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Amino acid

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Amino acid Codons
Alanine (Ala) GCT, GCC, GCA, GCG
Arginine (Arg) CGT, CGC, CGA, CGG, AGA, AGG
Asparagine (Asn) AAT, AAC
Aspartic acid (Asp) GAT, GAC
Cysteine (Cys) TGT, TGC
Glutamic acid (Glu) GAA, GAG
Glutamine (Gln) CAA, CAG
Glycine (Gly) CGT, GGC, GGA, GGG
Histidine (His) CAT, CAC
Isoleucine (Ile) ATT, ATC, ATA
Leucine (Leu) TTA, TTG, CTT, CTC, CTA, CTG
Lysine (Lys) AAA, AAG
Phenylalanine (Phe) TTT, TTC
Methionine (Met) ATG
Proline (Pro) CCT, CCC, CCA, CCG
Serine (Ser) TCT, TCC, TCA, TCG, AGT, AGC
Threonine (Thr) ACT, ACC, ACA, ACG
Tryptophan (Trp) TGG
Tyrosine (Tyr) TAT, TAC
Valine (Val) GTT, GTC, GTA, GTG

An amino acid is an organic molecule that possesses both carboxyl and amino groups. They serve as the monomers of proteins.[1]

There are twenty known naturally-occurring amino acids. As there are 64 possible codons, this means that more than one codon typically equates to one amino acid. In fact 61 of the 64 codons code for an amino acid (the other three are used as stop codes), with from one to six different codons coding for a particular amino acid.

Some organisms can synthesize all the amino acids from other molecules, but others (including humans) can't make certain amino acids, so they have to ingest them with food.

alanine

Almost all amino acids can exist in either of two mirror image forms, called L and D isomers, that rotate polarized light in opposite directions. Living organisms are composed of and produce only one form of each amino acid, usually the L form. Amino acids produced synthetically as well as those that occur naturally, i.e. other than in living things, have equal amounts of the two forms. Such a mixture is called racemic.

Amino acid dating

The L form of an amino acid can occasionally change into the D form. Given enough time, the pure L isomers produced by a living organism will eventually turn into a 50-50 mixture of the L and D isomers. This process is calle racemization. If enough is known about the past chemical environment of the amino acid to estimate the rate of transformation, the ratio of D to L isomers can be used to estimate the time since the organism produced the amino acid. A D/L ratio near zero indicates a short time, a D/L ratio approaching one indicates a relatively long time. The rate of transformation can be influenced by many factors. The most important of these is temperature, but humidity and pH (acidity) are also important.

This method is used in forensic science to determine the age at death of an body. The dentin of teeth contains aspartic acid, which is isolated from metabolic process by the enamel once the tooth is fully formed. After that, the transformation of L to D proceeds at a constant temperature and chemical environment. At death, the temperature drops significantly so that the transformation is effectively stopped. Thus the D/L ratio in teeth allows a calculation of the age at death with only a few years uncertainty.

In the simplest model, one might expect the rate of racemization to be constant, but it turns out that the rate actually drops over time. This was shown, for example, in a study of coral.[2] Comparison of the D/L ratios in the annual growth rings produced in the last 350 years indicate that the initially rapid rate of racemization (0.6% per year) slows in older growth bands to 0.04% per year.

Although the chemistry of racemization can be investigated by studies of actual samples at elevated temperatures, in practice, changes in the racemization rate over time and sensitivity to temperature and chemical environment make it difficult to extract an absolute date from a D/L ratio. More commonly, the method is used to provide relative dating at a single site, or it is combined with an age obtained by another method to infer the average temperature of the site in the past.

The rough effect of temperature has been reported as follows:

As a rule of thumb, sites with a mean annual temperature of 30°C have a maximum range of 200 ka and resolution of about 10 ka; sites at 10°C have a maximum age range of ~2 m.y., and resolution generally about 20% of the age; at -10°C the reaction has a maximum age of ~10 m.y., and a correspondingly coarser resolution.[3]

In summary, a 20 degree change in temperature results in a factor of ten change in the racemization rate.

Origin of life

The racemic (50-50 mixture of L and D forms) is a problem for naturalistic origin-of-life proposals. Proteins comprise a combination of amino acids, with the shape of the proteins being determined by the particular amino acids and how they are arranged. A mixture of L and D forms produces a different shape than is produced by all one form, so even a single D form in an otherwise-pure set of L forms produces a mis-shaped protein.

It was such a mixture that caused the thalidomide disaster. Thalidomide comprised of the L form is a strong tranquilliser, but the artificially-produced thalidomide produced in the early 1960s included D forms, which resulted in birth defects when given to pregnant women.

The only practicable way to separate the two forms is by using another such "homochiral" substance, although circularly or elliptically polarized light or some other chiral influence could in theory be used, but in practice is unable to have sufficient effect. Nevertheless, several explanations for homochirality in naturalistic scenarios have been advanced, and many revolve around autocatalysis.[4] However, these have either proved insufficient for the task or involve scenarios which would not be feasible for an origin-of-life situation.[5][6]

The problem that this poses for naturalistic origin-of-life proposals is the circular problem that you need a catalytic amount of a substances in one form before you can separate any naturally-occurring mixture into all one form.

Naturalistic scientists saw some hope when amino acids were found in the Murchison meteorite and were found to have slightly more of the L form (seven to nine percent). This led some scientists to propose that the excess of the L-form in extraterrestrial sources, possibly due to the influence of polarized light, was strong enough to establish that form in early life on Earth. However, scientists were unable to rule out contamination of the meteorite, rendering even this example as dubious.[5]

References

  1. Campbell, Neil A., and Jane B. Reece. Biology. 7th ed. San Francisco: Pearson Education, 2005.
  2. Glenn A. Goodfriend, P.E. Hare, and Ellen R.M. Druffel. Aspartic acid racemization and protein diagenesis in corals over the last 350 years. Geochimica et Cosmochimica Acta, Volume 56, Issue 10, October 1992, Pages 3847–3850.
  3. The Amino Acid Geochronology Laboratory, Northern Arizona University. Method: Age Determinations
  4. Blackmond, Donna G. Asymmetric autocatalysis and its implications for the origin of homochirality. Proceedings of the National Academy of Sciences, USA 101:16, Tue. 20th April, 2004Tue. April 20th, 2004, 5732-5736.
  5. 5.0 5.1 Sarfati, Jonathan, Did life’s building blocks come from outer space?, Journal of Creation 16(2):17–20, August 2002.
  6. Sarfati, Jonathan, Origin of life: the chirality problem, Journal of Creation 12(3):263–266 December 1998.
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