Molecular Biology Techniques
Chapter Exam Questions
Course Introduction
Molecular Biology Techniques is a comprehensive course designed to introduce students to the fundamental laboratory methods used in modern molecular biology research. The course covers essential topics such as DNA extraction, PCR amplification, gel electrophoresis, molecular cloning, and the analysis of nucleic acids and proteins. Emphasis is placed on understanding the principles behind each technique, hands-on experience with laboratory equipment, and troubleshooting common experimental challenges. By the end of the course, students will have gained the practical skills and theoretical knowledge necessary to design and execute experiments that investigate biological processes at the molecular level.
Recommended Textbook
Molecular Diagnostics Fundamentals Methods and Clinical Applications 2nd Edition by Lela Buckingham
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Chapter 1: DNA
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Q1) Which of the following is a purine?
A) Thymine
B) Cytosine
C) Adenine
D) Alanine
Answer: C
Q2) The purpose of ligase is to:
A) Synthesize DNA
B) Cut DNA within the double helix
C) Chew DNA from the ends
D) Paste two ends of DNA together
Answer: D
Q3) Restriction endonucleases are enzymes that are produced by bacteria and
A) degrade viral proteins
B) digest DNA
C) have no laboratory applications
D) degrade lipids
Answer: B
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Page 3
Chapter 2: RNA
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Q1) The most frequently methylated base in vertebrates is:
A) Adenine
B) Cytosine
C) Guanine
D) Thymine
Answer: B
Q2) Alteration of the nucleotide sequence of RNA after transcription is called:
A) Methylation
B) RNA silencing
C) RNA editing
D) Capping
Answer: C
Q3) In an RNA molecule, adenine always base-pairs with:
A) Thymine
B) Cytosine
C) Uracil
D) Guanine
Answer: C
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Chapter 3: Proteins
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Sample Questions
Q1) What amino acid is used to initiate most proteins in eukaryotes?
A) Methionine
B) Alanine
C) Proline
D) Aminoacyl tRNA synthetase
Answer: A
Q2) Which of the following describes the general structure of an amino acid?
A) Planar carbon-nitrogen ring with deoxyribose sugar
B) Pentose sugar bound to phosphate and purine or pyrimidine base
C) Central carbon with carboxyl group, amino group, hydrogen, and a side chain
D) Polymer of molecules bound together by a peptide bond
Answer: C
Q3) What enzymes are important for faithful translation of genetic information from RNA to protein?
A) DNA polymerase
B) Amino-acyl tRNA synthetase
C) DNA ligase
D) Exonuclease
Answer: B
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Page 5
Chapter 4: Nucleic Acid Extraction Methods
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Q1) PolyT oligomers bound to a matrix resin column will selectively isolate which of the following?
A) Ribosomal RNA
B) GC-rich DNA
C) Transfer RNA
D) Messenger RNA
Q2) Nucleic acid concentration can be assessed relatively simply and quickly by which of the following procedures?
A) Electrophoresis
B) Enzyme immunoassay
C) Sequencing
D) Spectrophotometry at 260 nm
Q3) The most abundant form of RNA in all cells is:
A) Ribosomal
B) Transfer
C) Messenger
D) Small nuclear
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6
Chapter 5: Resolution and Detection of Nucleic Acids
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Q1) How does one prepare a 2% agarose gel?
A) Mix 0.01 g agarose/mL running buffer and heat.
B) Mix 0.02 g agarose/mL running buffer and heat.
C) Mix 2 g agarose/mL running buffer and heat.
D) Mix 1 g agarose/mL running buffer and heat.
Q2) A molecular biologist is to separate and analyze a mixture of nucleic acids that are about 100,000 bp in size. Which of the following methods will yield the best results?
A) Capillary electrophoresis
B) Rotating gel electrophoresis
C) Polyacrylamide gel electrophoresis
D) Traditional agarose gel electrophoresis
Q3) What concentration of agarose should be used for optimal separation of DNA fragments of 100, 250, and 350 bp in length?
A) 0.5%
B) 0.7%
C) 2.0%
D) 12.0%
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Chapter 6: Analysis and Characterization of Nucleic Acids and Proteins
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Q1) Which of the following enzyme/substrate combinations is used in the chromogenic detection of target sequences of nucleic acids after blotting procedures?
