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Genetics > Lec5miRNAsAndOtherNoncodingRNAs > Flashcards

Lec5miRNAsAndOtherNoncodingRNAs Flashcards

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Biology 101 flashcards
1
Q

what is TERC

A

RNA in telomerase

RNA THAT TELOMERASE uses, it is the template

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2
Q

What is mRNA

A

mature RNA gets translated into protein

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3
Q

what is rRNA

A

ribosomal RNA, makes the large and small subunit of the ribosome and function in translation

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4
Q

What is SnRNA

A

Small nuclear RNA, functions in splicing

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5
Q

What is SnoRNA

A

Small nucleOlar, function in chemically modifying rRNA

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6
Q

What is TERC

A

RNA added to telomerase

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7
Q

What is XIST

A

X chromosome inactivation, has binding sites for histone methylase

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8
Q

what is the function of microRNA

A

multiple imp roles in gene regulation, notably in development and implicated in same cancers

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9
Q

what is the function of Piwi binding RNA

A

derived from repeats; expressed only in germ line cells, where they limit excess transposon activity

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10
Q

what is the function of endogenous short interfering RNA

A

derived from pseudogenes, inverted repeats, involved in gene regulation in Somatic cells and may be involved in same types of transposon

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11
Q

What is the RNA interference (RNAi) pathway?

A

Pathway for destroying long ds RNAs from viruses or transposable elements

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12
Q

In the RNA interference (RNAi) pathway, what chops us the ds DNA?

A

dicer

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13
Q

Dicer chops up ds DNA and makes what? (RNAi)

A

22bp(ds) segments called siRNA

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14
Q

where are the siRNA going to go? and do?(RNAi)

A

go to argonaute

argonaute has a helicase component and it will separate the two strands in (siRNA)

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15
Q

What happens to the single fragments after argonaute? (RNAi)

A

One will be left behind and the other will be incorporated in the complex guide

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16
Q

The guide complex can go into two pathways:

A

RISC and RITS

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17
Q

The guide complex can go into two pathways: explain the RICS pathway (RNAi)

A

Use the guide RNA to look for its complementary sequence and endonuculease activity to chop it up

EXCAT W/C BP

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18
Q

The guide complex can go into two pathways: explain the RITS pathway (RNAi)

A

Transcriptional Silencing

  • If there was a release of one of the guide RNA’s next to the 5’ end of a newly synthesized RNA (we just started synthesis so CURRENTLY being synthesized) we are going to use the RITS complex. We can then bring in a histone methylates to close chromatin and stop transcription

** basically shutting down the virus

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19
Q

RNAi is a natural pathway; the pathway is also used for what besides ENDO siRNA

A

exogenous siRNA

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20
Q

What does dicer work with and recognize?

A

Dicer works with transposons and inverted repeats; dicer recognizes dsRNA

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21
Q

What does dicer produce?

A

siRNAs of about 22bps with overhangs

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22
Q

T/F dicer does not have sequence specificity for cleavage

A

TRUE

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23
Q

what produces produces single stranded RNA that can lead to W/C base pairing on RNAs for degradation (RISC) or for transcriptional silencing (RITS)

A

endonuclease Argonaute

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24
Q

what is argonaute?

A

Argonaute is an endonuclease that generates a 20 nucleotide gRNA strand

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25
Q

What is dicer?

A

Dicer: Divides long DS DNA (entire rotavirus genome)
**DS endonuclease*

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26
Q

What is argonaute

A

Argonaute: Helicase + Endonuclease

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27
Q

What is RISC?

A

RISC(RNA Interference silencing complex): Cleaves and degrades

28
Q

What is RITs

A

RITS (RNA Interference transcriptional silencing): Stops transcription

29
Q

What is guide strand

A

guide strand: Strand that will w/c base pair with target strand

30
Q

What is the passenger strand

A

passenger strand: Released by argonaute complex

31
Q

What are microRNAs?

A

MiRNA will ultimately W+C bp with mRNAs to INHIBIT TRANSLATION

32
Q

Can miRNAs W-C base pair with some mismatching or need perfect pairing?,

A

miRNAs can W-C base pair with some mismatching, which basically means one miRNA can regulate multiple mRNAs.

basically means one miRNA can regulate multiple mRNAs.

33
Q

What is the key feature of miRNA?

A

hair pin due to intramolecular bp and a cap

34
Q

What is the hair pin caused by (miRNA)

A

hair pin due to intramolecular bp

35
Q

If the ds has a cap, when do you add the cap?

A

when you modifying the primary transcript and can only be added when RNA pol 2 is phosphorylated

36
Q

miRNA are produced by what and how can we tell?

