BCH5413 3 Comprehensive Study Guide
A+ Exam Questions and Answers Verified
Solutions Latest Update 2026/2027
Answer:
DNA -> RNA -> Protein
■What is the meaning of the term transgenic?.
Answer:
A transgenic organism is one whose genome has been altered by the random introduction of a
foreign piece of DNA. Researchers often compare transgenic organisms to wild type or control
organisms to determine the effect the transgene has. The amount of DNA inserted can vary from
1-200 base pairs
■When determining if an additional copy of a gene added to a mouse genome using PCR, how
would you be able to distinguish between the endogenous gene and the transgene?.
Answer:
For PCR, I use two primers, one inside the transgene and one outside the transgene, so I can
distinguish the endogenous gene from the transgene. Since only the transgene can bind with these
two primers and be amplified.
■When determining if an additional copy of a gene added to a mouse genome using a Southern
blot, how would you be able to distinguish between the endogenous gene and the transgene?.
Answer:
Like PCR, I will use one probe to target the gene and another probe to target the vector in Southern
Blot. When there is only one band with the size of the gene, then it is an endogenous gene. If there
are two bands, one is with the size of the gene, another is the size of the vector, and it is the
transgene.
■endogenous factors that cause DNA damage.
Answer:
error in replicationbully addict formationoxidationalkylationhydrolysis
■What would be the purpose of creating a reporter gene as a transgene? What types of
,experimental questions might you be able to ask and answer?.
Answer:
Reporter genes are used to investigate the expression of other genes whose expression we need to
measure in a transgenic animal. Reporter genes "report" whether the gene of interest is expressed or
not, or the location of gene expression.In the lecture, the example of the HKβ subunit gene is given,
in which using a reporter gene, scientists want to investigate the location of expression of the HKβ
subunit gene in the tissues of a transgenic mouse. LacZ gene is used as a reporter and the HKβ
control region is placed in front of the LacZ gene in a plasmid vector. Now the tissues that
expressed the HKβ subunit gene also expressed the reporter LacZ gene and it became easier for the
scientists to locate the expression of the HKβ subunit gene because of the blue color of the tissues,
expressed by the LacZ gene whose product is β-galactosidase.Other reporter genes mentioned in
the textbook include the luciferase gene from firefly and the bacterial gene cat that encodes
chloramphenicol acetyl transferase enzyme (CAT).
■When creating a knockout animal, why do you need to engineer ES cells?.
Answer:
**Able to perform manipulation of the genome but the cells still grow into a whole organism. ES
cells give rise to all body tissue types. iPS cells: take cells that are differentiated and cause them too
undifferentiated.**ES cells = pluripotent, used to knock out genes of interest.
■When creating knockout ES cells, why do you need to isolate cells that are sensitive to G418
AND ganciclovir?.
Answer:
To tell you where your transgene is being expressed!G418 neomycin analog kills cell without
neomycin-resistance gene (cells with no integration)Gangcyclovir kills cells containing thymidine
kinase gene (cells
with non-specific recombination)Cells that grow on medium will have homologous recombination
between the plasmid and WT gene
■When creating a knockout mouse, the chimeric animal is mated with one that is black and normal
for the gene of interest. From this cross, three possible offspring can be produced. Explain the
genetics of each of the three and what you would do next with the desired offspring..
Answer:
possible progeny genomes include: A/X+ (brown, no gene of interest), A/X- (brown, gene of
interest), a/X+ (black, no gene of interest) in which A/X- is the most desirable genome.I would then
mate two heterozygous brown mice (X+X-) containing the gene of interest to produce a
,homozygous brown knockout mouse (X-X-) and screen by southern blot.
■exogenous factors that cause DNA damage.
Answer:
UV, chemicals, x-rays, ionizing radiation
■emethanesulfate (EMS).
Answer:
DNA alkylation medicine for cancer
■Where in the genome are loxP sites located in a Cre/Lox model?a. Adjacent to the Cre locus
expressed in a desired cell typeb. On either side of the gene that is to be knocked outc. Random
sites throughout the genome.
