All GRE Subject Test: Biochemistry, Cell, and Molecular Biology Resources
Example Questions
Example Question #1 : Help With Separation Techniques
A new RNA virus was identified, and the high-throughput sequencing of the genome resulted in two unique contigs. Which method would provide insight into the genome structure of this virus?
A PCR with primers against the sequenced regions
A Northern blot analysis using probes from the sequenced regions
A denaturing protein gel to visualize all proteins in the viral particles
A Southern blot analysis using probes based on closely related virus
A Northern blot analysis using probes from the sequenced regions
Obtaining two distinct contigs from a sequencing reaction suggests that either this virus has two separate chromosomes, or that there is some type of error in the sequencing reaction.
The most direct way to test this would be to run a Northern blot analysis with probes against the two potential chromosomes. If they are unique chromosomes, we would expect to see a band that matches the length of the sequenced product on the gel per chromosome. If it is an error, both probes should yield a band of the same size, suggesting that there is only one chromosome.
A Southern blot tests for the presence of DNA; therefore, that would not be useful. A protein gel would also not be useful in this case since we are trying to determine the presence of RNA. A PCR will also not be fruitful since it cannot be conducted on RNA.
Note that a reverse-transcription PCR could potentially be useful because it would convert the RNA into DNA; in that case, you can design mulitple combinations of primers if you think it is a single chromosome.
Example Question #21 : Gre Subject Test: Biochemistry, Cell, And Molecular Biology
Which of these options is an important step in the process of DNA extraction and isolation?
Precipitation of DNA with an alcohol
Removal of contaminants by an organic solvent
Homogenization of cells or tissues
Removal of proteins from sample
All of these
All of these
These are all important steps to create a usable DNA extraction. First, the tissues are homogenized, generally chemically or mechanically. The proteins are then removed from the sample by denaturation. Any contaminants can be removed by multiple methods with organic solvents. Depending on the situation, some other steps are involved, such as removal of RNA from the extract. Lastly, the DNA is precipitated via an alcohol into a pure DNA extract.
Example Question #22 : Gre Subject Test: Biochemistry, Cell, And Molecular Biology
What is the main denaturing agent in a western blot gel that disrupts secondary, tertiary, and quaternary protein structure?
Tetramethylethylenediamine (TEMED)
Acrylamide
Ammonium persulfate
Ethylenediaminetetraacetic acid (EDTA)
Sodium dodecyl sulfate (SDS)
Sodium dodecyl sulfate (SDS)
The correct answer is SDS. SDS disrupts non-covalent bonds in proteins ultimately denaturing these proteins. Both ammonium persulfate and TEMED are reagents used to polymerize (or solidify) SDS-page gels for western blot applications. EDTA chelates cations in solution preventing the activity of proteases that may degrade the primary amino acid structure. Acrylamide is the substance that is polymerized in the SDS-gel, giving the viscous physical characteristics to the gel.
Example Question #7 : Help With Separation Techniques
White blood cells and red bloods cells differ in numerous physical properties, one of which is a significant difference in the density of the two cell types. Red blood cells do not have nuclei, making them much less dense and easy to separate out from white blood cells through simple centrifugation techniques. However, there are numerous white blood cell subtypes with similar densities, presenting a challenge in studying specific white blood cell types as they are more difficult to separate out. We can take advantage of the fact that different white blood cell types express different cell-surface molecules.
Which of the following techniques would be most useful to utilize different cell-surface molecules to separate out different types of white blood cells?
Southern blotting
Co-immunoprecipitation
X-ray crystallography
Flow cytometry
Centrifugation
Flow cytometry
Flow cytometry utilizes antibodies specific to a protein expressed by a single cell type. Antibodies can be coated onto magnetic beads, and those antibodies will bind only cells with the proper proteins, thus becoming "stuck" to the beads which can be separated out from the sample. Centrifugation will not be able to detect such small differences, and is only useful if the density is different. Co-IP is more appropriate when looking for proteins that interact or colocalize. Southern blotting is for DNA detection, and X-ray crystallography is for understanding protein structure.
Example Question #1 : Help With Identification Techniques
Of the following choices, which technique would be the most useful for identifying the binding site of a recently discovered transcription factor?
PCR
Northern blotting
Western blotting
DNA footprinting
DNA footprinting
One function of DNA footprinting involves looking for binding sites by using nucleases to cleave DNA. Wherever the transcription factor is bound should be blocked and protected from cleavage. A sample of DNA can be run in a gel without transcription factors bound and compared to a gel run with DNA that has been exposed to the transcription factor. The difference in DNA sequence can be analyzed based on cleavage differences to identify the transcription factor binding region.
Northern blotting helps identify gene expression by looking at RNA. Western blotting helps identify specific proteins in a sample. PCR helps amplify a sample of DNA.
