Help w/ FA 2010 biochem p. 72

[WashMe]

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OK so I admit that I've forgotten biochem and I'm having trouble understanding a figure on pg. 72 of FA.

Under "Functional organization of the gene," what are they representing? It seems like DNA because it has "T" instead of "U" and it is showing promoter, enhancer, etc., however it is written in the 5'-->3' direction. Shouldn't it be written in 3'-->5' direction (i.e., the direction that RNApol2 will read it)? Also, assuming it is 3'-->5', how does AATAAA yield AAUAAA in the resultant mRNA, allowing for polyadenylation?

My only guess is that they aren't showing the template DNA strand, but are showing the irrelevant strand (the one complementary to the one that is actually transcribed) for some reason. FA doesn't address this in the errata, so I'm probably just confused.

Thanks! 🙂

 

[WashMe]

bump. I now don't think this is the "non-template" DNA strand, because I thought the TATA base sequence was on the actual template strand... ideas?

 

[hoqhuuep]

I'm not sure about all of it, but I can clarify this one point...

coding strand = non-template strand = AATAAA
non-coding strand = template strand = TTATTT

messenger RNA gets "pressed" off of template strand = AAUAAA

 

[WashMe]

I'm not sure about all of it, but I can clarify this one point...

coding strand = non-template strand = AATAAA
non-coding strand = template strand = TTATTT

messenger RNA gets "pressed" off of template strand = AAUAAA

ahah! Thanks, this makes sense to me. I guess my only other questions is:

Does RNApol (or TBP) recognize the TATA box on the coding strand, even though it is not operating on that strand?

 

[hoqhuuep]

I could be wrong, but my understanding was that the TATA box was just a bunch of A's and T's upstream on both strands, as they're complementary anyways.

RNApol just looks for whatever melts easiest, and since that implies A:T (C:G shares 3 H bonds, A:T shares 2), its specificity isn't tied to a specific sequence but rather a lower binding strength.