Category: Objective Questions

Genetic Engineering Multiple Choice Questions on “Mutagenesis using PCR and Recovery of Mutated Sequences”.

1. A megaprimer method is a ____ stage approach and uses _____ oligonucleotide primers.
a) two, two
b) two, three
c) one, two
d) one, three
Answer: b
Explanation: A megaprimer method is an approach of carrying out mutagenesis by using PCR. It is a two stage approach and uses three oligonucleotide primers.

2. Choose the correct statement.
a) There are two flanking primers and they are having mutations
b) There is one primer which anneals the target sequence and is having mutation
c) Either of the flanking primers or the primer is annealing to the target sequence is having mutation
d) One of the flanking primer and the primer annealing to the target sequence is having mutation
Answer: b
Explanation: In the megaprimer approach three primers are used. There are two primers which flank the target sequence and a third primer anneal to the target sequence. The mutation is there in the third primer.

3. PCR using the mutagenic primer and one of the flanking primers is used to carry out amplification and generates a product corresponding to the part of the gene. It is called as megaprimer.
a) True
b) False
Answer: a
Explanation: Megaprimer is produced when amplification is carried out by using mutagenic primer and one of the flanking primers. It corresponds to the part of the gene.

4. Sometimes mutagenesis is carried out with the help of primers. Choose the correct statement with respect to it.
a) Double stranded circular molecule is used as a template
b) Mutation is introduced into one of flanking primers
c) Single stranded circular molecule is used as a template
d) After amplification, mutation is introduced into one strand
Answer: a
Explanation: Double stranded circular molecules are used as a template. Mutation is introduced into both of the primers and then amplification is carried out. After amplification is carried out, mutation can be introduced either in one strand or both the strands.

5. If PCR is used to introduce random mutations rather than specific mutations, it is called as ___________
a) mutagenic PCR
b) error-prone PCR
c) random PCR
d) general PCR
Answer: b
Explanation: At times, PCR is used to introduce random mutations, rather than specific mutations and this type of PCR is called as error-prone PCR. There can be either one or many mutations.

6. For the selection of the molecules having mutated sequence, which of the statement is true?
a) It is suitable for methods which are PCR based
b) It is suitable for methods which are not PCR based
c) It is suitable for both PCR and not PCR based
d) Selection of molecules with the mutant sequence is not possible
Answer: b
Explanation: Selection is done either of molecules having a mutant sequence or degradation of wild type molecules is carried out. For selection of molecules having a mutant sequence, it can be used for methods which are not PCR based.

7. Choose the incorrect statement for the methodology of selection of molecules with mutant sequences.
a) A vector is used which is having antibiotic resistance gene
b) Apart from antibiotic resistance gene, a second antibiotic resistance gene is also present
c) There are two mutagenic primers which are used
d) The second strand synthesis is carried out by only one primer
Answer: d
Explanation: A vector is used which is having conventional antibiotic resistance and along with a second antibiotic resistance gene. The second gene is inactivated because of point mutation. Also, there are two mutagenic primers used. The first primer is used for directing the incorporation of mutation. The second primer makes the inactive gene inactive. Both the primers are used for second strand synthesis.

8. Once second strand synthesis is carried out, it is introduced into the host. Host is having which mutation?
a) mutS mutation
b) mutD mutation
c) mutE mutation
d) mutG mutation
Answer: a
Explanation: The host is having a mutS mutation. And because of this mutation, no mismatch repair takes place.

9. Replication by first strand leads to the formation of mutated molecules and functional antibiotic resistant gene.
a) True
b) False
Answer: b
Explanation: Replication can be either by first strand or second strand. First strand replication leads to generation of wild type molecules and the antibiotic resistance is inactive. If the replication is carried out by second strand, mutated sequence is formed and the antibiotic resistance gene becomes active.

10. In a phosphothiorate nucleotide, oxygen atom is replaced by with atom?
a) Magnesium
b) Calcium
c) Sodium
d) Sulphur
Answer: d
Explanation: In a phosphothiorate nucleotide, oxygen atom is replaced by a sulphur atom. Because of this replacement the DNA molecule becomes resistant to attack by nucleases.

