Buckingham - Chapter 5 - Analysis and Characterization of Nucleic Acids and Proteins

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

A. One

B. Two

C. Three

D. Four

A. One

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

A. One

B. Two

C. Three

D. Four

B. Two

3. 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. One

B. Two

C. Three

D. Four

C. Three

4. 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. One

B. Two

C. Three

D. Four

D. Four

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

B. The distance between restriction enzyme recognition sites

6. 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

B. Nonspecific digestion of DNA by a restriction enzyme

7. What is 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

A. Ability to analyze specific regions of DNA without cloning them

8. What determines the specificity in terms of the gene that is detected in the Southern blot?

A. Nitrocellulose membranes

B. Agarose gel

C. Restriction enzymes

D. Labeled probe

D. Labeled probe

9. 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

B. Gel electrophoresis

10. Which of the following solutions has the highest stringency?

A. 0% formamide

B. 10% formamide

C. High-salt buffer

D. 50% formamide

D. 50% formamide

11. 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

B. HCl

12. What process facilitates denaturation of long DNA fragments?

A. Precipitation

B. Removal of bases from the ends of the molecules

C. Dephosphorylation

D. Depurination

D. Depurination

13. Which of the following conditions are the least stringent?

A. 40% formamide, 1X SSC (salt), 50°C

B. 50% formamide, 1X SSC, 55°C

C. 50% formamide, 0.5X SSC, 55°C

D. 40% formamide, 0.2X SSC, 60°C

A. 40% formamide, 1X SSC (salt), 50°C

14. 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.

A. Decrease the incubation temperature.

15. 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

C. Restriction enzyme digestion, electrophoresis, denaturation, probe hybridization

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

A. Analyze a specific gene region in a complex background

B. Measure gene expression

C. Investigate DNA binding proteins

D. Determine antigen/antibody interactions

B. Measure gene expression

17. Which of the following is a method of transferring nucleic acids from a gel to a membrane substrate?

A. Capillary

B. Transduction

C. Electrostatic

D. Ionic

A. Capillary

18. Which of the following will bind specifically to a sequence of interest, thus facilitating the analysis of that sequence?

A. Restriction enzymes

B. Probes

C. Hybridomas

D. Digoxygenin

B. Probes

19. What is the melting temperature (Tm) of the following hybrid?

AGCTATGCCGGCTAGCAC

TCGATACGGCCGATCGTG

A. 40°C

B. 50°C

C. 58°C

D. 65°C

C. 58°C

20. The melting temperature of nucleic acid is the temperature at which

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.

B. half of the double-stranded DNA is single stranded.

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

A. Nitrocellulose

B. Agarose

C. Acrylamide

D. Formamide

A. Nitrocellulose

22. 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

D. Alkaline phosphatase with nitroblue tetrazolium and 5-bromo-4-chloro-3-indolyl phosphate

23. A hybridization assay is run under the following conditions: 40% formamide with 0.5X SSC at 70oC. 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 in order to get results that are closer to expected?

A. Decrease formamide.

B. Increase the temperature.

C. Increase the SSC concentration.

D. Decrease the temperature.

B. Increase the temperature.

24. After chromogenic signal detection, circular colorless areas are observed on the membrane, eliminating 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

D. Bubbles or incomplete contact between the membrane and the gel

25. 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

A. Dot blot

26. Western blot probes are what type of molecules?

A. DNA

B. RNA

C. Protein

C. Protein

27. The specificity of western blots depends on what interaction?

A. DNA-RNA complementarity

B. RNA-RNA complementarity

C. DNA antigens

D. antigen-antibody recognition

D. antigen-antibody recognition

28. 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

C. Reverse dot blot

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

A. Macroarray

B. Southern blot

C. Dot blot

D. Microarray

D. Microarray

30. 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, whereas 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, whereas gene expression arrays do not.

A. CGH arrays detect gain or loss of DNA regions; gene expression arrays detect changes in gene expression.