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Trends in MB and BT > RNA Transcription > Flashcards

RNA Transcription Flashcards

1
Q

Rnase P

A

Ribozyme. Generate mature tRNA from pre-RNA. Endonuclease. Has a protein part and a RNA part. Protein part to prevent RNA-RNA repulsion. RNA part is catalyst

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2
Q

Ribozyme

A

RNA molecules that catalyze specific reactions, such as splicing & formation of peptide bonds during protein synthesis

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3
Q

Pseudoknots

A

Energetically unfavorable for translation, can be used for regulation. Used for modulating gene expression in gag-pol operon (virus)

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4
Q

How does region 2 of sigma factor interact with the promotor?

A

Binds to the -10 element and stabilize melted DNA

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5
Q

How does region 4 of sigma factor interact with the promotor?

A

Recognizes and binds to -35 using helix-turn-helix

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6
Q

Rho-independent termination

A

Hairpin structure followed by multiple A(:U)

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7
Q

Stepwise assembly of eukaryotic pol II preinitiation complex

A

TFIID/TBP -> TFIIA -> TFIIB -> TFIIF/RNA pol II -> TFIIE -> TFIIH

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8
Q

How is eukaryotic DNA transcribed despite histone proteins?

A

FACT removes H2A.H2B dimers from nucleosome

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9
Q

Formation of 5’ RNA cap

A

Dephosphorylation of 5’ end?. Happens before polyA-tail

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10
Q

Differences between transcription in prokaryotes and eukaryotes

A

Coupled transcription/translation in bacteria
Splicing, 5’ cap and polyA tail in eukaryotes.
TATA, TFII-X in eukaryotes, sigma factor and -10 and -35 consensus seq. in bacteria

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11
Q

Autocatalytic property of RNA

A

If in alkaline solutions, the 2’ OH group can attack the phosphodiester bond and cleave itself. In acidic conditions, this doesnt happen

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12
Q

Topoisomerase role in transcription

A

DNA is only unwound inside the RNA pol which could cause positive supercoiling in front of it

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13
Q

RNA polymerase holoenzyme

A

Core enzyme (2 beta (beta and beta prime) subunits, 2 alpha subunits), Sigma subunit. Resembles crab claw with catalytic center in cleft.

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14
Q

RNA pol beta subunits

A

Main body of the polymerase, contains catalytic center

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15
Q

RNA pol alpha subunits

A

Responsible for enzyme assembly and transcription start

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16
Q

Sigma factor

A

Recognize promotor region in bacteria. 4 factors. Involved in initiation, release lead to elongation step as it blocks RNA exit site.

17
Q

Sigma factor 2

A

Recognizes -10 (TATAAT), flips bases into body of sigma factor, melts open the DNA

18
Q

Sigma factor 1.1

A

Neg aas, stop polymerase from moving until sigma 2 unwinds DNA

19
Q

Sigma factor 4

A

Interacts with major groove at -35 with helix turn helix DNA binding. Blocks RNA exit tunnel

20
Q

Consensus sequence in bacteria

A

A form of gene regulation, the closer to the consensus sequence the higher expression

21
Q

Consensus sequence in eukaryotes

A

TATA box (-30), then the start point and some downstream promotor elements

22
Q

Main RNA polymerase in eukaryotes

A

RNA pol II, makes pre mRNA and snoRNA.

23
Q

Other RNA pol in eukaryotes

A

RNA pol I makes rRNA, RNA pol III makes tRNA

24
Q

TFIID+TBP

A

Binds to TATA box (at minor groove), causes distortion of DNA and sets landmark for RNA pol. Recruits -A and -B

25
Q

TFII-E

A

Helicase loader, recruits TFIIH and melts DNA

26
Q

TFII-H

A

H for Helicase. Also kinase, will start phosphorylating RNA pol “tail”, causing promotor release.

27
Q

TFIIF

A

Sits on RNA pol

28
Q

Histone acetylase

A

Adds acetyl groups to histone tails, decreasing interaction of histone-DNA, making it possible to unpack DNA

29
Q

Promotor escape in eukaryotes

A

Phosphorylation of serine-5 on RNA pol tail leads to promotor escape and capping

30
Q

Proofreading in RNA pol

A

Hydrolytic editing - stimulate RNase activity?
Phosphorylatic editing - PPi are allowed to do “backwards” reaction , GnB controls that the strand is not distorted, if it is then neutralizes metal ion which slows down addition of next NTP -> higher chance of backwards PPi reaction.

31
Q

Rho dependent termination

A

Rho binds to specific seq. when that RNA is exposed. Helicase that unwinds RNA-DNA hybrid. ATPase.

32
Q

Functional domains on Rho hexamer

A

P, Q and R-loop. P is ATP binding and activity, Q and R is RNA binding.

33
Q

TFIIS

A

Elongation factor that stimulates RNA proofreading by hydrolytic editing

34
Q

Hammerhead ribozyme

A

Forms 2’ 3’ cyclic phosphate by attack of 2’ OH at 3’ diphosphate linkage, sequence specific ribonuclease. Self cleaving RNA in viruses.

Trends in MB and BT (5 decks)

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