GRE Subject Test: Biochemistry, Cell, and Molecular Biology : Laboratory Practices

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

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All GRE Subject Test: Biochemistry, Cell, and Molecular Biology Resources

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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?

Possible Answers:

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

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 #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?

Possible Answers:

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

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 #2 : 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 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

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 #3 : Help With Biochemical Tagging

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

Possible Answers:

Human influenza hemagglutinin (HA) tag

Sodium dodecyl sulfate (SDS) tag 

FLAG tag

Polyhistidine (His) Tag

Glutathione S-transferase (GST) 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 #14 : Gre Subject Test: Biochemistry, Cell, And Molecular Biology

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

Possible Answers:

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

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 #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? 

Possible Answers:

Live cell imaging 

Northern blot

Indirect immunofluorescence

Western blot

Electrophoretic mobility super shift assay

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. 

Example Question #11 : Laboratory Practices

What methods were used in early DNA cloning to generate labeled DNA?

Possible Answers:

All of these

Nick translation

End labeling

PCR generation of a new strand with a radioactive label

Synthesis of complementary strands

Correct answer:

All of these

Explanation:

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?

Possible Answers:

Dialysis

Centrifugation

SDS-PAGE

Western blotting

Correct answer:

Centrifugation

Explanation:

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. 

Possible Answers:

Southern blotting

Co-immunoprecipitation

Mass spectrometry 

FRET

Correct answer:

Co-immunoprecipitation

Explanation:

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?

Possible Answers:

Covalent bond

Ionic bond

Metallic bond

Van der Waals bond

Correct answer:

Van der Waals bond

Explanation:

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.

All GRE Subject Test: Biochemistry, Cell, and Molecular Biology Resources

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