MCQs on Primers
1 - Question
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.
2 - Question
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.
3 - Question
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.
4 - Question
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.
5 - Question
Both the primers, the start primer and the end primer should have a nearly same melting temperature.
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.
6 - Question
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.
7 - Question
Which of the following is favoured for primer design?
a) The melting temperature should be different for both the primers
b) Primers should be long in length
c) Primers should not be complementary to each other
d) Matching should be of whole primer to the template
Explanation: Primers should not be complementary to each other. It is so because if they are complementary, primer dimer formation takes place. If primer dimer is formed, proper elongation won’t be taking place.
8 - Question
What will happen if the amino acid sequence is used directly for primer designing?
a) There would be certainty because the genetic code is unique for each amino acid
b) There would be uncertainty as the genetic code is degenerate and none of the amino acid is having a unique code
c) There would be uncertainty as the genetic code is degenerate but some of the amino acids such as methionine are having a unique codon
d) The amount of uncertainty or certainty is a matter of chance
Explanation: If the amino acid sequence is used directly, there would be uncertainty. It is so because the genetic code is degenerate. It means that one codon can correspond to many amino acids. There are some exceptions such as methionine which are having a unique codon.
9 - Question
In the case of uncertainty, if more than one nucleotide is included at a position it is called ____________
a) mixed site
b) polynucleotide site
c) unique site
d) degenerate site
Explanation: If uncertainty is there at times, more than one nucleotide can be included in one position. And in this condition it is called a mixed site.
10 - Question
What is the property of inosine?
a) Having narrow range of pairing capabilities
b) Having a broad range of pairing capabilities
c) The pairing capability is the same as the normal nucleotides
d) It is abbreviated as A
Explanation: It is having a broad range of pairing capabilities and thus can be used in order to have less amount of uncertainty.