Transcription in Prokaryotes

Question 1

How are base pairs in a gene organized? (?)

Answer 1

Every base pair in a gene is numbered

Question 2

What are the numbers in the transcribed region?

Answer 2

the pairs in the transcribed region have positive numbers

Question 3

What are the numbers in the promoter?

Answer 3

have negative numbers

Question 4

Where is the first base in the promoter?

Answer 4

Is the base just before the transcriptional start site.

Question 5

What does RNA polymerase do?

Answer 5

Creates the RNA strand during transcription

Question 6

What does RNA pol have the ability to do?

Answer 6

to separate and unwind the template and coding strands.

Question 7

What direction does RNA pol move in?

Answer 7

3’ to 5’ direction

Question 8

What is the orientation of the RNA strand synthesized by RNA pol? What does that mean?

Answer 8

antiparallel it means it is synthesized 5’ to 3’

Question 9

What kind of bond can RNA pol form between individual ribonucleotides?

Answer 9

phosphodiester bonds

Question 10

Which end can RNA pol add ribonucleotides to?

Answer 10

to the 3’ end

Question 11

Does RNA pol need a primer?

Answer 11

NO

Question 12

What are the six subunits of E. coli RNA pol?

Answer 12

1 and 2. Alpha
3. Beta
4. Beta prime
5. Omega
6. Sigma

Question 13

Which subunits are found in the core enzyme?

Answer 13

beta, beta prime, and the omega

Question 14

What can the sigma factor do?

Answer 14

it has the ability to attach and detach from the other subunits

Question 15

What is a holoenzyme?

Answer 15

it is when the sigma factor is bound to the core enzyme.

Question 16

What are the three stages of transcription?

Answer 16

1. Initiation
2. Elongation
3. Termination

Question 17

What happens during initiation?

Answer 17

All events that are necessary to begin synthesis of the RNA strand

Question 18

What happens during elongation?

Answer 18

It includes most of the events involving transcription synthesis.

Question 19

What happens during termination?

Answer 19

Steps that are required to end termination

Question 20

What are steps in the initiation stage?

Answer 20

1. Attachment of the holoenzyme to the DNA molecule
2. Attachment to the gene promoter
3. Separation and unwinding of the template and coding strands
4. Addition of the first few ribonucleotides to the RNA strand

Question 21

What happens when the holoenzyme encounters a DNA molecule?

Answer 21

it attaches to the DNA and then slides along the helix.

Question 22

What happens when the holoenzyme encounters a promoter?

Answer 22

it stops and forms a tighter attachment to the DNA at that site

Question 23

What recognizes the promoter sequence in a holoenzyme?

Answer 23

Sigma factor

Question 24

What is the function of the promoter with RNA pol?

Answer 24

The promoter functions to orient RNA polymerase on the DNA molecule

Question 25

Where does strand separation begin?

Answer 25

In the A—T rich region within a promoter

Question 26

What does the holoenzyme do during strand separation?

Answer 26

It breaks H bonds in the A—T rich region, separates the template form the coding strand, and unwinds them

Question 27

What is an open complex?

Answer 27

The area where the template and coding strand are separated

Question 28

What does the holoenzyme do once the strands are separated?

Answer 28

It starts transcription of the new RNA strand

Question 29

Where does the holoenzyme start RNA synthesis?

Answer 29

It begins RNA synthesis at the transcriptional start site and adds the first 8-9 ribonucleotides of the new RNA strand

Question 30

When does the sigma factor detach from the core enzyme?

Answer 30

The sigma factor detaches once RNA synthesis begins and the first few ribonucleotides of the new RNA strand are added

Question 31

What does the detachment of the sigma factor signify?

Answer 31

It marks the end of the initiation stage and the beginning of the elongation stage

Question 32

What occurs during the elongation stage?

Answer 32

The remainder of the RNA strand is synthesized

Question 33

What does the core enzyme do during elongation?

Answer 33

It moves along the DNA, unwinding the template and coding strands as it moves

Question 34

What happens as RNA pol moves along the template strand?

Answer 34

The position of the open complex changes

Question 35

How many base pairs long is the open complex?

Answer 35

About 17 base pairs of DNA

Question 36

What is within the open complex?

Answer 36

The bases of the RNA strand are H bonded to the bases of the template strand

Question 37

What happens as the template and coding strands are being rewound?

Answer 37

Bonded bases within the RNA strand are displaced from the template strand

Question 38

What happens as a consequence as bonded bases in the RNA strand are displaced from the template strand?

Answer 38

Only RNA within the open complex is bonded to the template strand

Question 39

When does the termination stage begin?

Answer 39

When the core enzyme encounters a terminator within the template strand

Question 40

What does the terminator do?

Answer 40

It participates in a process that releases the newly synthesized RNA strand It also detaches the core enzyme from the template strand

Question 41

What is the attachment of the core enzyme to the template strand dependent on?

Answer 41

The pairing between bases in the template and RNA strands within the open complex

Question 42

What happens to the base pairs between the template and RNA strands during termination?

Answer 42

The pairing is disrupted RNA strand and template strand are detached Core enzyme and DNA are detached

Question 43

What are the different ways RNA synthesis is terminated in E. coli?

Answer 43

Rho-dependent Rho-independent This is gene specific termination

Question 44

What is Rho-dependent termination?

Answer 44

A protein called Rho attaches to the open complex to disrupt H bonds between the RNA and template. RNA is released and †he core enzyme detaches from DNA

Question 45

What is Rho-independent termination?

Answer 45

The protein called Rho is not required. Sequences within the terminator are sufficient to disrupt bonds between RNA and template strands. Once RNA is released, RNA pol detaches from DNA