11. What is the function of ung gene?
a) It is responsible for deamination of cytosine
b) It is responsible for deamination of uracil
c) It is responsible for removal of uracil
d) It is responsible for removal of cytosine
Answer: c
Explanation: Ung gene is responsible for the removal of uracil. It does it by the enzyme Uracil-N-glycosylase and apyrimidinic site is created.

12. DpnI cuts ________ strands.
a) methylated
b) non-methylated
c) phosphorylated
d) non-phosphorylated
Answer: a
Explanation: DpnI is the restriction enzyme which is meant for cutting the DNA strands which are methylated.

Bioinformatics online test focuses on “Database Searching with the Smith – Waterman Method”.

1. The rigorous dynamic programming method is normally not used for database searching because it is slow and computationally expensive.
A. True
B. False

Answer: A
Explanation: Heuristics such as BLAST and FASTA are developed for faster speed. However, the heuristic methods are limited in sensitivity and are not guaranteed to find the optimal alignment. They often fail to find alignment for distantly related sequences.

2. FASTA and BLAST are __________ but __________ for larger datasets.
A. faster, more sensitive
B. faster, less sensitive
C. slower, less sensitive
D. slower, more sensitive

Answer: B
Explanation: Empirical tests have indeed shown that the exhaustive method produces superior results over the heuristic methods like BLAST and FASTA. But heuristic methods are better and practical when it comes to assess larger datasets with comparatively low sensitivity.

3. Scan PS is a web-based program that implements a modified version of the Needleman-Wunsch algorithm.
A. True
B. False

Answer: B
Explanation: ScanPS (Scan Protein Sequence) is a web-based program that implements a modified version of the Smith–Waterman algorithm optimized for parallel processing. The major feature is that the program allows iterative searching similar to PSI-BLAST, which builds profiles from one round of search results and uses them for the second round of database searching. Full dynamic programming is used in each cycle for added sensitivity.

4. Par Align is a web-based server that uses parallel processors to perform exhaustive sequence comparisons using either a parallelized version of the Smith–Waterman algorithm or a heuristic program for further speed gains.
A. True
B. False

Answer: A
Explanation: The heuristic subprogram first finds exact ungapped alignments and uses them as anchors for extension into gapped alignments by combining the scores of several diagonals in the alignment matrix. The search speed of ParAlign approaches to that of BLAST, but with higher sensitivity.

5. In Smith–Waterman algorithm, in initialization Step, the _________ row and ________ column are subject to gap penalty.
A. first, first
B. first, second
C. second, First
D. first, last

Answer: A
Explanation: In Smith–Waterman algorithm, first row and first column are set to 0. In the Needleman Wunsch algorithm, First row and first column are subject to gap penalty.

6. Local sequence alignments are necessary for many cases out of which one is repeated.
A. True
B. False

Answer: A
Explanation: It can also be used for modular organization of genes and proteins (exons, domains, etc.) Also it can be used in cases of sequences diverged so that similarity was retained, or can be detected, just in some sub-regions.

7. In SW algorithm, to align two sequences of lengths of m and n _________ time is required.
A. O(mn)
B. O(m²n)
C. O(m²n³)
D. O(mn²)

Answer: B
Explanation: The Smith–Waterman algorithm is quite demanding of time. Hence if two sequences of lengths of m and n have to be aligned, the required time is O(m²n). It requires O(mn) calculation steps.

8. One of the challenges in SWA is obtaining correct alignments in regions of low similarity between distantly related biological sequences.
A. True
B. False

Answer: A
Explanation: It is because mutations have added too much ‘noise’ over evolutionary time to allow for a meaningful comparison of those regions. Local alignment avoids such regions altogether and focuses on those with a positive score, i.e. those with an evolutionarily conserved signal of similarity.

9. Score can be negative in Smith–Waterman algorithm.
A. True
B. False

Answer: B
Explanation: Negative score is set to 0. In Needleman–Wunsch algorithm, the Score can be negative. Also, in Smith–Waterman algorithm, in tracing back step, it begins with the highest score, ends when 0 is encountered.

10. The function of the scoring matrix is to conduct one-to-one comparisons between all components in two sequences and record the optimal alignment results.
A. True
B. False

Answer: A
Explanation: The scoring process reflects the concept of dynamic programming. The final optimal alignment is found by iteratively expanding the growing optimal alignment.

