Eukaryotic Transcription

Question 1

DNA sequence promoter elements in eukaryotes and their locations:

Answer 1

• Core promoter (TATA; 25bp from start)
• Proximal promoter (C/G rich; <120bp from start)
• Enhancers (>250bp from start)

Question 2

The “core” promoter region of eukaryotic class II genes typically includes a:

Answer 2

• TATA box

Question 3

Where is the TATA box in relation to the transcription start site?

Answer 3

• -25
  
  • 25 base pairs upstream from the transcription start site

Question 4

Core promoter:

Answer 4

• typically a TATA box
• -25 from transcription start site

Question 5

TATA Box:

Answer 5

• core promoter (-25)
• “nucleation site” for assembly of a transcription complex
• functionally comparable to the –10 and –35 regions of a bacterial promoter

Question 6

What is the transcription complex consist of?

Answer 6

1. set of general transcription factors (GTFs)
2. a RNA polymerase II

• binds to the nucleation site / TATA box

Question 7

Proximal promoter location and function:

Answer 7

• <120 bp from start
• binding site for certain activator proteins

Question 8

Enhancers location and function:

Answer 8

• typically >250 bp from start
• function in either orientation
• function upstream, downstream or even with a gene
• binding site for transcription activators

Question 9

Enhancers are the binding sites for transcriptional activators that either:

Answer 9

1. make direct contact components of the RNA polymerase II transcriptional machinery
2. recruit chromatin remodeling complexes to the regulatory and promoter regions

Question 10

What promoter region serves as the binding site for “housekeeping” genes?

Answer 10

• proximal promoter region
• <120bp away from start

Question 11

How many eukaryotic nuclear polymerases exist?

Answer 11

• 3
  
  • RNA Pol I
  • RNA Pol II
  • RNA Pol III

Question 12

What polymerase is specific for rRNA?

Answer 12

RNA Pol I

Question 13

What polymerase is specific for mRNA?

Answer 13

RNA Pol II

Question 14

What polymerase is specific for tRNA?

Answer 14

RNA Pol III

Question 15

RNA Pol III transcribes:

Answer 15

• small RNAs
  
  • tRNA
  • some snRNAs
  • 5S rRNA

Question 16

Is there a eukaryotic counterpart to the σ subunit of bacterial RNA polymerases?

Answer 16

• no
• promoter recognition is conferred by GTFs in eukaryotic transcription

Question 17

How do eukaryotic RNA polymerases recognize specifc DNA sequences (promoters)?

Answer 17

• recruitment of general transcription factors
• RNA polymerases cannt recognize DNA sequences on their own

Question 18

How many subunits are in RNA Pol II?

Answer 18

• 12 (Rpb1 - Rpb12)
• some subunits are homologous to each of the bacterial RNA polymerase subunits

Question 19

The general transcription factors (GTFs) specific to RNA Pol II:

Answer 19

1. TFIIA
2. TFIIB
3. TFIID (includes TBP, the TATA binding protein)
4. TFIIE
5. TFIIF
6. TFIIH

Question 20

What are the core promoter elements of RNA Pol II?

Answer 20

• BRE (TFIIB recognition element; -35)
• TATA (TBP binding; -25)
• INR (initiator; +1)
• DPE (downstream promotor element; +30)

Question 21

TFIID:

Answer 21

• RNA Pol II - specific GTF
• contains TBP subunit (binds TATA)
• recognizes core promoter and tells Pol II where to bind

Question 22

In eukaryotes, the proximal promoter is rich in what bases?

Answer 22

C/G

Question 23

What are the two notable features of eukaryotic RNA pol II transcription that do not occur either in bacteria or by RNA pol I or RNA pol III?

Answer 23

• modifications to the 5’ and 3’ ends of the mRNA
• 5’ 7-methylguanosine “CAP”
• 3’ Poly-A tail (100-250 amino residues)

Question 24

The 5’ 7-methyguanosinine CAP is added to the mRNA shortly after:

Answer 24

• Initiation
  
  • just as the nascent mRNA polymer emerges from the RNA pol II enzyme complex

Question 25

Function of 5’ 7-methylguanosinine CAP:

Answer 25

• stabilizes/protects mRNA from nuclease digestion
• recognized by ribosome
  
  • thereby facilitating protein synthesis

Question 26

Many activators stimulate transcription by:

Answer 26

• binding GTFs, either to recruit or stabilize their binding to the core promoter.

Question 27

Steps in the assemply of the RNA Pol II Preinitiation Complex (PIC):

Answer 27

• TFIID (TBP subunit) binds to TATA box
• TFIIB binds, allowing RNA Pol II and TFIIF to form complex
• TFIIE and TFIIH bind
  
  • involved in promoter melting clearance (enable RNA pol II to initiate transcription)

Question 28

What two RNA Pol II GTFs are involved in involved in promoter melting clearance?

Answer 28

1. TFIIE
2. TFIIH

Once completed, transcription begins in 5’ to 3’ direction.

Question 29

The three steps of eukaryotic transcription:

Answer 29

1. initiation
2. elongation
3. termination

Question 30

Transcription termination by RNA pol II involves the addition of:

Answer 30

a poly(A) tail to the 3’ end of mRNA

Question 31

Eukaryotic transcriptional termination is specified by:

Answer 31

• distinct sequences in the DNA template
• involves two enzymatic reactions

Question 32

The two enzymatic reactions involved in termination of eukaryotic transcription:

Answer 32

1. endonucleolytic cleavage of the new mRNA transcript
2. addition of poly(A) tail to 3’ end of mRNA
   
   • typically 100 – 250 amino acid residues in length

Question 33

Are the 3’ poly-A tail and the 5’ 7-methylguanosine cap encoded by the DNA sequence?

Answer 33

• no
• they are specific to transcription by RNA Pol II, which produces mRNA

Question 34

Function of the 3’ Poly-A tail:

Answer 34

1. mRNA stabilization
2. transport of mRNA from the nucleus to the cytoplasm
3. efficient translation