A) Horseradish peroxidase with Luminol/H<sub>2</sub>O<sub>2</sub>/p-iodophenol
B) Alkaline phosphatase with 1-2 dioxetane derivatives
C) Horseradish peroxidase with disodium 3-(4-methoxyspiro {1,2-dioxetane-3,2'-(5'-chloro) tricyclo [3.3.1.1] decan}4-yl)-1-phenyl phosphate
D) Alkaline phosphatase with nitroblue tetrazolium and 5-bromo-4-chloro-3-indolyl phosphate
Q2) Which of the following bind(s) specifically to a sequence of interest, thus facilitating the analysis of that sequence?
A) Restriction enzymes
B) Probes
C) Hybridomas
D) Digoxigenin
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8
Chapter 7: Nucleic Acid Amplification
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Q1) Which of the following steps can be taken to minimize mis-priming in a PCR procedure?
A) Use high-quality deoxynucleotides, buffers, and enzymes.
B) Seclude the polymerase from the template and primers before amplification.
C) Load the samples carefully for gel electrophoresis of PCR products.
D) Keep the reaction mix at room temperature prior to amplification.
Q2) A PCR reaction that uses more than one primer pair is called:
A) Long-range PCR
B) Multiplex PCR
C) Signal amplification
D) Quantitative PCR
Q3) Starting with a single target, how many copies are produced in a PCR reaction of 30 cycles?
A) 30
B) 30<sup>2</sup>
C) 2<sup>30</sup>
D) 2 x 30
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9
Chapter 8: Chromosomal Structure and Chromosomal Mutations
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Q1) Which of the following is involved in connecting the centromere to the spindles during chromosome segregation in mitosis?
A) Kinetochore
B) Euchromatin
C) Histone protein H1
D) Heterochromatin
Q2) A chromosome that has the centromere in the center of the chromosome is called:
A) Acrocentric
B) Telocentric
C) Metacentric
D) Holocentric
Q3) Which of the following is an advantage of interphase FISH as compared with metaphase FISH?
A) Examination of 20 spreads in interphase FISH has increased sensitivity.
B) One can identify mutations anywhere in the chromosome in interphase FISH.
C) Interphase FISH allows identification of all chromosomes.
D) Results are available faster in interphase FISH procedures than metaphase FISH procedures.
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Chapter 9: Gene Mutations
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Q1) A reference segment of DNA has the following sequence: GCTCACCATGG. The fourth nucleotide is changed to an A in a particular genetic disease. How would this mutation be denoted?
A) 4C>A
B) 8A>C
C) 4delC
D) C4A
Q2) Which of the following methodologies was used in the Human Haplotype Mapping Project?
A) Melt curve analysis
B) Denaturing gradient gel electrophoresis
C) Protein truncation test
D) Inversion probe assay
Q3) What is MALDI-TOF?
A) An HPLC method
B) Gel-based electrophoresis
C) A type of mass spectrometry
D) ELISA performed under controlled conditions
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Chapter 10: DNA Sequencing
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Q1) Cycle sequencing was made possible through the development of what reagents?
A) Fluorescent dyes
B) dITP
C) Labeled primers
D) Heat-stable polymerases
Q2) Dideoxycytidine is added to one of four sequencing reactions. All of the DNA fragments produced in that reaction end with which of the following nucleotides?
A) dG
B) ddC
C) dC
D) ddG
Q3) In the Sanger sequencing method, which of the following when incorporated into the growing strand are used to determine the identity of the base at a particular position in a piece of DNA?
A) ribonucleotides
B) deoxyribonucleotides
C) dideoxyribonucleotides
D) amino acids
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Chapter 11: DNA Polymorphisms and Human Identification
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Q1) Which of the following polymorphisms are tandem repeats of 1-8 bp?
A) Restriction fragment length polymorphisms
B) Short tandem repeats
C) Variable number tandem repeats
D) Single nucleotide polymorphisms
Q2) Mitochondrial polymorphisms used for human identification are found in what part of the mitochondrial genome?
A) In the mitochondrial tRNA genes
B) At the origin of transcription
C) In the hypervariable regions
D) Anywhere on the circular genome
Q3) Two elderly women who had been adopted into different families as infants discover circumstantially that they may have the same biological mother. Which of the following analyses would give the best information toward proving their maternal lineage?
A) Y-STR
B) Mitochondrial DNA
C) RFLP-PCR
D) SNP haplotypes
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13
Chapter 12: Detection and Identification of Microorganisms
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Q1) In the interpretation of pulsed field gel electrophoresis patterns, what is the minimum number of bands that can differ between two organisms before those organisms are determined to be unrelated?
