Binghamton University - BIOL 311 -
Exam 2 – RVB Final Test Questions
and Actual Answers 2026 Updated.
What is Molecular Biology - Answer A group of processes and techniques used to
manipulate, analyze, expand, and express nucleotide sequence to understand/control gene
function
Genomics - Answer Wide reaching expansive term, key element is genes
Gene transfects - Answer Inserting intact genes through viruses, liposomes, nanoparticles
Example of gene transfection - Answer GFP linked to a gene of interest
Editing genes - Answer Adding or removing genes or single bases
Examples of gene editing (3) - Answer CRISPR-Cas-9, 62 pig retroviruses removed (clean pig),
xenograft transplantation
Controlling gene expression - Answer Knockin/Knockout transgenic animals and cells
Example of controlling gene expression (3) - Answer siRNA, shRNA, antisense RNA
DNA sequencing device - Answer Oxford Nanopore technologies MinION, for alpha
hemolysin and rapid DNA sequencing
Oxford Nanopore technologies MinION process - Answer Uses bacterial pores, pull protein
through the pore, bases are different sizes and have different electric currents
Transciptome - Answer The set of ALL RNA in a cell (mRNA)
Proteomics - Answer Huge field, structural, expression, mining, function, post translational
modification, the study of proteins
Epigenetics - Answer Inheritable non-base changes in DNA due to environment, DNA
methylation, histone phosphorylation
,DNA methylation - Answer Methyl group added to a base of DNA, turns down activity of a
gene (smoking)
Histone phosphorylation - Answer Nuclear packing protein that wraps DNA, can control gene
expression
What are epigenetics influenced by - Answer Lifestyle choices, diet, aging
Metabolome - Answer Default term for everything else, sugars, amino acids, lipids,
nucleotides (involved in metabolism)
Experiment example of studying metabolome - Answer Cancer cell in tube stained with dye,
measure metabolic action by seeing where cell goes (pathway of least energy)
Secretome - Answer What cells secrete, exosomes, cfDNA, proteins, vesicles (biomarkers)
What do stem cells secrete - Answer Factors in exosomes that are important to tissue repair
Benefit of stem cell exosomes - Answer Introducing non-autologous cells is risky
(oncogenes), exosomes can immunomodulate
What can immunomodulation of stem cell exosomes do? - Answer Dampen acute
respiratory distress syndrome (ARDS) and multiple organ failure (MOF)
Mutations - Answer Critical to understanding gene function, caused by UV light (DNA dimers
-> skin cancer) and chemicals (ethyl methane)
Point mutation - Answer One base change
Who discovered temperature sensitive mutants - Answer L.H. Hartwell, it is a yeast
Advantages of Yeast - Answer Simple growth medium
Can exist as haploids/diploids
Generate temperature sensitive mutants
5 steps to generate temperature sensitive mutants - Answer 1.) add mutagen to yeast
2.) incubate at 23C (permissive)
,3.) plate out yeast
4.) incubate 23C
5.) Replice plate/incubate (23 or 36C)
Non permissive temperature - Answer 36C - proteins are denatured
What can temperature sensitive yeasts test - Answer Gene function, take 2 haploid yeast
with different genes and fuse, incubate at 36C, growth indicates on different genes
(compliment) no growth = on same genes (combat)
Restriction nucleases - Answer Enzyme, cleaves nucleotides, found in bacteria to ward off
viruses (cleave viral DNA)
Who discovered restriction nucleases - Answer Nathan Smith, nobel prize in 1978, 600+
discovered
Gene splicing/Transfection - Answer Taking a DNA fragment and transfecting it, vector DNA
(carrier) and put in plasmid
Uses of Nucleic acid hybridization (probe) (7) - Answer 1.) FISH
2.) Antisense RNA
3.) Southern Blots
4.) Northern Blots
5.) cDNA microarrays
6.) Molecular beacons
