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Contemporary Lab Skills - Exam 2

Description

Covering Polymerase Chain Reaction, Electrophoresis, and more
Jo O'Bar
Quiz by Jo O'Bar, updated more than 1 year ago
Jo O'Bar
Created by Jo O'Bar over 3 years ago
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Resource summary

Question 1

Question
What does PCR stand for?
Answer
  • Polymerase Chain Reaction
  • Polyamorous Consensual Relationship
  • Polymorphic Chain Reaction
  • Polymorphic Contrasting Reaction

Question 2

Question
PCR is typically the [blank_start]first[blank_end] step in DNA analysis.
Answer
  • first
  • second
  • third
  • last

Question 3

Question
What is the main significance of PCR vs other methods?
Answer
  • PCR avoids the DNA cloning process
  • PCR promotes the DNA cloning process
  • PCR promotes the RNA cloning process
  • PCR avoids the RNA cloning process

Question 4

Question
PCR amplifies all included DNA segments, which allows us to measure general information about the DNA, such as length and total composition.
Answer
  • True
  • False

Question 5

Question
What determines the segment of DNA that is amplified by PCR?
Answer
  • Primers
  • Template DNA
  • Buffer
  • dNTPs

Question 6

Question
DNA amplification after PCR is [blank_start]less[blank_end] than 10^[blank_start]6[blank_end]x
Answer
  • less
  • greater
  • 6
  • 5
  • 10
  • 12

Question 7

Question
PCR amplification requires [blank_start]little[blank_end] template DNA, but is highly [blank_start]susceptible[blank_end] to contamination.
Answer
  • little
  • a large amount of
  • susceptible
  • resistant

Question 8

Question
______________ is a thermostable DNA polymerase used to automate the repetitive steps in the polymerase chain reaction (PCR) technique.
Answer
  • Taq polymerase
  • Qat polymerase
  • Thermopolymerase
  • Therm polymerase

Question 9

Question
Which of the following is a requirement of PCR?
Answer
  • Thermocycler
  • Template DNA
  • Primers
  • Thermostable DNA polymerase
  • Agarose Gel
  • Electric Current

Question 10

Question
What kind of primers are used in PCR?
Answer
  • Forward
  • Reverse
  • One-way
  • Two-way

Question 11

Question
Using dNTP, or [blank_start]deoxynucleotide triphosphate[blank_end], during the [blank_start]extension[blank_end] phase of PCR provides single bases ready to go into DNA and double it, like building blocks.
Answer
  • deoxynucleotide triphosphate
  • deoxynucleic triptophosphorous
  • deoxynucleotide triptophosphate
  • deoxynucleic triphosphate
  • extension
  • replication
  • conditioning

Question 12

Question
DNA polymerases (DNAPs)... - Add dNTPs to [blank_start]elongate[blank_end] primer - Require pre-existing [blank_start]oligonucleotide[blank_end] (primer) with free [blank_start]3' -OH[blank_end] - Read DNA template strand & inserts complementary [blank_start]deoxyribonucleotide (dNTP)[blank_end] of the next unpaired nucleotide in the template - Form [blank_start]phosphodiester[blank_end] bond between [blank_start]3' -OH[blank_end] of [blank_start]oligonucleotide[blank_end] & [blank_start]5' -PO4[blank_end] of [blank_start]deoxyribonucleotide (dNTP)[blank_end] - DNA synthesis proceeds [blank_start]5'-->3'[blank_end] - Template strand read [blank_start]3'-->5'[blank_end]
Answer
  • elongate
  • compress
  • oligonucleotide
  • phosphodiester
  • 3' -OH
  • 5' -OH
  • 3' -PO4
  • 5' -PO4
  • deoxyribonucleotide (dNTP)
  • DNA polymerase (DNAP)
  • deoxyribose (dRTP)
  • 3' -OH
  • 5' -PO4
  • oligonucleotide
  • phosphodiester
  • phosphodiester
  • oligonucleotide
  • deoxyribonucleoide (dNTP)
  • 5' -PO4
  • 3' -OH
  • 3' -PO4
  • 5' -OH
  • 5' -OH
  • 3' -PO4
  • deoxyribonucleotide (dNTP)
  • oligonucleotide
  • phosphodiester
  • 5'-->3'
  • 3'-->5'
  • 3'-->5'
  • 5'-->3'

