BIOL 308 > RNA Processing > Flashcards

RNA Processing Flashcards

(51 cards)

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1
Q

what 3 things happen to the pre mRNA before it goes to the nucleus ?

A
  1. 5’ methylated guanosine cap
  2. introns are removed by splicing
  3. 3’ ends are cleaved and poly A tail is added
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2
Q

what is heterogenous nuclear RNA(hnRNAs) ?

A

it is the collection of transcript made by RNAP II
hnRNAs = pre-mRNA +snRNA that are covered by hnRNProteins

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3
Q

what are 4 reason why the 5’ capping methyl guanonise is key

A
  1. protection from degrations
  2. enhanced splicing
  3. enhanced 3’ processing
  4. Stimulates translation
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4
Q

how does the methylation of the 5’ end work?

A

cap enzymes bind to CTD and RNA triphosphatase cleaves phosphate at 5’ end then RNA guanylytransferase adds GMP to a diphosphate then RNA methyl trans add a methyl group

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5
Q

similar to the reason of why methyl capping is key what is the one differen in reasoning for poly a tail

A

PAB binding site and mRNA stabilization

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6
Q

what is the polyadenylation signal

A

A and U site AAUAAA then a gu rich sequence to add a poly a tail

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7
Q

what are the 2 transcription termination models ?

A
  1. allosteric (anti-term) model
  2. torpedo model
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8
Q

what is the allosteric model?

A

where transcription of PAS cause a change in RNAP II that cause termination

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9
Q

what is the torpedo model ?

A

a 5-3 endonuclease decays the rna and slow down the polymerase and disengages it

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10
Q

what are the 3 mechanism of splicing and facts

A

Group I introns : rare in Rrna uses ribozyme can self splice 2 trans , G
Group II introns: rare in genes uses ribozyme can self splice 2 trans
Nuclear mRNA: use for most genes ,A uses splisomes 2 trans , A

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11
Q

what is the difference betwween trans splicing and alt splicing

A

in alternative exons in the same mrna are connected in different ways but in trans exons are linked

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12
Q

what is the 5 types of pre translational control ?

A
  1. Localization of mRNA
  2. RNA Editing
  3. Post transcriptional gene silencing
  4. transcriptional control switch
  5. mRNA longevity and Stability
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13
Q

why do eukaryotes mRNA need additional processing prior to translation

A

to prevent making faulty protein

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14
Q

what does poly-A polymerase do ?

A

it adds adenosine to the 3’ end on mRNA to protect it

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15
Q

what is the Role of CTD tail in polyadenylation ?

A

recruit enzymes necessary for polymerization

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16
Q

what is the Role of CPSF in polyadenylation and what does it bind to ?

A

cleavage and polyadenylation factor that binds to poly A sequence

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17
Q

what is the Role of CStF in polyadenylation and what does it bind to

A

cleavage stimulation factor that binds to G/U region

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18
Q

what is the Role of CFI & II in polyadenylation ?

A

cleavage factor 1 & 2 where mRNA is cleaved

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19
Q

what is the Role of PAP in polyadenylation ?

A

poly (A) polymerase binds

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20
Q

what is the 5 order of polyadenylation with the enzymes?

A
  1. CTD tail
  2. CPSF.
  3. CStF
  4. CFI & II
  5. PAP
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21
Q

what does PAB II do ?

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A

speeds up polyadenylation

22
Q

what is alternative splicing

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A

commonly within higher organisms pre-mRNA is spliced in different ways to make different functional isoforms of a protein

23
Q

what is trans splicing

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A

rare but generation of unique mRNAs by linking exons of 2 different pre mRNA

24
Q

what is the constitutive splicing and what is it used in?

