Amino Acids

Bernard Murray bernard at elsie.nci.nih.gov
Mon Jan 16 00:34:31 EST 1995


In article <jimgalt-1501951631580001 at pm035-11.dialip.mich.net>, jimgalt at umich.edu (Jim Galt) writes:
> I am writing a program to help people remember amino acid structures,
> codes, etc. and I was wondering if anyone would like to share their tips
> on how to remember which is which. Thank you in advance for your help.
> Jim Galt

As far as the one-letter amino acid codes are concerned, the original
paper on the nomenclature (which I don't have to hand) gave a logical
reason for most of the choices;
A, C, G, H, I, L, M, P, S, T, V  are initial letters
glu-E
F-enylalanine
asparageeN
R-ginine
tYrosine
I think W was chosen for tryptophan as the letter is suggestive of the
double-ring indole structure.
X = unknown

The remainder are the ones that take a little more memory;
D for aspartic acid as this is next to E for the other acidic residue

K = Lysine (why?)
Q = Glutamine (? near N)
B = D or N  (Asx) (why?)
Z = E or Q  (Glx) (why?)

I learned the structures as hierarchies (eg. G -> A -> V) (A -> P -> Y)
As soon as you have to recognise them in a 3-D structure you can get
quite fast at it.  If you have to write your own coordinate files
(eg. for CHARMM or AMBER) you even get to learn the numbering system
for the atoms.  Eventually its all just familiarity - a friend of mine
can fluently read the derived peptide sequence when given a cDNA.

The ambiguity codes for nucleotides are much less obvious.
		Have fun,
			Bernard

Bernard Murray, Ph.D.
bernard at elsie.nci.nih.gov  (National Cancer Institute, NIH, Bethesda MD, USA)




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