molbio Flashcards
(132 cards)
1
Q
component of a nucleotide is bound to carbon 5 of deoxyribose
A
phosphate group
2
Q
component of a nucleotide is bound to carbon 1 of deoxyribose
A
nitrogenous base
3
Q
DNA polymerase attaches nucleotides to the _ end of the growing strand
A
3’
4
Q
these are short RNA strands that anneal to the template strand to initiate DNA synthesis by the DNA polymerase enzyme
A
primers
5
Q
sample that is least likely to produce high yield DNA
A
serum
6
Q
reagent used to precipitate DNA and RNA from extracts
A
ethanol
7
Q
chaotropic salts are added to silica-based matrices to facilitate _
A
DNA/RNA binding
8
Q
Chelex resin beads are useful in DNA isolation because they _
A
adsorb contaminants
9
Q
binding, washing, and elution steps are performed for which isolation methods
A
solid-phase isolation method
10
Q
The following methods can be used to isolate mitochondrial DNA from chromosomal DNA, EXCEPT:
a. Differential centrifugation
b. RNAse digestion
c. Agarose gel electrophoresis
d. PCR
e. Density gradient centrifugation
A
b. RNAse digestion
11
Q
which isolation method is an aqueous layer and organic layer formed
A
phenol/chloroform method
12
Q
in phenol/chloroform method, DNA and RNA are harvested from which layer
A
aqueous phase
13
Q
in the Chelex method of DNA isolation, DNA are released from the cells through
A
boiling
14
Q
when determining the concentration of RNA through spectrophotometry, the absorbance reading is multiplied by a factor of _
A
40
15
Q
what is the dsDNA concentration from an absorbance of 0.216
A
10.8 µg/mL (multiply to 50)
16
Q
A
17
Q
DNA and RNA concentrations may be determined through spectrophotometry by measuring absorbance at _
A
260 nm
18
Q
DNA to protein ratio is also known as the
A
A260/A280 ratio
19
Q
which electrophoresis format requires complete denaturation of the sample
A
capillary electrophoresis
20
Q
Which electrophoresis method employs currents applied in alternating directions
A
pulse field gel electrophoresis
21
Q
Which electrophoresis method is performed in the vertical orientation
A
Polyacrylamide gel electrophoresis
22
Q
best used if attempting to resolve DNA fragments that are more than 200 kbps long
A
Pulse field gel electrophoresis
23
Q
agarose gels are used for electrophoresis in the _ concentration range
A
0.5 – 5.0%
24
Q
it can be done to shorten the run time of a gel electrophoresis protocol
A
increase the voltage
25
in DNA electrophoresis, bromphenol blue is used as a _
tracking dye
26
Tris Borate EDTA (TBE) is a reagent used for
electrophoresis buffer
27
Ficoll or glycerol is incorporated into the loading buffer in order to _
make the DNA/RNA sink into the wells
28
28
a device for the visualization of electrophoresis bands
transilluminator
29
what DNA stain will not fluoresce using blue light
Ethidium Bromide
30
a stain that requires a post-electrophoresis color development procedure and cannot be incorporated into the gel prior to the electrophoresis run
silver stain
31
may be added to the electrophoresis buffer in order to keep the DNA in a denatured state
Formamide
32
when determining the optimal voltage for DNA electrophoresis, it is common practice to multiply the length (cm) of the gel to _
5-10 volts
33
true about restriction sites (3)
double stranded DNA only
palindromic sequences
4-8 bp long
34
Restriction enzymes produce 2 types of cuts. Which type is best for gene splicing?
Sticky end cut
35
the pattern that shows the number and size of DNA fragments after restriction digestion and electrophoresis is known as _
RFLP
36
the visual representation of the location of known restriction sites along a section of DNA is known as
restriction map
37
a probe used to immobilize target DNA or RNA onto a solid surface
capture probe
38
These methods utilize hybridization and electrophoresis technology, EXCEPT:
a. Reverse dot blot
b. S1 Mapping
c. Southern blot
d. Northern blot
a. Reverse dot blot
39
Light emission through chemiluminescence is employed in _
hybridization protection
40
Compute the melting temperature of the following DNA sequence: ATCTCGAATGTAAGTACG
50°C (count A&T then multiply to 2°C, count G&C then multiply to 4°C)
41
in reverse dot blots, labels are bound to the _
sample DNA
42
a method that consists of restriction enzyme digestion, DNA electrophoresis, transfer of DNA
into a membrane, and staining with sequence-specific probes
southern blot
43
a method that is appropriate for determining how many copies of a particular chromosome is found within a cell
in situ hybridization
44
The following are examples of in-solution hybridization technology, EXCEPT:
a. Hybridization protection
b. Hybrid capture
c. Northern blot
d. S1 mapping
c. Northern blot
45
synthetic nucleic acid analogs used as probes are _
nuclease resistant
46
a solid support hybridization method that uses a glass slide for immobilizing the blots
microarrays
47
which type of restriction enzyme is used for restriction enzyme mapping
type 2
48
a method that involves alkaline hydrolysis and treatment with H2O2 to generate the positive
signal
hybridization protection
49
The following factors increase the stringency of hybridization reactions
a. high temperature
b. low salt concentration
c. low probe concentration
d. low sequence complexity
d. low sequence complexity
50
which step in a PCR cycle is usually accomplished at a temperature of 72°C
extension
51
which PCR technology is used to preferentially amplify one strand of the target sequence over the other and therefore produce mostly ssDNA products?
