Q.1 What is the main purpose of Polymerase Chain Reaction (PCR)?
To cut DNA into smaller pieces
To amplify a specific segment of DNA
To measure the amount of proteins in a cell
To change the shape of DNA molecules
Explanation - PCR is a technique used to create millions of copies of a specific DNA sequence, making it easier to study or analyze.
Correct answer is: To amplify a specific segment of DNA
Q.2 Which of the following is NOT a component of a standard PCR reaction?
DNA polymerase
Primers
RNA
dNTPs
Explanation - PCR uses DNA polymerase, primers, dNTPs, and a template DNA; RNA is not a standard component.
Correct answer is: RNA
Q.3 What role do primers play in PCR?
They provide the energy for the reaction
They guide the DNA polymerase to the start and end of the target sequence
They are the enzyme that synthesizes DNA
They are the building blocks of DNA
Explanation - Primers are short DNA sequences that anneal to the template and define the region to be amplified.
Correct answer is: They guide the DNA polymerase to the start and end of the target sequence
Q.4 In the PCR cycle, what temperature is used for denaturation?
94–98 °C
50–65 °C
70–80 °C
30–40 °C
Explanation - Denaturation melts the double‑stranded DNA, separating it into single strands, typically at ~95 °C.
Correct answer is: 94–98 °C
Q.5 Which enzyme is most commonly used in PCR?
Taq DNA polymerase
DNA ligase
RNA polymerase
Reverse transcriptase
Explanation - Taq polymerase is heat‑stable and can withstand the high temperatures of PCR cycles.
Correct answer is: Taq DNA polymerase
Q.6 How many cycles are typically performed in a PCR experiment?
2–5
10–20
20–40
80–100
Explanation - PCR usually involves 20–40 cycles to exponentially amplify the target DNA.
Correct answer is: 20–40
Q.7 What is the purpose of the annealing step in PCR?
To melt the DNA strands
To allow primers to bind to the template
To extend the new DNA strand
To purify the reaction mixture
Explanation - Annealing occurs at a lower temperature where primers can hybridize to complementary sequences on the DNA template.
Correct answer is: To allow primers to bind to the template
Q.8 During which step of PCR is the new DNA strand synthesized?
Denaturation
Annealing
Extension
Elution
Explanation - Extension (or synthesis) takes place at around 72 °C where DNA polymerase adds nucleotides to the primer.
Correct answer is: Extension
Q.9 Which of these is a common source of PCR failure?
Using a high‑fidelity polymerase
Contamination with foreign DNA
Adding too many primers
Running the reaction for too many cycles
Explanation - Foreign DNA can be amplified unintentionally, leading to incorrect results; contamination is a major issue in PCR.
Correct answer is: Contamination with foreign DNA
Q.10 What is a 'hot‑start' PCR polymerase?
An enzyme that starts the reaction at low temperatures
A polymerase that is activated only at high temperatures
A polymerase that works only with RNA templates
An enzyme that stops the reaction once completed
Explanation - Hot‑start enzymes are inactive at room temperature and become active after the initial high‑temperature activation step, reducing non‑specific amplification.
Correct answer is: A polymerase that is activated only at high temperatures
Q.11 In PCR, what is the 'template DNA'?
The DNA that will be amplified
The primers used in the reaction
The polymerase enzyme
The nucleotides added during synthesis
Explanation - The template DNA contains the target sequence that is copied during PCR.
Correct answer is: The DNA that will be amplified
Q.12 Which type of PCR can detect RNA viruses directly?
Standard PCR
Nested PCR
Real‑time PCR
Reverse‑transcription PCR (RT‑PCR)
Explanation - RT‑PCR first reverse‑transcribes RNA into cDNA, then amplifies the cDNA using PCR.
Correct answer is: Reverse‑transcription PCR (RT‑PCR)
Q.13 What is the function of dNTPs in a PCR reaction?
They act as primers
They serve as the building blocks for new DNA strands
They stabilize the polymerase
They inhibit nonspecific binding
Explanation - dNTPs (deoxynucleotide triphosphates) are the substrates that DNA polymerase uses to build the new DNA strand.
Correct answer is: They serve as the building blocks for new DNA strands
Q.14 Which factor most directly influences the annealing temperature of primers?
