PCR and DNA Sequencing: A Comprehensive Guide for Medical Students

Question 1

Which of the following is NOT a crucial component for a PCR reaction?

Accepted Answer

DNA Ligase

Answer

Template DNA

Answer

Primers

Answer

DNA Polymerase

Question 2

What is the primary purpose of the initial denaturation step in PCR?

Accepted Answer

To melt the DNA strands

Answer

To extend the DNA strands

Answer

To anneal the primers

Answer

To amplify the DNA fragments

Question 3

The key advantage of next-generation sequencing over Sanger sequencing is:

Accepted Answer

Higher throughput

Answer

Longer read lengths

Answer

Lower cost

Answer

Increased accuracy

Question 4

The purpose of using fluorescently labeled nucleotides in Sanger sequencing is to:

Accepted Answer

Differentiate between different nucleotides

Answer

Prevent hairpin loop formation

Answer

Increase the sensitivity

Answer

Reduce sequencing errors

Question 5

True/False: Cluster generation is an integral technique used in Next-generation sequencing.

Accepted Answer

True

Answer

False

Question 6

Which component of the PCR reaction is responsible for synthesizing new DNA strands complementary to the template DNA?

Accepted Answer

Taq polymerase

Answer

DNA template

Answer

dNTPs

Answer

Reverse transcriptase

Question 7

What is the primary purpose of the denaturation step in PCR?

Accepted Answer

To separate the DNA strands and make the template accessible for primer annealing.

Answer

To extend the DNA primers.

Answer

To amplify the DNA product.

Answer

To anneal the primers to the template.

Question 8

Which of the following sequencing methods utilizes capillary electrophoresis to separate DNA fragments based on their size?

Accepted Answer

Sanger sequencing

Answer

Next-generation sequencing

Answer

Pyrosequencing

Answer

Nanopore sequencing

Question 9

What is the main advantage of next-generation sequencing (NGS) over traditional Sanger sequencing?

Accepted Answer

Higher throughput, allowing for the sequencing of larger amounts of DNA in a shorter time.

Answer

Lower cost, making it more accessible for researchers.

Answer

Longer read lengths, providing more comprehensive sequence information.

Answer

Increased specificity, reducing the risk of sequencing errors.

Question 10

What is the role of reverse transcriptase in quantitative real-time PCR (qPCR)?

Accepted Answer

To convert RNA molecules into complementary DNA (cDNA) molecules.

Answer

To amplify the cDNA molecules.

Answer

To quantify the amplified product in real time.

Answer

To separate the DNA strands during PCR.

Question 11

What is the purpose of using a DNA ladder in DNA sequencing?

Accepted Answer

To determine the size of the DNA fragments generated during sequencing.

Answer

To identify specific DNA sequences based on their sequence complementarity.

Answer

To amplify the DNA product for downstream applications.

Answer

To separate the DNA strands during electrophoresis.

Question 12

In PCR, what is multiplexing and how does it facilitate high-throughput analysis?

Accepted Answer

Simultaneous amplification of multiple DNA targets in a single PCR reaction.

Answer

Increased specificity by eliminating non-specific amplifications.

Answer

Requirement for specialized instruments and reagents not used in standard PCR.

Answer

Exclusive applicability to Sanger sequencing.

Question 13

What is a major ethical concern surrounding the use of DNA sequencing in forensic investigations?

Accepted Answer

Potential invasion of privacy

Answer

Risk of false positive results

Answer

High cost of the technology

Question 14

In the context of diagnosing genetic diseases, how is PCR employed?

Accepted Answer

Detecting and identifying mutations in genes linked to genetic diseases

Answer

Establishing paternity or familial connections through DNA fingerprinting

Answer

Cloning genes for research and therapeutic applications

Answer

Amplifying DNA for forensic analysis and identification

Question 15

In PCR, what is the primary purpose of the annealing step?

Accepted Answer

Allowing primers to bind to the single-stranded DNA template

Answer

Separating the double-stranded DNA template into single strands

Answer

Extending the newly synthesized DNA strands

Answer

Amplifying the target DNA sequence exponentially

Question 16

Which enzyme is responsible for synthesizing new DNA strands during the elongation step of PCR?

