Wednesday, November 22, 2006

Enjoy Your W!

No, this isn't revealing my politics. W is the single letter code for tryptophan, which is reputedly richly found in turkey meat (If you are a vegetarian, what vegetable matter is richest in W?)

Tryptophan is an odd amino acid, and probably the last one added to the code -- after all, in most genomes only a single codon and it is one of the rarest amino acids in proteins. It has a complex ring system (indole), which would also suggest it might have come last.

Why bother? Good question -- one I should know the answer to but don't. When W is conserved, is the chemistry of the indole ring being utilized where nothing else would do? That's my guess, but I'll need to put that on the list of questions to figure out sometime.

But why W? Well, there are 20 amino acids translated into most proteins (plus a few others in special cases) and they were named before anyone thought their shorthand would be very useful. There are clearly mneumonic three letter codes, but for long sequences a single letter works better -- once you are indoctrinated in them, the three letter codes become nice compact representations which can be scanned by eye. Some have even led to names of domains, such as WD40, PEST and RGD.

The first choice is to use the first letter of the name: Alanine, Cysteine, Glycine, Histidine, Isoleucine, Leucine, Methionine, Proline, Serine, Threonine and Valine follow this rule. If multiple amino acids start with the same letter, the smallest amino acid gets to take the letter. Some others are phonetically correct: aRginine, tYrosine, F:Phenylalanine. Others just fill in D:aspartate, E:glutamate, K:lysine, N: asparagine and Q:glutamine.

But Tryptophan? Perhaps it was studied early on by Dr. Fudd
, who gave long lectures about the wonders of tWiptophan.

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