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Techniques in Neuroscience > Exam III > Flashcards

Exam III Flashcards

1
Q

What Is not a step involved in forward genetic screening?
a. Define and describe a normal phenotype
b. Mutagenize the eggs/larva of an organism
c. Screen for abnormal phenotypes
d. Bind the DNA sequence of interest to a fluorescent reporter

A

d. Bind the DNA sequence of interest to a fluorescent reporter

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2
Q

BLAST is a/an
a. Mutagen
b. Online tool used to compare nucleotide sequences of DNA
c. Reporter molecule to visualize DNA
d. Membrane for visualizing proteins in a western blot

A

b. Online tool used to compare nucleotide sequences of DNA

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3
Q

Microarray is a technique used to
a. Compare protein content between samples
b. Indicate which proteins are active
c. Compare relative gene expression between experimental groups
d. Measure the charge of a protein

A

c. Compare relative gene expression between experimental groups

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4
Q

Microarray uses nucleic acid printed is as small dots on slides
a. RNA
b. Genomic DNA
c. cDNA
d. ribosomal RNA

A

c. cDNA

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5
Q

A restriction enzyme
a. Cuts DNA at specific sites
b. Joins segments of DNA
c. Separates double-stranded DNA into single-stranded DNA
d. Degrades mRNA

A

a. Cuts DNA at specific sites

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6
Q

PCR is a reaction used to
a. Make copies of DNA
b. Break DNA up into short segments
c. Identify the size of a DNA string
d. Make copies of proteins

A

a. Make copies of DNA

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7
Q

PCR uses changes in what to drive its reaction
a. Salt concentration
b. Temperature
c. Protein content
d. DNA copy number

A

b. Temperature

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8
Q

Which is not a required step in the PCR reaction
a. DNA strand separation ( denaturing)
b. Hybridization of DNA primer to source DNA
c. DNA synthesis
d. DNA cleavage

A

d. DNA cleavage

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9
Q

In biology, regarding genetics a vector is
a. A vehicle to carry DNA into a host
b. A measure with both magnitude and direction
c. Something that carries disease
d. Ribosomal RNA

A

a. A vehicle to carry DNA into a host

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10
Q

Regarding microarray, what must mRNA be converted to in order to perform the experiment
a. cRNA
b. tRNA
c. dDNA
d. dsDNA

A

d. dsDNA

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11
Q

Which technique is an example in a forward genetic screen?
a. RNAi
b. Genetic Knock out
c. Genetic Knock in
d. X ray irradiation

A

d. X ray irradiation

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12
Q

Which technique is used to analyze protein content?
a. Southern blot
b. Western blot
c. Northern blot
d. Eastern blot

A

b. Western blot

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13
Q

Which technique is used to analyze RNA content
a. Southern blot
b. Western blot
c. Northern blot
d. Eastern blot

A

c. Northern blot

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14
Q

Gel electrophoresis separates proteins, DNA, or RNA based on differences in
a. Charge
b. Size
c. Color
d. Sequence

A

b. Size

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15
Q

After running the protein down on the gel electrophoresis, the protein is then
a. Run in the other direction on the gel
b. Transferred to a membrane for analysis
c. Put into solution for analysis
d. Hybridized with dDNA

A

b. Transferred to a membrane for analysis

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16
Q

Modern DNA sequencing uses what to distinguish between nucleosides
a. Separate lanes in gel electrophoresis
b. Different fluorescent molecules
c. DAB
d. Biotin

A

b. Different fluorescent molecules

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17
Q

Which is a technique used to introduce genes into a cell physically?
a. Viral vector
b. Biolistics or the gene gun
c. Calcium phosphate transfection
d. All of the above

A

d. All of the above

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18
Q

Producing an antibody requires
a. Cell culture
b. Surgery
c. Injecting an animal with a foreign substance or antigen
d. Chromatography

A

c. Injecting an animal with a foreign substance or antigen

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19
Q

In the paper: Characterization of an Enhancer Region of the Galanin Gene that Directs Expression of the Dorsal Root Ganglion and Confers Responsiveness to Axotomy, the production of the beta-galactosidase and color change with c-gal indicated that
a. That galanin was not produced by those cells
b. That galanin was being produced by those cells
c. That someone was using a microwave during the experiment
d. The gene of interest was inserted into the plasmid

A

d. The gene of interest was inserted into the plasmid

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20
Q

Which technique does not use antibodies
a. Western blot
b. Immunoprecipitation
c. Immunohistochemistry
d. Southern blot

A

d. Southern blot

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21
Q

Preparing a sample for a western blot requires
a. Sequencing of the gene for that protein
b. Solubilization of the protein of interest
c. Cell fractionation
d. Dehydration of the sample

A

b. Solubilization of the protein of interest

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22
Q

Immunoprecipitation differs from coimmunoprecipitation in that
a. Immunoprecipitation assays all proteins in a complex
b. Immunoprecipitation uses an antibody to assay all proteins in the homogenate
c. Coimmunoprecipitation is used to assay the protein of the interest as well as all the other proteins it is attached to
d. Coimmunoprecipitation is used to assay only the protein of interest

A

c. Coimmunoprecipitation is used to assay the protein of the interest as well as all the other proteins it is attached to

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23
Q

In DNA gel electrophoresis, the darkness of the band indicates
a. The length of your DNA fragment
b. The density of your DNA fragment
c. The amount of DNA present
d. The DNA sequence

A

b. The density of your DNA fragment
of DNA present

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24
Q

The length or size of your DNA fragment can be identified by comparing
a. Your sample bands color to other sample bands
b. The density of your sample band to loading controls
c. The position of your sample band to ladder controls
d. Your sample density to a standard concentration curve

A

c. The position of your sample band to ladder controls

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25
Q

In western blotting, a semiquantitative analysis can be performed by comparing your sample bands to
a. Loading control
b. Ladder control
c. Standard curve
d. Its littermates

A

a. Loading control

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26
Q

How does one assay what proteins are present when performing a coimmunoprecipitation?
a. Western blot analysis following the precipitation
b. Northern blot analysis following the precipitation
c. Southern blot analysis following the precipitation
d. Easter blot analysis following the precipitation

A

a. Western blot analysis following the precipitation

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27
Q

Regarding the paper: fos-B Null mice display impaired adult hippocampal neurogenesis and spontaneous epilepsy with depressive behavior, what was the major finding regarding the Dentate Gyrus in fosB Null mice?
a. No dentate gyrus was present
b. The dentate gyrus was misshapen
c. The dentate gyrus was much larger
d. The dentate gyrus was much smaller

A

d. The dentate gyrus was much smaller

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28
Q
  1. Using the western blot results shown, which two fos products are shown as present in the fosBd/d mice?
    a. FosB
    b. dFosB
    c. dsdFosB
    d. dfosB and FosB
    e. dFosB and dsdFosB
A

e. dFosB and dsdFosB

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29
Q

Which is not a step involved in a forward genetic screen?
a. Define and describe a normal phenotype
b. Mutagenize the eggs/larva of an organism
c. Screen for abnormal phenotypes
d. Bind the DNA sequence of interest to a fluorescent reporter

A

d. Bind the DNA sequence of interest to a fluorescent reporter

How well did you know this?
1
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30
Q

Which is an example of a reverse genetic screen?
a. Microarray screen
b. X-ray irradiation of eggs
c. Genetic knockout
d. Immunoprecipitation

A

c. Genetic knockout

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31
Q

BLAST is a/an
a. Mutagen
b. Online tool used to compare nucleotide sequences of DNA
c. Reporter molecule to visualize DNA
d. Membrane for visualizing proteins in a western blot

A

b. Online tool used to compare nucleotide sequences of DNA

32
Q

Which of the following is commonly used as a reporter gene?
a. CAG
b. Lac Z
c. Galanin
d. Sciatic nerve

A

b. Lac Z

33
Q

Microarray is a technique used to
a. Compare protein content between samples
b. Indicate which proteins are active
c. Compare relative gene expression between experimental groups
d. Measure the charge of a protein

A

c. Compare relative gene expression between experimental groups

34
Q

Microarray uses what nucleic acid is printed in small dots on slides
a. RNA
b. Genomic DNA
c. cDNA
d. ribosomal RNA

A

c. cDNA

35
Q

A restriction enzyme
a. Cuts DNA at specific sites
b. Joins segments of DNA
c. Separates double-stranded DNA into single-stranded DNA
d. Degrades mRNA

A

a. Cuts DNA at specific sites

36
Q

PCR is a reaction used to
a. Make copies of DNA
b. Break DNA up into short segments
c. Identify the size of a DNA strand
d. Make copies of proteins

A

a. Make copies of DNA

37
Q

PCR uses changes in what to drive its reaction
a. Salt concentration
b. Temperature
c. Protein content
d. DNA copy number

A

b. Temperature

38
Q

Which technique is used to analyze protein content
a. Southern blot
b. Western blot
c. Northern blot
d. Eastern blot

A

b. Western blot

39
Q

For a western blot, after running protein on the gel electrophoresis, the protein is then
a. Run in the other direction of the gel
b. Transferred to a membrane for analysis
c. Put into solution for analysis
d. Hybridized with dDNA

A

b. Transferred to a membrane for analysis

40
Q

Modern DNA sequencing uses what to distinguish between nucleosides
a. Separate lanes in gel electrophoresis
b. Different fluorescent molecules
c. AB
d. Biotin

A

b. Different fluorescent molecules

41
Q

Producing an antibody requires
a. Cell culture
b. Surgery
c. Injecting an animal with a foreign substance or antigen
d. Chromatography

A

c. Injecting an animal with a foreign substance or antigen

42
Q

In the paper: Characterization of an Enhancer Region of the Galanin Gene That Directs Expression to the Dorsal Root Ganglion and Confers Responsiveness to Axotomy, the production of Beta-galactosidase and color change with x-gal indicated
a. That galanin was not produced by those cells
b. That galanin was being produced by those cells
c. That someone was using a microwave during the experiment
d. The gene of interest was inserted into the plasmid

A

b. That galanin was being produced by those cells

43
Q

Which technique does not use antibodies?
a. Western blot
b. Immunoprecipitation
c. Immunohistochemistry
d. Southern blot

A

d. Southern blot

44
Q

Preparing a sample of a western blot requires
a. Sequencing of the gene for that protein
b. Solubilization of the protein of interest
c. Cell fraction
d. Dehydration of the sample

A

b. Solubilization of the protein of interest

45
Q

Immunoprecipitation differs from coimmunoprecipitation in that
a. Immunoprecipitation is assays all proteins in a complex
b. Immunoprecipitation uses an antibody to assay all proteins in the homogenate
c. Coimmunoprecipitation is used to assay the protein of interest as well as the other proteins it is attached to
d. Coimmunoprecipitation is used to assay only the protein of interest

A

c. Coimmunoprecipitation is used to assay the protein of interest as well as the other proteins it is attached to

46
Q

In DNA gel electrophoresis, the darkness of the band indicates
a. The length of your DNA fragment
b. The density of your DNA fragment
c. The amount of DNA present
d. The DNA sequence

A

c. The amount of DNA present

47
Q

The length or size of your DNA fragment can be identified by comparing
a. Your sample bands color to other sample bands
b. The density of your sample band to loading controls
c. The position of your sample band to ladder controls
d. Your sample’s density to a standard concentration curve

A

c. The position of your sample band to ladder controls

48
Q

In western blotting, a semiquantitative analysis can be performed by comparing your sample bands to
a. Loading control
b. Ladder control
c. Standard curve
d. Its littermates

A

a. Loading control

49
Q

How does one assay what proteins represent when performing a coimmunoprecipitation?
a. Western blot analysis following precipitation
b. Northern blot analysis following precipitation
c. Southern blot analysis following the precipitation
d. Easter blot analysis following the precipitation

A

a. Western blot analysis following precipitation

50
Q

Using the western blot results shown above, drawn from the paper: fosB-Nul Mice Display Impaired Adult Hippocampal Neurogenesis and Spontaneous Epilepsy with Depresive Behavior, which two fos products areshown as present in the fosB44 mice?
a. FosB
b. Delta fos B
c. Delta 2Fos B
d. Delta fosB and FosB
e. Delta FosbB and delta2deltaFosB

A

e. Delta FosbB and delta2deltaFosB

51
Q

PCR and Sanger sequencing differ in that
a. Sangar sequencing makes use no deoxyribonucleosides
b. Only one primer is used
c. Temperature program has to change to allow for chain termination
d. Taq polymerase is used instead of Bam RI

A

d. Taq polymerase is used instead of Bam RI

52
Q

Answer the following questions using the diagram of a western blot below. Bands are shown in the experimental lanes with their “density” or thickness/darkness shown in white. Use the information presented here to answer the next questions.
Which loading control is shown in the above figure?
a. Ladder
b. YFP
c. Beta-actin
d. Undefeated
e. Defeated

A

c. Beta-actin

53
Q

Perform a semiquantitative analysis of the above western blot. Which group has the most YFP?
a. Defeated
b. Undefeated
c. Ladder
d. Beta-actin

A

a. Defeated

54
Q

Which group has the most beta-actin?
a. Defeated
b. Undefeated
c. Neither, they are assumed to be the same

A

c. Neither, they are assumed to be the same

55
Q

Using the information on the Western blot, how big would you say Beta-actin is?
a. 40kDa
b. 130kDA
c. 125
d. 100
e. 150

A

a. 40kDa

56
Q

Again using the information on the western blot above, how bid would you say YFP is?
a. 200
b. 450
c. 140
d. 90
e. 40

A

90

57
Q

The density in a western blot refers to
a. The specific gravity of the protein isolated by the procedure
b. The darkness and thickness of the stained band
c. The number of different proteins that were probed
d. The size of the protein isolated by the procedure

A

b. The darkness and thickness of the stained band

58
Q

Using the figure of a petri dish with yeast colonies plated on it, answer the following questions. The petri dish has been treated with x-gal and ampicillin. Use the figure of the plasmid next to it.
Which colonies took up the plasmid?
a. Cells labeled a
b. Cells labeled b
c. None of the colonies
d. All of the colonies

A

d. All of the colonies

59
Q

Using the figure of a petri dish with yeast colonies plated on it, answer the following questions. The petri dish has been treated with x-gal and ampicillin. Use the figure of the plasmid next to it.
Which colonies took up the gene of interest?
a. Cells labeled a
b. Cells labeled b
c. None of the colonies
d. All of the colonies

A

b. Cells labeled b

60
Q

Using the figure of a petri dish with yeast colonies plated on it, answer the following questions. The petri dish has been treated with x-gal and ampicillin. Use the figure of the plasmid next to it.
Which colonies are resistant to ampicillin?
a. Cells labeled a
b. Cells labeled b
c. None of the colonies
d. All of the colonies

A

d. All of the colonies

61
Q

Refer to the plasmid diagram. If the gene of interest were to be taken up, where would it be inserted?
a. Site e
b. Site f
c. Site c
d. Site d

A

c. Site c

62
Q

A lack of x-gal staining indicates
a. Lac-z gene disrupted by insertion of the gene of interest
b. Lac-z gene killed by ampicillin
c. Lac-z gene if functional
d. The lac-z gene is obsolete

A

a. Lac-z gene disrupted by insertion of the gene of interest

63
Q

JC-07 – Molecular Cloning- Bacon 2007 – Characterization of an ….

What gene is used as a reporter gene in the experiments described in this paper?
a. Galanin
b. lacZ
c. biotinylated Dextran Amine (BDA)
d. fluorescein

A

b. lacZ

64
Q

JC-07 – Molecular Cloning- Bacon 2007 – Characterization of an ….

The reporter gene is expressed when
a. The galanin gene is expressed
b. X-gal is present
c. The 15KB enhancer region is exercised from the gene
d. Mice are treated with a SMAD reporter assay

A

a. The galanin gene is expressed

65
Q

JC-07 – Molecular Cloning- Bacon 2007 – Characterization of an ….

When the reporter gene is expressed it is observed as
a. A fluorescent signal observed with a fluorescence microscope
b. A bioluminescent signal in the presence of H2O2
c. A color change in the presence of X-gal
d. A persistent biotin signal

A

c. A color change in the presence of X-gal

66
Q

JC-07 – Molecular Cloning- Bacon 2007 – Characterization of an ….

Using the above graph, which cells expressed galanin in the least?
a. The 20 kb transgene
b. The 4.6 kb transgene
c. The 4.6 delta23, 18 kb transgene
d. The 1.9 kb transgene

A

c. The 4.6 delta23, 18 kb transgene

67
Q

JC-07 – Molecular Cloning- Bacon 2007 – Characterization of an ….

