biochemistry for dummies (me, that is...)

[Goran]

I guess, since it says "answers all your questions", I can post even a stupid biochemistry 101 question.

So, how can I define amino acids in termsof ionization? Of course I can talk about pH, pK etc., but they are never unionized, even as solids; if I start with "dipolar ions"; they aren't always that, and bringing in the definition of "intramolecular neutralization"... So, can I say that they are alway"molecular ions" (although that term isn't quite propriate)... any suggestions?

[mith]

Note that it contains both an alkaline group and an acidic group. The term you're looking for is probably zwitterion.

[Goran]

Thanx...

I guess I'll start with zwitter ions in neutral water solutions... and then, I'll add that aa. can be precipitated nad crystalized and explain the whole intramolecular neutralization, the difference: pKa1 << pKa2 (so, the predominant form is always ionized..) and also add something abouth "ionic character" of aa.

Thing that bothers me a bit, is the correct definition of zwitter ions...
Different books give different definitions...
Is it when alpha-COO- and alpha-NH3+ are in that form (ionized) so the whole molecule is electrically neutral? What about ionizable side chains? Are they unionzed in zwitter ions... and finally, one definition is that "zwiter ion is form when pH=pI" - taking into consideration ionazble side chains, that could give zwitter ions with unionized alpha groups...

g. sh.

[blcr11]

The charge on an amino acid in solution depends on the pH of the solution. At its pI, the amino acid is neutral, below its pI it should be positively charged and above its pI it should be negatively charged. Same thing for peptides and proteins. The side chains ionize independently of the beta-amino and alpha-carboxy groups, when the side chains are ionizable, that is, which will include amino acids like Glu, Asp (and to a lesser extent their amides Gln and Asn), His, Tyr, Trp, Lys, and Arg, typically. You can argue about Pro, Cys, Ser, and Thr, which under certain circumstances may ionize, but not typically. The rest have strictly non-ionizable side chains.

The nature of the side chain will influence where the pI of the amino acid is. If the side chain is acidic, the pI of the entire free amino acid will be towards the acidic side of things. Contraiwise for basic side chains. For example the pI of Aspartic acid (an acidic side chain) is 2.97, and for Glycine (whose side chain is a hydrogen atom) is 5.97 and for the basic amino acid Lysine is 9.59.