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Amino acids (for Marshall)

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Old August 5th 03, 03:19 AM
Amy Dahl
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Default Amino acids (for Marshall)

I can't find the post where Marshall asked for an explanation
of amino acids, so I hope I answer the right questions.

Amino acids are the building blocks for proteins, analogous
to the way nucleotides are the building blocks for DNA and
RNA. They all include the chemical structure

\ |
N - C - C = O
/ | |

Where "C" represents a carbon atom, "N" a nitrogen atom,
"H" a hydrogen atom, "O" an oxygen atom, and R the part of
the molecule that varies from one amino acid to another.
Bond angles and certain other details are approximated
owing to limitations of the medium.


H -

portion of the molecule is called an "amino group," while
the part represented as

- C = O

may be called an "acid group." The same acid group is found
in all organic acids, not only the amino acids, but also fatty
acids, oxalic acid (has two of them), acetic acid, ascorbic acid
(Vitamin C), etc.

Amino acids differ one from another only in what is attached
at the site labeled "R." They can be joined together by a
bond between the amino part of one and the acid part of another,
called a peptide bond. A molecule of H2O is given off in the
process. The peptide bond can be represented

|| |
- C - N - (+ H2O)

Chains (a.k.a. polymers) of amino acids can be formed, connected
"head to tail," the amino end of one attached to the acid part of
the next, with that one's amino end attached to the acid part of
the next in line, etc. These chains are called "polypeptides," and
very long ones are called proteins.

* * * * * * * * * * * * * * * * * * * * * * * * * * * * * ** * * * *
So the relationship of a protein to amino acids is that a protein
is a polymer, i.e. a large molecule of a "long-chain" configuration,
made up entirely of amino acids.
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

Taurine, apparently, is an amino acid that exists "free" in
extracellular fluid, so its importance is other than as a
protein building block. (It is also readily lost in
cooking, so merely including "meat" in the recipe does
not guarantee adequate taurine.)

Proteins are varied and, of course, important. Specific proteins
are coded for in the DNA, and synthesized via an interesting
transcription process. An important feature of proteins is that
they are big molecules. Although their chemical configuration
may be represented as a long chain of amino acids, they do not
exist in a "stringy" state. Instead the "chain" is folded around
and back on itself into a specific structure, and it is the
structure that gives the protein its functionality--whether it be an
enzyme, a hormone, a receptor, a neurotransmitter, or hemoglobin,
or whatever. The structure is maintained by the interactions of the
"R groups" on the different amino acids. Some attract each other,
others repel, and the sulfur-containing amino acids can actually
form bonds with one another. So,

* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
The structure, and hence the function, of a protein depends
upon the precise sequence and correct identity of the amino
acids which comprise it.
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

This means that for the body to synthesize protein, it needs
not just "a quantity of protein," but the right amino acids
in the right proportions to make a specific protein. If the
amino acid profile of protein in the diet does not match
an organism's needs, one amino acid will be "limiting"--it
will be used up, then no more synthesis can occur, and the
remaining collection of leftover amino acids is useless and
must be excreted. The difference in amino acid composition
between what is supplied and what is needed means that not
all of the protein supplied can be utilized. "Biological
value" is a measure of how efficiently a given protein can
be utilized. Egg protein rates high, followed by milk
protein (casein), then meats and chicken. Vegetable sources
(grains, beans, etc.). are further down the scale of biological
value. I think "beans" rate at .68 or .70 ( compared to 1.0 for
egg) suggesting that all of the essential amino acids are
there, but that a certain amount are wasted.

Hope that clears up the relationship between amino acids and
protein. There's a lot more of interest--such as the problem
of getting, and getting rid of, nitrogen. The main work of
the kidneys, if I understand correctly, is to eliminate
nitrogen resulting from breakdown of amino acids--both
unused amino acids from the diet, and old proteins which
have been discarded and broken down. At the other end,
nitrogen in the air cannot be utilized by most organisms--
only by "nitrogen-fixing bacteria" which "reduce" it to a
form that can be incorporated into amino acids.

One of Strombeck's contentions is that protein which is
not highly *digestible* results in some protein/peptides
passing into the colon, where bacteria break them down.
The nitrogen containing amino groups become ammonia
(NH3) which is an irritant and can damage the intestinal
mucosa, causing an assortment of problems. Digestibility
and biological value are separate issues, but both affect
the efficiency of utilization of dietary protein.

Let me know if this makes sense or not.

Amy Dahl

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