Eukaryotic transcription

Question 1

Types of RNA polymerase

Answer 1

type I in nucleolus
type II in nucleus produces mRNA and snRNA
type III in nucleus

Question 2

Archaeal/eukaryotic RNAP stalk

Answer 2

formed by heterodimer of E and F subunits
Interacts with nascent RNA transcript
Stimulates transcription processivity
Enables efficient termination
Recruits RNA-processing factors in eukaryotes

Question 3

RNA polymerase 2 promoters

Answer 3

Frequently have short conserved Py2CAPy5 sequence (initiator) at start point

Core promoter includes initiator and often TATA box or DPE
Elements bind regulatory proteins and determine site of pol2 assembly

Question 4

TATA box

Answer 4

Component of RNA pol 2 promoters
AT rich octomer upstream of start-point
Recognised by TATA-box binding protein (TBP)

Question 5

BRE element

Answer 5

TFII-B recognition element

Interacts with TFIIB

Question 6

DPE element

Answer 6

Downstream promoter element

Common in TATA-less promoters

Question 7

Eukaryotic promoter opening

Answer 7

Pre-initiation complex (PIC) forms

involves general transcription factors

Question 8

TBP/TFIID

Answer 8

TFIID core is TBP and 8 to 16 TBP associated factors (TAFs)

TBP binds to TATA box in minor groove and bends DNA 80 TO 90 degrees

TFIIA stabilises binding

Question 9

TFIIB

Answer 9

Enters PIC after TBP
Binds BRE element
zinc binding N-domain interacts with Pol2 and TFIIF to recruit Pol2
C domain interacts with DNA, TBP and Pol2

Question 10

TFIIF

Answer 10

Functions in initiation and elongation
Binds to Pol2
Suppresses non-specific Pol2 DNA binding (controls access to DNA binding channel)

Question 11

TFIIE

Answer 11

Recruits TFIIH
stimulates TFIIH CTD kinase and helicase activities
regulates Pol2 jaw opening and closing

Question 12

TFIIH

Answer 12

ATP dependent helicase activity
required for open complex formation
Core TFIIH also functions in nucleotide excision repair

Question 13

Sequence of TF and polymerase assembly

Answer 13

TBP/TFIID and TFIIA
TFIIB
TFIIF and RNA polymerase II
TFIIE
TFIIH
formation of transcription initiation complex

Question 14

RNA capping

Answer 14

7-methylguanosine caps added to 5’ end of eukaryotic RNA

Protects RNA from 5’ to 3’ exonucleases
required for export to cytoplasm
necessary for efficient translation

Question 15

Polyadenylation

Answer 15

100-250 nucleotide poly-A tail added to 3’ end of mRNA

Cleavage at polyA site followed by polyadenylation

Question 16

RNA polymerase II termination

Answer 16

Recruitment of CPF (cleavage and polyadenylation factor) complex

RNA cleavage and polyadenylation

Elongation complex dissociation