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Molecular Biology Prelims > Midterms practice test > Flashcards

Midterms practice test Flashcards

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1
Q

If 20% of the nucleotides in an organism
are adenine, predict the percentage of
nucleotides that are guanine.
A. 20%
B. 30%
C. 40%
D. 60%

A

30%

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2
Q

Which of the following is not required for
DNA replication by PCR?
A. Oligonucleotide primers
B. DNA polymerase
C. DNAligase
D. Deoxynucleotides

A

DNAligase

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3
Q

A restriction enzyme recognizes the
sequence, 5’ CTAATAG 3’, and cuts as
indicated. Predict the ends that would
result on the complementary DNA strand.
A. 3’G5’ 3’ATATC5’
B. 3’GA5’ 3’TATC5’
C. 3’GATA5’ 3’TC5’
D. 3’GATAT5’ 3’C 5’

A

3’GATA5’ 3’TC5’

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4
Q

The absorbance of a 1:100 dilution of
isolated dsDNA solution, measured at
260 nm, is 0.062. What is a reasonable
estimate for the dsDNA concentration
of the sample, expressed in ug/mL?
A. 3.1
B. 6.2
C. 310
D. 5000

A

310

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5
Q

In the isolation of RNA, diethylpyrocarbonate (DEPC) is used to
A. Inhibit RNase
B. Lyse the cells
C. Precipitate the DNA
D. Remove buffer salts

A

Inhibit RNase

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6
Q

The technique that makes ssDNA from
an RNA template is called
A. Strand displacement amplification
B. Polymerase chain reaction
C. Ligase chain reaction
D. Reverse transcription

A

Reverse transcription

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7
Q

Purification resins used to isolate DNA
take advantage of the fact that DNA is
A. Double stranded
B. Negatively charged
C. Higher in concentration than RNA
D. Higher molecular weight than RNA

A

Negatively charged

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8
Q

After performance of DNA electrophoresis, the isolated bands in the kilobase size
range appear too close together. Which of
the following can be done with the next
run to improve the appearance/separation
of the bands in the samples?
A. Increase the percent agarose concentration of the matrix
B. Increase the running time of the
electrophoresis assay
C. Increase the sample volume applied
to the gel
D. Decrease the sample volume applied
to the gel

A

Increase the running time of the
electrophoresis assay

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9
Q

Which of the following is commonly used
as a label in molecular tests?
A. Biotin
B. DNase
C. RNase
D. 125I

A

Biotin

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10
Q

Which of the following is not an example
of target amplification?
A. Reverse transcription-PCR (RT-PCR)
B. Transcription mediated amplification
(TMA)
C. Branched chain DNA amplification
(bDNA)
D. Polymerase chain reaction (PCR)

A

Branched chain DNA amplification
(bDNA)

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11
Q

In forensic testing, DNA fingerprinting
can identify individuals with high
accuracy because
A. Human genes are highly conserved
B. Only a small amount of sample is
needed
C. Human gene loci are polymorphic
D. DNA is stable and not easily
contaminated

A

Human gene loci are polymorphic

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12
Q

A 5850-base plasmid possesses EcoRl
restriction enzyme cleavage sites at the
following base pair locations: 36, 1652,
and 2702. Following plasmid digestion,
the sample is electrophoresed in a 2%
agarose gel. A DNA ladder marker,
labeled M in Color Plate 56B, is included
in the first lane, with base pair sizes
indicated in lanes A through D. Which
lane represents the sample pattern that is
most likely the digested plasmid?
A. A
B. B
C. C
D. D

A
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13
Q

Which of the following is characteristic of
DNA chips (i.e., DNA microarrays)?
A. Allow detection and discrimination
of multiple genetic sequences at the
same time.
B. Thousands of oligonucleotide probes
are labeled and placed on glass or
silicon surfaces.
C. Unlabeled target sequences within the
patient sample are detected by
hybridization to labeled probes.
D. All the above

A

Allow detection and discrimination
of multiple genetic sequences at the
same time.

