Posted: Mar 09, 2010 5:22 pm
by eversbane
rainbow wrote:
OgreMkV wrote:

This article (popular) describes how the metabolism first hypothesis is unsound. popular
Rebecca M. Turk, Nataliya V. Chumachenko, and Michael Yarus. Multiple translational products from a five-nucleotide ribozyme. Proceedings of the National Academy of Sciences, Published online February 22, 2010 DOI: 10.1073/pnas.0912895107 journal reference

This article descibes how RNAs that are only 5 bases long can be fully functioning protein catalyst.

from the Discussion

Further, these particular reactions are central to metabolism,
resembling the substrate and product of biological aminoacyltRNA
synthesis. Transaminoacylation in this work is performed
more simply than elsewhere (9, 12, 17). In addition, observation
of RNA-peptide products provides the simplest polypeptide
synthesis from aminoacyl adenylate (12, 18, 19), or from any
other substrate, in the absence of protein catalysts. Essential intermediates
in protein biosynthesis therefore arise surprisingly
easily in the presence of very short RNAs.

So this simple 5 nucleotide RNA chain can catalyze the essential intermediates. In other words, it shows that more of the steps from chemistry to biology are possible than we had before.

The ultimate importance of these observations may lie partly
in the unknown number of other reactions that can be accelerated
by comparably small RNAs. This is because for each such minuscule
RNA reaction, there is a prima facie case that it would
become accessible even after the most primitive ribonucleotide

So if one RNA only 5 nuceotides long can do this kind of work... why can't more. The search is on!

To see this, consider that, to pick every possible RNA pentamer
sequence from arbitrary pentamers (with probability 0.9975),
one needs only accumulate 4.1 × 10−18 gm of RNA. To possess
every tetramer (with probability 0.9975) from a pool of arbitrary
tetramers, one would need 3.4 × 10−18 gm RNA. In a real polymerization,
one would have a distribution of lengths; nonetheless,
with only attograms of total RNA of distributed short lengths
from some geochemical source, one would have not only our
ribozyme, but every activity of comparable size.

So you only need 0.00000000000000000041 grams of RNA to have every possible (0.9975) combination of RNA pentamer. Which could provide huge number of catalytic reactions.

As an illustration, the ribozymic complexes characterized here
demonstrate that aminoacyl-RNA and peptidyl-RNAs could
have appeared in the presence of ≥9 nucleotides of polymeric
RNA, with six of these free to vary to other base pairs. We have
previously estimated that a population containing about 1 ng of
arbitrary-sequence RNA would be required before useful ribozymes
and other active RNA structures would probably occur
among this population
(20). This follows the so-called axiom of
origin (21), which estimates that theRNAworld would begin when
the amount of RNA exceeds the threshold for occurrence of ribozymes.
The finding of nine-nucleotide active centers reduces the
threshold for ribozyme activity about 7 orders of magnitude, to a
level much more easily breached by undirected geochemical syntheses
or by RNA-catalyzed RNA synthesis itself (22–24).

my emphasis

Hey look, 'undirected geochemical syntheses'! :lol:

The most intriguing possibility raised by these results is that an
RNA reaction center for phosphoester transfer may exist somewhere
near this size. This would make the polymerase/replicase
needed to initiate Darwinian evolution of RNAs, the founding
event of the RNA world, much more likely. On one hand, with
this few ribonucleotides to dispose in space, there may not be
other similar nucleotide structures that are both stable and capable
of catalysis. On the other hand, for obvious reasons, it will be
extraordinarily important to look

Hmmm... future work that can be done using the concepts in this paper. Something ID has never done.

I hope this isn't too deep. I'll be happy to explain further.

edit: correct quotes

Thank you Ogre, that is an interesting post.
Please could you open a new thread on it, since to discuss it further here would derail this thread?