RNA Metabolism: RNA Processing Flashcards

1
Q

Processing of eukaryotic Pre-mRNA

A

1) 5’ end (capped) 2) internal (splicing introns out) 3) 3’end (polyadenylation)

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2
Q

What is capping?

A

capping occurs when ser 5 is phosphorylated; nucleotide is added in wrong direction ( connected via 5 prime end with 3’OH on end); 7 methyl guanine (methylation allows for binding to protective proteins); tethered to ctd tail

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3
Q

What is the purpose of capping?

A

1) protects from exonuclease activity (exonuclease can’t work because of incorrectly placed nucleotide) 2) RNA transport into cytoplasm 3) Translation

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4
Q

3’ Polyadenylation

A

1) cleavage of RNA 10-30n downstream of 3’ UTR 2) addition of A’s (80-250) to generate a poly A tail

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5
Q

what are the only mRNAs that have poly A tails?

A

only those who are produced by RNAPII

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6
Q

CPSF

A

Cleavage/polyadenylation specificity factor (3 subunit protein) recognizes AAUAAA; recruits CtsF (cleavage factors); Recruits PAP (poly A polymerase).

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7
Q

AAUAAA

A

sequence recognized in RNA 3’ UTR that CPSF binds to.

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8
Q

What are the two different models of termination in eukaryotes?

A

Torpedo and allosteric termination.

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9
Q

Torpedo Termination

A

rat1/hxrn2 (exonuclease) tracks along with RNAP,. Pulls RNA out of RNAP. Once it pulls RNA out, RNAP disassociates.

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10
Q

Allosteric Termination

A

Proteins alter conformation of RNAP causing termination

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11
Q

Why is it more advantageous to have more introns?

A

1) Diversity 2) regulation via splicing produces different types of mRNAs and subsequently different proteins 3)

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12
Q

Group I/II splicing

A

Self-splicing; do not require specific factors or ATP; requires two transesterification reactions

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13
Q

Group I

A

self-splicer; uses guanine nucleoside cofactor; occurs in rRNAs of tetrahymena and mitochondrial regions; 1st cleavage performed by external cofactor guanine

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14
Q

Group II

A

self-splicer; uses an A residue within intron= forming a branched lariat structure; found in mitochondria and chloroplast pre-mRNAs; 1st cleavage is carried out by 2’OH of A within intron.

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15
Q

Group III

A

Eukaryotic; spliceosomal introns; the largest class;

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16
Q

Group IV

A

requires for some tRNAs- requires ATP and an endonuclease.

17
Q

Group III mRNA mechanism

A

Step I: cleavage at the 5’ splice site (GUintron; AGexon) and joining of the 5’ end of the introns to the branch point A within the intron, producing a lariat-like intermediate 2) Cleavage at the 3’ (AGintron; G exon) splice site and simultaneous ligation of the exons, resulting in excision of the intron as a lariat- like structure

18
Q

SnRNP

A

small nuclear ribonucleoprotein particles; involved in splicing;

19
Q

What makes up a spliceosome?

A

SnRNPs and pre-mRNA

20
Q

Model of snRNP mediated splicing of pre-mRNA

A

1) U1 finds 5’ GU exon-intron junction (recruited by ASF/SF2 a SR- Ser-Arg-rich region) 2) U2AF sits on pyrimidine track sits between A and 3’ GU of intron 3) U2AF recruits BBP 4) BBP replaced by U2 loop outed 5) U4 (masks U6’s ability to react with U2)/6 (catalytic activity binds to U2)/5; 5) tripothide interacts with U2 and U1. U1 exits, U4 exits, U6 can now interact with U2. 7) Adenine attacks junction forming lariat

21
Q

How does the spliceosome find the splice site reliably?

A

1) Coupling with RNAP. Spliceosomal machinery is present at high concentration at poly A signals 2) Associating splicing factors with CTD

22
Q

Exonic splicing enhancers

A

ESEs; binding sites for SR proteins; SR proteins interact with each other and recruit the splicing machinery.

23
Q

U5

A

helps in finding other splice sites; helps keep U4 and U6 together.

24
Q

U1

A

U1SnRNP binds to the 5’ splice junction

25
Q

U2

A

U2snRNP binds to the intron branch point and facilitates 2’, 5’-phosphodiester bond formation

26
Q

U4

A

masks the catalytic activity of U6 in the U4/U6/U5 tri snRNP complex;

27
Q

E complex

A

Early presplicing complex; defines the intron prior to splicing;

28
Q

U6

A

base pairs with 5’ site (same as U1), after U1 leaves.