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14
Q

The most useful feature of the molecules
streptavidin and biotin is that they bind
A. Specifically to nucleic acids
B. Only in neutral pH conditions
C. To each other with very high affinity
D. Directly to DNA immobilized on
nitrocellulose

A

Specifically to nucleic acids

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15
Q

What is the theoretic estimation of the
number of DNA target sequences present
(per original double-stranded DNA in
solution) following 15 cycles of PCR?
A. 30
B. 210 (i.e., 1024)
C. 215 (i.e., 32,768)
D. 220 (i.e., 1,048,576)

A

215 (i.e., 32,768)

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16
Q

“Star activity” for a restriction enzyme
refers to
A. An ability to cleave DNA at sequences
different from their defined recognition sites
B. The enzyme’s specificity for sites
of methylation within the nucleotide
sequence
C. The temperature and pH conditions
at which the enzyme will function
optimally
D. The percent increased accuracy of
the enzyme when placed in ideal
conditions of pH

A

An ability to cleave DNA at sequences
different from their defined recognition sites

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17
Q

“Star activity” for a restriction enzyme
refers to
A. An ability to cleave DNA at sequences
different from their defined recognition sites
B. The enzyme’s specificity for sites
of methylation within the nucleotide
sequence
C. The temperature and pH conditions
at which the enzyme will function
optimally
D. The percent increased accuracy of
the enzyme when placed in ideal
conditions of pH

A

An ability to cleave DNA at sequences
different from their defined recognition sites

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18
Q

If a DNA probe is added to nitrocellulose
after the transfer step but before the
blocking step, which of the following will
occur?
A. The probe will nonspecifically bind to
its DNA target.
B. Unoccupied spaces on the nitrocellulose will bind the probe.
C. The DNA target on the nitrocellulose
will be unable to bind the probe.
D. Bound probe will be washed away in
the next wash step.

A
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19
Q

Which of the following items is not used
in the preparation of a DNA probe for
Southern blotting using random hexamer
primers?
A. Template DNA
B. Three unlabeled deoxynucleotides
C. Dideoxynucleotides, with one of them
labeled
D. DNA polymerase

A

Dideoxynucleotides, with one of them
labeled

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20
Q

Which of the following is considered a
“high stringency” condition for DNA
probe protocols?
A. Using wash buffer with highly acidic
pH
B. Washing the matrix with high-salt
buffer
C. Radiolabeling the probe with 35S
rather than 32P
D. Washing the transfer membrane
(e.g., nitrocellulose or nylon) at high
temperature

A

Washing the transfer membrane
(e.g., nitrocellulose or nylon) at high
temperature

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21
Q

When compared to Southern blot
hybridization testing, PCR
A. Is less sensitive to DNA degradation
than Southern blot
B. Includes transfer of DNA onto a nylon
membrane
C. Requires no specialized equipment
D. Is more labor intensive

A

Is less sensitive to DNA degradation
than Southern blot

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22
Q

What enzyme recognizes and cuts
overlapping DNA sequences formed
between mutant or normal probes and
target sequences within samples?
A. Restriction endonuclease
B. DNAligase
C. Cleavase
D. RNaseH

A

Cleavase

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23
Q

Which of the following specimen types is
not used routinely as source material for
molecular genetic tests?
A. Whole blood
B. Buccal scrapings
C. Amniocytes
D. Rectal swabs

A

Rectal swabs

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24
Q

TaqMan probes used to increase specificity of real-time PCR assays generate a
fluorescent signal
A. At the beginning of each cycle during
the denaturation step
B. When the probes bind to the template
(i.e., during annealing)
C. When the probe is digested by 5’ —> 3’
exonuclease activity during extension
of primers (i.e., DNA synthesis)
D. When the reporter fluorophor on the
probe is separated from the quencher
molecule by a restriction enzyme

A

When the probe is digested by 5’ —> 3’
exonuclease activity during extension
of primers (i.e., DNA synthesis)

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25
Q

For the purpose of diagnosing genetic
diseases, what component of whole blood
is used for the extraction of DNA?
A. Leukocytes
B. Plasma
C. Platelets
D. Red blood cells

A

Leukocytes

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26
Q

Which of the following statements best
describes characteristics of RNase?
A. It degrades mRNA but not rRNA.
B. It is found in large concentrations on
hands.
C. Its activity can be eliminated by
autoclaving.
D. Its activity occurs in a limited temperature range between 25 and 65°C.

A

It is found in large concentrations on
hands.

