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Genetics > Lec4SplicingandprocessingofRNA > Flashcards

Lec4SplicingandprocessingofRNA Flashcards

1
Q

RNA pol 2 is with protein coding or noncoding genes?

A

Protein coding genes

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2
Q

What are genes doesRNA pol I transcribed? what do they give?

A

5.8S, 18S and 28 rRNA genes

TRANSCRIPTS THAT GIVE IVS

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3
Q

What genes are transcribed by RNA Pol II?

A

All protein-coding genes, plus snoRNA genes, mRNA genes, siRNA genes, IncRNA genes, and most snRNA genes

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4
Q

What is the binding site for RNA pol II?

A

Phos of CTD

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5
Q

What is phosphorylates RNA pol 2?

A

TFIIH will phosphorylate RNA pol 2 at the CTD portion which is the binding sites for proteins

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6
Q

What are the steps of mRNA processing? (steps to turn primary transcript to mRNA for transport)

A
  1. capping
  2. splicing
  3. poly a addition
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7
Q

What happens when we complete the steps of mRNA processing?

A

Once it is complete, we can export the mRNA from the nucleus

Also important with connecting the ribosomal proteins

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8
Q

The 5’ capping is what type of bond ?

A

5’ to 5’ phosphodiester bond

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9
Q

What is the cap on mRNA?

A

Cap is a 7 methyl Guanine

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10
Q

Does the methyl get adding during, before or after synthesis of guanine and phophodiester bond is formed?

A

AFTER

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11
Q

When does the cap get added to mRNA?

A

Methyl cap gets added after synthesis of guanine but also after the Phosphodiester bond is formed(similar to 5-methyl cytosine)

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12
Q

What happens when there is no 5’ cap?

A

Cannot get mRNA to the ribosome

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13
Q

What is the energy source of 5’ capping?

A

Unstable release of pyrophosphate

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14
Q

Is pyrophosphate stable?

A

no

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15
Q

T/F the MRNA cap is 7 methyl guanine and the methyl is added during the synthesis of guanine

A

False

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16
Q

When exons do not come together properly what happens?

A

medical defect

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17
Q

codons are divided by what?

A

intron

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18
Q

If 2 exons don’t come together at the right n.t then what happens?

A

then you can be out of frame and have a medical defect

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19
Q

What is a gene that causes a defect when exons do not come together properly?

A

An example of this is TECTA gene in the case that leads to deafness

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20
Q

What does the TECTA gene cause?

A

deafness

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21
Q

Codon are a part of ______ and separated by ______(noncoding DNA)?

A

Codons are part of exons and separated by noncoding DNA (introns)

we need to slice exons together to put the right codons together

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22
Q

What is this browser and label what 1. and 2. are dictated by the arrows

A

Genome.ucsc.edu
1. 5’UTR–> untranslated region
2. Exon

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23
Q

How many primary transcripts are there? why are they there?

A

there are 2 primary transcripts because there is alt. splicing to choose which exons come together

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24
Q

If there are 2 splicing alternatives, there will be how many transcripts?

A

TWO

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25
Q

Why do we put different exons together?

A

to get slightly different proteins

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26
Q

splicing is dependent on what?

A

dependent on n.t sequence in the introns mainly and little bit of exons

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27
Q

Where is the invariant adenine?

A

10-30 bp from the 3’ end of the intron

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28
Q

Why is the invariant adenine important?

A

A cannot vary and important for splicing exons together

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29
Q

What does the invariant adenine get ?

A

2’OH

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30
Q

what is attached here?

A

2’OH

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31
Q

What does the 2’OH attack?

A

2OH to attack the phosphodiester bond @ the 5’end of an intron

The OH is then attached to the exon that was cut off

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32
Q

Besides attaching the 5’ end, what else does OH do?

A

the newly added OH on the exon breaks phosphodiester bond at the 3’end of intron

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33
Q

Which end of the intron get attacked with the 2’OH?

A

5’ end of intron

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34
Q

What is temporary produced after the connecting of 5’ end of the intron to the 2’OH

A

lariat structure

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35
Q

what is the set of proteins that are important for making the lariant happen?

A

Splicesomes and individual proteins –> SnRNPs

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36
Q

What does SnRNP stand for and what are SnRNP’s made up of?

A

Small nuclear, ribonuclear particles

Made of polypeptides +RNA

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37
Q

What do SnRNPs do?

A

These SnRNP’s will come together on the primary transcript and will arrange the primary transcript so the invariant A will be positioned properly

38
Q

The snRNPs and related proteins make up what is termed the ______

A

Spliceosome

39
Q

What does this sequence allow?

A

Sequence that aligns to the RNA to allow for invariant A to attack the 5’ end of intron

40
Q

snRNAs are part of what?

A

snRNAs are part of ribonuclear-proteins, referred to as snRNPs, that form a complex, which in turn allows the snRNAs to catalyze the splicing of the mRNA.

41
Q

Which of the following is most likely to be a spliceosome subunit?
a. Primase
b. Telomerase
c. U5
d. Collagen

A

C

42
Q

What is the purpose of this sequence?

A

Interact with SnRNPs so anything with a U

43
Q

The invariant changes or never changes?

A

never changes

44
Q

since the invariant does not change we need to do what?

A

Invarient never changes so need to match to the 20,000 + Prim Transcripts (that’s why its imperfect)

45
Q

How do we trace alternative splicing?

A

We trace alternative splicing to the final polypeptide and which proteins are interacting with the final polypeptide

46
Q

If an exon is missing its most likely a protein that interacts with that exon is __ _____

A

not present

47
Q

What are HnRNPs?

