Discuss the bonds which comprise the tertiary structure of protein.

Bonds in a protein's tertiary structure occur entirely between the highly variable R-groups of the amino acyl residues. Firstly, hydrogen bonds further to those in the secondary structure may form between the R-groups of polar amino acids such as serine and aspartate. Ionic bonds (salt bridges) may also exist between basic and acidic side chains of amino acids (e.g. lysine and glutamic acid respectively). However, it must be noted that these are quite rare and much more heavily involved in the quaternary sturcture. Disulfide bridges are strong covalent bonds which form exclusively between cysteine residues and may unite distant regions of the polypeptide chain. Due to the typical reducing environment within cells, it is more common to find disulfide bridges within poteins in the hostile extracellular environment such as with the peptide hormone insulin. Despite each bond listed being indivually quite strong, it is the cumulative contribution of the hydrophobic effect and van der Waals' forces that exerts the key influence on tertiary structure. In an aqueous medium, hydrophobic amino acids will tend to congregate in the sheltered core of the structure while hydrophilic amino acids will associate with the water on the exterior. It is this total entropic drive along with the bonds from transient dipoles (van der Waals') in the core which shapes a protein's 3D conformation. 

The resultant structure may be globular with a myriad of possible functions including enzyme catalysis, membrane transport, reception of molecules or hormonal control. Alternatively, a more ordered and repetitive tertiary structure invariably results in a structural protein such as collagen.