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Cellular and Molecular Biology > Exam 3: Ch 8 Cytoplasmic Post-Transcriptional Control & rRNA/tRNA Processing > Flashcards

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

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1
Q

miRNA

A

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

imperfect binding

inhibits translation of the target mRNA

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2
Q

siRNA

A

short interfering RNA (single stranded) aids RNAi

causes degradation of target mRNA

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3
Q

pri-miRNA

A

very long transcript for one or more miRNAs

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4
Q

Exportin5

A

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

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5
Q

Dicer

A

cytoplasmic RNA-specific RNase

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

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6
Q

RNA-induced silencing complex (RISC)

A

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

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7
Q

binding of multiple RISCs to an mRNA

A

inhibits translation initiation through P bodies

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8
Q

P body

A

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

mRNA degradation in cytoplasm

contain decapping enzyme, exonucleases, and activators of decapping enzyme

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9
Q

do RNAi bind perfectly to complementary mRNA to induce degradation?

A

yes

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10
Q

RNAi

A

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

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11
Q

difference between RISC associated siRNA and miRNA

A

siRNA: base pairs perfectly with target RNA and induces cleavage

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

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12
Q

the ________ protein is responsible for cleavage of target RNA

A

Argonaute

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

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13
Q

does RNAi protect against viruses and transposons?

A

yes

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14
Q

plasmodesmata

A

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

transfer of siRNA

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15
Q

siRNA knockdown

A

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

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16
Q

cytoplasmic polyadenylation

A

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

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17
Q

cytoplasmic polyadenylation element (CPE)

A

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

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18
Q

CPEB in neurons

A

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

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19
Q

what does the concentration of an mRNA depend on

A

rate of synthesis

rate of degradation

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20
Q

how can cytokine synthesis occur in bursts?

A

transcription of their genes is rapidly turned on or off

mRNAs have short half-lives

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21
Q

3 pathways of cytoplasmic degradation

A

deadenylation-dependent pathway

deadenylation-independent decapping pathway

endonucleolytic pathway

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22
Q

deadenylation-dependent pathway (most mRNA)

A

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

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23
Q

deadenylation-independent decapping pathway

A

special 5’ sequences make the cap sensitive to decapping enzyme

short bursts like cytokines

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24
Q

endonucleolytic pathway

A

RNAi pathway

doesn’t involve decapping or deadenylation

25
Q

rapamycin

A

antibiotic that suppresses immune response in organ transplant patients

26
Q

TOR pathway (target of rapamycin)

A

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

27
Q

Rheb

A

a small monomeric G protein that regulates mTOR

active when bound to GTP (activates mTOR)

28
Q

autophage/macrophagy

A

degradation of cytoplasmic components in starved cells

this process is inhibited by mTOR in growing cells when there are enough nutrients

29
Q

eIF2 kinase

A

regulates global rate of cellular protein synthesis

trimeric G protein (GTP/GDP)

translation initiation factor brings charged tRNA to P site

30
Q

how to inhibit eIF2 kinase

A

phosphorylation at a serine

31
Q

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

A

ex. chaperone proteins that refold proteins after cellular stress

32
Q

adenovirus and PKR (protein kinase RNA)

A

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

33
Q

ferritin

A

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

34
Q

iron response element-binding protein (IRE-BP)

A

controls iron concentration by regulating translation of one mRNA and degradation of another

regulates ferritin and transferrin receptor

35
Q

mRNA surveilance

A

mechanisms that help cells avoid translation of improperly processed mRNA

36
Q

nonsense mediated decay (NMD)

A

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

37
Q

protein localization

A

mRNAs being translated in regions where the protein is actually needed

sequences in 3’ UTR direct this

38
Q

__% of total RNA in rapidly growing cells is rRNA

A

80%

39
Q

__% of total RNA in rapidly growing cells is tRNA

A

15%

40
Q

where does ribosome formation take place

A

nucleolus, some nucleoplasm, final steps in cytoplasm

41
Q

quality control step in ribosome formation

A

before nuclear export

ensures only functional ribosomal subunits are exported to the cytoplasm

42
Q

pre-rRNA transcription unit

A

encodes the subunits of the large and small ribosome

synthesis and processing occurs in nucleolus

43
Q

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

A

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

44
Q

snoRNAs

A

small nucleolar RNAs

hybridize to pre-rRNA and form snoRNPs to aid processing

45
Q

AAA ATPase family

A

class of proteins involved in large molecular movements

ex. folding of large rRNA into proper conformation

46
Q

what organisms have self-splicing group I introns

A

mitochondrial and chloroplast pre-rRNA

mRNA from E. coli bacteriophages

bacterial tRNA primary transcrips

47
Q

group I self-splicing sequences use ______ as a cofactor

A

guanosine

48
Q

ribozyme

A

RNA with catalytic ability

49
Q

pre-tRNAs undergo extensive modification in the _____

A

nucleus

50
Q

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

A

RNA pol III, nucleoplasm

51
Q

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

A

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

52
Q

3 modifications that happen to pre-tRNAs

A

base modification

cleavage

splicing

53
Q

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

A

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

54
Q

which exportin moves mature tRNAs through NPCs

A

exportin-t

55
Q

nuclear body

A

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

56
Q

Cajal nuclear body

A

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

57
Q

nuclear speckle nuclear body

A

discovered using Ab immunofluorescence to snRNPs

storage of snRNPs

58
Q

promyelocytic leukemia (PML) nuclear body

A

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

59
Q

other nucleoli functions

A

assembly of immature SRP RNP complexes involved in protein secretion and ER membrane insertion

also export of these to the cytoplasm

Cellular and Molecular Biology (34 decks)

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