MBG PART TWO: Lecture 5

Question 1

How many RNA polymerases do Eukaryotes have?

Answer 1

At least Three RNA polymerases

Question 2

What does RNA polymerase I transcribe?

Answer 2

Larger rRNAs

Question 3

What does RNA polymerase II transcribe?

Answer 3

Pre-mRNA, some snRNAs, snoRNAs, some miRNAs

Question 4

How does transcription undergo for Prokaryotes?

Answer 4

Sigma factor recognizes and binds to the -35 and -10 consensus sequences in the promoter region, properly positioning the RNA polymerase to begin transcription.

Question 5

Why is the -10 consensus sequences prone to?

Answer 5

Unwinding due to its AT rich content.

Question 6

What are the specific sequences for genes to be transcribed by RNA polymerases I, II, III?

Answer 6

Specific promoter sequences

Question 7

What are accessory promoters?

Answer 7

Recognize each of these specific types of promoters (through interaction with their DNA sequences) and bind/recruit the appropriate polymerase to begin transcription.

Question 8

What are Po.I, Pol. II, and Pol III only recruited to?

Answer 8

Their promoter specific accessory proteins.

Question 9

What does an RNA polymerase II promoter consist of?

Answer 9

A core promoter and a regulatory promoter that aid in positioning transcription proteins and RNA polymerase II to begin transcription.

Question 10

Where does the transcription start site?

Answer 10

+1

Question 11

Where is the TATA box?

Answer 11

-25

Question 12

Where is the TFIIB recognition element (BRE)?

Answer 12

-35

Question 13

What does initiation involve?

Answer 13

Step wise assembly of Transcription Factors of Pol. II (TFII A, B, D, E, F and H)

Question 14

What do these transcription factors replace?

Answer 14

The sigma factor in prokaryotes

Question 15

What does TFIID complex contain?

Answer 15

The TATA Binding Protein (TBP) and is first to assemble at the TATA box followed by the remaining general transcription factors (TFs) and Pol.II

Question 16

What does the TFIID complex form?

Answer 16

The preinitiation complex or PIC: that is sufficient to initiate basal (low levels) transcription.

Question 17

What does More Complex transcription regulation involve?

Answer 17

A multi-subunit complex called a “Mediator” that permits interactions with other activator/repressor proteins bound to upstream/downstream regulatory regions or enhancer sequences.

Question 18

What does Each Gene have?

Answer 18

A unique regulatory promoter, having distinct regulartory elements and unique cofactors to influence transcription.

Question 19

What does assembly of TF’s and Pol II cause?

Answer 19

11-15 bp of surrounding DNA to unwind.

Question 20

What are the 5 steps of Initiation for Eukaryotic Transcription?

Answer 20

1.) TFIID binds to TATA box in the core promoter

2.) Then transcription factors and RNA polymerase II bind to the core promoter

3.) Transcription factors bind to sequences in enhancers

4.) DNA loops out, allowing the proteins bound to the enchanter to interact with the basal transcription apparatus.

5.) Transcription factors bind to sequences in the regulatory promoter and interact with the basal transcription apparatus through the mediator.

Question 21

What is a Coactivator?

Answer 21

A coactivator is a type of transcriptional coregulator that binds to an activator to increase the rate of transcription of a gene or set of genes.

Question 22

What is an Enchancer?

Answer 22

An enhancer is a short region of DNA that can be bound by proteins to increase the likelihood that transcription of a particular gene will occur. These proteins are usually referred to as transcription factors.

Question 23

What is Puffs (Balbini rings)

Answer 23

Where DNA is pulled apart in replication bubble (Sites of localized unwinding due to gene transcription)

Question 24

What does polymerase do when it moves downstream along a template strand?

Answer 24

Leaves transcription factors intact at the promoter for reinitiation of transcription with new polymerase.

Question 25

What does RNA polymerase maintain?

Answer 25

An 11-15 rNTPs transcription bubble during elongation.

Question 26

What do DNA-RNA hybrids bend at?

Answer 26

At a right angle (90 degrees)

Question 27

What does a right angle help with?

Answer 27

Opens up growing RNA molecule which makes it more accessible to nucleotides being added)

Question 28

How does the 90 degree position the -OH group?

Answer 28

At the active site where new nucleotides are added to the 3' end of the growing chain.

Question 29

What happens to the newly separated RNA?

Answer 29

It is separated from DNA and exits through another cleft.

Question 30

In prokaryotes, what does Rho bind to?

Answer 30

The rut site and moves toward the 3' end.

Question 31

What is Rho in prokaryotes?

Answer 31

Rho factor) is a bacterial protein involved in the termination of transcription. Rho factor binds to the transcription terminator pause site, an exposed region of single stranded RNA

Question 32

What does RNA Pol I require for termination in Eukaryotes?

Answer 32

A termination factor similar to rho factor in prokaryotes.

Question 33

What does RNA Pol III require?

Answer 33

Ends after transcribing a terminator sequence that produces a string of U's that is downstream from a hairpin. Similar to rho-independent termination.

Question 34

What does the string of U's cause?

Answer 34

Causes the RNA polymerase to pause, and the inverted repeats in RNA fold into a hairpin which destabilizes DNA-RNA

Question 35

What does RNA Pol II do?

Answer 35

Transcription continues past termination sequence. - RNA is cleaved at the consensus sequence

Question 36

What are the Three stages of Termination?

Answer 36

1.) RNA polymerase II transcribes well past the coding sequence of most genes. 2.) Cleavage takes place at the 3' coding region of the RNA 3.) While RNA polymerase continues transcribing

Question 37

What does cleaved RNA result in?

Answer 37

2 RNAs: one that will encode a protein and the other with its 5' trailing out of the RNA polymerase

Question 38

What does Rat1 (5' -> 3' exonuclease) do?

Answer 38

Attaches at the 5' end and degrades the remaining RNA strand

Question 39

How is transcription terminated?

Answer 39

When Rat1 reaches the transcription machinery (recall how rho binds a consensus sequence and moves up the RNA, but does not degrade it)

Question 40

What does a transcription unit not have?

Answer 40

Enhancer

Question 41

What would be the result if the specific sigma subunit of bacterial RNA polymerase were mutated?

Answer 41

RNA polymerase would initiate transcription at random on the DNA.

Question 42

What is the function of the DNA regulatory promoter?

Answer 42

Binds transcription factors that can positively or negatively influence transcription.

Question 43

Which of the following are required for transcription in eukaryotes?

Answer 43

- RNA polymerase - Several transcription factors

Question 44

Which eukaryotic RNA polymerase transcribes mRNA?

Answer 44

RNA polymerase II

Question 45

Which subunit of prokaryotic RNA polymerase directs to its target gene?

Answer 45

Sigma

Question 46

What does a rho independent transcription termination include?

Answer 46

- Inverted hairpins that when transcribed fold into a hairpin - A region in the RNA molecule that causes RNA polymerase to pause.