PHILLIPS CH10

Question 1

precursor RNA (pre-RNA)

Answer 1

needs to be modified to make the functional mature RNA

Question 2

3 benefits of RNA processing

Answer 2

1) regulation of gene activity
2) diversity - alternative splicing
3) quality control (defected mRNAs degraded)

Question 3

ribonucleoproteins (RNPs)

Answer 3

protein and RNA, many RNA processing complexes

Question 4

guide RNA

Answer 4

base pairs with pre-RNAs and guide the RNP to the correct place for processing

Question 5

initial transcript

Answer 5

tRNA and rRNA transcripts are made as long precursors that must be processed, ensures that similar amounts of each RNA are made

Question 6

RNase III

Answer 6

recognizes double-stranded RNAs, excises bacterial rRNAs, binds stem-loop structures in pre-RNAs and cleaves the dsRNAs

Question 7

RNase P

Answer 7

endonuclease that does 5’ trimming of tRNAs

Question 8

tRNA modifications

Answer 8

help folding/stability, increase specificity of interactions with other molecules

Question 8

addition of CCA to tRNA 3’ ends

Answer 8

CCA sequence at the 3’ ends of tRNAs is the attachment site for the amino acid\

not encoded by the genome, CCA adding enzyme adds nucleotides sequentially

Question 9

ribose 2’-O-methylation

Answer 9

RNA modification
2’ OH is changed to OCH3

Question 10

pseudouridylation

Answer 10

uridine is modified to pseudouridine (know structure) for H bonding capacity

Question 11

small nucleolar RNAs (snoRNAs)

Answer 11

guide enzymes to the correct site (with base pairing of specific regions), associate with a complex of proteins to make snoRNP
60-300 nucleotides long

Question 12

eukaryotic mRNA 5’ cap

Answer 12

5’ capped with a 7-methylguanine nucleotide via a 5’-5’ triphosphate linkage. this guanine is then methylated at N7 (know structure)

Question 13

how is the mRNA 5’ cap added?

Answer 13

1) RNA 5’ triphosphatase removes a phosphate from 5’ end (PPP > PP)
2) guanosine monophosphate (GMP) attaches to end in a 5’-5’ triphosphate linkage (PP > GMPPP)
3) guanine is methylated (GMPPP > m7GMPPP)

Question 14

poly A tail

Answer 14

on the 3’ ends of all eukaryotic mRNAs
protects mRNAs from degradation, essential for translation

Question 15

polyadenylation site

Answer 15

site where pre-mRNAs are cleaved and the poly A tail is added

Question 15

3’ untranslated region (UTR)

Answer 15

sequence between stop codon and the polyadenylation site
part of the genome but not read in translation

Question 15

how is the poly A tail added?

Answer 15

cleavage at polyadenylation site
~200 adenosines are added by poly A polymerase

Question 16

how are processing and transcription coupled?

Answer 16

transcription past 3’ end processing signals leads to recruitment of 3’ end processing complex - transcription and processing occurs simultaneously

Question 17

spliceosome

Answer 17

RNP complex that removes eukaryotic introns
made of small nuclear ribonucleoproteins (snRNPs), snRNA, proteins

Question 18

alternative splicing

Answer 18

different removal of introns gives different transcripts from the same gene

Question 19

what is the process of RNA splicing?

Answer 19

2 transesterification reactions: intron detached from exon 1, exon 1 reacts with exon 2
a single phosphodiester bond is broken and replaced by another of similar energy (no ATP)

Question 20

group I introns

Answer 20

found in bacteria, viruses, lower eukaryotes
many can self splice
free guanosine attacks 5’ end of intron, released end of exon 1 attacks intron-exon 2 junction

Question 21

group II introns

Answer 21

in bacteria and organellar genes of plants/fungi
some self splice
2’OH of specific adenosine within intron attacks exon1-intron junction to form lariat structure
released exon 1 attacks 5’ exon 2

Question 22

splice site motifs

Answer 22

5’ splice site: GU
3’ splice site: AG
branch-point nucleotide: adenosine where lariat will be formed
polypyrimidine tract before the 3’ splice site

Question 23

what proteins recognize each splice site?

Answer 23

5’ splice site: U1 snRNP
branch-point nucleotide: branch pt binding protein BBP, U2 snRNP
polypyrimidine tract and 3’ splice site: U2AF

Question 24

drosophilia dscam gene

Answer 24

can make 38000 different mature transcripts due to alternative splicing

Question 25

RNA editing

Answer 25

base modification (more common), insertion & deletion (rare)

Question 26

two examples of RNA base modification

Answer 26

1) demination of adenosine to inosine via ADARs (adenosine deaminase that acts on RNA)
2) deamination of cytidine to uridine

Question 27

APOB

Answer 27

expressed in both liver and intestine
deamination of a cytidine results in formation of stop codon in intestine only > different functions
cholesterol transport & lipid absorption from food

Question 28

RNA half-life

Answer 28

time in which the amount of RNA is reduced by half

Question 29

factors affecting RNA stability

Answer 29

5’ cap + stem loop structures (can protect against exo acivity), 3’ poly A tail, splicing

Question 30

RNA degradation in bacteria

Answer 30

conversion of 5’ triphosphate to monophosphate stimulates degradation
endonuclease begins degradation process
addition of 3’ poly A tail to stem loop structure helps degrade (stem loop blocks endo)

Question 31

mRNA degradation in eukaryotes

Answer 31

1) remove poly A tail by deadenylation (poly A tail provides stability in eukaryotes, opposite in bacteria)
2) degradation 3-5’ by exosome
3) decapping enzymes remove 5’ cap, 5-3’ exonucleases can access + degrade

Question 32

northern blot

Answer 32

can identify specific RNA sequences

RNA separated by size on a gel, transferred to membrane, membrane is incubated with a ss probe (bp with DNA of interest)