BIOD 102 Portage Learning - Lab 1 Exam
(Microarray Analysis) (2026/2027)
Section 1: Microarray Principles & Methodology
Q1: What is the primary structural difference between a cDNA microarray and an
oligonucleotide microarray?
A. cDNA arrays use RNA as probes, while oligonucleotide arrays use DNA as probes.
B. cDNA arrays utilize long, PCR-amplified probes (500-2000 bp), while oligonucleotide
arrays use short, synthetic sequences (20-80 bp). [CORRECT]
C. Oligonucleotide arrays require reverse transcription, while cDNA arrays do not.
D. cDNA arrays are synthesized in situ, whereas oligonucleotide arrays are spotted by robots.
Correct Answer: B
Rationale: cDNA microarrays utilize long fragments of PCR-amplified cDNA, making them
more prone to cross-hybridization, whereas oligonucleotide arrays use short, synthetically
designed sequences for higher specificity. Both utilize DNA probes, and either can be spotted or
synthesized in situ depending on the specific platform.
Q2: In a Portage Learning virtual lab simulation, you observe a technician using a robotic arm
with tiny pins to deposit small droplets of DNA onto a glass slide. Which type of microarray
fabrication is being demonstrated?
A. In situ photolithographic synthesis
B. Inkjet printing synthesis
C. Contact spotting [CORRECT]
D. Electrochemical synthesis
Correct Answer: C
Rationale: Contact spotting involves a robotic arm using solid pins to physically touch the slide
and deposit pre-synthesized DNA samples. Photolithography and inkjet printing synthesize the
oligonucleotides directly on the slide without physical contact from pins.
.
,Q3: In a dual-channel microarray experiment, fluorescent dyes Cy3 and Cy5 are commonly used.
What is the primary purpose of incorporating these dyes during the lab workflow?
A. To amplify the cDNA signal before hybridization
B. To cleave the target DNA into smaller fragments for better probe binding
C. To allow the scanner to differentiate between the test and control samples co-hybridized
to the same slide [CORRECT]
D. To stabilize the double-stranded DNA bonds during the washing steps
Correct Answer: C
Rationale: Cy3 and Cy5 emit light at different wavelengths (green and red, respectively),
enabling a laser scanner to distinguish the expression levels of two distinct samples (e.g., healthy
vs. diseased) hybridized simultaneously to the same array.
Q4: When designing an oligonucleotide probe for a microarray to target a specific mRNA
transcript, which principle is most critical to ensure accurate binding?
A. The probe must be complementary to the target sequence and designed to minimize
secondary structure. [CORRECT]
B. The probe should have a high GC content only at the 5' end to anchor the binding.
C. The probe must contain repetitive sequences to increase the likelihood of hybridization.
D. The probe should be complementary to the intron regions of the gene of interest.
Correct Answer: A
Rationale: Accurate hybridization relies on strict complementary base pairing; therefore, probes
must match the target sequence. Avoiding secondary structures (like hairpins) in the probe
ensures it remains accessible for target binding. Introns are spliced out of mature mRNA, so
probes target exons.
Q5: Although RNA sequencing (RNA-seq) has largely replaced microarrays in modern
2026/2027 genomic labs, understanding microarray principles remains foundational. Which of
the following best explains why microarray knowledge is still required?
A. RNA-seq cannot measure gene expression levels, only sequence variations.
.
, B. Microarray data analysis skills (normalization, fold-change) are directly translatable to
RNA-seq, and decades of legacy microarray data exist in public databases. [CORRECT]
C. Microarrays are the only method capable of detecting Single Nucleotide Polymorphisms
(SNPs).
D. RNA-seq technology relies on physically spotting cDNA onto glass slides.
Correct Answer: B
Rationale: The bioinformatic concepts of normalization, differential expression, and false
discovery rates originated with microarrays and apply directly to RNA-seq. Additionally,
researchers still mine legacy microarray databases (like GEO) for comparative meta-analyses.
Q6: The fundamental mechanism that allows a labeled target cDNA to bind to its specific probe
on a microarray slide is:
A. Covalent bonding between the dye and the glass slide
B. Hydrogen bonding between complementary nucleotide base pairs [CORRECT]
C. Peptide bonding between amino acids on the probe and target
D. Ionic bonding between the phosphate backbone and the slide coating
Correct Answer: B
Rationale: Microarray hybridization relies on the spontaneous formation of hydrogen bonds
between complementary nitrogenous bases (A-T and G-C) of the target cDNA in solution and the
immobilized probe DNA on the slide.
Q7: In a dual-channel microarray experimental design, a researcher decides to hybridize a
healthy tissue sample labeled with Cy3 and a cancerous tissue sample labeled with Cy5 onto the
same slide. What is the main advantage of this co-hybridization approach?
A. It halves the number of arrays required and eliminates technical variations between
separate slides. [CORRECT]
B. It allows the researcher to detect three times as many genes as a single-channel array.
C. It prevents the occurrence of cross-hybridization between similar gene sequences.
D. It increases the dynamic range of the fluorescent scanner.
Correct Answer: A
.