Question 13

Question
Select all that apply to DNA polymerases for PCR
Answer
  • Thermostability is essential
  • Optimum polymerase activity at 72 degrees C, but can withstand up to 95 degrees C
  • Use exonuclease deficient forms
  • 3'-->5' exonuclease activity may modify/degrade primers under initial sub-optimal conditions
  • Optimum polymerase activity at 65 degrees C, but can withstand up to 82 degrees C
  • Use endonuclease deficient forms
  • 5'-->3' exonuclease activity may modify/degrade primers under initial sub-optimal conditions

Question 14

Question
Match the DNA polymerases with their description [blank_start]Thermus aquatics[blank_end] - Taq Polymerase - In hot springs [blank_start]Thermococcus litoralis[blank_end] - deep ocean vents ...- extends templates >12kb ...- proofreading ability - Manipulation of Vent -->Deep Vent ...- Greater thermostability ...-Lacks exonuclease (exo-) component [blank_start]Thermus maritima (UITma)[blank_end] - Extends long templates - Proofreading ability [blank_start]Thermus thermophilus (Tth)[blank_end] - RT at 70 degrees C + Mn^2+ - similar to RNA-PCR without cDNA [blank_start]Pfu DNA polymerase (marine bacterium)[blank_end] - Proofreading activity - Efficiently incorporates radiolabeled dNTPs - Good for generating DNA probes
Answer
  • Thermus aquatics
  • Thermococcus litoralis
  • Thermus maritima (UITma)
  • Thermus thermophilus (Tth)
  • Pfu DNA polymerase (marine bacterium)

Question 15

Question
How long are typical PCR primers?
Answer
  • 20-30 bp
  • 30-40 bp
  • 10-20 bp
  • 40-50 bp

Question 16

Question
Select all that apply to a good PCR primer
Answer
  • complement flanking DNA
  • not self-complementary
  • avoids potential secondary structure
  • matched GC content
  • similar melting temp
  • higher melting temp
  • complements itself
  • cannot complement flanking DNA
  • avoids potential tertiary structure

Question 17

Question
Using software such as Oligo and Primer to calculate precise times and temperatures for PCR primer is an option, but calculations made by the researcher should be accurate enough.
Answer
  • True
  • False

Question 18

Question
Which of the following are major components in a PCR reaction mixture?
Answer
  • Target DNA
  • Primers
  • DNA Polymerase
  • dNTPs
  • Buffer appropriate for enzyme
  • dNADs
  • deoxyribonuclease

Question 19

Question
Which of the following should be considered when choosing a buffer for PCR?
Answer
  • enzyme activity
  • primer/template binding
  • effective incorporation of dNTPs
  • optimization for Mg^2+
  • optimization for P^+
  • DNA length

Question 20

Question
The PCR cycle has which three steps?
Answer
  • Denaturation
  • Annealing
  • Extension
  • Buffering
  • Contraction

Question 21

Question
What is the significance of the denaturing phase of PCR?
Answer
  • It allows the selected region for amplification to be accessible to enzymes
  • It allows primers to anneal to the template DNA
  • It extends the primers beyond the target DNA

Question 22

Question
Denaturation of DNA occurs at what temperature?
Answer
  • 90 degrees C
  • 80 degrees C
  • 85 degrees C
  • 75 degrees C

Question 23

Question
Which of the following occurs during the annealing phase of PCR?
Answer
  • reaction mixture cooled to 40-65 degrees C
  • Primers anneal to template DNA
  • precise temperature is critical and must be defined to avoid synthesis of other products
  • template dsDNA denatured by heating above 90 degrees C
  • temperature is raised to 72 degrees C
  • primers extended beyond target DNA
  • Primers extended from 3' -OH by thermostable DNA polymerase