A

miRNAs have a cap and poly A tail on c terminal domain which then gets lost in the nucleus

Which tells us that they are produced by
RNA POLYMERASE 2

37
Q

Same as endo, what happens to break down the ds (miRNA)

A

dicer comes in then argonaute will break down the ds and produce the guide strand to go down a pathway

38
Q

What are the two pathways for miRNA

A

imperfect match–> block 3 UT (untranslated region)= does not allow for ribosome assembly so no TRANSLATION

perfect march–>RICS pathway

39
Q

What does miRNA interact with to stop translation

A

block 3UT

40
Q

miRNA can be transcribed from what?

A

INTRONIC REGIONS

41
Q

miRNA can prevent what?

A

miRNA can prevent premature gene translation (important in embryonic development)

42
Q

If miRNA pairs extensively, what happens?

A

rapid mRNA degradation with Argonaute cleavage

43
Q

If miRNA base pairs less extensively , what happens?

A

translational repression and eventually mRNA degradation (3UT region)

44
Q

miRNA does not have what pathway?

A

RITS

45
Q

Where of miRNA primary transcripts originate from?

A

Encoded by themselves or in introns protein coding genes (Via RNA polymerase 2)

46
Q

what is this?

A

miRNA

47
Q

Piwi RNA are the same as what? what is the one exception

A

Same as RISC Complex but in specialized cell (Germ cells)

48
Q

What does piRNAs regulate?

A

piRNAs regulate transposition (inhibit transposition)

49
Q

what do we target? (piwi)

A

Targets the RNAs coming off the pi transposons (represent sequences by viruses over millions of years)

50
Q

piRNA can be be involved in what?

A

piRNAs can be involved in both transposon degradation and transposon transcriptional silencing.

WE CAN DESTROY THE RNAS WITH THE ENDONUCLEASE AND GUIDE RNAS LIKE RISC

AND WE CAN SUCH DOWN
TRANSCRIPTION WITH RECRUITEMENT OF CHROMATIN MODIFYING PROTEINS (HISTONE METHYLASE) LIKE RITS

51
Q

what happens if the vestigial transposon complex is allowed to go on?

A

If this vestigial transposon complex is allowed to go on and DS RNA accumulate then the germ cells are destroyed, and we will not produce gametes

52
Q

T/F: piRNAs have a high relevance in gametogenesis; infertility results if piRNA proteins are not degraded

A

False: piRNAs have a high relevance in gametogenesis; infertility results if piRNA proteins are NOT degraded

53
Q

piRNAs can be involved in both?

A

piRNAs can be involved both in transposon degradation and transposon transcriptional silencing

54
Q

Without piwi proteins what happens?

A

Without piwi proteins, germ cells have large amounts of transposon transcription.

55
Q

What presence of what defines germ cell stem cells

A

DDX4

56
Q

what is one of the piwi proteins ?

A

One of the piwi proteins is an RNA helicase, termed ddx4.

57
Q

DDx4 is what?

A

The ddx4 protein was identified as being expressed in ADULT female ovaries infertility treatments.

RNA helicase and marker for stem cells to develop egg cells

Represents a family of proteins with a conserved domain, the dead box domain (section of polypeptide)

58
Q

what is the mouse equivalent of ddx4?

A

mouse vasa homolog (mvh) and its human equivalent, ddx4
Hope is to address infertility issues with these stem cells

59
Q

Total RNA binding domain count for exam:

A

SR (splicing enhancement, alternative splicing)

Dead box (RNA helicase)

60
Q

Another important list: effects of nonconding RNAs

A

RNA degradation: EXACT MATCH

Inhibition of translation: MiRNA

Gene/transcription silencing: PiRNA

miRNA inhibit Translation, Endo siRNA (RITS) inhibit transcription

61
Q

PiRNA and ddx4

A

PIWI family proteins: MILI, MIWI2 : they produce piRNAs

Mice without MILI and MIWI2 expressed retrotransposons and had MVH deficiencies

MVH=DDx4 in mice=RNA Helicase

VASA= V in MVH= essential for germ cell development

MVH may play some roles in piRNA production therefore DNA methylation of retrotransposons

62
Q

What are examples of PIWI family proteins?

A

MILI, MIWI2

63
Q

MILI and MIWI2 produce what

A

they produce piRNAs

64
Q

Mice without mili and miwi2 have?

A

Mice without MILI and MIWI2 expressed retrotransposons and had MVH deficiencies

65
Q

____=DDx4 in mice

A

MVH

66
Q

If you lack MVH in mice they have what?

A

infertility issues

67
Q

From a stem cell, we can get what?

A

oocyte

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