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27
Q

Which of the following is the least likely
inhibitor of PCR?
A. Heme
B. Sodium heparin
C. DEPC (diethylpyrocarbonate)
D. EDTA (ethylenediaminetetraacetic
acid)

A

EDTA (ethylenediaminetetraacetic
acid)

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28
Q

Frequently, DNA probes are used to detect
target sequences in Northern or Southern
blots. Hybridization occurs between DNA
probe and RNA or DNA on the blot,
respectively. To ensure that only exactly
matched complementary sequences have
bound together, the blot is washed under
stringent conditions. Stringency of the
wash steps to remove unbound and
mismatched probe can be increased by
A. High temperature, high NaCl
concentration, and high detergent (i.e.,
SDS) solution
B. High temperature, low NaCl concentration, and high detergent (i.e., SDS)
solution
C. High temperature, high NaCl
concentration, and low detergent (i.e.,
SDS) solution
D. Low temperature, high NaCl concentration, and high detergent (i.e., SDS)
solution

A

High temperature, low NaCl concentration, and high detergent (i.e., SDS)
solution

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29
Q

In RNA, which nucleotide base replaces
thymineofDNA?
A. Adenine
B. Cytosine
C. Guanine
D. Uracil

A

Uracil

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30
Q

The component parts of a dNTP include a
purine or pyrimidine base, a
A. Ribose sugar, and one phosphate
group
B. Deoxyribose sugar, and three
phosphate groups
C. Ribose sugar, and two phosphate
groups
D. Deoxyribose sugar, and two phosphate
groups

A

Deoxyribose sugar, and three
phosphate groups

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31
Q

The component parts of a dNTP include a
purine or pyrimidine base, a
A. Ribose sugar, and one phosphate
group
B. Deoxyribose sugar, and three
phosphate groups
C. Ribose sugar, and two phosphate
groups
D. Deoxyribose sugar, and two phosphate
groups

A

Deoxyribose sugar, and three
phosphate groups

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32
Q

Molecular typing of bacterial strains is
based on restriction fragment length
polymorphisms (RFLPs) produced by
digesting bacterial chromosomal DNA with
restriction endonucleases. Which of the
following techniques is used to separate the
large DNA fragments generated?
A. Ribotyping
B. DNA sequencing
C. Pulsed field gel electrophoresis
D. Reverse transcription-polymerase
chain reaction

A

Pulsed field gel electrophoresis

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33
Q

Which of the following amplification
methods does not employ isothermal
conditions?
A. Nucleic acid sequence-based
amplification (NASBA)
B. Polymerase chain reaction (PCR)
C. Strand displacement amplification
(SDA)
D. Transcription mediated amplification
(TMA)

A

Polymerase chain reaction (PCR)

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34
Q

The coding region of a human gene is called
A. Exon
B. Intron
C. SNP
D. VNTR

A

Exon

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35
Q

The central dogma is that DNA is used to
make RNA, which is then used to make
protein. In this scheme the two processes
that are involved (i.e., DNA to RNA and
RNA to protein) are termed
A. Replication and transcription
B. Synthesis and encryption
C. Transcription and translation
D. Initiation and elongation

A

Transcription and translation

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36
Q

How many chromosomes are contained in
a normal human somatic cell?
A. 22
B. 23
C. 44
D. 46

A

46

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37
Q

An ordered sequence of events makes up
the cell cycle. Which of the following
describes the correct sequence of events
starting at Gl?
A. G1,G2, S,M
B. G1,S,G2,M
C. G1,M,G2, S
D. G1,S,M, G2

A

G1,S,G2,M

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38
Q

Purified DNA remains stable indefinitely
when stored as
A. Small aliquots at 4°C
B. Large aliquots at 25°C
C. Small aliquots at -70°C
D. Large aliquots at -20°C

A

Small aliquots at -70°C

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39
Q

An advantage of amplification technologies for clinical laboratories is that
A. They require inexpensive test reagents
B. They lend themselves to automated
methods
C. Each target molecule sought requires a
unique set of primers
D. Contamination is not a concern when
performing these assays

A

They lend themselves to automated
methods

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40
Q

The assay method that detects the
expression of a gene rather than the mere
presence or structure of a gene is termed
A. RT-PCR
B. TMA
C. Multiplex PCR
D. Ribotyping

