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BIOL 3321 - cell and molecular bio > miRNA and siRNA > Flashcards

miRNA and siRNA Flashcards

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1
Q

what is coding RNA

A

RNA that codes for a protein; mRNA

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2
Q

what is noncoding RNA

A

RNA that doesn’t code for a protein; everything other than mRNA

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3
Q

which type of RNA, coding or noncoding, regulates gene expression

A

noncoding

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4
Q

what is the role of noncoding RNA

A

regulation of gene expression

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5
Q

what is another term for regulation of gene expression

A

RNA interference aka RNAi

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6
Q

what is RNAi

A

RNA interference (regulation of gene expression)

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7
Q

what is miRNA

A

microRNA

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8
Q

what is miRNA responsible for

A

regulating gene expression by inhibition

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9
Q

does miRNA activate or inhibit gene expression

A

inhibit

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10
Q

what does miRNA regulate specifically

A

the translation of specific mRNAs and the stability of specific mRNAs

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11
Q

what transcribes the gene for miRNA

A

RNA pol II

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12
Q

right after transcription of miRNA, what happens to the transcript

A

it folds into a hairpin structure

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13
Q

how many nucleotides is the hairpin structure of miRNA

A

70

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14
Q

what is the name of the miRNA gene once it’s transcribed

A

pri-miRNA

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15
Q

describe the structure of pri-miRNA

A

the hairpin structure is 70 nt long and has imperfect base pairing in the stem

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16
Q

how does pri-miRNA become pre-miRNA

A

hairpin is cleaved = pre-miRNA

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17
Q

what cleaves the pri-miRNA hairpin

A

Drosha protein with DGCR8

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18
Q

how many strands in the pri-miRNA

A

two; it’s dsRNA

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19
Q

what type of molecule is Drosha

A

an RNase

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20
Q

once the hairpin pri-miRNA is cleaved, what is the molecule called

A

pre-miRNA

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21
Q

what happens to pre-miRNA now that the hairpin has been cleaved by Drosha + DGCR8

A

it’s recognized by a nuclear export factor (Exportin5) and it’s transported out of the nucleus

22
Q

what transports pre-miRNA out of the nucleus

A

Exportin5

23
Q

what happens to the pre-miRNA once it’s in the cytoplasm

A

Dicer and TRBP cleaves it and processes it into miRNA

24
Q

what cleaves the pre-miRNA

A

Dicer and TRBP

25
Q

describe the structure of miRNA that was produced by Dicer and TRBP

A

double stranded RNA, 21-23 nucleotides long

26
Q

now that we have miRNA fully processed and it’s double stranded, what happens to it

A

one strand is selected and assembles into a RISC

27
Q

what is a RISC

A

RNA-induced silencing complex

28
Q

what is the RISC made up of

A

ss miRNA, an Argonaute protein, and other proteins

29
Q

what happens once RISC has one strand of the miRNA attached to it

A

miRNA guides the RISC to mRNA molecules with complementary sequences in the 3’ UTR

30
Q

when the miRNA strand is in the RISC, what two things bind once mRNA is around

A

5’ end of miRNA with the 3’ UTR of the mRNA

31
Q

once miRNA is bound to the 3’ UTR of mRNA, what happens

A

two possibilities, both including mRNA degradation

32
Q

what two types of pairing can occur between the 5’ miRNA and the 3’ UTR of mRNA

A

extensive and less extensive

33
Q

describe what occurs when miRNA is extensively bound to mRNA

A

Arg protein slices through the mRNA = rapid mRNA degradation

34
Q

extensive matches between miRNA and mRNA are common in ____

A

plants

35
Q

describe what occurs when miRNA is less extensively bound to mRNA

A

Arg doesn’t slice through the mRNA, leading to rapid translational repression and eventual degradation of mRNA (repression occurs via proteins that inhibit translation, and the mRNA may be moved to P bodies for degradation)

36
Q

less extensive matches between miRNA and mRNA are common in ____

A

humans

37
Q

T or F: in mammals, base pairing between miRNA and mRNA needs to be perfect in order to get translation inhibition

A

false; does not need to be perfect

38
Q

how many bases need to be matched between miRNA and mRNA to get translation inhibition

A

2-7

39
Q

what are the implications of not needing perfect base pairing between miRNA and mRNA

A

it allows one miRNA to regulate many different mRNAs

40
Q

what is another function of Dicer and Argonaute proteins other than controlling gene expression

A

they play a role in cellular defense against viruses and transposons by cleaving dsRNA

41
Q

describe the mechanism of Dicer and Argonaute defending against viruses

A

virus puts dsRNA into cytoplasm of the host cell, and this is recognized by TRBP and Dicer, which produce small fragments of siRNA. Argonaute cleaves siRNA so one strand is in a RISC, this complex then binds to virus RNA, and RNA is cleaved by Argonaute = rapid destruction

42
Q

what is siRNA

A

short interfering RNA

43
Q

what is the siRNA knockdown method

A

used to study the function of any gene by inactivating it with siRNA

44
Q

what is the role of siRNA in the siRNA knockdown method

A

siRNA will inactivate a gene of interest, allowing us to determine the function of that gene

45
Q

what is the first step of siRNA knockdown method called

A

in vitro production of dsRNA

46
Q

describe the in vitro production of dsRNA in the siRNA knockdown method

A

you take the gene of interest and clone it into a plasmid, making a sense and an antisense transcript. Hybridizing the two transcripts together = dsRNA, and now these can be put into cultured cells or whole organisms

47
Q

once we have dsRNA for siRNA knockdown, how does it get processed into siRNA

A

dsRNA is processed into siRNA by Dicer

48
Q

in siRNA knockdown, what occurs once Dicer forms the siRNA from the dsRNA

A

siRNA forms a RISC, and it directs the RISC to bind to any mRNA that has complementary sequences (note: the mRNA it will bind to is from an organism of interest when we want to determine the funciton of some of its genes)

49
Q

in siRNA knockdown, what occurs once siRNA and RISC binds to the mRNA with genes of interest

A

binding = mRNA is destroyed, so no protein is produced. Then we can observe the phenotype to determine the function of the destroyed gene

50
Q

in siRNA knockdown, how will we determine the function of a gene once we finish the procedure?

A

siRNA binding to mRNA destroyed it so no protein is produced, so we will observe the phenotype

BIOL 3321 - cell and molecular bio (19 decks)

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