The term "denaturation," when used in conjunction with proteins or nucleic acids, refers to a change in structural characteristics primarily due to __________.

Nuclear transport is a very important concept of study in modern cellular biology. Transport of proteins into the nucleus of an organism requires energy in the form of GTP, which is attached to a protein called Ras-related Nuclear protein (RAN).

RAN is a monomeric G protein found in both the cytosol as well as the nucleus and its phosphorylation state plays an important role in the movement of proteins into and out of the nucleus. Specifically, RAN-GTP and RAN-GDP binds to nuclear import and export receptors and carries them into or out of the nucleus. They also play a role in dropping off cargo that import and export receptors hold onto. RAN's functions are controlled by two other proteins: RAN guanine exchange factor (RAN-GEF) and RAN GTPase activating protein (GAP). RAN-GEF binds a GTP onto RAN, while RAN-GAP hydrolyzes GTP into GDP. As a result, there is a RAN-GTP and RAN-GDP concentration gradient that forms between the cytosol and nucleus.

One of the main roles of RAN is to bind to nuclear import and export receptors and carry them into or out of the nucleus. Given that import and export receptors are proteins, what can we say about the cooperativity displayed by RAN when it comes to binding to import and export proteins? 

Among the most important pH buffer systems in humans is the bicarbonate buffer, which keeps the blood at a remarkably precise 7.42 pH. The bicarbonate buffer system uses a series of important compounds and enzymes to make the system function. Figure 1 depicts the key reactions that take place.

The activity of this buffer system is mainly controlled by the renal and respiratory systems. The renal system excretes bicarbonate in the urine, while the respiratory system “blows off” carbon dioxide as needed. By balancing these two systems as needed, blood pH is maintained in such a narrow range.

Carbonic anhydrase is an organic enzyme. Which of the following is true of carbonic anhydrase? Assume no CO₂ or bicarbonate is lost in the reaction.

I. It lowers the activation energy for the conversion of carbon dioxide to carbonic acid

II. It shifts the equilibrium toward carbon dioxide in experimental conditions

III. It modifies chemical species at its allosteric site

Hemoglobin is the principal oxygen-carrying protein in humans. It exists within erythrocytes, and binds up to four diatomic oxygen molecules simultaneously. Hemoglobin functions to maximize oxygen delivery to tissues, while simultaneously maximizing oxygen absorption in the lungs. Hemoglobin thus has a fundamentally contradictory set of goals. It must at once be optimized to absorb oxygen, and to offload oxygen. Natural selection has overcome this apparent contradiction by making hemoglobin exquisitely sensitive to conditions in its microenvironment.

One way in which hemoglobin accomplishes its goals is through the phenomenon of cooperativity. Cooperativity refers to the ability of hemoglobin to change its oxygen binding behavior as a function of how many other oxygen atoms are bound to the molecule. 

Fetal hemoglobin shows a similar pattern of cooperativity, but has unique binding characteristics relative to adult hemoglobin. Fetal hemoglobin reaches higher saturation at lower oxygen partial pressure.

Because of cooperativity, adult and fetal oxygen-hemoglobin dissociation curves appear as follows.

Beyond its ability to carry oxygen, hemoglobin is also effective as a blood buffer. The general reaction for the blood buffer system of hemoglobin is given below.

H⁺ + HbO₂ ←→ H⁺Hb + O₂

The observed cooperativity of oxygen binding to hemoglobin can be explained by changes in shape to the hemoglobin molecule upon oxygen attachment. What kind of change would this be considered?

Cryptosporidium is a genus of gastrointestinal parasite that infects the intestinal epithelium of mammals. Cryptosporidium is water-borne, and is an apicomplexan parasite. This phylum also includes Plasmodium, Babesia, and Toxoplasma. 

Apicomplexans are unique due to their apicoplast, an apical organelle that helps penetrate mammalian epithelium. In the case of cryptosporidium, there is an interaction between the surface proteins of mammalian epithelial tissue and those of the apical portion of the cryptosporidium infective stage, or oocyst. A scientist is conducting an experiment to test the hypothesis that the oocyst secretes a peptide compound that neutralizes intestinal defense cells. These defense cells are resident in the intestinal epithelium, and defend the tissue by phagocytizing the oocysts. 

She sets up the following experiment:

As the neutralizing compound was believed to be secreted by the oocyst, the scientist collected oocysts onto growth media. The oocysts were grown among intestinal epithelial cells, and then the media was collected. The media was then added to another plate where Toxoplasma gondii was growing with intestinal epithelial cells. A second plate of Toxoplasma gondii was grown with the same type of intestinal epithelium, but no oocyst-sourced media was added.

Where is the likely site of the neutralizing toxin synthesis in cryptosporidium cells?

Of the following statements, which is true regarding the change in free energy (ΔG) of a reaction?

Drain cleaners a common household staple, used to open clogged drains in bathtubs and sinks. Human hair is a common culprit that clogs pipes, and hair is made predominately of protein. Drain cleaners are effective at breaking down proteins that have accumulated in plumbing. Drain cleaners can be either acidic or basic, and are also effective at breaking down fats that have accumulated with proteins.

A typical reaction—reaction 1—which would be expected for a drain cleaner on contact with human hair, would be as follows in an aqueous solution:

Another reaction that may occur, reaction 2, would take place as follows in an aqueous solution:

Protein that forms the hair discussed in the preceeding passage is considered strucutral protein. Functional proteins, such as enzymes, are the other major class. Which of the following is true of enzymes?

Drain cleaners a common household staple, used to open clogged drains in bathtubs and sinks. Human hair is a common culprit that clogs pipes, and hair is made predominately of protein. Drain cleaners are effective at breaking down proteins that have accumulated in plumbing. Drain cleaners can be either acidic or basic, and are also effective at breaking down fats that have accumulated with proteins.

A typical reaction—reaction 1—which would be expected for a drain cleaner on contact with human hair, would be as follows in an aqueous solution:

Another reaction that may occur, reaction 2, would take place as follows in an aqueous solution:

Protein that forms the hair discussed in the preceeding passage is considered strucutral protein.  Functional proteins, such as enzymes, are the other major class. Which of the following is expected in an enzymatic biological reaction?

I. Faster rate than non-enzymatic reaction

II. Enzymatic coupling to hydrolysis reactions

III. More product generation relative to amount of reactant than non-enzymatic reaction

A student observes an enzymatic chemical reaction that normally takes place in human blood. She performs an experiment to see how certain conditions affect the reaction with the enzyme fully saturated with substrate. What should she do to speed the reaction up?

In order to catalyze a reaction, an enzyme is required to __________.