RNA Transcription

Question 1

Rnase P

Answer 1

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

Question 2

Ribozyme

Answer 2

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

Question 3

Pseudoknots

Answer 3

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

Question 4

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

Answer 4

Binds to the -10 element and stabilize melted DNA

Question 5

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

Answer 5

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

Question 6

Rho-independent termination

Answer 6

Hairpin structure followed by multiple A(:U)

Question 7

Stepwise assembly of eukaryotic pol II preinitiation complex

Answer 7

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

Question 8

How is eukaryotic DNA transcribed despite histone proteins?

Answer 8

FACT removes H2A.H2B dimers from nucleosome

Question 9

Formation of 5’ RNA cap

Answer 9

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

Question 10

Differences between transcription in prokaryotes and eukaryotes

Answer 10

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

Question 11

Autocatalytic property of RNA

Answer 11

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

Question 12

Topoisomerase role in transcription

Answer 12

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

Question 13

RNA polymerase holoenzyme

Answer 13

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

Question 14

RNA pol beta subunits

Answer 14

Main body of the polymerase, contains catalytic center

Question 15

RNA pol alpha subunits

Answer 15

Responsible for enzyme assembly and transcription start

Question 16

Sigma factor

Answer 16

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

Question 17

Sigma factor 2

Answer 17

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

Question 18

Sigma factor 1.1

Answer 18

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

Question 19

Sigma factor 4

Answer 19

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

Question 20

Consensus sequence in bacteria

Answer 20

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

Question 21

Consensus sequence in eukaryotes

Answer 21

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

Question 22

Main RNA polymerase in eukaryotes

Answer 22

RNA pol II, makes pre mRNA and snoRNA.

Question 23

Other RNA pol in eukaryotes

Answer 23

RNA pol I makes rRNA, RNA pol III makes tRNA

Question 24

TFIID+TBP

Answer 24

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

Question 25

TFII-E

Answer 25

Helicase loader, recruits TFIIH and melts DNA

Question 26

TFII-H

Answer 26

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

Question 27

TFIIF

Answer 27

Sits on RNA pol

Question 28

Histone acetylase

Answer 28

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

Question 29

Promotor escape in eukaryotes

Answer 29

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

Question 30

Proofreading in RNA pol

Answer 30

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.

Question 31

Rho dependent termination

Answer 31

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

Question 32

Functional domains on Rho hexamer

Answer 32

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

Question 33

TFIIS

Answer 33

Elongation factor that stimulates RNA proofreading by hydrolytic editing

Question 34

Hammerhead ribozyme

Answer 34

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