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BMS > Transcription, RNA Processing (Hampsey) > Flashcards

Transcription, RNA Processing (Hampsey) Flashcards

1
Q

Rifampin in binds to

A

Bacterial RNAP

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2
Q

Prokaryotic RNAP consists of

A

Sigma subunit, associates with core enzyme (alpha, alpha, beta, beta, omega) to generate hold enzyme

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3
Q

What happens during prokaryotic transcription

1. Initiation

A

Holo-RNAP (sigma) binds promoter, principal site for regulation of transcription

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4
Q

What happens during prokaryotic transcription: Elongation

A

RNAP “leaves the station”; sigma dissociates from RNAP & promoter

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5
Q

What happens during prokaryotic transcription: Termination

A

DNA-RNA-RNAP complex disassembles..dependent on specific signals (Rho dependent or Rho independent)

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6
Q

Structure of a bacterial promoter, how many sigma binding sites?

A

2
-35 sequence (TTGACA)
Pribnow box (TATAAT)

**these consensus sequences are not exact, don’t want overly tight binding

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7
Q

Rho-dependent transcription termination

A

Travels along nascent mRNA, comes in contact with RNAP and dissociates complex to stop termination

*torpedo, ATP dependent

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8
Q

Rho-independent transcription termination

A
  • Stem and loop
  • mRNA folds up and makes this stem
  • still within RNAP and complex disassociates
  • 3’ end: UUUU-OH
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9
Q

True or false: there are DNA sequences that tell transcription to stop

A

TRUE…..Rho-dependent/independent transcription signals are encoded for by DNA

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10
Q

2 notable features of eukaryotic transcription

A

1) 5’-CAP

2) 3’ polyA tail

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11
Q

Alpha-amantin

A
  • eukaryotic transcription inhibitor

- binds RNAP III and inhibits elongation (just like rifampicin does this in bacteria)

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12
Q

DNA –> rRNA via

A

RNAP I

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13
Q

DNA–> mRNA via

A

RNAP II

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14
Q

DNA–>tRNA/ssRNA via

A

RNAP III

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15
Q

MRNA—>Protein via

A

Ribosome

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16
Q

These bind to regulatory proteins and activate stuff…
>250bp
-dsDNA, function in any direction, and are binding sites for transcription activators

A

Enhancers

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17
Q

CpG islands make up

A

Proximal promoter
-bind regulatory proteins for housekeeping genes & certain activator proteins
Ex: Sp1: most well characterized activator for proximal promoter

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18
Q

Core promoter is the

A

TATA box
-40 to +40
Transcription start site +1 (INR, DPE is +20)
Binding site for RNAP II and GTFs

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19
Q

What makes up core promoter

A

BRE (TFIIB recognition element) @ -35
TATA @ -25INR +1
DPE +30

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20
Q

Proximal promoter and Core promoter….

A

Span ~80 bp & flank start of transcription

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21
Q

What binds to dsDNA Pre initiation complex

A

GTFs
—>leads assembly of RNAP II
Recognize specific stuff in promoter, similar to sigma in bacteria

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22
Q

What positions RNAP II at the promoter

A

GTFs (they recognize promoter elements)

23
Q

GTFs specific to RNAPII

A

TFIIA, TFIIB, TFIID

24
Q

TFII B binds to

A

BRE of core promoter

25
Q

TFII D binds to

A

Promoter

  • includes TBP (TATA binding protein) + 14 TBP associated factors (TAFs)
  • nucleases assembly of transcription Pre initiation complex

> > > > TBP (part of TFDII) binds TATA > bend in promoter DNA> allows TFBII and other to bind»»TFIIE,TFIIH bind subsequently, involved in promoter melting so RNAP II transcription can begin

26
Q

Which GTF is the last to bind?

A

TFII H

-has helicase activity and can unwind DNA, then DNA can descend into active site of RNAPII

27
Q

TFIIH implicated in

A

XP (xeroderma pigmentosum)
TTD (trichotriodystrophy)
Cockade syndrome (CS)

28
Q

Many activators can stimulate transcription by binding GTFs in order to

A

Recruit or stabilize their binding to core promoter

29
Q

Where is the only place where 5’ to 5’ linkage occurs

A

7-methylguanosine cap at 5’ ends of mRNAs

  • via triphosphate linkage
  • as soon as mRNA emerges from RNAP it’s capped 4 protection
30
Q

What occurs during polyadenylation of a primary transcript

A

There is a cleavage signal: AAUAA, and 2 enzymatic reactions

1) cleavage by specific endnonuclease
2) addition of tail by polyApolymerase (not encoded in DNA, uses ATP)

31
Q

Why is polyadenylation of a primary transcript needed?

