The three groups of atoms that make up amino acids are:

1. Amino group (NH2): This group contains nitrogen and hydrogen atoms.

2. Carboxyl group (COOH): This group contains carbon, oxygen, and hydrogen atoms.

3. Side chain (R group): This group varies depending on the specific amino acid and determines its unique properties.

It's important to remember that the alpha carbon is the central carbon atom to which all three groups are attached.