PIONEER: MOLECULAR BIOLOGY & DIAGNOSTICS

from quizlet

Which component of a nucleotide is bound to carbon 5 of deoxyribose?

a. Ribose

b. Nitrogenous Base

c. Phosphate Group

d. None of the choices

c. Phosphate Group

DNA polymerase attaches nucleotides to the ____________ end of the growing strand.

a. 1'

b. 2'

c. 3'

d. 4'

e. 5'

c. 3'

These are short RNA strands that anneal to the template strand to initiate DNA synthesis by the DNA polymerase enzyme.

a. Probes

b. Primers

c. Dimers

d. Okazaki Fragments

b. Primers

Which of the following samples is least likely to produce high yield DNA?

a. Tissue

b. Whole Blood

c. Bacterial Colonies

d. Serum

e. CSF

d. Serum

Which of the following reagents is used to precipitate DNA and RNA from extracts?

a. Chaotropic salt

b. Ethanol

c. TE Buffer

d. Elution Buffer

b. Ethanol

Chaotropic salts are added to silica-based matrices to facilitate...

a. DNA/RNA precipitation

b. Washing

c. DNA/RNA binding

d. Elution

e. Precipitate proteins

c. DNA/RNA binding

Chelex resin beads are useful in DNA isolation because they...

a. Elute DNA from silica

b. Adsorb DNA from the lysate

c. Adsorb contaminants

d. Stabilize DNA

c. Adsorb contaminants

Binding, washing, and elution steps are performed for which of the following isolation methods?

a. Organic Isolation Mtd

b. Inorganic Isolation Mtd

c. Solid-Phase Isolation Mtd

d. Chelating Ion Exchange Mtd

c. Solid-Phase Isolation Mtd

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

b. RNAse digestion

In which isolation method is an aqueous layer and organic layer formed?

a. Phenol/chloroform method

b. Salting out

c. Solid-Phase Isolation

d. Chelating Ion Exchange Resin

no answer

When determining the concentration of RNA through spectrophotometry, the absorbance reading is multiplied by

a factor of...

a. 50

b. 33

c. 40

d. 43

c. 40

In the above method, DNA and RNA are harvested from which layer?

a. Interphase

b. Organic phase

c. Aqueous phase

c. Aqueous phase

In the Chelex method of DNA isolation, DNA are released from the cells through...

a. NaOH

b. Boiling

c. Grinding

d. Protease

b. Boiling

What is the dsDNA concentration from an absorbance of 0.216?

a. 9.29 µg/mL

b. 8.64 µg/mL

c. 7.128 µg/mL

d. 10.8 µg/mL

d. 10.8 µg/mL

DNA and RNA concentrations may be determined through spectrophotometry by measuring absorbance at...

a. 260 nm

b. 230 nm

c. 280 nm

d. 240 nm

a. 260 nm

The DNA to protein ratio is also known as the:

a. A280/A260 ratio

b. A260/A230 ratio

c. A260/A280 ratio

d. A240/A260 ratio

c. A260/A280 ratio

Which electrophoresis format requires complete denaturation of the sample?

a. Agarose gel electrophoresis

b. Tube gel electrophoresis

c. Polyacrylamide gel electrophoresis

d. Capillary electrophoresis

d. Capillary electrophoresis

Which electrophoresis method employs currents applied in alternating directions?

a. Denaturing gradient gel electrophoresis

b. Polyacrylamide gel electrophoresis

c. Pulse field gel electrophoresis

d. Capillary electrophoresis

b. Polyacrylamide gel electrophoresis

Which electrophoresis method is performed in the vertical orientation?

a. Agarose gel electrophoresis

b. Polyacrylamide gel electrophoresis

c. Capillary electrophoresis

d. All of the choices

b. Polyacrylamide gel electrophoresis

Which of the following method is best used if attempting to resolve DNA fragments that are more than 200 kbps

long?

a. Denaturing gradient gel electrophoresis

b. Polyacrylamide gel electrophoresis

c. Pulse field gel electrophoresis

d. Capillary electrophoresis

c. Pulse field gel electrophoresis

Agarose gels are used for electrophoresis in the ________________ concentration range.

a. 7-9%

b. 0.5 - 5.0%

c. 0.2 - 1.5%

d. 10-20%

b. 0.5 - 5.0%

Which of the following can be done to shorten the run time of a gel electrophoresis protocol?

a. Increase the concentration of the gel

b. Decrease the concentration of the buffer

c. Increase the voltage

d. Increase the concentration of the stain

e. Decrease the concentration of Ficoll

c. Increase the voltage

In DNA electrophoresis, bromphenol blue is used as a...

a. Tracking dye

b. DNA stain

c. Density gradient

d. Denaturing agent

a. Tracking dye

Tris Borate EDTA (TBE) is a reagent used for which of the following purposes?

