Exam Prep Chapter 6 Nucleic Acid Amplification

Chapter 6: Nucleic Acid Amplification

Multiple Choice

1. The specificity of the PCR reaction is determined by which of the following components?

A. Mg²⁺ concentration

B. Deoxynucleotides

C. DNA polymerase

D. Primers

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2. Which of the following steps can be taken to minimize mis-priming in a PCR procedure?

A. Use high-quality deoxynucleotides, buffers, and enzymes.

B. Seclude the polymerase from the template and primers before amplification.

C. Load the samples carefully for gel electrophoresis of PCR products.

D. Keep the reaction mix at room temperature prior to amplification.

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3. Which of the following is the correct order of the steps that occur in a standard PCR cycle?

A. Annealing, denaturation, and extension

B. Denaturation, extension, and annealing

C. Denaturation, annealing, and extension

D. Extension, annealing, and denaturation

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4. Starting with a single target, how many copies are produced in a PCR reaction of 30 cycles?

A. 30

B. 30²

C. 2³⁰

D. 2 × 30

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5. Complementarity of primer pairs at the 3' ends will result in what artifacts?

A. Primer dimers

B. Large mis-primed products

C. No amplification

D. 5' end degradation of the primers

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6. High GC content in a DNA sequence is more likely to have what property that interferes with PCR amplification?

A. Tendency to degrade

B. Enzyme inactivation

C. Lower T_m

D. Secondary structure

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7. A polymerase enzyme with high processivity would be used for which application?

A. Long-range PCR

B. Sequence-specific PCR

C. Signal amplification

D. Quantitative PCR

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8. A PCR reaction that uses more than one primer pair is called

A. long-range PCR.

B. multiplex PCR.

C. signal amplification.

D. quantitative PCR.

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9. What type of PCR starts with an RNA template?

A. Real-time PCR

B. Multiplex PCR

C. Reverse transcriptase PCR

D. Sequence-specific PCR

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10. What is the advantage of a nested PCR procedure?

A. Nested PCR is less labor intensive.

B. Nested PCR offers increased specificity and yield of product.

C. Nested PCR has a shorter reaction time than standard PCR.

D. Nested PCR is less expensive than standard PCR.

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11. What is TaqMan?

A. A qPCR probe system

B. A high-efficiency buffer used in PCR

C. A special PCR enzyme

D. A video game

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12. Real-time PCR differs from standard PCR in which way?

A. Standard PCR is faster.

B. Real-time PCR is less sensitive.

C. Real-time PCR is quantitative.

D. Standard PCR is more specific.

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13. What is the purpose of an amplification control in PCR?

A. To check for contamination

B. To distinguish true positives from false positives

C. To distinguish true negatives from false negatives

D. To protect the template from degradation

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14. Which of the following is the most likely source of PCR contamination?

A. Unfiltered dust particles

B. Environmental fungi

C. Eyelashes

D. PCR products from a previous reaction

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15. What enzyme system is used to avoid contamination in real-time PCR?

A. dUTP-UNG

B. SSP-PCR

C. UV-psoralen

D. SAP-ExoI

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16. Which of the following is the function of SYBR green in quantitative PCR?

A. Detection of the PCR product

B. Facilitation of amplification

C. Prevention of contamination

D. Minimization of mis-priming

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17. Which of the following is a method of signal amplification?

A. Transcription-mediated amplification (TMA)

B. Polymerase chain reaction (PCR)

C. Ligase chain reaction (LCR)

D. Branched DNA (bDNA) assay

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18. Which of the following techniques is a primer-directed in vitro enzymatic reaction for the production of multiple copies of a specific DNA fragment found in a clinical sample?

A. Strand displacement amplification

B. Polymerase chain reaction

C. Cleavage-based amplification

D. Hybrid capture assay

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19. In PCR, an instrument is used to increase and decrease the temperature at set intervals as programmed by the technologist in order to

A. prevent the Taq polymerase from being denatured.

B. avoid the formation of primer dimers on a post-PCR gel image.

C. determine the reaction that is occurring in the sample.

D. neutralize potential contamination from previous amplicons.

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20. Transcription-mediated amplification obtains

A. DNA from RNA.

B. RNA from DNA.

C. DNA from DNA.

D. DNA from RNA and RNA from DNA.

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21. Which of the following PCR controls ensures that the enzyme is active, the buffer is optimal, and the primers are priming the correct target sequence and must have a PCR product detected in order to be valid?

A. Positive control

B. Negative template control

C. Contamination control

D. Amplification control

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22. Which of the following PCR controls ensures that the reaction mix is not contaminated with amplicons from a previous PCR procedure and must not have a PCR product detected in order to be valid?

A. Positive control

B. Negative template control

C. Contamination control

D. Amplification control

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23. A PCR assay is performed, and the results are being analyzed. The positive control has a band at the expected size, the negative template control has a band at the same size as the positive control, the contamination control has no band, and the amplification control has a band of expected size. All of the patient samples that were run had a band the same size as the band seen in the positive and negative template control wells. How are these results interpreted?

A. This is an acceptable run, and the patients should all be reported as positive.

B. This run is not acceptable because the amplification control should not have a band.

C. This run is not acceptable because the contamination control should have a band.

D. This run is not acceptable because the negative template control should not have a band.

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24. Which of the following PCR modifications was developed to allow for the amplification of an RNA template?

A. Multiplex

B. Nested

C. Reverse transcriptase

D. Real time

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21. SYBR green fluorescence is detectable at which stage of the PCR amplification process?

A. Denaturation

B. Primer annealing

C. Primer extension

D. Hybridization

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26. Which modification of PCR uses short primers with random sequences that generate the amplification of many different products?

A. Reverse transcriptase

B. Real time

C. Nested

D. Arbitrarily primed

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27. Which of the following amplification procedures uses RNA polymerase to generate amplicons?

A. Q beta replicase

B. Reverse transcriptase PCR

C. Ligase chain reaction

D. Strand displacement amplification

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28. In which of the following nucleic acid–amplification procedures is target nucleic acid labeled with enough signal to be detectable?

A. Polymerase chain reaction

B. Strand displacement amplification

C. Transcription-mediated amplification

D. Hybrid capture assay

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29. Nucleic acid has been isolated from a urethral swab, and a PCR is performed on the sample in order to detect Neisseria gonorrhoeae. The positive control has a band of the expected size, the negative template control and the contamination controls do not have bands, and the amplification control has a band of the expected size. The patient sample has a band consistent with the amplification control band and does not have a band corresponding to the positive control band. How is this result interpreted?

A. The patient has a positive PCR result for N. gonorrhoeae.

B. The results are not acceptable because the control results are invalid.

C. The patient does not have N. gonorrhoeae, and it is a true-negative result.

D. The patient has a false-negative result for N. gonorrhoeae.

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30. TaqMan, molecular beacons, and Scorpion-type primers are all used in which of the following procedures?

A. Branched DNA assays

B. Quantitative PCR

C. Transcription-mediated amplification

D. Multiplex PCR

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