Transcription Initiation and Elongation Flashcards
What is the catalytic site of RNA Polymerase? What happens at this site?
The site in which the template strands enters.
o mRNA and DNA hybrid
o The coding strand is sequestered away from the catalytic site
What is the winding point of RNA Polymerase? What happens at this site?
o Re-annealing of DNA
What enzyme is responsible for the unwinding of DNA?
Helicase
What enzyme is responsible for the re-annealing of DNA?
Topoisomerase
What creates the transcriptional bubble? How does it move?
• DNA is melted (helix dissociated)
o The bases are unpaired, creating the bubble
• The bubble moves along the strand by Pol movement
What is the unwinding point? What happens at this point?
• Unwinding point: at the edge of Pol
o Separation of coding and template strands
What is the main component of RNA polymerase?
Holoenzyme
Which types are RNA are synthesized by RNA polymerase?
• All RNA is synthesized by the same Pol
o mRNA, tRNA, rRNA
What is the holoenzyme?
about 460 kDA o Initiation complex o Has 2 functional components 1. Core enzyme 2. σ subunit (σ factor)
What is the core enzyme?
o About 400 kDa o Made of multiple subunits: α2ββ’ω o Involved in all stages of transcription o α 1. Required for core assembly 2. CTD: C-terminal domain 3. Binding interactions with DNA and regulatory proteins o β and β’: catalytic site o ω: core assembly
What is the role of the β and β’ subunits of the core enzyme?
Catalytic site
What is the role of the ω subunit of the core enzyme?
Core assembly
What is the σ factor?
o Promoter recognition and binding
o More variable than core enzyme
What happens if RNA Pol doesn’t bind the promoter?
Non-sensical RNA is synthesized
What are the features of RNA Pol and DNA for transcription initiation to occur?
RNA Pol needs to precisely recognize and bind only the promoter sequence
o Requires high binding affinity
o Very limited DNA sequence
What are the features of RNA Pol and DNA for transcription elongation to occur?
o Elongation requires low binding affinity to allow for constant binding and release
o Needs to recognize all DNA sequences
What is the holoenzyme dilemma?
Initiation: - High binding affinity - Need to recognize very limited DNA sequence Elongation - Low binding affinity - Need to recognize all DNA sequences
What is the solution for the holoenzyme dilemma?
reversible association of the σ factor with the core enzyme
o Core enzyme is responsible for elongation
Too generalized for specific promoter recognition
o σ factor has a high binding affinity for promoter
Only recognizes promoter sequence
σ binds to promoter only after binding the core
α subunit of the core enzyme facilitates promoter recognition
What is the closed binary complex?
σ bound but DNA wound
o Holoenzyme + DNA
What is the open binary complex?
σ bound and DNA has unwound
o Holoenzyme + DNA
What is the ternary complex?
There is RNA (aborted transcripts)
o As long as σ is bound to the core, the core cannot move forward
o As RNA is synthesized, it is aborted, until σ is released
o Holoenzyme + DNA + RNA
What is the ternary elongation complex?
Core, DNA, RNA
When does initiation end?
As σ is released
