Exam 3: Ch 8 Cytoplasmic Post-Transcriptional Control & rRNA/tRNA Processing

Question 1

miRNA

Answer 1

short single stranded RNA that hybridize to 3’ UTR of target mRNA

imperfect binding

inhibits translation of the target mRNA

Question 2

siRNA

Answer 2

short interfering RNA (single stranded) aids RNAi

causes degradation of target mRNA

Question 3

pri-miRNA

Answer 3

very long transcript for one or more miRNAs

Question 4

Exportin5

Answer 4

nuclear transporter that moves pre-miRNAs out of the nucleus through FG-domain of nucleoporin

Question 5

Dicer

Answer 5

cytoplasmic RNA-specific RNase

acts with TRBP (Tar binding protein) for RNA to process pre-miRNA into double-stranded miRNA

Question 6

RNA-induced silencing complex (RISC)

Answer 6

complex of 1 strand of double-stranded miRNA and a protein called Argonaute

Question 7

binding of multiple RISCs to an mRNA

Answer 7

inhibits translation initiation through P bodies

Question 8

P body

Answer 8

sites of translational repression of mRNA bound by miRNA-RISC complexes

mRNA degradation in cytoplasm

contain decapping enzyme, exonucleases, and activators of decapping enzyme

Question 9

do RNAi bind perfectly to complementary mRNA to induce degradation?

Answer 9

yes

Question 10

RNAi

Answer 10

double stranded RNA induces degradation of all cellular RNAs that have a sequence matching one of the double stranded RNAs

Question 11

difference between RISC associated siRNA and miRNA

Answer 11

siRNA: base pairs perfectly with target RNA and induces cleavage

miRNA: recognizes target with imperfect base pairing and results in inhibition of translation

Question 12

the ________ protein is responsible for cleavage of target RNA

Answer 12

Argonaute

1 domain is homologous to RNase H enzymes that degrade RNA of an RNA-DNA hybrid

Question 13

does RNAi protect against viruses and transposons?

Answer 13

yes

Question 14

plasmodesmata

Answer 14

cytoplasmic connections between plant cells that traverse the cell walls between them

transfer of siRNA

Question 15

siRNA knockdown

Answer 15

one strand of ds siRNA with single stranded regions generates mature siRNA RISC complexes without inhibition of protein synthesis

researches use synthetic ds siRNA to knockdown expression of specific genes in human cells

Question 16

cytoplasmic polyadenylation

Answer 16

oocytes have mRNAs with short polyA tails that cant be translated

upon fertilization of the egg, the mRNAs are stabilized and a long polyA tail is added

Question 17

cytoplasmic polyadenylation element (CPE)

Answer 17

U rich area where CPE-binding protein (CPEB) binds to signal polyadenylation

Question 18

CPEB in neurons

Answer 18

postsyn neuron remembers which axon was stimulated, and leads to local synthesis of new proteins help the synapse

due to CPEB being present in dendrites…stimulates polyadenylation –> translation of mRNA in dendrites

Question 19

what does the concentration of an mRNA depend on

Answer 19

rate of synthesis

rate of degradation

Question 20

how can cytokine synthesis occur in bursts?

Answer 20

transcription of their genes is rapidly turned on or off

mRNAs have short half-lives

Question 21

3 pathways of cytoplasmic degradation

Answer 21

deadenylation-dependent pathway

deadenylation-independent decapping pathway

endonucleolytic pathway

Question 22

deadenylation-dependent pathway (most mRNA)

Answer 22

length of poly A tail slowly decreases with time from deadenylating nuclease

when short enough, tail can’t be stabilized by PABPI

decapping enzyme removes cap and exonuclease degrades

Question 23

deadenylation-independent decapping pathway

Answer 23

special 5’ sequences make the cap sensitive to decapping enzyme

short bursts like cytokines

Question 24

endonucleolytic pathway

Answer 24

RNAi pathway

doesn’t involve decapping or deadenylation

Question 25

rapamycin

Answer 25

antibiotic that suppresses immune response in organ transplant patients

Question 26

TOR pathway (target of rapamycin)

Answer 26

active mTOR stimulates overall protein synthesis by phosphorylating 2 critcal proteins that regulate translation aids in synthesis of translation factors and tRNAs eases assembly of ribosomes

Question 27

Rheb

Answer 27

a small monomeric G protein that regulates mTOR active when bound to GTP (activates mTOR)

Question 28

autophage/macrophagy

Answer 28

degradation of cytoplasmic components in starved cells this process is inhibited by mTOR in growing cells when there are enough nutrients

