I am given an amino acid with an ionizable side chain at a certain pH. How do I determine the net charge of that amino acid when there are mixed protonation states of one or more of the groups at that pH (pKa of side chain, for example, is really close to the pH)?
Amino acids have terminal carboxyl and amino groups; some amino acids have ionizable side chains. When determining the charge of an amino acid, you have to take into consideration the pH and the pKa's of each of these groups. When the pKa of one group (or more) is close enough to the pH, a fraction of the amino acids will be deprotonated at that group and the other fraction of amino acids will be protonated at that group in solution. Thus, when determining the average net charge across the ensemble (or a time-averaged charge of a single particle), you have to take this into account.
I am asking for the expected value of the net charge (which would not be an integer); this number is relevant, for example, for the migration speed of the amino acid (or a protein) in gel electrophoresis or the strength of interaction with ion exchange chromatography media.
For example, a carboxylic acid/carboxylate group at a pH equal to its pKa would have an average charge of minus one half because half of the functional groups would be protonated (charge of zero) and half would be deprotonated (charge of minus one).