Biotechnology 2nd Edition Clark Test

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Clark: Biotechnology, 2nd Edition

Chapter 9: Proteomics

1. The term proteomics refers to:

*a. Global analysis of the proteins produced in an organism.
b. All of the mRNA transcribed at a given time.
c. The genes that are expressed at a given time.
d. The epigenetic changes associated with the genome.
e. None of the above.

2. Techniques used to separate and study proteins include all of the following EXCEPT:
a. Isoelectric focusing.
*b. Agarose gel electrophoresis.
c. Polyacrylamide gel electrophoresis
d. Two-dimensional PAGE
e. All of the above can be used to separate and study proteins.

3. In order to separate proteins by size, one should

a. Run acrylamide electrophoresis on crude extracts.
b. Run agarose gel electrophoresis on crude extracts.
c. Run cleavage reactions to remove all acetyl, phosphate, AMP or ADP-ribosyl groups
prior to gel electrophoresis.
*d. Boil with sodium dodecyl sulfate to unfold and provide a uniform negative charge on
the protein prior to gel electrophoresis.
e. Proteins cannot be separated by size

4. Scientists will identify specific proteins using western blots. Which of the following is
the correct order of steps in performing this technique?
a. Proteins are reacted with antibody, PAGE is run, proteins are blotted to nitrocellulose
and the second antibody with enzyme reporter is applied.
*b. PAGE is run, proteins are blotted to nitrocellulose, and then primary antibody is
added followed by a secondary antibody with enzyme reporter.
c. PAGE is run; primary antibody is added, followed by a secondary antibody with
enzyme reporter.
d. PAGE is run, proteins are blotted to nitrocellulose, and an antibody with a reporter
enzyme is then added.

5. A refractive index detector is used to identify ___________ during HPLC.

a. Radioactively labeled molecules
*b. Any molecule that scatters visible light waves
c. Any molecules that absorbs one wavelength of light and emits a different wavelength
d. Any molecule that scatters UV light

6. An ultraviolet detector is used to identify ___________ during HPLC.

a. Radioactively labeled molecules
b. Any molecule that scatters light waves
c. Any molecules that absorbs one wavelength of light and emits a different wavelength
*d. Any molecule that scatters UV light

7. A fluorescence detector is used to identify ___________ during HPLC.

a. Radioactively labeled molecules
b. Any molecule that scatters light waves
*c. Any molecules that absorbs one wavelength of light and emits a different wavelength
d. Any molecule that scatters UV light

8. Elastase is a
a. cysteine protease
b. metalloprotease
c. threonine protease
*d. serine protease
e. aspartic protease

9. Papain is a
*a. cysteine protease
b. metalloprotease
c. threonine protease
d. serine protease
e. aspartic protease

10. Pepsin is a
a. cysteine protease
b. metalloprotease
c. threonine protease
d. serine protease
*e. aspartic protease

11. MALDI is a mass spectrometry technique that allows very large molecules such as
proteins to be analyzed. The best description of MALDI is:
a. Liquid samples containing proteins are adhered to a metal bar. The protein is ionized
and the ions detected by TOF.
b. Proteins are dissolved in liquid, which is turned into droplets. After heating, the
solvent evaporates and ions are released into the vacuum tube and detected by TOF.
*c. Proteins are embedded into 2-methoxycinnamic acid. Laser energy then causes
proteins to lose ions, move through a vacuum, and be detected by TOF.
d. None of the above describe MALDI.

12. In which of the following ways can mass spectrometry be used to determine the
sequence of large proteases?
a. Protein in extracts are digested with proteases and then separated by SDS-PAGE.
Individual peptides are sequenced by mass spectrometry and then the sequence is pieced
back together.
*b. Separate proteins via SDS-PAGE, isolate the protein of interest from the gel, digest
protein with proteases, separate the resulting peptides with HPLC, and then use MALDI
to determine the sequence of the individual peptides.
c. Proteins are purified with HPLC, and then digested with protease. Peptides are
purified with SDS-PAGE prior to mass spectrometry.
d. None of the above.

13. Which of the following changes in a protein CANNOT be detected using mass
spectrometry?
a. Cleavage with an endoprotease.
b. Cleavage with an exoprotease.
c. Phosphorylation.
d. Glycosylation.
*e. All of the above CAN be detected with mass spectrometry.

14. His 6 tags are used in purifying proteins because:

a. Histidine binds to Ni2+, so a Ni2+ column can be used to bind the protein of interest.
b. Six histidines can be added to either the amino-terminal end or the carboxy-terminal
end of the protein without disrupting overall structure.
c. The protein can be removed from the column using histidine or imidazole.
*d. All of the above.
e. Some of the above.

15. A “Strep” tagged protein is purified by

a. Using a column containing chitin followed by self-cleavage
b. Using a specific antibody bound to a column or bead
*c. Using streptavidin coated beads or column
d. Using a column containing nickel, followed by imidazole

16. A Flag-tagged protein is purified by

a. Using a column containing chitin followed by self-cleavage
*b. Using a specific antibody bound to a column or bead
c. Using streptavidin coated beads or column
d. Using a column containing nickel, followed by imidazole

17. Intein-tagged proteins are purified by

*a. Using a column containing chitin followed by self-cleavage
b. Using a specific antibody bound to a column or bead
c. Using streptavidin coated beads or column
d. Using a column containing nickel, followed by imidazole

18. His-tagged proteins are purified by

a. Using a column containing chitin followed by self-cleavage
b. Using a specific antibody bound to a column or bead
c. Using streptavidin coated beads or column
*d. Using a column containing nickel, followed by imidazole

19. Biopanning involves all of the following EXCEPT

a. Screening a series of surface proteins for ability to bind a target such as an antibody.
*b. A sequence of 6 histidine at the beginning of each peptide.
c. Use of a phage display library.
d. The bacteriophage M13
e. All of the above are involved in biopanning.

20. A two-hybrid system is used to study protein-protein interactions. Which of the

following is true of a two-hybrid system.
*a. Proteins are fused to either a DNA binding domain (bait) or an activation domain
(prey). When proteins interact, a reporter gene is turned on.
b. The system is designed to work using E. coli but does not work in other organisms.
c. The DNA binding domain and the activation domain are from the maltose binding
protein operon.
d. All of the above.
e. None of the above.

21. The significance of metabolomics is

a. It consists of all the small molecules in the biological system.
b. It indicates the flow in the complex network system with in the cell.
c. It can be studied with cells grown in C14 glucose or C13 glucose followed by
chromatography or NMR.
*d. All of the above.

22. In MuDPIT, the peptide fragments are separated first by .

a. 2D gel electrophoresis
b. isoelectric focusing
*c. 2D LC microcapillary column
d. HPLC
e. MALDI-TOF

23. Order the following SILAC details:

1. Proteins are isolated.
2. Cells are grown with and without stable isotope-tagged amino acids.
3. The ratio of the two peaks is analyzed.
4. Mass spectroscopy
5. Samples are mixed and analyzed by chromatography.
6. Cells are lysed.

a. 2, 1, 6, 4, 3, 5
*b. 2, 6, 1, 5, 4, 3
c. 1, 2, 6, 5, 4, 3
d. 2, 6, 1, 4, 5, 3
e. None of the above.

24. What is the best way to analyze whole metabolomes?

a. NMR
b. SILAC
c. MuDPIT
*d. MS
e. HPLC

25. Plant metabolomics is most valuable for all of the following traits except
.
a. flavor
b. scent
c. nutrient content
*d. disease resistance
e. pigment production