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Genetic Engineering Questions and Answers for Campus interviews focuses on “Synthesis of Proteins and Translation In Vitro”.

1. Little quantities of radiolabelled proteins are required for which of the following?
a) co or post translational targeting
b) modification of proteins
c) both co or post translational targeting and modification of proteins
d) crystallization for structural studies
Answer: c
Explanation: Protein synthesis is very important and they are having varied functions. Small quantities of radiolabelled proteins are required for co or post translational targeting and modification of proteins.

2. __________ quantities of _______ protein are required for determination of properties in biochemical and biological assays.
a) Small, non-radiolabelled
b) Small, radiolabelled
c) Large, radiolablelled
d) Large, non-radiolabelled
Answer: d
Explanation: At times, large and non-radiolabelled proteins are required for determination of properties in biochemical and biological assays. It is also required for carrying out the crystallization for structural studies.

3. Small quantities of radiolabelled RNA can be produced by translation in vitro which is done by transcription in vitro.
a) True
b) False
Answer: a
Explanation: If small quantities of radiolabelled RNA are required, it can be produced by translation in vitro which is accomplished by transcription in vitro.

4. For the production of unlabelled and huge amount of proteins, which of the following is true?
a) Transcription is carried out in vivo and translation in vitro
b) Transcription and translation both are carried out in vivo
c) Transcription and translation both are carried out in vitro
d) Transcription is carried out in vitro and translation in vivo
Answer: b
Explanation: For having, large and unlabelled proteins, transcription and translation both should be carried out in vivo.

5. How many methods are there, which are used for protein synthesis in vitro?
a) 1
b) 2
c) 3
d) 4
Answer: c
Explanation: There are basically three methods which are used for protein synthesis in vitro. They are based on a lysate of reticulocytes.

6. Reticulocytes are immature red cells, which are obtained from ___________
a) rabbit
b) pig
c) human
d) cow
Answer: a
Explanation: Reticulocytes are immature red blood cells which are obtained from rabbits. The lysate of this is used for transcription in vitro.

7. What is the use of adding micrococcal nuclease in the reticulocyte cells?
a) It degrades DNA
b) It degrades mRNA
c) It degrades proteins
d) It degrades RNA and untranslated DNA
Answer: b
Explanation: The micrococcal nuclease is added in the reticulocyte cells in order to degrade the mRNA. This mRNA produces a high amount of background in translational products.

8. Treatment of reticulocyte cells is done with EGTA. It chelates the calcium ions which are required for functioning of micrococcal nuclease.
a) True
b) False
Answer: a
Explanation: The treatment of reticulocyte cells is done with EGTA. It chelates the calcium ions and they are required for the functioning of micrococcal nuclease. It is required for cleavage of mRNA.

9. In ________ transcription and translation is coupled.
a) prokaryotes
b) eukaryotes
c) both prokaryotes and eukaryotes
d) both prokaryotes and eukaryotes, but favourable in eukaryotes
Answer: a
Explanation: In prokaryotes, transcription and translation are coupled. It means that as the transcription is initiated, translation also starts.

10. In which of the following systems, transcription and translation are carried out together?
a) Reticuloycte lysate
b) Wheat gram extract
c) Both in reticulocyte lysate and wheat gram extract
d) S-30 extract
Answer: d
Explanation: S-30 extract is the one in which transcription and translation are carried out together. In wheat gram extract and reticulocyte lysate, they are carried out separately.

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Genetic Engineering test focuses on “BAC Vector, M13 and its Derivatives – 2”.

1. What is the size of the DNA molecule which can be packed by the viral protein coat?
a) 100kbp
b) 200kbp
c) 500kbp
d) No size restriction
Answer: d
Explanation: There is no size restriction on the DNA molecule which is packaged by the viral coat protein. It is an advantage.

2. The uniform layer of cells is known as lawn and the holes peppered from infected cells are termed as __________
a) plaques
b) holes
c) colony
d) pothole
Answer: a
Explanation: The infected cells, which are from the infection by bacteriophage create holes and they are termed as plaques.

