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COB Molecular > Lec 9. Protein synthesis 2. RNA Maturation and Versatility > Flashcards

Lec 9. Protein synthesis 2. RNA Maturation and Versatility Flashcards

1
Q

What are the steps for mRNA processing?

A

Capping proteins then splicing proteins then polyadenylation proteins

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2
Q

Why is RNA sticky?

A

Nitrogenous bases want to base pair with respective complementary bases, can form 4 secondary structures that can become binding sites for proteins

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3
Q

What are the 4 secondary structures for RNA?

A

Three-nucleotide bulge, four-stem junction, hairpin loop, pseudoknot

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4
Q

what is the 5’ cap?

A

An upside down and backwards G with an extra methyl group at the 5’ end of an RNA*

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5
Q

What does the 5’ cap do?

A

Resistant to digestion by nucleases, serves as a recognition site for CBC proteins (Cap binding complex).

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6
Q

What do CBC proteins do?

A

Initiate splicing and polyadenylation, direct mature mRNA through the nuclear pores and recruits elFs once in cytoplasm

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7
Q

What are the 4 mRNA processing splicing types?

A

Group I introns, Group II introns, Spiceosomal introns, and tRNA introns

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8
Q

Who has group I introns?

A

Prok, euk, and organelles.

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9
Q

Where are group I introns usually found?

A

In rRNA genes of euk.

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10
Q

How are Group I introns removed?

A

Self-catalyzed

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11
Q

Once Group I introns are removed what are the results?

A

Either linear or circularized introns

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12
Q

Which of the 4 mRNA processing splicing types is most prevalent in humans?

A

Group I introns

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13
Q

Who has Group II introns?

A

Prok and euk organelles

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14
Q

How are Group II introns removed?

A

Self-catalyzed, some require a protein helper in vivo.

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15
Q

What is the result once Group II introns are removed?

A

Lariot structures that are precursors to spliceosomal introns.

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16
Q

Who has spiceosomal introns?

A

Euk only

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17
Q

How are Spiceosomal introns removes?

A

Protein-mediated

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18
Q

What is the end result once Spiceosomal introns are removed?

A

Lariat structure

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19
Q

Who has tRNA introns?

A

Euk and their organelles

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20
Q

How are tRNA introns removed?

A

Protein-mediated. The intron sits across the anticodon, in order to remove the intron we need to split the tRNA in half and stick it back together.

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21
Q

Alternative splicing is a way to

A

increase genetic diversity without a permanent change to the DNA sequence*

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22
Q

What is polyadenylation?

A

200 A’s at the 3’ end of an RNA.

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23
Q

What does this polyadenylation do?

A

Define the exact 3’ end of the RNA, it is also a binding spot for PABS (PolyA binding proteins).

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24
Q

What do PABPS do?

A

Resistant to digestion by nucleases, can bind to translation initiation factors (elFs) to circularize the mRNA and start translation

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25
Q

Pertaining to polyadenylation, what does co-transcriptional recruitment of CPSF to polyadenylation signal site do?

A

Our specificity factor, where we stop our DNA.

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26
Q

Where does CstF bind?

A

DSE (downstream element site)

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27
Q

What do CPSF and CstF do?

A

Interact through this complex of proteins and basically expose this site (NN) to be cleaved as our absolute end of our mRNA, so we need an ENDO nuclease to come in and clip at the NN.

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28
Q

What does Poly-A Polymerase (PAP) do?

A

Adds polyA tail

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29
Q

What does Poly-A Binding Proteins (PABPs) do?

A

Coat the polyA tail, will act with elFs and loop around the end of mRNA and help initiate translation

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30
Q

What is the difference between coding and noncoding RNAs?

A

Coding RNAs are coding for protein, if we are not coding for protein we are noncoding RNA.

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31
Q

What is the only coding RNA?

32
Q

What is the function for mRNAs?

A

code for proteins

33
Q

What is the function for rRNAs?

A

form basic structure of the ribosome and catalyze protein synthesize

34
Q

What is the function for tRNAs?

