Thinking Process
Ans. The experiment will not likely to be affected as recombinant DNA molecule is circular and closed, with no free ends.
Ques. Restriction enzymes that are used in the construction of recombinant DNA are endonucleases which cut the DNA at ‘specific’-recognition sequence? What would be the disadvantage if they do not cut the DNA at specific-recognition sequence?
Ans. If the restriction enzymes would cut DNA at random sites instead of at specific sites, then the DNA fragments obtained will not have ‘sticky ends’.
Ques. A plasmid DNA and a linear DNA (both are of the same size) have one site for a restriction endonuclease.
Ans. When a plasmid DNA and a linear DNA having one site for a restriction endonuclease are cut and separated, plasmid shows one DNA band, while linear DNA shows two band because of difference in their basic structure.
Ans. to be continued
Ques. How does one visualise DNA on an agarose gel?
Ans. A compound called ethidium bromide stains DNA, which on exposure with ultra-violet, (uv) radiation gives orange light band of DNA.
Ques. A plasmid without a selectable marker was choosen as vector for cloning a gene.
Ans. In a gene cloning experiment, first a recombinant DNA molecule is constructed, where the gene of interest is ligated to the vector (the step would not be affected) and introduced inside the host cell (transformation)
Ques. A mixture of fragmented DNA was electrophoresed in an agarose gel.
Ans. The reasons are as follows
(i) DNA sample that was loaded on the gel may have got contaminated with nuclease (exo or endo both) and completely degraded.
(ii) Electrodes were put in opposite orientation in the gel assembly that is anode towards the wells (where DNA sample is loaded).
(iii) Ethidium bromide was not added at all or was not added in sufficient concentration and so DNA was not visible.
Ques. Describe the role of $\mathrm{CaCl}_{2}$ in the preparation of competent cells?
Ans. $\mathrm{CaCl}_{2}$ is known to increase the efficiency of DNA uptake to produce transformed bacterial cells.
Ques. What would happen when one grows a recombinant bacterium in the bioreactor but forget to add antibiotic to the medium in which the recombinant is growing?
Ans. In the absence of antibiotic, there will be no pressure on recombinants to retain the plasmid (containing the gene of our interest).
Ques. Identify and explain $A, B$ and $C$ in the PCR diagram given below.
Ques. to be continued
Ans. Region to be amplified
(i) Denaturation of DNA Sample Unwinding of two strand of DNA by heating the sample at $92-94^{\circ} \mathrm{C}$.
(ii) Primer Annealing Primers get positioned on the exposed nucleotides as per base pairing rules.
(iii) Extension of Primers DNA polymerase recognises primers as ‘start’ tags and begins to extend the primers using the free nucleotides provided in the reaction and the genomic DNA as template.
Ques. Name the regions marked $A, B$ and $C$.
Ans. Region A Bam $\mathrm{HI}$
Region $B$ Pot I
Region $\mathrm{C}$ amp $^{R}$.
E. coli cloning vector pBR322 showing restriction sites (Hind III, Eco RI, Bam HI, Sal I, Pvu II, Pst I, Cla I), Ori and antibiotic resistance genes $\left(\mathrm{amp}^{\mathrm{R}}\right.$ and $\left.\mathrm{tet}^{\mathrm{R}}\right)$.
Rop codes for the proteins involved in the replication of the plasmid.
Ques. For selection of recombinants, insertional inactivation of antibiotic marker has been supercoded by insertional inactivation of a marker gene coding for a chromogenic substrate.
Ans. In selection of recombinants due to inactivation of antibiotics, the transformed cells are first plated on the antibiotic plate which has not been insertionally inactivated (i.e., ampicillin) and incubated overnight for growth of transformants.
Ques. Describe the role of Agrobacterium tumefaciens in transforming a plant cell.
Ans. A soil-inhabiting, plant pathogenic bacterium, Agrobacterium tumefaciens, infects broad-leaved crops including tomato, soyabean, sunflower and cotton, but not the cereals.
Ques. Illustrate the design of a bioreactor.
Ans. Bioreactors are vessels of large volumes (100-1000 L) in which raw materials are biologically converted into specific products.
(a)
(b)
(a) Simple stirred-tank bioreactor
(b) Sparged stirred-tank bioreactor through which sterile air bubbles are sparged