Study Questions – Exam 1, Spring 2006
1. The Nobel Prize winning polymerase chain reaction (PCR) performs DNA synthesis in
a test tube using a purified DNA polymerase from bacteria that live in hot springs (Taq
polymerase). It has became so a successful because it was possible to denature (unwind)
DNA using high heat while at the same time not denature the DNA polymerase enzyme.
1A. (2pts) How does DNA get denatured during replication in cells, even though the
temperature does not change? (answer in a few words)
The enzyme helicase binds to the DNA and breaks the hydrogen bonds holding the
base pairs together.
1B. (6pts) Although the Taq enzyme from the hot springs bacterium works fine at 95°C,
it does not work at 37°C, a temperature where the similar the E. coli enzyme is fully
active. How is it possible that Taq does not work at 37°C?
Taq has more hydrophobic interactions than the E. coli enzyme so that the ‘core’ of
the protein is very stable. At 37°C the Taq therefore has a more rigid tertiary
structure. This may prevent it from undergoing the shape changes necessary to bind
to DNA and catalyze DNA synthesis.
1C. (4pts) The PCR reaction requires the use of a DNA ‘primer’ in order to copy the
DNA template. Which end of the DNA template should the primer bind to? Justify your
answer with a clearly labeled diagram
The 3’ end, since DNA synthesis proceeds 5’->3’ and the primer must base in an
antiparallel orientation to the complementary template strand.
1D. (6pst) Unlike the PCR reaction, the primers used in the cell for DNA synthesis are
made of RNA. Why not just use RNA for all our information purposes? Answer by
explaining one advantage of DNA over RNA as an information storage molecule.
The 2’-H of DNA reduces the rate at which water can attack and hydrolyze the S-P
bond, compared to having the 2’-OH of RNA. This makes the DNA a more stable
polymer, preserving the information stored in the sequence of bases longer than
As it is found in the