Question 24

Question
Which of the following occurs during the extension phase of PCR
Answer
  • Temperature is raised to 72 degrees C
  • Primers extended from 3' -OH by thermostable DNA polymerase
  • Primers extended beyond target DNA
  • Sequence at 3' end contains sequence complementary to other primer
  • reaction mixture cooled to 40-50 degrees C
  • Primers anneal to template DNA
  • Template dsDNA denatured by heating above 90 degrees C

Question 25

Question
Successive PCR cycles yield fragments precisely delimited by the primer.
Answer
  • True
  • False

Question 26

Question
Which of the following applies to Agarose Gel electrophoresis (AGE) PCR?
Answer
  • Run PCR products on gel alongside size standards
  • Look for band of predicted size
  • Original method
  • Semi-quantitative at best
  • Monitor accumulation of PCR products
  • Quantitative
  • Use fluorescent-labeled primers, probes, or fluorochromes
  • Based on Fluorescent Resonance Energy Transfer (FRET)

Question 27

Question
Which of the following applies to Real-time PCR
Answer
  • Monitor accumulation of PCR products during cycling
  • Quantitative
  • Use fluorescent-labeled primers, probes, or fluorochromes
  • Based on fluorescent Resonance Energy Transfer (FRET)
  • Run PCR products on gel alongside size standards
  • Look for band of predicted size
  • Orignal method
  • Semi-quantitative at best

Question 28

Question
Label the types of Real-Time PCR
Image:
Real Time+Pcr (binary/octet-stream)
Answer
  • Light Cycler Primers
  • Molecular Beacons
  • UFO PCR
  • Photon Cycler Primers
  • Taqman PCR Assay
  • Reporter-Quencher Assay
  • Scorpion Assay
  • Inchworm Assay

Question 29

Question
What is the main benefit of using PCR over cloning?
Answer
  • PCR is faster
  • PCR produces more accurate results
  • PCR requires less preparation
  • PCR is generally cheaper

Question 30

Question
In PCR, "RAPD" stands for... [blank_start]Rapid[blank_end] [blank_start]Amplification[blank_end] of [blank_start]Polymorphic[blank_end] DNA
Answer
  • Rapid
  • Renentive
  • Amplification
  • Annealing
  • Polymorphic
  • Phosphodiester

Question 31

Question
Which of the following applies to RAPD PCR Analysis?
Answer
  • One or both primers are random sequences
  • Yields discrete bands on gel
  • Alteration in fragment length due to insertions/deletions between primer sites
  • Reproducibly identify and organism/species
  • Differentiate between various mutants
  • Based on insertions/deletions in gene sequence among individuals/genes
  • Amplification using 1 primer

Question 32

Question
Which of the following applies to AFLP PCR analysis?
Answer
  • Based on insertions/deletions in gene sequence among individuals/species
  • PCR amplification of specific gene(s)
  • Type of DNA fingerprint analysis
  • Amplification using 1 primer
  • One or both primers are random sequences
  • Yields discrete bands on gels
  • Alteration in fragment length due to insertions/deletions between primer sites

Question 33

Question
PCR is an effective replacement for cloning
Answer
  • True
  • False

Question 34

Question
Cloning PCR products involves which of the following?
Answer
  • In vitro protein synthesis
  • In vivo protein synthesis
  • In vitro DNA synthesis
  • In vivo DNA synthesis

Question 35

Question
What are the initial problems associated with Direct PCR sequencing?
Answer
  • sequencing requires ssDNA
  • Short PCR products re-anneal rapidly
  • Prevent annealing of sequencing primers
  • Bias amplification for 1 strand (primer ratio 100:1)
  • Use denaturants
  • Selectively remove 1 strand after sequencing

Question 36

Question
What are the solutions for problems associated with direct PCR sequencing?
Answer
  • Bias amplification for 1 strand (primer ratio 100:1)
  • Use denaturants
  • Selectively remove 1 strand after synthesis
  • Sequencing requires ssDNA
  • Short PCR products reanneal rapidly
  • Prevent annealing of sequencing primers

Question 37

Question
Select all the denaturants used for direct PCR sequencing
Answer
  • Formamide
  • Dimethylsulfoxide
  • Formaldehyde
  • Dihydrogen monoxide