a. Electrophoresis buffer

b. Elution buffer

c. DNA binding to silica

d. Lysis buffer

a. Electrophoresis buffer

Ficoll or glycerol is incorporated into the loading buffer in order to...

a. Track the migration of bands

b. Prevent bands from migrating beyond the gel

c. Make the DNA/RNA sink into the wells

d. Protect DNA/RNA from enzyme digestion

e. Improve transparency of the gel

c. Make the DNA/RNA sink into the wells

Which of the following is a device for the visualization of electrophoresis bands?

a. Thermal cycler

b. Utracentrifuge

c. Transilluminator

d. Nanodrop spectrophotometer

c. Transilluminator

Which of the following DNA stains will not fluoresce using blue light?

a. Ethidium Bromide

b. GelRed

c. SYBR Green

d. GelGreen

e. SYBR Gold

a. Ethidium Bromide

Which of the following stains require a post-electrophoresis color development procedure and cannot be

incorporated into the gel prior to the electrophoresis run?

a. SYBR Green

b. EtBr

c. Silver Stain

d. Gel Red

c. Silver Stain

Which of the following may be added to the electrophoresis buffer in order to keep the DNA in a denatured state?

a. Ficoll

b. Glycerol

c. Xylene Cyanol Green

d. Formamide

e. Bromphenol blue

d. Formamide

When determining the optimal voltage for DNA electrophoresis, it is common practice to multiply the length (cm)

of the gel to which of the following?

a. 15-20 volts

b. 2-5 volts

c. 5-10 volts

d. 10-15 volts

c. 5-10 volts

Which of the following is not true about restriction sites?

a. Double stranded DNA

only

b. Palindromic sequences

c. 4-8 bp long

d. All of the choices

e. None of the choices

e. None of the choices

Restriction enzymes produce 2 types of cuts. Which type is best for gene splicing?

a. Blunt end cut

b. Sticky end cut

b. Sticky end cut

The pattern that shows the number and size of DNA fragments after restriction digestion and electrophoresis is

known as...

a. RFLP

b. Restriction Map

c. Southern Blot

d. Karyotype

a. RFLP

The visual representation of the location of known restriction sites along a section of DNA is known as...

a. RFLP

b. Restriction Map

c. Southern Blot

d. Karyotype

b. Restriction Map

A probe used to immobilize target DNA or RNA onto a solid surface is known as the:

a. Tailed probe

b. Capture probe

c. Reporter probe

d. PNA probe

b. Capture probe

These methods utilize hybridization and electrophoresis technology, EXCEPT...

a. Reverse dot blot

b. S1 Mapping

c. Southern blot

d. Norther blot

a. Reverse dot blo

Light emission through chemiluminescence is employed in which of the following?

a. In Situ Hybridization

b. Sandwich Hybridization

c. Hybridization Protection

d. Hybrid Capture

c. Hybridization Protection

Compute the melting temperature of the following DNA sequence: ATCTCGAATGTAAGTACG

a. 75 oC

b. 50 oC

c. 46 oC

d. 92 oC

b. 50 oC

In Reverse Dot Blots, labels are bound to the...

a. Sample DNA

b. Capture probe

c. Reporter probe

d. PNA probe

a. Sample DNA

Which of the following methods consists of restriction enzyme digestion, DNA electrophoresis, transfer of DNA

into a membrane, and staining with sequence-specific probes?

a. Southern blot

b. Northern blot

c. Microarray

d. In situ hybridization

a. Southern blot

Which method is appropriate for determining how many copies of a particular chromosome is found within a cell?

a. Southern blot

b. Microarray

c. Macroarray

d. Northern Blot

e. In Situ Hybridization

e. In Situ Hybridization

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

Which of the following is true about synthetic nucleic acid analogs used as probes?

a. have lower affinities to the targets

b. less stable than normal DNA or RNA

c. nuclease resistant

d. naturally occurring

c. nuclease resistant

Which of the following solid-support hybridization methods uses a glass slide for immobilizing the blots?

a. Northern blot

b. Dot blot

c. Macroarrays

d. Microarrays

d. Microarrays

Which type of restriction enzyme is used for restriction enzyme mapping?

a. Type I

b. Type II

c. Type III

d. Type IV

b. Type II

Restriction enzyme digestion was used to treat a 600bp gene fragment to detect a point mutation. The presence

of point mutation at the restriction site prevents digestion. Based on the results below, which patient suffers from

a mutation only in one allele of the gene?

a. Patients A,B, and E

b. Patient C

c. Patient D

d. All of the choices

b. Patient C

Which of the following methods involve alkaline hydrolysis and treatment with H2O2 to generate the positive

signal?

a. sandwich method

b. Northern blot

c. RNAse protection

d. reverse dot blot

e. Hybridization protection

e. Hybridization protection

he following factors increase the stringency of hybridization reactions, EXCEPT...

