Cell Question Set

November 8, 1998

9-5
A. We estimate there are ~8.04 turns that separate the centers of bending of the two CAP-binding sites at the point of
minimum relative migration and ~7.45 at the point of maximum migration. (#nucleotides/10.6)
B. The relationship between the relative migration and the separation of the centers of bending are what we would
expect when the cis configuration moves the slowest and trans the fastest. The cis (minimal migration)
configuration occurs when the number of nucleotides separating the bends is a whole number where the trans
(maximal migration) configuration occurs when the number of nucleotides separating the bends is a half-number.
C. From fig. D we can determine that minimum migration takes place at a distance of 101 nucleotides between the
centers of bending. Divide that by 10.6 nucleotides per turn and we determine the bends to be separated by ~9.5
helical turns.
D. The minor groove of the helix faces the inside of the bend at the center of bending of the cap site. We know this
because the centers of binding are 9.5 turns apart. The final turn is only one half; therefore, the bends must have
opposite grooves facing the inside.

9-9
A. The araC protein is a positive regulator in this operon, because it increases the rate of transcription of
the arabinose operon. If it were a negative regulator, the presence of araC would decrease the
amount of araA gene product present when arabinose is present. Therefore, araC must increase the
affinity of RNA POL for the promoter and is a positive regulator.
B.
AraA Gene Product
Genotype Minus Arabinose Plus Arabinose
araC+ 1 1000
araC- 1000 1000

9-11
A. RNA POL needs ntrC to switch from closed promoter to open promoter complex. If it cannot switch
to the open promoter complex, transcription cannot occur.
B. The phosphorylation may be necessary to transcription because the promoter uses energy from the
hydrolysis of the phosphate group to change to the open promoter complex.
C.

9-12
A. Our data supports the formation of a loop in the DNA.
If the DNA bends to make a loop we would see
By looking at fig.9-6 we can get several indications that DNA forms a loop in its mechanism for repression.