Ch. 9 Proteomics Flashcards
Why is SDS used in the electrophoresis of proteins?
SDS coats the protein with a negative charge so that the sample can run through the gel.
What is an issue with 2D-PAGE?
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
Which one of the following is not used during Western blotting?
Non-fat dry milk
What is used during Western blotting?
- secondary antibody with a conjugated detection system
- agarose gel electrophoresis
- primary antibody that recognizes the protein
- nitrocellulose membrane
Which of the following statements about HPLC is NOT correct?
The downside to HPLC is that it is not very adaptable due to the availability of stationary phase material
There are two phases to HPLC:
Mobile and stationary
Applications for HPLC:
Separation, identification, and purification of proteins
Factors that affect resolution in HPLC:
- adjusting the experimental conditions
- changing the particle size of the stationary phase
- controlling temperature
Which of the following is NOT an example of protease activity?
Some proteases cleave the phosphodiester bond between nucleic acid residues
Phosphodiestrase enzyme -
Breaks down the phosphodiester bond present between nucleic acid residues
Examples of protease activity ‘d
- 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
Which of the following statement about mass spectroscopy is incorrect?
ESI is able to handle much larger ions than MALDI
MALDI -
Matrix assisted LASER desorption ionization
- a soft ionization method in which fragmentation is less enabling to identify macromolecular ion
ESI -
Electron spray ionization
- comparatively harder ionization method where there is a high chance of fragmentation
How is biopanning useful to proteomics research?
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
Which of the following is needed to perform yeast two-hybrid assays?
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
Proteins in a protein assay can be screened for binding to all of the following except ___.
Small hairprin RNAs
Proteins in a protein assay can be screened for binding to:
- enzyme substrate
- proteins
- signaling molecules
- DNAs
All of the following statements concerning metabolomics is true except …
NMR and MS methods in metabolomics are not very sensitive methods for studying the metabolome
True about metabolomics:
- 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
Which of the following statements is NOT true about sequencing peptides with mass spectroscopy?
The entire protein can be sequenced all at once using mass spectroscopy
True about sequencing peptides with mass spectroscopy:
- 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
Which of the following is used to quantify proteins with mass spectroscopy?
2H
Why are protein tags useful?
Tags allow the protein to be isolated and purified from other cellular proteins
For what is co-immunoprecipitation used?
To determine if a protein-of-interest binds to a specific DNA sequence
What is a problem associated with immuno-based arrays?
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
Which of the following has been extensively studied using protein interaction arrays?
Proteins that are able to bind to biotin and streptavidin
Which of the following methods is the best way to analyze a metabolome?
Thin layer chromatography
Which of the following would be the best method to identify thousands of different proteins simultaneously?
SILAC
