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YEAR 2 S1 MOLECULAR > Gerber L2 RNA Processing > Flashcards

Gerber L2 RNA Processing Flashcards

1
Q

mRNA accounts for how much of transcribed RNA

A

1.5%

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2
Q

what is the start codon

A

AUG

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3
Q

what is the stop codon

A

UAA, UGA, UAG

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4
Q

RNA binding proteins (RBPs) comprise what % of protein repertoire

A

3-11%

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5
Q

RNA binding proteins have what structure

A

modular structure comprised of RNA-binding motifs

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6
Q

the CARBOXY-TERMINAL domain of RNA Pol ll does what

A
  • acts as a scaffold for assembly and coordination
  • recruits RNA processing enzymes:
  • 5’ cap formation enzyme
  • splicing proteins
  • 3’ end processing factors
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7
Q

describe the structure of the 5’ cap

A
  • consists of 7-METHYL GUANOSINE attached to the 5’ most nucleotide through a 5’-P-P-P-5’
  • the 2’ OH group of ribose 1 and 2 can be methylated
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8
Q

what is the function of the 5’ cap in eukaryotic mRNAs

A
  • 5’ cap marks RNA molecules as mRNA (other RNAs don’t have cap)
  • regulates NUCLEAR EXPORT of mRNAs
  • protects mRNAs from RNA digesting enzymes
  • promotes translation through interaction with a translation initiation factor (eIF4e, the cap-binding protein)
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9
Q

what is splicing

A

moval of introns from the pre-mRNA

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10
Q

describe splicing

A

1) TRANSESTERIFICATION
- 2’OH group of branch-site adenosine (A) attacks the phosphate group at the 5’ splice-site intron
2) 3’OH group at 5’ splice-site attacks phosphate at 3’ splice site
3) Branched lariat is formed and rapidly degraded by nuclear exosome

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11
Q

snRNAs are what

A

small nuclear RNAs

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12
Q

what is the structure of the spliceosome

A

5 snRNAs

~170 proteins

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13
Q

how is splice site determined

give examples

A

CONSENSUS SEQ
base pairing between seq in non-coding RNA (snRNAs) and “splice-site” seq
1) U1 snRNA has a complementary seq to exonintron splice site, O base pairs
2) U2 snRNA : pre-mRNA annealing at branch point

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14
Q

where does U1 snRNP ( small nuclear ribonucleoproteins) assemble

A

1) U1 snRNP assembles at the 5’ splice site; U2 snRNPat the 3’splice site; Splicing factor 1 (SF1) at the branch-point A
2) trimeric snRNP complex (U4, U5, U6) joins to form the spliceosome
3) Rearrangement of base-pairing interactions to from catalytically active spliceosome. U1/U4 snRNPs released
4) Catalytic core catalyses the first transesterification reaction > intron lariat is formed
5) Further rearrangement joins the two exons in a second transesterification reaction.
6) The excised lariat intron is converted to a linear RNA by a debranching enzymes and degraded by the exosome

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15
Q

how does exon size compare with introns

A

~10x shorter than introns

  • avg length = ~150 bases
  • ~10 axons per gene

introns

  • avg ~1.5kb length
  • largest= 1.1Mb
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16
Q

which additional factors are used to guide snRNPs to splice sites

A

SR PROTEINS

  • serine arginine rich proteins bind preferentially to EXON seq
  • Heterogenous nuclear ribonucleoproteins (hnRNPs) preferentially bind intron sequences
17
Q

what is the purpose of alternative spliicing in euk

A

generating mRNA variants from the same gene

  • alternative exons can gen different transcripts which are translated
  • cell/tissue specific splicing
  • allows for high diversity
18
Q

give an extreme example of alternative splicing

A

DSCAM gene
functions:
- immune syst (pathogen phagocytosis)
- neurons (cell-surface molecule to specify neural connections)

19
Q

what is alternative splicing controlled by

A

activator and repressor (simply sits on the splice site and hinders the access of the spliceosome to the splicing reaction)

20
Q

mutations of splice sites can cause what?

A

DISEASE :(

1) BETA-thalassemia
- INHERITED blood disorder (autosomal recessive)
- severe anaemia due to low Hb
- mutation in splice sites in beta globin gene
2) MYOTONIC DYSTROPHY
- Neuromuscular disease, 2 types (DM1 and DM2)
- DM1: Depletion of a splicing factor (MBNL) leads to mis-splicing of pre-mRNA targets.
3) CF
4) PARKINSON’S
5) RETINITIS PIGEMENTOSA
6) PREMATURE AGEING
7) CANCER

21
Q

mechanism of 3’ cleavage

components

A

req protein complex consisting:

  • CPSF(cleavage and polyadenylation specificity factor)
  • CstF(cleavage stimulatory factor)
  • Two cleavage factors (CFI, CFII)
  • Poly(A) polymerase (PAP)
22
Q

mechanism of 3’ cleavage

A

1) CPSF binds to the AAUAAA
sequence, CstF to the U-rich
sequence, creating a loop.
2. PAP joins the complex; RNA is cleaved
3. CStF and CFs are released, and PAP
adds ~ 10 As to the new 3’ end.
4. Poly(A) binding protein II (PABPII) binds to the short poly(A) tail and
stimulates further addition of Adenosines
5. The whole poly(A) tail (~200 Adenosines) is
ultimately covered by PABPII.

23
Q

what is the function of the poly (A) tail in euk

A
  • Required for export of the mRNA from the nucleus to the cytoplasm (binding of PABPII)
  • Promotes translation initiation and translation
  • Stabilizes the mRNA > shortening of poly(A) tail may lead to reduced translation and eventual decay of the
    mRNA
24
Q

why is regulated cleavage and polyadenylation important

A

determines whether antibodies are secreted or remain membrane-bound

25
Q

what are the 5 patterns of alt splicing

A

1) exon/intron skipping
2) intron retention
3) alternative 5’ splice site
4) alternative 3’ splice site
5) mutually exclusive exons (dep on direction)

26
Q

how does cleavage and polyadenylation determine whether ABs are secreted or membrane bound

A
  • if resting B cell, low CstF
  • poly A tail added
  • causes splicing of intron
  • membrane domain to keep ABs membrane bound is encoded
  • AB attached to surface of membrane

or

  • signal comes to activate B lymphocytes
  • high CstF
  • O weak poly A site
  • splicing machinery assembles on weak poly A site
  • causes shorter pre-mRNA
  • HYDROPHILIC domain encoded
  • O ABs can be secreted
27
Q

how are substances exported out of the nucleus

A
  • small mol and proteins can diffuse through thr membrane

- macromolecules (RNP) need active transport

28
Q

how is mRNA exported out of the nucleus

A
  • cytoplasmic cap-binding protein (eIF4e)
  • nuclear cap-binding protein, nuclear poly A binding protein
  • nuclear export factors (NXF1/T1), these are released in cytoplasm and reimported to the nucleus. Req energy

YEAR 2 S1 MOLECULAR (7 decks)

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