Molecular Diagnostics- Molecular methods Flashcards
1
Q
- Which double-stranded DNA molecule has the
highest melting temperature?
A. An oligonucleotide with a repeating sequence of
A-A-A at the 5´ end
B. A molecule of 5,000 base pairs with a high
number of A-T base pairs
C. An oligonucleotide with a large number of
repeating C-G-C codons
D. A DNA polymer of 100,000 base pairs
A
C. An oligonucleotide with a large number of
repeating C-G-C codons
2
Q
- Which base pair sequence is most likely to serve as
a binding site for a restriction endonuclease?
A. A-T-T-C-A
T-A-A-G-T
B. C-T-A-C-T-G
G-A-T-G-A-C
C. C-A-C
G-T-G
D. A-A-G-C-T-T
T-T-C-G-A-A
A
D. A-A-G-C-T-T
T-T-C-G-A-A
3
Q
- Cloning a human gene into a bacterium in order
to make a large molecular probe requires which
vector?
A. Plasmid
B. Bacterial microsome
C. 30S bacterial ribosome
D. Single-stranded DNA
A
A. Plasmid
4
Q
- What process can be used to make a DNA probe
produce a fluorescent or chemiluminescent signal?
A. Enzymatic attachment of acridinium esters to
terminal ends of the probe
B. Substitution of biotinylated or fluorescent
nucleotides into the probe
C. Splicing the gene for β-galactosidase into the
probe
D. Heat denaturation of the probe followed by acid
treatment
A
B. Substitution of biotinylated or fluorescent
nucleotides into the probe
5
Q
- What term describes the products produced when
DNA is digested by restriction endonucleases?
A. Mosaicisms
B. Chimeras
C. Amplicons
D. Restriction fragment length polymorphisms
A
D. Restriction fragment length polymorphisms
6
Q
- The following figure shows a DNA size standard
(ladder) made by restriction enzyme digestion
(PstI) of lambda phage DNA that has been
separated by agarose gel electrophoresis. Which DNA band has the highest molecular weight ?
A. 1
B. 2
C. 3
D. 4
A
A. 1
7
Q
- What reagent is most commonly used to stain
DNA separated by electrophoresis?
A. Silver nitrate
B. Nicotinamide adenine dinucleotide
C. Cationic dye
D. Ethidium bromide
A
D. Ethidium bromide
8
Q
- Which technique is used to detect DNA
containing a specific base sequence by applying a
labeled probe to DNA bands immobilized onto
nitrocellulose paper following electrophoresis?
A. Southern blot
B. Northern blot
C. Dot blot
D. Western blot
A
A. Southern blot
9
Q
- Which of the following types of mutation causes
the premature termination of protein synthesis?
A. Missense
B. Nonsense
C. Insertion
D. Frame shift
A
B. Nonsense
10
Q
- In humans, which component of a gene is
translated into a protein?
A. Intron
B. Exon
C. Promoter
D. TATA box
A
B. Exon
11
Q
- Which statement best describes a DNA
polymorphism?
A. A point mutation arising in a gene
B. Any change in DNA that is associated with
abnormal function
C. A change in the base sequence of DNA that is
translated into an abnormal protein
D. A variation in DNA that occurs with a frequency
of at least 1%
A
D. A variation in DNA that occurs with a frequency
of at least 1%
12
Q
- Which of the following is the most common type
of polymorphism?
A. Single nucleotide polymorphism (SNP)
B. Variable number tandem repeat (VNTR)
C. Short tandem repeat (STR)
D. Short repetitive interspersed element (SINES)
A
A. Single nucleotide polymorphism (SNP)
13
Q
- Which of the following mechanisms facilitates
DNA separation by capillary electrophoresis?
A. Molecular sieving
B. Partitioning
C. Adsorption
D. Deflection
A
A. Molecular sieving
14
Q
- The polymerase chain reaction (PCR) involves
three processes. Select the order in which these
occur.
A. Extension→Annealing→Denaturation
B. Annealing→Denaturation→Extension
C. Denaturation→Annealing→Extension
D. Denaturation→Extension→Annealing
A
C. Denaturation→Annealing→Extension
15
Q
- In the PCR cycle, how is denaturation
accomplished?
A. Heat
B. Alkali treatment
C. Addition of sulfonylurea
D. Formamide
A
A. Heat
16
Q
- What is the composition of the primer used
in PCR?
