1. If the template DNA belongs to several individual rather than single one, this type of heterogeneity is known as ____________
a) Heterzygosity
b) Product heterogeneity
c) Population heterogeneity
d) Template heterogeneity
Explanation: If the template DNA belongs to several individuals then this type of heterogeneity is known as population heterogeneity. It also gives rise to heterogeneity in PCR products
2. Heterogeneity can also arise if DNA is damaged before amplification. Which of the following doesn’t cause DNA damage?
a) Amination of bases
b) Chemical cross-linking between the strands
c) Chemical cross-linking within the strands
d) Slowing down the polymerase
Explanation: There are various reasons for DNA damage such as chemical cross-linking both between and within the strands. Deamination of bases is also one of the reasons. If polymerase is slowed down there are chances of incorporation of incorrect bases
3. If cytosine is deaminated, which of the base is formed?
a) Thymine
b) Guanine
c) Adenine
d) Uracil
Explanation: If cytosine is deaminated it leads to the formation of Uracil. This Uracil is further read as Thymine during DNA synthesis.
4. Which of the statement is correct for misincorporation?
a) If direct sequencing has carried this misincorporation is a great problem
b) The erroneous molecules give strong signals than genuine molecules in case of misincorporation
c) If the misincorporation in cloned PCR products it is a problem
d) Even if the error is induced at an early stage it is not incorporated in many sequences
Explanation: If the misincorporation takes place and direct sequencing is carried out, it is not a major problem. It is so because only small portion of molecules have it and thus the signals are weaker than that of genuine molecules. If the misincorporation is in cloned PCR product, it is of great problem. It is so because if it is included at an early stage, they are incorporated in many sequences
5. Errors can be introduced because of many reasons such as polymerase error or because of heterogeneity. Which of the statement holds true?
a) The error caused because of polymerase is biased for the first position in the codon
b) The error caused because of polymerase is evenly distributed on all the positions in the codon
c) The error caused by sequence heterogeneity is mainly because of first position in the codon
d) The error caused by sequence heterogeneity is evenly distributed on all the codon positions
Explanation: The error caused by polymerase whether due to template change or not, it is always distributed evenly over all the codon positions. If the error is caused by sequence heterogeneity is concentrated on the third codon position. It generally doesn’t leads to amino acid substitution.
6. Which of the statement is incorrect for jumping PCR?
a) It is used in the case when the DNA fragment is degraded
b) In this type of PCR, the molecules are not long enough to span between the two primer sites
c) At the end of first round of synthesis, the extension of the molecule from the primer site to the end of the fragmented molecule takes place
d) It doesn’t leads to the formation of chimeric product
Explanation: Jumping PCR is used in the case when the molecule is not long enough to span between the two primer sites. At times, the whole amplification doesn’t take place at one go and hence molecule anneals to other fragment having another portion. Thus at times, PCR products longer than the template are designed. But the disadvantage is that it leads to the formation of chimeric products at times
7. What are the possibilities which can occur until the temperature has reached for primer annealing?
a) Extension doesn’t starts until the appropriate temperature is reached
b) Extension may start even when the temperature is low
c) At low temperature, there is specific annealing of primer taking place
d) There are more specific products which are generated
Explanation: Until the temperature has reached for primer annealing there are chances of extension by polymerase. It is so because at low temperatures primer can anneal in a non specific manner and thus non specific products are generated.
8. Hot-start PCR is a modification of PCR. Which of the following is not corresponding to it?
a) The basis is that extension is not started until the first cycle reaches its maximum temperature
b) The polymerase is added after the first cycle has reached its maximum temperature or melting temperature
c) It is satisfactory for small number of samples
d) It leads to generation of non specific products
Explanation: Hot-start PCR is a modification which is used in order to overcome the problem of the extension before the maximum temperature of first cycle is reached. Hence, polymerase is added only after the maximum temperature for first cycle is reached. Hence, there are more specific products which are generated because proper annealing of primers has taken place. It is suitable for a small number of samples but not for a large number of samples.
9. An alternative to adding polymerase at later stage is __________
a) Make the polymerase inactive by binding it to an antibody
b) Introduce the polymerase or Magnesium in clay beads
c) Make the polymerase inactive by attaching groups which cause stearic inhindrance
d) Introduction of polymerase or Magnesium in plastic wires
Explanation: An alternative to start the extension at higher temperature is to make the polymerase inactive by binding an antibody to it. The antibody detaches itself at a higher temperature and thus polymerase is activated at higher temperature. Also, the polymerase or Magnesium can be introduced into wax beads and these beads melt at higher temperatures. Magnesium is required for the polymerase to function.
10. The primer annealing temperature is often very low from the maximum temperature. This low temperature leads to some mismatches.
a) True
b) False
Explanation: The primer annealing temperature is often very low from the maximum temperature. Though the low temperature is for stable binding of the template and the primer but at times it leads to mismatches.