Amino acids

Simon Brocklehurst (smb@bioch.ox.ac.uk)
Tue, 7 Feb 1995 14:37:21 +0000 (GMT)

Hi everyone,
I've just been flicking through Jon Cooper's fantastic
new course material. With regard to the descriptions of the
amino acids, I have what will probably seem to many a minor
point to make. But given that we're really aiming at thinking
clearly about how structure relates to function on this course
(i.e. chemistry), I think it's worth mentioning. For the benefit of
those who are completely new to proteins I should point out that, quite
legitimately, Jon has provided descriptions of amino acids that
perhaps 99.9% of structural biologists would be happy with, _and_
use in everyday conversations. BUT just 'cos 99.9% use the definitions,
it doesn't make them correct!

Specifically, I don't like descriptions of the amino acid
residues D and E as acidic residues, and K and R as basic residues.
As Jon points out, D and E are negatively charged at physiological
pH, and so they are BASES if they are anything! Conversely K, R are
hydronated (whoops going into mega-pedant mode there, let's say
protonated), and therefore ACIDS...!!

What's wrong with calling D and E, anionic residues, and K and R
cationic residues? Maybe I'm being a pedant...? But a lot of people
seem to be unaware of what the words mean (as opposed to just
using the terms as jargon, but actually understanding what's what)
judging by the number of times people to correct me when I call D an
aspartate residue (which it is!) as opposed to and an aspartic acid
residue (which it [almost always] isn't ;-)). Or am I missing something
fundamental? Is anyone serious happy with effectively saying:

"Aspartic acid is so-called because it acts as a base?"

Byeeeeee,
-- Simon
_________________________________________________________________________
|
| ,_ o Simon M. Brocklehurst,
| / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry,
| \>> | University of Oxford, Oxford, UK.
| \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://nmra.ocms.ox.ac.uk/~smb/
|________________________________________________________________________