A

RT-PCR

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41
Q

Which of the following assays cannot be
accomplished using PCR methods
employing only Tag polymerase?
A. Diagnosis of Chlamydia trachomatis
and Neisseria gonorrhoeae infection
B. Detection of single base pair gene
mutations, such as in cystic fibrosis
C. Detection of HLA-A, B and DR
genotypes
D. Determination of viral load for HCV

A

Determination of viral load for HCV

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42
Q

One method to prevent “false-positive”
PCR results includes the use of dUTP in
the reaction mix, resulting in amplicons
containing U in place of T. The enzyme
used to decrease contamination is
A. Uracil-/V-glycosylase
B. Tag polymerase
C. SI nuclease
D. DNase

A

Uracil-/V-glycosylase

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43
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

An oligonucleotide with a large number of
repeating C-G-C codons

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44
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

A-A-G-C-T-T
T-T-C-G-A-A

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45
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

Plasmid

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46
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

Substitution of biotinylated or fluorescent
nucleotides into the probe

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47
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

Restriction fragment length polymorphisms

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48
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

Ethidium bromide

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49
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

Southern blot

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50
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

Nonsense

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51
Q

In humans, which component of a gene is
translated into a protein?
A. Intron
B. Exon
C. Promoter
D. TATA box

A

Exon

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52
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

A variation in DNA that occurs with a frequency
of at least 1%

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53
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

Single nucleotide polymorphism (SNP)

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54
Q

Which of the following mechanisms facilitates
DNA separation by capillary electrophoresis?
A. Molecular sieving
B. Partitioning
C. Adsorption
D. Deflection

A

Molecular sieving

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55
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

Denaturation→Annealing→Extension

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56
Q

In the PCR cycle, how is denaturation
accomplished?
A. Heat
B. Alkali treatment
C. Addition of sulfonylurea
D. Formamide

A

Heat

57
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

An oligonucleotide complementary to bases at
the 3´ end of the target

58
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

Deoxyribonucleotide triphosphates

59
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

it is heat stable

60
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

By labeling multiple primers with specific fluors

61
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

2n where n is the number of cycles

62
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

Add a heat-stable reverse transcriptase enzyme to
the master mix

63
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

The target DNA is bound by multiple
probes, and those are amplified instead of
the target DNA

64
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

Contamination of control sample with a trace
amount of template DNA

65
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

Using an internal control

66
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

Pretreatment of samples with high-intensity
ultraviolet light

67
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

By comparing PCR product to an internal
standard

68
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

The result should not be reported and the sample
should be repeated

69
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

The threshold cycle versus concentration

70
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

Each cycle generates a twofold increase in
product

71
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

Melting temperature

72
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

Background signal

73
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

SYBR green

74
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

Hybridization is performed directly on intact
chromosomes

75
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

A cell suspension containing maternal and fetal
blood

76
Q

FISH can distinguish each of the following
chromosomal abnormalities except:
A. Aneuploidy
B. Translocation
C. Deletion
D. Trinucleotide repeats

A

Trinucleotide repeats

77
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

The sample DNA

78
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

A primer is made to the polyA tail of mRNA

79
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

he amount of each target is larger on a
macroarray

80
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

Mass spectroscopy

81
Q

In the reverse transcriptase PCR, the cDNA is synthesized by:
a. reverse transcriptase
b. DNA polymerase
c. Oligo dT primers
d. RNAse H

A

reverse transcriptase

82
Q

disadvantages of using a nested PCR

A

susceptible to contamination

83
Q

What is the relationship of the fluorescent dye to the single stranded DNA in every PCR cycle?
a. direct relationship
b. inverse relationship
c. no relationship
d. none of these options

A

no relationship

84
Q

What will happen to the target DNA sequence if the annealing temperature is too high?
1. No hybridization takes place
2. Primers and templates remains dissociated
3. Production of mismatch hybrids
4. Amplification is more likely to occur at nontarget sites in the template molecule

a. 1 and 2
b. 2 and 3
c. 3 and 4
d. 2 and 4
e. 1 and 4

A

1 and 2

85
Q

What will happen to the target DNA sequence if the annealing temperature is too low?
1. No hybridization takes place
2. Primers and templates remains dissociated
3. Production of mismatch hybrids
4. Amplification is more likely to occur at nontarget sites in the template molecule

a. 1 and 2
b. 2 and 3
c. 3 and 4
d. 2 and 4
e. 1 and 4

A

3 and 4

86
Q

What would be the effect to the amplicons, if the denaturation temperature is too low?

