Question

In biological macromolecules like proteins, the hydrophobic residues tend to clump together in the interior of the folded structure. What is the best explanation for why this occurs?

• A. Hydrophobic residues bind each other, while polar residues cannot bind each other. Therefore the hydrophobic ones end up stuck to each other in the core of the protein.

• B. Polar residues tend to bind to water in the cytoplasm as well as to each other. The water and polar residues cannot bind to the hydrophobic ones, so in the lowest energy state the hydrophobic residues are pushed together in the middle.

• C. Protein folding machinery interprets the amino acid code to pack hydrophobic residues into the center of proteins. This process must be important, because the cell expends large amounts of ATP to precisely coordinate protein folding.

• D. Hydrophobic residues bind to each other in specific ways. For instance, Ala forms di-methyl bonds, and phenylalanine binds isoleucine. This creates a tightly bound hydrophobic inner core.

Answer 1

The hydrophobic residues tend to clump together in the interior of the folded structure can be explained by the hydrophobic effect which is responsible for the protein folding along with intramolecular hydrogen bonds and van der Waals forces.

The hydrophobic effect is a phenomenon in which the hydrophobic chain collapse into the core of the protein. Minimizing the number of exposed hydrophobic side chains to water is a driving force for the protein folding.