I am studying for my third biochemistry midterm, and there are a few questions w

Question

I am studying for my third biochemistry midterm, and there are a few questions within his slides in his powerpoint lectures I am not able to 100% explain and I cannot find their explanation online to a degree I feel would be what he is looking for as far as an exam response. If you could help explain this to me that would be much appreciated! Thank you!

Question 1 I need clarification on: Explain the functions of RNAP II’s CTD, clamp, wall, funnel, rudder, bridge, and trigger.

(for question 1 I was able to find a somewhat explanation of this, but it included terms like "lid" and "zipper" which my instructor did not specify in his powerpoint, so I am unsure how that relates or if it's something different. Please use the terms listed above for the explanation just to help make things clear for me)!

Questinon 2 I need clarification on: Explain why both the sequence and structure of DNA help recruit RNA polymerase.

(I kind of understand that the structure of the RNA is reflected by it's "complement" DNA strand, but I don't really understand how to properly explain how sequence and structure of DNA helps to recruit RNA Polymerase).

Thank you so much for any assistance you can provide! I greatly appreciate it!

Explanation / Answer

1. RNAP II's CTD or the carboxy terminal of RNA Polymerase II helps a variety of nuclear factors for their flexible binding scaffold. It serves as a substrate for nuclear Abl tyrosine kinase. Inclusion of various nuclear proteins for elongation of RNAP II complex requires phosphorylation of CTD.

The clamp or mobile domain serves to control access with the help of double stranded promoter DNA to the active site. It is at first in open state so as to reach RNAP II active site. The clamp then changes to closed state after effectively placing r clamping DNA in requisite place.

Wall - The active site of RNAP II is present at the bottom a deep cleft which is blocked by a domain called 'wall' of upstream end.

Funnel is the most conserved part of NTPwhich needs loading of NTP. It serves tracking of active center trigger loop and blocks elongation of mRNA.

Rudder serves in stabilization of nascent RNA in RNAP elongation complex by the help of various protein-RNA interactions. Reassociation of exiting RNA is prevented by rudder loop.

Bridge is the key component that coordinates module movement in RNAP.

Trigger helices helps in contact with NTP substrate in a NTP bound substrate complex. They facilitate helix distortions which is required for RNAP function.

The second loop is called lid. Lid serves as a wedge which drives apart both DNA and DNA strands near upstream part of transcription bubble. The third loop is called zipper. Both help in maintaining of transcription bubble at the upstream end.

2. The enzyme required for invivo transcription is RNA Polymerase. It copies the DNA sequence into RNA in transcription. When information from DNA is copied into messenger RNA, it controls the process of transcription. It helps in expressing correct genes in the required body cells.

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