Question 38

Question
How is one strand selectively removed after synthesis during direct PCR sequencing? (Select 2)
Answer
  • Incorporate biotin into 1 primer
  • Affinity chromatography with bound streptavidin removes biotinylated strand
  • Incorporate formamide into 1 primer
  • HPLC chromatography with bound streptavidin removes biotinylated strand
  • HPLC chromatography with bound straptovitamin removes biotinylated strand

Question 39

Question
This is a depiction of which kind of PCR sequencing?
Image:
Direct+Pcr+Sequencing (binary/octet-stream)
Answer
  • Direct PCR sequencing
  • PCR cycle sequencing

Question 40

Question
This is a depiction of which type of PCR sequencing?
Image:
Pcr+Cyle+Sequencing (binary/octet-stream)
Answer
  • PCR cycle sequencing
  • Direct PCR sequencing

Question 41

Question
Which of the following applies to PCR cycling?
Answer
  • Amplification using 1 primer
  • Uses about 20 PCR cycles to complete
  • Detected using Fluorescent ddNTPs
  • Detected using Radiolabeled ddNTPs
  • BIas amplification for 1 strand (primer ratio 100:1)
  • Use denaturants

Question 42

Question
RT-PCR stands for...
Answer
  • Reverse Transcriptase PCR
  • Reverse Terminal PCR
  • Repeating Transcriptase PCR
  • Repeating Terminal PCR

Question 43

Question
Reverse Transcriptase converts [blank_start]mRNA[blank_end] to [blank_start]cDNA[blank_end] during RT-PCR.
Answer
  • mRNA
  • cDNA
  • ddDNA
  • rRNA
  • cDNA
  • mRNA
  • rRNA
  • ddDNA

Question 44

Question
What are the steps of RT-PCR in the correct order? [blank_start]Isolate Poly(A)-mRNA[blank_end] [blank_start]Anneal Poly(dT) Primer to mRNA[blank_end] [blank_start]Reverse Transcriptase Synthesis of cDNA[blank_end] [blank_start]Remove RNA[blank_end]--Use cDNA in PCR
Answer
  • Isolate Poly(A)-mRNA
  • Anneal Poly(dT) Primer to mRNA
  • Reverse Transcriptase Synthesis of cDNA
  • Remove RNA

Question 45

Question
Electrophoresis is...
Answer
  • the separation of molecules using an electric field
  • the separation of molecules using a magnetic field
  • the visualization of molecules using an electric field
  • the visualization of molecules using a magnetic field

Question 46

Question
The migration distance is primarily determined by the ___________ ratio
Answer
  • charge:mass
  • charge:size
  • density:mass
  • density:size

Question 47

Question
What is the primary reason we use a matrix in electrophoresis?
Answer
  • It increases resolution of molecules with a similar charge:mass ratio
  • It decreases the time it takes to complete electrophoresis
  • It allows the charges from the positive and negative ends to traverse the entire mechanism
  • It gives the molecules something to adhere to

Question 48

Question
A matrix imposes a size constraint on molecule movement during electrophoresis
Answer
  • True
  • False

Question 49

Question
Select all that are common matrices for electrophoresis
Answer
  • Agarose (AGE)
  • Polyacrylamide (PAGE)
  • Starch
  • Cellulose (TLE)
  • Silica (TLE)
  • Paper
  • Sodium hydrogen carbonate (SHC)

Question 50

Question
Drag the types of electrophoresis to their applications [blank_start]Starch gel electrophoresis[blank_end] - Proteins Paper electrophoresis - Small molecules [blank_start]Thin-layer electrophoresis (TLE)[blank_end] - Small Molecules [blank_start]Free-flow electrophoresis[blank_end] - Molecules dissolved in liquid [blank_start]Agarose gel electrophoresis (AGE)[blank_end] - DNA (>2 kb) - RNA (>2 kb) [blank_start]Capillary electrophoresis[blank_end] - DNA - RNA -Proteins - Small molecules [blank_start]Polyacrylamide gel electrophoresis[blank_end] (PAGE) - Small DNAs (<2 kb) - Small RNAs (<2 kb)
Answer
  • Starch gel electrophoresis
  • Thin-layer electrophoresis (TLE)
  • Free-flow electrophoresis
  • Agarose gel electrophoresis (AGE)
  • Capillary electrophoresis
  • Polyacrylamide gel electrophoresis

