Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Y3 RNA World > RNA processing > Flashcards

RNA processing Flashcards

1
Q

Describe mG7 capping

A

Guanine is methylated which prevents degradation of mRNA at the 5’ end
mRNA without a cap is degraded in the cell
Important in RNA export and stability
Aids in quality control as mG7 is recognised by cap binding protein 20

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Why is the RNA pol II CTD important?

A

Acts as a platform for co-factors
Can be phosphorylated to aid in certain processes, e.g splicing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is the RNA pol II CTD heptapeptide that can be phosphorylated

A

YSPTSPS
(You should probably take some presents santa)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What does phosphorylated Ser on RNA pol II do?

A

S2- Phosphorylated by Cdk9/12/13 to help RNAPII elongate down the gene
S5- Phosphorylated by Cdk7 for capping and splicing
S7- Phosphorylated by Cdk7, function unknown

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What does phosphorylating T on the RNAPII CTD do?

A

Used for histone mRNA processing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What does the exon junction complex do?

A

Links mRNA biogenesis to quality control
Enhances mRNA export, protein synthesis and NMD
Suppresses inappropriate recognition of splice sites

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Outline the splicing process.

A
  1. U1 snRNP binds 5’ exon,
  2. U2 snRNP binds 3’ exon defined by SR proteins and branchpoint A. This displaces branchpoint A binding protein (BBP) and U2AF
  3. U5 and U4/U6 snRNP bind to these and form an intron lariat by binding together. Creates the active site of the spliceosome
  4. Intron lariat is cleaved and debranched from snRNPs and degraded
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Describe 3’ RNA end formation

A

Poly A tail forms 10-30nt upstream of the cleavage site
PABP binds to this
During formation, CPSF binds RNAPII to pause it and do quality checks

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

How are introns and exons defined?

A

Introns are bundled into hnRNPs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What can alternative splicing do?

A

Skips exons/introns
Alternative 5’ or 3’ splice sites
Alternative promotors
Intron retention leading to decay and downregulation of mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

How are exons defined

A

Exons are bound by SR proteins to enhance splice sites as recognition sequence is 4bp
5’ exon cap is bound by the CBC complex.
PABP binds poly A tail

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

How does Duchenne muscular dystrophy come about?

A

Alternative splicing of dystrophin gene leads to it being truncated as exons are skipped
Dystrophin translation is halted altogether

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

How is sex determined

A

Governed by splicing
U2AF binds to exon, blocking U2snRNP and driving exon inclusionn of sex lethal in males
Without U2AF exons skip from 2 to 4, allowing Sxl expression for females

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How does 3’ UTR shortening contribute to cancer

A

miRNA no longer recognises 3’ UTR and the gene is transcribed more
e.g, shorter poly A on the Ras oncogene means the miRNA Let7 no longer recognises it. Ras oncogene is upregulated, leading to lung cancer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How does U1 snRNP keep the poly A long?

A

U1 snRNP concentration determines length of mRNA
Suppresses polyadenylation cleavage in early poly A tails

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

How does mRNA <200-300nt export from the nucleus?

A
  1. hnRNP tetramers wrap 200-300 bases around it to act as a molecular ruler.
  2. RNA unravels when it gets to the NPC
  3. Once moved through, Dbp5 (RNA helicase) strips Nxf1 from mRNA
  4. Gle1 drives ATP hydrolysis of Dbp5, causing release
  5. Nup159 releases ADP from Dbp5
17
Q

How does the TREX complex promote mRNA export?

A
  1. CBP80 subunit of nuclear cap binding complex allows ALYREF to bind. ALYREF allows TREX to bind 5’ mRNA and recruit Nxf1
  2. Exon junction complex stabilises TREX on mRNA, allowing mRNA to be marked for export
  3. TREX ensures free Nxf1 exports mRNA before processing by changing its conformation to autoinhibit RNA binding domain
18
Q

How does spinal muscular atrophy come about?