asymmetric PCR
52
polymerase chain reaction is an example of _
target amplification
53
The following components can be found in both PCR and in vivo DNA replication, EXCEPT:
a. Primers
b. DNA polymerase
c. dNTPs
d. template DNA
e. Ligase
e. Ligase
54
Which of the following is NOT true about PCR?
a. amplifes select DNA sequences
b. employs RNA primers
c. Denaturaton occurs at 94-95C
d. utilizes thermostable DNA polymerase
e. multiple target sequences can be amplified
simultaneously
b. employs RNA primers
55
which PCR component that comes from the patient’s sample
template DNA
56
threshold cycle (Ct) value is generated when performing _
real time PCR
57
serves as a reagent blank for real time PCR tests
negative control
58
which DNA polymerases can be used for one-step RT-PCR due to its reverse transcriptase activity
Tth polymerase
59
which DNA polymerases is best for gene cloning due to its proof-reading ability
Vent polymerase
60
which PCR Control results indicate the presence of mispriming
Negative Template Control = positive
61
which PCR Control results is the best indicator of the presence of contamination with PCR products
Negative Control = positive
62
which PCR Control results indicate an “out of control” test run
Internal Amplification Control = negative
63
method to destroy contamination due to PCR products
dUTP-UNG
64
method to minimize mispriming by creating a high stringency environment at the start of PCR while gradually proceeding to the optimal environment
Touchdown PCR
65
not found in conventional PCR but necessary in real time multiplex PCR
DNA probe
66
Heat-activated DNA polymerases are used for _ (2)
1. preventing polymerization due to mispriming
2. One-Step RT-PCR
67
purpose of Hot-start PCR
prevent mispriming
68
which PCR modification allows detection of the accumulation of PCR products while amplification is ongoing
qPCR
69
Which PCR method employs two rounds of PCR where the second round uses a primer pair that bind to sites within the binding regions of the first primer pair
Nested PCR
70
primer of choice for RT-PCR when amplifying whole mRNA sequences
Oligo dT primers
71
Which primers are appropriate when attempting to amplify a completely unknown sequence
random hexamers
72
PCR method that utilizes several primer pairs to simultaneously amplify different target sequences
Multiplex PCR
73
73
The following are true about real-time PCR, except:
a. requires a thermocycler that detects fuorescence
b. Ct values are directly proportional to the amount of starting target DNA
c. also known as quantitative PCR
d. may utilize fluorescent probes to increase specificity
b. Ct values are directly proportional to the amount of starting target DNA
74
the ability of PCR to amplify only the target of interest is based on _
primer specificity
75
primers that have 2-3 complementary bases at their 3’ ends produce PCR products known as _
primer dimers
76
A PCR master mix contains all the reagents for PCR, EXCEPT:
a. DNA polymerase
b. Buffer
c. Primers
d. dNTPs
c. Primers
77
Which probe is degraded by the exonuclease activity of Taq polymerase during polymerization of a new DNA strand
TaqMan
78
which labeled probe is attached or tailed to the 5’ end of the primer
Scorpion-type
79
which uses two probes, one with a fluorophore and another with a catalyst that binds to adjacent sites in the target sequence
FRET
80
an isothermal amplification method whose products are in the form of RNA strands instead of DNA
Transcription Based Amplification (TBA)
81
The following are signal amplification methods, EXCEPT:
a. Branched DNA Amplification
b. Ligase Chain Reaction
c. Hybrid Capture
d. Cleavage-based Amplification
e. none of the choices
b. Ligase Chain Reaction
82
The following are probe amplification methods, EXCEPT:
a. Cycling Probe
b. Qβ Replicase
c. Strand Displacement Amplification
d. Ligase Chain Reaction
e. none of the choice
a. Cycling Probe
83
an isothermal probe amplification method that utilizes a restriction enzyme to create a nick at the 3’ end of the primer to initiate another round of DNA polymerization
Strand Displacement Amplification
84
a probe amplification method where the target sequence is first immobilized using capture probes bound to paramagnetic beads, followed by the amplification of the reporter probe using a phage RNA polymerase
Qβ Replicase
85
TaqMan probes, Molecular Beacons, and Scorpion-type Primers utilize which pair of tags/labels
Fluorophore and Quencher
86
label that is used in fluorescent resonance energy transfer (FRET)
Fluorophore and Catalyst
87
In Real-time PCR, molecular beacons emit fluorescence (before / after) displacement by the Taq polymerase
before
88
a target amplification method that is least appropriate when attempting to amplify a target sequence for subsequent electrophoresis or DNA/RNA sequencing
Loop-Mediated Isothermal Amplification
89
The following are components of RT-PCR, EXCEPT:
a. RNA template
b. RNA polymerase
c. Primers
d. dNTPs
e. none of the choices
b. RNA polymerase
90
a target amplification method that utilizes self-priming and strand displacement to achieve isothermal amplification
LAMP
91
In the dideoxy chain termination method of DNA sequencing, ddNTPs cause termination of the polymerization step because _
ddNTPs do not have the hydroxy group at the 3’ end
92
Denaturing Gradient Gel Electrophoresis is used when detecting mutations in _
dsDNA
93
How many probes are used for the Ligase Chain Reaction assays?