Question 29

eIF2 kinase

Answer 29

regulates global rate of cellular protein synthesis trimeric G protein (GTP/GDP) translation initiation factor brings charged tRNA to P site

Question 30

how to inhibit eIF2 kinase

Answer 30

phosphorylation at a serine

Question 31

some mRNAs can still be transcribed even though eIF2 has been phosphorylated

Answer 31

ex. chaperone proteins that refold proteins after cellular stress

Question 32

adenovirus and PKR (protein kinase RNA)

Answer 32

normally inhibition of protein synthesis helps stop producing progeny virions adenovirus virus-associated RNA binds to PKR with high affinity and stop protein kinase acitibty to prevent inhibition

Question 33

ferritin

Answer 33

intracellular iron-binding protein that binds and stores excess cellular iron

Question 34

iron response element-binding protein (IRE-BP)

Answer 34

controls iron concentration by regulating translation of one mRNA and degradation of another regulates ferritin and transferrin receptor

Question 35

mRNA surveilance

Answer 35

mechanisms that help cells avoid translation of improperly processed mRNA

Question 36

nonsense mediated decay (NMD)

Answer 36

causes degradation of mRNAs where 1 or more exons have been incorrectly spliced rapid degradation of mRNAs with stop codons before the last splice junction

Question 37

protein localization

Answer 37

mRNAs being translated in regions where the protein is actually needed sequences in 3' UTR direct this

Question 38

__% of total RNA in rapidly growing cells is rRNA

Answer 38

80%

Question 39

__% of total RNA in rapidly growing cells is tRNA

Answer 39

15%

Question 40

where does ribosome formation take place

Answer 40

nucleolus, some nucleoplasm, final steps in cytoplasm

Question 41

quality control step in ribosome formation

Answer 41

before nuclear export ensures only functional ribosomal subunits are exported to the cytoplasm

Question 42

pre-rRNA transcription unit

Answer 42

encodes the subunits of the large and small ribosome synthesis and processing occurs in nucleolus

Question 43

how can so many pairs of ribosomal subunits (40/sec in yeast) be synthesized, processed, and transported

Answer 43

pre-rRNA genes are packed with RNA pol I transcribing the gene simultaneously

Question 44

snoRNAs

Answer 44

small nucleolar RNAs hybridize to pre-rRNA and form snoRNPs to aid processing

Question 45

AAA ATPase family

Answer 45

class of proteins involved in large molecular movements ex. folding of large rRNA into proper conformation

Question 46

what organisms have self-splicing group I introns

Answer 46

mitochondrial and chloroplast pre-rRNA mRNA from E. coli bacteriophages bacterial tRNA primary transcrips

Question 47

group I self-splicing sequences use ______ as a cofactor

Answer 47

guanosine

Question 48

ribozyme

Answer 48

RNA with catalytic ability

Question 49

pre-tRNAs undergo extensive modification in the _____

Answer 49

nucleus

Question 50

mature cytosolic tRNAs are produced from larger precursors (pre-tRNAs) synthesized by RNA pol _ in the ______

Answer 50

RNA pol III, nucleoplasm

Question 51

what is present in all pre-tRNAs that isnt in mature tRNAs

Answer 51

a 5' sequence of variable length 5' end of mature tRNA is generated from endonucleolytic cleavage specified by the tRNA 3D structure by RNase P

Question 52

3 modifications that happen to pre-tRNAs

Answer 52

base modification cleavage splicing

Question 53

mechanism of pre-tRNA splicing is different than self-splicing introns and spliceosomes

Answer 53

splicing is catalyzed by protein, not RNA intron is excised in 1 step of simultaneous cleavage at both ends of the intron hydrolysis of GTP and ATP is required to join the two tRNA halves back together

Question 54

which exportin moves mature tRNAs through NPCs

Answer 54

exportin-t

Question 55

nuclear body

Answer 55

specialized nuclear domains that aren't surrounded by membrane regions of high concentrations of specific proteins and RNAs ex. nucleoli: sites of ribosomal subunit synthesis

Question 56

Cajal nuclear body

Answer 56

site of RNP-complex assembly for spliceosomal snRNPs and other RNPs

Question 57

nuclear speckle nuclear body

Answer 57

discovered using Ab immunofluorescence to snRNPs storage of snRNPs

Question 58

promyelocytic leukemia (PML) nuclear body

Answer 58

discovered using Ab immunoflurorescence sites of assembly and modification of protein complexes for DNA repair and apoptosis ex. p53 tumor suppressor protein defense vs. DNA viruses and post-translational modification

Question 59

other nucleoli functions

Answer 59

assembly of immature SRP RNP complexes involved in protein secretion and ER membrane insertion also export of these to the cytoplasm