While all amino acids contain a carboxyl group bonded to the central carbon, in peptide bond formation, this carboxyl group becomes part of an amide linkage and loses its ionizability.

Aspartic acid and glutamic acid, however, possess carboxyl groups in their side chains. Here's an interesting discussion involving aspartic acid representative of the kinds of issues that may arise in an MCAT passage:

A protease is a digestive enzyme designed to break down proteins. The acid protease, pepsin, contains two aspartate residues within its active site. This leads to an interesting control mechanism for pepsin activity in addition to the zymogenic control mechanism everyone is familiar with (Pepsin is stored as the inactive precursor pepsinogen ('zymogen' is the name for an inactive enzyme precursor)). The additional interesting control mechanism for pepsin is that it only functions within the acidic environment of the stomach. For the enzyme to be active, one of the side chains of aspartate must be ionized, the other not. This means that the optimum pH of pepsin is quite acidic, close to the pKa of the side-chains. Can you reason why the pH must be near the pKa using Henderson-Hasselbalch?