Basic Transcription Part 5 Flashcards Preview

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Flashcards in Basic Transcription Part 5 Deck (27):
1

shine-delgarno sequence

- now called ribosome binding site
- helps first ribosome bind and translate message

2

which step is the most difficult

- initiation

3

prokaryotic transcription unit

- polycistronic
- >1 gene included on transcript
- >1 start site and stop site

4

Type I RNA polymerase

- pre-rRNAs for 18, 5.8 and 28S rRNAs

5

Type II RNA polymerase

- pre-mRNA
- some snRNAs

6

Type III RNA polymerase

- pre-tRNAs
- 5S rRNA
- some snRNAs

7

what transcribes most protein coding genes

Type II RNA pol

8

organization of prokaryotic transcription unit

- Shine Delgarno
- Translation start codon
- Translation stop codon

9

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

10

what is the cleft lined with

- basic amino acids to bind DNA

11

4 mobile elements

- Core
- Clamp
- Shelf
- Jaw Lobe

- move relative to each other as transcription takes place

12

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

13

Shelf and Jaw Lobe

- move relatively little and can rotate parallel to the active site cleft

14

Clamp

- connected to the core through a set of flexible switches
- moves with a large swinging motion to open and close cleft

15

TFIID

- binds TATA box

16

TFIIB

- positions enzyme correctly for initiation - bridges TFIID and enzyme

17

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

18

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

19

3 loops of clamp

- zipper
- rudder
- lid

20

zipper

- initiates dissociation of template DNA

21

rudder

- initiates dissociation of RNA-DNA hybrid

22

lid

- maintains dissociation as RNA chain grows

23

bridge helix and template strand

- positions template strand for decoding

24

bridge helix

- oscillates between straight and bent

25

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

26

during translocation

- bridge helix shifts to bent state

27

when it shift back to straight state

- reopens space at 3'-end of RNA