Purine World

TomHendricks474_at_cs.com
Date: 03/26/05 

Date: Fri, 25 Mar 2005 20:56:06 -0500 (EST)

Here are some ideas:

1. A 'purine world' would have only A, and G bases.
In order to go further you would have to add U, but
U is liable to UV caused dimer damage So some type of
UV protection would have to be in place - even if it
is the protection of water, or night, before the code
could go further.
2. If UV is a factor then WC pairing would cut the
UV absorbency down. Thus double strands or folded
and bonded single strands, would be more stable in
this environment than single unfolded strands without bonding.
3. If a purine world first, then that would explain
the more important role ATP and GTP play. It would
also suggest that the importance of ATP and GTP occured
in a time of mostly purines. And we now have a clue
to what was going on when ATP and GTP became an
integral part of the origin - purines played a dominant
role.
4. The genetic code seems clear to me in these clues:
If we accept the scarce C base, as something that
came later ( and I do,see below) and IF we accept the
middle base as most protected and most important
(its 3 bases for a codon to allow one to be protected on
both sides), then we have
three rows to consider
_U_ (pyrimidine U), _A_ ,and _G_ ,(purine A and G).

Now note the code. Under the A and G center base rows
you see just about every type of amino acid coded for
but hydrophobic amino acids. This mostly purine world
of coding looks like it may have had a lot of experimentation,
a lot of variety. I suggest that most early coding had a purine
in the important 2nd position.

Now look at the _U_ row - all hydrophobic. This would be
a great 2nd act to the code to add to the purine coding mentioned
above. (Then the code would expand to different first bases
coupled with the key 2nd base. And later the wobble in 3rd position
to further separate purines from pyrimidines - see below)

I suggest then that a mostly purine in 2nd position world
coded for mostly hydrophilic amino acids, then a lesser set
of pyrimidine U in 2nd position added hydrophobic amino acids
to the code (and later C became a mutt of sorts - not part
of either group though mostly a 2nd 'U' in character, but
occassionaly acting like a second purine.
5. If this is so then you would have to have WC pairing without
C. I note that U in the anticodon position will pair with
both purines A and G. No need for C. Now that is in the wobble
position. But couldn't it originally be in the key 2nd position in
the first days of the origin of the code?
Also if the U must
be in the anticodon spot, then that suggest U was a key part
to the tRNA makeup, while the absence of U or pyrimdines
was a key to the proto mRNA makeup. This suggests other
clues.
Note as support for this that in the stem of tRNA's there
are UG pairing. It is also in the stem of the 5S ribosomal RNA
molecule stem.

6. The anti codon loop has seven nucleotides with the
anticodon being the middle three - and the most protected
as I suggested above.
7. Note in third position it doesn't matter which pyrimidine
it is - both U and C code for the same amino acid. And excluding one
stop codon, the same is true for 3rd position purine - A or G.
This too suggests that the purine pyrimidine split is an integral
part of every aspect of the code.
8. Also note that all three stop codons have a purine in the
all important 2nd protected key position. I think that too
supports a predominately purine world in the origin of the code.

Comment?

Tom
 

Relevant Pages

  • Re: Purine World
    ... >>> Inferred Order of Introduction of Amino Acids into the Genetic ... >>Place three only important in being either a purine or pyrimidine ... >>They divide evenly again with two purine A in 2nd and two purine G ... >>What does Hunt and Perplexed see in this array - if anything? ...
    (sci.bio.evolution)
  • Re: Purine World
    ... If a purine world first, ... > the more important role ATP and GTP play. ... > coded for mostly hydrophilic amino acids, ... Note in third position it doesn't matter which pyrimidine ...
    (sci.bio.evolution)
  • Re: Purine World
    ... >> Inferred Order of Introduction of Amino Acids into the Genetic Code" ... >I note that 8 of these 9 earliest have purine in place one. ... > and two pyrimidine U in 2nd and two pyrimidine C in 2nd. ... >What does Hunt and Perplexed see in this array - if anything? ...
    (sci.bio.evolution)
  • Re: Purine World
    ... >> Inferred Order of Introduction of Amino Acids into the Genetic ... > I note that 8 of these 9 earliest have purine in place one. ... > and two pyrimidine U in 2nd and two pyrimidine C in 2nd. ... > What does Hunt and Perplexed see in this array - if anything? ...
    (sci.bio.evolution)
  • Logic and the Code
    ... I wonder - if you had mostly purine nucleotides ... N, pyrimidine, N coding = phobic. ... purine code in RNA = philic amino acids. ... There are much fewer pyrimidines. ...
    (sci.bio.evolution)