Proteins are made up of polypeptide chains. These are chains of amino acids which are joined together by peptide bonds as a result of a condensation reaction. This produces water as a waste product.The primary structure of the polypeptide is determined by the specific sequence of the amino acids in the chain. These are important because each amino acid has a different side-chain which affects its biochemical properties.The secondary structure arises as a result of the hydrogen bonds forming between the amino acids. These can produce alpha-helices or beta-pleated sheets.The tertiary structure gives the polypeptide its 3D shape, and is determined by further hydrogen bonding and more ionic interactions - for example, disulfide bonds. Again, these are determined by the side chains of the amino acids.Finally, the quaternary structure is made up of at least 2 polypeptide chains.