There are 20 naturally occurring amino acids that are strung together in polypeptide chains to make proteins. All of the amino acids have the same general underlying structure:

with a central carbon atom, and branching off from that is a hydrogen, a basic amine group (-NH₂) on one end (hence the "amino" part of the name), and an acidic carboxyl group (-COOH) on the other end (thus the "acid" part of the name). Notice also the "R" group, which is different for every amino acid. The R group is what gives each amino acid its particular unique character, and confers its unique chemical behavior. When amino acids are strung together in a polypeptide chain, the amine group of one amino acid binds to the carboxyl group of the next amino acid, forming a peptide bond, so their basic and acidic properties no longer influence the chemical behavior of the protein. Rather it is the R groups left sticking out that are chemically significant, and that is where you should draw your attention as you look at the structure of the 20 amino acids. Notice what they all have in common (that general structure), and what they all have that is different (the R group).

There are 4 main classes of amino acids: neutral nonhydrophilic (in other words, uncharged and nonpolar), neutral hydrophilic (that is, uncharged and polar), basic hydrophilic, and acidic hydrophilic . In each case, it is the chemical nature of the R group that determines to which class the amino acid belongs.

For example, let's compare the following 3 amino acids: alanine, aspartic acid, and lysine.

alanine	aspartic acid	lysine

Notice that they share the general amino acid structure, and only differ in their R groups. Alanine's R group is CH₃, a methyl group, which is uncharged and nonpolar, which makes this amino acid behave in this way – it is neutral and hydrophobic. Aspartic Acid's R group ends in the acidic –COOH, a carboxyl group, which readily becomes negatively charged and is thus polar. This makes this amino acid behave as an acid and hydrophilic. Now look at lysine – at the end of its R group, there is the basic –NH₂, an amine group, which readily becomes positively charged and is thus polar. Lysine's chemical behavior is thus a base and is hydrophilic.

Here is the complete list of the 20 amino acids, along with details such as the chemical nature and the 3-letter and 1-letter codes biochemists use to refer to each amino acid.

9 of these amino acids are referred to as essential amino acids because we don't naturally synthesize an appreciable amount of them, so we rely on getting them from our diet. They are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. This is a particular challenge for vegetarians, because most plant material is not rich in lysine and tryptophan. The names of the essential amino acids are marked with a star.