4. Which of these events contributes the most in proper folding of a polypeptide to its
native state in an aqueous solvent?
a. loss of hydrogen bonding between the polar amino acids and water
b. hydrophobic effect which sequesters the non-polar residues away from water
c. formation of new inter-molecular hydrogen bonding between polar amino acids
d. formation of di-sulphide linkages between free cysteine residues located at a distance
along the primary sequence

The correct answer is b. hydrophobic effect which sequesters the non-polar residues away from water. The hydrophobic effect is the dominant driving force for proper folding of a polypeptide into its native state in an aqueous solvent.​

Explanation of Each Option

• a. loss of hydrogen bonding between the polar amino acids and water
  While hydrogen bonding between polar amino acids and water is disrupted during folding, this loss is not the primary driving force. Instead, the system compensates by forming new hydrogen bonds within the protein. The energy gain from intramolecular hydrogen bonding is significant, but it is secondary to the hydrophobic effect.​

• b. hydrophobic effect which sequesters the non-polar residues away from water
  The hydrophobic effect is the major contributor to protein folding. When non-polar (hydrophobic) amino acid residues are exposed to water, they disrupt the hydrogen bonding network of water, increasing the system’s free energy. By folding, the protein sequesters these residues into the core, minimizing their contact with water and releasing water molecules to increase entropy. This process is thermodynamically favorable and drives the folding process.​

• c. formation of new inter-molecular hydrogen bonding between polar amino acids
  Formation of hydrogen bonds between polar amino acids within the protein does stabilize the folded structure, but this is a secondary effect. The main driving force is the burial of hydrophobic residues, not the formation of new hydrogen bonds.​

• d. formation of di-sulphide linkages between free cysteine residues located at a distance along the primary sequence
  Disulfide bonds are important for the stability of some proteins, especially extracellular ones, but they are not the primary factor in the initial folding process. Disulfide bond formation typically occurs after the protein has already collapsed into a near-native structure, guided by the hydrophobic effect.​

Introduction
Protein folding is a fundamental process in molecular biology, where a linear polypeptide chain folds into a specific three-dimensional structure. The most crucial factor in this process is the hydrophobic effect, which drives the sequestration of non-polar amino acid residues away from water, leading to the formation of the native protein structure.​

Why the Hydrophobic Effect Matters
In an aqueous environment, water molecules form ordered shells around hydrophobic residues, increasing the system’s free energy. Folding allows these residues to cluster in the protein’s core, minimizing their contact with water and releasing water molecules, which increases entropy. This thermodynamic driving force is the main reason proteins fold rapidly and efficiently.​

Other Factors in Protein Folding
While hydrogen bonding and disulfide bond formation contribute to protein stability, they play supporting roles. Hydrogen bonds form within the folded structure, and disulfide bonds stabilize the final conformation, but neither is the primary initiator of folding.​

Conclusion
The hydrophobic effect is the dominant force in protein folding, ensuring that polypeptides adopt their functional, native conformations in water. Understanding this principle is essential for grasping the fundamentals of protein structure and function.​