Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

CMMB 411 > Topic 8 (Transcription) > Flashcards

Topic 8 (Transcription) Flashcards

1
Q

Where in the eukaryotic cell does transcription happen?

A

Nucleus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Where in the eukaryotic cell does translation happen?

A

Cytoplasm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are the major differences between DNA replication and RNA transcription?

A

DNA: copy the entire genome once an only once per cell cycle, and both strands serve as templates for new DNA synthesis
RNA: selectively copy only certain parts of the genome from one to multiple times and only one of the DNA strands serves as a template

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

The template strand is also called the:

A

Antisense or noncoding strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

The non-template strand is also called the:

A

Sense or coding strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

The RNA transcript dissociates from the template a few nucleotides behind the point of syntheses, which allows for:

A

Multiple transcriptional events of the same gene and translation to occur rapidly (prokaryotes)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

RNA Pol:

A

Catalyzes RNA synthesis in the absence of primers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

How do RNA Pol and DNA Pol differ in terms of proofreading? Why?

A

RNA Pol lacks extensive proofreading mechanisms (except its involvement with TCR); If RNA Pol makes a mistake, it is not severely detrimental to the cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

How many RNA Pol do eukaryotes have? Prokaryotes?

A

3; 1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Which subunits of RNA Pol are conserved among all organisms?

A

2 alpha and 2 beta subunits

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

RNA Pol I transcribes:

A

rRNA precursor (large RNA)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

RNA Pol II transcribes:

A

mRNA (protein coding)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

RNA Pol III transcribes:

A

tRNA and 5S rRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What are the phases of transcription?

A
  1. Initiation
  2. Elongation
  3. Termination
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is the +1 site?

A

It is the first nucleotide transcribed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

True/False? The +1 site is always an A (start codon = AUG)

A

False. It depends on the 5’ UTR. AUG is the first translated codon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Describe the GENERAL steps of transcription initiation

A
  1. Formation of a closed complex (DNA is not melted yet) by binding Pol to the promoter
  2. Closed complex transformed into an open complex
  3. Initial transcribing complex makes the first 10 ribonucleotides
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What determines which DNA stretch will undergo transcription?

A

The promoter

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What direction does transcription occur in?

A

5’-3’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

The transcription bubble is an example of what?

A

An open complex

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Describe the GENERAL steps of transcription elongation and termination

A
  1. Continual RNA synthesis
  2. Unwinds the DNA in front and reanneals it behind
  3. Emergence of the growing RNA from the template
  4. Proofreads
  5. Transcription stops and RNA product is released
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Prokaryotic vs eukaryotic transcription initiation

A

Prokaryotic: only have 1 RNA Pol and one initiation factor (sigma)
Eukaryotic: 3 RNA Pol and requires several initiation factors for promoter-specific initiation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What sequences make up the core promoter for RNA Pol II from 5’ to 3’?

A

BRE, TATA, Inr, DPE

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What protein binds BRE?

A

TFIIB

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What protein binds TATA?

A

TBP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What protein binds Inr?

A

TFIID

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What protein binds DPE?

A

TFIID

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Which sequence contains the +1 site?

A

Inr

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What is a core promoter?

A

Minimal sequence required for accurate transcription initiation in vitro

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

BRE stands for:

A

TFIIB recognition element

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

TATA stands for:

A

TATA box (element)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Inr stands for:

A

Initiator

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

DPE stands for:

A

Downstream promoter element

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What is unique about DPE?

A

It is included in the open reading frame

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

TBP stands for:

A

TATA binding protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What is contained upstream of the core promoter?

A

Regulatory sequences required for efficient transcription in vivo

37
Q

Sequence elements upstream of the core promoter (6)

A

Promoter proximal elements
Upstream activator sequences
Enhancers
Silencers
Boundary elements
Insulators

38
Q

How was the binding sequence of transcription factors (TFIIB, TBP, TFIID) discovered?

A

Each was added one at a time in vitro and transcription was measured to determine what order the TFs bound in

39
Q

Transcription factors require these two domains:

A

DNA-binding domain and activation domain

40
Q

What proteins is TBP associated with?

A

10 other TBP-associated factors (TAFs)

41
Q

What is the function of TFIIB?

