All GRE Subject Test: Biochemistry, Cell, and Molecular Biology Resources
Example Questions
Example Question #1 : Help With Biochemical Tagging
A scientist wants to observe the localization of a particular protein within a tissue sample. Which of the following tags would be most useful for accomplishing this task?
FLAG
GFP
TRX
His
GFP
Fluorescent tags are incredibly powerful tools for observing protein localization. GFP (green fluorescent protein) is a widely used fluorescent tag for just this purpose. All of the other answers are tags used for various functions. His and FLAG tags are commonly used to purify recombinant proteins. TRX tags are used for solubilization and to assist in recombinant protein folding in organisms that are chaperone-deficient.
Example Question #1 : Laboratory Practices
Which of the following describes information that might be obtained from a successful FRET (fluorescence resonance energy transfer) experiment?
Protein localization
All of the answers
Distance between two interacting proteins in vivo
Distances between domains on the same protein
All of the answers
FRET is a widely used technique to study protein-protein interactions as well as reaction kinetics. The technique works by attaching fluorophores to proteins that produce fluorescent light when stimulated by light of the appropriate wavelength. When attempting to detect distances between two objects, two fluorophores are used. The first one is stimulated by an external source and the second is stimulated by the light produced from the excited fluorophore. The presence or absence of the light produced by the second excited fluorophore can then help determine protein-protein interactions. The technique is also applicable to protein localization and detecting distances between domains.
Example Question #1 : Help With Biochemical Tagging
A scientist performs a FRAP (fluorescence recovery after photobleaching) experiment. To do so he labeled a protein with a fluorescent probe. Originally, the fluorescent color was ubiquitous throughout the entire sample. His results indicate that fluorescence did not return to anywhere near the normal level after bleaching his sample. What information can be concluded from this experiment?
The protein is being held in place by the cytoskeleton
The protein is unstable
The protein is embedded in a lipid raft
The protein is immobile
The protein is immobile
During FRAP experimentation, a section of membrane is labeled with fluorophores. High intensity exposure to a small region of the membrane is used to "bleach" this region, resulting in a small region of zero fluorescence. The lack of recovery of the fluorescence only gives us information about the mobility of the protein: it is immobile. If the protein were mobile, then tagged proteins would be able to move into the bleached region, returning it to fluorescence.
While it may be true that the protein is anchored to the cytoskeleton or part of a lipid raft, the result of the experiment does not directly lead to these conclusions. It does, however, point the researcher in the right direction about learning more about the functionality of his protein. FRAP does not tell us anything about the stability of the protein.
Example Question #2 : Help With Biochemical Tagging
Which of the following tags would help a researcher locate a protein in vivo?
I. GFP
II. GST
III. His
IV. myc
I, II, and III
I, II, III, and IV
II and III
I only
I only
GFP is a fluorescent tag that is incredibly useful in helping visualize a protein in vivo. The tag will glow green in the tissue where the protein is present.
All of the other choices describe tags that help purify recombinant proteins. Because all of these tags isolate proteins from a sample of lysed cell, they would not be useful in following a protein in vivo.
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?
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 would degrade the 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 #4 : 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 engineer a mutant protein that no longer retains the native function
None of these
To facilitate overexpression of the protein due to the presence of the tag
To facilitate detection by antibody specific to the tag
To facilitate knockdown of the protein due to the presence of 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 #5 : Help With Biochemical Tagging
Which of the following is not a consideration when biochemically tagging a protein?
The biochemical tag is in-frame with the coding sequence
The biochemical tag can be fused to the -terminus
The biochemical tag can be fused to the -terminus
The biochemical tag does not disrupt native protein folding
The biochemical tag should be constitutively and independently expressed
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 #6 : Help With Biochemical Tagging
Which of the following is not a common biochemical tag that scientists fuse to proteins of interest?
Polyhistidine (His) Tag
FLAG tag
Human influenza hemagglutinin (HA) tag
Glutathione S-transferase (GST) tag
Sodium dodecyl sulfate (SDS) 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 #7 : Help With Biochemical Tagging
When creating a green fluorescent protein (GFP) fusion protein, which of the following is true?
All of these
GFP must not disrupt the native protein fold
GFP must be in-frame with native protein
The expression fusion protein expression vector must be suitable for expression in the desired host
GFP is usually conjugated to either the N or C-termini
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 #8 : Help With Biochemical Tagging
Which of the following is not a technique for which biochemical tagging can be used to detect a protein?
Indirect immunofluorescence
Live cell imaging
Western blot
Northern 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.
All GRE Subject Test: Biochemistry, Cell, and Molecular Biology Resources
