Scientists use a process called Flourescent In-Situ Hybridization, or FISH, to study genetic disorders in humans. FISH is a technique that uses spectrographic analysis to determine the presence or absence, as well as the relative abundance, of genetic material in human cells. 

To use FISH, scientists apply fluorescently-labeled bits of DNA of a known color, called probes, to samples of test DNA. These probes anneal to the sample DNA, and scientists can read the colors that result using laboratory equipment. One common use of FISH is to determine the presence of extra DNA in conditions of aneuploidy, a state in which a human cell has an abnormal number of chromosomes. Chromosomes are collections of DNA, the totality of which makes up a cell’s genome. Another typical use is in the study of cancer cells, where scientists use FISH labels to ascertain if genes have moved inappropriately in a cell’s genome.

Using red fluorescent tags, scientists label probe DNA for a gene known to be expressed more heavily in cancer cells than normal cells. They then label a probe for an immediately adjacent DNA sequence with a green fluorescent tag. Both probes are then added to three dishes, shown below.  In dish 1 human bladder cells are incubated with the probes, in dish 2 human epithelial cells are incubated, and in dish 3 known non-cancerous cells are used. The relative luminescence observed in regions of interest in all dishes is shown below.

When probe DNA binds with target DNA, what is the main bonding mechanism likely at play?

In which of the following ways does RNA differ from DNA?

Which of the following is NOT found in both RNA and DNA?

Which of the following statements is not true about DNA and RNA?

DNA is comprised of a double-stranded helix in which purine bases are paired with pyrimidine bases. Which base pairing requires more energy to separate?

Humans must generate an enormous array of antibodies to account for all the possible patterns that they must recognize on pathogens. In fact, the diversity needed in antibody chains cannot be explained by DNA sequence variation. As a result, segments of DNA are physically rearranged in a process called VDJ rearrangement in order to create unique antibody chains. In order to carry out this process, DNA bonds must be broken. What kinds of intra-strand DNA bonds are most likely broken in this process?

In 2013, scientists linked a cellular response called the unfolded protein response (UPR) to a series of neurodegenerative diseases, including such major health issues as Parkinson’s and Alzheimer’s Disease. According to their work, the unfolded protein response is a reduction in translation as a result of a series of enzymes that modify a translation initiation factor, eIF2, as below:

In the above sequence, the unfolded protein sensor binds to unfolded protein, such as the pathogenic amyloid-beta found in the brains of Alzheimer’s Disease patients. This sensor then phosphorylates PERK, or protein kinase RNA-like endoplasmic reticulum kinase. This leads to downstream effects on eIF2, inhibition of which represses translation. It is thought that symptoms of neurodegenerative disease may be a result of this reduced translation.

During translation, the genetic code is used to convert a sequence of nitrogenous bases in mRNA to an amino acid sequence. Which of the following is a difference between the mRNA transcript and the original DNA?

I.  DNA has no hydroxol group at the sugar's 2' position

II.  DNA has thymine; RNA has uracil

III.  DNA is synthesized 5' to 3'; RNA is synthesized 3' to 5'

Once a sample of DNA is isolated, it is loaded on an agarose electrophoresis gel, as shown below. Once the sample has run, where will the student find the DNA?

Prions are the suspected cause of a wide variety of neurodegenerative diseases in mammals. According to prevailing theory, prions are infectious particles made only of protein and found in high concentrations in the brains of infected animals. All mammals produce normal prion protein, PrP^C, a transmembrane protein whose function remains unclear. 

Infectious prions, PrP^Res, induce conformational changes in the existing PrP^C proteins according to the following reaction:

PrP^C  + PrP^Res  → PrP^Res + PrP^Res

The PrP^Res is then suspected to accumulate in the nervous tissue of infected patients and cause disease. This model of transmission generates replicated proteins, but does so bypassing the standard model of the central dogma of molecular biology. Transcription and translation apparently do not play a role in this replication process.

This theory is a major departure from previously established biological dogma. A scientist decides to test the protein-only theory of prion propagation. He establishes his experiment as follows:

Homogenized brain matter of infected rabbits is injected into the brains of healthy rabbits, as per the following table:

Rabbit 1 and 2: injected with normal saline on days 1 and 2

The above trials serve as controls.

Rabbit 3 and 4: injected with homogenized brain matter on days 1 and 2

The above trials use unmodified brain matter.

Rabbit 5 and 6: injected with irradiated homogenized brain matter on days 1 and 2

The above trials use brain matter that has been irradiated to destroy nucleic acids in the homogenate.

Rabbit 7 and 8: injected with protein-free centrifuged homogenized brain matter on days 1 and 2

The above trials use brain matter that has been centrifuged to generate a protein-free homogenate and a protein-rich homogenate based on molecular weight.

Rabbit 9 and 10: injected with boiled homogenized brain matter on days 1 and 2

The above trials use brain matter that have been boiled to destroy any bacterial contaminants in the homogenate.

In Rabbits 5 and 6, irradiation is used to destroy nucleic acids.  What type of irradiation is likely to be used in this portion of the experiment?

How many hydrogen bonds does it take to hold adenine and thymine together? Cytosine and guanine?