Biology Made Easy - Guide to Levels of Protein Structure

Proteins are made by linking together amino acids by forming peptide bonds between the amino group of one amino acid and the carboxyl group of the other. A water molecule is lost in this step, and the two amino acid chain is called a dipeptide. Longer chains of amino acids are called polypeptides.

The primary structure of a protein is simply the order of amino acids in the polypeptide chain. These amino acids are held together by covalent peptide bonds. The order of amino acids is determined originally by the DNA, which is then transcribed into mRNA, and then finally translated into a polypeptide. An interaction that can be included in the primary structure is a disulfide bond. This interaction occurs when two cysteine residues are close enough to each other to form a covalent link between their sulphur atoms.

The secondary structure of a protein includes alpha-helices and beta-pleated sheets. These are interactions between different amino acid residues by hydrogen bonds. Hydrogen bonds are weak compared to covalent bonds, but the large number of them can make up for their relative weakness.

An alpha-helix looks like a coiled spring. The spiral has 3.6 amino acids per turn, so they are offset, which allows them to form hydrogen bonds between double bonded oxygens and the amino hydrogens.

A beta-pleated sheet occurs when the polypeptide folds so that chains of it are folded alongside each other. The chains can be in opposite directions or the same direction, based on the folding and possible looping formations that may occur. The folded chains are held close together by hydrogen bonds between the same groups as in the alpha-helix.

The tertiary structure of a polypeptide determines the 3-D shape of the folded protein. Each amino acid has a different side chain that makes it unique from the others, so these interact in different ways with others around them. Side chains can form ionic bonds with each other, hydrogen bond with each other, or interact via weak forces called van der Waals forces. Van der Waals forces occur between amino acids with large hydrocarbon side chains as temporary dipoles form. The disulfide bonds discussed in primary structure are sometimes included as tertiary structure as well.

The quaternary structure of a protein is when multiple polypeptides come together to form a multimer. Two polypeptides form a dimer, three form a trimer, and four form a tetramer. Not all proteins have multiple polypeptide subunits. The quaternary structure is held together by the same interactions found in tertiary structure.