RNA processing

Question 1

pol II makes

Answer 1

mRNAs

Question 2

pol III makes

Answer 2

tRNAs

Question 3

pol I makes

Answer 3

rRNAs

Question 4

what are types of RNA processing events? (5)

Answer 4

cleavage, splicing, capping, polyadenylation, editing

Question 5

how are ribosomal RNAs processed?

Answer 5

transcribed as polycistronic (equimolar) by pol I with a strong promoter, processed in nucleolus by RNAse III-family enzymes that cleave ds regions of RNA

Question 6

how are tRNAs processed? (4)

Answer 6

5’ tail cleaved off by RNAse P, 3’ end CCA added by CCA-adding enzyme, post-transcriptional mods and intron excision

Question 7

bacterial vs eukaryotic rRNA/tRNA mods?

Answer 7

Bacteria: number of distinct modifications rRNA
Eukaryotes: mostly 2’ -O Me and pseudoU rRNA
tRNAs: >100 diff mods

Question 8

template directed modification system

Answer 8

snoRNAs, produce 2’ O Me and pseudouridylation

Question 9

how is mRNA cap made?

Answer 9

transcript has PPP, 5’ phosphate removed, GMP added, then methylated to form m7GPPP - this is an unusual mod that is protective in that it’s not cleaved by standard enzymes

Question 10

how is mRNA 3’ end processed?

Answer 10

cleavage of U/GU rich region downstream of AAUAAA, then polyadenylation by poly(A) polymerase. Bound by PABP

Question 11

what mRNAs don’t have a polyA tail?

Answer 11

histone mRNAs, instead have a 3’ stem loop which is bound by SLBP to replace PABP

Question 12

why do we need cap and polyA tail? (5)

Answer 12

1. direction of downstream maturation (splicing/transcription termination)
2. Cytoplasm transport
3. APA/alternative capping can be regulatory
4. Stabilization
5. Translation initiation

Question 13

how are exons and introns defined?

Answer 13

by bound protein factors - SR proteins like exons, U1/U2 like introns near boundary, and hnRNPs in intron body

Question 14

ESEs

Answer 14

exonic splicing enhancers, recognized by SR proteins

Question 15

what chemistry does the spliceosome do?

Answer 15

sequential trans-esterification reactions, with products of ligated exons and a released intron in the form of a branched lariat

Question 16

what do snRNPs do?

Answer 16

form the spliceosome, U1/U2/U4/U6 - undergoes a series of structural rearrangements involving RNA:RNA interactions

Question 17

T/F. RNA binding proteins determine strength of splice sites in different tissues

Answer 17

True

Question 18

how is RNA spliced in order?

Answer 18

spliceosomes attach early onto nascent transcripts, interactions mediated by phosphorylation of CTD