Ch. 9 Proteomics

Question 1

Why is SDS used in the electrophoresis of proteins?

Answer 1

SDS coats the protein with a negative charge so that the sample can run through the gel.

Question 2

What is an issue with 2D-PAGE?

Answer 2

All of the above are issuers with 2D-PAGE.

• hydrophobic proteins may not run as expected due to the hydrophobic surfaces
• highly expressed proteins may cover up proteins that are not as abundant but running in the gel nearby
• some proteins may not migrate through polyacrylamide and therefore not be represented on the gel
• rare cellular proteins are hard to visualize with Coomassie blue protein stain

Question 3

Which one of the following is not used during Western blotting?

Answer 3

Non-fat dry milk

Question 4

What is used during Western blotting?

Answer 4

• secondary antibody with a conjugated detection system
• agarose gel electrophoresis
• primary antibody that recognizes the protein
• nitrocellulose membrane

Question 5

Which of the following statements about HPLC is NOT correct?

Answer 5

The downside to HPLC is that it is not very adaptable due to the availability of stationary phase material

Question 6

There are two phases to HPLC:

Answer 6

Mobile and stationary

Question 7

Applications for HPLC:

Answer 7

Separation, identification, and purification of proteins

Question 8

Factors that affect resolution in HPLC:

Answer 8

• adjusting the experimental conditions
• changing the particle size of the stationary phase
• controlling temperature

Question 9

Which of the following is NOT an example of protease activity?

Answer 9

Some proteases cleave the phosphodiester bond between nucleic acid residues

Question 10

Phosphodiestrase enzyme -

Answer 10

Breaks down the phosphodiester bond present between nucleic acid residues

Question 11

Examples of protease activity ‘d

Answer 11

• some proteases cleave within a protein sequence and other proteases snip off residues from either end
• some proteases contain serine, cysteine, threonine, or aspartic acid residues within their active sites
• proteases hydrolyze the peptide bond between amino acid residues
• metalloproteases contain metal ion cofactors within their active site

Question 12

Which of the following statement about mass spectroscopy is incorrect?

Answer 12

ESI is able to handle much larger ions than MALDI

Question 13

MALDI -

Answer 13

Matrix assisted LASER desorption ionization

• a soft ionization method in which fragmentation is less enabling to identify macromolecular ion

Question 14

ESI -

Answer 14

Electron spray ionization

• comparatively harder ionization method where there is a high chance of fragmentation

Question 15

How is biopanning useful to proteomics research?

Answer 15

All of the above.

• to express large amounts of protein on the cell surface of yeast
• to screen expression libraries in E. coli
• to alter the cell membrane structures of cells by expressing foreign proteins on the cell surface
• to isolate specific peptides that bind to a specific target protein

Question 16

Which of the following is needed to perform yeast two-hybrid assays?

Answer 16

All of the above are needed.

• two vectors are needed to express the bait and prey proteins
• a reporter gene under the control of the GAL4 recognition sequence
• the DBD of a transcription factor genetically fused to the protein of interest, also called the bait
• the AD domain of a transcription factor genetically fused to proteins that are being screened for interactions with bait

Question 17

Proteins in a protein assay can be screened for binding to all of the following except ___.

Answer 17

Small hairprin RNAs

Question 18

Proteins in a protein assay can be screened for binding to:

Answer 18

• enzyme substrate
• proteins
• signaling molecules
• DNAs

Question 19

All of the following statements concerning metabolomics is true except …

Answer 19

NMR and MS methods in metabolomics are not very sensitive methods for studying the metabolome

Question 20

True about metabolomics:

Answer 20

• can help produce fresher produce
• is the identification of small molecules and metabolic intermediates within a system
• prior to MS, cell extract is separated by chromatography
• in higher organisms, different cell types have different metabolomes

Question 21

Which of the following statements is NOT true about sequencing peptides with mass spectroscopy?

Answer 21

The entire protein can be sequenced all at once using mass spectroscopy

Question 22

True about sequencing peptides with mass spectroscopy:

Answer 22

• some purified proteins must be digested with proteases to eliminate undesirable characteristics such as hydrophobicity and solubility
• two rounds of mass spectroscopy are used to determine the sequence
• in order to determine the sequence, a pure sample of protein is obtained through 2D-PAGE or HPLC
• a database of protein ion spectra is used to compare the peaks of the unknown peptide to determine the sequence

Question 23

Which of the following is used to quantify proteins with mass spectroscopy?

Answer 23

2H

Question 24

Why are protein tags useful?

Answer 24

Tags allow the protein to be isolated and purified from other cellular proteins

Question 25

For what is co-immunoprecipitation used?

Answer 25

To determine if a protein-of-interest binds to a specific DNA sequence

Question 26

What is a problem associated with immuno-based arrays?

Answer 26

All of the above. - proteins that are bound to solid supports may not be representative of intracellular conditions - the antibody may cross-react with other cellular proteins, producing a false positive - low concentrations of some proteins may not be able to compete for active sites compared to those that are in abundance - proteins that are often found in complexes may have the antibody binding site masked by the other proteins in the complex

Question 27

Which of the following has been extensively studied using protein interaction arrays?

Answer 27

Proteins that are able to bind to biotin and streptavidin

Question 28

Which of the following methods is the best way to analyze a metabolome?

Answer 28

Thin layer chromatography

Question 29

Which of the following would be the best method to identify thousands of different proteins simultaneously?

Answer 29

SILAC