a. high temperature

b. low salt concentration

c. low probe concentration

d. low sequence complexity

d. low sequence complexity

Which step in a PCR cycle is usually accomplished at a temperature of 72oC?

a. Primer Annealing

b. Extension

c. Denaturation

b. Extension

Which PCR technology is used to preferentially amplify one strand of the target sequence over the other and

therefore produce mostly ssDNA products?

a. real-time PCR

b. RT-PCR

c. Asymmetric PCR

d. Nested PCR

c. Asymmetric PCR

The polymerase chain reaction is an example of...

a. probe amplification

b. target amplification

c. signal amplification

no answer

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

Which of the following is NOT true about PCR?

a. amplifies select DNA sequences

b. employs RNA primers

c. Denaturation occurs at 94-95C

d. utilizes thermostable DNA polymerase

e. multiple target sequences can be amplified

simultaneously

b. employs RNA primers

Which of the following PCR components comes from the patient's sample?

a. dNTPs

b. DNA probe

c. DNA polymerase

d. primers

e. template DNA

e. template DNA

The treshold cycle (Ct) value is generated when performing...

a. DNA sequencing

b. melting curve analysis

c. STR analysis

d. real time PCR

d. real time PCR

Which of the following serves as a reagent blank for real time PCR tests?

a. positive control

b. negative control

c. negative template control

d. internal amplification control

b. negative control

Which of the following DNA polymerases can be used for one-step RT-PCR due to its reverse transcriptase

activity?

a. Taq polymerase

b. Pfu polymerase

c. Vent polymerase

d. Tth polymerase

d. Tth polymerase

Which of the following DNA polymerases is best for gene cloning due to its proof-reading ability?

a. Taq polymerase

b. Pfu polymerase

c. Vent polymerase

d. Tth polymerase

c. Vent polymerase

Which of the following PCR Control results indicate the presence of mispriming?

a. Positive Control = negative

b. Negative Control = positive

c. Negative Template Control = positive

d. Internal Amplification Control = negative

c. Negative Template Control = positive

Which of the following PCR Control results is the best indicator of the presence of contamination with PCR

products?

a. Positive Control = negative

b. Negative Control = positive

c. Negative Template Control = positive

d. Internal Amplification Control = negative

b. Negative Control = positive

Which of the following PCR Control results indicate an "out of control" test run?

a. Positive Control = positive

b. Negative Control = negative

c. Negative Template Control = negative

d. Internal Amplification Control = negative

d. Internal Amplification Control = negative

Which of the following is a method to destroy contamination due to PCR products?

a. Hot-start PCR

b. Touchdown PCR

c. dUTP-UNG

d. SAP and ExoI

c. dUTP-UNG

Which of the following is a method to minimize mispriming by creating a high stringency environment at the

start of PCR while gradually proceeding to the optimal environment?

a. Hot-start PCR

b. Touchdown PCR

c. dUTP-UNG

d. SAP and ExoI

c. dUTP-UNG

Which of the following is not found in conventional PCR but necessary in real time multiplex PCR?

a. dNTPs

b. DNA probe

c. DNA polymerase

d. primers

b. DNA probe

Heat-activated DNA polymerases are used for...

a. preventing polymerization due to mispriming

b. One-Step RT-PCR

c. both A and B

d. neither A nor B

c. both A and B

What is the purpose of Hot-start PCR?

a. prevent contamination

b. remove contamination

c. prevent mispriming

d. prevent primer dimers

c. prevent mispriming

Which PCR modification allows detection of the accumulation of PCR products while amplification is ongoing?

a. Nested PCR

b. RT-PCR

c. Multiplex PCR

d. qPCR

d. qPCR

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.

a. Nested PCR

b. RT-PCR

c. Multiplex PCR

d. qPCR

a. Nested PCR

Which of the following is the primer of choice for RT-PCR when amplifying whole mRNA sequences?

a. target specific primers

b. Oligo dT primers

c. Random hexamers

b. Oligo dT primers

Which primers are appropriate when attempting to amplify a completely unknown sequence?

a. target specific primers

b. Oligo dT primers

c. Random hexamers

c. Random hexamers

A PCR method that utilizes several primer pairs to simultaneously amplify different target sequences is

called...

a. Nested PCR

b. RT-PCR

c. Multiplex PCR

d. qPCR

c. Multiplex PCR

The following are true about real-time PCR, except...

a. requires a thermocycler that detects fluorescence

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

The ability of PCR to amplify only the target of interest is based on...

a. DNA polymerase specificity

b. Primer specificity

c. dNTP specificity

d. all of the choices

b. Primer specificity

Primers that have 2-3 complementary bases at their 3' ends produce PCR products known as...