The GC content of the primer
The length of the primer
Both A and B
The type of polymerase used
Explanation - Annealing temperature is determined by primer length and GC content, which affect melting temperature.
Correct answer is: Both A and B
Q.15 Which of the following best describes the exponential phase of PCR amplification?
The amount of product increases linearly
The amount of product doubles each cycle
The amount of product stays constant
The amount of product decreases each cycle
Explanation - During the exponential phase, each cycle theoretically doubles the amount of DNA, leading to exponential growth.
Correct answer is: The amount of product doubles each cycle
Q.16 What is a major advantage of real‑time PCR over conventional PCR?
It uses fewer reagents
It provides quantitative data in real time
It eliminates the need for primers
It can be performed at room temperature
Explanation - Real‑time PCR monitors fluorescence during amplification, allowing quantification of the initial DNA amount.
Correct answer is: It provides quantitative data in real time
Q.17 Which fluorescent dye binds to double‑stranded DNA in real‑time PCR?
SYBR Green
DAPI
Ethidium bromide
Alexa Fluor
Explanation - SYBR Green intercalates into double‑stranded DNA and fluoresces, enabling detection in real‑time PCR.
Correct answer is: SYBR Green
Q.18 Which technique is used to confirm the size of the PCR product?
SDS‑PAGE
Thin‑layer chromatography
Gel electrophoresis
Western blotting
Explanation - Gel electrophoresis separates DNA fragments by size, allowing verification of expected PCR product size.
Correct answer is: Gel electrophoresis
Q.19 In nested PCR, why are two rounds of amplification performed?
To increase yield dramatically
To improve specificity by using two sets of primers
To reduce the total reaction time
To allow detection of RNA templates
Explanation - Nested PCR uses an outer primer pair then a second inner pair, reducing nonspecific amplification.
Correct answer is: To improve specificity by using two sets of primers
Q.20 Which of the following is NOT a typical application of PCR?
Genotyping individuals
Detecting infectious disease
Measuring protein concentration
Forensic DNA analysis
Explanation - PCR amplifies DNA, not proteins; protein concentration is measured by other techniques.
Correct answer is: Measuring protein concentration
Q.21 What does the term 'template switching' refer to in the context of PCR?
When primers switch between different DNA strands
When the polymerase jumps from one template to another
When the PCR tube is moved during the reaction
When the temperature cycle is altered mid‑run
Explanation - Template switching can lead to chimeric products and is often a concern in high‑throughput sequencing PCR.
Correct answer is: When the polymerase jumps from one template to another
Q.22 Which of the following is a characteristic of a 'touchdown' PCR protocol?
The annealing temperature is increased gradually each cycle
The annealing temperature is decreased gradually each cycle
The extension time is shortened each cycle
The number of cycles is halved after a set point
Explanation - Touchdown PCR starts with a high annealing temperature to enhance specificity, then lowers it to improve yield.
Correct answer is: The annealing temperature is decreased gradually each cycle
Q.23 Which component is responsible for preventing the primer from binding nonspecifically?
MgCl₂
dNTPs
BSA (bovine serum albumin)
The specificity of the primer sequence
Explanation - Proper primer design—matching target sequence and avoiding complementarity elsewhere—is key to preventing nonspecific binding.
Correct answer is: The specificity of the primer sequence
Q.24 What is the main limitation of standard PCR in quantifying nucleic acid?
It cannot amplify DNA
It requires a fluorescent probe
Its output is only qualitative after a certain point
It takes too long to perform
Explanation - Standard PCR plateaus after many cycles; thus, it does not provide accurate quantitative data beyond the exponential phase.
Correct answer is: Its output is only qualitative after a certain point
Q.25 What does the term 'cycling' refer to in PCR?
The repeated heating and cooling of the reaction mix
The continuous mixing of the reaction vessel
The creation of multiple copies of the same DNA strand
The movement of DNA fragments through a gel
Explanation - Cycling refers to the repetitive thermal steps of denaturation, annealing, and extension.
Correct answer is: The repeated heating and cooling of the reaction mix
Q.26 What is the typical size range of a PCR amplicon for most applications?