Accepted Answer

DNA polymerase

Answer

RNA polymerase

Answer

Reverse transcriptase

Answer

Ligase

Question 17

In PCR, the purpose of the annealing step is to:

Accepted Answer

Allow primers to bind to the complementary sequences on the template DNA

Answer

Separate the PCR products by size

Answer

Denature the DNA strands

Answer

Extend the primers and synthesize new DNA strands

Question 18

In DNA sequencing, the function of fluorescently labeled dideoxynucleotides is to:

Accepted Answer

Indicate the end of DNA synthesis at specific positions

Answer

Amplify the PCR products

Answer

Separate the PCR products by size

Answer

Hybridize to the template DNA

Question 19

Among the listed sequencing technologies, which one involves single-molecule sequencing?

Accepted Answer

Nanopore sequencing

Answer

Sanger sequencing

Answer

Pyrosequencing

Answer

Illumina sequencing

Question 20

Degenerate primers are commonly used in PCR to:

Accepted Answer

Amplify regions of DNA with unknown sequences

Answer

Increase the specificity of amplification

Answer

Amplify highly conserved regions of DNA

Answer

Reduce the cost of PCR

Question 21

In PCR, the difference between a forward primer and a reverse primer is that the:

Accepted Answer

Forward primer binds to the 5' end of the target DNA, while the reverse primer binds to the 3' end.

Answer

Forward primer is longer than the reverse primer.

Answer

Reverse primer is labeled with a fluorescent dye, while the forward primer is not.

Answer

Forward primer is used in the first PCR cycle, while the reverse primer is used in subsequent cycles.

Question 22

In Sanger sequencing, what is the primary function of dideoxy nucleotides?

Accepted Answer

Terminating DNA strand elongation

Answer

Enhancing DNA stability

Answer

Labeling DNA fragments

Question 23

Which of the following is **NOT** a requirement for Polymerase Chain Reaction (PCR)?

Accepted Answer

Restriction Enzymes

Answer

Template DNA

Answer

Primers

Answer

DNA Polymerase

Question 24

During PCR, what is the purpose of the denaturation step?

Accepted Answer

To separate the DNA strands

Answer

To amplify the DNA template

Answer

To add primers to the DNA

Answer

To extend the DNA strands

Question 25

What is the primary role of primers in PCR?

Accepted Answer

To bind to specific regions of the DNA template

Answer

To extend the DNA strand

Answer

To denature the DNA

Answer

To cleave the DNA

Question 26

What is the ideal annealing temperature range for most PCR reactions?

Accepted Answer

45-55°C

Answer

37°C

Answer

60-70°C

Answer

75-85°C

Question 27

Which of the following is NOT required for PCR to function?

Accepted Answer

RNA primer

Answer

DNA template

Answer

DNA polymerase enzyme

Answer

Deoxynucleotide triphosphates (dNTPs)

Question 28

The primary role of the annealing temperature in PCR is to:

Accepted Answer

Allow primers to bind to the DNA template specifically

Answer

Separate the DNA strands by breaking hydrogen bonds

Answer

Extend the primers by adding nucleotides

Answer

Terminate the PCR reaction by inactivating the polymerase

Question 29

The principle behind Sanger sequencing involves:

Accepted Answer

Chain termination using dideoxyribonucleotide triphosphates (ddNTPs)

Answer

Detection of pyrophosphate release during nucleotide incorporation

Answer

Fluorescence-based monitoring of nucleotide addition

Answer

Mass spectrometry analysis of DNA fragments

Question 30

PCR has numerous applications in medical research. Which of the following is NOT a common use of PCR?

Accepted Answer

Protein synthesis

Answer

Diagnosis of infectious diseases

Answer

Cancer detection and monitoring

Answer

Non-invasive prenatal testing

Question 31

In PCR, Taq polymerase primarily serves to:

Accepted Answer

Synthesize new DNA strands complementary to the template

Answer

Unwind the DNA template

Answer

Bind primers to the DNA template

Answer

Stop the PCR reaction by cleaving the DNA strands

Question 32

During PCR, which enzyme is responsible for synthesizing the new DNA strands?

Accepted Answer

DNA polymerase

Answer

RNA polymerase

Answer

DNA ligase

Answer

Reverse transcriptase

Question 33

In PCR, what is the primary purpose of the denaturation step?

