VCE Biology Question Thread

[cosine]

Welcome

Sounds fine to me, assuming you know basically how transcription factors work (which I'm sure you do).  P.S. here's where you could cut on your answers - avoid stuff like 'code for specific amino acids that serve to produce a functioning protein', just say 'code for a functioning protein'.

I am not 100% sure on how transcription factors work, just a little gap with the promoter region and etc. I will give a rundown of what I know, please fill in the gaps and unnecessary parts:

A DNA helicase unwinds the double standed DNA helix and RNA polymerase binds to the promoter region on this DNA template strand. Once binding, the RNA polymerase moves from the 3 prime to the 5 prime direction, simultaneously synthesising the mRNA transcript as complementary ribonucleotides are added onto the progressing mRNA strand. This is the part I don't get, what do the start and stop codons play a part in transcription? Is it just that as RNA polymerase moves along the promoter region, it will only start synthesising the mRNA molecule once it hits the start triplet? And likewise with the termination, once the RNA polymerase hits the stop triplet, the pre-mRNA transcript is complete and ready for post-transcription processing?

Also as the mRNA is being synthesised, when complementary nucleotides are added, they don't actually form hydrogen bonds with the complementary bases on the DNA, right? Do they just get 'attracted' to the DNA bases and form phosphodiester bonds with the adjacent nucleotides on the progressing mRNA transcript or?

Cheers.

[cosine]

My question involving spoilers on a VCAA 2013 question. Proceed at your own risk :p

Spoiler

On the 2013 VCAA exam I had an otherwise perfect answer talking about transcription but I said DNA helicase unravels and unwinds the DNA molecule. Before I marked it I read this thread and decided I would only give myself 1 out of the 2 available marks. Should I only get one mark or two for this question?

Knowledge is knowledge, now that you know DNA helicase unwinds DNA helices, you will probably not forget it, so I would say full marks because in future you will again put DNA helicase..

[katiesaliba]

It may be that in VCE they say it's RNA polymerase, but this is patently untrue. It's actually a so-called transcription factor called TFIIH (a DNA helicase) that unwinds the DNA strands.

(Image removed from quote.)

Hey guys,

Last year I emailed Andrew Douch (from Douchy's podcasts) about this question. Although Mr T-Rav is correct, you are not expected to know about transcription in this much detail for year 12. Instead, it is sufficient to state that RNA polymerase unwinds DNA and catalyses the anabolism of the pre-mRNA (also known as hnRNA) strand. 

[heids]

A DNA helicase unwinds the double standed DNA helix and RNA polymerase binds to the promoter region on this DNA template strand. Once binding, the RNA polymerase moves from the 3 prime to the 5 prime direction, simultaneously synthesising the mRNA transcript as complementary ribonucleotides are added onto the progressing mRNA strand. This is the part I don't get, what do the start and stop codons play a part in transcription? Is it just that as RNA polymerase moves along the promoter region, it will only start synthesising the mRNA molecule once it hits the start triplet? And likewise with the termination, once the RNA polymerase hits the stop triplet, the pre-mRNA transcript is complete and ready for post-transcription processing?

Also as the mRNA is being synthesised, when complementary nucleotides are added, they don't actually form hydrogen bonds with the complementary bases on the DNA, right? Do they just get 'attracted' to the DNA bases and form phosphodiester bonds with the adjacent nucleotides on the progressing mRNA transcript or?

Cheers.

You're going into too much depth there (that is, too much depth for me hahaha), I'm sure the stuff about hydrogen bonds is beyond the course. 

Re start and stop codons, they're related to translation not transcription.  Transcription starts at the promoter sequence on the DNA, and I'm not sure how it's stopped. (Stop showing up my ignorance! )  But start and stop is to do with when the translation into a polypeptide chain starts and stops.

On transcription factors, they're just proteins that make it harder or easier for the RNA polymerase to bind to the DNA - inhibiting factors make it harder, so transcription won't happen and the cell won't express the protein, and ones that promote/activate make it easier, so they basically start transcription happening.  I'd also know why we regulate gene expression.

