It depends on the pH of whatever solvent/solution it's in.
Example: Amino acid (AA) Alanine (Ala) is in the blood, which has a pH of around 7.4. Alanine has no R-functional groups, so it just has the amino group and carboxyl group, pka values are 9 and 2.5.
Since pH = 7.4, that amino group will still have its proton. pka of amino group = 9 and pH of blood = 7.4, pH < pka so stays protonated (or exists as NH3+).
But, since the carboxyl group usually has a proton whenever the pH is lower than 2.5, in a solution/solvent with a pH > 2.5, the carboxyl will lose that proton. In this case with a pH of 7.4, the carboxyl terminus will be deprotonated, giving it a negative charge (COO-). Total charge of Ala is neutral at pH = 7.4 (called zwitterion) since you have a protonated amino terminus and deprotonated carboxyl terminus.
At pH of something greater than 9, pH > pka of amino terminus so it will deprotonate that amino group's proton, giving that amino terminus no charge now (exists as NH2). Total charge of Ala is -1 since the carboxyl terminus will also be deprotonated.