Example Question #2 : Help With Identification Techniques
In a western blot, to what does the secondary antibody bind?
Ponceau S dye
Nitrocellulose membrane
Primary antibody
Protein of interest
Primary antibody
The secondary antibody is designed to interact specifically with the primary antibody. This is a crucial step because the secondary antibody will contain a detectable marker (usually a fluorescent marker).
The primary antibody interacts with the protein of interest. The membrane is blocked with milk or some other substance prior to addition of the antibodies to prevent nonspecific binding. Ponceau S dye is used to quickly and reversibly detect quantities of proteins on nitrocellulose membranes.
Example Question #3 : Help With Identification Techniques
A student researcher in a lab has just discovered a new species of bacteria. Since very little is known about this species, he decides to execute an experiment to test for peptidoglycan in the outer plasma membrane. He determines that the bacteria does not contain an outer layer of peptidoglycan.
What experiment did the student perform? Is this bacteria virulent?
The student performed a gram stain and the bacteria is virulent
The student performed a Western blot and the bacteria is virulent
The student performed a gram stain and the bacteria is not virulent
There is not enough information to deduce the experiment the student performed or determine the virulence of the bacteria
The student performed a Western blot and the bacteria is not virulent
The student performed a gram stain and the bacteria is virulent
The correct answer is the student performed a gram stain and the bacteria is virulent. A gram stain specifically stains peptidoglycan, which is in the outer membrane layer of some bacteria, purple. The presence of peptidoglycan marks a bacteria as gram-positive. If peptidoglycan is not present, the bacteria will not stain purple, and the bacteria is said to be gram-negative. Gram-negative bacteria contain an outer layer of lipopolysaccharides that confer antibiotic resistance and virulence. Since we know that the bacteria in question doe not have an outer peptidoglycan layer, we know that it is virulent.
Example Question #3 : Help With Identification Techniques
Northern, Southern, and Western blots, as originally invented by E. M. Southern, are techniques used in different areas of molecular biology. What can you learn from a Northern blot?
The length of DNA transcripts, the number of transcripts isolated, and the expression level
The size of a protein
The level of RNase activity
The length of RNA transcripts, the number of transcripts isolated, and the expression level
The length of DNA or RNA transcripts and the number of transcripts isolated
The length of RNA transcripts, the number of transcripts isolated, and the expression level
Northern blots are used to study RNA. When run on the gel used in a Northern, you can observe the length of the RNA (by how far it moves on the gel), the number of transcripts (the number of dark bands), and the expression level (how dark the bands are). Southern blots are used to study DNA, and Western blots are used to study proteins.
Example Question #4 : Help With Identification Techniques
A researcher barcodes a library of 3000 plasmids expressing unique growth enzymes and transforms them into bacteria. These 3000 transformed bacteria are then all grown in one large culture of minimal media. Why does the researcher barcode these plasmids?
To determine which enzymes are expressed in the transformed bacteria
To directly drive the transformed bacteria to proliferate profusely
To disrupt the expression of a specific gene in the transformed bacteria
To directly drive the transformed bacteria to become quiescent
To determine which plasmids promote proliferative bacteria growth
To determine which plasmids promote proliferative bacteria growth
The correct answer is to determine which plasmids promote proliferative bacteria growth. In this experiment, the researcher wants to identify enzymes that, when over expressed in bacteria, allow the bacteria to grow in unfavorable (minimal) conditions. Since this researcher grows all 3000 transformed bacteria, each expressing a different enzyme, in one minimal media culture, he needs to be able to identify which enzymes promote growth. A barcode is an engineered unique DNA sequence that can be inserted on the plasmid expressing the enzyme. The researcher barcodes each unique plasmid. If a certain enzyme promotes bacteria growth, there will be bacterial replication and replication of the plasmid. Sequencing of the entire bacterial culture will determine which barcodes are overrepresented. Each barcode is then associated with the unique enzymes that allow for proliferative growth in minimal media.
Example Question #4 : Help With Identification Techniques
A researcher wants to determine if two proteins form a complex in cells. What technique is best suited for this experiment?
Electrophoretic mobility shift assay
Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET)
Co-immunoprecipitation
TUNEL assay
Protein Binding Microarray
Co-immunoprecipitation
The correct answer is co-immunoprecipitation. During this experiment, protein-protein complexes are cross linked then pulled down by an antibody specific to one of the proteins of interest. Then, these protein elutes are run on a western blot and probed for with a second antibody specific for the other protein believed to be in complex. An electrophoretic mobility shift assay measures the DNA-binding ability of a protein. A TUNEL assay is a measure for apoptosis by quantifying fragmented DNA. Protein binding microarrays determine the preferred DNA binding sequences for a given protein. ChIA-PET measures distal chromatin interactions within the genome.
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