1. Besides enzymatic means, physical stress can also be used for cleaving the DNA. Which of the following statements is true?
a) Sonication, needles, syringes, etc all come under the category of physical stress
b) In physical stress, there are no chances of contamination
c) The ends obtained have unique sequences
d) They are less effective than DNase treatment
Explanation: Physical stress methods are used to cleave the DNA randomly and it also generates non-unique ends as the DNase treatment. These include the use of sonication methods, needles and syringes. There are chances of contamination from the metal probes used in the setup used.
2. Phosphatases refer to __________
a) the enzymes which add phosphate group at the end of the DNA molecule in the place of hydroxyl group
b) the enzymes which hydrolytically remove phosphate group from the DNA molecules and replace them with hydroxyl group
c) the enzymes responsible for removal of phosphate group from the DNA molecules and replace them with hydrogen
d) the enzymes responsible for replacing hydrogen in the DNA molecules with the phosphate group
Explanation: Phosphatases are the enzymes which remove phosphate group and then replace them with the hydroxyl group. Kinases are the enzymes which are responsible for the addition of the phosphate group in place of hydroxyl group
3. How is phosphatase related to the ligation reactions?
a) Phosphate group is not required for the ligation reaction to take place, thus phosphatase is helpful
b) It is helpful in ceasing the unwanted ligation
c) Phosphatases are not at all related to ligation reactions
d) They act as a catalyst in case of the ligation reaction
Explanation: Phosphatses are used to stop unwanted ligation. It is so because if phosphatases are present, phosphate would be removed from the ends and it would further block the ligation. It is so because the phosphate group is necessary for ligation to take place.
4. How can phosphatase activity terminated prior to a ligation reaction?
a) By heating
b) By cooling
c) By creating vibrations
d) By alternatively cooling and heating
Explanation: Heating leads to termination of phosphatase activity prior to a ligation reaction because heating leads to the inactivation of the phosphatase activity.
5. Basic classification of polymerases includes how many types?
a) 2
b) 3
c) 4
d) 5
Explanation: The types are- DNA dependent DNA polymerase, DNA dependent RNA polymerase, RNA dependent DNA polymerase, template independent polymerase and RNA dependent RNA polymerase. Out of these, RNA dependent RNA polymerases are not focused so much in comparison to other polymerases.
6. Polymerase can be defined as ______________
a) an enzyme used to synthesize a new DNA or RNA strand on the basis of pre-existing strand or at times without a pre-existing strand
b) an enzyme used for removal of nucleotides from the DNA or RNA strand
c) an enzyme which can synthesize only a new DNA strand, not an RNA strand
d) an enzyme which can synthesize either a new DNA or an RNA strand but only when a strand is there
Explanation: The synthesis of a new DNA or RNA strand can be done either on the basis of a pre-existing strand or without it. Those which don’t require a pre-existing strand are known as template free or template independent.
7. Which of the following activity is not possible in the case of DNA polymerase I?
a) 3’-5’ exonuclease
b) 5’-3’ exonuclease
c) 5’-3’ DNA synthesis
d) 3’-5’ DNA synthesis
Explanation: DNA polymerase is having the ability to synthesize DNA strand in 5’-3’ direction but not in 3’-5’ direction. Also, it is having exonuclease activity in both the directions, which means that it can remove bases in either of the direction but can synthesize only in 5’-3’ direction.
8. The E. coli DNA polymerase enzyme gives different domains with different activities on cleaving with protease subtilisin. Which of the following statements is correct with respect to the fragments generated?
a) The smaller fragment is having C terminal and the larger fragment is having N terminal
b) The smaller fragment is named as Klenow fragment and the intact molecule is called as Kornberg fragment
c) The smaller fragment is having 5’-3’ exonuclease activity whereas the larger fragment is having 5’-3’ polymerase and 3’-5’ exonuclease activity
d) Both the fragments are having 5’-3’ polymerase and 3’-5’ exonuclease activity
Explanation: The two fragments are generated of size 35kDa and 76kDa, with the N terminal in the smaller fragment. The larger fragment, which is of 76kDa is known as Klenow fragment and the intact molecule is called Kornberg fragment. The smaller fragment is having 5’-3’ exonuclease activity whereas the larger fragment is having 5’-3’ polymerase and 3’-5’ exonuclease activity.
9. Removal of single stranded portions produced due to exonucleolytic activity and due to polymerase activity are termed as _____________
a) polishing and end filling respectively
b) end filling and polishing respectively
c) polishing in both the cases
d) end filling in both the cases
Explanation: The single stranded ends generated due to exonucleolytic activity can either be removed by generating their complementary strand or removing the single stranded overhang. In both cases, it is termed as polishing. Whereas removal of single stranded regions generated because of polymerase activity is termed as end-filling.
10. Thermostable DNA polymerases are very important in PCR. How are they obtained?
a) They are obtained by heating the bacteria manually over high temperatures
b) They are isolated from extremely stable thermophilic bacteria which are often found growing in oceanic vents
c) They are found everywhere in nature
d) They are obtained by genetically modifying the E. coli bacteria with thermal stability property
Explanation: Thermostable DNA polymerases are found naturally in thermophilic bacteria which can be found growing in oceanic vents. They are having high stability and their DNA polymerases can function effectively even at high temperatures in-vitro.