DNA to RNA Kaplan example wrong: please clarify AAMC expectations

[redsox90]

Hey everyone,

The question is:

What would be the corresponding RNA sequence of the following DNA sequence? Pretty standard discreet but it does not specify which is the template vs coding strand. In the real world and I am assuming on the MCAT(??), you ALWAYS ASSUME YOU ARE READING THE CODING STRAND which is COMPLEMENTARY to the TEMPLATE STRAND. The coding strand is also known as the RNA-LIKE strand b/c it makes it easier to read the mRNA template formed.

DNA : 5'-GATTCAAGTAGTC-3'
RNA: 5'-GACUACUUGAAUC-3' (Kaplan answer)
RNA: 5'-GAUUGAAGUAGUC-3' (Correct answer using the given DNA sequence as a coding strand)

This Kaplan example is wrong, the correct answer is A.
Kaplan would be correct if the 5' and 3' labels were switched.

I would appreciate it if someone could clarify what the expectation of the AAMC on the real MCAT is, i.e. if we are given a single stranded DNA sequence are we supposed to use a convention that does not reflect reality where we assume we are reading the template strand and not the coding strand?? This is what I am talking about if anyone is confused:

Also, the naming conventions for strands are annoying (sense, anti-sense, template, coding) does anyone know what the AAMC uses so as to avoid ambiguity?

Thank you very much, hope someone knows what the deal is here.

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[Czarcasm]

I'm sure every MCAT has (hopefully) been proofread to avoid ambiguity like this. This question should have clarified it was the non-coding template of DNA (sense strand) and likely, that'd be the case on the MCAT as well - so I wouldn't stress it. As you already realized, both replication and transcription occur in the 5' to 3' direction (which means, their template must be read in the 3' to 5' direction). Translation also has a polarity of 5' to 3' which corresponds to the synthesis of N to C terminus of the polypeptide chain.

The terminology sense, antisense, template, nontemplate can be very confusing and unfortunately it is used to throw some people off. Just realize the sense strand is non-coding; it's sense because the DNA sequence resembles the transcribed mRNA (which codes for a functional protein product). But this sense strand does not code for the mRNA because of the complementarity nature of base pairing. So instead, we use an antisense (coding) intermediate to get there.

 

[justadream]

@Czarcasm

Isn't the non-coding template strand the ANTIsense strand (not the sense strand)?

 

[Czarcasm]

@Czarcasm

Isn't the non-coding template strand the ANTIsense strand (not the sense strand)?

Argh, you're right! Glad you caught that. I always seem to make that silly mistake. I rarely see the words coding and non-coding so I was thinking in terms of transcription. As you pointed out though, coding is also used in the same way sense and antisense terms are used (to describe the relationship between DNA and mRNA bp 'info'). I guess it might help to realize that anti and non essentially mean the same thing.

 

[justadream]

@Czarcasm

But anyways I take it your point was that AAMC will usually provide the template/non-coding/antisense strand and to get the RNA, you just do the simple conversion.

 

[kraskadva]

Hey everyone,

The question is:

What would be the corresponding RNA sequence of the following DNA sequence? Pretty standard discreet but it does not specify which is the template vs coding strand. In the real world and I am assuming on the MCAT(??), you ALWAYS ASSUME YOU ARE READING THE CODING STRAND which is COMPLEMENTARY to the TEMPLATE STRAND. The coding strand is also known as the RNA-LIKE strand b/c it makes it easier to read the mRNA template formed.

DNA : 5'-GATTCAAGTAGTC-3'
RNA: 5'-GACUACUUGAAUC-3' (Kaplan answer)
RNA: 5'-GAUUGAAGUAGUC-3' (Correct answer using the given DNA sequence as a coding strand)

View attachment 184769

This Kaplan example is wrong, the correct answer is A.
Kaplan would be correct if the 5' and 3' labels were switched.

I would appreciate it if someone could clarify what the expectation of the AAMC on the real MCAT is, i.e. if we are given a single stranded DNA sequence are we supposed to use a convention that does not reflect reality where we assume we are reading the template strand and not the coding strand?? This is what I am talking about if anyone is confused:View attachment 184770

Also, the naming conventions for strands are annoying (sense, anti-sense, template, coding) does anyone know what the AAMC uses so as to avoid ambiguity?

