Ls3-Ch12 Transcription

Front 1

01: What is the primary enzyme of transcription?

Back 1

RNA POLYMERASE II

Front 2

02: How big is the bubble that RNA Pol opens up?

Back 2

1.5 turns

Front 3

03: General Steps of transcription

Back 3

INITIATION
ELONGATION
TERMINATION

Front 4

04: What is a problem at the start of transcription?

Back 4

Errors in base pairing are common at the beginning

RNA POL puts in 8-12 bp at the start to stabilize it, then goes much faster

Front 5

05: what is the region where RNA Pol binds?

Back 5

PROMOTER

Front 6

06: What s the CONSENSUS SEQUENCE?

Back 6

best sequence for RNA Pol binding

Front 7

07: What are the regions for RNA Pol binding in E. Coli?

Back 7

UPSTREAM PROMOTERS

-10, -35, UP ELEMENT

Front 8

08: What binds to the promoters in E. Coli?

Back 8

σ Factor-binds -10, -35 regions

αCTD subunit binds UP ELEMENT

Front 9

09: How can RNA production be increased in E. Coli?

Back 9

binding of one RNA Pol recruits others

Front 10

10: Are the -10 and -35 site on the same or different sides of DNA?

Back 10

SAME: are 20 bp apart

Front 11

11: What base pairs are at the -10 and -35 site?

Back 11

-10: TATA box
-35: TTGACA

Front 12

12: What is the ISOMERIZATION of RNA Pol?

Back 12

moves from CLOSED to OPEN: positions the active site in an open DNA bubble.

forms channels for DNA and RNA to leave the cell

Front 13

13: what is the primer for transcription?

Back 13

NO PRIMER! RNA Pol makes its own in the beginning. goes very slowly since errors are common and possible

Front 14

14: describe TERMINATION

Back 14

RHO DEPENDENT: Rho protein recognizes certain DNA sequence, terminates, then RNA falls off

RHO INDEPENDENT: "intrinsic terminators." DYAD SYMMETRY: RNA forms a hairpin loop of G-C, followed by UUUUUU.
Hairpin forms spontaneously, pulls UUUU section out of polymerase

Front 15

15: Why is Eukaryotic transcription more complex?

Back 15

lots of GENERAL TRANSCRIPTION FACTORS needed to initiate vs only σ factor in prokaryotes

Front 16

16: How did we determine the main transcription factor for eukaryotes?

Back 16

took mushroom cells, burts, ran column to separate proteins.

Found three peaks of RNA Pol activity.

added ALPHA AMARATIN: stops transcription in RNA Pol II, all synthesis stopped, therefore it is main enzyme

Front 17

17: What is the name of the promoter in Eukaryotes? What are its parts?

Back 17

POL II CORE PROMOTER: made of various DNA ELEMENTS:

BRE, TATA (tata box), INR (initiator element), DPE (downstream promoter)

these are the MINIMUM sequence needed to start transcription

Front 18

18: What is formed right before transcription in Eukaryotes?

Back 18

PRE-INITIATION COMPLEX: RNA Pol binds to general transcription factors.

Front 19

19: Steps of eukaryotic transcription initiation

Back 19

1: TFIID with TBP region binds to TATA BOX. other regions are TAF (association factors)

2: TBP bends DNA.

3: TFIIB+TFIIA bind to TBP

4: TFIIF associates w/ Pol II, guides Pol onto DNA

5: TFIIE binds, recruits TFIIH which KINASES Pol from closed to open.

PRE-INITIATION COMPLEX is now formed

Front 20

20: In Eukaryotic initiation, what is the first thing that binds. what are its parts? Where does it bind?

Back 20

TFIID: has TATA BINDING PROTEIN (TBP) and TATA ASSOCIATION FACTORS (TAF).

binds to TATA BOX

Front 21

21: What does the TBP do?

Back 21

BENDS the DNA

Front 22

22: What happens after TBP?

Back 22

TFIIB+TFIIA bind

Front 23

23: What happens after TFIIB and TFIIA?

Back 23

TFIIF associates w/ Pol II, guides it onto DNA

Front 24

24: What happens after Pol II binds to DNA?

Back 24

TFIIE binds, recruiting TFIIH which kinases Pol II from closed to open

Front 25

25: What other factors help regulate transcription in eukaryotes?

Back 25

ACTIVATORS/REPRESSORS: bind to DNA, recruit Pol II

MEDIATOR: many subunits, bound to several activators. bind to Pol, TFIIB. associate with Pol II TAIL

CHROMATIN REMODELERS: also act...

Front 26

26: What binds during elongation?

Back 26

initiation factors drop off, new ones bind to C-TERMINAL TAIL of RNA Pol

Front 27

27: Describe elongation

Back 27

CAPPING ENZYME: puts 5' cap on first RNA end made. protects end

SPLICING ENZYME: removes introns, keeps exons

CLEAVAGE FACTORS: signal cleavage

Front 28

28 What are the general regions of mRNA? (from 5' to 3')

Back 28

5' Cap

5' Untranslated Region (UTR)

CODING region

3' UTR

AAA Tail (polyA)

Front 29

29: What is the name for the Pol II Tail? what is on it in elongation?

Back 29

CTD TAIL

is PHOSPHORYLATED.

CAPPING ENZYME, SPLICING ENZYME, CLEAVAGE FACTOR

Front 30

30: What happens to histones in elongation? (Eukaryotes)

Back 30

just like replication.

2A-2B removed, Tetramer put to the side.

histones removed briefly, reformed immediately.

Chaperones help.

Front 31

31: Describe RNA capping

Back 31

RNA TRIPHOSPHATE: cuts phosphate at 5' end, getting rid of Gamma Phosphate on A

GUANYLTRANSFERASE: connects 5' phosphate of A to 5' phosphate of G. is unnatural, and hard to degrade

METHYLTRANSFERASE: methylates G

Front 32

32: What happens to the 3' end of the RNA?

Back 32

POLYADENYLATION:

CstF (cleavage stimulation factor) and CPSF (Cleavage Polyadenylation Specificity Factor) transferred from CTD Tail to a specific sequence, causing RNA to be cut.

POLY A POLYMERASE: attaches to free 3' end, adds 1-200 AAA's

POLY-A BINDING PROTEIN: binds, helps tail form and stabilize.