A

Mutation in exon 7, means it is skipped.
Exon 6 and 8 join and the protein cannot bind oligomers
Antisense oligonucleotides that drive inclusion of exon 7 is treatment

19
Q

Why is the SMN protein important?

A

Key to producing snRNPs in cajal bodies so snRNA can be produced
SMN forms a ring around snRNA in cytosol, trimming the hypermethylation on the 3’ cap and allowing it to move the cajal body and make an active snRNP complex

20
Q

What is siRNA

A

short intefering RNA
21-25 nt
Mostly exogenous
dsRNA precursor
Target specific

21
Q

How is the chalcone synthase gene in petunias post-translationally silenced?

A

Chalcone synthase is required for a deeper purple
Overexpressing the gene leads to white and variegated petunias
Silencing persists despite miRNA being easy to degrade

22
Q

How is motor neuron disease caused?

A

Fus binds snRNP, TDP43 and SMN
Fus usually connects U1snRNP to RNAPII but is occupied
U1 snRNP is mislocalised to the cytosol in ALS as the Fus NLS is mutated
U1 snRNP depletion in nucleus leads to motor neuron cell death

23
Q

Describe miRNAs

A

21-25nt
Encoded by endogenous genes
Hairpin precursors
Recognise multiple targets
Achieves post-translational gene repression by
deadenylation
proteolysis
blocking initiation
blocking elongation

24
Q

Describe miRNA processing

A
  1. RNAPII generates pri-mRNA which contains hairpins
  2. DGCR8 and Drosha clamp the hairpin out of RNA
  3. Pre-miRNA is exported with exportin-5 to the cytosol
  4. Dicer cleaves pre-miRNA in the stem to generate an miRNA duplex. 5’ end has more A-T content, making it easier to unwind
  5. Dicer, TRBP and AGO form the RISC complex. AGO cleaves the passenger strand and unwinds DNA
25
Q

How is RNA silenced via an RNA pathway?

A
  1. Long dsRNA activates 2’, 5’ OligoA synthetase.
  2. This activates RNase L which degrades RNA
  3. Long dsRNA acitvates PKR via phosphorylation
  4. PKR phosphorylates EIF2α which blocks protein synthesis initiation
26
Q

What do lncRNAs do?

A

Regulate nearby genes when transcribed
Alter epigenetic chromatin modifications
Good transcriptional regulators
Involved in mRNA stability and histone modifications

27
Q

What makes lncRNAs good transcriptional regulators?

A

Tightly controlled spatial and temporal expression
Rapidly turned over
Has RNA recognition motifs (RRM)

28
Q

What protein-RNA binding domains exist?

A

RRM
hnRNP K-homology motif (KH)
Zinc finger domains (ZnF)
Non-canonical RNA binding domains- chromatin organisation

29
Q

How are lncRNAs strucutred?

A

5’ ends have mG7 caps
3’ end processing less well defined
Mainly polyadenylated
Sometimes spliced

30
Q

How do lncRNAs recruite genes?

A

Interact with nascent RNA during transcription
Base pair with another RNA and target DNA

31
Q

How can lncRNAs inhibit transcription?

A

Block transcriptional regulation factors by
acting as a decoy
Blocking active site
Allosteric effects

32
Q

What is Neat1?

A

lncRNA that regulates paraspeckle formation to localise transcriptional proteins

33
Q

What is HOTAIR?

A

lncRNA that acts in trans
Acts as a scaffold to hold the REST complex (H3K4 demethylation) and PRC2 (H3K27) trimethylation
Activates/deactivates HOX genes

34
Q

What is Xist?

A

lncRNA involved in X-inactivation
Coats inactive X-chromosome in cis to repress it
Silenced by Repeat A (RepA), which allows PRC2 to lay down trimethylation on the Xist promotor

35
Q

What is the difference of cis and trans genes

A

cis- affects genes proximal of lncRNA locus
trans- acts as a signal, scaffolds, guides to express distant genes

Y3 RNA World (3 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions