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Biochemistry > Lecture 7- Eukaryotic Transcription > Flashcards

Lecture 7- Eukaryotic Transcription Flashcards

1
Q

How many RNA Polymerase are there and name them?

A

3; RNA Polymerase I,II, III

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2
Q

Do RNA Polymerase share the same subunits?

A

They share some subunits

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3
Q

What is the fx. of RNA Polymerase I?

A

Synthesize precursors of ribosomal RNA

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4
Q

What is the fx. of RNA Polymerase II?

A

Synthesizes mRNA precursors. It recognizes promotors of varying sequences through assoc. proteins.

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5
Q

What is the Fx. of RNA Polymerase III?

A

Synthesizes precursors of ribosomal RNA, tRNA and other small RNA’s

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6
Q

How many subunits are on RNA Polymerase II?

A

12 subunits

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7
Q

What’s the difference between the subunits of Prokaryotic and Eukaryotic RNA Polymerase?

A

RBP1 subunit in Eukaryotic RNA Polymerase II has a long tail.

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8
Q

What sequence is on the strand that’s important for regulation?

A

YSPTSPS

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9
Q

What Amino Acid might be found on RBP1?

A

Prolines; loop typed structure

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10
Q

True or False. RBP1 forms a loop structure?

A

True

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11
Q

Fx. of Pol II

A

Catalyzes RNA Synthesis

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12
Q

Fx. TBP

A

Recognizes TATA Box

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13
Q

What is the TATA Binding Protein?

A

TBP

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14
Q

Fx. of TFIIA

A

Stabilizes binding of TFIIB and TBP to the promoter

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15
Q

Fx. of TFIIB

A

Binds to TBP; recruits Pol-II-TFIIF complex

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16
Q

Fx. of TFIIE

A

Recruits TFIIH; has ATPase and helicase activities

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17
Q

Fx. of TFIIF

A

Binds tightly to Pol II; binds to TFIIB and prevents binding of Pol II to nonspecific DNA sequences

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18
Q

Fx. of TFIIH

A

Unwinds DNA at promoter; phosphorylates Pol II whine the CTD; recruits nucleotide -excision repair proteins

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19
Q

Where is the initiation region?

A

+1

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20
Q

What are 4 steps of Transcription?

A

Assembly
Initiation
Elongation
Termination

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21
Q

What happens during assembly? what happens immediately after

A

TATA binding protein binds to the TATA Box

TFIIB, TFIIF-RNA Polymerase II, TFIIE, TFIIH.

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22
Q

What is the job of TFIIF after Assembly?

A

guiding RNA Pol II to the correct DNA sequence

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23
Q

What happens during assembly?

A

TBP binds to TATA box

TFIIB, TFIIF, TFIIE and TFIIH are all recruited to site.

TFIIF “Chaperone” guides RNA Pol II to correct DNA sequence.

TFIIH binding completes closed complex and TFIIH starts to unwind the DNA to create an open complex.

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24
Q

What causes initiation?

A

TFIIH phosphorylates RNA Pol II numerous times in its terminal domain, causing a structural change.

TFIIE and TFIIH are released as RNA Pol II synthesizes the first 60-70 nucleotides and starts elongating.

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25
Q

What happens during elongation?

A

TFIIF remains assoc. with RNA Pol II throughout Elongation. Additional elongation facts bind to the complex to enhance activity.

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26
Q

What causes termination?

A

Dephosphorylation of RNA Pol II,

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27
Q

True or False.

Prokaryotes can have transcription/translation simultaneously?

A

True

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28
Q

What are introns

A

Portions of non-coding sequences on DNA

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29
Q

What happens to introns?

A

They have to be spliced out.

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30
Q

Polycistronic mRNA Exists in ____.

A

Found in Prokaryotes

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31
Q

Why are polycistronic mRNA not common in Eukaryotes?

A

You need a 5’ cap to define the start site for protein biosynthesis.

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32
Q

What does the 5’ cap consist of?

A

7 methylguanosine

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33
Q

Wha happens to the 3’ end?

A

has to be cleaved and add a Poly A tail

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34
Q

What is the prokaryotic version of introns?

A

transpositrons

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35
Q

Introns get spliced after they leave RNA Pol II

A

True; happens in real-time

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36
Q

If I see a 5’-5’ Triphosphate Linkage what might that indicate?

A

5’ end cap of a mRNA

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37
Q

What groups are added to the first bases on a mRNA strand that might denote a 5’ end?

A

Methyl Groups placed on C2

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38
Q

5’ Cap protects mRNA from ______ .

A

Ribonuclease

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39
Q

5’ Cap might enhance binding assoc. with ____.

A

Ribosome

40
Q

Cap is methylated at ____. before of after it’s added mRNA

A

N7; after

41
Q

Cap comes from which nucleotide?

A

GTP

42
Q

At what point is the cap added in reference to transcription?

A

Early in transcription

43
Q

Enzymes that make up the cap are tethered to polymerase ______.

A

CTD

44
Q

Which nucleotides of mRNA are methyl groups added to?

A

1st/2nd

45
Q

What are the (4) enzymes in Cap synthesizing complex?

A

Phosphohydrolase

Guanylytranserase

Guanine-7-Methyltransferase

2-O’ Methyltransferase

46
Q

What is the fx. of Phosphohydrolase?

A

Attacking gamma phosphorous position with water.

Gamma-P has been kicked off.

47
Q

What is the fx. of Guanylyltransferase?

