Whoop whoop - nerd alert.When I wrote about the Great Western Binfo meeting I attended last November, I prefaced the piece with a too-clever-by-'arf
UUUAGAAUCGACGCAUAC AUCAAC ACCCACGAA UGGGAAUCCACCthinking it would serve as un p'tit amuse-cerveau for binfoes before the meat of the article. I suspect that it served, to the nearest whole number, solely as un p'tit amuse-Bob. Last week I had the honour to host the 2014 version of the meeting and I put
GUNAUHRAYGARin the header of the programme by way of continuing the tradition. It came up in conversation during the afternoon coffee break when I was chatting with two physicist-turned-binfoes. Somebody who was earwigging turned round and said "Oh I assumed that was a typo". Well, really! I know that The Blob is sprinkled with errurs of spelinge and I often blush when I re-read my e-mails, but if I write something that sounds like one of two trolls 'wrestling' then I do so deliberately. Because the p-t-bs are both fightin' sharp and quick on the uptake, it didn't take them long to crack the code. That led nicely into a discussion of the IUPAC codes for DNA/RNA bases and the amino acids that go to make proteins.
Cypherists are quite frustrated by the fact that, while there are 26 letters in the English alphabet, there are only 20 amino acids that commonly appear in protein sequence
|A Ala||C Cys||D Asp||E Glu||F Phe||G Gly||H His||I Ile||K Lys||L Leu|
|M Met||N Asn||P Pro||Q Gln||R Arg||S Ser||T Thr||V Val||W Trp||Y Tyr|
That's handy for geeky coders because it brings two more letters into the possible alphabet for writing English words in codons. In December I was well impressed by a couple of the Masters of Immunology knowing that there was a 21st amino acid selenocysteine which is incorporated into proteins in special circumstances in particular species by subverting UGA, one of the stop codons. Selenocysteine is interesting because it looks exactly like cysteine except that a selenium atom replaces cysteine's sulphur. And that's interesting because oxygen, sulphur and selenium are all in the same column of the periodic table of elements - ie. have similar chemical properties. A couple of days later one of the MScs e-mailed me to say "and let's not forget pyrrolysine". That's another oddity that was discovered in 2002 in the methyltransferase gene of Methanosarcina barkeri. It's since been found in methyltransferases from other species where it forms an essential part of the active site. Like selenocysteine, it is coded by a subverted stop codon, in pyrrolysine's case UAG. This is handy because IUPAC have elected to represent selenocysteine as Sec or U and pyrrolysine as Pyl or O, so we can write pretty much anything we want in codon-speak because the only letters uncodable are minority interest J and X. But even those are sorted because X (any AA) could be represented by codon NNN and you could use I for J like the Romans.
Emboss backtranseq could help you if you want to send a secret message to your geeky mol.bol girlfriend like
ATC TTCGCCAACTGCTAC TACTAGTGAAGG GACAGGGCCATCAACAGC
and ExPaSy will help her translate the DNA back into English. I hope you know what to do when you do get together - and no, there's more exciting things to do with her than "pull an all-nighter playing Dungeons & Dragons".
Yes siree Bob - there is a way to preserve the code and use all letters....................BJOUZX BZEN BAMMMMMMMMMM!!!!!ReplyDelete