A

the DNA will not completely denature and amplification efficiency will be low

87
Q

Which of the following are correct when using a Multiplex PCR?
1. A minimum of three primer sets designed for amplification of different targets are included in the same PCR reaction.
2. More than one target sequence in a clinical specimen can be amplified in a single tube.
3. The primers used must be selected carefully to have similar annealing temperatures should be complementary to each other.
4. The amplicon sizes should be different enough to form distinct bands when visualized by gel electrophoresis.

a. 1 and 2 b. 1 and 3 c. 2 and 3 d. 2 and 4

A

2 and 4

Multiplex PCR facts:
More than one target sequence in a clinical specimen can be amplified in a single tube.
The amplicon sizes should be different enough to form distinct bands when visualized by gel electrophoresis.
A minimum of one primer sets designed for amplification of different targets are included in the same PCR reaction.
The primers used must be selected carefully to have similar annealing temperatures but should not be complementary to each other.

88
Q

Which of the following is true about the length of a primer:

A

If the primers are too short, they might hybridize to nontarget sites and give undesired amplification products

89
Q

Which of the following troubleshooting procedures must be performed when the annealing time is too short?

A

use an annealing time of at least 30 seconds

90
Q

result if Too few cycles were used

A

Can lead insufficient
amplification

91
Q

result if Extension time is too short

A

incomplete
replication of the target

92
Q

result if Annealing times too short

A

Primers do not have enough
time to bind to the template

93
Q

Annealing temperature was too
high

A

Primers are unable to bind to the
template

94
Q

Denaturation temperature was
too low

A

incompletely
denature and amplification
efficiency will be low

95
Q

Denaturation time was too long

A

DNA might be degraded

96
Q

Denaturation time was too short

A

incompletely
denature and amplification
efficiency will be low

97
Q

TRUE OR FALSE
To use a more cycles when the temperature concentration was
high and used less cycles when the temperature concentration was low

A

False; they are inversely proportional

98
Q

TRUE OR FALSE
Rule of thumb (Annealing Temperature)
should be 5 C lower than the melting point of primer

A

TRUE

99
Q

Implies that data collection and analysis occur in a reaction proceeds

A

Real Time

100
Q

true or false
Annealing temperature is independent on the primers sequences and is the
critical factor for a successful PCR reaction.

A

False; it is dependent

101
Q

Statement 1- If the primers are too short, they might hybridize to nontarget sites and give
undesired amplification products.
Statement 2 - Long primers hybridize at a slower rate. The efficiency of
the PCR is therefore reduced if the primers are too long

A

1 Statement is true, 2 Statement is true

102
Q

Statement 1- If the primers are too short, they might hybridize to nontarget sites and give
undesired amplification products.
Statement 2 - Long primers hybridize at a slower rate. The efficiency of
the PCR is therefore reduced if the primers are too long

A. Neither Statements are correct
B. 1 Statement is true, 2 Statement is true
C. 1 Statement is false, 2 Statement is true
D. 2 Statement is false, 1 Statement is true

A

1 Statement is true, 2 Statement is true

103
Q

Statement 1:Nested PCR was developed to increase the sensitivity but has a low specificity
of PCR
Statement 2: The products of the first round of amplification are then subjected to a second
round of amplification using the first set of primers

A. Neither Statements are correct
B. 1 Statement is true, 2 Statement is true
C. 1 Statement is false, 2 Statement is true
D. 2 Statement is false, 1 Statement is true

A

1 Statement is false, 2 Statement is true

rationale: Nested PCR was developed to increase the sensitivity and specificity
of PCR

104
Q

All are true about the multiplex PCR , except

a. more than one target sequence in a clinical specimen
can be amplified in a single tube.
b. The primers used in multiplex reactions must be selected carefully to have
similar annealing temperatures and must be complementary to each
other.
c. The amplicon sizes should be different enough to form distinct bands when
visualized by gel electrophoresis
d. None of the above

A

The primers used in multiplex reactions must be selected carefully to have
similar annealing temperatures and must be complementary to each
other.