(Microarray Analysis) (2026/2027)
Section 1: Microarray Principles & Methodology
Q1: What is the primary structural difference between a cDNA microarray and an
oligonucleotide microarray?
A. cDNA arrays use RNA as probes, while oligonucleotide arrays use DNA as probes.
B. cDNA arrays utilize long, PCR-amplified probes (500-2000 bp), while oligonucleotide
arrays use short, synthetic sequences (20-80 bp). [CORRECT]
C. Oligonucleotide arrays require reverse transcription, while cDNA arrays do not.
D. cDNA arrays are synthesized in situ, whereas oligonucleotide arrays are spotted by robots.
Correct Answer: B
Rationale: cDNA microarrays utilize long fragments of PCR-amplified cDNA, making them
more prone to cross-hybridization, whereas oligonucleotide arrays use short, synthetically
designed sequences for higher specificity. Both utilize DNA probes, and either can be spotted or
synthesized in situ depending on the specific platform.
Q2: In a Portage Learning virtual lab simulation, you observe a technician using a robotic arm
with tiny pins to deposit small droplets of DNA onto a glass slide. Which type of microarray
fabrication is being demonstrated?
A. In situ photolithographic synthesis
B. Inkjet printing synthesis
C. Contact spotting [CORRECT]
D. Electrochemical synthesis
Correct Answer: C
Rationale: Contact spotting involves a robotic arm using solid pins to physically touch the slide
and deposit pre-synthesized DNA samples. Photolithography and inkjet printing synthesize the
oligonucleotides directly on the slide without physical contact from pins.
.
,Q3: In a dual-channel microarray experiment, fluorescent dyes Cy3 and Cy5 are commonly used.
What is the primary purpose of incorporating these dyes during the lab workflow?
A. To amplify the cDNA signal before hybridization
B. To cleave the target DNA into smaller fragments for better probe binding
C. To allow the scanner to differentiate between the test and control samples co-hybridized
to the same slide [CORRECT]
D. To stabilize the double-stranded DNA bonds during the washing steps
Correct Answer: C
Rationale: Cy3 and Cy5 emit light at different wavelengths (green and red, respectively),
enabling a laser scanner to distinguish the expression levels of two distinct samples (e.g., healthy
vs. diseased) hybridized simultaneously to the same array.
Q4: When designing an oligonucleotide probe for a microarray to target a specific mRNA
transcript, which principle is most critical to ensure accurate binding?
A. The probe must be complementary to the target sequence and designed to minimize
secondary structure. [CORRECT]
B. The probe should have a high GC content only at the 5' end to anchor the binding.
C. The probe must contain repetitive sequences to increase the likelihood of hybridization.
D. The probe should be complementary to the intron regions of the gene of interest.
Correct Answer: A
Rationale: Accurate hybridization relies on strict complementary base pairing; therefore, probes
must match the target sequence. Avoiding secondary structures (like hairpins) in the probe
ensures it remains accessible for target binding. Introns are spliced out of mature mRNA, so
probes target exons.
Q5: Although RNA sequencing (RNA-seq) has largely replaced microarrays in modern
2026/2027 genomic labs, understanding microarray principles remains foundational. Which of
the following best explains why microarray knowledge is still required?
A. RNA-seq cannot measure gene expression levels, only sequence variations.
.
, B. Microarray data analysis skills (normalization, fold-change) are directly translatable to
RNA-seq, and decades of legacy microarray data exist in public databases. [CORRECT]
C. Microarrays are the only method capable of detecting Single Nucleotide Polymorphisms
(SNPs).
D. RNA-seq technology relies on physically spotting cDNA onto glass slides.
Correct Answer: B
Rationale: The bioinformatic concepts of normalization, differential expression, and false
discovery rates originated with microarrays and apply directly to RNA-seq. Additionally,
researchers still mine legacy microarray databases (like GEO) for comparative meta-analyses.
Q6: The fundamental mechanism that allows a labeled target cDNA to bind to its specific probe
on a microarray slide is:
A. Covalent bonding between the dye and the glass slide
B. Hydrogen bonding between complementary nucleotide base pairs [CORRECT]
C. Peptide bonding between amino acids on the probe and target
D. Ionic bonding between the phosphate backbone and the slide coating
Correct Answer: B
Rationale: Microarray hybridization relies on the spontaneous formation of hydrogen bonds
between complementary nitrogenous bases (A-T and G-C) of the target cDNA in solution and the
immobilized probe DNA on the slide.
Q7: In a dual-channel microarray experimental design, a researcher decides to hybridize a
healthy tissue sample labeled with Cy3 and a cancerous tissue sample labeled with Cy5 onto the
same slide. What is the main advantage of this co-hybridization approach?
A. It halves the number of arrays required and eliminates technical variations between
separate slides. [CORRECT]
B. It allows the researcher to detect three times as many genes as a single-channel array.
C. It prevents the occurrence of cross-hybridization between similar gene sequences.
D. It increases the dynamic range of the fluorescent scanner.
Correct Answer: A
.
