On Tue, 29 Jun 2004 04:01:13 +0000 (UTC), Harlequin <use...@cox.net>
wrote:

John's note is quite interesting. I'd like to expand on it a
bit so here's a modified version of an article that was originally
posted to sci.bio.evolution a few months ago.

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                   The Racemization "Problem"

There are two different conformations of the common amino acids.
These conformatons are distinctly different structures that cannot
be superimposed. As an example, I've drawn the two conformations
of the amino acid serine to show that they are mirror images of
each other. Note that the main difference is the orientation of
the chemical groups around the central alpha-carbon atom.

http://cwx.prenhall.com/horton/
medialib/media_portfolio/text_images/FG03_02.JPG

All chiral organic molecules, such as these two conformations of
serine, share the property of having a carbon atom bonded to four
different groups. In this case, the four groups are -H, -NH3, -COO,
and -CH2-COH. When the groups are orientated as shown on the left
side of the figure the conformation is referred to as L-serine. The
other conformation is called D-serine. The terminology originated
from the observation that pure solutions of chiral molecules will
rotate polarized light to the right (D = dextro) or left (L = levo)
but in modern chemistry the assignment of D- or L- names is based
on the structures and not on the property of rotating light. Thus,
all amino acids that have the same conformation as L-serine will
be called L-amino acids (e.g., L-alanine, L-glutamate etc.)

Amino acids can be formed spontaneously by chemical reactions.
The products of these reactions are usually mixtures of both
conformations. These mixtures are called racemic mixtures where
"racemic" refers to the fact that the solution contains equimolar
amounts of each conformation.

Modern living cells contain an abundance of L-amino acids and very
low concentrations of D-amino acids. Proteins are composed almost
entirely of L-amino acids. This is easily explained by the fact
that these amino acids are not formed by spontaneous chemical
reactions. Instead, they are synthesized inside the cell by
enzyme-catalyzed reactions and these reactions are highly
stereospecific. In other words, only the L-amino acids are made
in abundance. Furthermore, only the L-amino acids are incorporated
into proteins by the protein synthesis reactions. The D-amino
acids aren't made and even if they were they would not serve as
substrates for protein synthesis.

There's no problem explaining why modern cells don't have
racemic mixtures of the amino acids and there's no problem
explaining why proteins contain only the L- conformations.
However, if we are interested in explaining the origin of life
then we have to account for the selection of one conformation
over the other since the standard senarios presume that life
first cells arose under conditions where racemic mixtures of the
two conformations were made spontaneously in chemical reactions.
This "problem" is known as the racemization problem or the
chirality problem.

One type of explanation concentrates on the possibility that
the ancient pre-life mixtures were naturally enriched in L-amino
acids relative to D-amino acids. Thus, the choice of L-amino acids
was dictated by the natural prevalence of this conformation over
its miror image. This explanation is based solid evidence of the
enrichment of L-amino acids in meteorites. I'd like to suggest a
slightly different senario that emphasizes the synthesis of amino
acids by primitive biological catalysts.

Let's assume that there was a primordial soup where amino acids
came together spontaneously to form short peptides. In the
beginning the soup contained racemic mixtures of the D- and
L-forms of amino acids. These amino acid molecules were formed
spontaneously by the kinds of chemical reactions that are
simulated in the laboratory. The soup also contained abundant
quantities of the most simple amino acid, glycine. Glycine has
only a single conformation since the alpha-carbon atom is
covalently attached to only three (not four) different groups.

Some of the random peptides acted as catalysts for chemical
reactions. The catalytic activty of random peptides has been
observed in laboratory experiments so this part of the senario
is not overly speculative. One kind of reaction, amino acid
synthesis, would have been especially favorable since it created
more amino acids and that led to more peptides. The simplest
pathway to more amino acids is from pyruvate (a common three
carbon organic acid) to alanine. Another is from oxaloacetate
(a common four carbon organic acid) to the amino acid aspartate.
Both of these reactions require a relatively simple addition of
ammonia to a keto group and both reactions would probably have
been catalyzed (inefficiently) by the same peptide.

Peptide-catalyzed chemical reactions tend to be stereospecific
because the peptide binds the substrates (e.g., pyruvate and
ammonia) in a specific orientation. It's likely that the early
products of this primitive reaction were L-alanine and
L-aspartate. They could have been D-alanine and D-aspartate but,
by chance, the L-amino acids were made by the first peptide
catalysts. This part of the senario is referred to as the
"frozen accident" hypothesis.

As the concentrations of L-alanine and L-aspartate increased
there were more and more peptides formed and the new peptides
were enriched in these two particular amino acids. Other simple
amino acid synthesis reactions were catalyzed in the primordial
soup. The most likely ones are the synthesis of glycine and serine
from glycerol or glycerate (common three carbon organic alcohols
or organic acids). Again, these catalyzed reactions will only
produce one stereoisomer (enantiomer) of the amino acid and
there would have been selection for those parts of the soup that
made L-serine (instead of D-serine) because the L-serine could
more easily combine with L-alanine and L-aspartate to make many
more peptides. (Recall that there's only a single form of glycine
so the racemization problem doesn't apply to glycine.)

