Dr.GH
Posts: 2333
Joined: May 2002
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More from my "Short outline,"
I want to mention a neat instance where both left and right amino acids are used in a living thing. It is very rare, but it does happen. Next time a creationist claims to be an "expert" and that amino acid chirality "proves" something supernatural, you can gob-smack-em. The protein is called Gramicidin A and it has 8 L-amino acids, 6 D-amino acids, and one glycine which is an amino acid that is neither L- or D- in its structure. I have found that even many biologists will bet an "adult beverage" that all proteins are exclusive L- amino acids.
Before we go forward another couple of basic chemical facts need to be added to the discussion. First, L- amino acids will randomly convert to D- amino acids over time, and D- forms will convert to L- forms. This is called "racemization" because eventually you will end up with equal amounts of L- and D- amino acids. The rate that this occurs at varies with the amino acid, and its surroundings. The fastest conversion happens to amino acid molecules all by themselves in hot water. Under cold, dry conditions when the amino acids are attached to one another, or better yet, if they are also attached to a mineral, racemization can be very slow. Very, very slow.
This means that if there is even a tiny advantage one way or the other, the favored form will become the dominant form.
There are larger arguments for a racemic origin of life.
Edward Trifonov (2004) confirmed two ideas, that the earliest amino acids were those easiest to form abiotically, that codons and aa's organized contemporaneously to form short ogliomers (what he didn't cite was the notion that oligomers can form spontaneously, are "selected" merely by being stable, and that RNAs (or Lacanzo and Miller's PNAs) imprint and replicate "successful" short peptides.) Trifonov wrote, "The amino-acid chronology itself is a quintessence of natural simplicity and opportunism: use first those amino acids that are available. When done with all codons, take from those amino acids that have too many."
The fact is that there are a growing list of short proteins with D- aa's, (most of the ones I know of are bacterial membrane components but there are also examples from yeasts to humans). Add to this, most bacteria have evolved enzymes that convert L-aa's to D-aa's for the same Miller/prebiotic amino acids. Again even we humans have enzymes to use D-aa's.
Trifonov, Edward N. 2004 "The Triplet Code From First Principles" Journal of Biomolecular Structure & Dynamics, ISSN 0739-1102 Volume 22, Issue Number 1,
Babbitt PC, Mrachko GT, Hasson MS, Huisman GW, Kolter R, Ringe D, Petsko GA, Kenyon GL, Gerlt JA.
1995 "A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids." Science. 1995 Feb 24;267(5201):1159-61.
Nathalie Chamond, Maira Goytia, Nicolas Coatnoan, Jean-Christophe Barale, Alain Cosson, Wim M. Degrave and Paola Minoprio
2005 "Trypanosoma cruzi proline racemases are involved in parasite differentiation and infectivity." Molecular Microbiology Volume 58 Issue 1 Page 46 - October 2005
Alexander Jilek, Christa Mollay, Christa Tippelt, Jacques Grassi, Giuseppina Mignogna, Johannes Müllegger, Veronika Sander, Christine Fehrer, Donatella Barra and Günther Kreil
2005 "Biosynthesis of a D-amino acid in peptide linkage by an enzyme from frog skin secretions" Published online before print March 9, 2005, PNAS | March 22, 2005 | vol. 102 | no. 12 | 4235-4239
Yamashita, Tatsuyuki, Ashiuchi, Makoto, Ohnishi, Kouhei, Kato, Shin'ichiro, Nagata, Shinji & Misono, Haruo
2004 "Molecular identification of monomeric aspartate racemase from Bifidobacterium bifidum." European Journal of Biochemistry 271 (23-24), 4798-4803.
Ian G. Fotheringham, Stefan A. Bledig, and Paul P. Taylor
1998 "Characterization of the Genes Encoding D-Amino Acid Transaminase and Glutamate Racemase, Two D-Glutamate Biosynthetic Enzymes of Bacillus sphaericus ATCC 10208" Journal of Bacteriology, August 1998, p. 4319-4323, Vol. 180, No. 16
K. Y. Hwang, C.-S. Cho, S. S. Kim, K. Baek, S.-H. Kim, Y. G. Yu and Y. Cho
1999 "Crystallization and preliminary X-ray analysis of glutamate racemase from Aquifex pyrophilus, a hyperthermophilic bacterium" Acta Cryst. (1999). D55, 927-928
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"Science is the horse that pulls the cart of philosophy."
L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"
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