Question

1) Indicate why alpha helices and beta sheets help "bury" hydrophobic amino acids in the interior of a folded polypeptide in an aqueous environment.

2) Explain what is meant by the statement "Protein folding is driven by hydrophobic interactions" and under what conditions this is true.

Answer 1

1. Protein folding is a process by which polypeptide chain folds to become biological active protein in its 3-D structure which is critical for it's function. There area four stages of protein foldings- primary, secondary, tertiary and quartnery.

Secondary structure include alpha helix and beta pleated. Hydorgen bonding plays an important role in Secondary protein folding. This hydrogen bond has the tendency for interacting nonpolar molecule with each other rather than with water. This leads to the burial of nonpolar side chains in the interior of proteins, which in turn leads to a “collapse” of the protein from an extended coil to a more compact, globular structure.

2. Yes - in protein folding, H-bond is a major driving force and it's is the distribution of nonpolar and polar proteins that governs this bond. The (hydrophobic) non- polar side chains in a protein such as those belonging to phenylalanine, leucine, isoleucine, valine, methionine and tryptophan tend to cluster in the interior of the molecule (just as hydrophobic oil droplets coalesce in water to form one large droplet). In contrast, polar side chains such as those belonging to arginine, glutamine, glutamate, lysine, etc. tend to arrange themselves near the outside of the molecule, where they can form hydrogen bonds with water and with other polar molecules. There are some polar amino acids in protein interiors, however, and these are very important in defining the precise shape adopted by the protein because the pairing of opposite poles is even more significant than it is in wat