7.) gel electrophoresis and band shift assay
gel band shift assay - Answer Detect DNA binding proteins, simple, bands at different
locations if gene or gene +protein
DNA gel electrophoresis - Answer Polyacrylamide gel good for small DNA (10-2000 bases)
Agarose Gel electrophoresis - Answer Separate larger DNA (200-20,000 bases)
Standard Gel Electrophoresis for apoptosis/necrosis - Answer DNA is cleaved, living cells are
one band, apoptosis have ladder (programmed), necrosis is smear (random), can show a mix
, Southern Blot - Answer GE blotting, genes can be detected, qualitative (MW) and
quantitative (compare)
How to do a southern blot - Answer Standard gel -> transfer paper, need DNA/RNA probe
and detected presence in fragments ONE GENE AT A TIME
Application of Southern Blot - Answer CODIS (system to combine DNA information in
forensics)
Repeating unique sequences
VNTRs and RFLPs
VNTRs - Answer Variable number tandem repeats, polymorphic marker (each person is diff),
can match DNA in bone marrow transplants (see success) or forensics (match suspect to DNA)
What do SNPs do - Answer Single nucleotide polymorphisms (98-99% of DNA is not coding),
predict symptom severity of autism spectrum disorder, drug tolerance, and personalized
medicine
Northern blots - Answer Analyzes gene function, separates mRNA ONE AT A TIME
Molecular beacons - Answer Probe region, fluorescence is quenched unless bound to target
RNA/DNA (identify)
Oligonucleotide Microarray - Answer cDNA microarray, analyze 8600 mRNA at a time, cluster
analysis, color intensity shows binding ability
Question of experiment with cDNA - Answer What mRNA are selectively
synthesized/transcribed in response to _______ (analyze transcriptome)
Process of using cDNA - Answer 1.) Two cells (one with and without)
2.) isolate all mRNA
3.) reverse transcriptase
4.) mix together and microarray
4 possibilities of microarrays - Answer No sticks
mRNA with
mRNA without
mRNA with both
Exam 2 – RVB Final Test Questions
and Actual Answers 2026 Updated.
What is Molecular Biology - Answer A group of processes and techniques used to
manipulate, analyze, expand, and express nucleotide sequence to understand/control gene
function
Genomics - Answer Wide reaching expansive term, key element is genes
Gene transfects - Answer Inserting intact genes through viruses, liposomes, nanoparticles
Example of gene transfection - Answer GFP linked to a gene of interest
Editing genes - Answer Adding or removing genes or single bases
Examples of gene editing (3) - Answer CRISPR-Cas-9, 62 pig retroviruses removed (clean pig),
xenograft transplantation
Controlling gene expression - Answer Knockin/Knockout transgenic animals and cells
Example of controlling gene expression (3) - Answer siRNA, shRNA, antisense RNA
DNA sequencing device - Answer Oxford Nanopore technologies MinION, for alpha
hemolysin and rapid DNA sequencing
Oxford Nanopore technologies MinION process - Answer Uses bacterial pores, pull protein
through the pore, bases are different sizes and have different electric currents
Transciptome - Answer The set of ALL RNA in a cell (mRNA)
Proteomics - Answer Huge field, structural, expression, mining, function, post translational
modification, the study of proteins
Epigenetics - Answer Inheritable non-base changes in DNA due to environment, DNA
methylation, histone phosphorylation
,DNA methylation - Answer Methyl group added to a base of DNA, turns down activity of a
gene (smoking)
Histone phosphorylation - Answer Nuclear packing protein that wraps DNA, can control gene
expression
What are epigenetics influenced by - Answer Lifestyle choices, diet, aging
Metabolome - Answer Default term for everything else, sugars, amino acids, lipids,
nucleotides (involved in metabolism)
Experiment example of studying metabolome - Answer Cancer cell in tube stained with dye,
