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

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

Flashcards in Exam 3: Ch 8 Cytoplasmic Post-Transcriptional Control & rRNA/tRNA Processing Deck (59):
1

miRNA

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

imperfect binding

inhibits translation of the target mRNA

2

siRNA

short interfering RNA (single stranded) aids RNAi

causes degradation of target mRNA

3

pri-miRNA

very long transcript for one or more miRNAs

4

Exportin5

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

5

Dicer

cytoplasmic RNA-specific RNase

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

6

RNA-induced silencing complex (RISC)

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

7

binding of multiple RISCs to an mRNA

inhibits translation initiation through P bodies

8

P body

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

mRNA degradation in cytoplasm

contain decapping enzyme, exonucleases, and activators of decapping enzyme

9

do RNAi bind perfectly to complementary mRNA to induce degradation?

yes

10

RNAi

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

11

difference between RISC associated siRNA and miRNA

siRNA: base pairs perfectly with target RNA and induces cleavage

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

12

the ________ protein is responsible for cleavage of target RNA

Argonaute

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

13

does RNAi protect against viruses and transposons?

yes

14

plasmodesmata

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

transfer of siRNA

15

siRNA knockdown

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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cytoplasmic polyadenylation

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

17

cytoplasmic polyadenylation element (CPE)

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

18

CPEB in neurons

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

19

what does the concentration of an mRNA depend on

rate of synthesis

rate of degradation

20

how can cytokine synthesis occur in bursts?

transcription of their genes is rapidly turned on or off

mRNAs have short half-lives

21

3 pathways of cytoplasmic degradation

deadenylation-dependent pathway

deadenylation-independent decapping pathway

endonucleolytic pathway

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deadenylation-dependent pathway (most mRNA)

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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deadenylation-independent decapping pathway

special 5' sequences make the cap sensitive to decapping enzyme

short bursts like cytokines

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endonucleolytic pathway

RNAi pathway

doesn't involve decapping or deadenylation

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rapamycin

antibiotic that suppresses immune response in organ transplant patients

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TOR pathway (target of rapamycin)

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

Rheb

a small monomeric G protein that regulates mTOR

active when bound to GTP (activates mTOR)

28

autophage/macrophagy

degradation of cytoplasmic components in starved cells

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

29

eIF2 kinase

regulates global rate of cellular protein synthesis

trimeric G protein (GTP/GDP)

translation initiation factor brings charged tRNA to P site

30

how to inhibit eIF2 kinase

phosphorylation at a serine

31

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

ex. chaperone proteins that refold proteins after cellular stress

32

adenovirus and PKR (protein kinase RNA)

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

ferritin

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

34

iron response element-binding protein (IRE-BP)

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

regulates ferritin and transferrin receptor

35

mRNA surveilance

mechanisms that help cells avoid translation of improperly processed mRNA

36

nonsense mediated decay (NMD)

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

protein localization

mRNAs being translated in regions where the protein is actually needed

sequences in 3' UTR direct this

38

__% of total RNA in rapidly growing cells is rRNA

80%

39

__% of total RNA in rapidly growing cells is tRNA

15%

40

where does ribosome formation take place

nucleolus, some nucleoplasm, final steps in cytoplasm

41

quality control step in ribosome formation

before nuclear export

ensures only functional ribosomal subunits are exported to the cytoplasm

42

pre-rRNA transcription unit

encodes the subunits of the large and small ribosome

synthesis and processing occurs in nucleolus

43

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

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

44

snoRNAs

small nucleolar RNAs

hybridize to pre-rRNA and form snoRNPs to aid processing

45

AAA ATPase family

class of proteins involved in large molecular movements

ex. folding of large rRNA into proper conformation

46

what organisms have self-splicing group I introns

mitochondrial and chloroplast pre-rRNA

mRNA from E. coli bacteriophages

bacterial tRNA primary transcrips

47

group I self-splicing sequences use ______ as a cofactor

guanosine

48

ribozyme

RNA with catalytic ability

49

pre-tRNAs undergo extensive modification in the _____

nucleus

50

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

RNA pol III, nucleoplasm

51

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

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

3 modifications that happen to pre-tRNAs

base modification

cleavage

splicing

53

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

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

which exportin moves mature tRNAs through NPCs

exportin-t

55

nuclear body

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

Cajal nuclear body

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

57

nuclear speckle nuclear body

discovered using Ab immunofluorescence to snRNPs

storage of snRNPs

58

promyelocytic leukemia (PML) nuclear body

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

other nucleoli functions

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

also export of these to the cytoplasm