A) 2
B) 3
C) 6
D) 7
Q2) A PCR assay using primers specific for the autolysin gene (lytA) was performed on a sputum specimen from a 10-year-old girl. The specimen was positive, and all controls were acceptable. Which of the following is the best interpretation of these results?
A) Definitive diagnosis of clinically significant Streptococcus pneumoniae pneumonia is made.
B) Streptococcus pneumoniae is present, but clinical significance is questionable.
C) Mycobacterium tuberculosis is detected, and the girl should be isolated.
D) The patient has Chlamydophila pneumoniae pneumonia.
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14
Chapter 13: Molecular Detection of Inherited Diseases
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Q1) How are transmission patterns determined?
A) Family history
B) Karyotyping
C) Environmental studies
D) Comparing unrelated individuals
Q2) A pedigree was examined over four generations of a family with an abnormal rate of genetic disease. Scientists observed that males and females alike were affected by the disease but only when their mother was also affected. The children of affected males were all normal. All the children of affected females were affected. Which of the following describes this inheritance pattern?
A) Mitochondrial related
B) Autosomal dominant
C) Autosomal recessive
D) Sex linked
Q3) What defines a congenital disease?
A) Always heritable
B) Present at birth
C) Limited to blood disorders
D) Symptoms delayed until puberty
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Page 15
Chapter 14: Molecular Oncology
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Q1) Specific translocations involving the EWS gene at 22q12 are useful for diagnosis of what types of tumors?
A) Lymphoma
B) PNET/Ewing's sarcoma
C) Adenocarcinoma
D) Adenoma
Q2) T-cell receptor gene rearrangements were analyzed by PCR using forward and reverse primers complementary to the V<sub>\(\gamma\)</sub>1 and J<sub>\(\gamma\)</sub>1 regions, respectively, of the T-cell receptor gene region. The products were separated by polyacrylamide gel electrophoresis and bands visualized using ethidium bromide. The lane corresponding to the patient had a sharp band. All controls were acceptable. How is this result interpreted?
A) The patient has a monoclonal (monotypic) T-cell population.
B) The patient is normal and has polyclonal T cells.
C) This is a false positive because of amplification of immunoglobulin genes.
D) The assay should be repeated because the wrong primers were used.
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Page 16
Chapter 15: Dna-Based Tissue Typing
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Q1) A husband volunteers to be the donor for his wife's organ transplant. In pre-transplantation testing, the woman's serum was mixed in vitro with lymphocytes from her husband. After a few hours, complement and Trypan blue were added to the culture well. The cells were observed under the microscope and determined to be viable. What is the interpretation of this assay?
A) The husband has antibodies that recognize his wife's cells.
B) The wife has antibodies that recognize her husband's cells.
C) The husband cannot donate his organ to his wife.
D) The husband can donate his organ to his wife.
Q2) The level of detail to which an allele is identified is called which of the following?
A) Resolution
B) Ambiguity
C) Specificity
D) Typing
Q3) A set of alleles on the same chromosome is called which of the following?
A) Polymorphism
B) Aneuploid
C) Haplotype
D) Histocompatibility
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Page 17
Chapter 16: Quality Assurance and Quality Control in the Molecular Laboratory
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Q1) An assay that detects an analyte associated with a particular disease only in patients who have that disease and not in patients who do not have the disease has which of the following?
A) Analytic specificity
B) Analytic sensitivity
C) Clinical specificity
D) Clinical sensitivity
Q2) A blood specimen is received in the laboratory for a PCR assay to detect cytomegalovirus (a DNA virus) on a Wednesday night. The PCR assay will not be performed until the next Monday morning. How should this specimen be stored to maintain the integrity of the nucleic acid prior to analysis?
A) Lyze RBCs, centrifuge, and store at 22<sup>o</sup>C
B) Lyze RBCs, centrifuge, and store at -20<sup>o</sup>
C) Whole blood stored at 22<sup>o</sup>-25<sup>o</sup>C
D) Whole blood stored at 35<sup>o</sup>-37<sup>o</sup>C
Q3) What is required for incorporating an FDA-approved test into a laboratory?
A) Proceed to use the test reagents according to the manufacturer's directions.
B) Validate test performance on reference and validation specimens.
C) Use the test, substituting reagents previously validated in the laboratory.
D) Request and review quality-assurance data from the manufacturer.
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