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A protein is a chain of amino acids, compounds that contain amine and carboxyl groups, along with different side groups denoted as R, attached to a core carbon. Amino acids are linked through covalent peptide bonds, and the repeating series of atoms along the core is called the polypeptide backbone.

The sequence begins at the N-terminus, with a free amino group, NH3+, and ends with the C-terminus, a free carboxyl group, COO-.

Each protein is unique, depending on the number of amino acids and their side chains. For example, thyroid-releasing hormone has 234 amino acids, whereas the elastic muscle protein connectin has over 34,000.

Moreover, there are 20 different side chains, which fall into one of four groups. Negative polar amino acids, like aspartic and glutamic acids, have side chains with a carboxyl group. Because of this, they act like an acid at neutral pH.

Positive polar amino acids act like bases, and have an amino group in their side chain.

Several amino acids are polar but uncharged. They tend to be hydrophilic, and make up the outer portion of a folded protein, where they are free to interact with the aqueous environment. Lastly, a large group of amino acids contain nonpolar side chains.

They can be simple, as in glycine, or complex, like proline and tryptophan. Nonpolar side chains generally make the amino acid hydrophobic, forming the core of many proteins.