Rationale: must not be complementary to each
other.

105
Q

Statement 1 - A reaction’s Ct is directly linked to the starting concentration of target
sequence
Statement 2 - In the linear part of the PCR amplification, the Ct is directly correlated with
the log of the number of nucleic acid target sequence copies initially present
in the sample

A. Neither Statements are correct
B. 1 Statement is true, 2 Statement is true
C. 1 Statement is false, 2 Statement is true
D. 2 Statement is false, 1 Statement is true

A

2 Statement is false, 1 Statement is true

rationale: In the linear part of the PCR amplification, the Ct is inversely correlated with
the log of the number of nucleic acid target sequence copies initially present
in the sample

106
Q

Uses two pairs of amplification and two rounds of PCR

a. multiplex PCR
b. RT PCR
c. Nested PCR
d. Digital PCR

A

Nested PCR

107
Q

Statement 1 - Random hexamers/decamers are 18-base long long single stranded
oligonucleotides of random sequences
Statement 2 - Oligo dT primers are 12-base long single stranded poly dT sequence
that will prime cDNA synthesis from mRNA with poly A tails

A. Neither Statements are correct
B. 1 Statement is true, 2 Statement is true
C. 1 Statement is false, 2 Statement is true
D. 2 Statement is false, 1 Statement is true

A

Neither Statements are correct

Rationale:
Random hexamers/decamers 6 to 10 long base
Oligo dT primers are 18-base long

108
Q

Primers in RT PCR

A

Oligo dT and random hexamers/decamers

109
Q

Statement 1: Denaturation: occurs for 20-30 seconds at 94 degrees Celsius.
Statement 2: Annealing: occurs for 20-30 seconds at 50-60 degrees Celsius
Statement 3:Elongation: typically run at 72-74 degrees Celsius for 5 to 15 minutes

A. Neither Statements are correct
B. 1 and 2 Statement is true, 3 Statement is false
C. 1 Statement is false, 2 and 3 Statement is true
D. 2 Statement is false, 1 and 3 Statement is true
E. All statements are true

A

2 Statement is false, 1 and 3 Statement is true

rationale:Annealing: occurs for 20-40 seconds at 50-60 degrees Celsius

110
Q

True or false
During the elongation step, the DNA polymerase will synthesize new
double stranded DNA.

A

TRUE

111
Q

Choose A – 1st false 2nd true
Choose B 1st true 2nd false
Choose C both false
Choose D both true

In qPCR, regardless of starting point, all reactions will end at the same, or similar, concentration. qPCR involves gathering of information during the reaction, when different reactions are still in the exponential phase.

A
112
Q

Choose A – 1st false 2nd true
Choose B 1st true 2nd false
Choose C both false
Choose D both true

Cycle threshold is the number of PCR cycles required to exceed the background fluorescence. It is also the number of which the fluorescence of the given sample crosses the threshold value

A
113
Q

The conventional PCR can only evaluate the end product of PCR reaction, which can be quantitatively but not qualitatively accurate. The qPCR eliminates the need for post amplification manipulation.

Choose A – 1st false 2nd true
Choose B 1st true 2nd false
Choose C both false
Choose D both true

A
114
Q

If the denaturation time is too short, the DNA will completely denature and amplification efficiency will be low. For the initial denaturation, use 3 min to activate the polymerase and to denature the template during cycling, use 30 sec.

Choose A – 1st false 2nd true
Choose B 1st true 2nd false
Choose C both false
Choose D both true

A
115
Q

If the annealing temperature is too high, primers are unable to bind to the template. The rule of thumb is to use an annealing temperature that is 5°C higher than the melting point of the primer.

Choose A – 1st false 2nd true
Choose B 1st true 2nd false
Choose C both false
Choose D both true

A
116
Q

Which generation of sequencing relied on cycles of the termination of DNA polymerization and recording of the incorporated nucleotides in each cycle?

a. Manual sequencing
b. Third generation sequencing
c. Second generation sequencing
d. None of these
e. First generation sequencing

A
117
Q

Production of a human protein in bacteria genetic engineering is possible because:
a. Bacterial cell can carry out the RNA splicing reactions
b. The genetic code is universal
c. The mechanism of gene regulation is identical in human and bacteria
d. The human chromosome can replicate in bacterial cell

A
118
Q

For protein detection, the most commonly used probe is?

