Question 1

The optimal way to detect PCR amplicons is to use which stain?
A)Methylene blue
B)Malachite green
C)Bromothymol blue
D)Ethidium bromide

Accepted Answer

The nucleic acid bands in the agarose gel are stained with the fluorescent dye,ethidium bromide,which allows them to be visualized on exposure to ultraviolet (UV)light.

Question 2

Nucleic acid sequencing methods are based on:
A)the ability of two nucleic acid strands that have complementary base sequences to bond specifically with each other and form a double-stranded molecule.
B)detecting phenotypic traits not detectable by conventional strategies.
C)the principles of complementary nucleic acid hybridization with those of nucleic acid replication.
D)determining the exact nucleotide sequence of a gene or gene fragment obtained from an organism.

Accepted Answer

The nucleotide sequence of a microorganism's genome is the blueprint for that organism;therefore,the knowledge of its nature is a valuable tool in identifying infectious agents in clinical specimens.

Question 3

Hybridization methods are based on:
A)the ability of two nucleic acid strands that have complementary base sequences to bond specifically with each other and form a double-stranded molecule.
B)detecting phenotypic traits not detectable by conventional strategies.
C)the principles of complementary nucleic acid hybridization with those of nucleic acid replication that are repeatedly applied through numerous cycles.
D)determining the exact nucleotide sequence of a gene or gene fragment obtained from an organism.

Accepted Answer

The ability of complementary nucleic acid strands to bond specifically with each other and form a double-stranded molecule is what drives hybridization methods.

Question 4

Gen-Probe Mycobacterium tuberculosis direct test uses which type of nucleic acid amplification test?
A)Nucleic acid sequence-based amplification (NASBA)
B)Transcription-mediated amplification (TMA)
C)Reverse transcriptase polymerase chain reaction (RT-PCR)
D)Standard displacement amplification (SDA)

Accepted Answer

Gen-Probe uses TMA to identify M.tuberculosis.

Question 5

An organism whose genetic makeup is 50% C-G bonds would have a(n)_________ melting temperature (Tm),compared with an organism with 20% C-G bonds.
A)higher
B)lower
C)equal
D)similar

Accepted Answer

The Tm is the temperature at which the DNA becomes single-stranded,or melts,and is dependent on its base sequence (i.e. ,stretches of double-stranded DNA with more cytosine and guanine molecules requiring more heat [energy] to break the three hydrogen bonds between these two bases,in contrast to adenine- and thymidine-base pairing,which has only two hydrogen bonds).

Question 6

Which of the following steps are crucial for the success of a nucleic acid amplification test,such as PCR?
A)Nucleic acid purification
B)Fluorescent resonance energy transfer (FRET)
C)Melting temperature analysis
D)Nucleic acid sequencing

Accepted Answer

Nucleic acids (DNA or RNA)serve as the template molecules for PCR,and therefore must be purified and included in the reaction to ensure success of the PCR.

Question 7

After PCR,the amplification control has failed to yield a product.What should you do?
A)Report out Indeterminate
B)Report out Negative because there was no amplification from the sample
C)Check the original DNA or RNA preparation.If it is adequate,repeat the amplification.If not,re-isolate the nucleic acid.
D)Repeat it using a higher concentration of amplification control in the reaction.

Accepted Answer

Amplification controls typically fail based on nucleic acid concentration or preparation.

Question 8

The enzyme that has the ability to synthesize DNA from ribonucleic acid (RNA)is called:
A)DNA polymerase.
B)RNAse.
C)helicase.
D)reverse transcriptase.

Accepted Answer

The reverse transcriptase enzyme has the ability to direct the synthesis of DNA from the viral RNA template.

Question 9

The target in the hybridization assay can be described as:
A)originating from the unknown organism to be detected or identified.
B)a reporter molecule that chemically forms a complex with the single-stranded probe DNA.
C)originating from an organism of known identity.
D)an enzyme that adds nucleotides during the replication process.

Accepted Answer

The target in the hybridization assay is the strand of DNA from the unknown organism to be detected or identified.

Question 10

Which type of hybridization method would be the optimal choice to use to detect a lesion infected with a particular virus?
A)Southern
B)In situ
C)Peptide nucleic acid
D)Sandwich

Accepted Answer

In situ hybridization allows a pathogen to be identified within the context of the pathologic lesion being produced.

Question 11

Determining the exact nucleotide sequence of a gene or gene fragment obtained from an unknown organism is based on which of the following methods?
A)Hybridization
B)Sequencing
C)Amplification (PCR)
D)Genotypic

Accepted Answer

The nucleotide sequence of a microorganism's genome is the blueprint for that organism;therefore,knowledge of its nature is a valuable tool in identifying infectious agents in clinical specimens.

Question 12

Analysis of the number of target molecules in the original clinical specimen can be determined using which of the following molecular techniques?
A)Arbritary Primed PCR
B)Peptide Nucleic Acid (PNA)FISH
C)Nested PCR
D)Quantitative PCR

Accepted Answer

Quantitative PCR (qPCR,also known as real-time PCR)utilizes a standard dilution of target template molecules run in parallel to quantify the number of molecules in the original specimen.

