Podcast
Questions and Answers
What is the nature of sigma dissociation from RNA Polymerase?
What is the nature of sigma dissociation from RNA Polymerase?
At which position downstream of the promoter does experimental evidence show σ may be bound to the core?
At which position downstream of the promoter does experimental evidence show σ may be bound to the core?
What is the purpose of Fluorescence Resonance Energy Transfer (FRET) in testing the σ cycle hypothesis?
What is the purpose of Fluorescence Resonance Energy Transfer (FRET) in testing the σ cycle hypothesis?
What occurs to the FRET efficiency when σ comes closer to the 3’end of DNA?
What occurs to the FRET efficiency when σ comes closer to the 3’end of DNA?
Signup and view all the answers
What is the role of the probe on σ in FRET?
What is the role of the probe on σ in FRET?
Signup and view all the answers
What is the consequence of σ changing its association with the core during elongation?
What is the consequence of σ changing its association with the core during elongation?
Signup and view all the answers
What is the effect of RNA polymerase on the DNA at the transcription start site?
What is the effect of RNA polymerase on the DNA at the transcription start site?
Signup and view all the answers
What is the characteristic of the bubble formed during transcriptional initiation?
What is the characteristic of the bubble formed during transcriptional initiation?
Signup and view all the answers
What is the consequence of local DNA melting at the promoter?
What is the consequence of local DNA melting at the promoter?
Signup and view all the answers
What is the function of RNA polymerase during transcriptional initiation?
What is the function of RNA polymerase during transcriptional initiation?
Signup and view all the answers
Study Notes
Protein Domains and Proteolysis
- Limited digestion of protein domains reveals that they resist proteolysis, while unstructured regions between domains are susceptible to digestion.
- The α subunit has two domains connected by an unstructured linker of approximately 13 amino acids.
Model for Function of the C-terminus of α Subunit
- In a core promoter, the C-terminus of the α subunit is not required for function.
- With a UP element present, the C-terminus contacts the element.
Elongation and RNA Polymerase Subunits
- Core polymerase continues to elongate RNA after initiation and σ has left the holoenzyme.
- RNA polymerase subunits can be separated and reconstituted to re-create an active enzyme.
- Combining subunits from different sources can help understand their functions.
- Core polymerase determines sensitivity to rifampicin.
β Subunit Function
- The β subunit is responsible for sensitivity to rifampicin.
- The β subunit also determines sensitivity to streptolydigin, an antibiotic that blocks elongation.
- The β subunit is involved in phosphodiester bond formation during elongation.
UP Element Recognition
- The α subunit of RNA polymerase recognizes the UP element.
- The C-terminal portion of the α subunit is required for recognizing the UP element.
DNase Footprinting Assay
- The DNase footprinting assay shows that the α subunit contacts the UP element.
α Subunit Structure
- The N- and C-terminal domains of the α subunit fold independently and are tethered together by a flexible linker.
Sigma Dissociation
- Sigma dissociation from RNA polymerase is a stochastic event that may not always occur after initiation.
- Sigma may remain weakly bound to the core during elongation.
FRET Analysis
- Fluorescence resonance energy transfer (FRET) can measure the position of σ relative to DNA without separation techniques.
- FRET analysis shows that σ may change its association with the core during elongation.
Local DNA Melting
- RNA polymerase causes melting of 10-17 base pairs at the transcription start site, creating a "bubble" that moves with the polymerase.
- This melting exposes the template DNA.
Studying That Suits You
Use AI to generate personalized quizzes and flashcards to suit your learning preferences.
Description
This quiz covers the structure and function of the α subunit in molecular biology, including its domains, proteolysis, and interactions with promoter elements.
