Slashdot Mirror
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
for $500 please Alex
...What is Organic Chemistry.
Somewhere, something incredible is waiting to be known. -- Carl Sagan
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."
The X-files already taught us there were more amino acids to be discovered. I just hope they find the 5th and 6th nucleotides again, so that there will be proof of extraterrestrials.
And whatever you do, don't let the smoking man get ahold of them, that's how they dissappeared the first time around. And no, he isn't dead. He obviously had the black army/CIA helicopters stage his death. What a drama queen.
The amino acid they discovered in 1986 is selenocysteine, which is also encoded for by a STOP codon (UGA in this case). Maybe there is an entire class of amino acids that are encoded in this manner, in between the 20 directly encoded amino acids and the multifarious post-translationally modified amino acids (e.g., hydroxyproline and hydroxylysine in collagen; gamma-carboxyglutamate in various clotting factors)
And you probably need more than just a STOP codon to incorporate pyrrolysine. With selenocysteine, you need enzymes to convert the serine residue on the tRNA to selenocysteine, an enzyme to activate the inorganic selenium, and a modified translation factor that recognizes this special case.
Ah! Here's the original article: Code Breakers. It's definitely worth a read.
Steven N. Severinghaus
Even more so now that researchers are looking for numbers 23 and 24.
Strange stuff indeed. That is the problem with this class of metaphysician. reality intrudes from time to time.
"It is a greater offense to steal men's labor, than their clothes"
Nor is it obvious why certain radicals are vital, and most are not. Some of the common radicals are missing in the vital amino acids. Hydrogen and methyl are there, but ethyl, propyl and higher n-alkanes are not. Yet isopropyl, and both 1 & 2-methylpropyl are. Wierd. Perhaps it has something to do with the way exclusionary mechanisms to keep undesirably amino acids out of the protein building machinery.
From an information-theory viewpoint, why are the DNA sequences largely incompressible? Are the three-base pair codons (6 binary digits each) equally probable? Those codons could be decoded into 64 possibilities, yet we have only 22 amino acids. Are some of the codons used for amino acid pairs? Or else we've got alot of missing acids. Untils those codons are themselves decoded (and any bigrams, tridgrams, etc), we should expect surprises. And what of the great expanse of alleged junk? Does nature have a signal-to-noise ratio approaching that of USENET? :)
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?
It's not surprising that there are tRNA's in rare organisms that encode for "non-standard" amino acids -- evolution just selected against them, since the common 20 are so prevalent and easy to produce or obtain from food. Humans actually use 22 amino acids, but two of them are not genetically encoded, but produced by modifying the finished protein (hydroxylation of proline and lysine during collagen biosynthesis. Rice and beans are not sufficient, you need vitamin C to make collagen) Some bugs live in places where "non-standard" amino acids are probably preferred to make proteins more suited to the enivronment -- extreme conditions like Antarctic ice, or thermal vents.
It's important to remember that amino acids aren't the only building blocks -- cell membranes are made of lipids, cholesterol, and polysaccharides (sugars). There are many possible modifications beyond the amino acid sequence. For instance, immune markers (blood type, etc.) are sugar chains which are tacked onto proteins. Sugars on the surface of viruses help them bind to cells. Another common modification is phosphorylation: addition of phosphate to a protein, which is a common method of activating (or deactivating) proteins.
The body also uses lipid derivatives, steroids, and most importantly vitamins to obtain chemical functions not provided by amino acids (catalysis, cell signaling, etc.)
This case is special not because of the use of a non-standard amino acid, but because it is an *additional* amino acid rather than a replacement. This means that the machinery of translation of an RNA codon to an amino acid (via tRNA) and the construction of the amino acid (via an enzyme) exists in parallel with the machinery for all the other existing amino acids. This is remarkably interesting because it represents a much larger genetic difference in the amino acid translating machinery, and a difference which we have never seen before.