There are four levels of protein structure. These are classified as follows:

• Primary Structure - this refers to the linear sequence of amino acids within a polypeptide.
• Secondary Structure - involves regular repeated structures within a polypeptide. These structures occur within a polypeptide; the entire polypeptide does not have the configuration. There are two main types of secondary structure:
  • a-helix (alpha helix) - certain sequences of amino acids will naturally adopt a helical configuration, with 3.6 amino acids per turn of the helix, all stabilized by hydrogen bonds between adjacent turns of the helix.
  • b-sheet (beta sheet) - sometimes, regions of the amino acid chain will double back on itself one or more times, forming a "sheet"-like structure that is stabilized by hydrogen bonds (indicated in the diagram by dotted lines) between adjacent regions of the chain. When viewed edge-on, the sheet has a zig-zag appearance due to the angles of the peptide bonds, so the b sheet is sometimes called a b "pleated" sheet.

  Both a-helix and b-sheet add rigidity and strength to polypeptides, so polypeptides requiring extra strength tend to have more secondary structure. For example, the silkmoth protein fibroin (the main protein component of silk) has extensive b-sheet within its structure. Most polypeptides contain at least some of both types of secondary structure.

• Tertiary Structure - refers to the three-dimensional configuration of a polypeptide. As a polypeptide is synthesized, it folds into a shape that is specific to that polypeptide. How a polypeptide folds is directly determined by the sequence of amino acids (in other words, the primary structure). This is because tertiary structure is stabilized by such chemical forces as disulfide bridges (covalent bonds between the sulfur groups on two separate cysteine residues within a polypeptide), hydrogen bonds, and hydrophobic interactions (some amino acids don't like to be in contact with water, so they try to cluster at the center of the folded polypeptide). Mutations that lead to change in one or more amino acids can change the shape of a polypeptide, which can affect its function. The shape of a polypeptide is intimately associated with its function. For example, enzymes act on their substrates via the active site, which is a cleft or crevice on the surface of the enzyme. If the shape of the active site changes, the substrates will no longer fit correctly, and the enzyme will not function as it did before.
• Quarternary Structure - some polypeptides serve as subunits in multi-subunit proteins. Such polypeptides would not be functional on their own. Quarternary structure refers to the relationships between polypeptides in a multi-subunit protein. In other words, quarternary structure describes the shape of the whole (intermolecular) complex, whereas tertiary structure described the (intramolecular) shape of a single polypeptide. Can you think of any examples of proteins we've encountered that were composed of multiple subunits?

Protein Modification

After synthesis is complex, polypeptides (and/or proteins) can experience a variety of modifications that affect their function. The following is a far-from-complete list of the types of modifications the polypeptides can undergo:

• Glycosylation - some polypeptides, particularly those that are secreted from the cell or inserted into the cell membrane, have carbohydrates attached to them. MN Blood typing, for example, uses antibodies to detect specific carbohydrates on cell-surface polypeptides of red blood cells. (For description of MN blood typing, see the module on Extensions of Mendelism).
• Modification of Amino Acids - some amino acids undergo chemical modification, and this can affect protein function. One common modification is phosphorylation (addition of a phosphate group) to certain amino acids (tyrosine, serine, or threonine). Phosphorylation is often used as a "switch", turning protein function on or off.
• Cleavage of Polypeptide Chains - some polypeptides, in order to function, must be cleaved (cut) enzymatically in a specific way. This allows the peptide to fold correctly and prevents activity of the polypeptide in situations where it might not be wanted. An example of this is insulin, which is a peptide hormone. Insulin is synthesized in a much longer form than the active molecule (the longer form is called pre-pro-insulin). To become active, the polypeptide must be cut specifically twice, producing two inactive pieces and the active hormone. This allows the accumulation of insulin polypeptides before they are necessary, but prevents insulin activity until it is needed.
• Complexing with Metals - some polypeptides are complexed with metal ions in order to become functional. Examples of this include iron being complexed with globin polypeptides to produce hemoglobin, and zinc complexed with zinc finger transcription factors.