50–200 bp
200–1500 bp
1500–5000 bp
5 kb–10 kb
Explanation - Most PCR assays produce products between 200 and 1500 base pairs, balancing yield and ease of analysis.
Correct answer is: 200–1500 bp
Q.27 Which additive is commonly used to improve PCR performance with GC‑rich templates?
DMSO (dimethyl sulfoxide)
BSA (bovine serum albumin)
Glycerol
Tris-HCl
Explanation - DMSO helps destabilize GC‑rich secondary structures, improving amplification of GC‑rich regions.
Correct answer is: DMSO (dimethyl sulfoxide)
Q.28 Which of the following is a key feature of multiplex PCR?
It uses a single primer pair to amplify multiple targets
It amplifies a single target in many different reactions
It uses different polymerases for each target
It allows simultaneous amplification of multiple targets in one reaction
Explanation - Multiplex PCR uses several primer pairs in one tube to detect multiple DNA sequences at once.
Correct answer is: It allows simultaneous amplification of multiple targets in one reaction
Q.29 What does the 'lag phase' refer to in PCR?
The period before the first cycle begins
The initial cycles where product accumulation is minimal
The final cycles where the reaction slows down
The period of primer synthesis
Explanation - At the start of PCR, the amount of DNA is too low for detection; this is the lag phase.
Correct answer is: The initial cycles where product accumulation is minimal
Q.30 Which of the following best describes the 'exponential phase' in PCR?
The product amount increases linearly
The product amount doubles each cycle until limiting resources
The reaction stops due to enzyme denaturation
The reaction proceeds at a constant rate
Explanation - During the exponential phase, each cycle ideally doubles the DNA, until reagents become limiting.
Correct answer is: The product amount doubles each cycle until limiting resources
Q.31 What is a 'primer-dimer'?
A complex of a primer and a polymerase
A small DNA fragment formed when primers anneal to each other
A large DNA molecule formed from multiple PCR products
A type of fluorescent probe
Explanation - Primer-dimers are nonspecific products formed when primers bind to each other instead of the target.
Correct answer is: A small DNA fragment formed when primers anneal to each other
Q.32 Which type of PCR is most suitable for detecting point mutations?
Standard PCR
Allele‑specific PCR
Nested PCR
Touchdown PCR
Explanation - Allele‑specific PCR uses primers that match specific mutations to differentiate alleles.
Correct answer is: Allele‑specific PCR
Q.33 Which component of PCR is required to provide the energy for DNA synthesis?
Primers
dNTPs
Mg²⁺ ions
Polymerase
Explanation - dNTPs donate phosphate groups that form the backbone of new DNA strands.
Correct answer is: dNTPs
Q.34 What is the most common cause of non‑specific amplification?
Too high annealing temperature
High primer concentration
Inadequate magnesium concentration
Low extension time
Explanation - Excess primer increases chances of off‑target binding, causing non‑specific products.
Correct answer is: High primer concentration
Q.35 Which of the following best describes a 'hot‑start' Taq polymerase?
An enzyme that is inactive at low temperatures and becomes active after a high‑temperature step
An enzyme that remains active throughout the reaction without any activation step
An enzyme that works only with RNA templates
An enzyme that needs a cold activation step
Explanation - Hot‑start enzymes prevent nonspecific amplification at lower temperatures.
Correct answer is: An enzyme that is inactive at low temperatures and becomes active after a high‑temperature step
Q.36 What is the purpose of adding BSA to a PCR reaction?
To stabilize the polymerase
To inhibit nonspecific binding
To act as a primer
To increase the melting temperature of DNA
Explanation - BSA helps to stabilize enzymes and can bind inhibitors, improving PCR efficiency.
Correct answer is: To stabilize the polymerase
Q.37 Which of the following is an advantage of using a high‑fidelity DNA polymerase over Taq?
Lower error rate during amplification
Higher processivity
Lower cost
It works at lower temperatures
Explanation - High‑fidelity polymerases possess proofreading activity, reducing mutations in the amplified product.
Correct answer is: Lower error rate during amplification
Q.38 In real‑time PCR, what does the 'Ct value' represent?
The cycle at which fluorescence reaches a threshold
The total number of cycles
The temperature of the reaction
The concentration of MgCl₂
Explanation - Ct (cycle threshold) is the cycle number where fluorescence exceeds background, inversely related to starting template quantity.