3. M13 doesn’t actually lyse the cells.
a) True
b) False
Answer: a
Explanation: M13 doesn’t actually lyse the cells. It infects the cells and retards the growth but doesn’t actually lyse the cells.

4. The plaques formed by M13 infection are called as __________
a) retarded plaques
b) true plaques
c) pseudoplaques
d) lysogenized plaques
Answer: c
Explanation: As the plaques created by M13 are because of slow growth and not because of lysis, these plaques are called as pseudoplaques.

5. M13 vector is tightly packed. Where is the available site to insert DNA?
a) In the gene II
b) Between gene II and IV
c) Between gene III and V
d) Between gene V and VIII
Answer: b
Explanation: The production of phage depends upon the insertion of DNA without disrupting any of the phage genes. Hence, M13 vector is tightly packed. One such site for the insertion of DNA is between gene II and gene IV. Here, the lacZ and MCS are also present.

6. Choose the incorrect statement with respect to the collection of single stranded molecules.
a) An infected culture is set up and after a while the cells are removed by centrifugation
b) The phage is in the supernatant and is precipitated by addition of glycol and sodium chloride
c) The phage pellet is resuspended and phenol is used for removal of protein
d) The single stranded molecules sediment at the bottom
Answer: d
Explanation: The collection of single stranded molecules is slightly different. An infected culture is set up and after a while cells are removed by centrifugation. The phage is present in the supernatant and is precipitated by addition of glycol and sodium chloride. It is followed by centrifugation. The phage pellet is resuspended and phenol is used for removal of protein. The single stranded molecules remain in the solution and thus can be precipitated further.

7. Choose the correct statement for Sanger’s method of sequencing.
a) They are also called as chain termination methods
b) Use of M13 vector is made for getting double stranded DNA
c) Use of dideoxynucleotide phosphate (ddNTP) is made
d) The use of M13 vectors is more preferred these days
Answer: a
Explanation: Sanger’s method of DNA sequencing is also known as the chain termination method of sequencing. Dideoxynucleoside triphospahte (ddNTP) are used as chain terminating agents. M13 vector is used to obtain the single stranded DNA. Now a days there are technologies available for sequencing on double stranded DNA, thus it reduces the use of M13 vectors these days.

8. Which of the statement doesn’t holds for phage display systems?
a) The filamentous phage is often used as phage display system
b) Coding sequences are inserted in one of the protein coating genes
c) The most common protein coding genes are gene II or gene VIII
d) The inserted is expressed along with other protein coat genes
Answer: c
Explanation: The filamentous phage is often used as phage display system. The coding sequences are inserted in one of the protein coding genes and the most common protein coding genes are gene III and gene VIII. The insert is expressed along with other protein coat genes.

9. Choose the correct statement for the synthesis of RNA probe?
a) Double stranded DNA is only used for probe synthesis
b) Single stranded DNA can be used for probe synthesis
c) Probes are prepared for RNA transcripts which are specific for only particular strand
d) Probes are prepared for RNA transcripts which are specific for both the strands
Answer: b
Explanation: RNA probe can be synthesized by single stranded DNA. This single stranded DNA can be obtained from filamentous phage. Probes are prepared for RNA transcripts which are specific for either of the DNA strands.

10. M13-plasmid vectors are often used. Which of the following is not a feature for this?
a) They are known as phagemid, plage or phasmid
b) Replication takes place through the origin of replication of M13 derivatives only
c) Replication from M13 requires proteins to be provided by helper phage
d) Some of the examples of these types of the combination are pUC 118, 119 and 120
Answer: b
Explanation: M13-plasmid vector hybridization is often used and they are referred to as phagemid, phasmid or plage. Replication can take place either by the origin of replication of the plasmid or by the origin of replication of M13. Replication from M13 requires additional protein to be provided from helper phage. Single-stranded DNA is produced after replication and is packaged in a protein coat. Some of the examples of this type of hybridization are pUC 118, 119 and 120.

11. The main advantage of phagemid is that it can be used for the generation of single or double stranded products without recloning.
a) True
b) False
Answer: a
Explanation: The main advantage of pahgemid is that it can be used for the generation of single or double stranded products without recloning. It is so because M13 can be used to produce single stranded products and the double stranded products are obtained by using the origin of replication of plasmid.

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