Question 51

Question
For nucleic acid gel electrophoresis (separation of DNA and RNA), an [blank_start]agarose[blank_end] matrix is used for general applications while [blank_start]polyacrylamide[blank_end] is used for sequencing and footprinting.
Answer
  • agarose
  • polyacrylamide
  • polyacrylamide
  • agarose

Question 52

Question
The phosphate in a nucleic acid's backbone has a strong [blank_start]negative[blank_end] charge proportional to the [blank_start]number of base pairs (bp)[blank_end], so it runs towards the [blank_start]positive[blank_end] end of the electrophoresis matrix.
Answer
  • negative
  • positive
  • positive
  • negative
  • number of base pairs (bp)
  • size of base pairs (bp)
  • proportion of bases (A/G/T/C)

Question 53

Question
Why is denaturing part of agarose electrophoresis?
Answer
  • Used to prevent the formation of secondary structure
  • Used to prevent the formation of tertiary structure
  • Used to prevent re-annealing
  • Used to prevent annealing

Question 54

Question
Which of the following is used in denaturing agarose gels (DNA)
Answer
  • alkaline buffers
  • formamide
  • formaldehyde
  • methylmercuric hydroxide
  • Detergents (e.g. SDS)

Question 55

Question
Which of the following is used in denaturing agarose gels (RNA)
Answer
  • formamide
  • formaldehyde
  • methylmercuric hydroxide
  • alkaline buffers
  • Detergents (e.g. SDS)

Question 56

Question
Which of the following is used in denaturing acrylamide gels?
Answer
  • Detergents (e.g. SDS)
  • alkaline buffers
  • formamide
  • formaldehyde
  • methylmercuric hydroxide

Question 57

Question
Polyacrylamide gels permit the resolution of individual bases
Answer
  • True
  • False

Question 58

Question
Pulsed-field electrophoresis (or orthogonal field electrophoresis) does not permit the separation of large DNAs.
Answer
  • True
  • False

Question 59

Question
Which of the following applies to pulsed-field electrophoresis?
Answer
  • effectively separates small chromosomes >10^6 bp
  • uses electric field conducted through a stiff rod snaking through the gel
  • one can alter the orientation of the field
  • effectively separates large chromosomes <10^10 bp
  • uses electric field conducted through a liquid phase via two small rods on either end (one cathode, one anode)
  • the field is fixed and can only go in one direction

Question 60

Question
Which of the following are general stains for nucleic acids?
Answer
  • Ethidium bromide (EtBr)
  • SYBRgreen
  • Psorelen
  • Methylene blue

Question 61

Question
During electrophoresis staining of nucleic acids, the stain intercalates between the ___________ of the nucleic acids.
Answer
  • bases
  • phosphodiester bonds
  • -OH bonds

Question 62

Question
Alignment of stain molecules to DNA after electrophoresis permits a strong fluorescent signal when stimulated with [blank_start]UV[blank_end].
Answer
  • UV
  • gamma radiation
  • an electric field

Question 63

Question
Proteins are typically separated by what kind of electrophoresis?
Answer
  • Polyacrylamide gel electrophoresis (PAGE)
  • Agarose gel electrophoresis (AGE)
  • Capillary electrophoresis
  • Free-flow electrophoresis

Question 64

Question
PAGE gels can come in what formats?
Answer
  • Slab gels
  • Rod (tube) gels
  • Box gels

Question 65

Question
PAGE buffer systems can either be [blank_start]continuous or discontinuous[blank_end].
Answer
  • continuous or discontinuous
  • high or low charge
  • long or short
  • simple or complex

Question 66

Question
Which of the following are components of a polyacrylamide gel?
Answer
  • Acrylamide
  • BIs-acrylamide
  • Buffer
  • Denaturants (optional)
  • Agarose

Question 67

Question
Which of the following are catalysts used for polymerization of PAGE preparation?
Answer
  • Ammonium persulfate (APS)
  • N,N,N'N'-Tetramethylenediamine (TEMED)
  • Bis-acrylamide
  • Acrylamide

