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CMB2001-Eukaryotic Gene Expression > CMB2001/L01 Transcription > Flashcards

CMB2001/L01 Transcription Flashcards

1
Q

Describe the central dogma.

A

DNA -> RNA -> Protein

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2
Q

Define transcription.

A

Transfer of genetic information from dsDNA to ssRNA

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3
Q

Briefly describe transcription in prokaryotes. (3)

A

RNA polymerase binds to promoter region with sigma70
Forms open complex and moves along DNA in transcription bubble
Sigma70 and RNA pol released

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4
Q

Define promoters.

A

Cis acting DNA regulatory element through which transcription is initiated and controlled

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5
Q

Where are promoters located?

A

Within 60bp of transcription start site

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6
Q

What defines the efficiency of transcription?

A

Similarity of promoter to consensus sequence

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7
Q

Give 3 eukaryotic promoters.

A

TATA box
Initiator (Inr)
MTE (motif tan element)
DPE (downstream core promoter element)
BRE (TFIIB recognition element)

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8
Q

Describe the TATA box. (3)

A

Eukaryotic promoter element
Located -31 to -26
Pyramidine-rich sequence
TATAA/TAA/TA/G

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9
Q

Describe the initiator (Inr).

A

Eukaryotic promoter element
-2 to +4
YYANA/TYYY

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10
Q

Describe the MTE (motif tan element). (3)

A

Eukaryotic promoter element
+18 to 28
CG/CAA/GCG/CG/CAAC

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11
Q

Describe the DPE (downstream core promoter region). (3)

A

Eukaryotic promoter element
+28 to 32
A/GGA/TCGTG

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12
Q

Describe the BRE (TFIIB recognition element). (3)

A

Eukaryotic promoter element
-37 to -32
G/CG/CG/AGGCC

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13
Q

How are eukaryotic promoters different from prokaryotic?

A

Eukaryotic promoters are looser and more flexible
Not all elements will be within one promoter

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14
Q

How can CpG islands affect gene transription?

A

Methylation is associated with silencing or switching off transcription

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15
Q

Which residues are often methylated in mammals?

A

C residues followed by G

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16
Q

Which residues escape methylation in mammals (hypomethylation)?

A

C residues in CpG islands

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17
Q

What are UAS/enhancers and URS/silencers?

A

Activator binding sites
Repressor binding sites

18
Q

Describe reporter analysis.

A

Reporter genes encode proteins whose levels can be measured easily
Amount of reporter protein provides measure of gene expression

19
Q

What can reporters be used to identify? (3)

A

When/where a gene is expressed
What signals it responds to
What factors and sequences control its expression

20
Q

What is the target gene and location of RNA pol I?

A

rRNA (28S, 18S, 5.8S)
Nucleolus

21
Q

What is the target gene and location of RNA pol II?

A

mRNA, snRNAs, miRNAs
Nucleus

22
Q

What is the target gene and location of RNA pol III?

A

tRNA, 5S RNAs, U6 RNA, 7S RNA
Nucleus

23
Q

Compare the structure of prokaryotic and eukaryotic RNA polymerase.

A

Similar structure but eukaryotic enzyme has more subunits
Bacterial - B, B’, a x2, w subunits
Eukaryotic pol II - 12 subunits

24
Q

Give the 6 general transcription factors (GTFs) in eukaryotes.

A

TFIIA
TFIIB
TFIID
TFIIE
TFIIF
TFIIH

25
Q

Give 3 features of eukaryotic GTFs.

A

RNA pol specific
Multi component factors
Form a complex on TATA box
Recruit RNA pol II to promoter
Direct initiation at start-site

26
Q

Give the order of pre-initiation complex assembly.

A

IID
IIA
IIB
IIF & RNA pol II
IIH & IIE

27
Q

Describe transcription initiation by RNA pol II. (5)

A

Helicase activity of TFIIH separates template strand at start-site (ATP using)
Transcription starts (promoter clearance) and pol II is extensively phosphorylated on C-terminus domain
TFIID & TFIIA may stay behind
TFIIB, TFIIE, TFIIH released
TFIIF moves down template with pol II

28
Q

What is the function of TFIID?

A

Binds to TATA box (core promoter)
Recruits TFIIB
13 subunits

29
Q

What is the function of TFIIA?

A

Stabilises TFIID binding
Anti-repression function
3 subunits

30
Q

What is the function of TFIIB?

A

Recruits RNA pol II - TFIIF
Important for start site selection
1 subunit

31
Q

What is the function of TFIIF?

A

Assists TFIIB recruit RNA pol II
Stimulates RNA pol II elongation
2 subunits

32
Q

What is the function of TFIIE?

A

Helps recruit TFIIH and modulates TFIIH activity
2 subunits

33
Q

What is the function of TFIIH?

A

Promoter melting and clearance
CTD kinase activity
DNA repair coupling
9 subunits

34
Q

What 2 parts can TFIIH be divided into?

A

CORE
CAK

35
Q

What does the CAK module of TFIIH contain?

A

A kinase that phosphorylates the CTD of RNA pol II

36
Q

What ATPase does TFIIH contain and what does it do?

A

XPB (or Ssl2)
Key role in promoter melting

37
Q

How does Ssl2(XPB) helicase form the open complex?

A

Uses energy from ATP hydrolysis
Pushes DNA into cleft where RNA polymerisation is catalysed
Creates torsional stress to form transcription bubble

38
Q

Describe the structure of TFIID.

A

Central RNA pol II transcription factor
TATA binding protein + TBP associated factors (TAFs)

39
Q

Describe TBP (TATA binding protein). (3)

A

Can direct assembly of PIC on TATA-containing promoter in vitro
Alone can NOT direct PIC assembly on TATA-less promoter
Can NOT support activated transcription

40
Q

What can TAFs do?

A

Promote interaction of TFIID with basal promoter elements
Interact with activators to promote transcription initiation

CMB2001-Eukaryotic Gene Expression (5 decks)

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