Nucleic acid microarrays and protein microarrays applications MCQs With Answer

Nucleic acid microarrays and protein microarrays applications MCQs With Answer

This quiz compilation is designed for M.Pharm students studying Principles of Drug Discovery. It focuses on practical applications, workflows, detection methods, surface chemistries, data analysis and clinical translation of nucleic acid and protein microarrays. Questions emphasize experimental design, troubleshooting (cross-hybridization, dye bias, normalization), and application areas such as gene expression profiling, SNP genotyping, comparative genomic hybridization, biomarker discovery, pharmacogenomics and proteomic interaction mapping. Each MCQ includes realistic options and exact answers to reinforce conceptual understanding and to prepare students for exams or laboratory decision-making when applying microarray technologies in drug discovery and translational research.

Q1. What is the primary application of nucleic acid microarrays in drug discovery?

• Protein–protein interaction mapping
• Gene expression profiling
• Small molecule screening
• Antibody epitope mapping

Correct Answer: Gene expression profiling

Q2. Which type of microarray uses PCR products or cloned cDNA fragments printed on a slide?

• Protein microarray
• Oligonucleotide microarray
• cDNA microarray
• Antibody array

Correct Answer: cDNA microarray

Q3. Typical oligonucleotide probes used in commercial gene expression arrays are usually how long?

• 8–12 nucleotides
• 25–70 nucleotides
• 150–500 nucleotides
• Over 1000 nucleotides

Correct Answer: 25–70 nucleotides

Q4. Reverse-phase protein arrays (RPPA) are characterized by which feature?

• Immobilization of capture antibodies to measure many analytes
• Spotting protein samples or lysates from many samples directly on the array
• Printing thousands of peptides to map epitopes
• Using aptamers as capture reagents for small molecules

Correct Answer: Spotting protein samples or lysates from many samples directly on the array

Q5. What is the most commonly used detection method for both nucleic acid and protein microarrays in research labs?

• Radioactive labeling and autoradiography
• Fluorescence detection with labeled probes or antibodies
• Mass spectrometry imaging
• Electrochemical sensing

Correct Answer: Fluorescence detection with labeled probes or antibodies

Q6. Dye bias observed in two-color microarray experiments is primarily caused by what?

• Differences in probe sequence length between arrays
• Differences in dye incorporation efficiency and fluorescence properties
• Scanner resolution being too low
• Unequal humidity during hybridization

Correct Answer: Differences in dye incorporation efficiency and fluorescence properties

Q7. Which normalization method is commonly used to correct intensity-dependent dye bias in two-color microarrays?

• Quantile normalization
• Loess (local regression) normalization
• Z-score normalization
• Median polish

Correct Answer: Loess (local regression) normalization

Q8. Comparative Genomic Hybridization (CGH) microarrays are primarily used to detect which genomic alteration?

• Single nucleotide polymorphisms (SNPs)
• Copy number variations (CNVs)
• Differential gene expression
• DNA methylation changes

Correct Answer: Copy number variations (CNVs)

Q9. Functional protein microarrays are best suited for which application?

• Absolute quantification of plasma biomarkers in clinical samples
• High-throughput study of protein activities and molecular interactions
• Direct sequencing of protein-coding genes
• Measuring mRNA expression across tissues

Correct Answer: High-throughput study of protein activities and molecular interactions

Q10. Aptamer arrays differ from antibody arrays because aptamers are what?

• Short peptides selected from phage libraries
• Nucleic acid ligands selected to bind proteins with high affinity
• Small molecule inhibitors immobilized on a surface
• Engineered antibodies with fluorescent tags

Correct Answer: Nucleic acid ligands selected to bind proteins with high affinity

Q11. Which surface chemistry is commonly used to achieve covalent immobilization of proteins or oligonucleotides through primary amines?

• Nitrocellulose membrane (non-covalent adsorption)
• Avidin–biotin coated slides (non-covalent strong affinity)
• Epoxy-activated glass surface for amine coupling
• Plain untreated glass

Correct Answer: Epoxy-activated glass surface for amine coupling

Q12. What is the main purpose of performing a blocking step after probe or antigen immobilization on microarrays?

• To increase hybridization temperature
• To reduce non-specific binding of labeled sample or antibodies
• To denature immobilized probes into single strands
• To fluorescently label the background surface

Correct Answer: To reduce non-specific binding of labeled sample or antibodies

Q13. If an experiment requires improving the limit of detection on a microarray, which strategy is most appropriate?

• Using much longer probes to increase binding energy
• Applying signal amplification methods such as enzymatic or tyramide amplification
• Washing with higher salt concentrations to remove background
• Reducing hybridization time to prevent saturation

Correct Answer: Applying signal amplification methods such as enzymatic or tyramide amplification

Q14. In gene expression microarray workflows, reverse transcription is used to convert which molecule into cDNA for labeling?

• Genomic DNA
• mRNA (messenger RNA)
• Protein
• Ribosomal RNA only

Correct Answer: mRNA (messenger RNA)

Q15. Cross-hybridization on nucleic acid microarrays reduces specificity by what mechanism?

• Degradation of probes by nucleases
• Non-specific adhesion of proteins to the surface
• Similar, non-target sequences binding to immobilized probes
• Fluorophore photobleaching during scanning

Correct Answer: Similar, non-target sequences binding to immobilized probes

Q16. Which statistical metric is commonly used to assess reproducibility across technical replicates in microarray experiments?

• Coefficient of variation (CV)
• P-value from a t-test
• Fold change
• Signal-to-noise ratio only

Correct Answer: Coefficient of variation (CV)

Q17. Which protein microarray format is created by spotting patient sera or lysates directly onto a slide for profiling many patient samples?

• Analytical antibody array where antibodies are immobilized
• Functional protein array containing purified proteins
• Reverse-phase protein array (RPPA)
• Aptamer array with immobilized nucleic acid ligands

Correct Answer: Reverse-phase protein array (RPPA)

Q18. Detection of phosphorylation events on protein microarrays is typically achieved using what approach?

• General total protein stains without specificity
• Phospho-specific antibodies that recognize modified residues
• Fluorescent dye incorporation during transcription
• Mass spectrometry directly on the slide without probes

Correct Answer: Phospho-specific antibodies that recognize modified residues

Q19. What is a principal technical limitation when attempting to multiplex many analytes using fluorescence-based microarrays?

• Probe length differences affecting binding kinetics
• Spectral overlap between fluorescent dyes limiting distinct channels
• Excessively high ambient humidity during printing
• Too many available scanner lasers

Correct Answer: Spectral overlap between fluorescent dyes limiting distinct channels

Q20. For clinical deployment of microarray-based diagnostic assays, what regulatory or translational issue is of primary concern?

• High purchase cost of scanners only
• Lack of rigorous standardization, analytical validation and reproducibility
• Inability to print arrays in academic labs
• Limited availability of fluorescent dyes

Correct Answer: Lack of rigorous standardization, analytical validation and reproducibility

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