Steps of Transcription

simsimjoey
Posts: 9
Joined: Wed Nov 22, 2017 9:59 am

Steps of Transcription

Postby simsimjoey » Wed Dec 13, 2017 2:49 am

Hi,

I'm currently studying biochemistry part and I am a bit frustrated about steps of transcription.

The review book states that for transcription to occur, the DNA helicase should be involved. But, campbell text book I'm using mentions initiation of transcription occurs with RNA polymerase binding to promoter with the help of transcription factor, which unwinds the DNA strands and initiates RNA synthesis as well.

So the questions are...

1. Which one is correct?
2. If the textbook is correct, how can RNA polymerase recognize promoter region in the first place if it's not unwinded? Would it be hard to recognize because bases are not revealed?
3. RNA pol, like DNA pol, requires a 3' end to function, yet there isn't any mentioning of primase being involved. Is it implied? and if so, are the primase used in replication and transcription the same?

Thanks in advance,

Joey
NS_Tutor_Sophia
Posts: 13
Joined: Tue Aug 01, 2017 11:49 am

Re: Steps of Transcription

Postby NS_Tutor_Sophia » Wed Dec 13, 2017 10:28 am

Hi simsimjoey, great question! There are some differences--but also some commonalities--between transcription and translation, and it can get pretty confusing! It turns out that both are indeed correct, and neither is mutually exclusive.

1 - First, we need DNA helicase to unwind the double helix because you're right, RNA polymerase can't access the DNA and transcribe if can't "fit" between the two antiparallel strands of DNA.
2 - RNA polymerase can now access the promter, so it binds there with help of transcription factors (in eukaryotes). Transcription factors can bind enhancer sequences to increase transcription (if they are activators) or silencer sequences to block transcription (if they are repressors), and enhancer and silencer sequences can be either upstream or downstream of the promoter, even thousands of nucleotides away!

Transcription, unlike DNA replication, does not require a primer or a primase enzyme. DNA primase is techincally a type of RNA polymerase, if you think about it, that synthesizes an RNA primer when there isn't a 3' -OH group available...but this is only true for DNA polymerase during DNA replication. DNA polymerase always requires a 3' -OH group to continue to synthesize DNA in the 5' to 3' direction, so it requires an RNA primer to start. That's where DNA primase comes in: it synthesizes a short RNA primer that ends in a 3' -OH group so now DNA polymerase can jump in and continue replicating the DNA. However, RNA polymerase does NOT require a 3' -OH group to initiate synthesis of RNA - this explains why DNA primase (a type of RNA polymerase) can lay down an RNA primer without the help of another primer, and this is also why RNA polymerase can initiate transcription without an RNA primer.

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What may be confusing here is that RNA polymerase CAN (and will :) ) initiate transcription in the absence of a 3' -OH group...but they synthesize in 5' to 3' direction, just like DNA polymerase does, so once RNA polymerase generates that very first nucleotide, it will catalyze a phosphodiester bond between the 3' end of that very first nucleotide and the 5' end of the next, and continue until it's transcribed the entire pre-mRNA product. As a result, pre-mRNA doesn't have a "primer" sequence that is distinct from the rest of the molecule.

In general, the level of detail that is in a biology textbook will be much greater than tested on the PCAT. It's a great way to build a strong foundation in molecular biology, but you can rely on your Review Book to understand any of the topics you will actually see tested on Test Day. Does this help?
Sophia Stone
PCAT Content Manager
Next Step Test Prep
simsimjoey
Posts: 9
Joined: Wed Nov 22, 2017 9:59 am

Re: Steps of Transcription

Postby simsimjoey » Wed Dec 13, 2017 12:46 pm

Thank you for your help. However, this part i'm not too sure of
this explains why DNA primase (a type of RNA polymerase) can lay down an RNA primer without the help of another primer, and this is also why RNA polymerase can initiate transcription without an RNA primer


What do you mean without the help of another primer...? Otherwise, I think I got it.
NS_Tutor_Sophia
Posts: 13
Joined: Tue Aug 01, 2017 11:49 am

Re: Steps of Transcription

Postby NS_Tutor_Sophia » Wed Dec 13, 2017 12:58 pm

What is meant by that is that DNA primase can lay down an RNA primer without requiring attachment to any other pre-formed sequences. Whereas DNA polymerase requires a primer to add nucleotides, DNA primase does not require a primer before it adds nucleotides (that then form a primer for DNA synthesis). In other words, DNA primase can synthesize a primer without any "help" from a 3' -OH group, just like any other type of RNA polymerase can synthesize a new strand of ribonucleotides without a having a free 3' -OH to start.
Sophia Stone
PCAT Content Manager
Next Step Test Prep

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