Still looking at how dimers on adjacent pyrimidine
bases, might effect the genetic code.
(Purines = A, G // Pyrimidines = U,C - and T in DNA
*   *   *
Why 3 bases in a codon?
May have 3 to prevent dimers. 
IF there were only two then the 4 possibilities
would be pur/pur (a dimer on the anticodon side)
pyr/pyr (a dimer on the codon side) 
or pur/pyr, and pyr/pur  - both
of which might have a dimer with the adjacent base
outside the 2 base codon.
Thus 2 is unlikely to code much of anything due to
dimer damage.

But with 3 you have a center position to prevent
dimers in the codon. Two possibilities that would
prevent dimers (adjacent pyrimidines)
pur/pyr/pur or pyr/pur/pyr.

The first would not have dimer problems with its
neighbor bases either, but 
the 2nd, pyr/pur/pyr could have
a dimer at either end with an adjacent pyr.

Now then - on the proto tRNA it has ways around the
dimer -on-either-end- of the anticodon problem 
(see that post)

But to prevent dimers on the proto mRNA side, 
you would be limited to only one coding -
alternating purines/pyrimidines such that there is
never two pyrimidines together.
Thus the only dimer free proto mRNA possibility 
would be a single strand with this coding:

pur/pyr/pur/pyr/pur/pyr/pur/pyr/pur/pyr/pur/pyr/
etc.

But that sets up some interesting coding!
First note that start codon is pur/pyr/pur or AUG
which fits in with the above very nicely.

Now see that stop codon is pyr/pur/pur with
the last two suggesting a dimer in the anticodon.
Stop = UAA, UAG, or UGA = all pyr/pur/pur.
Thus stop is two purines in a row with dimer
damage possible on the anticodon that has
two pyrimidines in a row.

Now back to our alternating pur/pyr proto mRNA code.
Note that no matter where the reading of the code
starts you will get either 
pur/pyr/pur or pyr/pur/pyr - thus any place along
the strand will code and continue to code through
out the entire message till you run out of 3 base
sets.

pur/pyr/pur = coding = hydroPHOBIC amino acids
pyr/pur/pyr = coding = hydroPHILIC amino acids

So the code would seem to code for alternate
phobic then philic  amino acids.

It also suggests that anywhere on the proto mRNA
where the bases don't alternate pur/pyr, the code
shuts down and ends coding.

*  *   *
Now I went further and studied the genetic code
to see what amino acids could be coded by 
either pur/pyr/pur or pyr/pur/pyr.
I found 9 that could, and 11 that could not.

Here are the 9 that could
Ala, Arg, Cys, His, Ile, Met, Thr, Tyr, Val (and start)

The 11 that could not are
Asn, Asp, Glu, Gln, Gly, Leu, Lys, Phe, Pro, Ser, Trp.

I wonder if any reader sees any pattern in these two
sets? Or has any
comment on any of the above.

Tom
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