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New Amino Acid Discovered
EricMargel writes: "As published in Science, researchers at the Ohio State University claim to have discovered the 22nd known amino acid, pyrrolysine, the first discovered since 1986." I hope rice and beans are still sufficient to get all the needed amino acids.
If I remember my high school biology correctly, there are 4 nucleotides, and it take 3 of them to encode an amino acid, basic math...4*4*4=64. We earthlings aren't even using half the code space provided by our current DNA system. Just 1 more and we're there at half.
If Mr. Edison had thought smarter he wouldn't sweat as much. --Nikola Tesla
Beano is the magic pill. Alpha-galactose. True, it's an enzyme, not a protein, but a protein isn't going to stop farts, which are mainly caused by sugars we can't digest but which the bugs in our intestines can.
woof.
The very fact that this amino acid was overlooked for so long suggests that it's direct importance to our lives is negligible; it's relevance is more about filling the final gaps in an overall picture.
In the article, Krzycki suggests that it also alters the way we should approach genetics:
"This shows us that the genetic code, and therefore, evolution is much more plastic than people might have thought."
"I think this work will cause researchers to start looking at genetic sequences that they might have thought at first were simply aberrations," he said. "Instead, they might signal discoveries like ours."
because it didn't tell us *which* codon they were working with. There are several codons which were understood to be interepreted as STOP signals, so based on this fragment of the article,
"Surprisingly, the codon Krzycki's team identified should have signaled a stop to protein building but it did not."
it must be one of those. They previously-known-to-be-stop codons are: UAA, UGA, and UAG (did I miss any?). So which one is it? If you know, please reply to this post.
For reference, here is a good page for more info on codons, their product amino acids and more.
Oddities in the genetic codes of different species have been observed before. While all known life froms have very similar genetic codes (this codon yields that amino acid) there have been some life forms that are exceptions. Several kinds of bacteria express a different amino acid for a specific codon than, say, a human cell would.
So finding a bacteria like what this artical describes is only a mild suprise.
Great detective work though. Alot of people would have decided it was alot easier to call this an abberation than to spend ~2 years finding out what was really going on.
"Never, never suspect the dreams within the dreams of dreaming children." ~The Amazon Quartet
This "new amino acid" is coded for by a triplet that formerly was only observed to be a stop codon. That is, when the translation machinery came upon the base sequence on the RNA it was reading to build the peptide chain, it ended the chain.
Now consider this. What if the cell produced the matching tRNA and associated "new amino acid" only intermittantly. When it was available, this stop-codon wouldn't be a stop codon at all and translation would continue, but when it was missing, translation would stop.
This raises another interesting question (that may already be answered). Some organisms can not synthesize all the amino acids and must obtain some of them from dietary sources. These amino acids are referred to as the essential amino acids for that organism. If their diet is deficient in these essential amino acids, they can't make all the proteins they need, and bad things generally happen.
So, the question is, what happens at a translational level in this situation? Does translation just stop, leaving shorter peptide chains? Are their situations where the products of partial translation have biological activity?
As for why only certain R groups are found, it's probably ultimately dictated by thermodynamics, with a little input from natural selection. Nature is very conservative with the building blocks it uses, and almost all of the amino acids used can be derived from glucose and its various metabolites. n>2 alkanes R groups would probably require a lot of energy to synthesize, particularly since they're hydrophobic and all these reactions happen in an aqueous environment. If you can't make it from glucose within the thermodynamic constraints of a biological system, you're unlikely to make it.
Probably because of thermodynamics as well, not all codons occur with equal probability. And because of the thermodynamic instability of the third base pair with regards to codons/anti-codons binding, many tRNAs are only specific for the first two bases (a phenomenon known as "wobble")
Because of thermodynamic and steric considerations, it would be difficult for ribosomes to accept dipeptide/tripeptide tRNAs, since the active sites on the enzymes have only so much leeway as to where they expect to physically find the atoms they're supposed to act on. While theoretically an alternate translation system could evolve, given the conservative nature of evolution, it would probably take a long time and require severe selective pressure.
Finally, as for "junk" DNA, a lot of it has been found to serve various structural functions with regards to the integrity of the genome. There are probably very few regions of even heterochromatin that don't have a function, and the sequences that are truly useless now probably had a function in the evolutionary past.
What is remarkable about selenocysteine and pyrrolysine is that they are actually encoded by the genome. This is in contrast to hydroxyproline and hydroxylysine (and gamma-carboxyglutamate, necessary for blood clotting) which are encoded by standard proline, lysine, and glutamate codons. It's not until the peptides are being modified in the endoplasmic reticulum and Golgi apparatus that the hydroxy- or carboxy- groups are added on.
You've got a point there, there is no evidence to suggest that they are selected for or against. In fact, it's possible that there could be as many as 30 amino acids genetically encoded. This is just a WAG, of course; 4^3 possible codons, but if you consider the last base to be a "wobble" base in every codon (i.e., purine or pyrmidine), that cuts it to 32, then you have a start and stop codon, cutting it to 30 (even this depends a lot on your tRNA's).
Frequency distribution of codons show that some codons are simply more common, and some amino acids can be coded 6 ways (e.g. serine) while there's only one way to code methionine. I suggested selection because the most likely way that this distribution occured was mutation of tRNA's and aminoacyl-tRNA synthetases for uncommon amino acids, which implies genetic selection. There's a raft in literature on genetic evolution I'm not familiar with though (have to admit I got a "C" on my paper about that)
It's possible to substitute synthetic tRNA's in the lab to insert non-standard amino acids -- no reason it's doesn't happen in nature, all it would take is a "mutated" (from the point of view of the codon table in Voet and Voet) aminoacyl-tRNA synthetase to attach a different compound to the tRNA. It would be interesting to study whether this was conserved since the beginning of time or emergence of a new pathway.
I guess "beans" is too general a term.
I've tried food combination myself, and some of it works, some of it doesn't really make a difference. The mixing carbs and proteins rule didn't really didn't make a difference for me, and I've found plenty of "health experts" who contradicted the rule and said it was fallacious. To eat all meals completely devoid of either carbs or protein doesn't make sense to me. I would be malnourished if I did this. Even the vegatables I typically eat have both protein and carbs.
There are some parts of food combining that are true for me. For example, if I eat bananas and oranges together (sweet fruits and acid fruits), I usually have indigestion.
I guess whatever works for you. Everyone's diet needs are different. I just can't imagine life without beans.