A

central to protein synthesis as adaptors between mRNA and amino acids

35
Q

What is the function for snRNAs?

A

Nuclear processes, splicing of pre-mRNA

36
Q

What is the function for snoRNAs?

A

help to process and chemically modify rRNAs

37
Q

What is the function for miRNAs?

A

regulate gene expression by blocking translation of specific mRNAs and cause their degradation

38
Q

What is the function for siRNAs?

A

turn off gene expression by directing the degradation of selective mRNAs and the establishment of compact chromatin structures

39
Q

What is the function for piRNAs?

A

Piwi-interacting RNAS bind to piwi proteins and protect the germ line from transposable elements

40
Q

What is the function for lncRNAs?

A

Scaffolds, regulate diverse cell processes including x-chromosome inactivation

41
Q

Where are rRNAs made?

42
Q

Where are snRNAs and snoRNAs matured and recycled in?

A

Cajal bodies

43
Q

What are speckles?

A

Stockpiles of snRNAs and other processing factors

44
Q

Where are snRNAs found?

45
Q

snRNAs are transcribed by what?

A

RNA pol I & II

46
Q

What is the size catagory for snRNAs?

47
Q

What are the role of snRNAs?

A

splicing out the introns

48
Q

Where are snoRNAs found?

49
Q

snoRNAs are transcribed by what?

A

RNA pol II(meaning they get a cap n tail but dont need them and actually need to remove them to be functional)

50
Q

What is the size category for snoRNAs?

51
Q

What is the role of snoRNAs?

A

modification of nucleic acids (tRNA,rRNA, and snRNAs), can be cleaved down to miRNAs or piRNAs.

52
Q

siRNA, miRNA, piRNAs are transcribed by what?

A

RNA pol II

53
Q

What is the size category for siRNA, miRNA, piRNAs?

54
Q

What is the role of miRNAs?

A

block translation by degrading RNAs

55
Q

What is the distinguishable feature of miRNAs?

A

Hairpin with a bulge

56
Q

What is the role of siRNAs?

A

Block translation by degrading RNAs, block transcription by promoting heterochromatin

57
Q

What is the distinguishable feature of siRNAs?

A

No bulge, no hairpin, just a ds RNA

58
Q

What are the steps to transcriptional silencing by siRNAs?

A

DCr1 cleaves ds RNa and makes siRNAs, RITS comes in with HMT to methylate.

59
Q

What does transcriptional silencing by siRNAs require?

A

sequence homology.

60
Q

What does transcription silencing by siRNAs do?

A

spreads a methyl mark that signals for heterochromatin. Happens on nucleus

61
Q

What are piRNAs role?

A

Makes short RNA and then silences transposons by methylating their DNA by interacting with PIWI

62
Q

lncRNAs are transcribed by what?

A

RNA pol II

63
Q

What is the size category for lncRNAs?

64
Q

What is the role of lncRNAs?

A

activating or inhibiting, scaffold for proteins or bind directly to DNA/RNA

65
Q

What are the 4 types of lncRNAs?

A

Signal,decoy,guide, scaffold

66
Q

What does the signal lncRNA do?

A

indicated transcriptional activity

67
Q

What does the decoy lncRNA do?

A

removes other regulatory RNAs

68
Q

What does the guide lncRNA do?

A

directs localization of RNA-protein complexes

69
Q

What does the scaffold lncRNA do?

70
Q

What is an example of signal lncRNA?

A

Xist and Tsix (complementary to each other)

71
Q

What does Xist do?

A

when expressed coats x chromosome and thus inactivating it , making it a bar body

72
Q

What is an example of decoy lncRNA?

73
Q

What does Gas 5 do?

A

Binds to glucocortcoid receptor, once bound its a decoy. Meaning that the actual gluco cant bind to the receptor and cant activate that gene

74
Q

What is an example of a guide lncRNA?

75
Q

What does HOTAIR do?

A

Localizes the repressive complex (PRC2). PCR2 is a histone methyl transferase that leaves a repressive mark.

76
Q

What does over expression of HOTAIR uually indicate?

COB Molecular (36 decks)

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