The primary structure of a protein consists of a sequence of amino acids joined together by peptide bonds. This is known as a polypeptide chain, which undergoes the most basic level of folding in the shape of alpha helices and beta sheets. These are held together by hydrogen bonds. in the tertiary structure, there are three bonds between the R-groups of amino acids which gives the protein its 3d shape. These are hydrogen, ionic and disulfide bridges, and the position of these bonds determine the unique structure of the protein and give it a specific function.