Because of the danger of UV caused dimers whenever two
pyrimidines are adjacent on an RNA strand, there are only
two ways to code for a safe anticodon (safe being where
there are no 2 pyrimidines side by side on either the
anticodon or the codon)
They are:
purine, pyrimidine, purine
(the 2nd position pyr would pair with a codon 2nd
position pur which some suggest is connected to
hydrophilic amino acids).
OR
pyrimidine, purine, pyrimidine
(the 2nd position pur would pair with a codon 2nd
position pyr which some suggest is connected to
hydrophobic amino acids).
So far so good. (see other posts for reasons why this would
mostly be purines matched with philic aa's)
BUT this 3 base anticodon is not isolated - there are bases
on both ends of the RNA strand that they are on.
Thus if you have purine, pyr, purine - you have purines on
both ends and no danger of dimers with their neighbor bases.
BUT, and here is where it gets interesting for me , if you
code pyr,pur,pyr there is a real danger of dimers from the
outside pyr in first or 3rd positions and a possible pyr
next to it in either the 37 or 33 position.
Such that 33 = pyr 34,35,36 = pyr, pur, pyr anticodon 37 =
pyr
thus you have dimer potential in 33 - 34 or 36 -37 position.
Thus it would be highly unlikely for an anticodon to safely
have pyr, pur, pyr coding -
(or for that matter its codon! on the mRNA)
But it seems the bases in tRNA have evolved to solve this.
In position 37 there is always a purine. Thus 36-37 can
never be two pyrimidines and there can never be a dimer
between this outside base and position 1 in the anticodon.
On the other end you have 3rd position wobble at base 34,
plus a guaranteed 2 pyrimidines at position 33 and 32.
(Perhaps this weak end is why there is wobble)
Summary I think it is more and more clear that dimers were a
major selection force on the genetic code. There are too
many coincidences if it isn't. And that somehow the mostly
purine coding was associated with hydrophilic amino acids
while only that coding completely free of UV dimers
(whatever environmental conditions that suggests) coded for
hydrophobic amino acids.
Comment?