Protonation and deprotonation of amino acids

Explanation:

The pH of an amino acid affects which atoms protonate and deprotonate. Let's start by looking at the generic structure of an amino acid.

https://iweb.langara.bc.ca/biology/mario/Biol2315notes/biol2315chap3.html

Notice something weird? The amino group is protonated but the carboxyl is not. Amino acids are amphoteric, meaning they can act like an acid and base. Also, amino acids are dipolar. Amphoteric, dipolar species are called zwitterions.

This is due to ammonium (amino) groups being less acidic than carboxylic acids. Look at the $p{K}_a$values of the ammonium and carboxyl groups. The $p{K}_a$ of the carboxylic acid is always lower than that of the ammonium group. As pH increases, it will be deprotonated before the ammonium group.

For the amino acids with protonated R groups, you need to pay attention to their $p{K}_a$ values. The atom with the lowest $p{K}_a$ will be deprotonated. Use the following link to find a list of the $p{K}_a$ values for all the amino acids.

$p{K}_a$ values for amino acids

The exact opposite would happen for protonation of amino acids. The $p{K}_b$ values for amino groups are lower than that of carboxyl groups, so the amino groups will be protonated before the carboxyl groups.

Here is the structures at increasing pHs for a generic amino acid. If you start at a high pH and decrease it, read the structures from right to left.
http://butane.chem.uiuc.edu/cyerkes/chem104A_S07/Lecture_Notes_104/lect27c.html

Here is an example of deprotonating a protonated R group (glutamic acid).
http://butane.chem.uiuc.edu/cyerkes/chem104A_S07/Lecture_Notes_104/lect27c.html

Note that this is the WRONG structure at a neutral pH. This is usually a trap answer on tests.