Thank you very much, hope someone knows what the deal is here.

No... Actually Kaplan is right on this one.
And FYI, template=coding=sense strand.

The example you give is a pretty standard one, and on the MCAT you will likely see this type of question exactly as Kaplan presents it. They will give just the single strand, and it should be used as the template/coding/sense strand. What you're forgetting is that the 5'end of one matches to the 3' end of the other. However, convention is to always write 5'-3'. What this means for the test is that you read all answers backwards (make sure to check the end labels in case of trickery, but I've always seen it this way)

So...
DNA : 5'-GATTCAAGTAGTC-3'
RNA: 5'-GACUACUUGAAUC-3' (Kaplan answer)

DNA : 5'-GATTCAAGTAGTC-3'
RNA: 3'- CUAAGUUCAUCAG-5' (Kaplan answer written backwards)

 

[justadream]

@kraskadva

Just want to clarify:

Coding = Sense = NON-template strand.

"Wherever a gene exists on a DNA molecule, one strand is the coding strand (or sense strand or non-template strand), and the other is the noncoding strand (also called the antisense strand [antisense is a general term for a sequence of DNA or RNA that is complementary to mRNA],[1] anticoding strand, template strand, or transcribed strand)."

http://en.wikipedia.org/wiki/Coding_strand

 

[kraskadva]

I'm not going to argue with you.
Just don't make the blanket assumption that Kaplan has the wrong answer or that the MCAT has typos, because typically that's not true.
Learn to read/translate a DNA sequence. It's not that hard.

 

[redsox90]

Here's a CLC genomics workbench file (this is the standard program used in molecular biology) of the sequence of interest, then the same sequence translated into RNA. Its always read 5' to 3' so once again the Kaplan answer is actually by all standard/official conventions, technically wrong.
DNA

RNA


The 5' end of the mRNA that is transcribed from that sequence is GAUUCAA blah.

Think about it like this: PolII reads' 3-5 so that it can add 5'-3' If you think about the unwound template and PolII using that bottom strand as the strand to "decide" what RNA bases to add.

 

[kraskadva]

I have no idea what you're trying to show in that pic...
And why are you all missing the point? I don't care which one you want to flip around, but the 5' end of one has go to the 3'end of the other. Read the question tag strand backwards or read the answer backwards, but one of them has to flip. The Kaplan answer is correct.

 

[justadream]

@kraskadva

I believe the OP wishes to clarify which strand (the template or non-template) is the sequence provided in the original question.

The provided sequence is:
DNA : 5'-GATTCAAGTAGTC-3'

Now the question is: is that the template strand or the non-template strand?

If you take that to be the template strand (as you have done), then you will get:
TEMPLATE DNA : 5'-GATTCAAGTAGTC-3'
RNA: 5'-GACUACUUGAAUC-3' (Kaplan answer)

If you take that to be the non-template strand, then you will have:
TEMPLATE DNA: 5'-GATTCAAGTAGTC-3'
NON-TEMPLATE DNA: Complement of template DNA
RNA: Complement of the "Complement of template DNA". This is also answer choice A (OP's "correct" answer)

I hope the AAMC would be more clear about this but I think the question is: What's the AAMC convention?

 

[kraskadva]

Ah...okay....
The AAMC is asking you to give the complementary strand to the given sequence. ("What would be the corresponding RNA sequence of the following DNA sequence?") i.e. the DNA sequence given is the template strand. This is always the convention in practice tests, MCAT and IRL.

Taking the given DNA sequence to be the non-template strand would be highly unusual, and would require them to explicitly mention this (which I have never seen among hundreds of practice & real problems). OP is over thinking a very simple question.

 

[justadream]

Ah...okay....
The AAMC is asking you to give the complementary strand to the given sequence. ("What would be the corresponding RNA sequence of the following DNA sequence?") i.e. the DNA sequence given is the template strand. This is always the convention in practice tests, MCAT and IRL.

Taking the given DNA sequence to be the non-template strand would be highly unusual, and would require them to explicitly mention this (which I have never seen among hundreds of practice & real problems). OP is over thinking a very simple question.

I sure hope it's like this lol.