Deck 6: Analysis and Characterization of Nucleic Acids and Proteins

Question 1

Which of the following is the correct order of steps when performing a Southern blot after isolation of the DNA?

A) Probe hybridization, restriction enzyme digestion, denaturation, electrophoresis
B) Denaturation, electrophoresis, probe hybridization, restriction enzyme digestion
C) Restriction enzyme digestion, electrophoresis, denaturation, probe hybridization
D) Electrophoresis, restriction enzyme digestion, probe hybridization, denaturation

Answer 1

Restriction enzyme digestion, electrophoresis, denaturation, probe hybridization

Question 2

A linear molecule with one restriction enzyme recognition site will yield how many fragments when digested by the restriction enzyme?

A) 1
B) 2
C) 3
D) 4

Answer 2

2

Question 3

The melting temperature of nucleic acid is the temperature when:

A) All of the double-stranded DNA is single-stranded
B) Half of the double-stranded DNA is single-stranded
C) A quarter of the double-stranded DNA is single-stranded
D) All of the single-stranded DNA is double-stranded

Answer 3

Half of the double-stranded DNA is single-stranded

Question 4

Which of the following is not a method of transferring nucleic acids from a gel to a membrane substrate?

A) Capillary
B) Vacuum
C) Electrophoretic
D) Ionic

Question 5

What is learned from the size of restriction fragments as determined by migration speed in gel electrophoresis?

A) The specificity of the restriction enzyme
B) The distance between restriction enzyme recognition sites
C) The rate of digestion of the enzyme
D) The number of restriction sites in the DNA

Question 6

Which of the following solutions has the highest stringency?

A) 0% formamide
B) 10% formamide
C) high-salt buffer
D) 50% formamide

Question 7

What process facilitates denaturation of long DNA fragments?

A) Precipitation
B) Removal of bases from the ends of the molecules
C) Dephosphorylation
D) Depurination

Question 8

Which of the following bind(s) specifically to a sequence of interest, thus facilitating the analysis of that sequence?

A) Restriction enzymes
B) Probes
C) Hybridomas
D) Digoxigenin

Question 9

What determines the specificity in terms of the gene or region that is detected in the Southern blot?

A) Nitrocellulose membranes
B) Agarose gel
C) Restriction enzymes
D) Labeled probe

Question 10

What is the next step in the Southern blot procedure after restriction enzyme digestion?

A) Denaturation
B) Gel electrophoresis
C) Blotting to a membrane
D) Probe hybridization

Question 11

A circular molecule has two sites for the restriction enzyme PstI and one site for the enzyme BamH1. How many fragments will result when digested with both enzymes?

A) 1
B) 2
C) 3
D) 4

Question 12

A circular molecule with one restriction enzyme recognition site will yield how many fragments when digested by the restriction enzyme?

A) 1
B) 2
C) 3
D) 4

Question 13

A Southern blot procedure has been performed, but the molecular weight markers are the only bands seen on the gel. Apparently, the probe did not bind to its target on the membrane. How might the stringency be adjusted so that the probe will bind?

A) Decrease the incubation temperature.
B) Decrease the salt concentration.
C) Increase the formamide concentration.
D) Increase the incubation temperature.

Question 14

In order to depurinate DNA after electrophoresis, the gel should be soaked in which of the following?

A) NaOH
B) HCl
C) Saline sodium citrate
D) Formamide

Question 15

What is the melting temperature (T_m) of the following hybrid: AGCTATGCCGGCTAGCAC
TCGATACGGCCGATCGTG

A) 40^oC
B) 50^oC
C) 58^oC
D) 65^oC

Question 16

What is star activity?

A) Optimal specific activity of a restriction enzyme
B) Nonspecific digestion of DNA by a restriction enzyme
C) Degradation of DNA ends
D) Re-ligation of cut DNA

Question 17

A northern blot allows you to do which of the following?

A) Analyze a specific region of DNA in a complex background
B) Measure gene expression
C) Investigate DNA binding proteins
D) Determine antigen/antibody interactions

Question 18

Which of the following conditions are the least stringent?

A) 40% formamide, 1X SSC (salt), 50^oC
B) 50% formamide, 1X SSC, 55^oC
C) 50% formamide, 0.5X SSC, 55^oC
D) 40% formamide, 0.2X SSC, 60^oC

Question 19

What was the great advantage to molecular analysis offered by Southern blot?

A) Ability to analyze specific regions of DNA without cloning them
B) A rapid method to eliminate DNA contaminants
C) A more efficient buffer system
D) Ability to analyze nanogram amounts of DNA

Question 20

A linear molecule has two sites for the restriction enzyme PstI and one site for the enzyme BamH1. How many fragments will result when digested with both enzymes?

A) 1
B) 2
C) 3
D) 4

Question 21

The specificity of western blots depends on what interaction?

A) DNA/RNA complementarity
B) RNA/RNA complementarity
C) DNA antigens
D) Antigen/antibody recognition

Question 22

Which of the following molecules comprises most membranes that bind to nucleic acids in blotting procedures?

A) Nitrocellulose
B) Agarose
C) Acrylamide
D) Formamide

Question 23

Western blot probes are what type of molecules?

A) DNA
B) RNA
C) protein
D) PNA

Question 24

A hybridization assay is run under the following conditions: 40% formamide with 0.5X SSC at 70^oC. When the bands were visualized, there were many more bands than expected in all wells on the membrane. Which of the following changes should be made to the hybridization conditions to get results that are closer to those expected?

A) Decrease formamide
B) Increase temperature
C) Increase SSC concentration
D) Decrease temperature

Question 25

How do gene expression arrays differ from comparative genome hybridization (CGH) arrays?

A) CGH arrays detect gain or loss of DNA regions; gene expression arrays detect changes in gene expression.
B) CGH arrays can interrogate hundreds of genes, while gene expression arrays test thousands.
C) CGH arrays are simpler to perform than gene expression arrays.
D) CGH arrays require co-hybridization with comparative reference nucleic acid, while gene expression arrays do not.

Question 26

After chromogenic signal detection on a northern blot, circular colorless areas are observed on the membrane, obliterating bands and parts of bands. What is the cause of this?

A) Incomplete electrophoresis of the nucleic acid
B) Loss of alkaline phosphatase activity
C) Incorrect stringency conditions for probe binding
D) Bubbles or incomplete contact between the membrane and the gel

Question 27

Which of the following methods is best suited for qualitative analysis of DNA, such as mutational analysis, where many samples are compared simultaneously?

A) Dot blot
B) Traditional Southern blot
C) Western blot
D) Northern blot

Question 28

The entire human genome can be analyzed at one time by which of the following methods?

A) Northern blot
B) Southern blot
C) Slot blot
D) Microarray

Question 29

Which of the following enzyme/substrate combinations is used in the chromogenic detection of target sequences of nucleic acids after blotting procedures?

A) Horseradish peroxidase with Luminol/H₂O₂/p-iodophenol
B) Alkaline phosphatase with 1-2 dioxetane derivatives
C) Horseradish peroxidase with disodium 3-(4-methoxyspiro {1,2-dioxetane-3,2-(5-chloro) tricyclo [3.3.1.1] decan}4-yl)-1-phenyl phosphate
D) Alkaline phosphatase with nitroblue tetrazolium and 5-bromo-4-chloro-3-indolyl phosphate

Question 30

The microarray or chip is an example of which of the following blotting procedures?

A) Southern blot
B) Dot blot
C) Reverse dot blot
D) Western blot