DNA-dependent synthesis of RNA Eukaryotic Transcription

Question 1

Central Dogma

Answer 1

• nucleic acids store information
  DNA transcription = RNA
  RNA translation = proteins

Question 2

T or F: RNA can hybridize with DNA genome

Answer 2

TRUE; T or F: RNA can hybridize with DNA genome

Question 3

Differentiate transcription vs replication

Answer 3

Transcription:
- only specific genes at one time = only portions are transcribed
- one strand

Replication:
- both strands of DNA are replicated
- whole strand is replicated

Question 4

Which strand is used by RNA polymerase to synthesize RNA from DNA ‘bubble’ ?

Answer 4

Antisense (non-coding) strand
- complementary to coding strand
- produces RNA product that is similar to coding strand

Question 5

Different cell types have __ DNA genomes but vary __ of genes from cell to cell

Answer 5

Different cell types have SIMILAR DNA genomes but vary EXPRESSION of genes from cell to cell

Question 6

Why is RNA Polymerase II important in synthesis processes ?

Answer 6

• synthesizes all proteins in higher cells
• largest polymerase (12 subunits)
• serines in sequence are susceptible to covalent modification
• active site holds DNA

Question 7

Which polypeptide chains make up the active site in RNA Polymerase II ? What is the substrate for the active site ?

Answer 7

B’ homolog and B homolog
- dsDNA (substrate) is separated in a transcription bubble

Question 8

Phases of transcription (4):

Answer 8

1. Assembly
2. Initiation
3. Elongation
4. Termination

Question 9

Sequence selectivity is needed for __

Answer 9

ELONGATION not initiation

Question 10

What are eukaryotic promoters ? What is their purpose ?

Answer 10

• integrated sequences in DNA
• accessory proteins identify promoters and recruit RNAP to start transcription

Question 11

Enhancers can be located __ and __

Answer 11

Enhancers can be located upstream (-ve) and downstream (+ve)
- they are not precise

Question 12

What are enhancers in transcription ?

Answer 12

DNA sequences downstream or upstream the transcription site

Question 13

What is TATA binding protein ?

Answer 13

• part of TFIID
• first protein to bind promoter in initiation (along with TBP-Associated factors)
• via H bonding and VWF
• binding distorts DNA/ unwinds duplex

TBP- TATA Binding Protein

Question 14

Describe the Pre-initiation Complex

Answer 14

1. TBP component of TFIID binds TATA box of promoter
2. TFIIA and TFIIB bind
3. TFIIF binds to RNAP II = subsequently escorts it to promoter complex
4. TFIIE and TFIIH (helicase) are recruited = opens complex
5. RNAPII starts transcription

Question 15

When does the Pre-initiation complex change from a closed to open system ?

Answer 15

When TFIIE and TFIIH (helicase) are recruited = completes PIC complex and unwinds DNA = transcription bubble

Question 16

Does the TBP/TFIIB/TFIIA subunit follow RNAP II or remain at the promoter ?

Answer 16

TBP/ TFIIB/ TFIIA remain at promoter for next RNAP II to bind

Question 17

Are inactive and active genes repaired with equal efficiency ?

Answer 17

No; active genes are already being transcribed and have recruited TFIIH for nucleotide-excision repair complex
- inactive genes are still wound DNA (less efficient to repair)

Question 18

What is a mediator in transcription ?

Answer 18

• interacts with assembled PIC to initiate transcription
• regulates expression of both protein-coding and most non-coding RNA genes
• gene expression in response to developmental/ environmental cues

Question 19

Do eukaryotes have precise transcription termination sites ?

Answer 19

No, termination sites are imprecise
- after transcription, eukaryotic transcripts have variable 3’ ends
- undergo (post-transcription) endonucleolytic cleavage = more consistent 3’ ends

Question 20

3 molecules that selectively inhibit RNA polymerase

Answer 20

1. Rifampin
2. Actinomycin D
3. α-amanitin

Question 21

How does Rifampin cause selective inhibition of RNAP II?

Answer 21

• prevents promoter clearance
• antibiotic; inhibits bacterial β subunit of RNAP

Question 22

How does Actinomycin D cause selective inhibition of RNAP II?

Answer 22

• inhibits bacterial AND eukaryotic RNAP
• intercalates into dsDNA; prevents movement of RNA and RNAP along template

Question 23

How does α-amanitin cause selective inhibition of RNAP II?

Answer 23

• inhibits eukaryotic RNAP
• blocks RNAP II, and blocks RNAP III at higher concentrations

Question 24

WIP Role of CTD in transcription ?

Answer 24

CTD of RBP1 is phosphorylated by TFIIH

RBP1 = ribosomal protein 1

Question 25

TFIID binds which promoter element ?

Answer 25

TATA box

Question 26

Which transcription factor phosphorylates RNA pol II ?

Answer 26

TFIIH

Question 27

Which transcription factor phosphorylates RNA pol II ? At which domain ?

Answer 27

TFIIH phosphorylates RNAP II at C-terminal Domain (CTD)

Question 28

Which of the following is phosphorylated to initiate transcription ?

a). N-terminal domain of RBP1
b). C-terminal domain of RBP1
c). N-terminal domain of RBP2
d). C-terminal domain of RBP2

Answer 28

b). C-terminal domain of RBP1

RBP1 = RNAP II largest subunit

Question 29

Sequence of Transcription factors recruited to the promoter

Answer 29

TFIID > TFIIA > TFIIB > TFIIF-RNAPII > TFIIE > TFIIH

Question 30

Location of DPE

Answer 30

Downstream Promoter Element: +28 to +33

Question 31

Location of MTE

Answer 31

Motif Ten Element: +15 to +26

Question 32

Location of TATA box

Answer 32

-31 to -25

Question 33

Location of BRE

Answer 33

TFIIB Recognition Element: -38 to -32

Question 34

Which of the following is a function of TBP?

a.
partially unwinds DNA

b.
recruits TFIIH

c.
phosphorylates CTD

d.
excision-repair

Answer 34

Which of the following is a function of TBP?

a.
partially unwinds DNA

Question 35

Yeast RNAPII has how many subunits ?

Answer 35

12 subunits