1. Taq polymerase incorporates which residue at 3’ end?
a) G
b) T
c) A
d) C
Explanation: It incorporates A residue at the 3’ end. This overhang is often useful in carrying out the cloning of these PCR products
2. Polymerases are also available from other Thermus species. Which of the following is correct?
a) Thermus flavus gives Tfl enzyme
b) Thermus thermopilus gives Tfl enzyme
c) They are having proof reading activity
d) Thermus flavus gives Tth enzyme
Explanation: Other Thermus species also provide polymerases. Thermus flavus gives Tfl enzyme and Thermus thermopilus gives Tth enzyme. They are also 3’-5’ proof-reading activity
3. Polymerases are available with proof reading activity. Which of the following are the characteristics of these types of polymerases?
a) They add A residue at 3’ end
b) They are obtained from Thermococcus litoralis
c) They can’t be obtained from archaebacteria
d) The marine bacteria from which they are obtained grow at temperatures lower than that of Thermus aquatics
Explanation: As these polymerases are having a proof-reading activity, they generally don’t add any residue at the end. They are obtained from bacteria such as Thermococcus litoralis and grow at temperatures above than that of Thermus aquatics. They can also be obtained from archaebacteria
4. Thermococcus litoralis grows at a temperature upto 98 degrees.
a) True
b) False
Explanation: Thermococcus litoralis grows at a temperature upto 98 degrees. The half life is also high, 90% of its activity is retained after 1 hour of incubation at 95 degrees
5. Primers are generally ____________
a) 20-30 nucleotides long
b) 40-50 nucleotides long
c) as long as the template is
d) taken according to the amount available
Explanation: Primers are generally short in length. They are 20-30 nucleotides long. It is easier to match short primers with the template in comparison to long primers. But in the case of eukaryotic DNA as a template, long primers are preferred
6. Which end of the primer should be matched properly in order to carry out the amplification?
a) 5’ end
b) 3’ end
c) Both of the ends should be matched properly
d) Anyone of the ends should match
Explanation: For carrying out the amplification, it is not necessary that the whole primer should match with the template. But it is necessary that 3’ end should match because if 3’ end is not matched the polymerase won’t be able to carry out elongation
7. Which of the following nucleotides should be there at 3’ end?
a) Any of A, T, G or C will work out
b) Either A or T
c) Either G or C
d) Specifically G
Explanation: At 3’ end, either G or C should be present. It is so because; these form three hydrogen bonds and thus are stronger. Whereas, A and T form only two hydrogen bonds and thus are comparatively less strong than G or C.
8. Melting temperature is given by ____________
a) 4(G+C) + 2(A+T)
b) 2(G+C) + 4(A+T)
c) 2(A+G) + 4(C+T)
d) 4(A+G) + 2(C+T)
Explanation: The melting temperature is that temperature at which the primers associate with the template. The melting temperature is decided by the amount of different nucleotides present.
9. Both the primers, the start primer and the end primer should have a nearly same melting temperature.
a) True
b) False
Explanation: Both the primers should have a nearly same melting temperature. It is so because then they would nearly bind at the same time as the temperature is being lowered for their annealing.
10. Why internal secondary structures are not preferred for primers?
a) Internal structures are very bulky and thus elongation is not preferred
b) Because of it, primer may fold back on itself and won’t be available for template
c) Internal secondary structures require more amount of template
d) If internal structures are present, no proof reading would be observed
Explanation: Internal structures are not preferred because if they are present the primer may fold back on itself. As the primer folds back on it, it is not available for the template. As an intramolecular reaction, self annealing is preferred over intermolecular annealing of primer to the template.