Chapter 20 - Eukaryotic Transcription

Question 1

What is required for eukaryotic transcription?

Answer 1

Chromatin must be in an open structure (non-condensed).
Promoter must be nucleosome-free.
Gene must include a core promoter and start point.
RNA Polymerase binds
Basal Transcription Machinery Binds
- Transcription factors that facilitate
binding of the RNA Polymerase to the
promoter.
- TFNX: N=Polymerase I, II, or III and
X=Unique Identifying Letter

Question 2

Transcription factors (generally)

Answer 2

Facilitate binding of the RNA Polymerase to the promoter.
TFNX:
N=Polymerase I, II, or III
X=Unique Identifying Letter

Question 3

Transcription factors (generally)

Answer 3

Facilitate binding of the RNA Polymerase to the promoter.
TFNX:
N=Polymerase I, II, or III
X=Unique Identifying Letter

Question 4

Enhancer

Answer 4

A cis-acting sequence that increases the utilization of
(most) eukaryotic promoters and can function in either
orientation and in any location (upstream or downstream)
relative to the promoter.

Question 5

Silencer (Repressor)

Answer 5

A short sequence of DNA that can inactivate expression of a gene in its vicinity.

Question 6

RNA polymerase I

Answer 6

Synthesizes 5.8S, 18S, and 28S rRNA in the nucleolus.

Question 7

RNA polymerase III

Answer 7

Synthesizes tRNA, 5S rRNA genes, small RNAs in the nucleoplasm.

Question 8

RNA polymerase II

Answer 8

Synthesizes hnRNA in the nucleoplasm; all RNA with the exception of those transcribed by RNA Polymerase I & III

Question 9

hnRNA

Answer 9

Heterogeneous nuclear RNA

Question 10

hnRNA

Answer 10

Heterogeneous nuclear RNA

Question 11

Promoter includes 2 components:

Answer 11

1. Core promoter

2. Upstream promoter element (UPE)

Question 12

Transcription from RNA Polymerase I promoter:

Answer 12

1. Upstream binding factor (UBF) binds the UPE
2. UBF wraps the DNA 360°
3. Recruits SL1 complex
4. RNAP I binds UBF/SL1 complex and initiates transcription

Question 13

SL1

Answer 13

Binds core promoter

Includes TATA binding protein (TBP)

Question 14

Upstream binding factor

Answer 14

Bind the Upstream Promoter Element (UPE)

Question 15

RNA polymerase III has two types of promoters:

Answer 15

1. Upstream promoters

2. Internal promoters

Question 16

Upstream promoters:

Answer 16

Consensus sequences upstream of the start point, bound by transcription factors

Analogous to RNA polymerase II-regulated promoters

Question 17

Internal promoters:

Answer 17

Consensus sequences located within the transcription unit

Supports initiation upstream.

Question 18

TFIIIC

Answer 18

binds downstream sites.
2. TFIIIB binds start point.
3. TFIIIC is removed from downstream
sites.
4. TFIIIB recruits RNAP III.

Question 19

TFIIIB

Answer 19

binds start point.

Question 20

TFIIIC

Answer 20

Binds downstream sites

Then removed from downstream sites

Question 21

TFIIIB

Answer 21

Binds start point
Removes TFIIIC
Recruits RNAP III

Question 22

TFIIIA

Answer 22

Binds downstream sites

Question 23

Basal transcription apparatus

Answer 23

RNA Polymerase II + basal transcription factors

Question 24

Core promoter:

Answer 24

The shortest sequence that enables binding of the basal transcription apparatus and initiation of transcription

Question 25

RNAP II Core Promoter:

Answer 25

- Initiator (Inr) - TATA box - Downstream Promoter Element (DPE)

Question 26

Initiator (Inr)

Answer 26

Short conserved sequence Py2CAPy5 at the start point.

Question 27

TATA box

Answer 27

A-T octomer 25 bp upstream of the start site that positions the RNAP II.

Question 28

Downstream Promoter Element (DPE)

Answer 28

Replaces TATA box

Question 29

TAF

Answer 29

TBP-associated factors

Question 30

TAF

Answer 30

TBP-associated factors

Question 31

TFIID

Answer 31

At RNAP II promoters, the TFIID serves as the positioning factor for RNAP and recognition of the promoter. Composed of TBP and TAFs Enables the binding of TFIIB

Question 32

TBP

Answer 32

Component of positioning factor that is required for RNAP (I, II, III) to bind core promoter. Binds TATA and TATA-less promoters with equal affinity. TBP binds the minor groove and forms a “saddle” around the DNA TBP widens the minor groove and bends-in towards the major groove

Question 33

TFIIB

Answer 33

``` Binds downstream of TFIID. Interacts with RNAP II at 2 points: • RNA exit site • Active center. Interaction with RNAP II orients the enzyme on the DNA ```

Question 34

TFIIB

Answer 34

``` Binds downstream of TFIID. Interacts with RNAP II at 2 points: • RNA exit site • Active center Interaction with RNAP II orients the enzyme on the DNA ```

Question 35

TFIIF

Answer 35

TFIIF and RNAP II are simultaneously recruited to the TFIID-TFIIB complex. TFIIF is bound to RNAP II prior to DNA localization of the enzyme. TFIIF guides RNAP II to and stabilizes it at the TFIID-TFIIB complex.

Question 36

TFIIE

Answer 36

Binds the basal apparatus. TFIIE is required to melt DNA to allow polymerase movement. Recruits TFIIH.

Question 37

TFIIH

Answer 37

- Helicase activity (DNA melting) which requires interaction with TFIIE. - Rapidly repairs damaged DNA to avoid RNAP II stalls. - Phosphorylates the C-terminal domain (CTD) of RNAP II (D)

Question 38

TFIIH

Answer 38

- Helicase activity (DNA melting) which requires interaction with TFIIE. - Rapidly repairs damaged DNA to avoid RNAP II stalls. - Phosphorylates the C-terminal domain (CTD) of RNAP II (D)

Question 39

Promoter clearance

Answer 39

Phosphorylation of the CTD is required for release the RNAP II from the promoter (or promoter clearance) Promoter clearance is required for elongation or transcription of the DNA template strand and extension of the RNA strand.

Question 40

What is required for gene transcription in eukaryotic cells?

Answer 40

Chromatin must be in an open structure (non-condensed). | Promoter must be nucleosome-free.

Question 41

Enhancer

Answer 41

An enhancer activates the promoter nearest to itself, and can be any distance either upstream or downstream of the promoter. Enhancers are the activating DNA sequence in close proximity to a gene promoter.

Question 42

Enhancer

Answer 42

An enhancer activates the promoter nearest to itself, and can be any distance either upstream or downstream of the promoter. Activate DNA sequence in close proximity to gene promoter. Usually work in cis with the promoter. Can be made to work in trans by promoter and enhancer via (1) a protein bridge or (2) interlocking two molecules. Bound by Co-regulatory Proteins called Activators or Repressors.

Question 43

Activators:

Answer 43

Complex of proteins that interact directly or indirectly | with the promoter to initiate gene transcription

Question 44

Repressors:

Answer 44

Complex of proteins that prevent gene transcription by | binding to an enhancer