Unraveling DNA Sequencing

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Who coined the term 'plasmid'?

James Watson

Francis Crick

Joshua Lederberg (correct)

Rosalind Franklin

What is the main function of plasmids in bacteria?

To provide antibiotic resistance

To exchange genes with other bacteria

To carry genes that benefit the survival of the organism (correct)

To replicate independently of chromosomal DNA

What is the normal number of copies of plasmid found in a single cell called?

Cellular replication

DNA number

Plasmid count

Copy number (correct)

What is the purpose of phenol-chloroform extraction in DNA purification?

To remove proteins and other contaminants from the DNA Signup and view all the answers

Which of the following is a key application of PCR in forensic science?

Amplifying and sequencing DNA to reveal a person's identity Signup and view all the answers

What is the purpose of annealing in the PCR process?

To bind the primers to the DNA template Signup and view all the answers

What is the typical range for the GC content of PCR primers?

40-60% Signup and view all the answers

What is the purpose of real-time PCR?

To monitor the formation of products as the reaction proceeds Signup and view all the answers

Which detection method in real-time PCR involves the use of a fluorescent reporter molecule and a quencher molecule?

Detection Method 2 Signup and view all the answers

What is the purpose of melting curve analysis in real-time PCR?

To assess the dissociation characteristics of double-stranded DNA Signup and view all the answers

Which method involves the synthesis of single-stranded DNA using single-stranded RNA as a template?

Reverse Transcription Signup and view all the answers

Which type of virus uses RNA as its genetic material and replicates through reverse transcription?

Retroviruses Signup and view all the answers

Which enzyme is added to the pyrosequencing reaction mixture to catalyze the reaction of PPi with adenosine 5’ phosphosulfate (APS)?

ATP sulfurylase Signup and view all the answers

What is the limitation of pyrosequencing when it comes to detecting homopolymeric regions?

Homopolymeric regions longer than 10 bases cannot be resolved. Signup and view all the answers

What triggers the release of visible light in pyrosequencing?

The reaction of ATP with luciferin Signup and view all the answers

Which sequencing technology utilizes reversible terminators?

Illumina sequencing Signup and view all the answers

Which of the following is a disadvantage of using qPCR for COVID-19 testing?

Poorer communities cannot afford the qPCR equipment Signup and view all the answers

What is the purpose of a Ct value in real-time PCR?

To determine the number of cycles it took to detect a real signal Signup and view all the answers

What is the purpose of a housekeeping gene in relative quantification of gene expression?

To normalize all Ct values to a baseline experimental condition Signup and view all the answers

How is the fold change in gene expression calculated in qRT-PCR?

Fold change = 2-Δ(ΔCt) Signup and view all the answers

Which of the following is NOT a method for rupturing cellular walls to isolate DNA and RNA from living cells?

Treatment with a hypertonic solution Signup and view all the answers

What is the purpose of centrifugation in the separation of DNA by cesium chloride?

To form a stable, linear gradient of CsCl Signup and view all the answers

Which macromolecule has the highest density and sinks to the bottom of the tube during centrifugation in the separation of DNA by cesium chloride?

RNA Signup and view all the answers

What is the main purpose of extracting nucleic acids from living cells?

To isolate DNA and RNA from living cells Signup and view all the answers

Which of the following is a step involved in RNA-seq library construction?

Fragmentation of RNA Signup and view all the answers

What is the purpose of depleting rRNAs from the total RNA pool in RNA-seq?

To reduce the amount of sequencing reads dominated by rRNAs Signup and view all the answers

Which primer can be used to specifically select for mRNAs in RNA-seq?

Oligo(dT) primer Signup and view all the answers

What is the advantage of using random hexamers for first strand cDNA synthesis in RNA-seq?

Reduces 3' end bias in the sequencing library Signup and view all the answers

What is the role of Ribonuclease H (RNase H) in second strand synthesis in RNA-seq?

Cleaves RNA in RNA:DNA hybrids Signup and view all the answers

What is the purpose of adding an 'A' base to the 3' ends of dsDNAs in RNA-seq library construction?

To enable adapter ligation Signup and view all the answers

Who discovered bacterial conjugation and won the Nobel Prize for it?

Joshua Lederberg Signup and view all the answers

What is the main function of plasmids in bacteria?

To carry genes that benefit the survival of the organism Signup and view all the answers

What is the normal number of copies of plasmid found in a single cell called?