four
94
How many probes are used for the FRET amplification assays?
one pair
95
The following are true about short tandem repeat (STR) technology, EXCEPT:
a. based on repeating DNA sequences found
in selected introns
b. also known as minisatellite DNA technology
c. used for human identification
d. sequences are 2-7 bp long
b. also known as minisatellite DNA technology
96
The following are true about RFLP technology, EXCEPT:
a. Southern blotting technology may be used to resolve bands
b. Depends on restriction enzyme digestion technology
c. May be used for human identifcation
d. used for tissue-typing to determine donor-recipient compatibility
e. also known as sequence-specific PCR
e. also known as sequence-specific PCR
97
gold standard method for DNA Sequencing
Dideoxy Chain Termination Method
98
Detection and characterization of 16s rRNA Gene is performed when analyzing _
bacteria
99
Point-of-care tests using LAMP have been developed that detect turbidity resulting from the production of _ as a byproduct of amplification
Mg Pyrophosphates
100
The following technologies are appropriate for DNA-based tissue typing, EXCEPT:
a. sequence specific probes
b. RFLP analysis
c. VNTR analysis
d. sequence specific PCR
c. VNTR analysis
101
Which of the following is NOT TRUE about the use of PAGE for single-strand conformation polymorphism determination?
a. can diferentiate between ssDNA fragments of the same lengths but dif sequences
b. utilizes the vertical gel format
c. uses an increasing gradient of denaturing agent in the gel
d. all of the choices
c. uses an increasing gradient of denaturing agent in the gel
102
process of producing RNA copy of a gene from a DNA template
transcription
103
The following are methods of DNA and RNA isolation, EXCEPT:
a. restriction digestion
b. salting out
c. phenol-chloroform method
d. magnetic beads
a. restriction digestion
104
base pairs that have three hydrogen bonds
Guanine-Cytosine
105
attached to the 3’ carbon
-OH
106
Which of the following is not a circular piece of double strand DNA?
a. Plasmid
b. Mitochondrial DNA
c. Okazaki Fragments
d. Bacterial Chromosome
c. Okazaki Fragments
107
Which of the following is NOT TRUE about restriction sites?
a. palindromic sequences
b. RNA only
c. double strand only
d. none of the choices
b. RNA only
108
steps in solid-phase isolation
lysis-binding-washing-elution
109
temperature where 50% of a given sequence is double-stranded
melting temperature
110
slows down the migration of DNA during electrophoresis
high gel concentration
111
mixed with the DNA sample before loading into the electrophoresis gel
Bromphenol Blue
112
an in-solution hybridization method that use both reporter and capture probes
hybrid capture
113
In positive hybridization protection assays, chemiluminescence is detected after _
addition of H2O2
114
In DNA and RNA electrophoresis, nucleic acid strands migrate
towards the anode
115
118
DNA bases pair
ATGC
adenine:thymine
cytosine:guanine
119
number of chromosomal pairs
23
120
normal human has how many pairs of autosomes
22
121
technique that produces an image of the chromosomes and identifies their abnormalities
karyotype
122
PCR & Restriction Fragment Length Polymorphism are examples of
molecular assay
123
PCR & Ligase chain reaction & branch-chain amplification are _
amplification methods
124
uses primers & a constant temperature coupled to a strand displacement reaction
loop-mediated isothermal amplification (LAMP)
125
gold standard for many molecular applications from mutation detection to genotyping
DNA sequencing
126
gold standard or method of choice for SARS-CoV-2/COVID-19 testing
nucleic acid amplification (ex. RT-PCR)
127
test that facilitates in vitro DNA synthesis
PCR
128
it rapidly produces (amplifies) millions to billions of copies of a specific segment of DNA
PCR
129
PCR mastermix components (5)
Taq DNA polymerase
buffer
primers
MgCl2
deoxyribonucleotide triphosphates (dNTPs)
130
template for PCR
dsDNA
131
function of thermocycler
amplifies DNA and RNA
132
these are small fragments of newly replicated DNA
Okazaki fragments
