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Study and Diagnosis of Disease > Lecture 01 - Eukaryotic Transcription > Flashcards

Lecture 01 - Eukaryotic Transcription Flashcards

1
Q

What is transcription

A

the DNA dependent synthesis of RNA

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2
Q

What makes transcription different than replication

A
  • 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
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3
Q

What is the coding strand used for

A

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

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4
Q

What is the antisense strand used for

A

used by RNA polymerase to synthesize the RNA

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5
Q

What does gene mean

A

specific DNA sequences associated with products

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6
Q

What is mRNA used for

A

to direct protein synthesis

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7
Q

What is tRNA used for

A

delivery of amino acids to ribosomes during translation

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8
Q

What is small interfering and micro RNA used for

A

sequence-specific inactivation of mRNA

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9
Q

What is large intergenic noncoding RNA used for

A

transcriptional control

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10
Q

What is small nuclear RNA used for

A

RNA splicing

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11
Q

What is small nucleolar RNA used for

A

sequence-specific methylation of rRNA

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12
Q

How do cells differentiate

A

expression of genes vary from cell to cell

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13
Q

What is an example of long term control

A

cell differentiation

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14
Q

What is an example of short term control

A

metabolic control

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15
Q

What does RNAP I do

A

transcription of rRNA precursors

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16
Q

What does RNAP II do

A

transcription of mRNA precursors

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17
Q

What does RNAP III do

A

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

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18
Q

What subunit is shared between RNAP I, II, III

A

omega homolog

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19
Q

What subunit is shared between RNAP I and II

A

alpha homolog

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20
Q

How many subunits does yeast RNA polymerase II have

A

12

21
Q

What is the largest subunit of yeast RNA polymerase II

A

Rpb1

22
Q

What are the phases of transcription

A

assembly, initiation, elongation, termination

23
Q

What does the clamp portion of Rpb2 do

A

locks over bound dNA to increase processivity

24
Q

Where are contacts between RNAP and hybrid duplex

A

the backbone

25
Q

What are enhancers

A

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

26
Q

What do accessory proteins do

A

identify promoters and recruit RNAP to transcription start site

27
Q

How many general transcription factors are there

A

6

28
Q

What is the TATA binding protein

A

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

29
Q

How does the TATA binding protein associate

A

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

30
Q

What is the pre-initiate complex

A

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

31
Q

What does TF2B interact with

A

RNAP2 and TBP

32
Q

What does TF2A do

A

stabilizes TBP and TAF binding

33
Q

What does TF2B do

A

stabilizes TBP binding, recruits RNAP2, influences start site selection

34
Q

What does TF2D do

A

recognizes TAT box, recruits TF2A and TF2B, regulatory function

35
Q

What does TF2E do

A

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

36
Q

What does TF2F do

A

facilitates promoter targeting, stimulates elongation

37
Q

What does TF2H do

A

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

38
Q

What initiates transcription

A

after the PIC is assembled Pol II CTD is phosphorylated

39
Q

How does TF2H repair errors in the DNA

A

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

40
Q

Where is repair of damaged DNA most effective

A

on actively transcribed genes and the template strand

41
Q

What is a cis acting enhancer

A

its on the same chromosome thats being transcribed

42
Q

What is a trans acting enhancer

A

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

43
Q

What is a mediator used for

A

regulating expression of most RNA polymerase II transcripts

44
Q

How is a mediator usually targeted

A

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

45
Q

What is endonucleolytic cleavage

A

post-transcription processing which creates more consistent 3’ ends

46
Q

What does ripfampicin do

A

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

47
Q

What does Actinomycin D do

A

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

48
Q

What does alpha-amanitin do

A

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

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