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Wobble Reason?



I may have a plausible cause for the wobble in 3rd position
and ask any good biochemist out there to comment.

I don't think it was to get to a future 20 aa's. Instead I think
it was the placement of the bases then and their stability in
their environment.
Specifically I think the first anticodon was 3 bases on the
acceptor stem and that the 3rd one - the one out on the limb -
started the wobble condition. This was later mimiced in the
3 bases of the anticodon that we know on the tRNA today.

1. IF there was a connection between the aa and 3 bases in
the acceptor stem (either directly or through an enzyme) and
2. IF these 3 bases were 73, 74, and 75 (with #76 coming later perhaps or just
too far out to fit.)

THEN they would mimic the anticodon. 

In both cases the 2nd base or  inside base of the 3 
would be protected on both sides by other bases. It would also be the
strongest position if and when all 3 were h-bonded to other  molecules.

The first base - #73 in the acceptor stem and #36 in the anticodon
would both have bases next to them and be in the 2nd most stable position.
But the 3rd in both would be in precarious positions.
In #75 it is out on a limb so to speak and would be the weakest of
the 3 bonds with only #76 beyond it (and it may not have been there.
In #34 it too would be in the weakest postion at the end of the anticodon
loop.

Therefore in both positions we have similar circumstances of h-bond fit.
And in both cases the outside base would be the weak wobble base, with
the strongest position being the 2nd and the next strongest the first position.

Also I would suggest that the acceptor stem 3-bases probably came first.
And later the anticodon followed.

Also it is likely that we now have at least 3 symbiotic conditions that would
link both ends: temp (hot or cold) pH (acid or base) and wet or dry.

Comment?
Tom Hendricks




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