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Molecular Biology of the Gene > RNA processing > Flashcards

RNA processing Flashcards

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1
Q

What is RNA processing?

A

Any type of reaction that modifies the RNA molecule after transcription.

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2
Q

What are the 4 events that can occur during RNA processing?

A
  1. 5’ end capping
  2. 3’ end processing - cleavage and polyadenylation
  3. Splicing
  4. RNA editing (doesn’t always happen).
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3
Q

In what order do the events of RNA processing happen?

A
  1. 5’ end capping
  2. Splicing
  3. Cleavage and polyadenylation (3’ end processing).
  4. RNA editing (if it occurs).
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4
Q

When do the RNA processing events occur?

A

Co-transcriptionally

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5
Q

Which 3 processes occur systemically to all RNAs during RNA processing?

A
  1. 5’ end processing
  2. Splicing
  3. Cleavage and polyadenylation
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6
Q

What are the biological roles of the 5’ CAP?

A

mRNA stability - protects RNA from degradation by 5’ exonucleases because it doesn’t resemble the proper substrate.
Aids with splicing and polyadenylation processes.
Translation initiation
In the nucleus the cap is bound by the cap-binding complex which is recognised by the nuclear pore complex facilitating export of the transcript from nucleus to cytoplasm.
In the cytoplasm the cap-binding complex is replcaed by the translation initiation factor eIF4E essential for translation initiation.

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7
Q

What are the biological roles of the polyA tail?

A

mRNA stability - protects RNA from degradation.
Translation efficiency
To promoter nuclear export

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8
Q

What is the biological role of splicing?

A

Source of genetic variation and complexity

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9
Q

What is the biological role of RNA editing?

A

Contributes to protein variability.

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10
Q

How is co-transcriptional RNA processing regulated?

A

By phosphorylation of the CTD of RNAP II by TFIIK.

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11
Q

Phosphorylation of which serine promotes interaction between RNAP II and the capping complex?

A

Serine 5 of the 52 heptapeptide repeat.

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12
Q

Phosphorylation of which serine promotes interaction between RNAP II and the spliceosome?

A

Serine 2 of the 52 heptapeptide repeat.

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13
Q

How long is the nascent pre-mRNA when RNAP II interacts with the capping enzyme complex?

A

22-40 nucleotides

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14
Q

What promotes interaction of RNAP II and the capping enzyme complex?

A

Phosphorylation of serine 5 of the 52 heptapeptide repeat of the CTD of RNAP II by TFIIK.

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15
Q

What promotes interaction of RNAP II and the spliceosome?

A

Phosphorylation of serine 2 of the 52 heptapeptide repeat of the CTD of RNAP II by TFIIK.

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16
Q

What is the 5’ cap?

A

7-methylguanosine linked to the pre-mRNA via a 5’-5’ phosphodiester linkage.

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17
Q

What are the 3 enzyme-mediated steps of capping?

A
  1. RNA triphosphatase cleaves the gamma phosphate from the 5’ end of the RNA.
  2. RNA guanyltransferase adds GMP from GTP to the RNA diphosphate and links guanosine to the beta-phosphate of your nucleotide.
  3. Guanine methylase methylates the guanosine.
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18
Q

What 3 enzymes constitute the capping enzyme complex?

A

RNA triphosphatase
RNA guanyltransferase
Guanine methylase

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19
Q

What are the 2 steps of 3’ end processing?

A

Cleavage and polyadenylation.

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20
Q

Which step of RNA processing is linked to eukaryotic transcription termination?

A

Cleavage and polyadenylation.

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21
Q

Between which 2 cis-acting sequences are most mRNA 3’ ends cleaved?

A

AAUAAA and G/U rich element.

22
Q

By how many nucleotides are the AAUAAA and G/U rich element separated?

A

20 nucleotides.

23
Q

Which trans-acting factor binds the AAUAAA cis-acting sequence?

A

CPSF-160

24
Q

Which trans-acting factor binds the G/U rich element?

A

CstF-64

25
Q

How many subunits is CPSF composed of?

A

5 subunits

26
Q

How many subunits if CstF composed of?

A

3 subunits

27
Q

Which cis-acting sequence does CPSF bind?

A

AAUAAA

28
Q

Which cis-acting sequence does CstF bind?

A

G/U rich element

29
Q

What is polyadeylation?

A

The process by which the polyA tail is synthesised.

30
Q

The AAUAAA and G/U rich elements are what types of sequence?

A

Cis-acting.

31
Q

What other enzyme does CPSF interact with?

A

PolyA polymerase

32
Q

Which enzyme catalyses the addition of 100-250 A residues?

A

PolyA polymerase.

33
Q

What is the role of polyA polymerase?

A

Catalyses the addition of 100-250 adenosine residues to form the polyA tail.

34
Q

How many mammalian mRNA-encoding gene express alternative polyadenylation isoforms?

A

70%

35
Q

What is alternative polyadenylation?

A

Differential usage of polyadenylation sites to form distinct mRNA isoforms with different properties to regulate the same mRNA in different ways in different tissues.

36
Q

What are the two types of alternative terminal exons generated through alternative polyadenylation?

A

Skipped temrinal exons

Composite terminal exons

37
Q

Where are the alternative polyadenylation sites usually located?

A

Within the 3’UTR

38
Q

mRNAs with what length 3’UTRs are usually translated at higher levels?

A

Shorter 3’UTR = translated at higher levels = higher protein levels.

39
Q

What kind of regulation is RNA editing?

A

Epigenetic

40
Q

What is RNA editing?

A

The process by which ORFs can be altered after transcription to specifically change the sequence of the RNA without altering the sequence of the parent strand.
It is a way of changing the genetic content of a cell without changing the genetic sequence.

41
Q

When was RNA editing first discovered?

A

In the 1980’s in trypanosomes.

42
Q

What are the 2 types of RNA editing mechanisms?

A
  1. Base modification RNA editing

2. Insertion or deletion RNA editing

43
Q

What is base modification RNA editing?

A

This results in an mRNA of the same length with altered sequence by changing 1 particular nucleotide into another.
There are two possible events A to I or C to U.
In both cases these are deamination events mediated by ADAR or CDAR enzymes (A to I and C to U respectively).
This changes the coding capacity of the RNA but leaves the genome unaltered.

44
Q

What are the two possible base modification events that can occur during RNA editing?

A

Adenosine converted to inosine.

Cytosine to uracil.

45
Q

Which enzymes convert A to I in base modification RNA editing?

A

ADAR enzymes.

46
Q

Which enzymes convert C to U in base modification RNA editing?

A

CDAR enzymes.

47
Q

What is insertion/deletion RNA editing?

A

Either insertion or deletion of an extra nucleotide.

This allows the length of the mRNA to be slightly shortened or lengthened and can change the ORF.

48
Q

Which base is most commonly added or removed during insertion/deletion RNA editing?

A

U

49
Q

What is the benefit of RNA editing?

A

Contributes to protein variability.

50
Q

What is the role of PolyA binding protein?

A

Increases the affinity of polyA polymerase for RNA for further extension of the polyA tail.

51
Q

What is splicing?

A

Removal of the introns and joining of exons to move from pre-mRNA to a fully spliced mRNA.

Molecular Biology of the Gene (5 decks)

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