RNA

Question 1

In what ways is RNA different from DNA?

Answer 1

RNA is shorter
RNA is single stranded (vs ds DNA)
RNA can form secondary loop and stem structures (e.g. tRNA)

Question 2

What is the most abundant form of RNA in the cell

Answer 2

rRNA

Question 3

RNA is synthesized ___’ to ___’

Answer 3

5’ to 3’

Question 4

Does RNA require a primer?

Answer 4

No

Question 5

What is the function of the beta subunit of RNA polymerase?

Answer 5

Contains the catalytic site

Question 6

What is the function of the sigma subunit of RNA polymerase?

Answer 6

Recognizes the promoter region of RNA

Question 7

Does transcription transcribe the whole genome?

Answer 7

No, there are discreet areas that are transcribed.

Question 8

How do promoters work in eukaryotes?

Answer 8

2 sequence elements at -35 and -10

Question 9

What piece of RNA polymerase recognizes and binds to the promoter region?

Answer 9

Sigma subunit

Question 10

What are the steps of transcription?

Answer 10

1. Initiation
2. Elongation
3. Termination

Question 11

What is the committed step of transcription initiation.

Answer 11

Moving from a closed promoter to an open complex with 2 open strands. Transcription bubble always 12 bases wide.

Question 12

RNA almost always starts with a ____.

Answer 12

Purine

Question 13

How long is the RNA-DNA hybrid in the beta subunit of RNA Polymerase?

Answer 13

8 bases

Question 14

What sequence signifies transcription rho-independent termination site?

Answer 14

GC-rich palindrome followed by UUU

(a self-complementary sequence!)

UUU forms a hairpin loop

Question 15

A small fraction of transcription termination is __________.

Answer 15

Rho-dependent

Question 16

How does rifampicin work?

Answer 16

It inhibits the formation of the first phosphodiester bond in transcription initiation

Question 17

How is eukaryotic transcription different than prokaryotic?

Answer 17

1. Three polymerases
2. No sigma subunit
3. Polymerase-protein interactions govern specificity

Question 18

What does RNA Polymerase I do?

Answer 18

Large rRNAs (28s, 18s, 5.8S) in the nucleolus

Question 19

What does RNA Polymerase III do?

Answer 19

Transcribes the precursors of small RNAs (tRNAs and 5S rRNAs)

Question 20

What does RNA Polymerase II do?

Answer 20

Transcribes the precursors of mRNAs

Question 21

Does RNA Polymerase II have a sigma factor?

Answer 21

No! Instead Pol II interacts with specific PROTEINS which bind core promoter regulatory elements

Question 22

What are key features of the eukaryotic promoter?

Answer 22

Further from beginning of transcription than prokaryotes

TATA box/basal element (-25)

Additional constitutive elements -40 to -110

Inducible elements -150

Question 23

What do constitutive elements in the eukaryotic promoter do?

Answer 23

Govern the RATE of transcription

Question 24

What do inducible elements do?

Answer 24

Cause initiation of transcription in response to hormones or very specific environmental stimuli

Question 25

What binding factors must proceed binding of Pol II?

Answer 25

TATA binding protein (TBP), TAF, TFIIA-F

Question 26

What is TFIIH?

Answer 26

A binding factor that phosphorylates Pol II to initiate transcription

Question 27

What type of protein binds to enhancers.

Answer 27

Activators

Question 28

What are the components of the core promoter?

Answer 28

Basal element
Constitutive element
Inducible element

Question 29

How does chromosome remodeling and histone acetylation/deacetylation affect transcription?

Answer 29

Affect efficiency of transcription initiation

Question 30

Are constitutive elements always on to some degree?

Answer 30

Yes

Question 31

How are death cap mushrooms toxic?

Answer 31

Alpha-amanitin inhibits RNA Pol II in eukaryotes.