Copy number Signup and view all the answers

What is the purpose of phenol-chloroform extraction in DNA purification?

To remove proteins and impurities from DNA Signup and view all the answers

Which enzyme is responsible for catalyzing the reaction of pyrophosphate (PPi) with adenosine 5’ phosphosulfate (APS) in pyrosequencing?

ATP sulfurylase Signup and view all the answers

What is the limitation of pyrosequencing when it comes to detecting homopolymeric regions?

Homopolymeric regions longer than 10 bases cannot be resolved Signup and view all the answers

Which sequencing technology utilizes reversible terminators?

Illumina sequencing Signup and view all the answers

What triggers the release of visible light in pyrosequencing?

Luciferase Signup and view all the answers

Which detection method in real-time PCR involves the use of two sequence-specific oligonucleotide probes labeled with different dyes?

Hydrolysis probe technique Signup and view all the answers

Which of the following is a key application of PCR in forensic science?

Amplifying and sequencing small amounts of DNA to reveal a person's identity Signup and view all the answers

What is the purpose of melting curve analysis in real-time PCR?

To assess the dissociation characteristics of double-stranded DNA during heating Signup and view all the answers

What is the purpose of annealing in the PCR process?

Allowing the primers to bind to the DNA template Signup and view all the answers

What is reverse transcription?

The synthesis of single-stranded DNA using single-stranded RNA as a template Signup and view all the answers

What triggers the release of visible light in pyrosequencing?

The release of pyrophosphate (PPi) during DNA synthesis Signup and view all the answers

What is the genetic material used by retroviruses?

RNA Signup and view all the answers

What is the purpose of real-time PCR?

To monitor the formation of PCR products as the reaction proceeds Signup and view all the answers

Which of the following is a disadvantage of using Loop-Mediated Isothermal Amplification (LAMP) for COVID-19 testing?

LAMP is prone to false positives Signup and view all the answers

What is the purpose of a cleavable hairpin beacon (CHB) in colorimetric detection of LAMP products?

To increase target specificity Signup and view all the answers

What is the purpose of a standard curve in absolute quantification of gene expression?

To compare results from actual experiments Signup and view all the answers

What is the purpose of normalizing Ct values to a housekeeping gene in relative quantification of gene expression?

To select the correct housekeeping gene Signup and view all the answers

Which of the following is NOT a method for rupturing cellular walls to isolate DNA and RNA from living cells?

Treatment with an isotonic solution Signup and view all the answers

What is the purpose of adding an 'A' base to the 3' ends of dsDNAs in RNA-seq library construction?

To facilitate the ligation of adapters Signup and view all the answers

What is the main function of plasmids in bacteria?

To store genetic information Signup and view all the answers

What is the purpose of melting curve analysis in real-time PCR?

To confirm the specificity of the PCR reaction Signup and view all the answers

Which step is involved in RNA-seq library construction?

Addition of 'A' base to 3' ends Signup and view all the answers

What is the purpose of adding an 'A' base to the 3' ends of dsDNAs in RNA-seq library construction?

To obtain an Illumina library Signup and view all the answers

What is the role of Ribonuclease H (RNase H) in second strand synthesis in RNA-seq?

To degrade only the RNA in RNA:DNA hybrids Signup and view all the answers

Which method involves the synthesis of single-stranded DNA using single-stranded RNA as a template?

Reverse Transcription (RT) Signup and view all the answers

What is the purpose of depleting rRNAs from the total RNA pool in RNA-seq?

To get rid of rRNAs Signup and view all the answers

What is the typical range for the GC content of PCR primers?

30-40% Signup and view all the answers

Which of the following methods can be used to isolate DNA and RNA from living cells?

Treatment with a detergent Signup and view all the answers

How are DNA molecules separated from RNA and protein in the process of cesium chloride centrifugation?

DNA molecules sink to the bottom of the tube Signup and view all the answers

What is the purpose of the polymerase chain reaction (PCR)?

To amplify specific DNA sequences Signup and view all the answers

What is the main function of plasmids in bacteria?

To transfer genetic material between bacteria Signup and view all the answers

Which enzyme is responsible for catalyzing the reaction of pyrophosphate (PPi) with adenosine 5’ phosphosulfate (APS) in pyrosequencing?

ATP sulfurylase Signup and view all the answers

What is the purpose of adding dATP-αS instead of natural dATP in pyrosequencing?