measure metabolic action by seeing where cell goes (pathway of least energy)
Secretome - Answer What cells secrete, exosomes, cfDNA, proteins, vesicles (biomarkers)
What do stem cells secrete - Answer Factors in exosomes that are important to tissue repair
Benefit of stem cell exosomes - Answer Introducing non-autologous cells is risky
(oncogenes), exosomes can immunomodulate
What can immunomodulation of stem cell exosomes do? - Answer Dampen acute
respiratory distress syndrome (ARDS) and multiple organ failure (MOF)
Mutations - Answer Critical to understanding gene function, caused by UV light (DNA dimers
-> skin cancer) and chemicals (ethyl methane)
Point mutation - Answer One base change
Who discovered temperature sensitive mutants - Answer L.H. Hartwell, it is a yeast
Advantages of Yeast - Answer Simple growth medium
Can exist as haploids/diploids
Generate temperature sensitive mutants
5 steps to generate temperature sensitive mutants - Answer 1.) add mutagen to yeast
2.) incubate at 23C (permissive)
,3.) plate out yeast
4.) incubate 23C
5.) Replice plate/incubate (23 or 36C)
Non permissive temperature - Answer 36C - proteins are denatured
What can temperature sensitive yeasts test - Answer Gene function, take 2 haploid yeast
with different genes and fuse, incubate at 36C, growth indicates on different genes
(compliment) no growth = on same genes (combat)
Restriction nucleases - Answer Enzyme, cleaves nucleotides, found in bacteria to ward off
viruses (cleave viral DNA)
Who discovered restriction nucleases - Answer Nathan Smith, nobel prize in 1978, 600+
discovered
Gene splicing/Transfection - Answer Taking a DNA fragment and transfecting it, vector DNA
(carrier) and put in plasmid
Uses of Nucleic acid hybridization (probe) (7) - Answer 1.) FISH
2.) Antisense RNA
3.) Southern Blots
4.) Northern Blots
5.) cDNA microarrays
6.) Molecular beacons
7.) gel electrophoresis and band shift assay
gel band shift assay - Answer Detect DNA binding proteins, simple, bands at different
locations if gene or gene +protein
DNA gel electrophoresis - Answer Polyacrylamide gel good for small DNA (10-2000 bases)
Agarose Gel electrophoresis - Answer Separate larger DNA (200-20,000 bases)
Standard Gel Electrophoresis for apoptosis/necrosis - Answer DNA is cleaved, living cells are
one band, apoptosis have ladder (programmed), necrosis is smear (random), can show a mix
, Southern Blot - Answer GE blotting, genes can be detected, qualitative (MW) and
quantitative (compare)
How to do a southern blot - Answer Standard gel -> transfer paper, need DNA/RNA probe
and detected presence in fragments ONE GENE AT A TIME
Application of Southern Blot - Answer CODIS (system to combine DNA information in
forensics)
Repeating unique sequences
VNTRs and RFLPs
VNTRs - Answer Variable number tandem repeats, polymorphic marker (each person is diff),
can match DNA in bone marrow transplants (see success) or forensics (match suspect to DNA)
What do SNPs do - Answer Single nucleotide polymorphisms (98-99% of DNA is not coding),
predict symptom severity of autism spectrum disorder, drug tolerance, and personalized
medicine
Northern blots - Answer Analyzes gene function, separates mRNA ONE AT A TIME
Molecular beacons - Answer Probe region, fluorescence is quenched unless bound to target
RNA/DNA (identify)
Oligonucleotide Microarray - Answer cDNA microarray, analyze 8600 mRNA at a time, cluster
analysis, color intensity shows binding ability
Question of experiment with cDNA - Answer What mRNA are selectively
synthesized/transcribed in response to _______ (analyze transcriptome)
Process of using cDNA - Answer 1.) Two cells (one with and without)
2.) isolate all mRNA
3.) reverse transcriptase
4.) mix together and microarray
4 possibilities of microarrays - Answer No sticks
mRNA with
mRNA without
mRNA with both