Question 68

Question
What are the functions of the catalysts used during PAGE preparation?
Answer
  • TEMED forms free radicals from APS
  • APS forms free radicals from TEMED
  • Bis-acrylamide forms free radicals from acrylamide
  • Acrylamide forms free radicals from bis-acrylamide

Question 69

Question
In PAGE gel preparation the free radicals made from the catalysts form form linkages from [blank_start]acylamide[blank_end] to acrylamide and [blank_start]acrylamide[blank_end] to [blank_start]bis-acrylamide[blank_end].
Answer
  • acrylamide
  • TEMED
  • APS
  • acylamide
  • TEMED
  • APS
  • bis-acrylamide
  • TEMED
  • APS

Question 70

Question
Which of the following can inhibit APS/TEMED catalysts during PAGE gel preparation?
Answer
  • low pH
  • oxygen
  • high pH
  • water

Question 71

Question
Select all that apply to %T
Answer
  • = Total acrylamides in gel (w/v)
  • = % Acrylamide + % Bis-acrylamide
  • Increased %T --> decreased pore size
  • = Cross-linkers in gel (w/v)
  • = % Bis-acrylamide
  • Increased %T --> increased pore size

Question 72

Question
Select all that apply to %C
Answer
  • = Cross-linkers in gel (w/v)
  • = % Bis-acrylamide
  • Increased %C --> decreased pore size
  • = Total acrylamides in gel (w/v)
  • = % Acrylamide + % BIs-acrylamide
  • Increased %C --> increased pore size

Question 73

Question
In a discontinuous buffer system... Velocity of Migration = [blank_start]Effective Mobility[blank_end] x [blank_start]Voltage[blank_end] - Proportion of charged molecules determines effective mobility Voltage = [blank_start]Current[blank_end] x [blank_start]Resistance[blank_end] - V = I x R Proteins accumulate in a [blank_start]narrow[blank_end] band (i.e. [blank_start]Stack[blank_end]) before entering the [blank_start]resolving[blank_end] gel Stacking gels have [blank_start]large[blank_end] pores ([blank_start]low[blank_end] %T, [blank_start]no molecular sieving[blank_end]) and a pH of [blank_start]6.8[blank_end]. Glycine is [blank_start]protonated[blank_end], so it has a [blank_start]slow[blank_end] migration and is the [blank_start]trailing[blank_end] ion. Proteins are [blank_start]differentially deprotonated[blank_end], so they have an [blank_start]intermediate[blank_end] migration. Chloride (Cl-) has [blank_start]high[blank_end] mobility and is the [blank_start]leading[blank_end] ion. Cl- moves [blank_start]away from[blank_end] the glycine, creating a [blank_start]low[blank_end] conductivity zone. The [blank_start]low[blank_end] conductivity zone attains a [blank_start]higher[blank_end] voltage gradient. At its steady-state, glycine and Cl- are moving at [blank_start]the same rate[blank_end] with a [blank_start]sharp[blank_end] boundary between them. As the glycine moves through the stacking gel, the [blank_start]Cl-[blank_end]overtakes the [blank_start]proteins[blank_end] [blank_start]in front of[blank_end] the boundary. Proteins have [blank_start]higher[blank_end] mobility than glycine in the trailing [blank_start]high-voltage[blank_end] gradient, so they move [blank_start]at[blank_end] the boundary. Resolving gels have [blank_start]smaller[blank_end] pores ([blank_start]higher[blank_end] %T, [blank_start]molecular sieving[blank_end]) and a pH of [blank_start]8.8[blank_end]. At the resolving gel, glycine [blank_start]deprotonates[blank_end] and [blank_start]increases[blank_end] mobility. The [blank_start]glycine[blank_end] overtakes the [blank_start]proteins[blank_end] and moves just behind the Cl-. Then the Proteins separate based on their [blank_start]charge:mass ratio[blank_end] and molecular sieving due to gel composition (%T, %C).
Answer
  • Effective Mobility
  • Size
  • Voltage
  • Mass
  • Current
  • Charge
  • Resistance
  • Reactability
  • narrow
  • wide
  • Stack
  • Resolution
  • resolving
  • stacking
  • large
  • small
  • low
  • high
  • no molecular sieving
  • molecular sieving
  • 6.8
  • 8.8
  • 8.6
  • 6.6
  • 8.8
  • 6.8
  • 6.6
  • 8.6
  • protonated
  • deprotonated
  • slow
  • fast
  • trailing
  • leading
  • differentially deprotonated
  • differentially deprotonated
  • protonated
  • deprotonated
  • intermediate
  • slow
  • fast
  • intermediate
  • high
  • low
  • leading
  • trailing
  • away from
  • towards
  • low
  • high
  • low
  • high
  • higher
  • lower
  • the same rate
  • different rates
  • sharp
  • undefined
  • Cl-
  • proteins
  • proteins
  • Cl-
  • in front of
  • behind
  • higher
  • lower
  • high-voltage
  • low-voltage
  • at
  • behind
  • in front of
  • smaller
  • larger
  • higher
  • lower
  • molecular sieving
  • no molecular sieving
  • deprotonates
  • protonates
  • increases
  • decreases
  • glycine
  • proteins
  • proteins
  • glycine
  • charge:mass ratio
  • mass

