Mammalian Genetics BCH5413 Exam
Questions and Correct Answers
Question 1
Explain how you would determine the directionality of your cloned fragment in a
TOPO vector.
Correct Answer
Digest the plasmid with a restriction enzyme that cuts in 2 places and run an
agarose gel, depending on the band sizes and where the restriction sites are
located, you can tell which direction the insert is found in
Question 2
Which gene is responsible for exon shuffling?
Correct Answer
Interrupted gene
Question 3
Why is it significant that histones have a basic pH?
Correct Answer
Histones have a (+) charge, causing the attraction of (-) charged DNA
Question 4
What is the advantage of using beads containing oligo T nucleotides for isolating
RNA when creating a cDNA library?
Correct Answer
mRNA has a polyA tail that will bind to the oligo T nucleotides, trapping it in the
column for elution (tRNA and rRNA can be washed away) with a low-salt buffer
Page 1 of 171
,Question 5
How is the DNA isolated that is bound to the protein of interest in ChIP?
Correct Answer
An Ab specific to the protein of interest is added, allowing for immunoprecipitation
that pulls the protein out of solution, bringing the DNA sequence with it
Question 6
Why are ddNTPs needed in Sanger sequencing?
Correct Answer
ddNTPs are missing an -OH group on the 3' C, making it impossible to add the next
dNTP, causing the strand to be terminated; the fragments are then separated by
size
Question 7
What happens in a RT-PCR reaction if the gene of interest wasn't expressed?
Correct Answer
No detection of the target gene will happen because the probe was not able to
attach to the target sequence
Question 8
Why would an investigator want to create a genomic library?
Correct Answer
To catalogue all of the mRNA present in an organism
Question 9
T/F: If bacterial cells have taken up any plasmid, the colonies will be white in blue-
white selection.
Correct Answer
True (the white colonies will contain the plasmid of interest)
Page 2 of 171
,Question 10
What is attached to the 4' C in DNA's 5-C sugar?
Correct Answer
It completes the ring structure (connects the 5' C and 3' C to the oxygen in the ring)
Question 11
Why might an investigator carry out a ChIP experiment?
Correct Answer
ChIP assays can be used to show the interaction between a DNA sequence and a
protein
Question 12
T/F: Blunt ends give better ligation than sticky ends.
Correct Answer
False (sticky ends are easier to ligate than blunt ends)
Question 13
Why would there be a region of no bands in a DNA footprinting gel?
Correct Answer
The region of no bands is where the DNA is protected from degradation of DNase
by the protein it's interacting with
Question 14
A technique for determining the exact DNA sequence that binds to a protein in DNA-
protein interactions using DNase for degradation.
Correct Answer
DNA footprinting
Page 3 of 171
, Question 15
What are the 2 advantages of TaqMan over SYBR Green?
Correct Answer
(1) TaqMan is very specific because the probe only attaches to the sequence of
interest; (2) the probes can be labeled with different dyes, allowing for detection of
multiple sequences within only one reaction
Question 16
What modification needs to happen in PCR to CLONE a fragment of DNA instead of
just amplifying it?
Correct Answer
Primers with a "sticky end" sequence will incorporate these into the amplified DNA,
allowing for ligation into a vector with matching "sticky ends"
Question 17
A normal feature in yeast shuttle vectors that allows for selection in yeast (a marker
gene).
Correct Answer
URA3
Question 18
What are 3 differences between DNA and RNA?
Correct Answer
(1) DNA has thymine and RNA has uracil; (2) DNA has an -H on its 2' C and RNA has
an -OH group; (3) DNA is normally double-stranded while RNA is normally single-
stranded
Question 19
What is the negative control for a DpnI digestion?
Correct Answer
Digest the WT plasmid with DpnI (there should be no colonies)
Page 4 of 171
Questions and Correct Answers
Question 1
Explain how you would determine the directionality of your cloned fragment in a
TOPO vector.
Correct Answer
Digest the plasmid with a restriction enzyme that cuts in 2 places and run an
agarose gel, depending on the band sizes and where the restriction sites are
located, you can tell which direction the insert is found in
Question 2
Which gene is responsible for exon shuffling?
Correct Answer
Interrupted gene
Question 3
Why is it significant that histones have a basic pH?
Correct Answer
Histones have a (+) charge, causing the attraction of (-) charged DNA
Question 4
What is the advantage of using beads containing oligo T nucleotides for isolating
RNA when creating a cDNA library?
Correct Answer
mRNA has a polyA tail that will bind to the oligo T nucleotides, trapping it in the
column for elution (tRNA and rRNA can be washed away) with a low-salt buffer
Page 1 of 171
,Question 5
How is the DNA isolated that is bound to the protein of interest in ChIP?
Correct Answer
An Ab specific to the protein of interest is added, allowing for immunoprecipitation
that pulls the protein out of solution, bringing the DNA sequence with it
Question 6
Why are ddNTPs needed in Sanger sequencing?
Correct Answer
ddNTPs are missing an -OH group on the 3' C, making it impossible to add the next
dNTP, causing the strand to be terminated; the fragments are then separated by
size
Question 7
What happens in a RT-PCR reaction if the gene of interest wasn't expressed?
Correct Answer
No detection of the target gene will happen because the probe was not able to
attach to the target sequence
Question 8
Why would an investigator want to create a genomic library?
Correct Answer
To catalogue all of the mRNA present in an organism
Question 9
T/F: If bacterial cells have taken up any plasmid, the colonies will be white in blue-
white selection.
Correct Answer
True (the white colonies will contain the plasmid of interest)
Page 2 of 171
,Question 10
What is attached to the 4' C in DNA's 5-C sugar?
Correct Answer
It completes the ring structure (connects the 5' C and 3' C to the oxygen in the ring)
Question 11
Why might an investigator carry out a ChIP experiment?
Correct Answer
ChIP assays can be used to show the interaction between a DNA sequence and a
protein
Question 12
T/F: Blunt ends give better ligation than sticky ends.
Correct Answer
False (sticky ends are easier to ligate than blunt ends)
Question 13
Why would there be a region of no bands in a DNA footprinting gel?
Correct Answer
The region of no bands is where the DNA is protected from degradation of DNase
by the protein it's interacting with
Question 14
A technique for determining the exact DNA sequence that binds to a protein in DNA-
protein interactions using DNase for degradation.
Correct Answer
DNA footprinting
Page 3 of 171
, Question 15
What are the 2 advantages of TaqMan over SYBR Green?
Correct Answer
(1) TaqMan is very specific because the probe only attaches to the sequence of
interest; (2) the probes can be labeled with different dyes, allowing for detection of
multiple sequences within only one reaction
Question 16
What modification needs to happen in PCR to CLONE a fragment of DNA instead of
just amplifying it?
Correct Answer
Primers with a "sticky end" sequence will incorporate these into the amplified DNA,
allowing for ligation into a vector with matching "sticky ends"
Question 17
A normal feature in yeast shuttle vectors that allows for selection in yeast (a marker
gene).
Correct Answer
URA3
Question 18
What are 3 differences between DNA and RNA?
Correct Answer
(1) DNA has thymine and RNA has uracil; (2) DNA has an -H on its 2' C and RNA has
an -OH group; (3) DNA is normally double-stranded while RNA is normally single-
stranded
Question 19
What is the negative control for a DpnI digestion?
Correct Answer
Digest the WT plasmid with DpnI (there should be no colonies)
Page 4 of 171
