Basic Transcription Part 5 Flashcards
shine-delgarno sequence
- now called ribosome binding site
- helps first ribosome bind and translate message
which step is the most difficult
- initiation
prokaryotic transcription unit
- polycistronic
- > 1 gene included on transcript
- > 1 start site and stop site
Type I RNA polymerase
- pre-rRNAs for 18, 5.8 and 28S rRNAs
Type II RNA polymerase
- pre-mRNA
- some snRNAs
Type III RNA polymerase
- pre-tRNAs
- 5S rRNA
- some snRNAs
what transcribes most protein coding genes
Type II RNA pol
organization of prokaryotic transcription unit
- Shine Delgarno
- Translation start codon
- Translation stop codon
compare the subunit composition of E coli RNA polymerase with eukaryotic RNA polymerase II.
- E. coli has 2 alpha’s, 1 beta, 1 beta’ and one omega
- RNA pol II has 12 subunits
what is the cleft lined with
- basic amino acids to bind DNA
4 mobile elements
- Core
- Clamp
- Shelf
- Jaw Lobe
- move relative to each other as transcription takes place
Core
- RPB 3, 10, 11, and 12 and regions of RPB 1 and 2 form active center
- comprised mainly of subunits common to all cellular polymerases
Shelf and Jaw Lobe
- move relatively little and can rotate parallel to the active site cleft
Clamp
- connected to the core through a set of flexible switches
- moves with a large swinging motion to open and close cleft
TFIID
- binds TATA box
TFIIB
- positions enzyme correctly for initiation - bridges TFIID and enzyme
elongation complex
- clamp closed over template and RNA product
- DNA-RNA hybrid at an angle to downstream DNA
- forced by closing of clamp and facilitated by ssDNA between hybrid and downstream DNA
organization of elongation complex
- Mg2+ positioned to bind to phosphate linking nucleotides +1 and -1
- base of nucleotide +2 points upward
- base of nucleotide +1 points down to pair with last nucleotide added to RNA chain
- 90 degree twist of DNA
3 loops of clamp
- zipper
- rudder
- lid
zipper
- initiates dissociation of template DNA
rudder
- initiates dissociation of RNA-DNA hybrid
lid
- maintains dissociation as RNA chain grows
bridge helix and template strand
- positions template strand for decoding
bridge helix
- oscillates between straight and bent
bridge helix in straight conformatin
- active site open for nucleotide addition
- pol adds new nucleotide, filling in space between 3’ end of RNA and straight bridge helix
during translocation
- bridge helix shifts to bent state
when it shift back to straight state
- reopens space at 3’-end of RNA