Question 74

Question
Denaturing protein electrophoresis is generally conducted using _________ to separate proteins.
Answer
  • SDS-PAGE
  • Urea gels
  • Starch gels
  • Sucrose gels

Question 75

Question
The "SDS" in SDS-PAGE stands for...
Answer
  • sodium dodecylsulfate
  • sodium dioxycarbonate
  • sodium dioxysulfate
  • sodium dodecylcarbonate

Question 76

Question
Select all that apply to the SDS detergent used in SDS-PAGE
Answer
  • Linearizes protein
  • Coats protein with negative charges
  • Coats protein with positive charges
  • Compresses protein

Question 77

Question
SDS-PAGE requires __________ for complete disruption of secondary structure
Answer
  • a reducing agent
  • a buffer
  • a catalyst

Question 78

Question
Which of the following are examples of reducing agents used during SDS-PAGE?
Answer
  • beta-Mercaptoethanol (BME)
  • Dithiothreitol (DTT)
  • Dithioerythritol (DTE)
  • Sodium dodecylsulfate
  • Ampholytes

Question 79

Question
When using an SDS detergent for PAGE... Separation is based on [blank_start]chain length[blank_end] It has a slightly negative charge at pH 7, so the molecules run towards the positive pole
Answer
  • chain length
  • chain linearization
  • chain charge

Question 80

Question
Which of the following applies to Urea gels during denaturing protein electrophoresis?
Answer
  • Disrupts hydrogen bonds (H-bonds) to for primary structure
  • Does not alter charges on protein for the given buffer system and pH
  • Separation is based on the charge:mass ratio
  • Alters charges on protein for the given buffer system and pH
  • Creates hydrogen bonds (H-bonds) for secondary structure
  • Separation is based on the chain length
  • Sometimes used for 1st dimension of 2D-PAGE

Question 81

Question
Which of the following are examples of gel matrices used for non-denaturing protein electrophoresis?
Answer
  • polyacrylamide
  • starch
  • Sucrose
  • Glucose

Question 82

Question
Which of the following are examples of native gels used for non-denaturing protein electrophoresis?
Answer
  • Sucrose
  • Glucose
  • Polyacrylamide
  • Starch

Question 83

Question
Select all that apply to native gels
Answer
  • Separation by charge:mass ratio
  • Maintain protein activity
  • Halt/dampen protein activity
  • Separation by chain length

Question 84

Question
Select all that apply to isoelectrofocussing (IEF) gels
Answer
  • Separation based on pI of protein
  • Ampholytes generate pH gradient
  • Proteins migrate to isoelectric point
  • Used during non-denaturing protein electrophoresis
  • Used during denaturing protein electrophoresis
  • Separation based on charge:mass ratio
  • Glycine and Cl- generate charge gradient