Peptides that are formed from all L-amino acids with no D-amino
acids are more stable than peptides that have mixtures of the two
conformations of amino acids so there would have been a sort of
feedback mechanism where the synthesis of new L-amino acids
created opportunities for stable forms of new catalysts.

L-serine is the precursor to L-cysteine so it's likely that
L-cysteine was also one of the early amino acids to accumulate
in the primordial soup. This was an important addition to the
repertoire since L-cysteine has a sulfur group and that leads to
many more possibilities for catalytic active sites in the peptides.
Note that once L-serine began to accumulate in the soup it led
directly to the stereospecific L-cysteine. You can't make
D-cysteine from L-serine so there's no racemization problem once
L-serine accumulates.

L-glutarate (from alpha-ketoglutartic acid, a common five-carbon
organic acid) is another good candidate for the primitive amino
acids. (It's quite possible that L-alanine, L-asparate, and
L-glutamate were all made by the same primitive enzyme using very
similar 3, 4, and 5-carbon substrates.)

At this point there are all kinds of peptides containing various
combinations of L-alanine, L-aspartate, L-serine, glycine,
L-cysteine, and L-glutamate since these six amino acids have
become much more abundant that the ones formed spontaneously by
uncatalyzed reactions that produce a racemic mixture. This is
probably the time when there was a shift to encoding peptides in
a sequence of nucleotides.

This is an important point. The shift to more and more complex
peptides did not have to take place in a random mixture of both
forms of all 20 amino acids. It could have taken place under
conditions where there was already a significant enrichment of
a small number of L-amino acids due to catalytic biosynthesis
from organic acid precursors. I'm suggestng that the first real
proteins contained only six different amino acids and the fact
that five of these were L-amino acids required only one or two
chance events.

There's some suggestive evidence to indicate that the primitive
genetic code was much simpler than the one we see today and may
have only had codons for the six initial amino acids. The other
L-amino acid synthesis pathways arose later on and the genetic
code expanded when codons were "stolen" from the precursors of
these new L-amino acids.

One of the primitive codons for aspartate, for example, might
have been AXX (any codon beginning with A). L-aspartate is the
precursor to: L-lysine (AAA, AAG), L-asparagine (AAU, AAC),
L-threonine (ACX), L-methionine (AUG), and L-isoleucine (AUU,
AUC, AUA). The idea is that the new amino acids were originally
synthesized on L-aspartate that was attached to its tRNA adaptor
and they were incorporated into proteins at some positions in
place of L-asparate. (This hypothesis on the origin of the
genetic code was developed by my former colleague Jeff Wong. The
idea came to him while teaching an undergraduate course in
biochemistry ... but that's another story.)

I don't have any good ideas about how the transition to encoded
peptides happened but that's not directly relevant to the
racemization problem.

The important points are ....

  1. The most primitive catalysts were probably not very big.

  2. The first important step was synthesis of new stereospecific  
     amino acids which meant that the process was no longer
     dependent on the original pool of spontaneously formed
     amino acids.  

  3. The first peptides and polypeptides (proteins) probably
     contained only six amino acids. These are the amino acids
     that can be easily made from readily available precursors.

If one thinks about the origin of life in this way it will help
to understand why biochemists don't think the "racemization
problem" is a real problem. This scheme will also help in
understanding why some *particular* amino acids came to be
enriched in proteins and not all of the other amino acids that
were in the primordial soup in the very beginning.

The common amino acids that we see today are the ones that can
easily be synthesized from common organic acids that were present
under pre-biotic conditions. Once the six types of amino acids
began to accumulate (because of catalyzed reactions and not
spontaneous reactions) then these were the ones that were most
likely to be strung together to make proteins. There must have
been other strange amino acids (e.g., citrulline, gamma-
aminobutyrate) present in the primordial soup but they were only
present at much, much lower concentrations and were shut out of
the lottery. Later on, the repertoire of amino acids expanded to
the current 20 (actually 23) by building on the first ones.
There's nothing magical about this.

In the beginning there may have been lucky catalysts formed by
the random association of amino acids (and nucleotides) but once
the synthesis of amino acids and the formation of peptide bond
arose, the synthesis of real stable polypeptides got under way.
It's important to realize that catalysis by primitive peptides
and nucleotides is an important part of any speculations about
abiogenesis. There are two important advantages of catalysis:

   (a) they greatly increase the rates of reactions so that
       the formation of products no longer depends on slow
       spontaneous chemical reactions;
   (b) catalyzed reactions are specific so only particular
       kinds of bonds are formed (e.g. L-amino acids, peptide
       bonds.)

The formation of peptide bonds is greatly aided by attaching
an amino acid to a nucleotide to form an "activated" amino acid.
This was probably the way peptide bond formation evolved. It's
consistent with the mechanism we see today where amino acids are
attached to transfer RNA (tRNA). It's also consistent with the
creation of a primitive genetic code and the evolution of the
genetic code. (The modification of existing amino acids to create
new ones would likely have occurred while they were attached to
nucleotides.)

Larry Moran