A protein has three structures -- sometimes, when combined with another protein, even four. * The primary structure is the amino acid sequence. The amino acid sequence is what identifies each protein. * The secondary structure is determined by the helixes, sheets, and loops that occur in different parts of the protein. * The tertiary structure is the overall three-dimensional shape of the protein. Finding a good tertiary structure is the major goal of Foldit. * The quaternary structure is multiple polypeptide units interacting. In Foldit, symmetry puzzles work with the quaternary shape formed when multiple copies of a protein bond with each other.