An amino acid contains both an amino group and a carboxyl group. The amino acids used to build ordinary proteins are mostly α-amino acids, meaning that both functional groups are attached to the same central carbon, called the α carbon.

A generic α-amino acid can be represented as

$$\mathrm{H_2N-CH(R)-COOH},$$

where $R$ is the side chain. The amino group, carboxyl group and backbone hydrogen are common to the standard amino-acid framework; the side chain is what distinguishes one amino acid from another.

For example:

• glycine has $R=H$;
• alanine has $R=CH_3$;
• serine has $R=CH_2OH$;
• aspartic acid has $R=CH_2COOH$;
• lysine has a longer side chain ending in an amino group.

Side chains create different chemical behavior

Side chains can be grouped approximately by the kinds of interactions they support in water:

• nonpolar side chains are dominated by hydrocarbon-like groups and interact relatively weakly with water;
• polar uncharged side chains contain groups such as hydroxyls or amides that can interact strongly with water;
• acidic side chains contain groups that can donate protons and therefore can become negatively charged;
• basic side chains contain groups that can accept protons and therefore can become positively charged.

These categories are useful but not permanent charge labels. The protonation state of an ionizable side chain depends on the surrounding acid-base conditions; that dependence is treated quantitatively in the next acid-base unit.

Chirality

For most standard amino acids, the α carbon is attached to four different groups and is therefore a stereogenic center. Glycine is the exception because its side chain is another hydrogen, so its α carbon is achiral.

Proteins made by ribosomes overwhelmingly use amino acids of the L stereochemical family. The L/D naming convention is historical and is not identical to the R/S system, although most common L amino acids happen to have S configuration at the α carbon.

Changing a side chain can change size, charge, polarity, hydrogen-bonding ability and steric behavior. Because proteins are chains of amino acids, those local differences become the raw material from which protein folding, binding and catalysis emerge.