Answer:
b. On either side of the gene that is to be knocked out
■GC base pairing when guanine is exposed to EMS.
Answer:
guanine to 06-ethylguanine and bins to thymine
■EMS as a cancer treatment.
Answer:
interferes with transcriptional and DNA replication
■alkylation event that does not change base pairing.
Answer:
attacks phosphodiester bond
■In which organism was the CRISPR system discovered?.
Answer:
System of bacterial natural immunity. From studying natural immunity in bacteria.
■In the immunization phase, what happens to the foreign viral DNA?.
, Answer:
Phase 1(immunization phase): how the bacterial cell makes itself immunePhase 2 (immunity
phase): how it uses that to protect itself from a second infection.The foreing viral DNA is cleaved
into smaller pieces called spacers. The spacers are incorporated into the CRISPR locus; part of that
region of the chromosome has the spacers in it. The small pieces of viral DNA are separated from
each other by black boxes called repeats.
■In the immunity phase, what RNAs are present in the Cas9 complex? And what is their role?.
Answer:
pre-CRISPR RNA-contains the spacers and repeatsRNase III-cleave the RNase between the spacer
and the spacer and repeat, cleaves between these spacers and repeats from the rest of the spacers
and repeatstracrRNA-tracer binds to the repeat, which makes a recognition site for the RNase III
■endogenous sources of oxidative stress.
Answer:
respiration, stress
■What happens in a new infection from a previously recognized viral DNA?.
Answer:
The second time the bacteria encounter the same viral RNA, it will go into the cell and it will
complementary base pair with the spacer because it was made from the same viral DNA. The viral
DNA will then get cleaved by the CRISPRS
■exogenous sources of oxidative stress.
Answer:
smoking, alcohol, pollution, water, pesticides, medications, food (meat)
■What is the importance of PAM sequence in CRISPR Cas9 technology?.
Answer:
THE PAM sequence is present in the invading viral DNA, and it is not present as part of the spacer.
So the cell or the cas9 complex recognizes that the viral DNA is non-self and it will get cleaved.
■Result of oxidative damage.
Answer:
A+ Exam Questions and Answers Verified
Solutions Latest Update 2026/2027
Answer:
DNA -> RNA -> Protein
■What is the meaning of the term transgenic?.
Answer:
A transgenic organism is one whose genome has been altered by the random introduction of a
foreign piece of DNA. Researchers often compare transgenic organisms to wild type or control
organisms to determine the effect the transgene has. The amount of DNA inserted can vary from
1-200 base pairs
■When determining if an additional copy of a gene added to a mouse genome using PCR, how
would you be able to distinguish between the endogenous gene and the transgene?.
Answer:
For PCR, I use two primers, one inside the transgene and one outside the transgene, so I can
distinguish the endogenous gene from the transgene. Since only the transgene can bind with these
two primers and be amplified.
■When determining if an additional copy of a gene added to a mouse genome using a Southern
blot, how would you be able to distinguish between the endogenous gene and the transgene?.
Answer:
Like PCR, I will use one probe to target the gene and another probe to target the vector in Southern
Blot. When there is only one band with the size of the gene, then it is an endogenous gene. If there
are two bands, one is with the size of the gene, another is the size of the vector, and it is the
transgene.
■endogenous factors that cause DNA damage.
Answer:
error in replicationbully addict formationoxidationalkylationhydrolysis
■What would be the purpose of creating a reporter gene as a transgene? What types of
,experimental questions might you be able to ask and answer?.
Answer:
Reporter genes are used to investigate the expression of other genes whose expression we need to
measure in a transgenic animal. Reporter genes "report" whether the gene of interest is expressed or
not, or the location of gene expression.In the lecture, the example of the HKβ subunit gene is given,
in which using a reporter gene, scientists want to investigate the location of expression of the HKβ
subunit gene in the tissues of a transgenic mouse. LacZ gene is used as a reporter and the HKβ
control region is placed in front of the LacZ gene in a plasmid vector. Now the tissues that
expressed the HKβ subunit gene also expressed the reporter LacZ gene and it became easier for the
scientists to locate the expression of the HKβ subunit gene because of the blue color of the tissues,
expressed by the LacZ gene whose product is β-galactosidase.Other reporter genes mentioned in
the textbook include the luciferase gene from firefly and the bacterial gene cat that encodes
chloramphenicol acetyl transferase enzyme (CAT).
