Flexi Says: The secondary structure of a protein refers to local coiling or folding. The intermolecular forces in secondary structures include hydrogen bonding, van der Waals forces, and dipole-dipole interactions between amino acids. Tertiary structure refers to the overall three-dimensional shape of an entire protein chain. Because of the ways that proteins can fold in on themselves, tertiary structure often involves interactions between amino acids that are very far apart in the primary sequence. The tertiary structure involves covalent bonds, dipole-dipole interactions, and hydrophobic interactions between amino acids.
