AAMC Practice Exam 2

[Starling314]

Thoughts from people who've taken AAMC's newest practice exam

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[5words]

Wait, they have released a new Test?

 

[twist2]

scored a 515 on first and a 521 on the second. Taken one week apart. Not sure if the real exam will be this straight forward .

 

[DaAlienist]

Can use some help with this question.

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Is the blurb about the protein being non-functional irrelevant to the question? The explanation makes it seem this is really just a Q on the minutiae of Southern blotting. That is all their explanation mentions.

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Is it common knowledge (or expected for the MCAT I guess) that restriction endonucleases used in Southern blotting specifically target palindromic sequences that are 4-6 nucleotides long? Is this a thing? Aren't there hundreds of restriction enzymes that can be used in Southern Blotting? Am I supposed to memorize the Hind endonucleases?

Any help or guidance would be appreciated.

 

[doctor_crane]

DaAlienist, I think that that question is a very rare question. The MCAT is designed so that no one will get every question correct, so this would be a harder question that only people with an in-depth understanding of southern blotting can answer. I'd not stress about it because on your MCAT, it may be some in-depth question about physics, biochemistry, or something else that they'd not expect most to answer correctly. On questions like this, best to not waste a lot of time on it and guess, but if you can remember that mutations for southern blots require the creation or destruction of a palindromic sequence, that is all you need to know for this question. Don't worry about specific details like the HindIII sequences.


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[DaAlienist]

DaAlienist, I think that that question is a very rare question. The MCAT is designed so that no one will get every question correct, so this would be a harder question that only people with an in-depth understanding of southern blotting can answer. I'd not stress about it because on your MCAT, it may be some in-depth question about physics, biochemistry, or something else that they'd not expect most to answer correctly. On questions like this, best to not waste a lot of time on it and guess, but if you can remember that mutations for southern blots require the creation or destruction of a palindromic sequence, that is all you need to know for this question. Don't worry about specific details like the HindIII sequences.


Sent from my iPhone using SDN mobile

So, long story short, you have to have memorized a minute detail about Southern blotting to get this question correct? Is this common knowledge that restriction enzymes generally prefer or specifically target palindromic sequences? I had not heard of this before, yet the AAMC states it as if it is something one should know.

Anyone with lab experience of a more thorough bio backgrounds care to weight in?

 

[desperadoflakes]

Yeah, it's expected that you read about common techniques used in the lab, and especially electrophoresis questions. This is a hard question, and the only way to get it right is to know "southern blot" = "restriction site" and knowing that restriction sites are palindromic

 

[BUMedHopeful93]

I don't get this .. Is this an error on AAMC's part or did I actually get this wrong

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[Spectar]

I don't get this .. Is this an error on AAMC's part or did I actually get this wrong

Looks like you got it right. I think that question is full of errors - they are asking for moles but you have to answer in molecules.

 

[doctor_crane]

So, long story short, you have to have memorized a minute detail about Southern blotting to get this question correct? Is this common knowledge that restriction enzymes generally prefer or specifically target palindromic sequences? I had not heard of this before, yet the AAMC states it as if it is something one should know.

Anyone with lab experience of a more thorough bio backgrounds care to weight in?

Like I said, the MCAT will ALWAYS have things you have never heard of (basically impossible to know everything). I did not know this aspect of southern blotting until I saw your post. In times like this, you can hope to be able to reason by eliminating choices you know are wrong so you can guess and move on.
The best you can do is do practice problems and learn from your mistakes. Also be sure to review the practice MCAT books (these books will not have everything you need to know, but they give you a basic knowledge of everything that has a chance to be on the MCAT).


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[DaAlienist]

eliminating choices you know are wrong so you can guess and move on...

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I get that, but with this Q, how are you able to eliminate ANY of the wrong answers without knowing this random fact about Southern blotting. I'm not doubting the AAMC will give me Qs like this, but I hate that it appears to only reward pure, random memorization, not thinking involved.

Thank you.

 

[desperadoflakes]

The point is it's not a random fact about southern blotting, it's an obvious fact if you read about southern blotting

 

[DaAlienist]

The point is it's not a random fact about southern blotting, it's an obvious fact if you read about southern blotting

I don't think you know what obvious means. It is a fact about southern blotting. A fact that you cannot know unless you study southern blotting in detail, not something the AAMC typically does with its science (or at least purports not to do).

The fact the AAMC chose to hinge this question entirely on one aspect of restriction endonucleases is random, not the fact itself. Can you point me to a resource where this fact is stated or presented as common knowledge or fundamental to understanding Southern Blotting?? I have honestly never learned that Southern blotting restriction enzymes specifically target 4-6 bp long palindromic sequences (as their terrible explanations say). Are there not hundreds of restriction enzymes to use? How many of them target palindromic sequences such that the AAMC would consider this a fair question?

