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TomHendricks474
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 Posted: Thu Dec 04, 2003 1:38 am Post subject: tRNA evolution |
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More and more I think the major clue to the origin of life
lies in tRNA. I was thinking last night about how it could
first start and came up with this scenario.
We start with a single strand of nucleotides.
It has folds caused by the order of nucleotides, h-bonding
and other forces.
The folds are bordered on both ends by unfolded stretches.
Thus we have a folded portion with acceptor like stems on
both ends.
Through chemical selection the fold became more precise,
and at some point one of the acceptor stems folded over on
itself to make the anticodon loop. Thus leaving the other
end as our present day acceptor stem.
All of this makes sense, fits the basic facts, and is easy to visualize.
But that raises more questions:
1. Why was a folded proto tRNA selected that is that
size and shape?
2. Why was a folded proto tRNA selected that size and shape with
two single strand proto-acceptor stems on each end.
3. Why are the two ends pointing in the same direction?
3. What did those two acceptor strands - h-bond to
(if it was an h-bond)?
4. Why are the two proto acceptor strands 76 a apart?
What does that fit?
5. Why would connecting both ends to another molecule (s)
help this one better survive its environment.
6. Somehow the proto tRNA attaching to peptide bonds
was an advantage -
how did it do it? Why did it do it?
I firmly believe some biochemist out there sees the missing
fact - sees some connection between the tRNA ends and the peptide
bond that the tRNA exactly fits. And they>ve probably said
something like, 'that>s curious". If you are he - and you see
the reason proto tRNA in the shape it is, is best adapted to
symbiotic behavior with a peptide bonds - let me know!
Tom Hendricks |
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Jim Menegay
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| Posted: Fri Dec 05, 2003 1:48 am Post subject: Re: tRNA evolution |
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As to why tRNA has the shape it has, there was a lot of theorizing about that
in the 1970s from Eigen>s group and from a guy named Kuhn (I think). You
definitely should become familiar with Eigen>s "hypercycle" theory if you
are interested in this aspect of OOL.
As to what selective advantage tRNAs got from binding amino acids, and later
discharging them, one of the most interesting ideas is the "genomic tag" model
of Weiner (Alan, I think) and Nancy Maizels. They wrote a number of papers
about it in the late 1980s and it also appears in editions of Watson>s
textbook from that era. I think you will find their theory particularly
interesting.
What are the best modern theories? I>m not sure, but you should be able to
find them by doing a citation search. The papers I mention will definitely
be cited in newer theories.
Maybe someone with a better memory and/or library research tools can provide
the exact citations. |
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TomHendricks474
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| Posted: Fri Dec 05, 2003 1:48 am Post subject: Re: tRNA evolution |
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<< More and more I think the major clue to the origin of life
lies in tRNA. I was thinking last night about how it could
first start and came up with this scenario.
We start with a single strand of nucleotides.
It has folds caused by the order of nucleotides, h-bonding
and other forces.
The folds are bordered on both ends by unfolded stretches.
Thus we have a folded portion with acceptor like stems on
both ends.
New stuff:
Let>s take this idea further. We have a folded nucleotide strand of RNA with
two naked ends - each with bases.
At some point I suggest that there are 3 bases on each end. There are at least
3 bases because that allows for one MIDDLE base. And a protected 2nd position
middle base is essential.
Here>s a possibility for those 3 and in both cases we are listing them in this
direction - from the folded strand out toward the naked out-on-a-limb end.
I suggest at both ends we have
these 3 bases: G/N/Wobble -
Where G is always the first base
Where N = A,U,C, or G as possibilities for the 2nd base
Where there is wobble in the third base. because it is the most exposed.
We have now the possibility of 4 codons that happen to code for the four most
produced amino acids in most prebiotic experiments:
(G N Wobble)
G G wobble = Glycine
G C wobble = Alanine
G A wobble = Aspartic Acid
G U wobble = Valine
Now note that glycine and alanine are some what neutral in not being either
hydrophobic or philic, but that
Aspartic acid is philic, and Valine is phobic.
And in similar conditions of heat/wet and dry/pH; I would think both ends would
be selected when their codons matched. And when they did not match they would
not be selected.
Also when both end>s codons matched , the number of h-bonds would match too.
Thus both would be denatured at the same time - thus they would both release
their h-bonds at both ends at the same time. etc. That would be selected for.
IF any of this has a basis in fact, then they suggest
two immediate questions:
1. why would G be favored in first position or in the position next to the RNA
folded portion.
2. how would these codon ends connect to AA>s - what part of the AA>s would
they connect to - and how would tt help in a prebiotic chemical symbiosis
between the RNA and the AA>s?
Comment?
Tom Hendricks
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TomHendricks474
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| Posted: Sat Dec 06, 2003 11:40 pm Post subject: Re: tRNA evolution |
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<< You
definitely should become familiar with Eigen>s "hypercycle" theory if you
are interested in this aspect of OOL.
Yes but that>s not quite what I>m suggesting.
As to what selective advantage tRNAs got from binding amino acids, and later
discharging them, one of the most interesting ideas is the "genomic tag" model
of Weiner (Alan, I think) and Nancy Maizels. They wrote a number of papers
about it in the late 1980s and it also appears in editions of Watson>s
textbook from that era. I think you will find their theory particularly
interesting.
TH
I>ve seen them mentioned - but there>s nothing on the net or in old textbooks
I>ve go
Z**t. Does any reader know what was the jist of their ideas.
What are the best modern theories? I>m not sure, but you should be able to
find them by doing a citation search. The papers I mention will definitely
be cited in newer theories.
TH
I don>t think any of the modern hypothesis are correct.
If they aren>t based on life as a reaction to a heat cycle, I don>t think they
can be correct.
That>s why I>m looking still.
Maybe someone with a better memory and/or library research tools can provide
the exact citations.
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