To interfere with the luciferase reaction Signup and view all the answers

What is the limitation of pyrosequencing when it comes to detecting homopolymeric regions?

Homopolymeric regions longer than 10 bases cannot be resolved Signup and view all the answers

What triggers the release of visible light in pyrosequencing?

Luciferase Signup and view all the answers

Which detection method in real-time PCR involves the use of a fluorescent reporter molecule and a quencher molecule?

Detection Method 2 Signup and view all the answers

What is the purpose of melting curve analysis in real-time PCR?

To assess the dissociation characteristics of double-stranded DNA during heating Signup and view all the answers

Which type of virus uses RNA as its genetic material and replicates through reverse transcription?

Retrovirus Signup and view all the answers

What is the purpose of reverse transcription in molecular biology?

To generate single-stranded DNA using single-stranded RNA as a template Signup and view all the answers

Which of the following is a key application of qPCR in gene expression analysis?

Comparing the expression levels of different genes Signup and view all the answers

What is the purpose of a standard curve in absolute quantification of gene expression using qPCR?

To determine the amount of targeted nucleic acid in a sample Signup and view all the answers

What is the advantage of using relative quantification in gene expression analysis using qPCR?

It allows for the comparison of expression levels of different genes Signup and view all the answers

What is the formula to calculate the fold change in gene expression using qPCR?

Fold change = 2^(-Δ(ΔCt)) Signup and view all the answers

Which of the following is NOT a characteristic of plasmids?

They are responsible for bacterial conjugation Signup and view all the answers

Which of the following is TRUE about the copy number of plasmids?

The copy number of plasmids can vary from one to several hundreds in a single cell Signup and view all the answers

Which of the following is TRUE about CsCl density gradient centrifugation?

CsCl density gradient centrifugation separates plasmid DNA from chromosomal DNA using ethidium bromide Signup and view all the answers

What is the purpose of minipreparation of plasmid DNA?

To isolate plasmid DNA from bacteria Signup and view all the answers

Which step is involved in RNA-seq library construction?

Depletion of rRNAs Signup and view all the answers

What is the purpose of adding an 'A' base to the 3' ends of dsDNAs in RNA-seq library construction?

To facilitate adapter ligation Signup and view all the answers

What is the role of Ribonuclease H (RNase H) in second strand synthesis in RNA-seq?

To degrade RNA in RNA:DNA hybrids Signup and view all the answers

What is the purpose of depleting rRNAs from the total RNA pool in RNA-seq?

To reduce the dominance of rRNAs in sequencing reads Signup and view all the answers

What is the purpose of first strand cDNA synthesis with oligo(dT) in RNA-seq?

To capture an entire transcript Signup and view all the answers

What is the purpose of random hexamers in first strand synthesis in RNA-seq?

To reduce 3' end bias Signup and view all the answers

What is the purpose of real-time PCR?

To monitor the formation of PCR products Signup and view all the answers

What is the typical range for the length of PCR primers?

15 to 30 nucleotides Signup and view all the answers

What is the purpose of annealing in the PCR process?

To allow the primers to bind to the DNA template Signup and view all the answers

What is the purpose of denaturation in the PCR process?

To separate the DNA strands Signup and view all the answers

Unraveling DNA Sequencing

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Questions and Answers

Who coined the term 'plasmid'?

What is the main function of plasmids in bacteria?

What is the normal number of copies of plasmid found in a single cell called?

What is the purpose of phenol-chloroform extraction in DNA purification?

Which of the following is a key application of PCR in forensic science?

What is the purpose of annealing in the PCR process?

What is the typical range for the GC content of PCR primers?

What is the purpose of real-time PCR?

Which detection method in real-time PCR involves the use of a fluorescent reporter molecule and a quencher molecule?

What is the purpose of melting curve analysis in real-time PCR?

Which method involves the synthesis of single-stranded DNA using single-stranded RNA as a template?

Which type of virus uses RNA as its genetic material and replicates through reverse transcription?

Which enzyme is added to the pyrosequencing reaction mixture to catalyze the reaction of PPi with adenosine 5’ phosphosulfate (APS)?

What is the limitation of pyrosequencing when it comes to detecting homopolymeric regions?

What triggers the release of visible light in pyrosequencing?

Which sequencing technology utilizes reversible terminators?