Either way, there is no critical thinking in this question. It is just raw, "random" (as far as the MCAT science goes) memorization.

 

[Ismet]

Reminder that posting screenshots of AAMC material is a copyright violation and is not permitted on SDN. Please be aware that representatives from AAMC as well as testing companies regularly use SDN and can see when their material is being illegally reproduced.

 

[desperadoflakes]

I don't think you know what obvious means. It is a fact about southern blotting. A fact that you cannot know unless you study southern blotting in detail, not something the AAMC typically does with its science (or at least purports not to do).

The fact the AAMC chose to hinge this question entirely on one aspect of restriction endonucleases is random, not the fact itself. Can you point me to a resource where this fact is stated or presented as common knowledge or fundamental to understanding Southern Blotting?? I have honestly never learned that Southern blotting restriction enzymes specifically target 4-6 bp long palindromic sequences (as their terrible explanations say). Are there not hundreds of restriction enzymes to use? How many of them target palindromic sequences such that the AAMC would consider this a fair question?

Either way, there is no critical thinking in this question. It is just raw, "random" (as far as the MCAT science goes) memorization.

I'm not sure why you feel so strongly about this. The MCAT is a curved exam, they purposefully make it extremely difficult to get every question right. People who do get every question right are people that are both very good at critical thinking and also have a higher than average level of detail in their knowledge. Though I do feel like you're overestimating how obscure this specific piece of knowledge is. It really requires you to know two things:

1) The first step of southern blotting is digestion of your DNA sample with a restriction enzyme. You will read this fact in any description of the procedure.
2) Restriction enzymes (almost all of them) rely on palindromic sequences. This is obvious knowledge to anyone with lab experience in molecular cloning, or anyone who has read about restriction enzymes. The palindromic sequence is important for site specificity and for creating sticky ends (overhangs). In molecular cloning, you use a restriction enzyme to create compatible sticky overhangs on the two things you're splicing together. So let's say you want to clone a particular gene into a particular site in a particular plasmid. First you PCR amplify a piece of your DNA sample that includes your gene of interest. Then you use a restriction site that recognizes a site on your sample and on your plasmid, in a region of the plasmid that works for you. You use the enzyme to digest both.

So let's say your sequence is 5' GAATTC 3', and your restriction enzyme likes to cut at 5' G*A (* = cut site). So both your PCR amplified sample and your plasmid have this sequence:
5' GAATTC 3'
3' CTTAAG 5'

You digest both, and let's say you get this for example:
Plasmid:
5' G_____
3' CTTAA_

Gene of Interest:
5' _AATTC
3' _____G

Combining these digested samples and running a ligation protocol will allow them to anneal together to create a plasmid that now has your gene of interest. It also recreates the restriction site, so you could redigest if you need to.

New plasmid after annealing:
5' G'AATTC 3'
3' CTTAA'G 5'

You can see that the use of the palindromic sequence is crucial to the use of a restriction enzyme, because it lets you cut at extremely specific sites, and it allows you to create these sticky end overhangs that are extremely useful for cloning. Not all restriction enzymes create sticky ends - some cloning protocols call for blunt-ended ligation

Note: the specific cloning protocol I wrote out will run into some issues with self ligation and stuff, so its incomplete. dont read into it too far except for a basic understanding of how overhangs help in cloning.

 

[DaAlienist]

I'm not sure why you feel so strongly about this. The MCAT is a curved exam, they purposefully make it extremely difficult to get every question right. People who do get every question right are people that are both very good at critical thinking and also have a higher than average level of detail in their knowledge. Though I do feel like you're overestimating how obscure this specific piece of knowledge is. It really requires you to know two things:

1) The first step of southern blotting is digestion of your DNA sample with a restriction enzyme. You will read this fact in any description of the procedure.
2) Restriction enzymes (almost all of them) rely on palindromic sequences. This is obvious knowledge to anyone with lab experience in molecular cloning, or anyone who has read about restriction enzymes. The palindromic sequence is important for site specificity and for creating sticky ends (overhangs). In molecular cloning, you use a restriction enzyme to create compatible sticky overhangs on the two things you're splicing together. So let's say you want to clone a particular gene into a particular site in a particular plasmid. First you PCR amplify a piece of your DNA sample that includes your gene of interest. Then you use a restriction site that recognizes a site on your sample and on your plasmid, in a region of the plasmid that works for you. You use the enzyme to digest both.