Correct answer is: The cycle at which fluorescence reaches a threshold
Q.39 Which of the following can be used as a reference gene in quantitative PCR?
HIV‑1
β‑actin
Ribosomal RNA
Hemagglutinin
Explanation - β‑actin is a housekeeping gene often used as an internal control in qPCR.
Correct answer is: β‑actin
Q.40 What is the main reason for including a 'no‑template control' in a PCR experiment?
To confirm the reaction works
To check for contamination or primer-dimer formation
To determine the optimal Mg²⁺ concentration
To calibrate the thermocycler
Explanation - The control ensures no DNA is present; any amplification indicates contamination.
Correct answer is: To check for contamination or primer-dimer formation
Q.41 Which of the following best describes the 'melting curve' analysis?
A method to determine the GC content of a DNA fragment
A way to visualize the temperature at which DNA duplexes dissociate
A technique to separate proteins by size
A method to amplify DNA in a single step
Explanation - Melting curves plot fluorescence versus temperature, showing the melting temperature of PCR products.
Correct answer is: A way to visualize the temperature at which DNA duplexes dissociate
Q.42 What is the role of MgCl₂ in PCR?
It acts as a cofactor for polymerase
It prevents primer binding
It provides a buffer for pH
It stabilizes the template DNA
Explanation - Mg²⁺ ions are essential for polymerase activity and influence primer binding and specificity.
Correct answer is: It acts as a cofactor for polymerase
Q.43 Which step in PCR is most likely to lead to incomplete extension?
Denaturation
Annealing
Extension
Cycling
Explanation - If extension time is too short, polymerase may not fully synthesize the target strand.
Correct answer is: Extension
Q.44 Why is it important to keep the PCR reaction mixture in the cold before cycling?
To activate the polymerase
To prevent primer dimer formation
To keep the enzyme stable until the cycle starts
To reduce the melting temperature of DNA
Explanation - Cold storage helps maintain enzyme activity before the high‑temperature activation step.
Correct answer is: To keep the enzyme stable until the cycle starts
Q.45 What is a common use of PCR in forensic science?
To identify DNA fingerprints
To sequence proteins
To analyze blood types
To detect viruses
Explanation - PCR amplifies specific DNA regions used for DNA profiling in forensic investigations.
Correct answer is: To identify DNA fingerprints
Q.46 Which of the following is NOT a typical source of DNA for PCR?
Saliva swab
Blood sample
Protein extract
Bacterial culture
Explanation - PCR requires DNA or cDNA; proteins do not serve as templates.
Correct answer is: Protein extract
Q.47 What does the term 'amplicon' refer to?
The DNA polymerase used
The primer pair
The amplified DNA fragment
The template DNA
Explanation - An amplicon is the product of PCR amplification.
Correct answer is: The amplified DNA fragment
Q.48 Which type of PCR is designed to amplify DNA from a single cell?
Whole-genome amplification (WGA)
Quantitative PCR
Allele‑specific PCR
Touchdown PCR
Explanation - WGA methods amplify the entire genome from minute amounts, such as a single cell.
Correct answer is: Whole-genome amplification (WGA)
Q.49 Which of the following is a limitation of nested PCR?
Requires fewer cycles
High risk of contamination due to two rounds of amplification
Lower specificity
Cannot detect mutations
Explanation - Nested PCR involves multiple steps, increasing the chance of contaminant DNA entering the reaction.
Correct answer is: High risk of contamination due to two rounds of amplification
Q.50 Which of the following best explains why PCR products are typically double‑stranded?
Primers bind to single‑stranded DNA only
DNA polymerase copies both strands during each cycle
The reaction uses RNA as a template
Primers are designed to bind only one strand
Explanation - During extension, polymerase synthesizes a complementary strand, resulting in two double‑stranded copies.
Correct answer is: DNA polymerase copies both strands during each cycle
Q.51 In a PCR experiment, which parameter is most directly related to primer specificity?
The primer length
The GC content of the primer
Both A and B
The enzyme concentration
Explanation - Primer specificity depends on length and GC content, affecting melting temperature and binding.
Correct answer is: Both A and B
Q.52 What is the primary reason for adding a 'stop' step at the end of PCR?
