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

 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