A. A cocktail of enzymes and nucleotide
triphosphates that bind to the target
B. An oligonucleotide complementary to bases at
the 3´ end of the target
C. A small piece of dsDNA that attaches to the
template
D. A probe made of mRNA that binds downstream
from the target
A
B. An oligonucleotide complementary to bases at
the 3´ end of the target
17
Q
- The master mix solution used for PCR contains
which of the following reagents?
A. Deoxyribonucleotide triphosphates
B. Deoxyribonucleotide monophosphates
C. Deoxyribonucleosides
D. Ribonucleotide monophosphates
A
A. Deoxyribonucleotide triphosphates
18
Q
- What is the unique characteristic of the DNA
polymerase, Taq DNA polymerase, used in PCR?
A. It can be enzyme labeled
B. It is more efficient than eukaryotic polymerases
C. It is heat stable
D. It works with DNA of any species
A
C. It is heat stable
19
Q
- In PCR methods, how can several targets be
copied simultaneously and detected?
A. By following the increase in absorbance at
260 nm during melting
B. By labeling multiple primers with specific fluors
C. By substitution of hybridization probes for
primers
D. By analysis of adenosine tail signatures
A
B. By labeling multiple primers with specific fluors
20
Q
- Which formula predicts the number of PCR
products that can be produced?
A. 2n where n is the number of cycles
B. N4 where N is the number of cycles
C. p2 + 2pq + q2 = 1 where p and q are the number
of primers
D. N2/2 where N is the number of cycles
A
A. 2n where n is the number of cycles
21
Q
- How can PCR be applied to the detection of
human immunodeficiency and other RNA viruses?
A. The virus must be inserted into human DNA by
viral integrase prior to PCR
B. Substitute deoxyuridine triphosphate in place of
deoxythymidine triphosphate in the master mix
C. Add a heat-stable reverse transcriptase enzyme to
the master mix
D. Substitute ribonucleotide triphosphates for
deoxyribonucleotide triphosphates in the
master mix
A
C. Add a heat-stable reverse transcriptase enzyme to
the master mix
22
Q
- Which statement best describes the method of
branched DNA signal amplification?
A. The DNA template is amplified directly using
patented enzymes
B. Multiple primers are used to create branches of
the template DNA, permitting multiple
extension sites
C. The target DNA is denatured and hybridized to
RNA, and the hybrid molecules are amplified by
both DNA and RNA polymerases
D. The target DNA is bound by multiple
probes, and those are amplified instead of
the target DNA
A
D. The target DNA is bound by multiple
probes, and those are amplified instead of
the target DNA
23
Q
- A PCR reaction is performed, and the negative
control demonstrates the presence of a detectable
number of PCR products (amplicons) by capillary
electrophoresis. What is the most likely cause?
A. False-positive post-PCR hybridization reaction
due to low stringency
B. Dimerization of PCR primers
C. Contamination of control sample with a trace
amount of template DNA
D. Background signal from gel fluorescence or
inadequate removal of unbound probe
A
C. Contamination of control sample with a trace
amount of template DNA
24
Q
- How can a false-negative PCR test caused by the
presence of an inhibitor of the reaction in a
patient’s sample be detected?
A. Using a positive control
B. Using an internal control
C. Performing each test in duplicate
D. Performing serial dilutions of the sample
A
B. Using an internal control
25
Q
- All of the following are requirements for reducing
contamination in DNA amplification methods
except:
A. Use of aerosol barrier pipette tips when
transferring samples or reaction products
B. Preparation of reagents in a dead air box or
biological cabinet
C. A separate area for performing preamplification,
postamplification, and detection steps
D. Pretreatment of samples with high-intensity
ultraviolet light
A
D. Pretreatment of samples with high-intensity
ultraviolet light
26
Q
- Which method has been used successfully to
reduce contamination in the preamplification
stage of PCR?
A. Substitution of deoxyuridine triphosphate for
deoxythymidine triphosphate in the master mix
B. Use of low-molecular-size primers
C. Use of a denaturation temperature above 95°C
D. Pretreatment of samples with antisense RNA
A
A. Substitution of deoxyuridine triphosphate for
deoxythymidine triphosphate in the master mix
27
Q
- How are PCR methods adapted to yield
quantitative data?