To inactivate the polymerase
To prevent the polymerase from continuing to synthesize DNA
To allow the product to settle
To change the temperature of the tube
Explanation - A final hold step allows the reaction to stabilize and the polymerase to cease activity.
Correct answer is: To prevent the polymerase from continuing to synthesize DNA
Q.53 Which of the following best describes 'PCR inhibitors'?
Substances that enhance PCR efficiency
Compounds that prevent the amplification of DNA
Enzymes that break down DNA
Primers that bind nonspecifically
Explanation - Inhibitors such as hemoglobin or heparin can interfere with enzyme activity or binding, reducing PCR success.
Correct answer is: Compounds that prevent the amplification of DNA
Q.54 Which of the following is a typical use of PCR in plant genetics?
Measuring chlorophyll content
Sequencing mitochondrial DNA only
Detecting specific gene alleles associated with traits
Analyzing plant hormone levels
Explanation - PCR allows quick detection of allelic variations linked to desirable traits in plant breeding.
Correct answer is: Detecting specific gene alleles associated with traits
Q.55 Which component is typically added to PCR to reduce primer-dimer formation?
High MgCl₂
Low primer concentration
High primer concentration
Increased dNTPs
Explanation - Reducing primer concentration lowers chances of primers binding to each other rather than the template.
Correct answer is: Low primer concentration
Q.56 Which of the following best describes the 'exponential phase' of PCR?
The amount of product increases linearly
The product amount doubles each cycle
The product amount stays constant
The product amount decreases each cycle
Explanation - During the exponential phase, each cycle ideally doubles the DNA amount, leading to exponential growth.
Correct answer is: The product amount doubles each cycle
Q.57 Which of the following best explains why PCR requires a DNA polymerase that is heat‑stable?
Because the reaction is performed at low temperatures
Because the reaction cycles include high temperatures that denature regular enzymes
Because heat‑stable polymerases are cheaper
Because heat‑stable polymerases produce higher yields
Explanation - During denaturation, temperatures rise to ~95 °C; only heat‑stable enzymes survive to synthesize DNA.
Correct answer is: Because the reaction cycles include high temperatures that denature regular enzymes
Q.58 What is the primary advantage of using a 'hot‑start' polymerase for forensic DNA analysis?
It allows amplification at lower temperatures
It reduces nonspecific amplification, improving the reliability of DNA fingerprints
It speeds up the cycling process
It reduces the need for primers
Explanation - Hot‑start polymerases prevent nonspecific extension before the first denaturation, increasing data accuracy.
Correct answer is: It reduces nonspecific amplification, improving the reliability of DNA fingerprints
Q.59 Which of the following is a typical application of PCR in clinical diagnostics?
Measuring cholesterol levels
Identifying bacterial pathogens
Determining blood type
Assessing bone density
Explanation - PCR can quickly detect bacterial DNA, aiding in timely diagnosis of infections.
Correct answer is: Identifying bacterial pathogens
Q.60 Which of the following best describes the 'template switching' phenomenon in PCR?
The polymerase jumps from one template to another during synthesis
Primers switch between forward and reverse strands
The temperature cycle switches from denaturation to annealing
The reaction volume switches between tubes
Explanation - Template switching can create chimeric DNA products, affecting downstream analysis.
Correct answer is: The polymerase jumps from one template to another during synthesis
Q.61 Which of the following is NOT a component of the PCR mixture?
Nuclease-free water
Polymerase
Primer
Reverse transcriptase
Explanation - Reverse transcriptase is used only in RT‑PCR to convert RNA to cDNA; standard PCR does not need it.
Correct answer is: Reverse transcriptase
Q.62 What is the typical maximum length of a PCR product when using standard Taq polymerase?
500 bp
2 kb
5 kb
10 kb
Explanation - Standard Taq can reliably amplify up to ~2 kb; longer fragments require specialized enzymes or protocols.
Correct answer is: 2 kb
Q.63 Which of the following best describes the function of a 'no‑template control' (NTC) in a PCR run?
To ensure the polymerase is active
To detect contamination or nonspecific amplification
To calibrate the thermocycler
To determine the optimal primer concentration
Explanation - NTC contains all PCR reagents except DNA template; any amplification indicates contamination.
