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crazy person

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Hi all ! I was wondering if anyone could explained these two questions from the Physical/Chemical Section.

# 33) Why is the answer R and L ? Since site I and II will only recognize hydrophobic and anionic substrates.

For answer choice A, the answer is R and L ( leucine, which is hydrophobic and R, which is arginine is positive). For answer choice B, the answer is D and E ( which is aspartic acid that is negative charged and E is phenyalanine which is hydrophobic ) . so I don't get why R and L is the right answer

#38) I'm lost. How do I even begin to do this prolem ?

Thanks !
 

RaspberrySlushy

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So it says it recognizes hydrophobic and anionic residues, so that means it must itself have hydrophobic and cationic residues. L is hydrophobic and R has a positively charged side chain at almost all pH.

D and E both have negatively charged carboxyl side chains so would not recognize anionic residues b/c of electric repulsions.

As for 38 not sure how to explain over text. this was one of the Qs I used scratch paper for, to push arrows. The good thing is you only have to do that for reaction 2 since it shows where all the labeled carbons are going in (and all further runs have no effect on carbon arrangements).

Looking at reaction 2, it's an aldol condensation where the alpha carbon of acetyl CoA attacks the left carbonyl of acetoacetyl CoA. That's the only way to get the connectivity seen in the product. So from here I'd just draw the mechanism with the labeled carbons marked and it should just be two arrows and only one matters for where carbons end up.

Sorry no idea if that's helpful at all, really hard to explain o chem just in words!
 

Altius Premier Tutor

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I would add that complementarity is the key to MANY of these MCAT-2015 amino acid questions. Look forward to a lot of questions about predicting which a.a. -R group will be on the enzyme or the substrate/ligand. I think you might have been focused on "matching" instead of "complementing." It's kind of like saying that the DNA sequence GCT "Matches" GCT, but "CGA" is its "complement." Hydrophobic residues should BOTH be hydrophobic, so you could think of them as matching. Charges, though, need to be OPPOSITES to be complementary...very important! Polarity is complementary when matched (polar and polar stabilize each other, polar next to non-polar repel one another). Acids and bases complement each other. An a.a. with an R-group that can give up a proton is likely if we know an a.a. in the binding site is basic. Structures, especially when they ask about enzyme pockets, don't have to be exactly the same to match, they do have to have approximately the same 3-D shape so look at the more general arrangement of their backbone. Note that if they ask for a replacement or competitor for a ligand/substrate you need it to be the same shape. But if one is the enzyme pocket shape and one is the ligand/substrate shape they have to complement each other (i.e., fit together), which would predict different answers if asked about a 3-D shape for the binding pocket. Pretty much all example of this new MCAT-2015 question type, which is so far very common, is based off of these general principles just described.

For #38, this is an extremely common O-Chem or Biochem AAMC question approach. They used it all the time on the old exam and they are still using it. I'll give you something that will get you 95% of these right, but you have to practice. First, DRAW OUT the precursor and/or product given on your scratch paper. Second, you are going to think of it like playing the sesame street game "Which of these is not like the other?" When they ask you to predict a product, including when they ask for where a radiolabeled group will end up, move backwards. Look at the precursor and literally circle every difference in bond connectivity or functional group. Next, you have to ask how each "difference" could have been accounted for by some SIMPLE o-chem reaction (it will always be a simple, commonly-used one [unless they taught it to you in the passage]). Finally, COUNT and LABEL carbons. So many students lose track of a carbon atom, especially when looking at a line-bond drawing [or sometimes worse, a condensed formula like CH3COCOOCH2CH(OH)CH(CH3)2]. The crux is to get good at quickly seeing differences and recognizing what could have caused them. That comes with practice and won't happen just because you read this. Also, the second part (explaining how the differences got there) can't happen unless you have internalized the basic o-chem reactions--so it that's a weak area you'll need to shore that up. Good luck!
 

sas33

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I would add that complementarity is the key to MANY of these MCAT-2015 amino acid questions. Look forward to a lot of questions about predicting which a.a. -R group will be on the enzyme or the substrate/ligand. I think you might have been focused on "matching" instead of "complementing." It's kind of like saying that the DNA sequence GCT "Matches" GCT, but "CGA" is its "complement." Hydrophobic residues should BOTH be hydrophobic, so you could think of them as matching. Charges, though, need to be OPPOSITES to be complementary...very important! Polarity is complementary when matched (polar and polar stabilize each other, polar next to non-polar repel one another). Acids and bases complement each other. An a.a. with an R-group that can give up a proton is likely if we know an a.a. in the binding site is basic. Structures, especially when they ask about enzyme pockets, don't have to be exactly the same to match, they do have to have approximately the same 3-D shape so look at the more general arrangement of their backbone. Note that if they ask for a replacement or competitor for a ligand/substrate you need it to be the same shape. But if one is the enzyme pocket shape and one is the ligand/substrate shape they have to complement each other (i.e., fit together), which would predict different answers if asked about a 3-D shape for the binding pocket. Pretty much all example of this new MCAT-2015 question type, which is so far very common, is based off of these general principles just described.

For #38, this is an extremely common O-Chem or Biochem AAMC question approach. They used it all the time on the old exam and they are still using it. I'll give you something that will get you 95% of these right, but you have to practice. First, DRAW OUT the precursor and/or product given on your scratch paper. Second, you are going to think of it like playing the sesame street game "Which of these is not like the other?" When they ask you to predict a product, including when they ask for where a radiolabeled group will end up, move backwards. Look at the precursor and literally circle every difference in bond connectivity or functional group. Next, you have to ask how each "difference" could have been accounted for by some SIMPLE o-chem reaction (it will always be a simple, commonly-used one [unless they taught it to you in the passage]). Finally, COUNT and LABEL carbons. So many students lose track of a carbon atom, especially when looking at a line-bond drawing [or sometimes worse, a condensed formula like CH3COCOOCH2CH(OH)CH(CH3)2]. The crux is to get good at quickly seeing differences and recognizing what could have caused them. That comes with practice and won't happen just because you read this. Also, the second part (explaining how the differences got there) can't happen unless you have internalized the basic o-chem reactions--so it that's a weak area you'll need to shore that up. Good luck!
I am still having trouble with 38. Thanks so much for your long explanation, as it did help me get on the right track. However, I don't understand how C3 isn't also an answer since it's gaining a double bond?
 
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