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Question about ICE #1 Question 2
Christopher_4735
#1 Posted : Saturday, May 08, 2021 4:12:50 AM
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Question 2 asks:
Which of the following is the best explanation for why attempts at predicting the protein configuration based upon amino acid sequence have been unsuccessful?

A. It is impossible to know the amino acid sequence of a protein without knowing the DNA nucleotide sequence.
B. Chaperones help to determine the three dimensional shape of a protein.
C. The three-dimensional shape of a protein is based upon hydrogen and disulfide bonding between amino acids, and the number of possible combinations of bonding amino acids makes prediction difficult.
D. The amino acid sequence of the same protein may vary slightly from one sample to the next.

I completely see why C makes is right, but I am wondering why B is wrong. Both the answer at the back of the book and the instructor indicated that B is wrong because Chaperones do not 'determine' the product/3-D shape of the protein, and chaperones only stabilize the intermediate.

But that's not what choice B says. Choice B says that chaperones help determine the 3D shape. The way that chaperones help is through stabilizing intermediates to allow the rest of the protein to fold a certain way. In other words, without chaperones, the shape and configuration of a protein would undoubtedly be different, so chaperones do help with determining shape (but are not the only factor obviously).

So isn't the fact that we can't actually know how chaperones impact the 3D shape by looking at the amino acid sequence alone also a good reason why we can't predict the final shape based on looking at the sequence?
Anjali_5681
#2 Posted : Monday, May 10, 2021 7:48:28 PM
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This was a tough question!

For this question, I would say that answer B was not the best answer, and that answer C was more comprehensive. Between choosing the two answers here, I would consider which one is more correct, which is difficult to do because answer B sounds super tempting and is brought up in the passage.

I would say in this case, based on the passage information provided, chaperones merely assist in the folding. We cannot infer from the passage that the folding would produce shapes that would be different. It most likely would have taken longer for the protein to fold into the shape that it is meant to, without those proteins. Therefore, this makes answer B out of scope and not the best answer.

Looking at answer C, the content is correct, and furthermore, the answer specifically states that the reason for it being difficult to predict is the sheer number of possibilities from the number of intermolecular bondings possible, making it a very strong contender for the correct answer.

Hope that helps!
Christopher_4735
#3 Posted : Monday, May 10, 2021 10:42:30 PM
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I appreciate the response a lot.

Anjali_5681 wrote:

I would say in this case, based on the passage information provided, chaperones merely assist in the folding. We cannot infer from the passage that the folding would produce shapes that would be different. It most likely would have taken longer for the protein to fold into the shape that it is meant to, without those proteins. Therefore, this makes answer B out of scope and not the best answer.


To this point, I agree that we can't infer from the passage itself, but we actually do know that chaperones do impact the shape by assisting in folding. Since this isn't a CARS passage, we're allowed to use outside information about Bio/BioChem to assist us.

We know (from our knowledge of chaperones outside of this passage) that chaperones don't merely speed up the process, but hold certain parts of the protein stable while other parts of a protein are either translated or themselves folded into place. Without accounting for chaperones, we can't determine the shape/structure of a protein based on the amino acid sequence itself.

Maybe the right thing to do here is just not to overthink why there might be two potentially correct answer choices here in a non-AAMC question and hope something like this doesn't pop up on the actual exam.

Thanks for your help.
INSTR_Kennedy_135
#4 Posted : Thursday, May 27, 2021 6:05:00 PM
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Hello!

Process of elimination is best technique for this question!

Try rewording statement with because then add answer choices. " attempts at predicting the protein configuration based upon amino acid sequence have been unsuccessful because..."

Even if A were true it does not answer the question. B is false as chaperones do not determine the product, they only stabilize intermediates. D is false except in rare cases of neutral mutation. C is a direct response and is true.

Kennedy
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