This set of Protein Engineering Multiple Choice Questions & Answers (MCQs) focuses on “New Protein Molecule Design – DNA Shuffling”.
1. Which of the following strategy of protein engineering is based on high throughput protein engineering?
a) Slow evolution
b) Rational evolution
c) Natural evolution
d) Irrational protein design
View Answer
Explanation: Irrational protein design strategy of protein engineering is based on high throughput protein engineering. In this technique, detailed knowledge of the protein structure and function is not required.
2. Irrational protein design is also known as directed evolution.
a) False
b) True
View Answer
Explanation: The above statement is true. Irrational protein design is also known as directed evolution. The main premise of directed evolution is the random mutagenesis of the gene of interest, followed by a selection scheme for the new desired function.
3. What happens with the length of fragments in each PCR cycle?
a) It can either increase or decrease
b) It decreases
c) It remains constant
d) It increases
View Answer
Explanation: The average length of the fragments increases in each PCR cycle. It neither decreases nor it remains constant. Hence, after many cycles of PCR without adding primers, the molecules of original size are obtained.
4. Which of the following is a method of artificial evolution achieved by reassembling different fragments and includes the creation of novel mutations as well as recombination?
a) Phage display
b) Rational protein design
c) Error-prone PCR
d) DNA shuffling
View Answer
Explanation: The gene to be improved is cut into random segments. These segments are then reassembled by using a suitable DNA polymerase with overlapping segments or by using some versions of overlap PCR.
5. In DNA shuffling the gene to be improved is cut into random segments. What is the length of these segments?
a) 10-50 base pairs long
b) 2-10 base pairs long
c) 500-1000 base pairs long
d) 100-300 base pairs long
View Answer
Explanation: In DNA shuffling the gene to be improved is cut into random segments and the length of these fragments is 100-300 base pairs. These segments are reassembled by using a suitable DNA polymerase with overlapping segments.
6. A more powerful variant of DNA polymerase is to start with several closely related (i.e. homologous) versions of the same gene from different organisms.
a) False
b) True
View Answer
Explanation: The above statement is true. A more powerful variant of DNA polymerase is to start with several closely related (i.e. homologous) versions of the same gene from different organisms. The genes cut at random with appropriate restriction enzymes and the segments mixed before assembly. The result is a mixture of genes that have recombined different segments from different original genes.
7. Which of the following is not true for DNA shuffling?
a) It involves random DNA fragmentation
b) It recombines beneficial mutations from different molecules
c) It involves many cycles of PCR
d) It involves the addition of primers
View Answer
Explanation: DNA shuffling involves random DNA fragmentation. It also recombines beneficial mutations from different molecules. It involves many cycles of PCR. But, in DNA shuffling there is no addition of primers. Hence, the statement “It involves the addition of primers” is not true.
8. Which step is performed before the partial digestion of the library of genes by restriction enzymes?
a) Reassembly
b) X-ray crystallography
c) Protein assay
d) Random mutagenesis
View Answer
Explanation: Random mutagenesis is performed before the partial digestion of the library of genes by restriction enzymes. It is done to generate random point mutations at different sites in the gene. Reassembly, X-ray crystallography, or Protein assay are not performed before the partial digestion of the library of genes by restriction enzymes.
9. Which of the following is a method to recombine fragments generated in DNA shuffling?
a) RT-PCR
b) Error-prone PCR
c) Random PCR
d) Overlap PCR
View Answer
Explanation: Overlap PCR is a method to recombine fragments generated in DNA shuffling. RT-PCR, error-prone PCR, and random PCR are methods that can be used to recombine fragments generated in DNA shuffling.
10. DNA shuffling is also known as sexual PCR.
a) False
b) True
View Answer
Explanation: The above statement is true. In the DNA shuffling technique fragments are generated with the help of nuclease. These fragments then go through PCR without added primers. Hence, DNA shuffling is also known as sexual PCR.
11. Which of the following is not a step of the DNA shuffling technique?
a) Polymerase extension
b) Denaturation
c) Annealing
d) Phage display
View Answer
Explanation: Phage display is not a step of the DNA shuffling technique. Polymerase extension, denaturation, and annealing are the steps in the DNA shuffling technique. The DNA shuffling technique starts with several copies of a gene containing point mutation.
12. Which of the following can be used to create random fragments of DNA?
a) DNA ligase
b) EcoR I
c) BamH I
d) DNase I
View Answer
Explanation: DNase I can be used to create random fragments of DNA. DNase I is an endonuclease that non-specifically cleaves DNA to release fragments of DNA. EcoR I and BamH I cut the DNA specifically at restriction sites. Hence, it does not cleave the DNA randomly. DNA ligase joins the fragments of DNA.
13. The fragmentation of DNA in the DNA shuffling technique occurs at specific sites in DNA.
a) True
b) False
View Answer
Explanation: The above statement is false. The fragmentation of DNA in the DNA shuffling technique occurs at random sites in the DNA. It uses DNase I for the random fragmentation. Hence, The fragmentation of DNA in the DNA shuffling technique does not occur at specific sites in DNA.
14. Which step comes after DNA fragmentation in DNA shuffling technique?
a) Polymerase extension
b) Annealing
c) DNase I treatment
d) Denaturation
View Answer
Explanation: The step which comes after DNA fragmentation in the DNA shuffling technique is denaturation. The double-stranded DNA fragments are generated in the DNA fragmentation step. These fragments are then denatured by increasing the temperature so that double-stranded DNA is separated into single-stranded ones.
15. The three steps of denaturation, annealing, and polymerase extension are repeated for multiple cycles.
a) False
b) True
View Answer
Explanation: The above statement is true. The three steps of denaturation, annealing, and polymerase extension are repeated for multiple cycles. The average length of fragments increases in each cycle of PCR.
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