Why do we consider amino acids with high side chain pKa's basic, yet with a higher pKa, less of the amino acid will exist in basic form at equilibrium compared to acid form at physiological pH?
What will the concentration of the base be given the high pKa of these amino acid side chians. The answer is that the higher the pKa, the lower the concentration of the base, since with 1) with a higher pKa, then 2) you will have a lower Ka (pKa = - logKa) and therefore 3) a lower concentration of base, due to Ka = the conjugate base (times H3O+) / acid, then the numerator, the conjugate base will be lowered in concentration with a lower Ka. This can also be confirmed with the Henderson-Hasselbach equation, where pH = pKa + log [A-]/[HA] and since pkA is increasing will make pKa > pH, meaning pH - pKa = a negative number = log [A-]/[HA], where [A-]/[HA] would then equal 10^negative number, meaning the concentration of the acid will be greater than the concentration of the base.
My question is, when you look at titration curves, we know that parts of an amino acid will act more as a base, than an acid, at higher pKa's. Meaning, if you have the amine group of an amino acid, with a pkA of 9-10, it doesn't want to give up it's hydrogen, until the pH is pretty high (10-12). Why are amino acids with high overall pKas considered basic, yet, when you look at a molecule's pKa at a high pKa, less of the molecule will exist as the base at equilibrium (meaning it is wrong to say that a molecule with a high pKA will exist primarily it is basic form)?