GRE Subject Test: Biochemistry, Cell, and Molecular Biology : Help with Biochemical Tagging

Study concepts, example questions & explanations for GRE Subject Test: Biochemistry, Cell, and Molecular Biology

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Example Questions

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Example Question #7 : Gre Subject Test: Biochemistry, Cell, And Molecular Biology

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?

Possible Answers:

His

FLAG

GFP

TRX

Correct answer:

GFP

Explanation:

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 #8 : Gre Subject Test: Biochemistry, Cell, And Molecular Biology

Which of the following describes information that might be obtained from a successful FRET (fluorescence resonance energy transfer) experiment? 

Possible Answers:

All of the answers

Protein localization

Distances between domains on the same protein

Distance between two interacting proteins in vivo

Correct answer:

All of the answers

Explanation:

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 #9 : Gre Subject Test: Biochemistry, Cell, And Molecular Biology

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?

Possible Answers:

The protein is immobile

The protein is being held in place by the cytoskeleton

The protein is unstable

The protein is embedded in a lipid raft

Correct answer:

The protein is immobile

Explanation:

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 #1 : 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

Possible Answers:

II and III

I only

I, II, and III

I, II, III, and IV

Correct answer:

I only

Explanation:

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 #2 : Help With Biochemical Tagging

Why would EDTA be detrimental to an assay for the detection of a protein that has a 6-His tag?

Possible Answers:

EDTA does not detect a 6-His tag

The 6-His tag would bind to EDTA and not be able to bind the antibody

EDTA is a cation chelator, which would prevent detection of the protein

EDTA would degrade the 6-His tag

Correct answer:

EDTA is a cation chelator, which would prevent detection of the protein

Explanation:

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 #6 : 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?

Possible Answers:

To facilitate detection by antibody specific to the tag

To facilitate knockdown of the protein due to the presence of the tag

None of these

To engineer a mutant protein that no longer retains the native function

To facilitate overexpression of the protein due to the presence of the tag

Correct answer:

To facilitate detection by antibody specific to the tag

Explanation:

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 #3 : Help With Biochemical Tagging

Which of the following is not a consideration when biochemically tagging a protein? 

Possible Answers:

The biochemical tag should be constitutively and independently expressed

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 does not disrupt native protein folding

Correct answer:

The biochemical tag should be constitutively and independently expressed

Explanation:

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 #4 : Help With Biochemical Tagging

Which of the following is not a common biochemical tag that scientists fuse to proteins of interest?  

Possible Answers:

Sodium dodecyl sulfate (SDS) tag 

Human influenza hemagglutinin (HA) tag

Glutathione S-transferase (GST) tag

Polyhistidine (His) Tag

FLAG tag

Correct answer:

Sodium dodecyl sulfate (SDS) tag 

Explanation:

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 #5 : Help With Biochemical Tagging

When creating a green fluorescent protein (GFP) fusion protein, which of the following is true?

Possible Answers:

The expression fusion protein expression vector must be suitable for expression in the desired host

GFP must be in-frame with native protein

GFP must not disrupt the native protein fold

GFP is usually conjugated to either the N or C-termini

All of these

Correct answer:

All of these

Explanation:

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 #6 : Help With Biochemical Tagging

Which of the following is not a technique for which biochemical tagging can be used to detect a protein? 

Possible Answers:

Electrophoretic mobility super shift assay

Northern blot

Indirect immunofluorescence

Live cell imaging 

Western blot

Correct answer:

Northern blot

Explanation:

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. 

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