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

mechanisms of post-transcriptional gene control Flashcards

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
what type of proteins will bind to trigger mRNA degradation during the nonsense mediated decay surveillance system
Upf proteins
26
what does the nonsense mediated system prevent
prevents defective mRNAs from being translated in the cytoplasm
27
where can mRNA be translated
on a free ribosome in the cytoplasm or on ribosomes on the ER
28
T or F: many mRNAs are directed to specific intracellular locations prior to efficient translation
true
29
describe the 3 different localization paths an mRNA can take once it leaves the nucleus
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
30
where are mRNA localization signals found
in the 3' UTR region of the mRNA
31
where is the 3' UTR region
right after the stop codon and before the poly(A) signal
32
what does localization of mRNA enable the cell to do
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
33
what does tRNA-met need help from to bind to the ribosome for translation
eIF2
34
what is eIF2
eukaryotic translation initiation factor 2
35
where does tRNA-bind to on the ribosome
the P site
36
when the tRNA-amino acid is bound to the P site, what happens
the small ribosomal subunit binds at the 5' cap and begins scanning for the first AUG
37
what happens to initiation factors once the ribosome finds the start codon
they dissociate
38
at what point in initiation of translation does the large ribosomal subunit bind
once small subunit finds the start codon and the initiation factors dissociate
39
how is translation initiation regulated
repressors may bind to the 5' UTR of the mRNA to inhibit translation
40
for translation initiation control, where do repressors bind
to the 5' UTR of the mRNA
41
what is the effect of too much iron in the cell
this can generate free radicals
42
what do free radicals do
they damage cellular macromolecules
43
why is precise iron regulation required
too much iron can generate free radicals, which will damage cellular macromolecules
44
where is iron stored in the body
in a protein called ferritin
45
what is the role of the protein ferritin
stores iron in the body
46
what special element is part of the ferritin mRNA
an iron-response element (IRE)
47
where is the IRE located
at the 5' UTR of the ferritin mRNA
48
what is the structure of the IRE
forms a stem loop structure
49
what is another name for IRE-BP
aconitase
50
what recognizes the IRE sequence
the iron-response element binding-protein (IRE-BP)
51
is the IRE-BP an activator or a repressor for ferritin translation
a repressor
52
is IRE-BP active or inactive when iron is low? explain
active; it represses ferritin translation so ferritin cannot store iron
53
is IRE-BP active or inactive when iron is high? explain
inactive; it cannot repress ferritin translation, therefore ferritin is made and can store the excess iron
54
what is the sequence surrounding AUG
5'-ACCAUGG-3'
55
what happens when the consensus recognition sequence surrounding AUG differs from ACCAUGG
the ribosome may skip over the first start codon and go to the second or third
56
what is the name for when a ribosome skips past the first AUG codon and goes to the next
leaky scanning
57
what controls/prevents leaky scanning from occuring
concentration of eIF4F in the cell
58
describe how eIF4F prevents leaky scanning
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
which terminus does leaky scanning effect
the N-terminus
60
since leaky scanning affects the N terminus, what is the result of this
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
describe the early stages of mRNA degradation
a deadenylase interacts with the 5' cap and starts to remove the adenines of the tail (mRNA is circular)
62
what is the shape of mRNA during degradation
circular
63
once a critical length is reached for the poly A tail during degradation, how many mechanisms may come into play
2
64
describe the 2 mechanisms of mRNA degradation
1. decapping followed by rapid 5' to 3' degradation 2. continued 3' to 5' degradation via exonucleases
65
explain how decapping occurs during mRNA degradation
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
describe the translation-degradation relationship
anything that increases one process will decrease the other
67
T or F: endonucleases are another form of mRNA degradation
true! this is the third form of degradation
68
describe degradation of mRNA via endonucleases
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
T or F: endonuclease degradation involves decapping
false; no decapping occurs
70
T or F: endonuclease degradation involves deadenylation
false; no deadenylation occurs, only splitting the mRNA into fragments
71
T or F: endonuclease degradation involves exonucleases
true; endonuclease creates fragments, exonuclease degrades those fragments
72
how is iron brought into a cell
via the transferrin receptor
73
how can we control the amount of iron brought into a cell
by changing the stability of the transferrin receptor mRNA
74
how does IRE-BP interact with transferrin mRNA
it recognizes and binds sequences of transferrin mRNA within the 3' UTR
75
in regards to iron and the transferrin receptor, explain what occurs when we have low iron
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
in regards to iron and the transferrin receptor, explain what occurs when we have high iron
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
which part of the cell does mRNA degradation take place
in the cytoplasm
78
where in the cytoplasm does mRNA degradation take place
in P bodies
79
where in the cell are P bodies located
in the cytoplasm
80
what are P bodies
major sites of mRNA degradation
81
what do P bodies have in them that make them good for mRNA degradation
exonucleases
82
T or F: P bodies are dynamic
true
83
what does it mean for P bodies to be dynamic
they can grow and shrink depending on the amount of degradation
84
once the mRNA is out of the nucleus, describe the different fates it can have
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
what two processes can occur within P bodies
nonsense mediated decay, and repression of mRNA
86
give an example of a post translational event
modification of amino acid side chains by kinases and phosphatases
87
what do kinases do
attach phosphates to the hydroxyl groups of Ser, Thr, and Tyr
88
what do phosphatases do
removes phosphate groups

BIOL 3321 - cell and molecular bio (19 decks)

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