Most proteins are folded into a complex globular shape. Each protein molecule consists of one or more chains of amino acid monomers. The amino acids are linked by peptide bonds, so a protein polymer is often called a polypeptide. Because they are so complicated, proteins are usually described in terms of four levels of structure. Each protein has a unique primary structure - a particular number and sequence of amino acids making up the polypeptide chain. Twenty different amino acids are used to build proteins. Theoretically, the various amino acids could be linked in almost any sequence, forming an almost infinite variety of different proteins. This illustration shows some of the amino acids making up the primary structure of a protein. The structure of a single generalized amino acid is shown below. The main backbone of every amino acid is the same. This is what forms the backbone of the polypeptide chain. It is the R-group which projects out from the backbone that makes each of the twenty kinds of amino acids unique. Different amino acids have different properties that affect the folding of a protein. Thus, primary structure ultimately determines the shape of a protein, which determines its function. In most proteins, parts of the polypeptide chain are coiled or folded, forming twists and corrugations. This is secondary structure. The turns and folds of secondary structure contribute to the protein's overall shape. One kind of secondary structure is the alpha helix, where the chain twists. Another is the beta pleated sheet, where the chain folds back on itself or where two regions of the chain lie parallel to one another. Secondary structure results from hydrogen bonding between atoms along the polypeptide backbone. Oxygen and nitrogen atoms along the backbone are highly electronegative, and when bound to hydrogen atoms, O and N have partial negative charges while the H atoms have partial positive charges. These negatively and positively charged atoms are attracted to one another at regular intervals along the chain, causing parts of the protein to twist or fold back upon itself. Superimposed on primary and secondary structure is tertiary structure, irregular loops and folds that give the protein its overall three-dimensional shape. The irregular folding of the tertiary structure results from interactions among the R groups of amino acids. Acidic and basic R groups ionize, and these positively and negatively charged groups may form ionic bonds. Polar forces also contribute to tertiary structure. Hydrophilic or polar R groups may hydrogen bond with one another, or turn outward and hydrogen bond with the surrounding water. Hydrophobic, non-polar R groups cluster on the inside of the protein, away from water. Tertiary structure may be further stabilized by strong covalent bonds between sulfur atoms in certain R groups. Some proteins consist of two or more polypeptide chains. The fourth level of protein structure, quaternary structure, results from the combination of two or more polypeptide subunits. Quaternary structure is in turn stabilized by the same sorts of attractions that stabilize tertiary structure. Hemoglobin, the oxygen-carrying protein of blood, is an example of a protein with quaternary structure. It consists of two kinds of polypeptide chains. Two of each, a total of four chains, make up each hemoglobin molecule.