Question 13

Which enzyme recognizes a specific nucleotide sequence (~4 to 8 nucleotides in length)and catalyzes the digestion of the nucleic acid at that site,causing a break in the DNA strand?
A)Ligase
B)Gyrase
C)Helicase
D)Endonuclease

Accepted Answer

Endonucleases recognize a specific nucleotide sequence (usually 4 to 8 nucleotides in length)known as the enzyme's recognition or restriction site.

Question 14

The ability of two nucleic acid strands,a probe and a target,which have complementary base sequences that specifically bond with each other and form a double-stranded molecule,drives which of the following methods?
A)Hybridization
B)Sequencing
C)Amplification (PCR)
D)Genotypic

Accepted Answer

The ability of complementary nucleic acid strands to bond specifically with each other and form a double-stranded molecule drives hybridization methods.

Question 15

The enzyme that is commonly used for primer extensions in the PCR method works best at what temperature?
A)25°C
B)56°C
C)72°C
D)94°C

Accepted Answer

Taq polymerase is the enzyme commonly used for primer extensions,which occurs at 72°C.

Question 16

Complementary nucleic acid hybridization,which is coupled with nucleic acid replication and applied repeatedly through numerous cycles,is based on which of the following methods?
A)Hybridization
B)Sequencing
C)Amplification (PCR)
D)Genotypic

Accepted Answer

In PCR-based methods,the target nucleic acid is amplified by nucleic acid replication;these methods are repeatedly applied through numerous cycles.

Question 17

The probe in the hybridization assay can be described as:
A)originating from the unknown organism to be detected or identified.
B)a reporter molecule that chemically forms a complex with the single-stranded probe deoxyribonucleic acid (DNA).
C)originating from an organism of known identity with a known sequence.
D)the enzyme needed to elongate the strand.

Accepted Answer

The probe in a hybridization assay is made from a known organism that is the same as the organism being sought in the assay.

Question 18

Target nucleic acid amplification (polymerase chain reaction [PCR])methods are based on:
A)the ability of two nucleic acid strands that have complementary base sequences to bond specifically with each other and form a double-stranded molecule.
B)detecting phenotypic traits not detectable by conventional strategies.
C)the principles of complementary nucleic acid hybridization with those of nucleic acid replication that are repeatedly applied through numerous cycles.
D)determining the exact nucleotide sequence of a gene or gene fragment obtained from an organism.

Accepted Answer

In PCR-based methods,the target nucleic acid is amplified by nucleic acid replication;these methods are applied repeatedly through numerous cycles.

Question 19

Analytical sensitivity is concerned primarily with which of the following PCR parameters?
A)Target specificity
B)Limit of detection
C)Head-to-head comparison to a gold-standard test
D)Gram staining

Accepted Answer

The defined limit of detection of a PCR-based test is the lower threshold of reproducible detection of the target molecule in a given sample type.

Question 20

Predict which of the following DNA oligonucleotide probes would have the highest melting temperature (Tm)when hybridizing to the target sequence 5'-GTGCCTGAATGCAATGTCA-3'.
A)3'-CACGGA-5'
B)3'-CATGGA-5'
C)3'-TTACAG-5'
D)3'-TTACTG-5'

Accepted Answer

DNA with more cytosine and guanine molecules require more heat [energy] to break the three hydrogen bonds formed between these two bases,in contrast to adenine- and thymidine-base pairing,which has only two hydrogen bonds.In addition,single nucleotide mismatches that reduce the complementarity of the hybridization (i.e.no hydrogen bonds formed between noncomplementary bases)will lower the melting temperature.

Quiz 8: Nucleic Acid-Based Analytic Methods for Microbial Identification and Characterization

The optimal way to detect PCR amplicons is to use which stain?

Nucleic acid sequencing methods are based on:

Hybridization methods are based on:

Gen-Probe Mycobacterium tuberculosis direct test uses which type of nucleic acid amplification test?

An organism whose genetic makeup is 50% C-G bonds would have a(n) _________ melting temperature (Tm) ,compared with an organism with 20% C-G bonds.

Which of the following steps are crucial for the success of a nucleic acid amplification test,such as PCR?

After PCR,the amplification control has failed to yield a product.What should you do?

The enzyme that has the ability to synthesize DNA from ribonucleic acid (RNA) is called:

The target in the hybridization assay can be described as:

Which type of hybridization method would be the optimal choice to use to detect a lesion infected with a particular virus?

Determining the exact nucleotide sequence of a gene or gene fragment obtained from an unknown organism is based on which of the following methods?

Analysis of the number of target molecules in the original clinical specimen can be determined using which of the following molecular techniques?

Which enzyme recognizes a specific nucleotide sequence (~4 to 8 nucleotides in length) and catalyzes the digestion of the nucleic acid at that site,causing a break in the DNA strand?

The ability of two nucleic acid strands,a probe and a target,which have complementary base sequences that specifically bond with each other and form a double-stranded molecule,drives which of the following methods?

The enzyme that is commonly used for primer extensions in the PCR method works best at what temperature?

Complementary nucleic acid hybridization,which is coupled with nucleic acid replication and applied repeatedly through numerous cycles,is based on which of the following methods?

The probe in the hybridization assay can be described as:

Target nucleic acid amplification (polymerase chain reaction [PCR]) methods are based on:

Analytical sensitivity is concerned primarily with which of the following PCR parameters?

Predict which of the following DNA oligonucleotide probes would have the highest melting temperature (Tm) when hybridizing to the target sequence 5'-GTGCCTGAATGCAATGTCA-3'.