This set of Molecular Biology MCQs focuses on “Properties of DNA Polymerase – 2”.
Explanation: Only 1 active site is dedicated for the addition of all the four types of dNTPs in the DNA polymerase. This is due to the identical geometry of all the four types of dNTPs.
2. How does the polymerase recognize the correct dNTP for addition?
a) Structure of dNTP
b) Molecular weight of dNTP
c) Purine and pyrimidine orientation
d) Ability of hydrogen bond formation
Explanation: Only 1 active site is dedicated for the addition of all the four types of dNTPs in the DNA polymerase. This is due to the identical geometry of all the four types of dNTPs. The polymerase recognizes the correct dNTP for addition is by the ability of hydrogen bond formation of the new bases with the existing bases on the template strand.
3. DNA polymerase can distinguish between dNTPs and rNTPS due to ___________
a) Structural differentiation
b) Steric exclusion
c) Steric hindrance
d) Enzyme substrate mismatch
Explanation: DNA polymerase shows an impressive ability of distinguishing between dNTPs and rNTPS. This is facilitated by the steric exclusion of the rNTPS from the DNA polymerase active site which is too small to accommodate the 2’-OH of rNTPs.
4. When we compare the structure of DNA polymerase to the structure of a body part, it resembles to _________________
a) Right hand
b) Left hand
c) Right foot
d) Left foot
Explanation: From the studies of the atomic structures of the various DNA polymerases bound to the primer:template junction it reveals that the structure resembles partially to that of a closed right hand. Based on the analogy to a hand the three domains of polymerase are called the thumb, fingers and palm.
a) Contains primary elements of the catalytic site
b) Binds to 2 divalent ions
c) Composed of α helix
d) Brings about the environmental changes around 3’-OH of dNTP
Explanation: The palm domain of the DNA polymerase is composed of β sheet and contains the primary elements of the catalytic site. In particular, this region of the polymerase binds to 2 divalent metal ions that bring about the chemical environmental changes around 3’-OH of dNTP for its polymerization.
6. The two divalent metal ions of the active sites of DNA polymerase are major catalytic elements that bring about changes required for the joining of the dNTPs.
Explanation: One of the metal ions reduces the affinity of the 3’-OH for its hydrogen. This generates a 3’-O- that is primed for nucleophilic attack of the α – phosphate of the incoming dNTP. The second metal ion coordinates the negative charges of the β – and γ – phosphates of the dNTPs and stabilizes the pyrophosphate produced by the joining the primer and the incoming nucleotide.
7. Mismatched DNA does not affect the rate of activity of DNA polymerase.
Explanation: Te accuracy of the base – pairing is monitored by the palm domain of the polymerase. The palm makes extensive hydrogen bond contacts with the base pairs in the minor groove of the newly synthesized strand. These contacts are not base pair specific but only bond if the base – pairing is correct. Thus mismatched DNA dramatically slows the rate of activity of DNA polymerase.
8. Which is the rate limiting step of DNA replication?
a) Formation of the RNA primer
b) Binding of primer to the DNA template
c) Binding of DNA polymerase to the primer:template junction
d) Binding of first dNTP to the primer
Explanation: The rate of DNA synthesis is dramatically increased by adding multiple nucleotides per binding site. It is the initial step of binding the DNA polymerase to the primer:template junction the slowest step.
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