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Biochemistry > Lecture 7- Eukaryotic Transcription > Flashcards

Lecture 7- Eukaryotic Transcription Flashcards

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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
What happens during elongation?
TFIIF remains assoc. with RNA Pol II throughout Elongation. Additional elongation facts bind to the complex to enhance activity.
26
What causes termination?
Dephosphorylation of RNA Pol II,
27
True or False. | Prokaryotes can have transcription/translation simultaneously?
True
28
What are introns
Portions of non-coding sequences on DNA
29
What happens to introns?
They have to be spliced out.
30
Polycistronic mRNA Exists in ____.
Found in Prokaryotes
31
Why are polycistronic mRNA not common in Eukaryotes?
You need a 5' cap to define the start site for protein biosynthesis.
32
What does the 5' cap consist of?
7 methylguanosine
33
Wha happens to the 3' end?
has to be cleaved and add a Poly A tail
34
What is the prokaryotic version of introns?
transpositrons
35
Introns get spliced after they leave RNA Pol II
True; happens in real-time
36
If I see a 5'-5' Triphosphate Linkage what might that indicate?
5' end cap of a mRNA
37
What groups are added to the first bases on a mRNA strand that might denote a 5' end?
Methyl Groups placed on C2
38
5' Cap protects mRNA from ______ .
Ribonuclease
39
5' Cap might enhance binding assoc. with ____.
Ribosome
40
Cap is methylated at ____. before of after it's added mRNA
N7; after
41
Cap comes from which nucleotide?
GTP
42
At what point is the cap added in reference to transcription?
Early in transcription
43
Enzymes that make up the cap are tethered to polymerase ______.
CTD
44
Which nucleotides of mRNA are methyl groups added to?
1st/2nd
45
What are the (4) enzymes in Cap synthesizing complex?
Phosphohydrolase Guanylytranserase Guanine-7-Methyltransferase 2-O' Methyltransferase
46
What is the fx. of Phosphohydrolase?
Attacking gamma phosphorous position with water. | Gamma-P has been kicked off.
47
What is the fx. of Guanylyltransferase?
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
When is the cap Methylated?
Cap is methylated on N-7 and after it is added to mRNA; after attack on GTP Guanine 7-Methyltransferase
49
5' cap comes from___
Guanylate
50
What adds the Methyl group to capping?
Guanine-7- Methyltransferase
51
SAM is the source of what?
Methyl group
52
SAM gives his methyl to____.
5' end of mRNA during capping. Putting it on 7 methyl guanosine
53
What is the fx. of 2' O Methyltransferase?
It determines where it wants to add the methyl groups. Either 1' OH or 2'OH
54
The methyl groups are derived from ______.
S-adenosylmethionine
55
What happens after 7-methylguanosine is formed?
Capped 5' end is released from the capping enzymes and bound to the cap-binding complex.
56
What is Actinomycin D
Deforms the DNA and prevents movement of RNA Polymerase.
57
Rifampicin
binds to beta subunit of bacterial RNA poly. and prevents extension past the promoter.
58
Alpha-Amanitin
Blocks RNA Pol II, but not bacterial RNA polymerase. Prevents predators from destroying the mushroom population.
59
Poly A tails are on what end?
3' end
60
Poly A Tail cause degradation of bacterial
True
61
Tail length transcribes life or RNA
True
62
Bacterial love Poly A Tails.
False; they degrade poly a tail
63
What is the recognition seq. to lay down poly A tail?
AAUAAA
64
How many residues make up Poly A tails?
80-250
65
True or false | Poly A tails in Eukaryotic contribute to mRNA enzymatic destruction
False; Poly A Tails help protect mRNA from enzymatic destruction
66
What is the difference in Poly A tails destruction in Eukaryotic vs Prokaryotic mRNA?
Prokaryotic: stimulate decay Eukaryotic: prevent degradation
67
What generates the free 3' hydroxyl group that defines the end of mRNA?
Cleavage
68
What happens to RNA Polymerase when Enzyme Complex reccog. binds to transcript what does RNA Pol II do?
RNA Polymerase leaves
69
Endonuclease
It cuts the transcript
70
Poly A Polymerase
Put out 80-250 AA residues on the tripped end
71
Intron
Non-Coding
72
Exon
Coding
73
Which are longer? Exon or Intron
Intron
74
How many types of Introns are there?
4
75
Group 1/2 self-splice
True
76
In what major way do Group 1/2 differ?
Mechanism
77
Majority of eukaryotic introns are?
Spliceosomal Introns
78
Group 1 Introns use ____ to initiate splicing process
Guanylate
79
During Group 1 Intron nucleotide attacks, which end is attacked first and then what happens?
3' end; it generates a 3' OH that will then attack at the 5' end of the second exon.
80
What happens after the introns after they are cut out?
Released/Degraded
81
Do Group 1 Introns appear to have consensus splice sites?
No
82
Group 1 Introns do NOT appear to have _______.
consensus splice sites
83
Explain process of Group I Introns
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
Adenosine is used in which intron group of splicing?
Group II Introns
85
Which Intron group produces a lariat structure?
Group II Introns
86
Which intron group uses a 2' oH
Group II Introns
87
Does Group II Introns have consensus splice sites?
Yes
88
What does the Lariat Structure have?
3 Phosphodiester Bonds
89
Describe the process of Group II Intron
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
What nucleases are o the 5" and 3' end during Group II Introns?
5' GU 3' AG
91
Consensus Splice Site in | Group II
GU-AG
92
What is a notable feature about the Lariat Structure
3 Phosphodiester Bonds
93
In what ways are the structures directed in the Lariat Structure?
(2) runs 5' - 3' | (1) runs 2' to 5'
94
How many RNA complexes are involved in spliceosomal introns?
5
95
True or False | Group II Introns are self splicing?
True

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