a. primer monomers

b. primer dimers

c. primer trimers

d. primer oligomers

b. primer dimers

A PCR master mix contains all the reagents for PCR, EXCEPT...a. DNA polymerase

b. Buffer

c. Primers

d. dNTPs

c. Primers

Which of the following probes is degraded by the exonuclease activity of Taq polymerase during

polymerization of a new DNA strand?

a. TaqMan

b. Molecular Beacon

c. Scorpion-type

d. FRET

a. TaqMan

Which of the following is a labeled probe attached/tailed to the 5' end of the primer?

a. TaqMan

b. Molecular Beacon

c. Scorpion-type

d. FRET

c. Scorpion-type

Which of the following uses two probes, one with a fluorophore and another with a catalyst that binds to

adjacent sites in the target sequence?

a. TaqMan

b. Molecular Beacon

c. Scorpion-type

d. FRET

d. FRET

Which of the following is an isothermal amplification method whose products are in the form of RNA strands

instead of DNA?

a. Reverse Transcriptase-PCR (RT-PCR)

b. Loop Mediated Isothermal Amplification

(LAMP)

c. Ligase Chain Reaction

d. Transcription Based Amplification (TBA)

d. Transcription Based Amplification (TBA)

Which of the following is 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?

a. Cycling Probe

b. Qβ Replicase

c. Strand Displacement Amplification

d. Ligase Chain Reaction

b. Ligase Chain Reaction

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

Which of the following is 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?

a. Ligase Chain Reaction

b. Strand Displacement Amplification

c. Branched-DNA Amplification

d. Hybrid Capture

b. Strand Displacement Amplification

Which of the following is 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?

a. Cycling Probe

b. Qβ Replicase

c. Strand Displacement Amplification

d. Ligase Chain Reaction

b. Qβ Replicase

TaqMan probes, Molecular Beacons, and Scorpion-type Primers utilize which pair of tags/labels?

a. Biotin and Streptavidin

b. Fluorophore and Catalyst

c. Fluorophore and Quencher

d. Enzyme-Substrate

c. Fluorophore and Quencher

Which type of label is used in fluorescent resonance energy transfer (FRET)?

a. Biotin and Streptavidin

b. Fluorophore and Catalyst

c. Fluorophore and Quencher

d. Enzyme-Substrate

b. Fluorophore and Catalyst

In Real-time PCR, molecular beacons emit fluorescence...

a. before displacement by the Taq polymerase

b. after displacement by the Taq polymerase

a. before displacement by the Taq polymerase

Which of the following is a target amplification method that is least appropriate when attempting to amplify a

target sequence for subsequent electrophoresis or DNA/RNA sequencing?

a. Polymerase Chain Reaction

b. Loop-Mediated Isothermal Amplification

c. Transcription-Based Amplification

b. Loop-Mediated Isothermal Amplification

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

Which of the following is a target amplification method that utilizes self-priming and strand displacement to

achieve isothermal amplification?

a. RT-PCR

b. LAMP

c. qPCR

d. TBA

b. LAMP

In the dideoxy chain termination method of DNA sequencing, ddNTPs cause termination of the

polymerization step because...

a. ddNTPs do not have the hydroxy group at the 3' end

b. ddNTPs do not have the phosphate group at the 5' end

c. ddNTPs are tagged with a fluorescent dye

d. all of the choices

a. ddNTPs do not have the hydroxy group at the 3' end

Denaturing Gradient Gel Electrophoresis is used when detecting mutations in...

a. ssDNA

b. dsDNA

c. ssRNA

d. all of the choices

b. dsDNA

How many probes are used for the Ligase Chain Reaction assays?

a. one

b. two

c. three

d. four

e. five

d. four

How many probes are used for the FRET amplification assays?

a. one pair

b. two pairs

c. three pairs

d. four pairs

a. one pair

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

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 identification

d. used for tissue-typing to determine donor-recipient compatibility

e. also known as sequence-specific PCR

e. also known as sequence-specific PCR

Which of the following is the gold standard method for DNA Sequencing?

a. Next Generation Sequencing

b. Bisulfide DNA Sequencing

c. Maxam-Gilbert Method

d. Dideoxy Chain Termination Method

d. Dideoxy Chain Termination Method

Detection and characterization of 16s rRNA Gene is performed when analyzing...

a. HLA compatibility

b. Viruses

c. Bacteria

d. Paternity tests

e. Tumor markers

c. Bacteria

Point-of-care tests using LAMP have been developed that detect turbidity resulting from the production of

___________________ as a byproduct of amplification.

a. Barium Sulphates

b. Mg Pyrophosphates

c. Ca Oxalates

d. Ca Carbonates

b. Mg Pyrophosphates

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

Which of the following is NOT TRUE about the use of PAGE for single-strand conformation polymorphism

determination?

a. can differentiate between ssDNA fragments of the same lengths but diff 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 ge