L-aspartic acid is an α-amino acid. Shown in the structure attached. The original structure of l-aspartic acid is the structure containing no charges. It contains an amine functionality and a carboxylic functionality like all amino acids and has an R-group, which in this case is another carboxylic acid group. Amino acids are amphoteric which means it can act as an acid as a base, since the -NH₂ group is basic, and the -COOH group is acidic.
The physiological pH, which is the pH of various body fluids such as blood, is generally around 7.4. This is a mostly neutral pH. A carboxylic acid has a pKa value of around 3-4. If the pH of a solution is higher than the pKa of the acid in that solution, then the acid will dissociate and give up it's protons. In this example, the carboxylic functional group has a pKa of 3.9, which is less than the pH of 7.4. Therefore, at physiologic pH, the carboxylic acid functionality will be deprotonated in the form -COO⁻.
We must also consider the basic amine, -NH₂, functional group. This basic group has the ability to be protonated under the right pH conditions. When an amine is protonated, it becomes an ammonium group of the form -NH₃⁺. This ammonium group has a pKa of around 9. If the pH is greater than 9, then this group will be deprotonated, but in our case, the physiological pH is 7.4 which is less than 9. Therefore, the amine group will be protonated at a physiological pH.
The correct structure to represent l-aspartic acid is shown in the image that has charges, with a deprotonated carboxylic acid group, -COO⁻, and a protonated amine group, -NH₃⁺.
This is true for the pure amino acid. However, when this amino acid is part of a protein chain and has formed peptide bonds using the amine and carboxylic groups, what is left is the free carboxylic acid chain. The same rules apply to this carboxylic acid, and therefore, at physiological pH, this carboxylic acid will be the one to be deprotonated, as the other carboxylic acid will have reacted to form a peptide bond.
