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MBG Flashcards > Transcription 1 > Flashcards

Transcription 1 Flashcards

Corden Lecture 1

1
Q

What’s defines a transcription unit?

A

Promoter, Genes, Terminator

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2
Q

T/F. Bacteria couple transcription to translation

A

true

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3
Q

T/F. Eukaryotes couple transcription to translation

A

False, couple transcription to processing

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4
Q

4 Eukaryotic RNA Polymerase Families and Transcription Targets

A

1 - rRNA
2 - mRNA, small regulatory RNAs
3 - tRNA, 5S RNA, snRNA

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5
Q

RNA Polymerase Characteristics (3)

A

5’ -> 3’ chain elongation
Conserved a.a. between species are in catalytic active site
Multi-subunit

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6
Q

Function: Sigma Factor (3)

A
  1. Destabalize nonspecific binding to non-promoter DNA
  2. Stabilize specific binding to promoter DNA
  3. Accelerate search for promoter DNA
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7
Q

Structure: Sigma Factor Regions and Functions (4)

A

Region 1.1 - binds RNA pol where template strand would be
Region 2 - binds -10 of promoter
Region 3.2 - binds RNA pol, important for abortive initiation
Region 4 - binds -35 of promoter

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8
Q

Transcription Initiation Steps (3)

A

Promoter Binding, Promoter Unwinding, Promoter Clearance

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9
Q

Mechanism of Promoter Melting in Bacteria

A

1) Sigma factor binds promoter
2) Isomerizes A in -10 region
3) Twist in downstream region leads to relief of negative supercoil, allow ATP independent melting
4) DNA replaces Region 1.1 of sigma factor
5) Open complex is formed

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10
Q

Mechanism of Abortive Transcription in Bacteria

A

1) Open complex is formed
2) Oligonucleotides are formed in active site
3) With enough [NTP], oligonucleotide will displace region 3.2 of sigma factor
4) Get promoter clearance

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11
Q

Two types of promoters in Eukaryotes

A

Sharp type promoters: Have TATA box and specific initiator site

Borad type promoters: nonspecific transcription start site, usually consists of CpG islands

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12
Q

RNA Pol II Promoter Elements (3)

A

TATA box, Inr, BRE (B recognition element), DPE (downstream promoter element)

Optional: MTE, DCE, XCPE1

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13
Q

Function: TFIIA

A

Stabilize binding of TBP and TFIIB

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14
Q

Function: TFIIB

A

Promoter recognition, stabilize early transcribing complex, binds BRE

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15
Q

Function: TFIID

A

Consists of TBP, TAFs,
involved in promoter recognition, DNA bending to interact w/ regulatory factors
binds TATA, INR, DPE

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16
Q

Function: TFIIE

A

Recruit TFIIH

17
Q

Function: TFIIF

A

capture non-template strand upon melting

optional: suppress non-specific DNA binding

18
Q

Function: TFIIH

A

unwind promoter DNA with 3’->5’ ATP dependent helicase

Phosphorylate CTD

19
Q

What happens if you mutate TFIIB?

A

Get altered start site selection

20
Q

What is the Pol II-CTD?

A

Repeating heptapeptide that can be modified. Different residues are modified depending on state of transcription

21
Q

Function: DSIF

A

Binds to NELF to initiate promoter proximal pausing

22
Q

Function: NELF

A

Locks Pol II in inactive conformation by locking DNA-RNA hybrid

23
Q

Function: P-TEFb

A

inactivates DSIF and NELF through phosphorylation, allows Pol II release

24
Q

Why does Pol II pause at promoters? (2)

A

1) Ensure that 5’ end of mRNA is capped.

2) Adds layer of regulation, especially for developmental genes or genes involved in stimuli

25
Q

How does RNA Pol translocate?

A

Thermal ratchet mechanism. Brownian motions allows Pol to move, but NTP binding + hydrolysis traps it in forward translocated state

26
Q

What kind of supercoils appear in front and behind Pol and what enzymes deal with them?

A 
Behind: Negative supercoils, Topoisomerase
In front (bacteria): Positive supercoils, gyrase
27
Q

What are the two types of pause sites in elongation?

A

Class 1 (bacteria) is related to rho-independent terminators.

Class 2: weak hybrids (rU:dA hybrid) cause Pol backtrack

28
Q

Mechanism: Backtracking

A

1) Stalled polymerase backtracks
2) RNA goes through secondary channel
3) GreB (Bacteria) / TFIIS (Eukaryotes) cleaves RNA
uses Mg2+ ions to facilitate cleavage

29
Q

Mechanism: Rho Independent Termination

A

1) GC rich dyad sequence is transcribed
2) Dyad sequence forms hairpin and causes pausing
3) rU:dA hybrid downstream is unstable, causes release

30
Q

Mechanism: Rho-Dependent Termination

A

1) C-rich rut site is transcribed
2) Rho binds the site, uses ATP hydrolysis to move along RNA
3) crashes into Pol and destabilizes complex

31
Q

What protein regulates Rho?

A

NusG
Negatively regulates during normal elongation
Positively regulates when there is stress (ribosome stalls)

32
Q

Eukaryotic Termination Pathways (2)

A

Allosteric model and Torpedo Model

MBG Flashcards (12 decks)

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