Lecture 4: PCR

Question 1

Question: Which of the following correctly compares how DNA is separated during Polymerase Chain Reaction (PCR) and in a living cell during replication?

A) In PCR, DNA separation is initiated by helicase, whereas in a living cell, heat is used to break the hydrogen bonds between DNA strands.
B) In PCR, heat is used to separate DNA strands, while in a living cell, helicase enzymes unwind and separate the DNA strands.
C) In PCR, both heat and helicase are used to separate DNA strands, while in a living cell, only helicase is involved.
D) In both PCR and living cells, heat is used to separate DNA strands during replication.

Answer 1

b)

Question 2

Why is it important for the 3’ end of a primer to perfectly match the target DNA sequence when designing primers for PCR?

A) DNA polymerase can only add nucleotides to the 5’ end of the primer, so the 3’ end match is irrelevant.
B) A mismatch at the 3’ end allows the primer to bind more tightly to the DNA template, improving PCR efficiency.
C) A 3’ end match ensures that DNA polymerase can properly extend the primer and amplifies the target sequence with high specificity.
D) The 3’ end match is important only for binding, but mismatches do not affect primer extension.

Answer 2

c)

Question 3

Which of the following components is NOT required for a PCR reaction?

A) DNA template
B) DNA polymerase
C) Ribosomes
D) Primers

Answer 3

c) ribosomes

Question 4

What is the main purpose of the annealing step in PCR?

A) To denature the DNA into single strands
B) To allow primers to bind to the template DNA
C) To synthesize new DNA strands
D) To break down the template DNA

Answer 4

B) to allow the primers to bind to the template strand

Question 5

At what temperature does the DNA denaturation step typically occur in PCR?

A) 37°C
B) 72°C
C) 94–98°C
D) 50–65°C

Answer 5

c) about 95 degrees celcius

Question 6

What role do dNTPs play in a PCR reaction?

A) They act as primers for DNA synthesis.
B) They provide the heat necessary for denaturation.
C) They are the building blocks for synthesizing the new DNA strands.
D) They stabilize the DNA polymerase enzyme.

Answer 6

C)

Question 7

Which enzyme is most commonly used in PCR due to its ability to withstand high temperatures?

A) Ligase
B) RNA polymerase
C) Taq polymerase
D) Helicase

Answer 7

c) Taq polymerase

Question 8

Which of the following best describes the relationship between the denaturation step in PCR and a similar process in natural DNA replication?

A) Denaturation in PCR is analogous to the action of primase adding RNA primers in DNA replication.
B) Denaturation in PCR is analogous to the action of helicase unwinding the DNA strands in DNA replication.
C) Denaturation in PCR is analogous to DNA polymerase synthesizing new DNA strands in DNA replication.
D) Denaturation in PCR is analogous to the ligase joining Okazaki fragments in DNA replication.

Answer 8

b)

Question 9

In the annealing step of PCR, what is the role of the primers?

A) To break hydrogen bonds between DNA strands
B) To provide a starting point for DNA polymerase
C) To synthesize new DNA strands
D) To add dNTPs to the growing DNA chain

Answer 9

b)

Question 10

How does Taq polymerase function during the extension step of PCR?

A) It adds RNA primers to the template strands.
B) It synthesizes new DNA strands in a 3’ to 5’ direction.
C) It synthesizes new DNA strands in a 5’ to 3’ direction.
D) It unwinds the DNA strands for replication.

Answer 10

c)

Question 11

Which component is essential for complementary base pairing during PCR extension?

A) Primers
B) dNTPs
C) DNA template
D) All of the above

Answer 11

d)

Question 12

Which enzyme is primarily responsible for synthesizing new DNA strands during DNA replication?

A) DNA ligase
B) DNA helicase
C) DNA polymerase
D) RNA primase

Answer 12

c) DNA polymerase

Question 13

What is the purpose of applying heat during the denaturation step of PCR?

A) To allow primers to anneal to the DNA
B) To break hydrogen bonds between the DNA strands
C) To synthesize new DNA strands
D) To cool down the reaction mixture

Answer 13

B) To break hydrogen bonds between the DNA strands

Question 14

During the annealing step in PCR, what occurs when the temperature is lowered?