A. By comparing PCR product to an internal
standard
B. By applying a conversion factor to the PCR
signal that converts it to copies per milliliter
C. By determining the mass of PCR product using
ultraviolet spectrophotometry
D. By making serial dilutions of the sample
A
A. By comparing PCR product to an internal
standard
28
Q
- A PCR analysis of a vaginal sample for Chlamydia
trachomatis gives a negative result (optical density
of biotinylated reaction product below the cutoff
point). The internal control result is also below the
cutoff. Positive and negative controls produced
acceptable results. What action should be taken?
A. The test should be reported as negative
B. The sample should be diluted and the test
repeated
C. The result should not be reported and the sample
should be repeated
D. A preliminary result of negative should be
reported but should be confirmed by further
testing using a different method of analysis
A
C. The result should not be reported and the sample
should be repeated
29
Q
- In real-time PCR analysis, the absolute
concentration of PCR product is determined
by plotting which two values?
A. Fluorescent intensity versus melting temperature
B. The threshold cycle versus concentration
C. The well factor versus threshold cycle
D. The melting temperature versus concentration
A
B. The threshold cycle versus concentration
30
Q
- In real-time PCR, quantitation can be done
without standards of known copy number.
Relative quantitation (estimated concentration) is
possible because:
A. Each cycle generates a twofold increase in
product
B. Each cycle threshold represents a 10-fold increase
in product
C. The fluorescence of two samples can be
compared directly
D. Concentration is proportional to fluorescence at
the endpoint of the PCR reaction
A
A. Each cycle generates a twofold increase in
product
31
Q
- Which real-time PCR parameter can be used to
detect the presence of a contaminant?
A. Threshold cycle
B. Baseline
C. Melting temperature
D. Relative fluorescent intensity
A
C. Melting temperature
32
Q
- In real-time PCR, what value is needed in order to
determine the threshold?
A. Background signal
B. Melting temperature
C. Maximum fluorescence
D. Threshold cycle
A
A. Background signal
33
Q
- In real-time PCR, which of the following methods
is not based on using a probe?
A. TaqMan
B. Molecular beacon
C. Scorpion
D. SYBR green
A
D. SYBR green
34
Q
- Which statement accurately describes the process
of fluorescent in situ hybridization (FISH)?
A. Hybridization is performed on DNA extracted
from cells
B. Hybridization is performed directly on intact
chromosomes
C. Hybridization probes are attached to histones
associated with the chromosomes
D. Hybridization occurs by attachment to the probe
only at the centromere
A
B. Hybridization is performed directly on intact
chromosomes
35
Q
- Which type of specimen would be unsuitable for
FISH analysis?
A. Paraffin-embedded tissue
B. Cells with chromosomes in metaphase
C. Cells with chromosomes in interphase
D. A cell suspension containing maternal and fetal
blood
A
D. A cell suspension containing maternal and fetal
blood
36
Q
- FISH can distinguish each of the following
chromosomal abnormalities except:
A. Aneuploidy
B. Translocation
C. Deletion
D. Trinucleotide repeats
A
D. Trinucleotide repeats
37
Q
- In microarray and macroarray analysis, which
molecules are labeled?
A. The immobilized DNA molecules
B. The sample DNA
C. Both target and sample molecules
D. The substrate matrix
A
B. The sample DNA
38
Q
- How can all of the mRNA within a sample be
amplified to prepare microarray probes?
A. A specific primer for each mRNA must be
synthesized
B. A primer is made to the polyA tail of mRNA
C. Nonspecific attachment of T7 polymerase occurs
when the cells are treated with detergent
D. Random primer sets are used under low
stringency conditions
A
B. A primer is made to the polyA tail of mRNA
39
Q
- What is the difference between a microarray and a
macroarray DNA assay?
A. The number of targets is larger on a macroarray
B. The molecular size of each target is larger on a
macroarray
C. The amount of each target is larger on a
macroarray
D. The substrate used for a macroarray is different
from a microarray
A
C. The amount of each target is larger on a
macroarray
40
Q
- Protein microarray analysis requires the use of
which of the following techniques to generate
protein profile data?
A. Electrophoresis
B. Mass spectroscopy
C. Thin-layer chromatography
D. Gas chromatography
A
B. Mass spectroscopy
