Number: 207 (Read 0 times) Date: 25 Mar 94 18:43:42 To: All Subject: Complexity, Amino Aci

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Number: 207 (Read 0 times) Date: 25 Mar 94 18:43:42 From: Ken Cox To: All Subject: Complexity, Amino Acids, and the Face of God From: kcc@achilles.wustl.edu (Ken Cox) Organization: Washington University, St. Louis MO In article , Deaddog wrote: >A desperate attempt to redress my own s/n. I must admit that at first I didn't understand what Deaddog was saying in this post. Oh, I got his major point -- that given one molecule there are often several reaction paths to get to another, and that the paths that cells use to perform very similar transformations often vary wildly, which isn't really what you would expect from an intelligent designer. But I didn't understand the chemistry. Well, I still don't understand the first of the two reaction -- the dephosphorylation one. But since (according to Deaddog) it's a clever sneaky reaction that _is_ the sort of thing a good designer might come up with, it isn't important to the main point. However, after a bit of bookwork I did manage to grasp the second reaction, the one with the panda's thumbprints all over it. I thought it might be helpful for others if I presented a more detailed explanation of the reactions, with pictures. A caveat: Chemistry is not my field, and I am sure that I have made a number of minor mistakes, but the major reaction paths are correct. Deaddog is discussing the formation of amino acids, the building blocks of proteins. An amino acid looks like this: H H O | | || H--N--C--C--O--H | R (H = hydrogen, C = carbon, N = nitrogen, O = oxygen, R we'll get to below.) The thing at the top is the amino acid backbone. It consists of an amino group NH2, a central carbon (the alpha carbon), and a carboxyl group COOH. The alpha carbon is attached to the amino group, the carboxyl group, a hydrogen atom, and a side group R. The side group differs among the various amino acids and gives them different chemical properties. Deaddog is describing the formation of two amino acids, histidine and tryptophan (I'll condense the drawing of the amino and carboxyl groups now): H H | | NH2--C--COOH NH2--C--COOH | | H--C--H H--C--H | | C3H3N2 C8H6N Histidine Tryptophan As you can see, the R groups of these amino acids start with CH2 (the beta carbon) then have something more stuck on the end. In histidine the "something more" is imidazole, C3H4N2, with the beta carbon taking the place of one of imidazole's H's. In tryptophan it is indole, C8H7N, again with the beta carbon in place of an H. In the synthesis of histidine by a cell, one precursor molecule is imidazole glycerol phosphate, which looks like this: H | OH--C--H | OH--C--H | PO3--C--H | C3H3N2 Imidazole glycerol phosphate (Warning: I probably have the phosphate PO3 in the wrong place, and I may have an OH for an H or vice-versa, but it doesn't matter much for this discussion.) Deaddog calls this "glycerol-3-phosphate on a stick", which is true -- the glycerol is the chain of three carbons, and the "stick" is the imidazole. The resemblance to histidine is obvious, especially if I draw the IGP a little differently: H H | | OH--C--CH2OH NH2--C--COOH | | PO3--C--H H--C--H | | C3H3N2 C3H3N2 Imidazole GP Histidine As you can see, just three minor differences -- a CH2OH for the carboxyl COOH, an OH in place of the amino NH2, and a PO3 where an H should be. (If I've misplaced the phosphate or written OH for H, the number of differences might be two or four. Details, details.) This suggests turning one into the other by replacing or modifying the three (or whatever) groups. This is the reaction path used by cells. According to Deaddog, it takes five steps and is a little expensive, energy-wise. Now look at the synthesis of tryptophan. Its immediate precursor is indole glycerol phosphate, which looks a lot like imidazole glycerol phosphate but has indole instead of imidazole: H | OH--C--H | OH--C--H | PO3--C--H | C8H6N Indole glycerol phosphate And of course it also looks like tryptophan: H H | | OH--C--CH2OH NH2--C--COOH | | PO3--C--H H--C--H | | C8H6N C8H6N Indole GP Tryptophan So we have exactly the same problem as before -- turning the glycerol phosphate into the beta, alpha, and carboxyl carbons in the tryptophan. But the cell does not solve the problem in the same way! Instead, once it has the indole glycerol phosphate in hand (so to speak), it finds another amino acid, serine: H | NH2--C--COOH | H--C--H | OH Serine Of course the serine already has the amino acid backbone, and also has the beta carbon (CH2) that we need in tryptophan (and in histidine, for that matter). Once the cell has found the serine and dragged it over to the indole glycerol phosphate, it removes the glycerol-3-phosphate from the indole glycerol phosphate and the OH group from the serine's R group, leaving: H | NH2--C--COOH | H--C--H | | C8H6N Serine without OH Indole GP without the GP It then glues these two pieces together to get the tryptophan. Deaddog says this takes one step, and implies it is much cheaper, energy-wise, than the long path used to make histidine. (Is it?) To repeat Deaddog's point: These are almost identical transformations, differing only in indole versus imidazole (a component which is not modified by either reaction). Yet the cell uses two entirely different reaction paths to perform these transformations. Is this the mark of intelligent design? Ken Cox kcc@siesta.wustl.edu

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