My question involving spoilers on a VCAA 2013 question. Proceed at your own risk :p

Spoiler

On the 2013 VCAA exam I had an otherwise perfect answer talking about transcription but I said DNA helicase unravels and unwinds the DNA molecule. Before I marked it I read this thread and decided I would only give myself 1 out of the 2 available marks. Should I only get one mark or two for this question?

If in doubt, leave it out.

Basically, this is too much depth for VCE, so you're safer to leave it out as you never know when you'll make a mistake - and even if you have all the info to score full marks, an incorrect statement takes off a mark.  (Not commenting on this particular case, just in general).

[vox nihili]

I wouldn't say that RNA polymerase is what is taught as correct, rather that it's a common misconception among students.  Anyways, you wouldn't have to write either; you don't have to go into that level of detail on transcription (it's never mentioned in the assessors' reports I think, not totally sure).

Thanks for the clarification. Personally, I didn't know. Either way, that RNA polymerase unwinds DNA is patently untrue; it doesn't have a helicase domain.

Hey guys,

Last year I emailed Andrew Douch (from Douchy's podcasts) about this question. Although Mr T-Rav is correct, you are not expected to know about transcription in this much detail for year 12. Instead, it is sufficient to state that RNA polymerase unwinds DNA and catalyses the anabolism of the pre-mRNA (also known as hnRNA) strand. 

Thanks too for the clarification. Have missed you on this thread!

Don't call pre-mRNA hnRNA though; nobody uses that!

I am not 100% sure on how transcription factors work, just a little gap with the promoter region and etc. I will give a rundown of what I know, please fill in the gaps and unnecessary parts:

A DNA helicase unwinds the double standed DNA helix and RNA polymerase binds to the promoter region on this DNA template strand. Once binding, the RNA polymerase moves from the 3 prime to the 5 prime direction, simultaneously synthesising the mRNA transcript as complementary ribonucleotides are added onto the progressing mRNA strand. This is the part I don't get, what do the start and stop codons play a part in transcription? Is it just that as RNA polymerase moves along the promoter region, it will only start synthesising the mRNA molecule once it hits the start triplet? And likewise with the termination, once the RNA polymerase hits the stop triplet, the pre-mRNA transcript is complete and ready for post-transcription processing?

Also as the mRNA is being synthesised, when complementary nucleotides are added, they don't actually form hydrogen bonds with the complementary bases on the DNA, right? Do they just get 'attracted' to the DNA bases and form phosphodiester bonds with the adjacent nucleotides on the progressing mRNA transcript or?

Cheers.

Just to clarify, transcription:

DNA strand unwound (mysteriously)
RNA pol binds
New RNA strand

Then enter processing.

It really is that easy in VCE. In reality it's pretty simple too. As bangali_lok just said, TFs just help RNA pol get into the strand...among other things but we won't worry about that because I'll get carried away.

[Bruzzix]

And here we approach the limitations of the vce bio course..

[heids]

And here we approach the limitations of the vce bio course..

Yes, but they're necessary limitations.  Half the state don't know that a transcription factor or DNA helicase is even a thing.  Because you can always go deeper with Bio, even when you're years and years into uni, at every level you have to have a cut-off point.  VCE Bio is already more content-heavy than many other VCE subjects, and *most* people struggle to learn all that's in it already (as an average human bean, I certainly did).

[katiesaliba]

I am not 100% sure on how transcription factors work, just a little gap with the promoter region and etc. I will give a rundown of what I know, please fill in the gaps and unnecessary parts:

A DNA helicase unwinds the double standed DNA helix and RNA polymerase binds to the promoter region on this DNA template strand. Once binding, the RNA polymerase moves from the 3 prime to the 5 prime direction, simultaneously synthesising the mRNA transcript as complementary ribonucleotides are added onto the progressing mRNA strand. This is the part I don't get, what do the start and stop codons play a part in transcription? Is it just that as RNA polymerase moves along the promoter region, it will only start synthesising the mRNA molecule once it hits the start triplet? And likewise with the termination, once the RNA polymerase hits the stop triplet, the pre-mRNA transcript is complete and ready for post-transcription processing?  Yep. Don't worry about this too much, because you're not expected to know this in great detail. However, for interests sake, transcription also has a lot to do with factors (e.g. activators, enhancers, silencers, repressors) that regulate the process in eukaryotes. The promotor region is simply the site where the RNA polymerase binds, thus it determines where RNA synthesis will begin. The termination region is where RNA polymerase and the pre-mRNA molecule are released.

