Transcription

Question 1

Explain the Beadle and Tatum experiment

Answer 1

discovered one gene, one enzyme by growing mutants in selective media

Question 2

Replication differs from transcription how?

Answer 2

1. produces an exact copy of self
2. uses dNTPs
3. produces dsDNA
4. requires DNA pol

Question 3

Transcription differs from replication how?

Answer 3

1. produces a functional compenent
2. uses NTPs (T is now U)
3. produces ss molecule
4. requires RNAP (RNA pol)

Question 4

What are the 9 required parts of a gene?

Answer 4

1. -35 and -10 TATA boxes
2. +1 transcription start site
3. 5’ UTR
4. Shine-Delgarno sequence
5. Start codon
6. coding sequence
7. stop codon
8. 3’ UTR
9. termination site

Question 5

monocistronic

Answer 5

one RNA, one protein

Question 6

polycistronic

Answer 6

one RNA, many proteins

Question 7

Why is polycistronic transcription important?

Answer 7

it ensures coordinated expression of multiple components at the same time from the same locus (ex: members of a coordinated pathway)

Question 8

Sigma factor

Answer 8

needed for initiation of RNA synthesis

Question 9

RNAP core

Answer 9

catalyzes DNA transcription to RNA

Question 10

What are the 2 RNAP holoenzyme parts?

Answer 10

Sigma factor + RNAP core

Question 11

How do you identify the UP element?

Answer 11

1. it has a similar consensus sequence that interacts with the C-terminus of alpha RNAP
2. it is an A/T rich sequence located -40 to -60

Question 12

What does the UP element do?

Answer 12

stabilizes RNAP association

Question 13

What binds TATA boxes?

Answer 13

sigma 70

Question 14

What binds UP?

Answer 14

alpha subunit of RNAP

Question 15

Two ways to repress transcriptional initiation?

Answer 15

1. proteins bind within core promopter elements (-35 and -10) and prevent sigma 70 or RNAP binding
2. proteins bind away from the promotor but induce DNA structure the occludes the promotor (ex: loop with -35 and -10 in bend)

Question 16

What is the first step in transcription initation?

Answer 16

assembly of the RNAP holoenzyme

Question 17

Assembly of the RNAP holoenzyme

Answer 17

1. sigma factor binds to TATA box while the alpha subunit of RNAP binds UP to form RPc (closed)
2. melting of the -10 TATA box to “flip out” the DNA into the RNAP to form RPo (open)

Question 18

Where is the RNA polymerization phosphodiester bond formed?

Answer 18

formed between the 3’ -OH and the 5’ alpha phosphate

Question 19

RNA polymerization direction

Answer 19

reads 3’ to 5’ on template to produce 5’ to 3’ RNA

Question 20

4 ePEC roles (elemental pause state)

Answer 20

1. coordinates transcription and translation
2. facilitates RNA folding
3. provides regulation via proteins
4. transcriptional termination

Question 21

intrinsic termination

Answer 21

1. hairpin loop formation 7-8 nt from end
2. 7-8 nt U rich tract after
3. pressure from hairpin forces RNAP off

Question 22

Rho dependant termination

Answer 22

1. rut sequence in RNA gets threaded into rho
2. force of RNA wrapped around in rho pulls RNA off

Question 23

RNA base pairing is …

Answer 23

flexible and messy due to modified nucleosides

Question 24

nucleosides are modified when?

Answer 24

following transcription

Question 25

modified nucleosides are important why?

Answer 25

For structural RNAs

Question 26

tRNA modification

Answer 26

is required for function