Lecture 29

Question 1

RNA molecules are a result of ________ of DNA

Answer 1

transcription

Question 2

types of RNA

Answer 2

rRNA - function and structure

mRNA - informational role. Carries information from genome to the ribosome

tRNA - functional role, carries the amino acids for protein synthesis

-All three of these forms of RNA interact with the ribosome and are needed for protein synthesis.

Question 3

4 main points about RNA

Answer 3

1) Has ribose rather than deoxyribose sugars 2) has uracil instead of thymine 3) usually occurs as single strands not double strands 4) It comes in at least three different forms that serve different functions (mRNA, tRNA, rRNA)

Question 4

What is RNA polymerase?

Answer 4

the enzyme that copies DNA into RNA

Question 5

5 subunits of RNA polymerase

Answer 5

alpha, beta, beta ‘, omega and sigma (there are two alpha subunits)

Question 6

omega subunit needed for?

Answer 6

needed for enzyme assembly, but not for synthesis of RNA

Question 7

alpha and betas are needed for what?

Answer 7

synthesis of RNA

Question 8

sigma factor needed for?

Answer 8

recognition of the promoter region of the gene and initiates transcription

Question 9

the subunits of RNA polymerase interact to form the active enzyme _________ , but the sigma factor is not as tightly bound as the others and easily dissociates, leading to the formation of the RNA polymerase _______ enzyme. What is the function of these separate units?

Answer 9

holoenzyme, but becomes core enzyme without sigma subunit.

core enzyme functions to make RNA, while subunit functions to recognize the appropriate site on the DNA for RNA synthesis to begin

Question 10

To initiate RNA synthesis correctly, RNA polymerase must first recognize the initiation sites on the DNA called?

Answer 10

promoters, whic is a specific DNA sequence to which RNA polymerase binds

Question 11

E. coli has how many different promoter sequences, and they are all recognized by the same sigma factor ________. If you compare the promoter sequences, you will see that they are not identical. However, two shorter sequences (shown in red) within the promoter region are highly conserved between promoters, and it is these that sigma recognizes.

Answer 11

six different promoter sequences

-sigma factor ^70 (70 kilodaltons)

Question 12

Both of these shorter sequences precede the site where transcription starts at the _______ site. One of the red regions is _______ bases before the start of transcription, and is called the _______ region and the _______. Which bases occur most often at each position at this location?

Answer 12

transcription starts at the +1 site

• 10 bases before the start of transciption, called the -10 region and is referred to as the pribnow box
• TATAAT

Question 13

The second region of conserved sequences in the promoter is about _______ bases from the start of transcription. What region is this? Also, what is the consensus seq?

Answer 13

about 35 bases before the start of transciption, -35 region.

consensus sequence is TTGACA

Question 14

Note that although sigma recognizes the promoter seqs on the 5’ to 3’ (dark green) strand of DNA, the RNA pol core enzyme will actually transcribe the light green strand running ________because the core enzyme works only in the ________ direction .

Answer 14

3’to 5’

5’ to 3’ direction

reads the DNA strand from 3’ to 5’ synthesizes from 5’ to 3’

Question 15

Once RNA polymerase (in green here) has bound to a promoter, transcription can proceed, this is called? What happens in this process?

Answer 15

Elongation

In this process the DNA double helix at the promoter is opened up to form a transcription bubble.

Question 16

As the polymerase moves, it unwinds the DNA in short segments. This transient unwinding exposes the ________ (aka the what strand?)

Answer 16

template strand

(aka the antisense or minus strand of DNA).

Question 17

Like DNA, RNA is synthesized in the _____ direction.It starts to make an RNA polymer from ribonucleotides _________ ? RNA synthesis continues until RNA polymerase reaches a site on the DNA called the ____________.

Answer 17

5’ to 3’

(ATP,GTP,CTP and UTP)

terminator

Question 18

It’s important that only the genes needed are transcribed. So a specific protein factor, called what in E. coli? – is needed to terminate the mRNA strand after it is transcribed. What is this entire process called?

Answer 18

Rho dependent termination, and the specific protein factor is known as Rho in E. coli

Question 19

During Rho-dependent termination, the direct binding of this ______utilizing Rho protein to the RNA physically destabilizes RNA polymerases’ interaction with DNA, and RNA pol falls off the DNA, transcription stops.

Answer 19

ATP utilizing

Question 20

termination of RNA synthesis is governed by?

Answer 20

specific base sequences on the DNA

Question 21

In bacteria, a common termination signal on the DNA is a GC rich sequence containing an inverted repeat with a central nonrepeating segment. . When such a DNA seq is transcribed, the RNA forms a stem loop structure by intra-strand base pairing. Such stem loop structures followed by a run of adenosines (AAAA) in the DNA template and therefore a run of uridines (UUUUU) in the mRNA are effective transcription terminators.

Answer 21

This is due to the formation of a stretch of U:A base pairs that holds the RNA and DNA template together. This structure is very weak as U:A base pairs have only 2 hydrogen bonds each. The RNA pol pauses at the stem loop and the DNA and RNA come apart at the run of uridines., this terminates transcription without the addition of any extra factors are referred to as intrinsic terminators