AAMC thinks you can see 3bp resolution in Gel Electrophoresis? (B/B Section Bank Spoilers)

[DerDudelsack]

Anyone else have issues with this problem on the AAMC B/B Section Bank? The answer says the best way to distinguish between alternative splicing here is to do gel electrophoresis with the cDNA, amplifying with primers specific to exons 1 and 4. Is it just me or is the AAMC crazy for thinking that you're going to see the 3bp difference in size with gel electrophoresis?

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[Thoth]

If you run it long enough, you can see anything.

 

[DrHart]

I won't lie, going through the q packs and section bank... there are definitely a few really crappy questions. I remember this as one of them. I think this was a question where elimination of other answers was more useful.

You can rule out C and D because genomic DNA won't indicate where splicing takes place.
B was tough. Working with mRNA is hard (cDNA is more stable). If you probe for exon 3, you'll get a result for the 16 residue (exons 1, 3, 4) but a blank result for the 17 residue (exons 1, 2, 4).
With option A you can directly compare two band sizes (in theory, I know 3bp would take a long time to resolve). The point is you design the experiment to get positive data when both isoforms are present - not just positive data when one isoform is present and negative data when the other one is present.
****ty question imo

 

[LIC2015]

If you run it long enough, you can see anything.

This is not true at all.

The problem with conventional gel electrophoresis is that ethidium bromide and DNA run in opposite directions along the gel. Even the more modern DNA intercalating molecules like SYBR dyes won't stain for more than ~60 mins without running toward the negative terminal of the rig. Thus, there is only a relatively small window of time during which you can separate DNA, and no one can achieve 3bp resolution with a gel. You need sequencing technology to achieve that sort of precision.

 

[LIC2015]

View attachment 208267
Anyone else have issues with this problem on the AAMC B/B Section Bank? The answer says the best way to distinguish between alternative splicing here is to do gel electrophoresis with the cDNA, amplifying with primers specific to exons 1 and 4. Is it just me or is the AAMC crazy for thinking that you're going to see the 3bp difference in size with gel electrophoresis?

The question is ridiculous. I remember thinking the same thing when I saw it a few months ago.

 

[andelJ94]

I won't lie, going through the q packs and section bank... there are definitely a few really crappy questions. I remember this as one of them. I think this was a question where elimination of other answers was more useful.
View attachment 208283
You can rule out C and D because genomic DNA won't indicate where splicing takes place.
B was tough. Working with mRNA is hard (cDNA is more stable). If you probe for exon 3, you'll get a result for the 16 residue (exons 1, 3, 4) but a blank result for the 17 residue (exons 1, 2, 4).
With option A you can directly compare two band sizes (in theory, I know 3bp would take a long time to resolve). The point is you design the experiment to get positive data when both isoforms are present - not just positive data when one isoform is present and negative data when the other one is present.
****ty question imo

SMH, I hated this question and many of the AAMC questions are this awful or worse. They're not scientifically wrong, per se, just really roundabout and, to me, illogical.

With these questions I end up having to literally eliminate the wrong answers, in order to arrive at a final answer I may not understand, but at least I have found problems with the other choices. This one though. Choice B would work right? Though it would be tougher to perform.

My best reasoning (the AAMC explanations suck, WHY?????) is because the question explicitly asks for a test that would indicate the presence of both isoforms, and that is the ONLY thing that makes choice A correct and choice B incorrect.

Am I crazy?

 

[DrHart]

SMH, I hated this question and many of the AAMC questions are this awful or worse. They're not scientifically wrong, per se, just really roundabout and, to me, illogical.

With these questions I end up having to literally eliminate the wrong answers, in order to arrive at a final answer I may not understand, but at least I have found problems with the other choices. This one though. Choice B would work right? Though it would be tougher to perform.

My best reasoning (the AAMC explanations suck, WHY?????) is because the question explicitly asks for a test that would indicate the presence of both isoforms, and that is the ONLY thing that makes choice A correct and choice B incorrect.

Am I crazy?

That was why I ended up going with A.
A would (theoretically) show you both isoforms on one gel. B would only show you one (You can't assume that a sample that doesn't probe is the other isoform - because there is no proof.)

Agreed that AAMC explanations are trash. I worked on a lot of EK problems and felt like their explanations were great. Started on AAMC content and felt like the explanations were useless.

 

[andelJ94]

Thanks!