In the quaternary structure of a protein the polypeptide is folded through the mechanism of amino acids rotating around bonds and folding into a alpha-helix or beta-pleated sheet structure and stabilized by bonds. amino are the building blocks of proteins. They are made up of a center carbon atom bound to a positively charged group and a negatively charged group and a side chain. In the secondary structure of a protein the amino acid side chains of the folded polypeptide interact, forming a complex three-dimensional shape. primary structure formed by amino reactions link amino acids together, forming a linear chain. The of a protein exists if multiple polypeptides bind together to form a functional protein.