Correct answer is: To detect contamination or nonspecific amplification
Q.64 What is the primary advantage of using 'touchdown PCR'?
It reduces the number of cycles needed
It improves specificity by starting with a high annealing temperature
It eliminates the need for primers
It allows amplification of RNA directly
Explanation - Touchdown PCR begins with a higher annealing temperature to reduce nonspecific binding, then gradually lowers it.
Correct answer is: It improves specificity by starting with a high annealing temperature
Q.65 Which of the following best explains why DNA polymerase requires Mg²⁺ for activity?
Mg²⁺ acts as a cofactor, stabilizing the enzyme and aiding dNTP incorporation
Mg²⁺ provides the necessary heat for the reaction
Mg²⁺ is a template for new DNA strands
Mg²⁺ prevents primer-dimer formation
Explanation - Mg²⁺ ions stabilize the negative charges on dNTPs and help form the active site of the polymerase.
Correct answer is: Mg²⁺ acts as a cofactor, stabilizing the enzyme and aiding dNTP incorporation
Q.66 Which type of PCR uses a fluorescent probe that only emits light when it is hydrolyzed?
Standard PCR
Nested PCR
Real‑time PCR (probe-based)
Touchdown PCR
Explanation - Probe-based qPCR uses labeled probes that are cleaved during amplification, emitting fluorescence.
Correct answer is: Real‑time PCR (probe-based)
Q.67 What does the abbreviation 'qPCR' stand for?
Quantitative PCR
Qualitative PCR
Quick PCR
Quadruplex PCR
Explanation - qPCR (quantitative PCR) is another term for real‑time PCR, measuring DNA amounts during amplification.
Correct answer is: Quantitative PCR
Q.68 What is the main function of the 'extension temperature' setting in a PCR protocol?
To melt the DNA strands
To allow polymerase to synthesize the new strand
To enable primer annealing
To deactivate the polymerase
Explanation - The extension step temperature (≈72 °C) optimizes polymerase activity for strand synthesis.
Correct answer is: To allow polymerase to synthesize the new strand
Q.69 Why is it important to use high‑purity reagents in PCR?
To ensure the reaction runs faster
To prevent contamination and nonspecific amplification
To lower the temperature needed for denaturation
To increase primer length
Explanation - Impurities or contaminants can inhibit enzymes or produce false positives, compromising results.
Correct answer is: To prevent contamination and nonspecific amplification
Q.70 Which of the following is a typical application of PCR in agriculture?
Sequencing the entire crop genome
Measuring soil pH
Detecting GMO presence
Estimating crop yield
Explanation - PCR can amplify specific transgene sequences to confirm the presence of genetically modified organisms.
Correct answer is: Detecting GMO presence
Q.71 What is the most common purpose of including a 'positive control' in a PCR experiment?
To confirm the reaction can produce an amplification product
To measure the temperature accurately
To ensure no contamination is present
To determine the optimal number of cycles
Explanation - Positive controls contain known DNA to verify that the PCR reagents and conditions work correctly.
Correct answer is: To confirm the reaction can produce an amplification product
Q.72 Which of the following best describes the 'annealing temperature' of a PCR primer?
The temperature at which the polymerase becomes active
The temperature at which the primer binds to the template
The temperature at which DNA melts
The temperature at which the reaction is held at the end
Explanation - Annealing temperature is chosen based on primer melting temperature for optimal binding.
Correct answer is: The temperature at which the primer binds to the template
Q.73 In which scenario would you use 'high‑fidelity PCR'?
When you need maximum amplification speed
When accurate sequencing of the product is required
When working with very low template amounts
When you want to reduce reagent cost
Explanation - High‑fidelity polymerases have proofreading activity, reducing errors for sequencing applications.
Correct answer is: When accurate sequencing of the product is required
Q.74 What is a 'primer set' in PCR?
Two primers that bind to opposite strands of the DNA
One primer that initiates synthesis
A set of fluorescent dyes
The polymerase and buffer mixture
Explanation - A primer set includes a forward and reverse primer that flank the target region.
Correct answer is: Two primers that bind to opposite strands of the DNA
Q.75 Which of the following is a common method to check for PCR contamination?