■When creating a knockout animal, why do you need to engineer ES cells?.
Answer:
**Able to perform manipulation of the genome but the cells still grow into a whole organism. ES
cells give rise to all body tissue types. iPS cells: take cells that are differentiated and cause them too
undifferentiated.**ES cells = pluripotent, used to knock out genes of interest.
■When creating knockout ES cells, why do you need to isolate cells that are sensitive to G418
AND ganciclovir?.
Answer:
To tell you where your transgene is being expressed!G418 neomycin analog kills cell without
neomycin-resistance gene (cells with no integration)Gangcyclovir kills cells containing thymidine
kinase gene (cells
with non-specific recombination)Cells that grow on medium will have homologous recombination
between the plasmid and WT gene
■When creating a knockout mouse, the chimeric animal is mated with one that is black and normal
for the gene of interest. From this cross, three possible offspring can be produced. Explain the
genetics of each of the three and what you would do next with the desired offspring..
Answer:
possible progeny genomes include: A/X+ (brown, no gene of interest), A/X- (brown, gene of
interest), a/X+ (black, no gene of interest) in which A/X- is the most desirable genome.I would then
mate two heterozygous brown mice (X+X-) containing the gene of interest to produce a
,homozygous brown knockout mouse (X-X-) and screen by southern blot.
■exogenous factors that cause DNA damage.
Answer:
UV, chemicals, x-rays, ionizing radiation
■emethanesulfate (EMS).
Answer:
DNA alkylation medicine for cancer
■Where in the genome are loxP sites located in a Cre/Lox model?a. Adjacent to the Cre locus
expressed in a desired cell typeb. On either side of the gene that is to be knocked outc. Random
sites throughout the genome.
Answer:
b. On either side of the gene that is to be knocked out
■GC base pairing when guanine is exposed to EMS.
Answer:
guanine to 06-ethylguanine and bins to thymine
■EMS as a cancer treatment.
Answer:
interferes with transcriptional and DNA replication
■alkylation event that does not change base pairing.
Answer:
attacks phosphodiester bond
■In which organism was the CRISPR system discovered?.
Answer:
System of bacterial natural immunity. From studying natural immunity in bacteria.
■In the immunization phase, what happens to the foreign viral DNA?.
, Answer:
Phase 1(immunization phase): how the bacterial cell makes itself immunePhase 2 (immunity
phase): how it uses that to protect itself from a second infection.The foreing viral DNA is cleaved
into smaller pieces called spacers. The spacers are incorporated into the CRISPR locus; part of that
region of the chromosome has the spacers in it. The small pieces of viral DNA are separated from
each other by black boxes called repeats.
■In the immunity phase, what RNAs are present in the Cas9 complex? And what is their role?.
Answer:
pre-CRISPR RNA-contains the spacers and repeatsRNase III-cleave the RNase between the spacer
and the spacer and repeat, cleaves between these spacers and repeats from the rest of the spacers
and repeatstracrRNA-tracer binds to the repeat, which makes a recognition site for the RNase III
■endogenous sources of oxidative stress.
Answer:
respiration, stress
■What happens in a new infection from a previously recognized viral DNA?.
Answer:
The second time the bacteria encounter the same viral RNA, it will go into the cell and it will
complementary base pair with the spacer because it was made from the same viral DNA. The viral
DNA will then get cleaved by the CRISPRS
■exogenous sources of oxidative stress.
Answer:
smoking, alcohol, pollution, water, pesticides, medications, food (meat)
■What is the importance of PAM sequence in CRISPR Cas9 technology?.
Answer:
THE PAM sequence is present in the invading viral DNA, and it is not present as part of the spacer.
So the cell or the cas9 complex recognizes that the viral DNA is non-self and it will get cleaved.
■Result of oxidative damage.
Answer:
