5.) Transcription

Question 0

The name of the strand that is complementary to the RNA transcript is called the ________________, whereas the name of the strand that is identical in sequence to the RNA transcript is called the ______________.

Answer 0

Template strand.

Non-template/sense/coding strand.

Question 1

Compare and contrast DNA polymerases to RNA polymerases.

Answer 1

1. ) RNA Polymerases do not require a primer
2. ) Nascent RNA does not remain hybridized to template DNA
3. ) RNA is less permanent than DNA, thus transcription is much less accurate than replication
4. ) RNA and DNA polymerases are structurally unrelated.

Question 2

What is/are the product(s) of RNA polymerase I? II? III?

Answer 2

RNA Polymerase I: 5.8S, 18S, and 28S rRNA’s (70% of RNA synthesis activity).

RNA Polymerase II: mRNA, snoRNA and some snRNA

RNA Polymerase III: tRNA, 5S RNA,, snRNA (splicing, poly(A)), scRNA (SRP, signal recognition particle).

Question 3

What RNA polymerase synthesizes mRNA?

Answer 3

RNA polymerase II

Question 4

What are some of the differences between Bacterial vs. Eukaryotic RNA Polymerases?

Answer 4

1. ) Bacterial RNA polymerase requires only a single protein for initiation whereas eukaryotic RNA polymerases require many additional proteins (general transcription factors).
2. ) Eukaryotic transcriptional initiation must deal with the packing of DNA into nucleosomes.

Question 5

What are the 3 general elements of the promoter region?

Answer 5

1. ) Distal Region
2. ) Proximal Region
3. ) Core region

Question 6

What are the elements of the core promoter region?

Answer 6

1. ) BRE: TFIIB Recognition Element - upstream extension of TATA box.
2. ) TATA: TATA box
3. ) Inr: initiator
4. ) DPE: Downstream promoter element.

Question 7

If genes can be located on either strand, how is the direction and location of synthesis specified?

Answer 7

Via Promoter regions on the 5’ end of the gene.

Question 8

True or False: Core promoter elements are typically palindromic.

Answer 8

False: They need to convey a direction, can’t do that with palindromic sequences.

Question 9

What role does the TATA box play in transcription?

Answer 9

It is part of the core promoter region. In combination with the BRE, it will “tell the RNA polymerase” to bind at that site and transcribe in “this” direction.

Question 10

What are the important components for a successful initiation complex?

Answer 10

TFIID (which has the TBP) will associate with the TATA box and recruit TFIIB. Their binding promotes the association of TFIIE, H, and F. TFIIF is a protein subunit on RNA Polymerase II. Once associated, with the help of TFIIH and many dNTPs, a helicase is activated to begin the unwinding of DNA and the CTD (C-terminal domain) of the RNA polymerase II is phosphorylated. This phosphorylation activates RNA poly II and transcription will begin.

Question 11

What is the importance of the CTD on RNA polymerase II.

Answer 11

This is phosphorylated by TFIIH to begin the process of transcription.

Question 12

How does eukaryotic Initiation differ from prokaryotic initiation?

Answer 12

Eukaryotic initiation requires:

1. ) An enhancer region, which is the binding site for an activator protein.
2. ) A mediator that binds tot he initiation complex
3. ) A chromatin remodeling complex, also binds to the initiation complex
4. ) Histone-modifying enzyme (histone acetylase) which will also bind to the initiation complex.

Question 13

How might supercoiling aid or inhibit transcription?

Answer 13

The negative supercoiling that forms behind the direction of transcription aids in the opening of the helix.
The positive supercoiling that forms in front of the direction of transcription will inhibit helix opening. This is where topoisomerases will remove the tension.

Question 14

How is elongation different in Eukaryotes vs. Prokaryotes?

Answer 14

Eukaryotes form a primary transcript that needs to be modified in order to be active. Introns and exons need to be processed.

Prokaryotes don’t need post transcriptional modification for a protein to be translated.

Question 15

Describe the different components of mRNA.

Answer 15

1. ) 5’ cap (phosphates)
2. ) Poly A tail.
3. ) Coding sequence (this is the protein sequence)
4. ) Non-coding sequence - these are sequences that aren’t translated into a protein.

Question 16

What is the difference between eukaryotic mRNA and Prokaryotic mRNA?

Answer 16

Prokaryotic mRNA has non-coding sequences in between coding sequences. Possible to produce multiple different proteins from one transcript. Half-life is short, usually minutes

Eukaryotic mRNA only has non-coding sequences on either end of its transcript. Half life is long, can be minutes to tens of hours.

Question 17

What is the importance of the mRNA 5’ cap?

Answer 17

1. ) Aids in mRNA transport
2. ) protects from 5’ to 3’ exonuclease degradation in cytoplasm
3. ) targets transcription to ribosome for translation.

Question 18

What is the importance of a poly A tail?

Answer 18

1. ) Participates in termination of transcription
2. ) aids in mRNA nuclear export
3. ) protects from 3’ to 5’ exonuclease degradation in cytoplasm
4. ) targets transcription to ribosome for translation.

Question 19

The 5’ cap of mRNA is composed of…

Answer 19

a 5’ to 5’ triphosphate bridge and a 7methylguanosine head group.

(probably not high yield)

Question 20

What does it mean to say that RNA polymerase II is an RNA factory?

Answer 20

Essentially it is saying that RNA polymerase II brings along all of the necessary factors that are necessary to synthesize a mature RNA. Ie, it contains the necessary “ingredients” to make the 5’ cap and poly A tail. It can splice the RNA.
Capping factors
Splicing proteins
3’ end processing proteins.

Question 21

What is the importance for phosphorylating the CTD?

Answer 21

Note this is the CTD of RNA poly II. It initiates transcription. More specifically, through a cascade of events, phosphorylation first promotes the binding of capping factors which will bind to the mRNA as it is synthesized. Then another phosphorylation event occurs that allows the binding of a splicing protein, which will associate co-translationally.

Question 22

The main point of regulation for RNA synthesis is during the ___________ phase.

Answer 22

Initiation

Question 23

Regulation during the elongation phase occurs by manipulating…

Answer 23

5’ capping
RNA splicing
3’ Polyadenylation.

Question 24

What is a lariat structure?

Answer 24

This is an intron that is looped after it is removed from the mRNA.

Question 25

Discuss the role of RNA splicing.

Answer 25

??

Question 26

What is the significance of RNA splicing?

Answer 26

??