Running the reaction at a higher temperature
Adding more primer
Using a negative control
Increasing the number of cycles
Explanation - A negative control contains no template DNA; any amplification indicates contamination.
Correct answer is: Using a negative control
Q.76 Why is it necessary to use 'deoxy' nucleotides (dNTPs) in PCR?
To make the DNA more stable
To provide the building blocks for new DNA strands
To act as primers
To inactivate the polymerase
Explanation - dNTPs are the substrates that DNA polymerase uses to synthesize the new DNA strand.
Correct answer is: To provide the building blocks for new DNA strands
Q.77 Which of the following best explains the 'exponential amplification' observed in PCR?
Each cycle results in a linear increase in product
Each cycle results in the product doubling
The product decreases over time
The product remains constant
Explanation - In exponential amplification, each cycle theoretically doubles the number of DNA molecules.
Correct answer is: Each cycle results in the product doubling
Q.78 In which scenario would you prefer 'touchdown PCR' over standard PCR?
When the target region has low GC content
When high specificity is needed
When using a high‑fidelity polymerase
When amplifying RNA templates
Explanation - Touchdown PCR starts with a high annealing temperature to reduce nonspecific binding, increasing specificity.
Correct answer is: When high specificity is needed
Q.79 Which of the following is an application of PCR in forensic science?
Analyzing blood sugar levels
DNA fingerprinting
Measuring blood pressure
Assessing bone density
Explanation - PCR amplifies DNA regions used for forensic profiling and identification.
Correct answer is: DNA fingerprinting
Q.80 What is the main difference between conventional PCR and real‑time PCR?
Real‑time PCR uses a fluorescent probe and can quantify DNA in real time
Conventional PCR is faster
Real‑time PCR requires a different polymerase
Conventional PCR uses RNA templates only
Explanation - Real‑time PCR monitors fluorescence to quantify DNA during amplification, while conventional PCR is qualitative.
Correct answer is: Real‑time PCR uses a fluorescent probe and can quantify DNA in real time
Q.81 Which component of PCR is responsible for adding new nucleotides to the growing DNA strand?
Primers
DNA polymerase
dNTPs
MgCl₂
Explanation - DNA polymerase catalyzes the formation of phosphodiester bonds to extend the DNA strand.
Correct answer is: DNA polymerase
Q.82 What is a 'hot‑start' polymerase and why is it used?
An enzyme that is inactive until heated, preventing nonspecific amplification
An enzyme that works at low temperatures only
An enzyme that is inactivated after each cycle
An enzyme that needs no Mg²⁺
Explanation - Hot‑start polymerases prevent activity at room temperature, reducing primer-dimers and off‑target amplification.
Correct answer is: An enzyme that is inactive until heated, preventing nonspecific amplification
Q.83 Which of the following best describes the role of a 'template DNA' in PCR?
It is the DNA that is copied during the reaction
It is the polymerase enzyme
It is the primer sequence
It is the fluorescent dye
Explanation - Template DNA contains the sequence to be amplified.
Correct answer is: It is the DNA that is copied during the reaction
Q.84 What does the term 'primer-dimer' refer to?
Two primers annealing to each other instead of the template
A polymerase that has dimethyl sulfoxide bound
A DNA fragment that is too small
A type of fluorescent probe
Explanation - Primer-dimers form when primers bind to each other, producing nonspecific small fragments.
Correct answer is: Two primers annealing to each other instead of the template
Q.85 In a PCR experiment, what would cause a 'no‑product' result?
Insufficient primer concentration
Excess of MgCl₂
High template DNA concentration
Too many cycles
Explanation - Low primer concentration can prevent effective binding and subsequent amplification.
Correct answer is: Insufficient primer concentration
Q.86 Which of the following is an advantage of multiplex PCR?
It amplifies only one target
It requires no primers
It can detect multiple targets in one reaction
It eliminates the need for a thermocycler
Explanation - Multiplex PCR uses several primer pairs in a single tube to amplify several sequences simultaneously.
Correct answer is: It can detect multiple targets in one reaction
Q.87 Which of the following best explains why PCR requires a thermocycler?
To mix the reagents thoroughly
To apply precise temperature changes for denaturation, annealing, and extension
To keep the reaction at a constant temperature
To sterilize the reaction mixture
Explanation - PCR cycles require controlled heating and cooling at specific temperatures for each step.
