Lecture 4 - DNA

Question 1

What is the depth and width of MAJOR groove?

Answer 1

12A wide 7A deep, 5 base pairs

Question 2

What is the Helix-turn-Helix?

Answer 2

DNA binding proteins which have a recognition and stabilising helix.

Stabilising helix - turn - recognition helix
N -> C

Question 3

What is a symmetrical dimer used for?

Answer 3

Placing the recognition helixes between adjacent major grooves (34A)

Question 4

Give examples of symmetrical dimer

Helix-turn-helix

Answer 4

Lac repressor
CAP
trp repressor

Question 5

What is the angle of DNA bending when CRP interacts with RNA polymerase?

Answer 5

> 90 degrees

This is believed to help open the double helix region to begin transcription

Question 6

Why is lac repressor a tetramer when the minimum requirement is a dimer?

Answer 6

To form a “repression loop” - 93bp of promoter DNA

CAP+cAMP is also bound WITHIN the loop.
RNA Pol. can bind more strongly to this repression loop.

Ultimately, it brings the positive and negative control circuits together into one unified mechanism

Question 7

What is the i(-d) gene?

Answer 7

A defect (N-terminus) of the protein to bind to DNA. 
This prevents DNA being held in a loop. Only 1 defective site is required.
i(-d) is transdominant to i+

Question 8

Where is the repressor loop region found?

Answer 8

Between O3 and O1 (auxilliary operators)

Question 9

What is another example of DNA repression loop?

Answer 9

Arabinose operon. ONE regulator protein (AraC) exerts BOTH positive and negative control depending on presence of the inducing sugar.

Question 10

Classify the following into either a tetramer or dimer:
Trp repressor
Lac repressor
CAP

Answer 10

Trp - dimer
Lac - teramer
CAP - dimer