A

Antibody

119
Q

1st statement: Chain-termination DNA sequencing is based on the principle that during DNA synthesis, addition of a nucleotide triphosphate requires a free hydroxyl group on the 3’ carbon of the sugar of the first nucleotide of the growing DNA strand.

2nd statement: However, if a synthetic dideoxynucleotide that lacks a hydroxyl group at the 5’ carbon of the sugar moiety is incorporated at the end of the growing chain, DNA synthesis stops because a phosphodiester bond cannot be formed with the next incoming nucleotide.

a. Only the second statement is true
b. Both statements are true
c. Only the first statement is true
d. Both statements are false

A
120
Q

A technique of centrifugation that uses repeated centrifugation with a progressive speed that will fractionate the cell homogenates into their components.

A

differential centrifugation

121
Q

All are the example criteria for selecting a technique for protein quantification and purification, EXCEPT:

A

Storage temperature

122
Q

the process by which a sample is broken into identical parts so that removing one portion of it does not disrupt and still accurately reflects the remaining sample’s molecular composition.

A

Homogenization

123
Q

The technique used to detect the presence of DNA or RNA in a Non-fractionated DNA sample is?

A

Dot Blot Technique

124
Q

Which of the following cell lysis detergent are not example of non-ionic type detergent?
a. Tween 80
b. Triton X-100
c. NP-40
d. Tween 20
e. Sodium dodecyl sulfate

A
125
Q

Before DNA sequencing, the template DNA must first be prepared by ensuring that there is enough single-stranded version of the DNA to be used. Which among the following is not used to prepare the template DNA?

A

Phage vector B7

126
Q

The most widely used device to separate a homogenate into different parts or fractions.

A

Centrifugation

127
Q

The principle techniques to remove contaminants and detergent from proteomic samples use saturated salts to precipitate proteins in the form of ammonium sulfate precipitation or sodium sulfate.

A

Salting out

128
Q

was the first of the high-throughput DNA sequencing technologies to be made commercially available.

A

pyrosequencing

129
Q

1st statement: Because the Klenow polymerase has low processivity, it can only synthesize a relatively short DNA strand before dissociating from the template. This limits the length of sequence that can be obtained from a single experiment to about 250 bp.
2nd statement: To improve this short synthesis problem, most sequencing today makes use of a more specialized enzyme, such as Sequenase which is a modified version of the DNA polymerase encoded by bacteriophage T5. Sequenase has high processivity and no exonuclease activity and so is ideal for chain-termination sequencing, enabling sequences of up to 750bp to be obtained in a single experiment.
a. Only the second statement is true
b. Both statements are true
c. Only the first statement is true
d. Both statements are false

A
130
Q

Which among the following is not a method of how manual sequencing was automated.
a) replacement of radioactive labels by fluorescent labels
b) use of thermal cyclers
c) use of fluorescent detection systems,
d) use of capillary gel electrophoresis
e) none of these

A
131
Q

Which of the following substances/chemicals will not interfere with the Lowry colorimetric method?

A

Tris buffer

132
Q

What is the color reaction of Bicinchonic acid assay?

A

Deep-blue reaction

133
Q

What is the chemical reactant used in Bradford assay?

A

Deep-blue reaction

134
Q

What is the chemical reactant used in Bradford assay?

A

Coomassie brilliant blue

135
Q

The principle of this colorimetric assay is based on the complex formation of cupric ions with the proteins.

A

Biuret reaction

136
Q

This type of buffer for 2DE disrupts the non-covalent and ionic bonds between amino acid residues

A

Chaotropic agents

137
Q

What is the difference between the Urea-PAGE and SDS-PAGE?

A

Urea-PAGE Denature RNA strands, while the SDS-PAGE denature proteins and coat with them in negative charges.

138
Q

This device is used for identification of each protein in the sample which undergo digestion, ionization and fragmentation.

A

Mass spectrometry

Molecular Biology Prelims (9 decks)

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