MCQs on Gel electrophoresis, Oligonucleotide & Microarrays – 1
1 - Question
Gel electrophoresis separates nucleic acid molecules based on ____________
a) charge on molecules
b) size of the molecules
c) nature of the molecules i.e. whether DNA or RNA
d) chemical properties of the nucleic acids
Explanation: Gel electrophoresis separates nucleic acid molecules on the basis of their size. The nucleic acid molecules move through the gel because of the force provided by the applied electric field.
2 - Question
The charge present on the DNA backbone is negative. The force required to accelerate the molecules towards anode is directly proportional to the number of ____________
a) sugar molecules
b) nitrogenous bases
c) phosphate groups
d) both phosphate group and sugar molecules
Explanation: The DNA backbone is negatively charged because of the phosphate groups. Hence, the force required to move the molecules towards anode is directly proportional to the number of phosphate groups present.
3 - Question
Force is defined as mass per unit acceleration. As the number of phosphate molecules increases, the charge also increases which increases the force required. The acceleration is dependent on the size of the molecules
Explanation: As the charge increases, which is because of the number of phosphate molecules, the size also increases. As, the size increases, it also results in increase of mass. Thus, now the force and also the acceleration are independent of size until a retarding force is present. But, in the case of gel electrophoresis, the retarding force is provided by gel and thus separation takes place on the basis of size.
4 - Question
Which one of the following will travel fastest through the gel if the amount of DNA present is same in all?
d) Supercoiled and circular will move at same speed and faster than nicked
Explanation: The supercoiled form of DNA will travel the fastest. It is so because; the movement through the gel is based on the size. The smaller the molecule is the less retarding force it experiences when it moves. Hence, supercoiled which is having the smallest size will move the fastest.
5 - Question
How is the size of molecules under analysis measured?
a) By measuring the distance moved through a ruler
b) By measuring the amount of visualising dye used
c) By running a standard molecule, whose size is known in parallel
d) There is no exact criterion for doing so
Explanation: The size of the DNA molecules is measured by a standardized molecule. It is known as DNA ladder. The molecules under analysis are compared with the DNA ladder
6 - Question
Gel matrices are generally of two types Agarose and Polyacrylamide. Which of the statements is correct with respect to agarose gels?
a) Agarose is a polysaccharide which is obtained from red algae
b) Agarose is a polysaccharide obtained from fungus
c) It is composed of glucose residues
d) It is obtained via dissolving in its water by boiling in water and then cooling it
Explanation: Agarose is a polysaccharide which is obtained from red algae. It is composed of galactose residues. Agarose gel is obtained via dissolving in it a buffer by boiling it and then cooling it. It leads to the formation of agar in conjunction with other polysaccharides, agropectin.
7 - Question
Polyacrylamide gels are the other types of gels which are commonly used. Which of the following statement is not correct with respect to these types of gels?
a) They are obtained via polymerization between acrylamide and bis-acrylamide
b) The components added for initiating polymerization are ammonium persulphate and TEMED
c) It is casted in horizontal and flat trays
d) TEMED catalyses the formation of free radicals from persulphate ions which leads to initiation of cross-linking
Explanation: Polyacrylamide gels are made up by the polymerization of acryl amide and bis acryl amide units. The polymerization takes place because of TEMED and ammonium persulphate, as TEMED catalyses the formation of free radicals from persulphate. These gels are usually casted in vertical trays whereas the agarose gels are casted in horizontal and flat trays.
8 - Question
If the amount of agarose added is more, the molecular under analysis should have the following characteristic:
a) small size
b) large size
c) size has no relation with the amount of agarose
d) the amount of molecules under analysis matters
Explanation: In the case of agrose gels, the separation takes place because of size. If the amount of agarose is more, smaller size molecules will be able to move easily as in comparison to larger size molecules. It is so because; the movement is through the pores. More the amount of agarose, smaller the size of the pore.
9 - Question
In the case of electrophoresis of single stranded DNA or RNA, which type of gels are used?
c) The routine agarose gel
d) The routine polyacrylamide gel
Explanation: In the case of single stranded molecules, denaturing gels are used. It is so because, if denaturing gels are not there, there are chances of formation of secondary structures which hinder the movement of nucleic acids. Thus to avoid this, denaturing agents such as urea, etc. are added.
10 - Question
At times, a specific fragment of the molecules of DNA which are analyzed needs to be separated. One of the methods is digesting the gels simply. Which of the following statement is not correct in with respect to it?
a) The gelling temperature has an important role to play
b) For higher gelling temperatures, digestion of DNA is done via the addition of agarase or some chaotropic agents
c) For lower gelling temperatures, simply slicing out of target DNA is done which is followed by melting
d) The DNA can be extracted via the addition of sodium or any positively charged group
Explanation: For the method of solubilising DNA, the gelling temperature is very important. For lower gelling temperatures simply the target DNA can be sliced out and further melting is done. But for higher gelling temperatures, either agarase or chaotropic agents are added. After this, the required DNA is obtained via purification which is done by the addition of silica or solvent extraction can also be done.