So let's say your sequence is 5' GAATTC 3', and your restriction enzyme likes to cut at 5' G*A (* = cut site). So both your PCR amplified sample and your plasmid have this sequence:
5' GAATTC 3'
3' CTTAAG 5'

You digest both, and let's say you get this for example:
Plasmid:
5' G_____
3' CTTAA_

Gene of Interest:
5' _AATTC
3' _____G

Combining these digested samples and running a ligation protocol will allow them to anneal together to create a plasmid that now has your gene of interest. It also recreates the restriction site, so you could redigest if you need to.

New plasmid after annealing:
5' G'AATTC 3'
3' CTTAA'G 5'

You can see that the use of the palindromic sequence is crucial to the use of a restriction enzyme, because it lets you cut at extremely specific sites, and it allows you to create these sticky end overhangs that are extremely useful for cloning. Not all restriction enzymes create sticky ends - some cloning protocols call for blunt-ended ligation

Note: the specific cloning protocol I wrote out will run into some issues with self ligation and stuff, so its incomplete. don't read into it too far except for a basic understanding of how overhangs help in cloning.

Thanks for the details. My only issue with the questions was the palindromic detail. I feel strongly because I have worked with blotting and restrictive enzymes before, and I never read their target sequences had to be palindromic. All the other stuff you wrote above was known to me.

I did some digging, and the best I can find is some textbooks and Wikipedia say that "many" restriction enzymes target palindromic sequences. I don't see how the AAAMC can then justify their questions with this. Because "many" RE target palindromic sequences, that should be my default thought when I hear restriction enzyme?

This is fine if the AAMC wants it this way, and is consistent, but to claim that anyone who studied REs would conclude they must be talking about a RE with a palindromic target sequence seems a bit arbitrary. Not unfair per se, but, for lack of a better term, his is lame. I guess if you know palindromic is a typical, if not majority target for REs, and there is only 1 answer with a palindromic sequence, it is the "best" answer to this question.

Just for my own sanity, can you link me a resource or refer me a book which states that the prevailing RE targets are palindromic. I am fine with the AAMC deciding that RE target = palindromic, but I would like to see the actual science behind it, if it is anywhere.

 

[DaAlienist]

Reminder that posting screenshots of AAMC material is a copyright violation and is not permitted on SDN. Please be aware that representatives from AAMC as well as testing companies regularly use SDN and can see when their material is being illegally reproduced.

Is education, commentary, or review not fair use, even for copyright material? The U.S. definition of fair use is "the doctrine that brief excerpts of copyright material may, under certain circumstances, be quoted verbatim for purposes such as criticism, news reporting, teaching, and research, without the need for permission from or payment to the copyright holder."

More Information on Fair Use | U.S. Copyright Office

Are you saying that SDN will not allow any posting of copyright material, even if covered under fair use? Or are you saying that screen-shotting is not enough of a transformation to qualify for fair use?

I want to be sure because I understand you cannot afford to irk the AAMC, I just wanted to point out the potential inconsistency.

Caution will be exercised in the future.

 

[desperadoflakes]

Thanks for the details. My only issue with the questions was the palindromic detail. I feel strongly because I have worked with blotting and restrictive enzymes before, and I never read their target sequences had to be palindromic. All the other stuff you wrote above was known to me.

I did some digging, and the best I can find is some textbooks and Wikipedia say that "many" restriction enzymes target palindromic sequences. I don't see how the AAAMC can then justify their questions with this. Because "many" RE target palindromic sequences, that should be my default thought when I hear restriction enzyme?

This is fine if the AAMC wants it this way, and is consistent, but to claim that anyone who studied REs would conclude they must be talking about a RE with a palindromic target sequence seems a bit arbitrary. Not unfair per se, but, for lack of a better term, his is lame. I guess if you know palindromic is a typical, if not majority target for REs, and there is only 1 answer with a palindromic sequence, it is the "best" answer to this question.

Just for my own sanity, can you link me a resource or refer me a book which states that the prevailing RE targets are palindromic. I am fine with the AAMC deciding that RE target = palindromic, but I would like to see the actual science behind it, if it is anywhere.

Sure, here you go.

Restriction enzyme - Wikipedia

 

[bonedoc82]

Congrats to everyone and good luck to others! 4th year Orthopedic surgery resident here! Contact here or PM with questions!

Dr. Webb

 

[Ismet]

Is education, commentary, or review not fair use, even for copyright material? The U.S. definition of fair use is "the doctrine that brief excerpts of copyright material may, under certain circumstances, be quoted verbatim for purposes such as criticism, news reporting, teaching, and research, without the need for permission from or payment to the copyright holder."

More Information on Fair Use | U.S. Copyright Office

Are you saying that SDN will not allow any posting of copyright material, even if covered under fair use? Or are you saying that screen-shotting is not enough of a transformation to qualify for fair use?

