Protein Synthesis

Here's a quote from Strickberger on 2 ways protein synthesis
might have evolved. I agree with both. And think both
happened at the same time.

"Protein synthesis might then have evolved through (2 ways)
specific amino acids directly interacting with specific
nucleotide sequences...."

One idea is that first coding would favor two divisions
hydrophilic or hydrophobic and later this would be refined
to what we have today. But I say why have two at first?
That seems unrealistic and highly complicated and refined
for the origin.

Instead I suggest that the first peptides to be selected
were all or mostly hydrophilic. Thus those that could react
in water were exclusively selected at first. Hydrophobic
would be a later reaction against water.

Almost all nucleotides (and they are sparse in prebiotic
experiments) are purines. Also pyrimidines may have been
selected against because of UV caused dimers. Also we have 3
bases in a codon to separate bases and prevent dimers. For
these and other reasons most of the earliest RNA strands
would be purines, and would NOT be two pyrimidines together
( could make dimer).

Thus we have two separate conditions going on at the
same time:
1. chemical selection favoring hydrophilic amino acids.
2. chemical selection favoring purine nucleotides.

Together they set up the first match mostly hydrophilic
amino acids with mostly purine coding. (Any mismatch would
be chemically selected against)

Later (in a way that is still very murky) its opposite would
be chemically selected for due to the improvements they
would bring: hydrophobic amino acids , and pyrimidine
nucleotides

******

"...or, perhaps through indirect placement of amino acids
into such sequences by intermediary adaptor molecules that
brought amino acids to the nucleotide chain."

I think the 'intermediary adaptor molecules were
polyphosphate chains (pre-ATP). Any nucleotides or peptides
that were in the vicinity of polyphosphate chains would have
the advantage they gave (chemical energy) and would be
chemically selected.

Those isolated without polyphosphate chains would have no
chemical energy source.

Thus we would have islands of prebiotic chemistry where
there was polyphosphate chains. The rest of the prebiotic
soup would be mostly inert to change.

Comment?

<< "...or, perhaps through indirect placement of amino acids
into such sequences by intermediary adaptor molecules that
brought amino acids to the nucleotide chain."

Those isolated without polyphosphate chains would have no
chemical energy source.

Thus we would have islands of prebiotic chemistry where
there was polyphosphate chains. The rest of the prebiotic
soup would be mostly inert to change.

***

Follow up:

There is some interesting evidence that seems to support
the above.

1. RNA binding to ATP "Some cellular RNA molecules catalyse
reactions that include bindng to ATP, the common energy
transfer molecule. - Sassanfar and Szostak

2. RNA binding to amino acids "Zhang and Cech demonstrated
that even a selected non cellular ribozyme can perform
... amino acid binding function (peptide formation)

Therefore I suggest: All the following 3 things happened at
about the same time and in the same temperature zones and
that each step helped the other 2 better survive.

3. RNA strands evolve to tRNA,mRNA, etc.
4. polyphosphate chains evolve to ATP
5. amino acids evolve to protein.

And RNA was connected to ATP was connected to Amino acids
was connected to RNA etc.

Let's go further and say this:

Job one for the above set of 3 was polymerization, or
getting the water out. At first the sun/dry/ heat cycle did
that. Then a sun substitute chemically evolved (involving
polyphosphate chains or ATP) that allowed chemical energy in
water as well as the original sun energy outside of water. (
In water monomers would be more safe from UV dimer damage on
pyrimidines) and Job 2 making variants from these longer
polymerized molecules whether they were nucleic acids,
proteins, polysachharides, lipids,, and Job 3 Chemical
selection on these variants that produced ribozymes,
denatured and annealed hybrids of all kinds of folded and or
paired nucleotide strands, etc.

Selection pressure would be mostly from the heat cycle. Then
out of two identically thermal stable molecules, that which
best survives would be chemically selected.

Tom Hendricks

Protein Synthesis

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