Chapter 6, Problem 15P

The CAP protein is shown bound to DNA in Fig. 6.15. CAP binds a specific sequence of base pairs in DNA (N = any base):

5′ TGTGANNNNNNTCACA 3′

3′ ACACTNNNNNNAGTGT 5′

a.	In a long double-stranded DNA molecule with random base sequence and an equal number of A–T and G–C base pairs, how many different kinds of DNA sequences could be bound by CAP?
b.	In the same DNA molecule, how frequently would a CAP binding site of any type be present? Of a particular type?
c.	CAP protein binds DNA as dimer; two identical CAP protein subunits bound to each other bind DNA. Can you detect a special feature of the DNA site that CAP binds that suggests that two identical protein subunits bind the DNA? (Hint: Try reading the sequence in the 5′-to-3′ direction on each strand.)
d.	CAP protein binds to the major groove of DNA. Do you expect that DNA helicase is required for CAP to bind DNA?