Accepted Answer

To separate the DNA strands

Answer

To amplify the DNA

Answer

To synthesize new DNA strands

Answer

To sequence the DNA

Question 34

Sanger sequencing is based on the principle of:

Accepted Answer

Chain termination

Answer

Pyrosequencing

Answer

Fluorescence resonance energy transfer

Answer

Nanopore sequencing

Question 35

One of the limitations associated with PCR is:

Accepted Answer

Amplification of non-specific products

Answer

High cost

Answer

Low sensitivity

Answer

Long reaction time

Question 36

What is the primary function of primers in PCR?

Accepted Answer

To define the region of DNA to be amplified

Answer

To synthesize new DNA strands

Answer

To denature the DNA

Answer

To sequence the DNA

Question 37

Forward and reverse primers differ in that:

Accepted Answer

Forward primers bind to the 5' end, while reverse primers bind to the 3' end of the target DNA

Answer

Reverse primers bind to the 5' end, while forward primers bind to the 3' end of the target DNA

Answer

They are both used to synthesize new DNA strands

Answer

They are both used to denature the DNA

Question 38

In PCR, the annealing temperature refers to:

Accepted Answer

The temperature at which the primers bind to the target DNA

Answer

The temperature at which the DNA is denatured

Answer

The temperature at which the new DNA strands are synthesized

Answer

The temperature at which the PCR reaction is stopped

Question 39

In PCR, which advantage makes Pfu polymerase preferable to Taq polymerase?

Accepted Answer

Higher accuracy (fidelity) in DNA synthesis

Answer

Faster DNA amplification speed

Answer

Greater thermostability at elevated temperatures

Question 40

In PCR, the primary purpose of the annealing step is to:

Accepted Answer

Allow primers to bind to the target DNA sequence

Answer

Extend the newly synthesized DNA strand

Answer

Separate the two DNA strands

Question 41

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

Accepted Answer

DNA polymerase

Answer

Reverse transcriptase

Answer

Helicase

Answer

Restriction enzyme

Question 42

The principle behind Sanger DNA sequencing is:

Accepted Answer

Chain-termination using dideoxynucleotides

Answer

Hybridization of labeled probes to a DNA sequence

Answer

Next-generation sequencing using high-throughput technologies

Answer

Electrophoresis of fluorescently labeled DNA fragments

Question 43

A major limitation of PCR is the potential for:

Accepted Answer

Amplifying non-specific products

Answer

Low sensitivity

Answer

High cost of reagents

Answer

Inability to sequence DNA fragments

Question 44

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

Accepted Answer

RNA polymerase

Answer

dNTPs

Answer

Primers

Answer

Taq polymerase

Question 45

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

Accepted Answer

To allow primers to hybridize to complementary sequences on the target DNA.

Answer

To extend the primers.

Answer

To denature the DNA template.

Question 46

Which of the following is a significant limitation of Sanger sequencing?

Accepted Answer

It has a limited read length, typically shorter than 1000 base pairs.

Answer

It is a time-consuming process.

Answer

It requires expensive equipment.

Question 47

What is the primary role of fluorescently labeled nucleotides in DNA sequencing?

Accepted Answer

To enable the detection and differentiation of DNA fragments of different lengths.

Answer

To amplify the DNA sample.

Answer

To terminate DNA synthesis.

Question 48

What is the fundamental difference between a sense and an antisense primer?

Accepted Answer

A sense primer is complementary to the coding strand, while an antisense primer is complementary to the non-coding strand of the DNA.

Answer

A sense primer is longer than an antisense primer.

Question 49

Which of the following factors does NOT influence the efficiency of PCR?

Accepted Answer

Primer length

Answer

DNA concentration

Answer

Temperature

Answer

Primer sequence

Question 50

What is the primary purpose of a thermal cycler in PCR?

Accepted Answer

To precisely control the temperature of the reaction.

Answer

To amplify DNA samples.

Answer

To separate DNA fragments by size.

Question 51

Which of the following is a key advantage of next-generation sequencing compared to Sanger sequencing?

Accepted Answer

The ability to sequence much longer DNA fragments.

Answer

It is less expensive.

Answer

It provides higher accuracy.

Question 52

What is the primary function of DNA ligase in PCR?

Accepted Answer

To covalently join DNA fragments.

Answer

To separate DNA fragments by size.

Answer

To denature the DNA template.

Answer

To extend the primers.