acids: Glycine - GGwobble Glutamic Acid or Aspartic acid - GAwobble.
(note with glycine there is no chirality. With the other two there is. Perhaps that set up L-aa's.)
(note there are added carboxyl groups on the 2 side chains of the acids GAwobble - that suggests a
clue of some sort because the h-bonding is the unpaired base + the carboxyl group on the aa )
With a later addition of a 2nd position C or U, (GCwobble, or GUwobble) I believe you can easily
evolve all aa variants.
Etc. etc.
It seems to me all this is feasible, all this is selected in the early earth climate, all this is
symbiotic from the start, all this is thermally the most stable, etc.
But it is certainly also extremely sketchy and vague. Somehow I tend to think the pieces are coming
together though.
Comment?
Thus if rna to rna end on one end has GAG
