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BIOL 3321 - cell and molecular bio > mechanisms of post-transcriptional gene control > Flashcards

mechanisms of post-transcriptional gene control Flashcards

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1
Q

how does the cell know when the mRNA has been fully processed?

A

a fully processed mRNA will have a collection of proteins on it

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2
Q

list the collection of proteins found on a fully processed mRNA

A

cap-binding complex
SR proteins
hnRNP proteins
PABPs
exon junction complex

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3
Q

what are exon junction complexes

A

a group of proteins that assemble onto the mRNA at a site where there was an intron

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4
Q

what directs the EJC to a site on the mRNA where there was an intron

A

the spliceosome

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5
Q

what does the presence of an EJC indicate

A

that a successful splicing event has occured

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6
Q

T or F: there is lots of RNA debris in the nucleus

A

true

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7
Q

what type of RNA debris is in the nucleus

A

introns, pre-mRNAs not properly spliced or polyadenylated, cleavage products following polyadenylation

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8
Q

how does the cell get rid of nuclear debris?

A

via the nuclear RNA exosome

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9
Q

where does the mRNA go after processing

A

leaves the nucleus via the nuclear pore complex

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10
Q

what binds to the mRNA to facilitate it’s transport through the nuclear pore complex after its processed

A

nuclear export receptors

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11
Q

what leaves the mRNA before it can move through the nuclear pore complex once it’s done being processed

A

some nucleus-restricted proteins

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12
Q

after the mRNA is out of the nucleus, what type of proteins bind to it (give specific examples)

A

ones required for translation: eIF4E/eIF4G

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13
Q

what is remodeling

A

describes how proteins associated w/ mRNA are replaced by a new set of proteins as the mRNA is transported through the nucleus

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14
Q

give examples of remodeling in mRNA

A

CBC is replaced by eIF4E/EIF4G, PABPN1 is replaced by PABPC1

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15
Q

once the mRNA is out of the nucleus and all the proper proteins are attached, what must happen before translation can occur

A

nonsense-mediated decay

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16
Q

what form is mRNA in while it waits for translation

A

circular

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17
Q

why is mRNA circular as it waits for translation

A

occurs due to protein interactions at the 5’ and 3’ end

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18
Q

what is the purpose of mRNA being circular as it waits for translation/during translation

A

increases efficiency of translation because when the ribosome is done, the start site is right there so it can easily go again

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19
Q

when does nonsense mediated decay occur

A

before mRNA enters the cytoplasm

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20
Q

purpose of nonsense-mediated mRNA decay surveillance system

A

its a quality control system that the cell uses to make sure that the mRNA to be exported is not defective

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21
Q

what does the nonsense-mediated mRNA decay surveillance system do

A

it looks for a nonsense codon within the reading frame of the mRNA to recognize improperly spliced mRNAs

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22
Q

list the nonsense (stop) codons

A

UAA, UAG, UGA

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23
Q

when would a nonsense codon be present within an mRNA?

A

when there is an intron still present

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24
Q

describe how nonsense mediated decay surveillance system works

A

as soon as the 5’ end of mRNA leaves the nuclear pore, it meets a ribosome that does a test run to test for in-frame nonsense codons. If the final stop codon is reached and there are no EJCs remaining, translation can occur, but if it reaches a codon and there are still downstream EJCs then Upf proteins will bind and trigger mRNA degradation

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25
Q

what type of proteins will bind to trigger mRNA degradation during the nonsense mediated decay surveillance system

A

Upf proteins

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26
Q

what does the nonsense mediated system prevent

A

prevents defective mRNAs from being translated in the cytoplasm

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27
Q

where can mRNA be translated

A

on a free ribosome in the cytoplasm or on ribosomes on the ER

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28
Q

T or F: many mRNAs are directed to specific intracellular locations prior to efficient translation

A

true

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29
Q

describe the 3 different localization paths an mRNA can take once it leaves the nucleus

A
  1. mRNA move along cytoskeleton where they’re trapped by anchor proteins
  2. mRNAs diffuse through cytoplasm until they’re trapped at their site by anchor proteins
  3. mRNA is degraded unless it’s bound by proteins that protect and anchor it
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30
Q

where are mRNA localization signals found

A

in the 3’ UTR region of the mRNA

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31
Q

where is the 3’ UTR region

A

right after the stop codon and before the poly(A) signal

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32
Q

what does localization of mRNA enable the cell to do

A

place the mRNA in the cell where that protein is needed, regulate gene expression independently in dif regions of the cell, and it allows for the establishment of asymmetry in the cell

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33
Q

what does tRNA-met need help from to bind to the ribosome for translation

A

eIF2

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34
Q

what is eIF2

A

eukaryotic translation initiation factor 2

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35
Q

where does tRNA-bind to on the ribosome

A

the P site

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36
Q

when the tRNA-amino acid is bound to the P site, what happens

A

the small ribosomal subunit binds at the 5’ cap and begins scanning for the first AUG

37
Q

what happens to initiation factors once the ribosome finds the start codon

A

they dissociate

38
Q

at what point in initiation of translation does the large ribosomal subunit bind

A

once small subunit finds the start codon and the initiation factors dissociate

39
Q

how is translation initiation regulated

A

repressors may bind to the 5’ UTR of the mRNA to inhibit translation

40
Q

for translation initiation control, where do repressors bind

A

to the 5’ UTR of the mRNA

41
Q

what is the effect of too much iron in the cell

A

this can generate free radicals

42
Q

what do free radicals do

A

they damage cellular macromolecules

43
Q

why is precise iron regulation required

A

too much iron can generate free radicals, which will damage cellular macromolecules

