Chapter 6: 6.3 Prokaryotic Transcription

Question 1

How many steps can transcription be broken down into? What are they?

Answer 1

3 steps:
1. Initiation
2. Elongation
3. Termination

Question 2

What enzyme synthesizes the complementary RNA strand?

Answer 2

RNA polymerase

Question 3

What is the site that transcription starts at designated as?

Answer 3

+1

Question 4

Define:

Sigma factor

Answer 4

Subunit of RNA polymerase
* Can bind to specific DNA sequences within the promoter region of a gene

Question 5

In the Inititation stage:

What does the sigma subunit bind to?

Answer 5

1. The -35 box
2. The -10 box

Question 6

Where are the -35 and -10 boxes located?

Answer 6

In the promoter region

Question 7

Why is it called the -35 box and the -10 box?

Answer 7

1. -35 box = ~35 bases upstream from the +1 site
2. -10 box = ~10 bases upstream from the +1 site

Question 8

In the Inititation stage:

Where do the remaining subunits of RNA polymerase bind?

Answer 8

To the promoter

Question 9

What is the RNA polymerase complex referred to as?

Answer 9

Holoenzyme

Question 10

In the Inititation stage:

The RNA polymerase is able to orient itself near the – —- and to move in the direction of ————-

Answer 10

1. +1 site
2. Transcription

Question 11

In the Inititation stage:

RNA polymerase:
1. Binds to ——– ——
2. It reads DNA – – –
3. It synthesizes RNA in – – –

Answer 11

1. Template strand
2. 3’ to 5’
3. 5’ to 3’

Question 12

True or False:

The promoter sequence is the same between genes and bacteria

Answer 12

False, they can vary but are still recognized by Sigma because they are relatively similar

Question 13

Comparing the sequences for the -35 box and -10 box of different genes can yield what?

Answer 13

A consensus sequence
* The most common nucleotide at a particular position

Question 14

State:

The consensus sequence of -34 region

Answer 14

TTGACG

Question 15

State:

The consensus sequence of -10 region

Answer 15

TATAAT

Question 16

The closer to consensus a sequence is…

Answer 16

The higher the affinity the Sigma has for the promoter

Question 17

In the Elongation stage:

When does the elongation start?

Answer 17

Starts when the polymerase releases the sigma subunit

Question 18

In the Elongation stage:

What happens?

(4 points)

Answer 18

• RNA polymerase orientates at the +1 site
• Moves along the template strand in the 3’ to 5’ direction
• Creates a complementary RNA copy by base pairing
• Uses Uracil instead of Thymine (RNA)

Question 19

In the Elongation stage:

The RNA strand is created ————- to the template strand

Answer 19

Complementary

Question 20

True or False:

The RNA strand is identical to the coding (non-template) strand

Answer 20

True

Question 21

In the Termination stage:

What are the two types of termination signals?

Answer 21

1. Rho-dependent termination
2. Formation of a hairpin (Rho-independent)

Question 22

Describe:

Rho-dependent termination

Answer 22

Uses a protein called Rho that binds to the new RNA strand and causes RNA Polymerase to fall off upon their encounter

Question 23

How does Rho-independent termination work?

Answer 23

1. RNA polymerase reaches a termination sequence in the DNA
2. Region with C-G folds onto itself to form a hairpin loop
3. The region with a run of A-U is not very stable, and in combination with the hairpin, causes the polymerase to dissociate

Question 24

In the Rho-independent termination:

What is a termination sequence?

Answer 24

Typically a region of DNA with lots of C and G nucleotides and a poly A sequence

Question 25

In the Elongation stage:

What does a formation of a hairpin loop cause?

Answer 25

Causes polymerase to pause