DB Lecture 23: Basal Transcription

Question 1

List the RNA polymerases.

Answer 1

RNA pol I (transcribes mostly rRNA)
RNA pol II (transcribes protein-coding genes)
RNA pol III (transcribes mostly tRNA genes)

Question 2

What is the core promoter?

Answer 2

a DNA sequence located in the immediate vicinity of the +1 site
where RNA pol II binds (directed by other protein factors)

Question 3

What are consensus sequences?

Answer 3

similar sequences found at the promoter regions of many genes
e.g. TATA box

Question 4

What is a TATA box?

Answer 4

promoter “consensus” sequence located around -25 to -30 composed of varying number of TA repeats

Question 5

What is the composition of a TFII protein?

Answer 5

TBP (TATA binding protein) and several TAFs (TBP-associated factors

Question 6

What are the kinds of TFIIDs?

Answer 6

A, B, C, D, E, F, H

Question 7

What composes a pre-initiation complex?

Answer 7

various TFIIDs and a mediator

Question 8

List the steps of transcription.

Answer 8

formation of the pre-initiation complex
initiation
elongation
termination

Question 9

What event initiates transcription?

Answer 9

hyperphosphorylation of the carboxy-terminal domain of the largest RNA pol II subunit (consisting of multiple repeats of a short, serine rich sequence) by TFIIH (a protein kinase)

Question 10

What is the first nucleotide in the pre-mRNA?

Answer 10

a nucleoside 5’-triphosphate (which will have a cap shortly after transcription initiation)

Question 11

What happens during the elongation phase of transcription?

Answer 11

helicase unwinds the double stranded DNA template ahead of the elongating transcription complex and topoisomerase relieves the tension created by the unwinding

Question 12

What is the rate of transcription initiation?

Answer 12

the rate at which re-initiation (the binding of another RNA pol II complex to the promoter region after one leaves the promoter region) occurs

Question 13

How does initiation of RNA synthesis differ from initiation of DNA replication?

Answer 13

DNA replication requires pre-existing 3’ hydroxyl to begin

RNA synthesis can begin de novo

Question 14

Describe the “torpedo model” for transcription termination.

Answer 14

when RNA pol II transcribes past polyadenylation signal, the nascent RNA is cleaved to allow poly(A) addition
=> generation of new 5’ end which is unprotected and bound by a 5’ exonuclease that begins to degrade the RNA in the 5’ to 3’ direction
when 5’ exonuclease catches up to the elongatign RNA pol II, some conformational change occurs that causes release of RNA pol II from the DNA template
RNA pol II is returned to its hypophosphorylated state by CTD phosphatase (allowing for recycle RNA pol II)

Question 15

What are cis elements?

Answer 15

consensus sequences on the DNA itself

intrinsic part of the DNA sequence

Question 16

What are trans elements?

Answer 16

transcription factor proteins that bind consensus sequences

factors that exist outside the DNA itself and bind to the DNA

Question 17

What are promoter-proximal elements?

Answer 17

cis elements that are bound by “constitutive” (unregulated) transcription factors
generally located close to the core promoter

Question 18

What are enhancers?

Answer 18

cis elements that are bound by regulated transcription factors
can be located far away from promoters (upstream or downstream)
comprise several DNA sequence boxes recognized in a sequence-specific manner by regulated transcription factors

Question 19

How do enhancers increase the rate of transcription initiation?

Answer 19

recruitment of co-activators that affect formation of the pre-initiation complex or accessibility of the DNA for transcription initiation