A

Binds the pre-initiation complex after TBP and may function in bridging between TATA-bound TBP and RNA Pol II. Also responsible for the directionality of transcription

42
Q

How is TFIIB responsible for the directionality of transcription?

A

Binds upstream (5’) of TBP, so RNA Pol II is prevented from binding there and must bind downstream. Defines asymmetric assembly of the pre-initiation complex and unidirectional transcription

43
Q

What is the function of TFIIF?

A

Recruited to the promoter with Pol II. This complex stabilizes the DNA-TBP-TFIIB complex and recruits TFIIE and TFIIH

44
Q

What is the function of TFIIE?

A

Recruits and regulates TFIIH

45
Q

What is the function of TFIIH?

A

Controls ATP-dependent transition of the pre-initiation complex to the open complex, phosphorylates Pol II C-terminal domain and causes promoter melting and escape. Also functions in NER

46
Q

What are 5 examples of TAFs (TBP-associated factors)?

A

TFIIB, TFIID, TFIIF, TFIIE, TFIIH

47
Q

What is the pre-initiation complex?

A

Protein complex containing Pol and general transcription factors

48
Q

What part of the DNA does TBP bind?

A

Minor groove of the TATA element through its beta-sheet

49
Q

What is unique about TBP associating with DNA?

A

Uses a beta-sheet to associate, while other TFs usually use alpha-helices to associate with the major groove

50
Q

Describe the DNA conformational change when TBP binds

A

Minor groove is induces to be widened to almost flat, and the DNA is bent away from the TBP

51
Q

Describe the steps to the assembly of the pre-initiation complex

A
  1. TFIID, TBP, and 11 TAFs recognize the TATA element. TBP binds TATA
  2. TFIIA and TFIIB bind upstream of the TATA
  3. Pol II with TFIIF binds
  4. TFIIE and TFIIH bind to complete the pre-initiation complex
  5. C-terminal domain of RNA Pol II becomes phosphorylated, promoter escape occurs, and transcription elongation begins
52
Q

The C-terminal tail of RNA Pol II contains what?

A

Tyr residue repeats for phosphorylation

53
Q

Why are additional proteins necessary for transcription initiation in vivo?

A

The DNA template in vivo is in chromatin form

54
Q

What is the function of the activator proteins for transcription initiation?

A

Recruits Pol and stabilizes Pol:promoter interaction and binds to chromatin remodeling complexes

55
Q

What is the function of the chromatin remodeler for transcription initiation?

A

Modifies nucleosome structure to facilitate transcription

56
Q

What is the function of the HAT protein for transcription initiation?

A

Part of the chromatin remodeling complex, acetylates histone tails (loosens interaction)

57
Q

What is the function of the mediator complex for transcription initiation?

A

Bridges the C-terminal domain of the Pol and the activator and regulates TFIIH

58
Q

Which modifier complex subunit is required for Pol II transcription in vivo?

A

Med17

59
Q

True/False? Mediator complexes have a similar shape and size to RNA Pol

A

False. Similar shape but larger size

60
Q

How are mediator complexes organized?

A

Into modules (sub-complexes of multiple subunits

61
Q

How does transcription elongation overcome the obstacle of chromatin?

A

FACT dimers

62
Q

What does FACT stand for?

A

FAcilitates Chromatin Transcription

63
Q

Describe the function of FACT on DNA that has already been transcribed

A

Restores H2A:H2B dimer to the existing hexamer

64
Q

Describe the function of FACT on DNA yet to be transcribed

A

Disassembles H2A:H2B dimers from the octamer

65
Q

What happens to initiation factors after initiation?

A

They dissociate from Pol II

66
Q

Recruitment of elongation factors depends on what?

A

The phosphorylation state of the CTD (C-terminal domain) of RNA Pol II

67
Q

What are elongation factors? Provide 2 examples

A

Factors that stimulate elongation; ELL protein family and TFIIS

68
Q

What are the functions of TFIIS?

A

Increases rate of elongation by limiting Pol’s pause time and proofreads the new transcript

69
Q

What are the RNA processing enzymes? How are they recruited?