Also as the mRNA is being synthesised, when complementary nucleotides are added, they don't actually form hydrogen bonds with the complementary bases on the DNA, right? Do they just get 'attracted' to the DNA bases and form phosphodiester bonds with the adjacent nucleotides on the progressing mRNA transcript or? Hydrogen bonds will briefly form - hence, the attraction. A significant difference between RNA and DNA is the structure of the pentose sugar involved, not their associated nitrogenous bases (excluding thymine/uracil of course).

Cheers.

Thanks too for the clarification. Have missed you on this thread!

Don't call pre-mRNA hnRNA though; nobody uses that!

I've missed this thread! haha
See, I usually wouldn't. However, I came across the terminology in the sem 2 biol practice exam, so I'm trying to ingrain it in me.

[cosine]

Cheers. Sorry, getting carried away with this haha.. I can tell bangali lok is fainting inside at the depth of detail haha xD (forgive me, master).

SO as simple as:

- DNA unwinds
- RNA polymerase binds to promoter region
- RNA polymerase moves along the template DNA strand in the 3 prime to 5 prime direction
- As it moves along, complementary ribonucleotides are added onto the progressing mRNA transcript, synthesising it in the 5 prime to 3 prime direction
- When the transcription comes to a halt, the mRNA is release and is ready for post-transcription processing.

[grannysmith]

I've missed this thread! haha
See, I usually wouldn't. However, I came across the terminology in the sem 2 biol practice exam, so I'm trying to ingrain it in me.

Heeey!! Welcome back!

[katiesaliba]

Cheers. Sorry, getting carried away with this haha.. I can tell bangali lok is fainting inside at the depth of detail haha xD (forgive me, master).

SO as simple as:

- DNA unwinds
- RNA polymerase binds to promoter region
- RNA polymerase moves along the template DNA strand in the 3 prime to 5 prime direction
- As it moves along, complementary ribonucleotides are added onto the progressing mRNA transcript, synthesising it in the 5 prime to 3 prime direction
- When the transcription comes to a halt, the mRNA is release and is ready for post-transcription processing.

The DNA doesn't unwind before RNA polymerase is bound though. To directly quote my lecture: "RNA polymerase binds and DNA is denatured in this region. DNA strands separate".  The ribonucleotides would then be added.
Also, make sure you write pre-mRNA. Other than that, all good!

Heeey!! Welcome back!

Hey hey! 

[Biology24123]

Cheers. Sorry, getting carried away with this haha.. I can tell bangali lok is fainting inside at the depth of detail haha xD (forgive me, master).

SO as simple as:

- DNA unwinds
- RNA polymerase binds to promoter region
- RNA polymerase moves along the template DNA strand in the 3 prime to 5 prime direction
- As it moves along, complementary ribonucleotides are added onto the progressing mRNA transcript, synthesising it in the 5 prime to 3 prime direction
- When the transcription comes to a halt, the mRNA is release and is ready for post-transcription processing.

Swap 1st and 2nd step

[cosine]

Swap 1st and 2nd step

How can RNA polymerase bind to promoter region if the helix has not been unwinded? o.O

[katiesaliba]

How can RNA polymerase bind to promoter region if the helix has not been unwinded? o.O

http://www.mun.ca/biology/desmid/brian/BIOL3530/DEVO_10/ch10f03.jpg

[vox nihili]

I've missed this thread! haha
See, I usually wouldn't. However, I came across the terminology in the sem 2 biol practice exam, so I'm trying to ingrain it in me.

Hmmm Dawn's (yes?) trolling I think.

How can RNA polymerase bind to promoter region if the helix has not been unwinded? o.O

All complicated, in VCE Biology you'd get away with either one.


Actual reason is because of the order of things binding to the strand. A lot of TFs facilitate the binding of RNA pol to the DNA.