44
Q

where is iron stored in the body

A

in a protein called ferritin

45
Q

what is the role of the protein ferritin

A

stores iron in the body

46
Q

what special element is part of the ferritin mRNA

A

an iron-response element (IRE)

47
Q

where is the IRE located

A

at the 5’ UTR of the ferritin mRNA

48
Q

what is the structure of the IRE

A

forms a stem loop structure

49
Q

what is another name for IRE-BP

A

aconitase

50
Q

what recognizes the IRE sequence

A

the iron-response element binding-protein (IRE-BP)

51
Q

is the IRE-BP an activator or a repressor for ferritin translation

A

a repressor

52
Q

is IRE-BP active or inactive when iron is low? explain

A

active; it represses ferritin translation so ferritin cannot store iron

53
Q

is IRE-BP active or inactive when iron is high? explain

A

inactive; it cannot repress ferritin translation, therefore ferritin is made and can store the excess iron

54
Q

what is the sequence surrounding AUG

A

5’-ACCAUGG-3’

55
Q

what happens when the consensus recognition sequence surrounding AUG differs from ACCAUGG

A

the ribosome may skip over the first start codon and go to the second or third

56
Q

what is the name for when a ribosome skips past the first AUG codon and goes to the next

A

leaky scanning

57
Q

what controls/prevents leaky scanning from occuring

A

concentration of eIF4F in the cell

58
Q

describe how eIF4F prevents leaky scanning

A

when concentrations of eIF4F are high in the cell, the first AUG codon will be used regardless of the presence of a nonoptimal consensus sequence

59
Q

which terminus does leaky scanning effect

A

the N-terminus

60
Q

since leaky scanning affects the N terminus, what is the result of this

A

the signal sequence that dictates where proteins will go = located at the N terminus, so changing the N terminus can change where proteins are directed

61
Q

describe the early stages of mRNA degradation

A

a deadenylase interacts with the 5’ cap and starts to remove the adenines of the tail (mRNA is circular)

62
Q

what is the shape of mRNA during degradation

A

circular

63
Q

once a critical length is reached for the poly A tail during degradation, how many mechanisms may come into play

A

2

64
Q

describe the 2 mechanisms of mRNA degradation

A
  1. decapping followed by rapid 5’ to 3’ degradation
  2. continued 3’ to 5’ degradation via exonucleases
65
Q

explain how decapping occurs during mRNA degradation

A

due to the short A tail, the interaction between the cap, eIFs, and PABPs is not stable, so the cap is left unprotected. A decapping enzyme then comes in

66
Q

describe the translation-degradation relationship

A

anything that increases one process will decrease the other

67
Q

T or F: endonucleases are another form of mRNA degradation

A

true! this is the third form of degradation

68
Q

describe degradation of mRNA via endonucleases

A

this doesn’t involve decapping or deadenylation. The mRNA will have a sequence within the 3’ UTR that the endonuclease will recognize, so then it will do internal cleavage, and those fragments will be degraded via exonucleases

69
Q

T or F: endonuclease degradation involves decapping

A

false; no decapping occurs

70
Q

T or F: endonuclease degradation involves deadenylation

A

false; no deadenylation occurs, only splitting the mRNA into fragments

71
Q

T or F: endonuclease degradation involves exonucleases

A

true; endonuclease creates fragments, exonuclease degrades those fragments

72
Q

how is iron brought into a cell

A

via the transferrin receptor

73
Q

how can we control the amount of iron brought into a cell

A

by changing the stability of the transferrin receptor mRNA

74
Q

how does IRE-BP interact with transferrin mRNA

A

it recognizes and binds sequences of transferrin mRNA within the 3’ UTR

75
Q

in regards to iron and the transferrin receptor, explain what occurs when we have low iron

A

low iron = we want the transferrin receptor to be made so it can bring iron in. No iron = iron doesn’t bind to IRE-Bp = active conformation = IRE-BP binds to recognition sequence on the mRNA = masks endonucleolytic site = translation occurs and receptor is made so iron is brought in

76
Q

in regards to iron and the transferrin receptor, explain what occurs when we have high iron

A

we don’t want the receptor to be made. Excess iron = it binds to IRE-BP and inhibits it from binding to the mRNA = no masking of the endonucleolytic site = mRNA is degraded

77
Q

which part of the cell does mRNA degradation take place

A

in the cytoplasm

78
Q

where in the cytoplasm does mRNA degradation take place

A

in P bodies

79
Q

where in the cell are P bodies located

A

in the cytoplasm

80
Q

what are P bodies

A

major sites of mRNA degradation

81
Q

what do P bodies have in them that make them good for mRNA degradation

A

exonucleases

82
Q

T or F: P bodies are dynamic

A

true

83
Q

what does it mean for P bodies to be dynamic

A

they can grow and shrink depending on the amount of degradation

84
Q

once the mRNA is out of the nucleus, describe the different fates it can have

A

right to translation and from there to a P body or stress granule, or it can go right to the P body from the nucleus

85
Q

what two processes can occur within P bodies

A

nonsense mediated decay, and repression of mRNA

86
Q

give an example of a post translational event

A

modification of amino acid side chains by kinases and phosphatases

87
Q

what do kinases do

A

attach phosphates to the hydroxyl groups of Ser, Thr, and Tyr

88
Q

what do phosphatases do

A

removes phosphate groups

BIOL 3321 - cell and molecular bio (19 decks)

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