Rodgers 03-26 Flashcards
Where can one find single subunit RNAPs?
viruses, mitochondria, chloroplasts
How is the core enzyme defined in RNAP? How is holoenzyme defined?
core= containing beta, beta’ subunits (together with alpha’ alpha” and omega). holo= containing the sigma factor
Where does sigma interact with the DNA
at the -10 and -35 promoter elements
How do eukaryotic and archeal RNAPs differ from bacteria
more subunits (from more TF interactions)
how many regions in sigma factor
4
What inorganic ion is needed for catalysis at the RNAP active site
Mg++
How do elements of the eukaryotic and archea RNAP regulate transcription
Through their interaction with the growing RNA strand
describe the common active site motif of RNAP
the Asp residues in each beta barrel coordinate Mg++ ions that bind PP on the new NTP, catalyze the 3’OH attack on the new NTP
describe the catalytic cycle
1) bridging helix tightly bind P of the new NTP 2) trigger loop conformation change the closes the active site, binding other two P’s 3) PPi released, trigger loop returns to more distant conformation the translocate the DNA
how does RNAP perform backtracked endonuclease activity
when the RNA enters the substrate entry/exit site, it pulls internal RNA back to the active site for PPi or H2O attack
How does the RNAP escape the promoter
by building enough force in the open DNA to make the scrunched initiation complex before elongation complex is free
Participants in the DNA translocation mechanism
fork loop, rudder, bridge and trigger
Why must RNAPs pause when a nucleosome is encountered
must wait for thermodynamic loosening of the DNA from the histone- may take longer depending on the modifications present on the histone
rho-independent termination
secondary structure of RNA (stem loop) forces the DNA to close and RNAP falls off. Aided by secondary structure binding proteins.
rho-dependent termination
C-rich RNA sequences are bound by rho helicase, which translocates toward the RNAP until forced termination
