pKa of argnine and lysine EK question

[rlaboss]

EK has a question:

What could be a reasonable explanation for the difference in pKa between the side chains of lysine and arginine?

A. Lysine's side chain has a more stable conjugate base than arginine's side chain

B. Arginine's side chain has a more stable conjugate base than Lysine's side chain

C. Lysine's side chain has a more stable conjugate acid than arginine's side chain

D. Arginine's side chain has a more stable conjugate acid than Lysine's side chain

The answer they go with is A so they're saying the terminal NH2 is more stable than the uncharged terminal guanidium of arginine. I would think the answer should be D because the reason arginine is more basic and able to hold onto the proton is because of its resonance.

What do you guys think?
-rylaboss

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[aldol16]

I don't like this question because I believe that both A and D are correct statements and are simply two sides of the same coin. Saying that lysine's conjugate base is more stable than arginine's is the same thing as saying that arginine's conjugate acid is more stable than lysine's. The root of the confusion is that they are looking at specific chemical entities, which they should not be doing when talking about a thermodynamic process. Take this: Lys-NH3 (A) <---> Lys-NH2 (B) and Arg-NH3 (C) <---> Arg-NH2 (D). These are thermodynamic equilibria and should be referred to as such. The reason that lysine is more acidic than arginine is because the equilibrium between A and B lies more to the right than the equilibrium between C and D. In other words, B is stabilized relative to A more so than D is stabilized relative to C. You can't directly compare B and D or A and C. You have to take all four into account, by looking at the equilibria.

 

[rlaboss]

I don't like this question because I believe that both A and D are correct statements and are simply two sides of the same coin. Saying that lysine's conjugate base is more stable than arginine's is the same thing as saying that arginine's conjugate acid is more stable than lysine's. The root of the confusion is that they are looking at specific chemical entities, which they should not be doing when talking about a thermodynamic process. Take this: Lys-NH3 (A) <---> Lys-NH2 (B) and Arg-NH3 (C) <---> Arg-NH2 (D). These are thermodynamic equilibria and should be referred to as such. The reason that lysine is more acidic than arginine is because the equilibrium between A and B lies more to the right than the equilibrium between C and D. In other words, B is stabilized relative to A more so than D is stabilized relative to C. You can't directly compare B and D or A and C. You have to take all four into account, by looking at the equilibria.

Your referring to the equilibria specifically at physiological pH, correct?

 

[UBLI-EINSTEIN]

"A" should be a better answer than "D" in terms of this question. The question is asking about "pKa".
So you can translate question to something like: Why is there a difference in acidity (pKa) between Lys and Arg?
Then it comes to be a simple simple organic chemistry concept: Acidity can be evaluated through the stability of its conjugate base.
Thus I think "A" would be a better answer than "D".

This is a kind of tricky and stupid questions. "D" is correct but "A" is better.
I don't think this kind of questions will be on the exam, but if at some point you get confused for whatever reasons, there can be an answer which "seems better than the other"

 

[aldol16]

Your referring to the equilibria specifically at physiological pH, correct?

Yes.