B/B Section Bank #74, reasoning? (sooner than later please, testing on 4/20)

[sapientnarwhal]

---

Members don't see this ad.

PLEASE CAREFULLY CONSIDER THE ALTERNATIVE EXPLANATION I HAVE PROVIDED. I WOULD LIKE FEEDBACK ON MY REASONING, PLEASE DO NOT SIMPLY RESTATE THE ANSWER.

So I understand that the 2nd and 3rd variants are involved in binding to prorenin. However, the 4th variant results in a decreased Km (same as decreased Kd). This does not necessarily mean WT A269 is involved in binding of the substrate. If anything, this indicates that the mutant A269K introduces a novel binding site/interaction with the substrate. The 2nd and 3rd variants suggest that WT V109 and WT W140 are involved in prorenin binding because non-conservative AA substitutions at these residues lead to a reduction in substrate affinity.

The basis for my reasoning follows that if a substrate-interaction is lost, the Kd will increase. So why must the opposite imply that this residue is involved in the actual binding to prorenin? If the question asks us to determine which variants actually bind to the substrate, why should a substitution result in a lower Kd (i.e. strong binding to substrate). This does not necessarily mean the WT residue bound the substrate. Not every active site residue is involved in substrate binding.

I definitely understand that the A269K Kd value relative to WT implies that it is located in the active site, but this does not necessarily mean that the WT A269 residue binds to the substrate.

NOTE: the question asks for residues involved in binding to prorenin.

@NextStepTutor_1 I tagged you in this, as you have been extremely helpful in clarifying questions and info. I was wondering if you could offer any feedback.

 

[DelayedGratification]

This is pretty simple. Of all of the substitutions/mutations shown, Tryptophan 140 to Leucine, Aspartate 201 to Asparagine, and Alanine 269 to Lysine, all cause a change in Kd. If the Kd changes, the amino acid must have a role in ligand binding in the active site.

On the other hand, Valine 169 to Glutamate had no effect.

 

[sapientnarwhal]

This is pretty simple. Of all of the substitutions/mutations shown, Tryptophan 140 to Leucine, Aspartate 201 to Asparagine, and Alanine 269 to Lysine, all cause a change in Kd. If the Kd changes, the amino acid must have a role in ligand binding in the active site.

On the other hand, Valine 169 to Glutamate had no effect.

@DelayedGratification

Please carefully read my explanation. The basis for my reasoning follows that if a substrate-interaction is lost, the Kd will increase. So why must the opposite imply that this residue is involved in the actual binding to prorenin? If the question asks us to determine which variants actually bind to the substrate, why should a substitution result in a lower Kd (i.e. strong binding to substrate). This does not necessarily mean the WT residue bound the substrate. Not every active site residue is involved in substrate binding.

There could be alternative explanations (e.g. this substitution led to a conformational change or change in active site dynamics/structure such that the affinity is increased etc.), but this is likely beyond the assumptions the passage and question stem required us to make.

 

[NextStepTutor_1]

Hi @sapientnarwhal -

I appreciate the request, and am very glad to have been of help! I think you've answered your own question to some extent, in that it all depends on whether you interpret "involved in binding the protein" (1) as applying to any amino acid at the active site, even if it makes a non-direct contribution, or (2) as specifically binding (i.e. coming into direct contact with and stabilizing through some charge-based interaction). It sounds like you're arguing for (2), but the AAMC chose (1). To some extent, the main lesson to be drawn here is how the AAMC thinks about things. But I think their interpretation is somewhat reasonable if you keep in mind that the "binding" in question is almost certainly a reversible charge- and sterics-based interaction rather than the formation of a covalent bond, and the topography of the active site in terms of charge and sterics is shaped by all of its constituent parts. Disrupting any of them might disrupt (or enhance) the active site, so in that sense, all of them may be "involved" in what the active site does.

That said, it seems like a large part of what's going on here may be continuing to calibrate your thought process to the reasoning the AAMC is looking for. It is often the case that the underlying question or reasoning on the MCAT is pretty simple -- a question like this is couched in technical/experimental terms that may intimidate many students, but it boils down to "which variants cause something else to change". A very common pattern is that a question involves first some complex digging around to determine what they're talking about, followed by a relatively simple application of that insight. That seems to be what's happening here. What you personally think about questions like this is up to you, but my personal suggestion is that for Test Day your goal is to align yourself as best as you can w/ AAMC-style thinking and that the day after Test Day is the time to vent about the imperfections of standardized testing 🙂.

(More on the other S/B question later, but I hope this is helpful, if maybe a bit frustrating).