Question 85

Question
Which of the following are examples of protein stains? (Drag to correct spot) Standard: [blank_start]Coomassie Brilliant Blue[blank_end] [blank_start]Ruby Red[blank_end] Most sensitive: [blank_start]Silver[blank_end]
Answer
  • Coomassie Brilliant Blue
  • Methylene Blue
  • Ruby Red
  • Sybergreen
  • Silver

Question 86

Question
[blank_start]Protein stains[blank_end] (is/are) used for total protein visualization in electrophoresis (steady-state). [blank_start]Autoradiography[blank_end] (is/are) used for visualizing newly synthesized proteins after electrophoresis.
Answer
  • Protein stains
  • Autoradiography
  • Autoradiography
  • Protein stains

Question 87

Question
Select all that apply to Autoradiography
Answer
  • Used for In vivo labeling
  • Visualizes bands with x-ray film
  • Intensifying screens
  • increased spot density means increased quantity in band
  • Increased spot density means decreased quantity in band
  • Visualizes bands with UV light

Question 88

Question
Rf = Distance of [blank_start]Migrated Band[blank_end] / Distance of [blank_start]Migrated Dye[blank_end]
Answer
  • Migrated Band
  • Migrated Dye
  • Migrated Dye
  • Migrated Band

Question 89

Question
Migration in SDS-PAGE should be determined with a _________ function
Answer
  • linear
  • logarithmic

Question 90

Question
Rf is typically used when molecular weight markers (MWM's) run on the gel with the sample.
Answer
  • True
  • False

Question 91

Question
2D enhanses esolution over 1D PAGE.
Answer
  • True
  • False

Question 92

Question
Why do we use 2-Dimensional Gel Electrophoresis?
Answer
  • A 1D band may contain several proteins, so 2D resolves overlying proteins.
  • 1D just seemed so boring that we had to add another dimension. It is the 21st century, after all.
  • 1D band only transports the proteins halfway; 2D is needed for the proteins to travel the rest of the gel.

Question 93

Question
Select all that apply to protein separation in the first dimension (electrophoresis).
Answer
  • IEF or native gel
  • separation based on charge:mass ratio
  • ampholytes generate pH gradient
  • proteins migrate to isoelectric point
  • separate on SDS-PAGE gels
  • separation based on size
  • posttranslational modifications occur

Question 94

Question
Select all that apply to protein separation in the second dimension (electrophoresis).
Answer
  • separate on SDS-PAGE gels
  • separation based on size
  • Look for reproducible results
  • Posttranslational modifications occur
  • IEF or native gel
  • Separation based on charge:mass ratio
  • Proteins migrate to isoelectric point

Question 95

Question
Why do posttranslational modifications occur after separation in the second dimension (electrophoresis)>
Answer
  • ARG & mature spot may not be the same
  • proteins don't follow the laws of physics during electrophoresis
  • proteins migrate to the isoelectric point, not based on size

Question 96

Question
Select all components of In vitro translation systems (electrophoresis)
Answer
  • ribosomes
  • protein synthesis factors
  • tRNAs
  • mRNA
  • Amino acids (one radiolabeled)
  • rRNA
  • cDNA
  • Ampholytes

Question 97

Question
What are the uses of In vitro translation of proteins?
Answer
  • Analyze major mRNAs present
  • Pro-protein production
  • Resolves overlying proteins

Question 98

Question
What is the basic procedure of In vitro translation of proteins? 1. [blank_start]Extract mRNAs[blank_end] 2. [blank_start]Translate mRNAs In vitro[blank_end]
Answer
  • Extract mRNAs
  • Copy mRNAs
  • Translate mRNAs In vitro
  • Label mRNAs In vitro

Question 99

Question
___________ is the transfer of macromolecules from gel to membrane filter following electrophoresis.
Answer
  • Blotting
  • Translation
  • Visualization
  • Staining

Question 100

Question
What are some of the advantages of analyzing macromolecules using probes instead of in gels?
Answer
  • More sensitive detection
  • Need less DNA/RNA/protein to complete
  • Probe detects only molecule of interest (not all molecules on gel visualized)
  • Reduce volumes of expensive reagents
  • Probes make you feel like a cool alien
  • Faster visualization
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