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Wednesday, June 21, 2017

Introduction to Biochemistry - Quiz 2.2.1


When water is exposed to a hydrophobic molecule, it has a more restricted conformation because they must be all aligned in order to form hydrogen bond. Therefore, hiding the hydrophobic surfaces away can increase water's entropy. Although the folding of protein reduce energy, it also significantly reduce its conformational entropy, that's why the increase of water's entropy is important here.


The effect of increasing water's entropy by folding is called the hydrophobic effect and is one of the major force for the folding. Folding does decrease chain conformational entropy, but that is an inhibitor, not a driving force, folding does not increase chain conformational entropy. Water's entropy got increased by the folding, not decrease. Finally, the word "enthalpy" alone is vague, what it really means in this context should be the overall reduction of potential energy by pulling the opposite charges closer, that is indeed a driving force.

Therefore the answers should be "The hydrophobic effect" and "Enthalpy".


Enthalpy and The hydrophobic effect drives protein folding as we discussed above. Increased entropy of water is basically the same as hydrophobic effect, therefore that is not an answer either. The only remaining choice is "Chain conformational entropy". Indeed, the folding decrease the chain's flexibility to change conformation, therefore it reduces entropy and disfavor protein folding.


Hydrogen bond is the key player in stabilizing the secondary structure for both alpha helix and beta sheets. Salt bridges are strong, but we don't have formal charges around in the protein chain. The other forces are weaker than hydrogen bonds.


Protein folding does have an effect on all of the given factors, but in terms of scale, a folded protein is pretty much stuck, but the unfolded one have a lot of freedom to move around, so if I have to guess, i would guess "Chain conformational entropy".

And I am right :)

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