BCH5413 PRACTICE EXAM 2026 SOLVED
QUESTIONS WITH FULL EXPLANATIONS
◉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
◉Who developed the nobel prize for PCR?. Answer: kary mullis
,◉PCR consists of what cycles... Answer: Consists of alternate cycles
of denaturation, primer annealing, and elongation are performed
◉For each cycle, the PCR reaction ___ the existing number of copies
of DNA sequence. Answer: doubles
* 2^N
**30 cycles creates ~1 million copies
◉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
◉What does Taq stand for. Answer: Thermus aquaticus
- thermostable Pol allowed automation
◉What is the most common use of PCR. Answer: generate DNA
fragments for cloning, sequencing, or to make probes
,◉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)
◉PCR for genotyping: triplex PCR
- primers used. Answer: Two different forward primers:
1. wild type
2. knockout
One reverse primer
◉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
◉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)
◉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
◉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
◉PCR and DNA footprinting
QUESTIONS WITH FULL EXPLANATIONS
◉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
◉Who developed the nobel prize for PCR?. Answer: kary mullis
,◉PCR consists of what cycles... Answer: Consists of alternate cycles
of denaturation, primer annealing, and elongation are performed
◉For each cycle, the PCR reaction ___ the existing number of copies
of DNA sequence. Answer: doubles
* 2^N
**30 cycles creates ~1 million copies
◉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
◉What does Taq stand for. Answer: Thermus aquaticus
- thermostable Pol allowed automation
◉What is the most common use of PCR. Answer: generate DNA
fragments for cloning, sequencing, or to make probes
,◉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)
◉PCR for genotyping: triplex PCR
- primers used. Answer: Two different forward primers:
1. wild type
2. knockout
One reverse primer
◉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
◉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)
◉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
◉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
◉PCR and DNA footprinting