A

Beta O- is nucleophile; hits alpha-P atom in GTP (electrophile). It kicks off beta/gamma from GTP.

This moves G-Alpha to make a 5’-5’ Triphosphate

48
Q

When is the cap Methylated?

A

Cap is methylated on N-7 and after it is added to mRNA;
after attack on GTP
Guanine 7-Methyltransferase

49
Q

5’ cap comes from___

A

Guanylate

50
Q

What adds the Methyl group to capping?

A

Guanine-7- Methyltransferase

51
Q

SAM is the source of what?

A

Methyl group

52
Q

SAM gives his methyl to____.

A

5’ end of mRNA during capping. Putting it on 7 methyl guanosine

53
Q

What is the fx. of 2’ O Methyltransferase?

A

It determines where it wants to add the methyl groups. Either 1’ OH or 2’OH

54
Q

The methyl groups are derived from ______.

A

S-adenosylmethionine

55
Q

What happens after 7-methylguanosine is formed?

A

Capped 5’ end is released from the capping enzymes and bound to the cap-binding complex.

56
Q

What is Actinomycin D

A

Deforms the DNA and prevents movement of RNA Polymerase.

57
Q

Rifampicin

A

binds to beta subunit of bacterial RNA poly. and prevents extension past the promoter.

58
Q

Alpha-Amanitin

A

Blocks RNA Pol II, but not bacterial RNA polymerase. Prevents predators from destroying the mushroom population.

59
Q

Poly A tails are on what end?

A

3’ end

60
Q

Poly A Tail cause degradation of bacterial

A

True

61
Q

Tail length transcribes life or RNA

A

True

62
Q

Bacterial love Poly A Tails.

A

False; they degrade poly a tail

63
Q

What is the recognition seq. to lay down poly A tail?

A

AAUAAA

64
Q

How many residues make up Poly A tails?

A

80-250

65
Q

True or false

Poly A tails in Eukaryotic contribute to mRNA enzymatic destruction

A

False; Poly A Tails help protect mRNA from enzymatic destruction

66
Q

What is the difference in Poly A tails destruction in Eukaryotic vs Prokaryotic mRNA?

A

Prokaryotic: stimulate decay

Eukaryotic: prevent degradation

67
Q

What generates the free 3’ hydroxyl group that defines the end of mRNA?

A

Cleavage

68
Q

What happens to RNA Polymerase when Enzyme Complex reccog. binds to transcript what does RNA Pol II do?

A

RNA Polymerase leaves

69
Q

Endonuclease

A

It cuts the transcript

70
Q

Poly A Polymerase

A

Put out 80-250 AA residues on the tripped end

71
Q

Intron

A

Non-Coding

72
Q

Exon

A

Coding

73
Q

Which are longer? Exon or Intron

A

Intron

74
Q

How many types of Introns are there?

A

4

75
Q

Group 1/2 self-splice

A

True

76
Q

In what major way do Group 1/2 differ?

A

Mechanism

77
Q

Majority of eukaryotic introns are?

A

Spliceosomal Introns

78
Q

Group 1 Introns use ____ to initiate splicing process

A

Guanylate

79
Q

During Group 1 Intron nucleotide attacks, which end is attacked first and then what happens?

A

3’ end; it generates a 3’ OH that will then attack at the 5’ end of the second exon.

80
Q

What happens after the introns after they are cut out?

A

Released/Degraded

81
Q

Do Group 1 Introns appear to have consensus splice sites?

A

No

82
Q

Group 1 Introns do NOT appear to have _______.

A

consensus splice sites

83
Q

Explain process of Group I Introns

A

3’ OH of Guanylate (Nucleophile) attacks 5’ (Electrophile) Phosphoryl.

Kick off exon as a leaving group. Frees up 3’ OH Exon.

Guanylate is covalently bound to intron.

Now, free 3 OH’ (Nucleophile) attacks P on 3’ Intron.

Now (2) exon are fused

84
Q

Adenosine is used in which intron group of splicing?

A

Group II Introns

85
Q

Which Intron group produces a lariat structure?

A

Group II Introns

86
Q

Which intron group uses a 2’ oH

A

Group II Introns

87
Q

Does Group II Introns have consensus splice sites?

A

Yes

88
Q

What does the Lariat Structure have?

A

3 Phosphodiester Bonds

89
Q

Describe the process of Group II Intron

A

2’ OH of Adenosine of Intron (Nucleophile) attacks the 5’ splice site to form a lariat structure.

2’ OH (Nucleophile), Attacks P atom in phosphodiester linkage that bridges exon and intron. It will sever the bond.

Electrons now kick off exon. Now we have a free 3’ OH

Now we form a Lariat Structure.

3’ OH (Nucleophile) hits phosphorous bride between intron and exon.

Kicks off intron as leaving group. Now we have a phosphodiester bond bt. exon.

90
Q

What nucleases are o the 5” and 3’ end during Group II Introns?

A

5’ GU

3’ AG

91
Q

Consensus Splice Site in

Group II

A

GU-AG

92
Q

What is a notable feature about the Lariat Structure

A

3 Phosphodiester Bonds

93
Q

In what ways are the structures directed in the Lariat Structure?

A

(2) runs 5’ - 3’

(1) runs 2’ to 5’

94
Q

How many RNA complexes are involved in spliceosomal introns?

A

5

95
Q

True or False

Group II Introns are self splicing?

A

True

Biochemistry (12 decks)

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