Correct answer is: To apply precise temperature changes for denaturation, annealing, and extension
Q.88 What is the main benefit of using a 'touchdown PCR' approach?
It reduces the need for a thermocycler
It improves primer specificity by starting with a higher annealing temperature
It shortens the reaction time
It eliminates the use of polymerase
Explanation - Higher initial annealing temperatures help reduce nonspecific primer binding.
Correct answer is: It improves primer specificity by starting with a higher annealing temperature
Q.89 In PCR, what is a 'lag phase'?
The initial cycles where product accumulation is minimal
The stage where polymerase activity stops
The final cycles before the reaction ends
The time between each cycle
Explanation - The lag phase occurs when product amount is too low to detect, before exponential growth begins.
Correct answer is: The initial cycles where product accumulation is minimal
Q.90 Which of the following best describes the function of the 'extension temperature' setting in PCR?
It determines the temperature for DNA denaturation
It allows polymerase to synthesize the new strand
It sets the temperature for primer annealing
It activates the polymerase
Explanation - The extension step temperature (usually ~72 °C) optimizes polymerase activity for DNA synthesis.
Correct answer is: It allows polymerase to synthesize the new strand
Q.91 Which of the following is a typical application of PCR in plant genetics?
Measuring chlorophyll content
Sequencing mitochondrial DNA only
Detecting specific gene alleles associated with traits
Analyzing plant hormone levels
Explanation - PCR enables rapid identification of alleles linked to desirable traits in breeding programs.
Correct answer is: Detecting specific gene alleles associated with traits
Q.92 What is the typical length range of a PCR amplicon for most applications?
50–200 bp
200–1500 bp
1500–5000 bp
5 kb–10 kb
Explanation - Most PCR assays produce products between 200 and 1500 base pairs, balancing yield and analysis ease.
Correct answer is: 200–1500 bp
Q.93 Which component of PCR is essential for the enzyme to attach to the DNA template?
Primers
dNTPs
MgCl₂
Polymerase
Explanation - Primers hybridize to the template, providing a free 3’ end for polymerase to extend.
Correct answer is: Primers
Q.94 Which of the following is a characteristic of a high‑fidelity DNA polymerase?
It has proofreading activity that reduces errors
It works best at room temperature
It has no need for Mg²⁺
It cannot amplify GC‑rich regions
Explanation - High‑fidelity polymerases possess 3’→5’ exonuclease activity to correct misincorporations.
Correct answer is: It has proofreading activity that reduces errors
Q.95 What is the primary purpose of adding BSA to a PCR reaction?
To stabilize the polymerase
To inhibit primer binding
To act as a primer
To increase the melting temperature of DNA
Explanation - BSA helps stabilize enzymes and can bind inhibitors, improving PCR efficiency.
Correct answer is: To stabilize the polymerase
Q.96 Which of the following best describes the 'exponential phase' in PCR?
The product amount doubles each cycle
The product amount increases linearly
The product amount stays constant
The product amount decreases each cycle
Explanation - During the exponential phase, each cycle ideally doubles the DNA amount, leading to exponential growth.
Correct answer is: The product amount doubles each cycle
Q.97 In PCR, which step is most likely to cause nonspecific amplification?
High annealing temperature
Low primer concentration
High extension time
High magnesium concentration
Explanation - Excess Mg²⁺ can lower primer specificity, leading to off‑target amplification.
Correct answer is: High magnesium concentration
Q.98 Which of the following is NOT a typical component of a PCR reaction mix?
DNA polymerase
Primers
RNA
dNTPs
Explanation - PCR amplifies DNA; RNA is not a standard component unless performing RT‑PCR.
Correct answer is: RNA
Q.99 Which of the following best explains why PCR requires a DNA polymerase that is heat‑stable?
Because the reaction cycles include high temperatures that denature regular enzymes
Because heat‑stable polymerases are cheaper
Because they produce higher yields
Because they do not need Mg²⁺
Explanation - During denaturation, temperatures rise to ~95 °C; only heat‑stable enzymes survive.
Correct answer is: Because the reaction cycles include high temperatures that denature regular enzymes