MCQs on Precautions and Drawbacks
1 - Question
Which of the statement holds for long-range PCR and in its relation?
a) It is the PCR in which longer templates are used
b) DNA polymerases which don’t have proof-reading activity give larger products
c) DNA polymerases’ processivity is not a measure to have larger products
d) It is PCR in which a mixture of enzymes is used to have larger products
Explanation: Long range PCR is the PCR in which a mixture of enzymes is used to have larger products. If DNA polymerases are having proof reading activity then we can obtain larger products because in this case chain terminators are not used. Also, the processivity of the enzymes is also very important.
2 - Question
Which of the following conditions don’t contribute to wrong annealing to primer?
a) Chance complementarity
b) Conditions of annealing
c) The original sequence of the primers
d) Both the conditions of annealing and the original sequence don’t play any role
Explanation: There are cases when wrong annealing of the primer takes place. It can happen because of chance complementarity, conditions of annealing such as ionic concentration and temperature. The original sequence of the primers is very important.
3 - Question
How can the specificity of primer annealing be increased?
a) Use of short primers
b) Raising temperature
c) Adjusting the concentration of sodium ions
d) Using polymerase with proof reading activity
Explanation: The specificity of primers annealing can be increased in various ways such as increasing temperature, using long primers. If long primers are used there are increased chances of having correct matching. Also, if the magnesium ion concentration is adjusted, annealing can be done more effectively. It is so because they stabilize primer-template binding.
4 - Question
There are basically two types of contamination, laboratory and external. If a PCR product is found to be contaminated by bacteria. It comes under laboratory contamination.
Explanation: Laboratory contamination consists of aerosols in pipettes from previously formed PCR products or related DNA sequences. External contamination includes contamination from bacteria, fungi and other human contamination.
5 - Question
Which can be used as a precaution in order to minimize contamination?
a) Careful use and design of pipettes
b) Placing the pre-PCR and post-PCR stages in the same rooms
c) Extracting the DNA along with surface layers
d) Use of primers carefully is not very important
Explanation: Pipettes are very important in minimizing contamination. Thus they should be designed and used carefully. The pre-PCR and post-PCR stages should be places in separate rooms. While extraction of DNA surface layers should be removed because they might be containing bacteria. Sometimes the use of species specific primers is also very important, thus they should be used carefully.
6 - Question
During amplification, there are chances of having a product of a mixture of different sequences. There are various ways to detect it. Which of the statement is true in regard to it?
a) Direct sequencing can’t be used in the case if the template DNA is heterozygous at the locus
b) Direct sequencing can be used if the template DNA is heterozygous at the locus
c) If cloning is done before sequencing, then it is detected via using only a single clone for sequencing
d) In the case several recombinants are used, it can’t go undetected
Explanation: If the template DNA is heterozygous at the locus, it can be detected via using direct sequencing. It is so because it would give rise to two different signals at the same nucleotide position at the sequence output. If the cloning is done before sequencing, a single clone won’t be helpful to detect heterogeneity. It is because single clones are derived from a single PCR product. Also, if several recombinants are used, there are chances that they go undetected.
7 - Question
If the template DNA belongs to several individual rather than single one, this type of heterogeneity is known as ____________
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.
8 - Question
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.
9 - Question
If cytosine is deaminated, which of the base is formed?
Explanation: If cytosine is deaminated it leads to the formation of Uracil. This Uracil is further read as Thymine during DNA synthesis.
10 - Question
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.
11 - Question
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.
12 - Question
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.