I want to be sure because I understand you cannot afford to irk the AAMC, I just wanted to point out the potential inconsistency.

Caution will be exercised in the future.

Taking a screenshot of a question in order to ask a question about it will not fall under fair use. You're not teaching, researching, etc and there's no transformation of the material happening.

We have always allowed people to paraphrase questions in order to ask questions. We have always disallowed copying questions verbatim or posting screenshots of questions that are only available behind a paywall and/or are covered by a copyright. Same applies to MSAR data, USN&WR data that's behind the paywall, etc. First and foremost we want to protect our members against possible legal action from what they post here.

I apologize for any apparent inconsistency in moderation in this forum, we don't currently have a moderator specifically assigned to the MCAT forums so sometimes these fly under our radar until they get reported or we see them.

 

[DaAlienist]

Sure, here you go.

Restriction enzyme - Wikipedia

Yeah, I had already seen that and mentioned it in my post. The only thing Wikipedia says is that "many" are palindromic. Nor most, not a majority, just the vague term "many". To me, this is what made the Q frustrating and "random." Saying "Manyx X are Y" to me, does not lead to inferring that "If X, then Y" the way the AAMC does here with RE targets and palindromic sequences.

As I stated before, the AAMC is free to be as arbitrary as they want, so long as they are consistent. I actually looked up the reference cited in the Wiki article and got this:

Finally, I have closure. If research shows that X is usually Y, then it stands to reason that the AAMC can expect us to connect X and Y. It sucks that I had to go to a 2001 research paper, and there is no consensus in standard Biology textbooks (none that I have read or that any here have offered). But at least I know the scientific justification for the AAMCs choice is there.

Long story short, according to the AAMC, when we see restriction enzyme, barring any other info, they will target palindromic sequences.

P.S. The AAMC sucks, and the MCAT is a beast. I am glad it will be over soon.

 

[DaAlienist]

Taking a screenshot of a question in order to ask a question about it will not fall under fair use. You're not teaching, researching, etc and there's no transformation of the material happening.
a moderator specifically assigned to the MCAT forums so sometimes these fly under our radar until they get reported or we see them.

Thank you for the clarification!

 

[DaAlienist]

AAMC PRACTICE TEST 2 - BIO/BIOCHEM Q45 AAMC Mistake

Does anyone get an error in this question?

I just took PT 2 and Q45 in Bio/biochem asks "Under anaerobic conditions, how many moles of ATP are produced from the consumption of 5 moles of glucose?"

I figured the answer is either 10 or 20. Glycolysis produces 4 mol ATP per round, but the body only gains 2 net ATP. Thus, depending on how the AAMC means it, I get:

5 moles glucose x 4 ATP/ 1 rd = 20 moles ATP OR 5 moles glucose x 2 net ATP/1 rd = 10 moles ATP
​

But, all of the answers have powers of 10^24 in them.

Did the AAMC screw up and calculate the # of molecules of ATP and not moles? How simple is this to differentiate? Am I missing something about why you would need to multiply by Avogadro's Number in order to calculate total moles? That seems backwards to me.

I paid good $ for these tests and now I am missing points on my practice tests due to AAMC mistakes. The explanation even follows my logic, but you cannot get the Q right except by random chance because they screwed up the answers.

You had 1 job AAMC, how do you mess that up?

 

[mariposas905]

AAMC PRACTICE TEST 2 - BIO/BIOCHEM Q45 AAMC Mistake

Does anyone get an error in this question?

I just took PT 2 and Q45 in Bio/biochem asks "Under anaerobic conditions, how many moles of ATP are produced from the consumption of 5 moles of glucose?"

I figured the answer is either 10 or 20. Glycolysis produces 4 mol ATP per round, but the body only gains 2 net ATP. Thus, depending on how the AAMC means it, I get:

5 moles glucose x 4 ATP/ 1 rd = 20 moles ATP OR 5 moles glucose x 2 net ATP/1 rd = 10 moles ATP
​

But, all of the answers have powers of 10^24 in them.
View attachment 219705

Did the AAMC screw up and calculate the # of molecules of ATP and not moles? How simple is this to differentiate? Am I missing something about why you would need to multiply by Avogadro's Number in order to calculate total moles? That seems backwards to me.

I paid good $ for these tests and now I am missing points on my practice tests due to AAMC mistakes. The explanation even follows my logic, but you cannot get the Q right except by random chance because they screwed up the answers.

You had 1 job AAMC, how do you mess that up?

Yup, I think that's a mistake too lol, I put the same answer you did

 

[desperadoflakes]

lol