SUGGESTED ESSAY-TYPE QUESTIONS FOR NEXT EXAM:
(1) DNA - negative supercoils can be titrated out by “unwinding agents”. Ethidium
bromide, a planar molecule, “intercalates” itself between the stacked DNA base
pairs, thereby unwinding the supercoils. However, the linking number of the DNA is
not changed! Explain the physical basis for the ability of ethidium bromide to
“unwind” these supercoils.
(You will have to look at the definition of the linking difference. In this definition, Lo
refers to the linking number for relaxed B-DNA. This number reflects the number
of base pairs that stack in one helical turn. Does this number change when ethidium
bromide is intercalated?)
(2) Eukaryotic DNA do not have a DNA gyrase activity, as do bacteria. How, then,
are negative supercoils introduced into eukaryotic DNA such that the DNA can be
compacted?
(3) Specific DNA-binding proteins mainly contact DNA through hydrogen bonds in
the major groove of B-DNA.
(a) Why might sequence-specific binding be more common in the major
groove than in the minor groove?
(b) What hydrogen-bond contacts can proteins make with the bases in the
major groove? Are these different from those in the minor groove?
(4) In what ways do HTH proteins and the met repressor represent two general
modes of DNA-protein interaction?
(5) Explain the phenomenon of “indirect readout”.
(6) Explain the function each of the two zinc fingers in the cys4 estrogen receptor.
(7) Describe the assembly of the eukaryotic preinitiation complex.
(8) A hypothetical new eukaryotic RNA polymerase is discovered. To study the
enzyme, an in vitro assay is developed with an inhibitor or RNA chain elongation,
3’-deoxy-5’-[-32P] CTP. You are surprised by the fact that no 32P is found in the
transcribed RNA! What does this result tell you about the mechanism of the
polymerase?