RNA Pol II Promoters and Transcription Initiation

Question 1

In which groove does TBP bind (on DNA)?

Answer 1

In the MINOR GROOVE

Question 2

What molecules are required to bring RNA polymerase II to the transcription initiation start site and help it initiate transcription away from +1?

Answer 2

GTFs - GENERAL TRANSCRIPTION FACTORS

Question 3

Where do General Transcription Factors (GTFs) bind?

Answer 3

They bind to the PROMOTER of the gene.

Question 4

What are the roles of GTFs?

Answer 4

• POSITION RNA Pol II at start site
• ASSIST IN INITIATION

They help find a particular sequence of a particular gene that is open, bind to it and make this address that can be recognized by other factors that will come in, bring Pol II and initiate gene transcription.

Question 5

Where can transcription initiation be observed?

Answer 5

IN VIVO and IN VITRO

Question 6

Is transcription initiation an ATP dependent reaction?

Answer 6

YES

Question 7

What happens when transcription of a gene is activated?

Answer 7

There is UP TO 1000X OR MORE mRNA SYNTHESIZED.

Question 8

In single-cellular organisms, why is gene transcription regulated?

Answer 8

It is regulated to ADJUST TO CHANGES IN THE NUTRITIONAL AND PHYSICAL ENVIRONMENT.

Question 9

What directs the regulation of gene transcription in multicellular organisms?

Answer 9

Genes are regulated TO ENSURE COORDINATION DURING EMBRYONIC DEVELOPMENT AND TISSUE DIFFERENTIATION.

Question 10

Name all four promoter elements.

Answer 10

TATA BOX - -31 to -26

B RECOGNITION ELEMENT (BRE) - -37 to -32

INITIATOR ELEMENT (Inr) - -2 to +4

DOWNSTREAM PROMOTER ELEMENT (DPE) - +28 to +32

Question 11

Genes that are highly transcribed use which promoter sequence?

Answer 11

TATA BOX

Question 12

What is necessary for a promoter sequence to function?

Answer 12

SPACIAL CONFORMATION that surrounds it.

If you removes genes between these sequences, they do not work. You interfere with initiation and their ability to work.

*When you play with the sequence and not the distance between promoters, it does not have an effect.

Question 13

Except being necessary to transcription initiation, what do all promoter sequences have in common?

Answer 13

They all interact with different parts of the TFIID complex

TATA BOX - TBP
BRE - TFIIB
(others not mentioned)

They also all help place Pol II over the start site.

Question 14

What is +1?

Answer 14

It is the FIRST rNTP.

Question 15

What percentage of genes use CpG islands?

Answer 15

70%

Question 16

What is a CpG island?

Answer 16

A C-G rich stretch of 20-50bps that act as a promoter sequence. It is used for most of the stuff that the cell needs.

• Sloppy mechanism that can’t give it directionality, nothing to position them at a start site.

They are found in genes that do not have a TATA Box or a Inr.

Question 17

What happens when a gene does not have a TATA Box or a Inr?

Answer 17

Transcription of some genesINITIATES AT MULTIPLE ALTERNATIVE SITES within a 100-1000 bp region.

These contain CpG Islands, which is a substitute for TATA Box.

Question 18

What is the major downside to CpG islands?

Answer 18

RNA Pol II DOES NOT KNOW WHICH WAY TO GO.

In the wrong direction, RNA Pol II cannot give anything (will make something, but it will be gibberish) and RNA Pol II needs to be directed into the right direction. If it is not, it will simply go in which ever direction it wants.

It will give nothing approximately half of the time.

Question 19

What is the difference between a promoter-proximal element and an enhancer element?

Answer 19

PROMOTER-PROXIMAL ELEMENT:
Within 100-200 bp of the promotor and CAN REGULATE TRANSCRIPTION.

ENHANCER ELEMENT:
LONG DISTANCE TRANSCRIPTION CONTROL ELEMENTS that can be thousands of kb away from the transcription start site.

Basically, the difference is DISTANCE FROM THE PROMOTER. They both are cell-type specific and influence the probability and rate of the expression of a particular gene.

Question 20

What is the use of linker-scanning mutations?

Answer 20

Used to FIND PROXIMAL-PROMOTER ELEMENTS of a gene. It is good for short stretches of DNA.

Question 21

What can deletion analysis be used for?

Answer 21

To FIND ENHANCER ELEMENTS of a gene.

Question 22

What are used as promoters in eukaryotes?

Answer 22

TATA BOX
Inr
CpG ISLANDS