Flexi Says: A protein may have up to four levels of structure. The lowest level, a protein’s primary structure, is its sequence of amino acids. The secondary structure is the 3-D arrangement of amino acids chains into spiral or flat ribbon shapes by the formation of hydrogen bonds. The tertiary structure is the folding of the secondary structures into large 3-D lattices. The quaternary structure is formed by the assembly of two or more polypeptides (amino acid chains) into one functional shape.