All GRE Subject Test: Biochemistry, Cell, and Molecular Biology Resources
Example Questions
Example Question #3 : Help With Biochemical Tagging
Why would EDTA be detrimental to an assay for the detection of a protein that has a 6-His tag?
EDTA is a cation chelator, which would prevent detection of the protein
EDTA would degrade the 6-His tag
The 6-His tag would bind to EDTA and not be able to bind the antibody
EDTA does not detect a 6-His tag
EDTA is a cation chelator, which would prevent detection of the protein
EDTA is a chelator of metal cations. In order to detect a 6-His tag, nickel beads are used. If EDTA is in the solution, it will chelate the nickel from the beads and prevent detection of the protein.
Example Question #1 : Help With Biochemical Tagging
Researchers often fuse a hemagglutinin (HA) or a FLAG tag to proteins to study their cellular localization and function. What is the purpose of this tag?
To facilitate knockdown of the protein due to the presence of the tag
None of these
To facilitate overexpression of the protein due to the presence of the tag
To engineer a mutant protein that no longer retains the native function
To facilitate detection by antibody specific to the tag
To facilitate detection by antibody specific to the tag
When tagging the N-terminus of a protein, the main purpose is to detect this protein by a widely commercial antibody to the tag. Many proteins that researchers intend to study do not have a specific antibody, and therefore, the utilization of a HA or FLAG tag allows easy detection. The tag is not intended to alter the native protein's function nor change its expression level in cells.
Example Question #2 : Help With Biochemical Tagging
Which of the following is not a consideration when biochemically tagging a protein?
The biochemical tag should be constitutively and independently expressed
The biochemical tag does not disrupt native protein folding
The biochemical tag can be fused to the -terminus
The biochemical tag can be fused to the -terminus
The biochemical tag is in-frame with the coding sequence
The biochemical tag should be constitutively and independently expressed
One of the purposes of biochemically tagging a protein is to facilitate its detection. As such, it is important that the tag is expressed only when the protein is expressed. Additionally, the in-frame tag is typically fused to the or -terminus of the protein to ensure minimal disruption in native protein folding and structure.
Example Question #3 : Help With Biochemical Tagging
Which of the following is not a common biochemical tag that scientists fuse to proteins of interest?
Human influenza hemagglutinin (HA) tag
Sodium dodecyl sulfate (SDS) tag
FLAG tag
Polyhistidine (His) Tag
Glutathione S-transferase (GST) tag
Sodium dodecyl sulfate (SDS) tag
Researchers commonly use FLAG, His, HA and GST tags when biochemically tagging proteins for experiments. Often, these tags are fused in-frame to the -terminus of the protein to minimize disruption of native protein folding. Sodium dodecyl sulfate (SDS) is an anionic detergent, that when applied to proteins, destroys their folded secondary and tertiary structure. SDS is most commonly used in Western blots.
Example Question #14 : Gre Subject Test: Biochemistry, Cell, And Molecular Biology
When creating a green fluorescent protein (GFP) fusion protein, which of the following is true?
GFP must be in-frame with native protein
GFP is usually conjugated to either the N or C-termini
All of these
GFP must not disrupt the native protein fold
The expression fusion protein expression vector must be suitable for expression in the desired host
All of these
All of the answer choices are true. Creating fluorescently tagged proteins is a common laboratory practice to visualize subcellular localization of proteins. Fusion proteins are subcloned into expression vectors, therefore, it is important that the expression vector is suitable for expression in the species one wishes to express the protein. Furthermore, to minimize disruption of native protein fold, fluorescent tags are usually added to either the N or C-termini. Finally, to ensure that translation is not disrupted, the fusion must be in-frame with the native protein.
Example Question #15 : Gre Subject Test: Biochemistry, Cell, And Molecular Biology
Which of the following is not a technique for which biochemical tagging can be used to detect a protein?
Live cell imaging
Northern blot
Indirect immunofluorescence
Western blot
Electrophoretic mobility super shift assay
Northern blot
The correct answer is Northern blot. A Northern blot is used to detect or quantify RNA in a sample to measure gene expression. A biochemically tagged protein can be detected by Western blot using an antibody specific to the tag. Cell culture cells expressing a tagged protein can also be detected using an antibody specific to the tag by indirect immunofluorescence. Tagging a protein with a fluorescent protein allows researchers to track a protein's localization and movement in cells with live cell imaging. Finally, an electrophoretic mobility shift assay (EMSA) detects a protein's ability to bind DNA, but a super shift incubates the protein of interest with an antibody to determine which protein is binding DNA. In this case, a tagged protein can be probed on an EMSA.
Example Question #11 : Laboratory Practices
What methods were used in early DNA cloning to generate labeled DNA?
All of these
Nick translation
End labeling
PCR generation of a new strand with a radioactive label
Synthesis of complementary strands
All of these
These are all possible methods for generating a labeled DNA probe that is easier to visualize in a heterogeneous sample. In nick translation, DNase is used to nick the DNA of interests, then DNA Polymerase I replaces some nucleotides with their labeled analogues. End labeling involves the use of labeled nucleotides that prevent further elongation at the ends of the DNA molecule. PCR with a radioactive label is another method of cloning labeled DNA.
Example Question #1 : Help With Separation Techniques
Which of the following techniques would be most useful to isolate intact ribosomes from cells?
Dialysis
Centrifugation
SDS-PAGE
Western blotting
Centrifugation
Ribosomes have relatively small molecular weights in comparison to cell organelles, and relatively large molecular weights in comparison to macromolecules (such as proteins). Several rounds of centrifugation, using slightly different conditions, is a feasible way to isolate intact ribosomes.
SDS-PAGE is an excellent technique for separating denatured proteins based on molecular weight. Western blotting is used to detect the presence specific proteins in a sample. Dialysis is often used in protein purification procedures.
Example Question #12 : Laboratory Practices
__________ is a technique used to pull a protein complex out of a solution by targeting one member of the complex with an antibody.
Southern blotting
Co-immunoprecipitation
Mass spectrometry
FRET
Co-immunoprecipitation
The only answer that will viably pull a protein complex out of a solution is co-immunoprecipitation. Co-immunoprecipitation involves using a large amount of antibody for a specific protein to capture the protein of interest and anything that is associated with it (namely the protein complex). The proteins can then be eluted from the antibody and analyzed.
FRET involves fluorescently labeling two proteins to look for, amongst other possible uses, protein-protein interactions in vivo. Southern blotting is a technique used to separate and identify a specific DNA sequence in a solution. Mass spectrometry can be used to analyze and sequence proteins, but does not directly involve the use of antibodies.
Example Question #3 : Help With Separation Techniques
Ethidium bromide is commonly used to detect presence of DNA in DNA gels under UV light. What type of bond does ethidium bromide form with double-stranded DNA to emit fluorescence?
Covalent bond
Ionic bond
Metallic bond
Van der Waals bond
Van der Waals bond
Ethidium bromide intercalates into the hydrophobic interior of the DNA double helix and remains bound through Van der Waals interactions. The binding of ethidium bromide to DNA leads to a conformational shift that increases its fluorescence.
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