post transcriptional processing

Question 1

the primary transcript must undergo ____________ to generate a mature, translation-ready ______. A mature ______ has a 5’ and a 3’ ________________ flanking a _____________. the 5’ end has a “_____” and the 3’ end a “___________”

Answer 1

RNA processing; mRNA; mRNA; untranslated region (UTR); coding sequence; cap; poly-A tail

Question 2

the ________ is assembled on the 5’ end of mRNA molecules by ________________.
- the 5’ cap provides __________________________
- also important for ___________________

Answer 2

5’ cap; capping enzyme; protection from 5’ to 3’ exonucleases; translation initiation

Question 3

phosphorylation of RNA pol II CTD is necessary for:

Answer 3

-promoter escape (transcription initiation)
-as docking sites for RNA processing enzymes including capping enzyme, cap-binding complex, cleavage/termination complexes, RNA splicing factors

Question 4

_______ continues transcription beyond the termination sequence

Answer 4

RNA pol II

Question 5

_____________ occurs with cleavage of the endonuclease-> RNA pol II dissociates

Answer 5

termination

Question 6

3’ end undergoes ____________ by ______________ or __________________, one of the termination factors
- a _________ is 50-100 nucleotides long

Answer 6

polyadenylation; polyadenylate polymerase; or poly A polymerase; poly A tail

Question 7

most mRNAs in mammals undergo splicing to remove ______ sequences and link ______ sequences. The order of exons in a mRNA is identical to their organization 5’ -> 3’ in the gene.

Answer 7

intron; exon

Question 8

the ______ governs RNA splicing. A splice junction linking the 5’ exon to the 3’ exon is formed during splicing. All the intervening intron sequence is excised.

Answer 8

GU/AG rule

Question 9

5’ end of an intron is ____. the _______________ is immediately upstream

Answer 9

GU; 5’ splice site

Question 10

3’ end of an intro is ____. the _______________ is immediately downstream

Answer 10

AG; 3’ splice site

Question 11

within the intron is the __________.

Answer 11

branch point A

Question 12

spliceosome

Answer 12

nuclear complex responsible for removing intron sequences and ligation of exon sequences 5’->3’ to generate a mRNA

Question 13

U1 snRNP

Answer 13

binds to 5’ splice site in RNA

Question 14

U2 snRNP

Answer 14

binds to the branch site and aligns it for the 1st splicing reaction

Question 15

U4 snRNP

Answer 15

binds to and sequesters U6 snRNP

Question 16

U5 snRNP

Answer 16

aligns the pre-RNA for the 2nd splicing reaction

Question 17

U6 snRNP

Answer 17

promotes catalysis of splicing reactions

Question 18

splicing mechanism
1. ________ is recruited to 5’ splice site
2. _______ is recruited to branch site A
3. _______ and ____________ bind to the complex to complete spliceosome assembly.
4. Dynamic rearrangement of spliceosome initiates splicing activity
- both U1snRNP and U4 snRNP exit; spliceosome is now in the catalytically active conformation

Answer 18

U1 snRNP; U2 snRNP; U5 snRNP; U4 snRNP/U6 snRNP

Question 19

___, ___, and ______ rearrange aligning the 5’ and 3’ splice sites for the 2nd reaction

Answer 19

U2, U5, and U6 snRNA

Question 20

small nuclear ribonuclear protein (snRNP)

Answer 20

complexes that make up the bulk of a spliceosome

Question 21

__________ formation requires unusual __________________________

Answer 21

lariat; 2’-5’ phosphodiester bond

Question 22

1st transesterification reaction

Answer 22

2’ OH of branch point A attacks 5’ P of intron

Question 23

2nd transesterification reaction

Answer 23

3’ OH of exon attacks 5’P of downstream exon

Question 24

a ___________ resulting from an error in selection of a 3’ splice site= hemophilia

Answer 24

splicing defect

Question 25

alternative splicing

Answer 25

mechanism for developmental or tissue-specific production of differing mRNA (& thus proteins) from a single gene

Question 26

____________ (serine/arginine rich) promote splicing by binding ______________________

Answer 26

SR proteins; exonic splicing enhancers (ESE)

Question 27

____________________________ bind to __________________ and inhibit splicing

Answer 27

heterogeneous nuclear ribonuclear proteins (hnRNP); exonic splicing silencers (ESS)

Question 28

RNAi

Answer 28

group of mechanisms in eukaryotes involving small ncRNAs that reduce expression of specific genes

Question 29

___________ and ______________ act on mature mRNA in the cytoplasm.

Answer 29

microRNA (miRNA) and small interfering (siRNA)

Question 30

miRNA

Answer 30

regulates both whether an mRNA can be translated and its stability

Question 31

siRNA

Answer 31

regulates mRNA levels by direct endonuclease cleavage
- mech more important in plants

Question 32

miRNA/RISC

Answer 32

represses translation and increases turnover of target mRNAs
- a miRNA has imperfect base pairing to the target mRNA 3’ UTR

Question 33

siRNA/RISC

Answer 33

cleaves a target mRNA using an endonuclease activity
- siRNA cleavage requires perfect base pairing between the siRNA and the target mRNA coding sequence

Question 34

______ action occurs if there is perfect base pairing between siRNA and a target mRNA
- usually a target site is located in the coding sequence of an mRNA

Answer 34

siRNA

Question 35

________ action occurs if the base pairing is imperfect
- usually, the target site is in the 3’ UTR of an mRNA

Answer 35

miRNA