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Anatomy > molec of gene > Flashcards

molec of gene Flashcards

1
Q

RNA pol II is ______ to bind promoter

A

unable

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2
Q

General transcription factors: 1. 2. 3. and are analogous to __

A
  1. recruit RNA pol II to promoter 2. melt DNA at promoter 3. allow RNA pol II to start RNA synthesis to sigma factor
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3
Q

GTFs + RNA pol at promoter=

A

pre-initiation complex

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4
Q

pre-initiation complex=

A

GTFs + RNA pol at promoter

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5
Q

The 6 GTFs are TFII_

A

ABDEFH

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6
Q

Human TFIIF has _____ subunits

A

2

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7
Q

GTFs Work in a Step-Wise Fashion TFIID: TBP: TFIIA: TFIIB

A

recognizes TATA box

binds and distorts TATA

box stabilizes TFIID binding

recruits Pol II

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8
Q

TFIID in initiation

A

recognizes TATA box

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9
Q

TBP

A

binds and distorts TATA box

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10
Q

TFIIA

A

stabalizes TFIID binding

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11
Q

TFIIB

A

recruits RNA Pol II

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12
Q

TBP _______, using a beta- sheet inserted into the minor groove, then TFIIB can bind a b-sheet on TBP

A

bends DNA,

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13
Q

Draw Step wise binging of GTFs to promoter

A
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14
Q

Action of TFIIE

A

involved in transition of closed to open transcription complex

  • recruits TFIIH
  • modulates IIH activities
  • promoter escape
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15
Q

Action of TFIIH

A
  • promoter melting
  • promoter escape
  • helicase activities!
  • associated kinase activity
  • essential for NER
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16
Q

Pol II CTD “Tail” composed of

A

composed of a series of 7-amino acid repeats

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17
Q

phosphorylation of CTD tail on ____ leads to ___

A

Ser residues, leads to release of GTFs and promoter escape

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18
Q

The TATA box is recognized by

A

TFIID

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19
Q

____is the primary point of regulation of gene expression.

A

Initiation of transcription

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20
Q

Transitioning from initiation to elongation requires______

A

phosphorylation of the Pol II CTD

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21
Q

TFIIH controls the _______

A

ATP dependent transition into open complex

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22
Q

TFIIH mediates _____

A

promoter melting

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23
Q

2 transcription factors that transtion it from open to closed

A

TFIIE and H

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24
Q

CTD tail is part of

A

RNA pol

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25
Q

CTD tail is phosphorylated by __ at ______in order to ______

A

TFIIH, at serine residues, to initiate promoter esacpe,

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26
Q

Factors that stimulate elongation

A

TFIIS and SPT5

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27
Q

TFIIS and SPT5

A

stimulate elongation

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28
Q

TFIIS

A

reduces pausing of RNA pol II to aid in elongation

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29
Q

SPT5

A

recruits and stimulates 5’ capping enzyme

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30
Q

SPT5 and TFIIS are both recruited to

A

phosphorylated CTD tail of RNA pol II

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31
Q

draw basic elongation model

A
32
Q

TFIIS activates ________within RNA polymerase to _____

A

RNAse activity, proofread during transcription

33
Q

Capping the 5’ end of the RNA occurs

A

as soon as RNA emerges from RNA pol

34
Q

How does the capping machinery disengage?

A

Dephosphorylation of CTD tail @ Ser5 disengages capping machinery.

35
Q

Function of the 5’ Cap (3)

A
  1. prevents degradation of pre-mRNA in nucleus
  2. cap-binding protein (CBC) is needed for export
  3. bound by small subunit of ribosomes
36
Q

Termination and Polyadenylation factors

A

CPSF and CstF

37
Q

CPSF

A

involved in termination and polyadenylation

cleavage and polyadneylation specific factor

38
Q

CstF

A

cleavage stimulating factor

involved in termination and polyadenylation

39
Q

Termination and Polyadenylation Steps

A
  1. The poly-A signal sequence is transcribed.
  2. CPSF and CstF bind the signal sequence in the RNA transcript.
  3. CstF mediates RNA cleavage beyond the sequence and is released.
  4. Poly-A polymerase (PAP) adds ~200 A’s to the 3’ end.

•does not use a template

5.Poly-A binding proteins (PABP) bind the poly-A tail.