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A

same introns will consistently be taken out used in simple transcription units

25
what is the difference between Group I and Group II introns?
Group I uses branch G and Group II uses branch site A for transesterification
26
what is the 4 step splicing general reaction what occurs at each transesterification?
1. @ 1st trans : phosphate ester bond between 5' from intron and 3' from exon 2. 5' from intron bonds to 2' from branching site A 3. @ 2nd trans: ester bond between 5' of exon 2 and 3' intron is freed 4. 5' of exon bond to 3' of exon and release the intron lariat
27
what are 4 key factors that are involved in splicing ?
1. SR proteins 2. RNA binding domains (RBD) 3. helicases 4. proteins that recognize single strand regions
28
what do snRNAS AND Sm proteins assist with ?
the splice and branch site recognition and bind
29
what is the 10 step specific constitutive spliceosomal splicing?
1. U1 attaches to 5' intron 2. U2 binds to branch point A via ATP 3. U4/U6, U5 bind as a complex to 3' intron 4. U4 and U6 change conformation due to binding of spliceosome 5. U6 leaves U4 which displaces U1 6. U1 AND U4 leave via ATP 7. Spliceosomes is activated with U2, U5 , U6 snRNPs 8. 1st trans and 2nd trans happen 9. lariat is degraded 10. snRNPs released
30
what does u5 and u2-u6 do ?
u5 positions and hold , u2-u6 has catalytic activity
31
what does is the difference between complex and simple transcriptional unit ?
complex has alternative splicing simple has constitutive splicing
32
what are the 3 regulators of Alternative splicing and how do they do it ?
1. intro and exons; ESE or ISE (exon splice enhancers , ESS or ISS ( Exons splicing silencers 2. Splicing Activators- has SR protein for attracting splicing machinery 3. Splicing Repressors- bind RNA but cant call splice machinery
33
what 3 things does the role of alternative splicing is key ?
1. Tissue: hepatocytes- cons , fibroblast- alter 2. Developmental 3. Sex Determination- in dros splice determines sex
34
what does the U1A protein do?
it inhibits polyadenylation but not cleavage by binding to an upstream site
35
what is alternative polyadenylation (APA) ?
it is an alternative way to regulate gene expression
36
what is discontinuous group II trans splicing ?
plant organelles genes in complex units
37
what is the role of the cytoskeleton ?
for transport and local translation of specific mRNAs
38
how can mRNA transported through the nuclear pore into cytoplasm
the recognition of 5' cap and exons junction complex , polyadenyl that make up the hnRNPs
39
why is localized the mRNA important ?
its is put in different part of the cell for specific functional control or for spatial and temporal control for protein to build complex struct
40
what are two types of RNA editing?
1. Deamination of A to I(ionsine) 2. Deamination of C to U
41
what does RNA editing do and what mediates it ?
U deletion or addition through TUTASE that is by gRNA guide RNA
42
what is the anchor region of gRNA ?
binding of gRNA to mRNA due to complementarity
43
what is the editing region of gRNA ?
partial complementarity with mRNA that guides deletion of U's
44
what enzyme deminates A to I and what is the consequence of having I?
ADAR, adenosine deaminase and in translation the I is read as a G so it affect stop codon, branch points and splice point
45
what is RNA interference ?
double or single strand RNA gene silencing by binding
46
what are the 4 roles of small RNAs
1. Regulator factor in pre-translation 2. chromatin silencing 3. suppression of mobilization 4. defense against viral infection
47
What is the 3 step process of making siRNA and miRNAs
1. DICER cuts imperfect hairpins into miRNAs and DiICER cuts dsRNAs into small interfering RNA snRNAs 2. siRNAs and miRNAs become single strand RNAs in the RNA induced silencing complex 3. depending on the % of completerity with target mRNA RISC can stop translation
48
what are the two type of translational control switch iron response elements and where an what do they do
1. Ferritin mRNA - in 5' UTR control translation 2. Transferrin mRNA- in 3' UTR controls degradation
49
what occurs when iron is low in the cell ?
IRE-BP (trans factor) is active ferritin trans is stopped and transferrin is translated no degradation
50
what occurs when iron is high in the cell
IRE-BP (trans factor) is inactive ferritin is synthesized but transferrin is not
51
what determines the amount of mRNA in the cell ?
the balance between mRNA degradation and synthesis
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