Topic 3, Lecture 1

Question 1

What is RNA polymerase II’s basic interaction with DNA?

Answer 1

RNA polymerase II is going to move down the double stranded DNA and unwind while reading and copying only one strand of the DNA.

Question 2

What is the structure of RNA polymerase II?

Answer 2

Horseshoe

Question 3

What is different about RNA from DNA (in this context)?

Answer 3

They contain uracil instead of thymine.

Question 4

What is the importance of the ribose sugar on RNA?

Answer 4

There is a reactive -OH group on the RNA. It hangs off the side of carbon-2.

Question 5

What is peculiar about the tertiary structure of RNA?

Answer 5

RNA can make classic Watson-Crick binding between its own base pairs. This gives RNA a function.

Question 6

What is the function of RNA polymerase I?

Answer 6

Synthesizes rRNA genes

Question 7

What is the function of RNA polymerase II?

Answer 7

Synthesizes all protein-coding genes, snoRNA genes, miRNA genes, siRNA genes, IncRNA genes, and most snRNA genes

Question 8

What is the function of RNA polymerase III?

Answer 8

Synthesizes tRNA genes, 5S rRNA genes, some snRNA genes, and genes for other small RNA’s

Question 9

Give all of the other words that could mean the same as “template strand”.

Answer 9

Noncoding, Antisense, Complementary

Question 10

Give all of the other words that could mean the same as “nontemplate strand”.

Answer 10

Coding, Sense, Identical

Question 11

Which way does RNA polymerase II read the DNA? Which way does the RNA get synthesized?

Answer 11

Read: 3’ to 5’
Code: 5’ to 3’

Question 12

Which end of the RNA is each new ribonucleotide added?

Answer 12

3’ end

Question 13

Describe the exchange between the triphosphate linkage and the phosphodiester bond.

Answer 13

Basically, there are three phosphates in the triphosphate. Each phosphate group has a name: alpha phosphate, beta phosphate, and gamma phosphate. The overactive hydroxyl group on the 2’-C really wants one of those phosphates. The hydroxyl group “clips” the bond between the alpha and beta phosphates. The alpha phosphate gets snatched up by that hydroxyl group, while the beta and gamma phosphate groups float away because we don’t need them anymore.

Question 14

Why does the cell prefer the phosphodiester bond over the triphosphate linkage?

Answer 14

It is more energetically favorable.

Question 15

Why is it important that the phosphodiester bond and triphosphate linkage exchange does not require an intake of energy?

Answer 15

If the polymerization (attachment) of the alpha phosphate and the hydroxyl group required ATP, the cell wouldn’t be functional because it would require too much energy. This is why it is soooo important that the polymerization between the alpha phosphate and the hydroxyl group MUST be energetically favorable.

Question 16

Describe the function of TFIID.

Answer 16

TFIID recognizes TATA box and other DNA sequences near the transcription start point.

Question 17

Describe the function of TFIIB.

Answer 17

TFIIB recognizes BRE element in promoter and accurately positions RNA polymerase at the start site of transcription.

Question 18

Describe the function of TFIIH.

Answer 18

Unwinds DNA at the transcription start point by phosphorylating Ser5 of the RNA polymerase C-terminal domain (CTD) and releases RNA polymerase from the promoter.

Question 19

Describe the function of the TATA box binding protein.

Answer 19

The TATA box binding protein binds to the minor groove of the TATA box and forms a saddle-like structure. This action bends the DNA like the hand to shoulder example.

Question 20

Describe why all of the accessory proteins are important in relation to the mediator.

Answer 20

While the mediator does bring the RNA polymerase II to the transcription site, the mediator cannot recognize the TATA box sequence so TFIID assists in the recognition of the TATA box and other DNA sequences near the transcription point. Then, TFIIB places RNA polymerase II at the start site of transcription.

Question 21

What are the two functions of the CTD?

Answer 21

Recruits and activates RNA processing factors and stimulates chain elongation (which makes the nascent protein longer)

Question 22

Describe mRNA production factories.

Answer 22

mRNA synthesis takes place in groups that are very similar to nuclear neighborhoods. These neighborhoods are held together by aggregation factors that are essentially glue that has an affinity for everything.