Which of the following is a disadvantage of using qPCR for COVID-19 testing?

What is the purpose of a Ct value in real-time PCR?

What is the purpose of a housekeeping gene in relative quantification of gene expression?

How is the fold change in gene expression calculated in qRT-PCR?

Which of the following is NOT a method for rupturing cellular walls to isolate DNA and RNA from living cells?

What is the purpose of centrifugation in the separation of DNA by cesium chloride?

Which macromolecule has the highest density and sinks to the bottom of the tube during centrifugation in the separation of DNA by cesium chloride?

What is the main purpose of extracting nucleic acids from living cells?

Which of the following is a step involved in RNA-seq library construction?

What is the purpose of depleting rRNAs from the total RNA pool in RNA-seq?

Which primer can be used to specifically select for mRNAs in RNA-seq?

What is the advantage of using random hexamers for first strand cDNA synthesis in RNA-seq?

What is the role of Ribonuclease H (RNase H) in second strand synthesis in RNA-seq?

What is the purpose of adding an 'A' base to the 3' ends of dsDNAs in RNA-seq library construction?

Who discovered bacterial conjugation and won the Nobel Prize for it?

What is the main function of plasmids in bacteria?

What is the normal number of copies of plasmid found in a single cell called?

What is the purpose of phenol-chloroform extraction in DNA purification?

Which enzyme is responsible for catalyzing the reaction of pyrophosphate (PPi) with adenosine 5’ phosphosulfate (APS) in pyrosequencing?

What is the limitation of pyrosequencing when it comes to detecting homopolymeric regions?

Which sequencing technology utilizes reversible terminators?

What triggers the release of visible light in pyrosequencing?

Which detection method in real-time PCR involves the use of two sequence-specific oligonucleotide probes labeled with different dyes?

Which of the following is a key application of PCR in forensic science?

What is the purpose of melting curve analysis in real-time PCR?

What is the purpose of annealing in the PCR process?

What is reverse transcription?

What triggers the release of visible light in pyrosequencing?

What is the genetic material used by retroviruses?

What is the purpose of real-time PCR?

Which of the following is a disadvantage of using Loop-Mediated Isothermal Amplification (LAMP) for COVID-19 testing?

What is the purpose of a cleavable hairpin beacon (CHB) in colorimetric detection of LAMP products?

What is the purpose of a standard curve in absolute quantification of gene expression?

What is the purpose of normalizing Ct values to a housekeeping gene in relative quantification of gene expression?

Which of the following is NOT a method for rupturing cellular walls to isolate DNA and RNA from living cells?

What is the purpose of adding an 'A' base to the 3' ends of dsDNAs in RNA-seq library construction?

What is the main function of plasmids in bacteria?

What is the purpose of melting curve analysis in real-time PCR?

Which step is involved in RNA-seq library construction?

What is the purpose of adding an 'A' base to the 3' ends of dsDNAs in RNA-seq library construction?

What is the role of Ribonuclease H (RNase H) in second strand synthesis in RNA-seq?

Which method involves the synthesis of single-stranded DNA using single-stranded RNA as a template?

What is the purpose of depleting rRNAs from the total RNA pool in RNA-seq?

What is the typical range for the GC content of PCR primers?

Which of the following methods can be used to isolate DNA and RNA from living cells?

How are DNA molecules separated from RNA and protein in the process of cesium chloride centrifugation?

What is the purpose of the polymerase chain reaction (PCR)?

What is the main function of plasmids in bacteria?

Which enzyme is responsible for catalyzing the reaction of pyrophosphate (PPi) with adenosine 5’ phosphosulfate (APS) in pyrosequencing?

What is the purpose of adding dATP-αS instead of natural dATP in pyrosequencing?

What is the limitation of pyrosequencing when it comes to detecting homopolymeric regions?

What triggers the release of visible light in pyrosequencing?

Which detection method in real-time PCR involves the use of a fluorescent reporter molecule and a quencher molecule?

What is the purpose of melting curve analysis in real-time PCR?

Which type of virus uses RNA as its genetic material and replicates through reverse transcription?

What is the purpose of reverse transcription in molecular biology?

Which of the following is a key application of qPCR in gene expression analysis?

What is the purpose of a standard curve in absolute quantification of gene expression using qPCR?

What is the advantage of using relative quantification in gene expression analysis using qPCR?

What is the formula to calculate the fold change in gene expression using qPCR?