A

hnRNPs: heterogenous nuclear ribonuclear proteins

Proteins that will block formation of spliceosome and proteins that contact the spliceosome

48
Q

What is SR?

A

SR= Serine + Arginine

The SR proteins stimulate the formation of the splicesome

49
Q

What is A common “reason” for alternative splicing ?

A

to generate membrane bound and secreted forms of a protein, with the secreted form often generated bc the exon encoding the membrane binding regions of a protein is not included

50
Q

Info on IgM… I did not know how to form a question

A

In the case of IgM, either secreted or membrane bound versions are produced depending on alternative splicing.

51
Q

Does the PIC interact with TATA box or Exon splicing sequence?

A

TATA box

52
Q

Splicing can be enhanced by what?

A

RNA sequences and proteins that bind to the sequences

53
Q

What are the RNA sequences that affect splicing

A

ISS: Intron sequence silence
ISE: Intron sequence enhance
ESS: Exon sequence silencer
ESE: Exon sequence enhancer

54
Q

What is ISS

A

Intron sequence silence

55
Q

What is ISE

A

Intron sequence enhance

56
Q

What is ESS

A

Exon sequence silencer

57
Q

What is ESE

A

Exon sequence enhancer

58
Q

What is important about this article ?

A

INDUCIBLE SPLICING WITH INSULIN

59
Q

Key points for splicing?

A

Phosphodiester bond hydrolyzes at the 5’ end of the intron for phosphodiester bond formation with the 2’-OH of a consensus adenine nucleotide located close to the 3’ end of the intron: lariat formation

Consensus sequences in the pre-mRNA transcript provide binding sites, via W-C base pairing, for RNA-containing proteins (small nuclear ribonuclear proteins, snRNPs), which position the intron and exon sequences for the splicing reactions (NOT PERFECT WC BP)

The snRNPs make up the spliceosome

The spliceosome function is regulated by SR and hnRNPs, particularly for alternative splicing.

60
Q

If we mutate a sequence in the intron what happens?

A

It can effect splicing

61
Q

If we change the g to an t, what happens?

A

It can skip an exon or retain/keep an intron

62
Q

Almost all primary transcripts have this sequence

A

AAUAAA

63
Q

What is important about the sequence AAUAAA

A

Which is an indication of where it should be cut off @ the 3’ end and where the Poly A tail starts

64
Q

mRNAs have a polyA addition/cleavage signal, what is it ?

A

AAUAAA

65
Q

The polyA tail is added in a template _____ manner

A

INDEPENDENT

66
Q

T/F the PolyA tail is added in a template dependent manner

A

false

67
Q

The poly A tail doesn’t have what?

A

a template

68
Q

What attaches to the RNA pol II then causes what?

A

Cleavage and polyadenylation specific factor (CPSF)

binds the polyA signal site of the emerging mRNA; recruits polyA polymerase.

69
Q

What is the landing cite for cpsf?

A

AAUAAA

70
Q

What is the sites on the RNA pol II that allow the binding of enzymes (ex.CSPF)

A

Phos. on CTD

71
Q

What phosphorylates CTD?

A

TFIIH

72
Q

What is AAUAAA

A

Signal sequence landing site for CSPF

73
Q

What is poly A pol?

A

Adds poly tail

74
Q

What is Poly a binding protein

A

Coats the poly A as its synthesized

75
Q

What happens when poly A are not added

A

RNA is rapidly degraded

76
Q

Cleavage of the pre-mRNA occurs when?

A

Cleavage of the pre-mRNA occurs AFTER binding of PAP

77
Q

The polymerization of polyA tails requires what?

A

ATP and the binding of poly A binding proteins (PABPs).

78
Q

mRNA processing proteins are recruited to where and how?

A

mRNA processing proteins are recruited to RNA polymerase II by phosphorylated amino acids in RNA pol II.

79
Q

Does rRNA participate in splicing

A

NOOOOO

gives IVS

80
Q

Since there is no splicing of rRNA, how do we modify rRNA if needed

A

Chemical modifications of NT @ a specific spot

81
Q

T/F Ribosomal RNA is never going to vary

A

True

82
Q

What are two example of chemical modifications?

A

Pseudouridine and 2-O-methylated n.t.

helps with stability

83
Q

in rRNA what are guide RNAs?

A

snoRNAs

84
Q

What do snoRNAs do?

A

direct the position of the base modifications for rRNAs

84
Q

What is important about the nucleolus in rRNA

A

Nucleolus: Building up ribosome and match up of almost all RNA polypeptide

Partners like telomerase

85
Q

What are Small Nucleolar RNA

A

rRNA modifying enzyme

86
Q

What are small nuclear RNA

A

RNA modifying enzymes

86
Q

With SnoRNA is it perfect match or not?

A

PERFECT MATCH W-C BP (RNA is not changing)

87
Q

What causes deafness in Brazilian family?

A

Deletion in the 5’ end of intron 16, included the last two bases of donor splice site (nucleotide change)

deletion in the TECTA gene

88
Q

What is the function of the ZP (zona pellucida) domain of the TECTA protein?

A

Most likely, to mediate polymerization with other proteins. Thus, if one allele encodes a defective copy of TECTA, the overall product of the polymerization process is likely to be defective. In other words, one bad apple can spoil the entire matrix of polymerized proteins.

Mutation of ZP-domains can result in severe pathologies, such as infertility, deafness, and cancer

Genetics (12 decks)

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