Lecture 17

Question 1

Initation

Answer 1

RNA pol binds to DNa
DNA unwound at the promoter
Very short chains are synthesized and released

Question 2

Elongation

Answer 2

Polymerase synthesizes RNA

Question 3

What is the elongation process also known as?

Answer 3

processivity

Question 4

Necessary for elongation

Answer 4

core enzyme

Question 5

Core enzyme

Answer 5

alpha 2, beta, beta prime, omega

Question 6

Required for initiation of transcription

Answer 6

Holoenzyme

Question 7

Holoenzyme

Answer 7

alpha 2, beta, beta prime, omega, sigma

Question 8

What does the initial holoenzyme complex cover?

Answer 8

75 bp (-55 to +20)

Question 9

Is the core enzyme or holoenzyme binding faster?

Answer 9

core enzyme is fast, but holoenzyme is more specific so it’s even faster

Question 10

Sigma 70 promoters, amino acids, and preferred sequence

Answer 10

1000 promoters
613 amino acids
TTGACA to TATAAT

Question 11

UP element

Answer 11

AT rich region located upstream of -35 box

expressed in highly expressed genes

Question 12

-35 box alpha helix

Answer 12

4.2

Question 13

-10 box

Answer 13

Pribnow box

TATAAT

Question 14

Down mutation

Answer 14

decreases promoter efficiency and expressed at a lower level

cant bind as well

Question 15

Up mutation

Answer 15

crank up expression

better binding

Question 16

-35 mutations

Answer 16

affect inital binding

Question 17

-10 mutations

Answer 17

affect melting rxn to open the complex

Question 18

amino acids in 2.4 alpha helical region

Answer 18

arg, thr, gln, trp, tyr

Question 19

What prevents sigma from binding DNA all the time?

Answer 19

sigma changes structure to expose binding sites when it attaches to the holoenzyme. DNA displaces the N-terminus when the complex forms.

Question 20

Hairpin

Answer 20

intrastrand pairing (G-C rich)
sequence located upstream of terminator sequence initates pause and release

Question 21

Rho factor

Answer 21

extrinsic terminator

Question 22

Process of rho factor

Answer 22

1. Rho attaches to rut site
2. Rho translocates
3. RNA pol catches on hairpin and Rho catches up
4. Rho unwinds DNA-RNA hybrid
5. RNA released from DNA

Question 23

Rut Site

Answer 23

rich in C poor in G

at the 3’ end of the RNA

Question 24

Rho properties

Answer 24

hexamer

Question 25

Rho n terminal

Answer 25

RNA binding domain

Question 26

Rho C terminal

Answer 26

ATPase domain

Question 27

How is initiation selective?

Answer 27

sigma factors can substitute and bind to different promoters

Question 28

Cascade of sigma factors

Answer 28

1 sigma factor is required to transcribe the gene coding for the next sigma factor

Question 29

Antiterminator protein

Answer 29

can overcome termination events

there are multiple types

Question 30

Intercistronic region

Answer 30

the region of DNA between 2 coding sequences

Question 31

In vivo

Answer 31

In living cell

Question 32

In vitro

Answer 32

in a test tube