A

5’ capping enzymes, splicing factors, and 3’ polyadenylation and cleavage factors; phosphorylation state of CTD

70
Q

Describe the sequence of events following the phosphorylation of the CTD

A
  1. Capping enzyme is recruited to CTD tail
  2. Capping enzyme moves to 5’ end of new transcript, splicing machinery recruited to CTD
  3. 5’ capping enzyme dissociates, splicing machinery associates with the transcript, and polyadenylation and cleavage factors are recruited to the CTD
71
Q

What stage of transcription is the capping enzyme recruited?

A

Promoter escape

72
Q

What stage of transcription is splicing machinery recruited?

A

Elongation

73
Q

Describe the steps of 5’ cap formation

A
  1. RNA triphosphatase removes the gamma phosphate at the 5’ end of the transcript
  2. Guanylyltransferase adds the GMP moiety to the terminal beta-phosphate
  3. Methyltransferase adds a methyl group to the guanine base (7-methylguanylate cap)
74
Q

How many phosphates separate the first transcribed base and the 7’methylguanylate cap?

A

3 (beta and alpha from base and alpha from cap)

75
Q

What is the function of the 5’cap?

A

Stabilizes the transcript and signals the transcript is correctly processed

76
Q

Describe the steps of 3’ polyadenylation

A
  1. RNA Pol encounters and transcribes the poly-A signal (AAUAAA)
  2. Phosphorylated CTD recruits polyadenylation enzyme (CSPF and CstF)
  3. RNA Pol II transcribes until it falls off the template
  4. CSPF and CstF and other proteins cleave downstream of the poly-A signal, CSPF stays on the transcript
  5. Poly-A polymerase (PAP) adds ~200 adenines to the 3’ end of the poly-A signal
  6. Poly-A binding protein (PBP) coats the As to stabilize them and protect them from 3’-5’ exonuclease
77
Q

What is the function of the poly-A tail?

A

Stabilizes mRNA and signals correct 3’ end processing

78
Q

Describe the torpedo model of termination

A
  1. 5’-3’ exonuclease (Rat1/hXrn2) binds RNA Pol II
  2. Termination signal is transcribed and mRNA falls off while RNA Pol keeps transcribing
  3. exonuclease degrades the uncapped end of the newly synthesized RNA coming out of RNA Pol, which is faster than synthesis
  4. RNA Pol dissociates from the template
79
Q

Describe the allosteric model of termination

A
  1. Termination signal is transcribed and mRNA falls off while RNA Pol keeps transcribing
  2. As RNA Pol transcribes, its processivity decreases as a result of a conformational change
  3. RNA Pol falls off, leaving the second RNA strand to be degraded
80
Q

Why is RNA Pol I transcription so high?

A

There are many isoforms of rRNA that need to be transcribed by RNA Pol I

81
Q

True/False? RNA Pol II is the only eukaryotic RNA Pol that is protein coding

A

True

82
Q

Describe RNA Pol I transcription initiation

A
  1. UBF dimer binds upstream control element (UCE)
  2. SL1 (TBP + 3 TAFs) binds the core promoter upstream of +1
  3. Pol I binds
83
Q

What is unique about RNA Pol III transcription?

A

The start site is upstream of the promoter

84
Q

Why are the promoters internal to tRNA and 5S RNA?

A

Because they’re transcribed by RNA Pol II, their promoters are transcribed because the start site is upstream of the promoter

85
Q

Describe RNA Pol II initiation

A
  1. TFIIC binds Box A and B
  2. TFIIB and TBP bind just upstream of the start site
  3. RNA Pol III is recruited to TFIIB and TBP
  4. TFIIC is displaced by RNA Pol III binding
86
Q

What are the themes of eukaryotic gene regulation?

A
  • transcription initiation is the primary point of gene regulation
  • nucleosomes and their modifiers have a profound influence on gene expression
  • transcription is controlled by activators and repressors
  • regulation of RNA splicing is also important for gene expression
87
Q

What are the 6 upstream sequence elements required for efficient transcription in vivo?

A
  • promoter proximal elements
  • upstream activator sequences
  • enhancers
  • silencers
  • boundary elements
  • insulators
88
Q

SLIDE 44 - 65

A

CMMB 411 (8 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions