Final answer:
The net charge of amino acids comes from their carboxyl and amino groups in the backbone, but can also be influenced by ionizable side chains and their ionic, hydrogen, and disulfide bonding interactions.
Step-by-step explanation:
The net charge of amino acids primarily comes from the carboxyl and amino groups in the backbone, which are proton donors or acceptors, respectively. However, the overall charge of an amino acid molecule can also be affected by its side chains, especially when these side chains contain groups that can be ionized (gain or lose a proton). Ionic bonding involving the side chains can contribute to an amino acid's net charge at a given pH level. For example, an aspartic acid carboxylate ion (negative charge) can attract a lysine ammonium ion (positive charge), influencing the local electrostatic environment and potentially the protein's structure. Ionic interactions, hydrogen bonding involving polar amino acid side chains, and disulfide linkages between cysteine side chains further contribute to the three-dimensional structure and stability of proteins.