Molecular Biology of the Gene 7th Edition by Richard Losick, James Watson, Michael Levine, Tamara Baker, Alexander Gann

Exercise 1

Researchers studying ? repressor binding to the three binding sites in the right operator produced the data in the table below. In the experiment, they performed a DNase I protection assay (footprinting assay) using the DNA containing all three binding sites for a range of repressor concentrations From this, they calculated the relative concentration of repressor dimers required to occupy a specific binding site on half of the DNA molecules present (values given in table).

A. Based on the data for wild-type DNA and the information in Chapter 18, explain why the relative concentrations for O R1 and O R2 are almost the same despite the fact that O R1 has a 10-fold higher affinity for ? repressor than O R2 does (information from this chapter).
B. Based on the data for wild-type DNA and the information in Chapter 18, explain why the relative concentration of repressor needed to bind O R3 is much higher than for O R1 and O R 2.
C. Based on the data for mutant DNAs X and Y, identify the binding site ( O R1 , O R2 , or O R3 ) that included the mutation in each respective mutant. Explain your choices.
D. Given what you know from this chapter, explain why the relative repressor concentration required to bind O R3 goes down to 5 for Mutant X relative to wild-type DNA in terms of the mechanism for ? repressor binding DNA.