FL 4 c/p #21

cecie_icy
Posts: 3
Joined: Sun Jan 15, 2017 12:59 pm

FL 4 c/p #21

Postby cecie_icy » Wed Oct 04, 2017 9:17 pm

Can someone please explain this answer clearly?
NS_Tutor_Andrew
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Posts: 512
Joined: Mon May 23, 2016 1:47 pm

Re: FL 4 c/p #21

Postby NS_Tutor_Andrew » Wed Oct 04, 2017 11:05 pm

Hi cecie_icy,

This is definitely a challenging question! For questions like this, it can be very helpful to break down the answer choices to see what specifically you have choose between. The first thing that should jump out at you is that C and D involve a hydroxyl group attacking, while A and B involve an amide nitrogen attacking. If you can figure out which is correct, you've eliminated two answer choices.

In order to do this, you need to go to the passage, figure out that the reaction they're talking about is exemplified in step 1 of Fig. 1 (although technically Fig. 1 is for a jellyfish CP, not sgBP), and identify what happens in that step in loose terms. Even just visually, comparing the molecule before and after step 1, we can see that in step 1, a ring is formed, and the way this happens is that a bond is formed between a nitrogen and a carbonyl carbon. (This is what the arrow in the image in the explanation illustrates). Recognizing this allows you to eliminate C and D.

Your next task is to compare A and B. Both answer choices talk about the attack of an amide nitrogen onto an electrophilic carbonyl carbon, but they differ based on the specific structures that they refer to. Let's take the first half of each answer choice: A says that the amide nitrogen is on Gly64, and B says that it's on Gln62. Thus, you want to examine the rest of the structure associated with that N. It happens to be part of a glycine amino acid (the giveaway is that no carbon-containing R group is drawn; glycine's side chain is -H, which is not illustrated in bond-line notation). Since it's part of a glycine amino acid, A must be right. Don't worry about the numbers 62 vs. 64 here -- it's enough to distinguish between Gly and Gln.

This is enough to get you the right answer. However, you might wonder about the second half of the answer choice (the reference to Gln62). If you're paying close attention, you'll notice that the carbonyl C involved in step 1 in Fig. 1 is actually part of a serine amino acid, not a glutamine amino acid. So, what's up with that? Well, Fig. 1 doesn't illustrate exactly the same thing that the question is asking about -- the question asks about sgBP, not jellyfish CP, and paragraph 2 tells us that sgBP has a glutamine in the corresponding position. Moreover, paragraph 1 tells us that CPs have a structure of X-Tyr-Gly, so we can infer that "X" = serine in the CP shown in Fig. 1 but glutamine in sgBP. Paragraph 1 also confirms for us that steps 1 and 2 in Fig. 1 apply to this entire set of molecules, so we can be confident in using Fig. 1 to reason about the mechanism in sgBP.

Hope this is helpful! Thanks for the question and please feel free to reach out with follow-up :).
Andrew D.
Content Manager, Next Step Test Prep.

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