The 4.6 delta 23, 18 kb transgene refers to a construct with what modification?
a. It is missing the entirety of the upstream enhancer region
b. It has putative SMAD and STAT binding sites specifically removed
c. It has putative CREB binding sites added
d. It is a complete knockout of the gene

A

b. It has putative SMAD and STAT binding sites specifically removed

68
Q

JC-08 – Manipulating Genes – Yutsudo 2013 – fosB-Null Mice

How big is the delta2deltaFosB product?
a. 25kDA
b. 37kDa
c. 50kDa
d. 6
e. 24

A

a. 25kDA

69
Q

JC-08 – Manipulating Genes – Yutsudo 2013 – fosB-Null Mice

How big is the FosB product?
a. 40kDa
b. 37kDa
c. 50kDa
d. 6kDa
e. 24kDa

A

a. 40kDa

70
Q

JC-08 – Manipulating Genes – Yutsudo 2013 – fosB-Null Mice

Which fos products are present in the wild-type mice?
a. All of them
b. Delta 2 delta FosB and FosB
c. Delta 2 delta fosb and delta fosB
d. fosB
e. none of them

A

a. All of them

71
Q

JC-08 – Manipulating Genes – Yutsudo 2013 – fosB-Null Mice

At which point is the smallest concentration of delta2deltafosB in the FosB d/d mice?
a. Cant tell no loading control
b. C
c. 6
d. 24

A

a. Cant tell no loading control

72
Q

JC-08 – Manipulating Genes – Yutsudo 2013 – fosB-Null Mice

Which protein is not present in the d/d samples?
a. fosB
b. Delta fosB
c. Delta2Delta FosB
d. Delta2DeltaDosbB and Delta FosB

A

a. fosB

73
Q

Briefly describe the process of microarray and how it can compare relative gene expression

A

Microarrays involve immobilizing DNA probes on a solid surface to measure mRNA levels. After isolating RNA from samples, they are converted to labeled cDNA and hybridized to the array. The intensity of hybridized signals indicates gene expression, allowing comparison between conditions (e.g., treated vs. untreated)

74
Q

Compare monoclonal and polyclonal antibodies including how they are produced.

A

Monoclonal: Produced by a single B-cell clone fused with myeloma cells, creating hybridomas. Recognize one specific epitope.
Polyclonal: Generated by immunizing an animal, yielding a mix of antibodies from multiple B-cell clones. Recognize multiple epitopes.

75
Q

What is an immediate early gene, and what is it used for in research?

A

Immediate early genes are rapidly expressed without new protein synthesis after stimulation. Used as markers for cell activation and signaling pathway studies.

76
Q

Describe the process of DNA sequencing.

A

DNA sequencing determines nucleotide order using methods like Sanger sequencing (dye-labeled dideoxynucleotides halt elongation) or NGS (massive parallel sequencing of short DNA fragments).

77
Q

Describe how the PCR technique is modified to sequence DNA

A

The Polymerase Chain Reaction (PCR) is modified for DNA sequencing primarily through the Sanger sequencing method, which involves chain termination. In this technique:
* Template DNA Preparation: The target DNA is denatured into single strands to serve as a template.
* Reaction Mixture: A single-stranded DNA template, a primer, DNA polymerase, regular deoxynucleotide triphosphates (dNTPs), and fluorescently labeled dideoxynucleotide triphosphates (ddNTPs) are added.
* Incorporation of ddNTPs: During DNA synthesis, ddNTPs randomly incorporate instead of dNTPs. Unlike dNTPs, ddNTPs lack a hydroxyl group at the 3’ end, causing termination of DNA elongation.
* Fragment Generation: This results in DNA fragments of varying lengths, each ending at a ddNTP.
* Separation by Size: The fragments are separated using capillary electrophoresis, with shorter fragments moving faster.
* Detection and Sequencing: A laser excites the fluorescently labeled ddNTPs, and a detector records the emitted light, indicating the sequence of bases.
* By reading the sequence of terminated fragments, the DNA’s nucleotide order is determined. This method ensures accurate sequencing, especially for smaller DNA regions.

Techniques in Neuroscience (4 decks)

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