BCH5413 Practice Exam Explanations
Questions and Answers Verified Solutions
Latest Update 2026/2027
Question:
Western blot analysis: controls
- positive, negative, equal loading, cross reaction, other.
Answer:
Positive: make sure reagents worked correctly
Negative: test to see if NO signal when required reagent is mising
Equal Loading: did you really put the same amount of sample in each lane
Cross-reactions: could one of your reagents be detecting something else
Other experimental conditions: think about the result that you want to get, then ask how it could
possibly arise in an incorrect manner and test for that possibility
Question:
Who developed the nobel prize for PCR?.
Answer:
kary mullis
Question:
PCR consists of what cycles...
Answer:
Consists of alternate cycles of denaturation, primer annealing, and elongation are performed
Question:
For each cycle, the PCR reaction ___ the existing number of copies of DNA sequence.
Answer:
,doubles
* 2^N
**30 cycles creates ~1 million copies
Question:
What are the reaction components of PCR.
Answer:
- template
DNA
- primers (forward and reverse)
- dNTP's (A,T,C,G)
- Taq Pol
- buffer + magnesium
- water
Question:
What does Taq stand for.
Answer:
Thermus aquaticus
- thermostable Pol allowed automation
Question:
What is the most common use of PCR.
Answer:
generate DNA fragments for cloning, sequencing, or to make probes
Question:
What restriction enzymes are used in PCR for cloning.
Answer:
BamH1 and HindiIII
- leaves sticky ends convenient for cloning if a vector has compatible
end sites (ligation of sticky ends to vector)
,Question:
PCR for genotyping: triplex PCR
- primers used.
Answer:
Two different forward primers:
1. wild type
2. knockout
One reverse primer
Question:
PCR for genotyping
- how primers work.
Answer:
- knock out one gene with a different
sequence
- knock out strand has forward primer for its sequence
- wild type has a forward primer for its sequence
- one reverse primer for both matching wild type and knockout
Question:
PCR for genotyping
- what the primers show on gel.
Answer:
Heterozygote +/-
- will show forward primer and reverse primer (two bands)
Homozygote wild type +/+
- will show only foward primer (heavier top band)
Homozygote knockout -/-
- will show only reverse primer (lighter lower band)
Question:
Bisulfite PCR.
, Answer:
- determines the methylation status of
every C in a DNA sequence
*useful in eukaryotic promoter analysis and in determining methylation status of a region of DNA
Question:
Bisulfite PCR
- what happens when DNA is treated with bisulfite.
Answer:
- C's are
converted to U, which changes a GC basepair to an AT basepair during PCR
- 5 methyl C is resistant to this treatment, and so GC basepairs in the
sequence CpG remain in the sequence
- once the DNA is treated, PCR primers are chosen (avoiding CpG in
the primer sequence and change all C's to T's)
- after PCR, the DNA fragment is sequenced
Question:
PCR and DNA footprinting
- what it is used for
- when it occurs.
Answer:
DNA footprinting is used to analyze sequence-specific DNA-protein interactions
- DNA footprinting occurs when digestion of a specific region of DNA
is prevented by binding of a protein. The protection can be either to digestion by DNases, or to
chemical modification. The second process gives greater resolution
Question:
Ligation-mediated PCR.
Answer:
a technique conducted after the DNA was exposed to DNase, and is used to amplify a rare
footprinted fragment by a PCR step
- must be followed by southern blotting and probing
Questions and Answers Verified Solutions
Latest Update 2026/2027
Question:
Western blot analysis: controls
- positive, negative, equal loading, cross reaction, other.
Answer:
Positive: make sure reagents worked correctly
Negative: test to see if NO signal when required reagent is mising
Equal Loading: did you really put the same amount of sample in each lane
Cross-reactions: could one of your reagents be detecting something else
Other experimental conditions: think about the result that you want to get, then ask how it could
possibly arise in an incorrect manner and test for that possibility
Question:
Who developed the nobel prize for PCR?.
Answer:
kary mullis
Question:
PCR consists of what cycles...
Answer:
Consists of alternate cycles of denaturation, primer annealing, and elongation are performed
Question:
For each cycle, the PCR reaction ___ the existing number of copies of DNA sequence.
Answer:
,doubles
* 2^N
**30 cycles creates ~1 million copies
Question:
What are the reaction components of PCR.
Answer:
- template
DNA
- primers (forward and reverse)
- dNTP's (A,T,C,G)
- Taq Pol
- buffer + magnesium
- water
Question:
What does Taq stand for.
Answer:
Thermus aquaticus
- thermostable Pol allowed automation
Question:
What is the most common use of PCR.
Answer:
generate DNA fragments for cloning, sequencing, or to make probes
Question:
What restriction enzymes are used in PCR for cloning.
Answer:
BamH1 and HindiIII
- leaves sticky ends convenient for cloning if a vector has compatible
end sites (ligation of sticky ends to vector)
,Question:
PCR for genotyping: triplex PCR
- primers used.
Answer:
Two different forward primers:
1. wild type
2. knockout
One reverse primer
Question:
PCR for genotyping
- how primers work.
Answer:
- knock out one gene with a different
sequence
- knock out strand has forward primer for its sequence
- wild type has a forward primer for its sequence
- one reverse primer for both matching wild type and knockout
Question:
PCR for genotyping
- what the primers show on gel.
Answer:
Heterozygote +/-
- will show forward primer and reverse primer (two bands)
Homozygote wild type +/+
- will show only foward primer (heavier top band)
Homozygote knockout -/-
- will show only reverse primer (lighter lower band)
Question:
Bisulfite PCR.
, Answer:
- determines the methylation status of
every C in a DNA sequence
*useful in eukaryotic promoter analysis and in determining methylation status of a region of DNA
Question:
Bisulfite PCR
- what happens when DNA is treated with bisulfite.
Answer:
- C's are
converted to U, which changes a GC basepair to an AT basepair during PCR
- 5 methyl C is resistant to this treatment, and so GC basepairs in the
sequence CpG remain in the sequence
- once the DNA is treated, PCR primers are chosen (avoiding CpG in
the primer sequence and change all C's to T's)
- after PCR, the DNA fragment is sequenced
Question:
PCR and DNA footprinting
- what it is used for
- when it occurs.
Answer:
DNA footprinting is used to analyze sequence-specific DNA-protein interactions
- DNA footprinting occurs when digestion of a specific region of DNA
is prevented by binding of a protein. The protection can be either to digestion by DNases, or to
chemical modification. The second process gives greater resolution
Question:
Ligation-mediated PCR.
Answer:
a technique conducted after the DNA was exposed to DNase, and is used to amplify a rare
footprinted fragment by a PCR step
- must be followed by southern blotting and probing
