17. Below is a folding energy funnel describing folding energy landscape of a pr

Question

17. Below is a folding energy funnel describing folding energy landscape of a protein. The width of the funnel indicates the entropy of the protein, and the height corresponds to its free energy a) if A corresponds to the native structure, what does B correspond to? b) Does this protein have multiple folding pathways or just one? c) The native state A have the lowest entropy, does it violate the 2nd law of thermodynamics? Why or why not? d) Does the native state also has the lowest enthalpy. What makes the enthalpy to decrease as the protein fold?(

Explanation / Answer

Answers:

a: B corresponds to a molten globule state.

b: This protein has one folding pathway since there's only one peak represented in the funnel.

c. It does not violate the 2nd law of thermodyanamics. Reason: The native state of protein is the most stable form of the protein and is characterised by low entropy  because all protein atoms are kept by mutual interaction in a well defined geometry. When placed in a polar solvent the hydrophobic sidechains of the protein are unable to form polar interactions thus the dissociative degrees of freedom available to the molecule decreases and entropy decreases. This leads to the aggregation of the hydrophobic regions.While the entropy of the polypeptide has decreased as it enters a more ordered state, the overall entropy of the system increases, contributing to the thermodynamic favourability of a folded polypeptide.

d: Intramolecular enthalpy is also relatively low because many attractive interactions are satisfied

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