A

For mRNA stabilization, transport of mRNA from nucleus to cytoplasm
-uses ATP

32
Q

Direction of flow of genetic information

A

5’ to 3’

33
Q

What’s the organization of a human B-glob in gene?

A

3 exonuclease, 2 introns

-before RNA translated, splicing occurs

34
Q

How is b-glob in gene processed?

A

Bglobin gene-[transcription, 5’ cap, poly a tail]->primary transcript (with introns)-[splicing]->B globin mRNA

35
Q

5’ splice site of upstream exon

A

AG|GUAAGU

First exon always begins with a GU

36
Q

3’ splice site of downstream exon

A

CAG|G

***exon always ends with AG

37
Q

Exon begins/ends with

A

GU…….AG

38
Q

Where is there the only 2’ to 5’ PD bond?

A

Lariat intermediate (which eventually becomes intron)

39
Q

Transesterification reaction

A

1) cleave PH bond btwn exon 1, intron 1 (2’OH branch site of intron) —->form the 2’-5’ PD bond
2) 3’-OH of exon 1 cleaves PD bond btwn intron, exon 2
- –>exon 1 joined to exon 2, intron released as lariat

40
Q

Spliceosome assembly is de novo from _____

A

SNURPs

41
Q

SNURPs recognize

A

5’ splice site (AG|GU) U1
Branch sit
3’ splice site(AG|G)
Branch site U2

+U4U5U6 complex –>basically scrunched it up

42
Q

Spliceosome assembly requires

A

ATP

43
Q

B-thalassemia is an intron mutation..what kind?

A 
Point mutation (substitution)
-now machinery thinks this is splice site and have 6 extra amino acids as a consequence
44
Q

Tamoxifen

A
  • antagonist
  • binds to estrogen receptor as a competitive inhibitor
  • fails to induce conformational change required for transcription activation
45
Q

How do steroid hormones work?

A

Directly stimulate transcription as hormone-receptor complexes…receptors are transcription factors; bind to dsDNA (promoter) and can cause conformational changes

DNA-Hormone-Receptor Comoplex interacts with coactivator complex –> RNAP II transcriptional machinery stimulated

46
Q

Steroid hormones bind ____ and recruit chromatin remodeling proteins

A

Enhancer sequences

47
Q

How do coactivators work?

A

Recruit/stabilize RNAP II/GTF to core promoter
-clear a path for RNAP II by altering chromatin DNA template

By remodeling chromatin, can now recruit coactivator complex (how estrogen works)

48
Q

What do histone acetyltransferases (HATs) do?

A

Acetylation of histone lysine residue in N-terminal tails of H3, H4 –>chromatin modification

*reversible by histone deactylases (HDACs)

49
Q

ATP-dependent remodeling complexes (aka remodeling engine) does what?

A

Remodel nucleosomes via ATP hydrolysis

–> TFs bind to DNA and promote gene transcription

50
Q

Mechanism of glucocorticoid receptor

A

Cortisol binds -> conformational Chang win receptor -> zinc finger binding domain uncovered -> steroid receptor complex interacts with specific regulatory DNA sequences (GRE)
-hormone receptor complex (w/ coactivator proteins) controls transcription of targeted genes

51
Q

MMTV (mouse mammaery tumors virus)

A

-DNA virus

  • breach cell carcinoma
  • MMTV has DNA sequence identical to estrogen enhancer, integrates next to Wnt-1-protooncogene so WNt1 now regulator of cell proliferation under control of estrogen
52
Q

TFIIH

A

Couples transcription with DNA damage repair

Issue with TFII H associated with some is eases (XP,TTD,CS) since DNA rapier altered

53
Q

Alpha amantin

A

Binds to RNAP II , inhibits elongation of transcription

54
Q

Rifampicin

A

Antibiotic,binds to RNAP of bacteria

BMS (7 decks)

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