Lecture 01 - Eukaryotic Transcription

Question 1

What is transcription

Answer 1

the DNA dependent synthesis of RNA

Question 2

What makes transcription different than replication

Answer 2

• only specific genes are transcribed at a time
• only one strand is typically transcribed
• regulatory sequences in DNA designate beginning and end of DNA segments that are templates for transcription

Question 3

What is the coding strand used for

Answer 3

it matches the sequence of the RNA an is used as as a reference

Question 4

What is the antisense strand used for

Answer 4

used by RNA polymerase to synthesize the RNA

Question 5

What does gene mean

Answer 5

specific DNA sequences associated with products

Question 6

What is mRNA used for

Answer 6

to direct protein synthesis

Question 7

What is tRNA used for

Answer 7

delivery of amino acids to ribosomes during translation

Question 8

What is small interfering and micro RNA used for

Answer 8

sequence-specific inactivation of mRNA

Question 9

What is large intergenic noncoding RNA used for

Answer 9

transcriptional control

Question 10

What is small nuclear RNA used for

Answer 10

RNA splicing

Question 11

What is small nucleolar RNA used for

Answer 11

sequence-specific methylation of rRNA

Question 12

How do cells differentiate

Answer 12

expression of genes vary from cell to cell

Question 13

What is an example of long term control

Answer 13

cell differentiation

Question 14

What is an example of short term control

Answer 14

metabolic control

Question 15

What does RNAP I do

Answer 15

transcription of rRNA precursors

Question 16

What does RNAP II do

Answer 16

transcription of mRNA precursors

Question 17

What does RNAP III do

Answer 17

transcription of 5S, rRNA, tRNA and other small RNA precursors

Question 18

What subunit is shared between RNAP I, II, III

Answer 18

omega homolog

Question 19

What subunit is shared between RNAP I and II

Answer 19

alpha homolog

Question 20

How many subunits does yeast RNA polymerase II have

Answer 20

12

Question 21

What is the largest subunit of yeast RNA polymerase II

Answer 21

Rpb1

Question 22

What are the phases of transcription

Answer 22

assembly, initiation, elongation, termination

Question 23

What does the clamp portion of Rpb2 do

Answer 23

locks over bound dNA to increase processivity

Question 24

Where are contacts between RNAP and hybrid duplex

Answer 24

the backbone

Question 25

What are enhancers

Answer 25

variable in terms of location, specific sequences of DNA where proteins can bind

Question 26

What do accessory proteins do

Answer 26

identify promoters and recruit RNAP to transcription start site

Question 27

How many general transcription factors are there

Answer 27

6

Question 28

What is the TATA binding protein

Answer 28

the first protein to bind to a promoter in initiation which distorts the DNA partially unwinding the duplex

Question 29

How does the TATA binding protein associate

Answer 29

via hydrogen bonding, van der waals interactions and aromatic sidechain interactions

Question 30

What is the pre-initiate complex

Answer 30

when TF2D binds to the TATA box of the promotor, then TF2B and TF2A bind which becomes a stable complex. TF2F binds to RNAP2 and escorts it to the complex where it binds. TF2E and TFH are recruited which completes the complex

Question 31

What does TF2B interact with

Answer 31

RNAP2 and TBP

Question 32

What does TF2A do

Answer 32

stabilizes TBP and TAF binding

Question 33

What does TF2B do

Answer 33

stabilizes TBP binding, recruits RNAP2, influences start site selection

Question 34

What does TF2D do

Answer 34

recognizes TAT box, recruits TF2A and TF2B, regulatory function

Question 35

What does TF2E do

Answer 35

its an alpha 2 beta 2 heterotetrametric, recruits TF2H and stimulates its helicase activity, enhances promoter melting

Question 36

What does TF2F do

Answer 36

facilitates promoter targeting, stimulates elongation

Question 37

What does TF2H do

Answer 37

contains an ATP-dependent helicase that functions in promoter melting and clearance

Question 38

What initiates transcription

Answer 38

after the PIC is assembled Pol II CTD is phosphorylated

Question 39

How does TF2H repair errors in the DNA

Answer 39

at the site of a DNA lesion Pol II halts and TF2H interacts with the lesion and recruits entire nucleotide-excision repair complex

Question 40

Where is repair of damaged DNA most effective

Answer 40

on actively transcribed genes and the template strand

Question 41

What is a cis acting enhancer

Answer 41

its on the same chromosome thats being transcribed

Question 42

What is a trans acting enhancer

Answer 42

it is on a different chromosome that comes close and the mediator proteins bind

Question 43

What is a mediator used for

Answer 43

regulating expression of most RNA polymerase II transcripts

Question 44

How is a mediator usually targeted

Answer 44

sequence-specific DNA-binding transcription factors that work to control gene expression programs in response to developmental or environmental cues

Question 45

What is endonucleolytic cleavage

Answer 45

post-transcription processing which creates more consistent 3' ends

Question 46

What does ripfampicin do

Answer 46

inhibits bacterial beta subunit of RNA polymerase, prevents promotor clearance, antibiotic

Question 47

What does Actinomycin D do

Answer 47

inhibits bacterial and eukaryotic RNA polymerase, intercalates into dsDNA preventing movement of RNA and RNAP along the template, anti-cancer agent

Question 48

What does alpha-amanitin do

Answer 48

inhibits eukaryotic RNA polymerase, blocks RNAP2 and at higher concentrations RNAP3, does not block bacterial polymerase or RNAP1