  • protect the transcript from degradation
  • allow for export
40
Q

draw diagram of termination and capping steps of transcription

A
41
Q

Draw structure of a gene

A

promoter, exon, intron, etc

42
Q

gene with longest coding region

A

TITIN

43
Q

titin bps

A

280,000

44
Q

titin aas and location

A

38000 and c’some 2

45
Q

longest human gene, bps, aas, and its location

A

dystophin at 2.4 mil bps and 3500 AAs, on the X

46
Q

average interon

A

3300 bps

47
Q

average exon

A

1500 bps

48
Q

spicosome structure

A

150 proteins

5snRNAs and 5snRNPs

49
Q

snRNA types

A

U 1,2,4,5,6

50
Q

purpose of snRNA

A
  1. recognition of mRNA splice sites via complementary bps
  2. recognize eachother via bps
  3. catalytic activities
51
Q

3 critical sequences at in pre-mRNA

A

1 and 2. short conserved sequences at each (5 and 3) splice junction

  1. conserved sequence within intron, containing branch site
52
Q

BASIC mechanism of mRNA splicing

A
  1. 5’ splice site is cut
    - upstream exon is held in place by the spicosome
    - 5 intron is attached to the branch point
  2. 3’ splice site is cut
    - the up and dwn stream exons are joined by phosphodiester bond
    - releasing the lariet from the sequence
53
Q

_______is required to assemble and operate the splicing machinery

A

ATP

54
Q

Detailed mRNA splicing mechanism

A
  1. U1 binds complementary to and then cleaves at 5’ junction (AG|GU)
  2. U2AF attaches at 3’ end, then BPP binds, then U2 binds, connecting att snRNPs and forming the splicosome
  3. BPP and U2AF leave
  4. U5/U6 attach to splicosome
  5. transesterification attaches 5’ G to OH of branch site A to form lariet loop
  6. U1 leaves
  7. 3’ end is cleaved, and exons are joined
  8. splicosome releases taking lariet loop with it
55
Q

How is INAPPROPRIATE SPLICING prevented?

A

Active site formation is a late step!

Only occurs after 5’ and 3’ splice sites + branch point are recognized by multiple components of spliceosome

All spliceosome components are successfully assembled.

56
Q

Potential Errors During Splicing

A
  1. 5’ splice site is recognized, but the nearest 3’ splice site is missed
  2. A sequence similar to splice site is treated as one (“pseudo” splice sites).
57
Q

What mechanisms exist to ensure ACCURATE SPLICING? (2)

A

RNA pol II and ESEs

58
Q

RNA pol II role in splicing accuracy

A
  • ‘cotranscriptional’ loading
  • IMMEDIATELY deposits splicing machinery at the 5’ splice site
  • insures interaction with FIRST 3’ splice site (avoids competition from downstream sites!)
59
Q

ESEs

A

Exonic Splicing Enhancers

  • sequences spread throughout exons, and bound by special proteins!
  • rich in Ser-Arg these proteins (SR proteins) interact with early spliceosome subunits
60
Q

Function of ESEs in Splice Site Selection

A

SR proteins bind to ESEs

  • interact with U2AF and deposit at 3’ splice site
  • interact with U1 and deposit at 5’ splice site
61
Q

3 classes of splicing

A

nuclear pre-mRNA

Group I and II introns

62
Q

Nuclear pre-mRNA splicing

A

2 tranesterifications, branch site A, major and minor splicososomes

most common

63
Q

group II splicing

A

rare 2 transest, branch A, RNA enzyme

64
Q

group II splice

A

rare, 2 transest, branch G, ribozyme

65
Q

splice diagrams comparing

A
66
Q

•Nuclear pre-mRNA splicing may have evolved from ___

A

Group II

67
Q

How does ALTERNATIVE SPLICING

occur?

A

SR proteins are expressed differentially:

  1. different varieties in different cell types
  2. different varieties during development

varying levels of SR proteins

controlled by physiological signals

68
Q

Additional Ways Alternative Splicing Occurs

A

•alternative promoters

•

•alternative poly(A)sites

•

•

•trans-splicing

69
Q

Mechanisms Ensure Mutually Exclusive Splicing

A
  1. steric hindrance
  2. major and minor splice site combinations
  3. nonsense-mediated decay (NMD)
70
Q

Human Disorders Result From Defects in Splicing

A

15% of diseases that are caused by point mutations alter splice sites!

b-thalassemia

TTGGT → TTAGT

familial isolated growth hormone def type II

Frasier syndrome

impaired kidney/gonad development

dementia

defective cytoskeleton protein

cystic fibrosis

71
Q

Some Human Disorders Result From Defects in Splicing

A

Splicing machinery defects

retinitis pigmentosa

retinal degeneration, blindness

spinal muscular atrophy

loss of spinal neurons

Cancer

72
Q

why are there introns?

A
  1. alternitive splicing
  2. formation of new genes via exon shuffling
73
Q

Exon Shuffling

A

The rearrangement of exons by RECOMBINATION, resulting in NEW GENES

Some supporting evidence:

  1. Exon boundaries often coincide with protein DOMAINS.
  2. Genes show evidence of exon DUPLICATION and DIVERGENCE.
  3. Related exons appear in unrelated genes.
74
Q

Reshuffling of Exons, how and favorability?

A

Recombination IN INTRONS may lead to reshuffling of exons.

Recombination IN EXONS may lead to their disruption.

SO: short exons, long introns favors…?

Conservation of splice sites between all genes allows interchangeability.

Alternative splicing may allow the original and reshuffled message to be spliced!

75
Q
A

Anatomy (6 decks)

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