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Biotechnology I > Ch. 9 Proteomics > Flashcards

Ch. 9 Proteomics Flashcards

1
Q

Why is SDS used in the electrophoresis of proteins?

A

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

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2
Q

What is an issue with 2D-PAGE?

A

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
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3
Q

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

A

Non-fat dry milk

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4
Q

What is used during Western blotting?

A
  • secondary antibody with a conjugated detection system
  • agarose gel electrophoresis
  • primary antibody that recognizes the protein
  • nitrocellulose membrane
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5
Q

Which of the following statements about HPLC is NOT correct?

A

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

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6
Q

There are two phases to HPLC:

A

Mobile and stationary

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7
Q

Applications for HPLC:

A

Separation, identification, and purification of proteins

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8
Q

Factors that affect resolution in HPLC:

A
  • adjusting the experimental conditions
  • changing the particle size of the stationary phase
  • controlling temperature
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9
Q

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

A

Some proteases cleave the phosphodiester bond between nucleic acid residues

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10
Q

Phosphodiestrase enzyme -

A

Breaks down the phosphodiester bond present between nucleic acid residues

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11
Q

Examples of protease activity ‘d

A
  • 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
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12
Q

Which of the following statement about mass spectroscopy is incorrect?

A

ESI is able to handle much larger ions than MALDI

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13
Q

MALDI -

A

Matrix assisted LASER desorption ionization

  • a soft ionization method in which fragmentation is less enabling to identify macromolecular ion
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14
Q

ESI -

A

Electron spray ionization

  • comparatively harder ionization method where there is a high chance of fragmentation
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15
Q

How is biopanning useful to proteomics research?

A

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
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16
Q

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

A

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
17
Q

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

A

Small hairprin RNAs

18
Q

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

A
  • enzyme substrate
  • proteins
  • signaling molecules
  • DNAs
19
Q

All of the following statements concerning metabolomics is true except …

A

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

20
Q

True about metabolomics:

A
  • 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
21
Q

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

A

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

22
Q

True about sequencing peptides with mass spectroscopy:

A
  • 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
23
Q

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

A

2H

24
Q

Why are protein tags useful?

A

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

25
Q

For what is co-immunoprecipitation used?

A

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

26
Q

What is a problem associated with immuno-based arrays?

A

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
27
Q

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

A

Proteins that are able to bind to biotin and streptavidin

28
Q

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

A

Thin layer chromatography

29
Q

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

A

SILAC

Biotechnology I (14 decks)

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