A) DNA polymerase synthesizes new DNA strands.
B) Primers anneal to their complementary sequences on the template strands.
C) The DNA strands are denatured into single strands.
D) The dNTPs are added to the reaction mixture.

Answer 14

b) primers anneal to their complimentary sequences on the template strands

Question 15

After the first cycle of PCR, how many double-stranded DNA molecules are produced if you start with one double-stranded molecule?

A) 1
B) 2
C) 4
D) 8

Answer 15

b) 2

Question 16

After the second cycle of PCR, how many double-stranded DNA molecules are produced if you start with one molecule?

A) 2
B) 4
C) 8
D) 16

Answer 16

b) 4

Question 17

What happens to the synthesized DNA strands that do not match the target size during PCR?

A) They are amplified more efficiently than the correct size.
B) They will eventually be paired with the correct primers and amplified.
C) They are less likely to be amplified in subsequent cycles.
D) They are removed from the reaction mixture.

Answer 17

c)

Question 18

How does PCR ensure that only the target DNA region is amplified over time?

A) By using multiple enzymes
B) By incorporating fluorescent markers
C) By gradually eliminating non-target strands through successive cycles
D) By increasing the temperature during each cycle

Answer 18

c)

Question 19

In the formula {# of Starting DNA Molecules} times (2^n), what does
𝑛 represent?

A) The number of DNA primers
B) The number of cycles
C) The number of starting DNA molecules
D) The total number of amplified DNA strands

Answer 19

b) the number of cycles

Question 20

What is the maximum number of DNA molecules you would have after performing 4 cycles of PCR starting with 1 molecule of DNA?

A) 4
B) 8
C) 16
D) 32

Answer 20

c) 16

Question 21

What happens if the 3’ end of a primer does not match the template DNA sequence?

A) DNA polymerase will extend the primer efficiently.
B) The primer will anneal correctly to the template.
C) DNA polymerase will be unable to extend the primer efficiently.
D) The PCR reaction will be unaffected.

Answer 21

c)

Question 22

The presence of which functional group at the 3’ end of the primer is crucial for DNA synthesis?

A) -NH2
B) -OH
C) -SH
D) -COOH

Answer 22

b) -OH

Question 23

If a primer has a mismatch at its 3’ end, what is likely to occur during PCR?

A) Efficient amplification of the target DNA
B) No amplification of the target DNA
C) Only partial amplification of the target DNA
D) Increased efficiency of DNA polymerase

Answer 23

b) no amplification of target DNA

Question 24

Why might you choose a Taq polymerase with proofreading capabilities for gene cloning?

A) It is faster than other Taqs.
B) It produces more copies of DNA.
C) It reduces the likelihood of errors in the cloned DNA.
D) It is less expensive.

Answer 24

c)

Question 25

What do the bands in gel electrophoresis primarily represent?

A) The total amount of DNA in a sample
B) Specific sizes of DNA fragments
C) The sequence of the DNA
D) The origin of the DNA

Answer 25

b)

Question 26

How can you determine the size of DNA fragments from a gel electrophoresis?

A) By comparing the bands to a DNA ladder of known sizes
B) By measuring the intensity of the bands
C) By calculating the total length of the gel
D) By observing the color of the bands

Answer 26

A)

Question 27

What does the intensity of a DNA band in gel electrophoresis indicate?

A) The temperature during the electrophoresis process
B) The size of the DNA fragment
C) The relative amount of DNA in that fragment
D) The sequence of the DNA fragment

Answer 27

c)

Question 28

Why is band intensity not always directly proportional to the amount of DNA present?

A) Different DNA fragments migrate at different speeds.
B) Staining efficiency and loading inconsistencies can vary.
C) The gel can absorb DNA differently.
D) Only certain sizes of DNA can be detected.

Answer 28

b)

Question 29

What is the primary purpose of Reverse Transcription PCR (RT-PCR)?

A) To quantify DNA in real time
B) To convert RNA into complementary DNA (cDNA)
C) To amplify DNA directly from genomic samples
D) To analyze protein expression levels

Answer 29

b)

Question 30

Which of the following statements correctly differentiates qPCR from RT-PCR?

