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RBH
11 Apr 2009, 12:19 AM
This is a cross post of something I just put up on the Panda's Thumb.

One of the "criticisms" (scare quotes to indicate creationist blather) of science is that it doesn't (and, some say, can't) account for the emergence of life on earth. Now a new paper coming out in Astrobiology (pre-pub version online here (http://arxiv.org/abs/0904.0402) shows that 10 of the 20 amino acids in life on earth are thermodynamically favored, and would likely emerge under a variety of conditions.

The implications are profound, as Supernova Condensate (http://invaderxan.livejournal.com/80849.html) notes. Among those implications is that life elswhere is likely to have some characteristics in common with life on earth at the biochemical level. The abstract of the paper:Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth via meteorites. We combine observational and experimental data of amino acid frequencies formed by these diverse mechanisms and show that, regardless of the source, these ten early amino acids can be ranked in order of decreasing abundance in prebiotic contexts. This order can be predicted by thermodynamics. The relative abundances of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated. The remaining amino acids were incorporated into proteins after pathways for their biochemical synthesis evolved. This is consistent with theories of the evolution of the genetic code by stepwise addition of new amino acids. These are hints that key aspects of early biochemistry may be universal. More discussion at Supernova Condensate (http://invaderxan.livejournal.com/80849.html), where I found the story.

lpetrich
11 Apr 2009, 03:32 AM
I'd mentioned some related results in The Earliest Molecular Evolution (http://secularcafe.org/showthread.php?t=940). In Molecular evolution before the origin of species (http://www.ncbi.nlm.nih.gov/pubmed/12225777), Brian Davis came up with a "code age" of various amino acids that is the number of steps required to make them from members of the Krebs cycle. And in Evolution of Amino Acid Frequencies in Proteins Over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code (http://www.ncbi.nlm.nih.gov/pubmed/12270892), Brooks, Fresco, Lesk, and Singh had concluded that reconstructed ancestral proteins were enriched in amino acids common in prebiotic syntheses. From the paper that the OP's reference refers to, A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code (http://arxiv.org/abs/0904.0402), the average abundance order is

Glycine, Alanine, Aspartate, Glutamate, Valine, Serine, Isoleucine, Leucine, Proline, Threonine

Brian Davis had estimated a "code age" of amino acids from the amount of metabolic steps needed to make them from Krebs-Cycle members; he views the Krebs Cycle as a very early metabolic pathway.

Age | Amino Acids
02 | Aspartate, Glutamate, Asparagine, Glutamine
04 | Alanine, Proline, Serine, Valine
05 | Cysteine, Glycine
06 | Threonine
07 | Isoleucine, Leucine, Methionine
09 | Arginine
10 | Lysine
11 | Phenylalanine, Tyrosine
13 | Histidine
14 | Tryptophan

I've underlined all the prebiotic ones; they are all among the "younger" amino acids. The exceptions are asparagine and glutamine, which are aspartate and glutamate with the side-chain -COOH turned into -CONH2, and cysteine and methionine, which both contain sulfur.

RBH
11 Apr 2009, 03:38 AM
On Panda's Thumb Gary Hurd pointed out this paper (http://www.google.com/url?sa=t&source=web&ct=&cd=2&url=http%3A%2F%2Fwww.colorado.edu%2Fphysics%2Fphys 7450%2Fphys7450_sp05%2Fdownloads%2Ftripletcode.pdf&ei=nA7gScWtDaCWtgPj042xCQ&usg=AFQjCNEVOQQXywtNVoaGZew50z7SLKgc0A&sig2=QPDDp7tmTdxtUdcT-Ts9aw) on the Triplet Code from First Principles, which he considers more important than the thermodynamic one I described above. I haven't read Gary's reference yet, so can't say one way or the other.

lpetrich
11 Apr 2009, 09:38 AM
Its author, Edward N. Trifonov, first collected 60 hypotheses of the order of acquisition of amino acids and found some consensus orders. Here's the one for single-factor analyses; I've underlined the prebiotic AA's:

glycine, alanine, valine, serine, proline, aspartate, threonine, glutamate, leucine, isoleucine, asparagine, arginine, histidine, glutamine, lysine, phenylalanine, cysteine, methionine, tryptophan, tyrosine

He then ordered the codons in order of their binding strength and worked out the order of addition of amino acids with the help of that order and some other hypotheses.

The most stable codon pair is GGC - GCC, and it accounts for glycine and alanine, respectively. These are the smallest biological amino acids and the most abundant in prebiotic syntheses. The next one is GAC - GUC, which gets aspartate and valine, which are close in line.

Making the third codon wobbly gives glycine GGG, GGA, and GGU, alanine GCG, GCA, and GCU, aspartate GAG, GAA, and GAU, and valine GUG, GUA, and GUU. The opposites of the glycine ones are CCC - proline, UCC - serine, and ACC - threonine. Etc. But GAG and GAA get reassigned to glutamate, a similar but bigger amino acid, by "codon capture". Third-codon expansions and codon captures continue, filling out the genetic code.

The order that Trifonov finds is close to the consensus orders he had earlier found, though not an exact match.

This causes some problems for Brian Davis's "code ages" of proteins, because the cysteine in ferredoxin makes that protein younger than several of the others, and that cysteine is necessary for bonding to that protein's iron ions.