Amino acids are organic compounds that contain an amine group, a carboxylic acid group, and a side chain (-R group). Depending on the pH of the solution, these different ends and -R groups may be protonated or deprotonated. A neutral amino acid that contains both a positive and a negative charge is called a zwitterion (i.e. when the amino end is protonated to form -NH3+ and the carboxyl group is deprotonated to form −CO2−).
Amino acids are classified by the chemical properties given them by their side chains: non-polar (hydrophobic), polar, acidic, and basic. The primary structure of a protein is the linear sequence of amino acids, and the protein’s secondary structure is determined by interactions between side chains on nearby amino acids.