Introns and Exons

[i61164]

I am working on a question that is really bothering me...

I won't post the exact question since it's probably against some copyright law, but it deals with a hypothetical gene. According to the answer key, the gene in question looks like this:

3'---start codon---(5' untranslated region)---1st intron---1st exon---etc.---5'

I don't know why they think that the 1st intron comes before the 1st exon. Everything I have seen shows it the other way around. The question is really convoluted, but it boils down to "What is downstream of the 1st exon?" I thought it was the 5' untranslated region, but they say it's the 1st intron. Also up for debate is my understanding of the term "downstream." Even though DNA is read 3' to 5', upstream and downstream should be based on how it is synthesized 5' to 3', so downstream is toward the 3' end (and closer to the start codon of the gene).

What do you guys think (besides the obvious that this question is just crap)?

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[fakin' the funk]

I am working on a question that is really bothering me...

I won't post the exact question since it's probably against some copyright law, but it deals with a hypothetical gene. According to the answer key, the gene in question looks like this:

3'---start codon---(5' untranslated region)---1st intron---1st exon---etc.---5'

I don't know why they think that the 1st intron comes before the 1st exon. Everything I have seen shows it the other way around. The question is really convoluted, but it boils down to "What is downstream of the 1st exon?" I thought it was the 5' untranslated region, but they say it's the 1st intron. Also up for debate is my understanding of the term "downstream." Even though DNA is read 3' to 5', upstream and downstream should be based on how it is synthesized 5' to 3', so downstream is toward the 3' end (and closer to the start codon of the gene).

What do you guys think (besides the obvious that this question is just crap)?

The gene is always set up so that it starts 5' and ends 3'. The TATA box is 5' to the transcription start site. Just note that the RNAP actually reads the COMPLEMENTARY strand in a 3' to 5' direction, synthesizing the nascent RNA transcript 5' to 3', to create an exact copy of the "coding" strand, only in RNA form. This might clear up part of the confusion.

 

[i61164]

That is a good point, what I have drawn is the template strand. In the answer key to the problem in question it says "The 5'UTR should be located immediately upstream of the translation start codon," which only makes sense to me if they are talking about upstream on the template strand.

5'UTR refers to an untranslated region of mRNA which looks like this:

5' cap---5'UTR---coding sequence---3'UTR---poly A tail

The coding strand would look the same:

5'---start codon---5'UTR---coding sequence---3'UTR---3'

Like I said, the problem is convoluted, but basically there is a mutation in the 5'UTR region of the gene (disease gene). It turns out that there is also another gene on the complementary strand (gene X). The start codon of the disease gene lines up with the end of the first exon of gene X. Which part of gene X lines up with the mutation? Answer: the first intron of gene X.

 

[ertugrul]

Also up for debate is my understanding of the term "downstream."

Sorry for illustration but it's best that I can do
Note: dots are background, I had had to put them otherwise it ignores spaces and aligns all to left

...UPstream<--->DOWNstream................................................................
....................|.......................................................................................
....................|.......................................................................................
....................|-------------------------->Transcription starting point.............
....................|.......................................................................................
5'---|Promoter|===========|----------3' : Coding (antitemplate) strand.........
3'---|..region..|===========|----------5' : Template strand.........................
.............................................................................................................
.............................||.............................................................................
.............................||.............................................................................
...................TRANSCRIPTION....................................................................
.............................||.............................................................................
.............................\/.............................................................................
............................................................................................................
...................5'===========3' : mRNA..........................................