A) qPCR is used for quantifying RNA, while RT-PCR is used for quantifying DNA.
B) qPCR measures DNA amplification in real time, whereas RT-PCR converts RNA into cDNA before amplification.
C) qPCR does not require any enzymes, while RT-PCR requires reverse transcriptase only.
D) qPCR is primarily qualitative, whereas RT-PCR is primarily quantitative.

Answer 30

b)

Question 31

What does a match at multiple STR loci between a suspect and crime scene sample indicate?

A) The two samples come from unrelated individuals.
B) The two samples are likely from the same individual.
C) The samples are contaminated.
D) The analysis is inconclusive.

Answer 31

b)

Question 32

in the context of plasmids, what does “stringent control” refer to?

A) Plasmids replicate independently of the chromosome.
B) Plasmids replicate only when the bacterial chromosome replicates.
C) Plasmids cannot be used as vectors.
D) Plasmids are larger than bacterial chromosomes.

Answer 32

b)

Question 33

What form of plasmid DNA runs the fastest during gel electrophoresis?

A) Linear form
B) Nicked circular form
C) Supercoiled form
D) Concatamer

Answer 33

c)

Question 34

Which component is essential for a plasmid to function as a vector in gene transformation?

A) A bacterial origin of replication
B) A promoter for gene expression
C) A selectable marker
D) All of the above

Answer 34

d) all of the above

Question 35

What is a primary function of plasmids in bacteria?

A) They encode essential proteins for survival.
B) They serve as the main source of genetic information.
C) They confer advantages such as antibiotic resistance.
D) They replicate only during cell division.

Answer 35

c)

Question 36

Which of the following describes a selectable marker in a plasmid?

A) A region that regulates gene expression.
B) A gene that allows bacteria to survive in the presence of antibiotics.
C) A section that contains multiple restriction enzyme sites.
D) A DNA sequence that prevents plasmid replication.

Answer 36

b)

Question 37

What is the purpose of a Multiple Cloning Site (MCS) in a plasmid?

A) To ensure plasmid stability during replication.
B) To facilitate the insertion of genes by providing multiple restriction enzyme sites.
C) To regulate the expression of the plasmid’s genes.
D) To encode antibiotic resistance.

Answer 37

b)

Question 38

Which component of a plasmid acts as an “on switch” for gene expression?

A) Selectable marker
B) Multiple Cloning Site (MCS)
C) Promoter sequence
D) Origin of replication

Answer 38

c) promotoer sequence

Question 39

What is the primary mechanism of DNA transfer in transformation?

A) Direct contact between two bacterial cells
B) Uptake of free DNA from the environment
C) Viral-mediated transfer of DNA
D) Plasmid transfer through a pilus

Answer 39

B) Uptake of free DNA from the environment

Question 40

Which of the following best describes transduction?

A) The transfer of DNA through direct contact between bacteria.
B) The uptake of free DNA by a bacterial cell.
C) The transfer of DNA via a bacteriophage.
D) The replication of plasmids within a single bacterium.

Answer 40

c)

Question 41

What role does the pilus play in bacterial conjugation?

A) It helps bacteria take up free DNA from the environment.
B) It acts as a protective barrier against viruses.
C) It forms a connection between donor and recipient bacteria for DNA transfer.
D) It is involved in the replication of bacterial DNA.

Answer 41

c)

Question 42

Which mechanism of gene transfer is most commonly associated with the spread of antibiotic resistance genes among bacteria?

A) Transformation
B) Transduction
C) Conjugation
D) All of the above

Answer 42

C) conjugation

Question 43

Which method of gene transformation involves applying an electric current to create pores in the cell membrane?

A) CaCl₂ Treatment
B) Lipofection
C) Electroporation
D) Microinjection

Answer 43

c) electroporation

Question 44

Which transformation method is considered to have the highest efficiency for introducing DNA into cells?

A) CaCl₂ Treatment
B) Electroporation
C) Lipofection
D) Heat-Shock Method

Answer 44

b)

Question 45

Which of the following methods is typically NOT used for transforming bacterial cells?

A) Lipofection
B) CaCl₂ Treatment
C) Microinjection
D) Ballistic gene gun
E) all of the above

Answer 45

e) all of the above

Electroporation is commonly used