MCAT Biology : Organic Chemistry, Biochemistry, and Metabolism
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Example Questions
Example Question #23 : Amino Acids
A researcher stains a transmembrane protein. The membrane-spanning region of the protein is stained red, whereas the other regions are stained blue. Which of the following will you most likely find in the red region?
I. Glycine, which has a side chain of
II. Cysteine, which has a side chain of
III. Alanine, which has a side chain of
I and II
None of these amino acids will be found in the red region
I and III
II and III
I and III
The question states that the membrane-spanning region of the transmembrane protein is stained red; therefore, you will find only hydrophobic amino acids in this region. Recall that an amino acid has a central carbon that has a hydrogen group, carboxylic acid group, amino group, and a side chain attached. The differences between amino acids arise from the different side chains.
A hydrophobic amino acid contains nonpolar side chains. Glycine and alanine contain 
Example Question #24 : Amino Acids
Sildenafil (commonly called Viagra) is a common drug used to treat erectile dysfunction and pulmonary arterial hypertension. Sildenafil's effect comes from its ability to cause vasodilation in smooth muscle cells. For this problem, we're only going to consider its effects on erections in males.
Erectile dysfunction is a common medical problem in older men. Its most significant effect is the prevention of erections. Erections occur when there is an increase in blood flow via enlargement of an artery (vasodilation). Understanding the mechanism by which vasodilations occur is important in order to treat erectile dysfunction.
Erections occur when nitric oxide 
Which of the following amino acids is most likely used to synthesize nitric oxide?
Proline
Leucine
Arginine
Tyrosine
Aspartic acid
Arginine
Let's consider nitric oxide, which has the chemical formula 
In most biological contexts, oxygen is relatively easy to derive since it can be derived from lots of sources, such as water or air. However, the nitrogen in nitric oxide is the more difficult atom to obtain.
All of the listed amino acids have a backbone that has an amino group, but only one has nitrogen within its side chain, and that is arginine. Since arginine has 3 nitrogen atoms on its side chains, it is the most likely candidate to be stripped of its nitrogen to form nitric oxide.
Example Question #1 : Protein Structure
Which of the following statements is NOT true regarding the comparison of the alpha-helix structure to the beta-sheet structure in proteins?
Each may occur in typical globular proteins
Each is stabilized by inter-chain hydrogen bonds
The peptide bond in each is planar and trans
Each is an example of secondary structure
All possible hydrogen bonds between the peptide carbonyl oxygen (C=O) and the amide hydrogen (N-H) are formed in each
Each is stabilized by inter-chain hydrogen bonds
Alpha-helices and beta-sheets are secondary structure motifs that occur when sequences of amino acids are linked by hydrogen bonds. These secondary structures are an integral part of globular proteins, such as hemoglobin. Alpha-helices resemble a coiled spring, with hydrogen bonding occurring in an intra-chain arrangement between carbonyl oxygens and amide hydrogens that is parallel to the central axis. Beta sheets, on the other hand, may have either inter- or intra-chain hydrogen bonding between carbonyl oxygens and amide hydrogens. Thus, the correct answer (and false statement) is that each is stabilized by interchain hydrogen bonds.
Example Question #1 : Protein Structure
Which of the following describes the folding of soluble globular proteins?
Two of the answers are true
Most hydrophilic amino acid residues are protected from water
The energy of the system (protein + water) is at a maximum
Most hydrophobic amino acids are internal, away from solvent water
None of the answers are true
Most hydrophobic amino acids are internal, away from solvent water
Globular proteins are representative of the quaternary structure of a class of proteins, an example of which is hemoglobin. In a soluble molecule the surface of the molecule must interact with water. Any hydrophobic portions of the molecule must remain internal and away from water, while hydrophilic portions will remain on the exterior portion interacting with water molecules. A soluble globular protein is folded so as to minimize the energy of the system. Thus, the correct answer is that most hydrophobic amino acids are internal, away from solvent water.
Example Question #3 : Protein Structure
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 opitimized 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
What portions of the amino acids in hemoglobin likely mediate the differences in the binding and non-binding regions of hemoglobin?
Peptide bond
Alpha carbon
Amino termini
Side chains
Carboxy termini
Side chains
Side chains are the principal point of variety in amino acids. When amino acids contribute to differential functions of proteins, it is typically the side chains that mediate how the amino acids behave in specific environments. All other answers are static components of amino acids and proteins, and would not change regardless of position in the protein. As such, they would not be capable of explaining regional differences.
Example Question #4 : Protein Structure
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.
After conducting the experiment described in the passage, the scientist attempts to determine the overall three dimensional shape of the protein toxin secreted by the cryptosporidium oocysts. What is the scientist investigating?
Global structure
Secondary structure
Regional structure
Tertiary structure
Primary structure
Tertiary structure
The tertiary structure of a polypeptide chain is defined as the overall shape. It is determined by the primary structure, or sequence of amino acids, and the secondary structures in the polypeptide, which are usually composed of beta-sheet or alpha-helix conformations.
Example Question #1 : Protein Structure
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.
Which of the following is the LEAST important force that promotes protein folding?
Hydrogen bonding
Van der Waals interactions
Dipole interactions
Covalent bonding
Metallic bonding
Metallic bonding
Metallic bonding adheres to the "nuclei in a sea of electrons" model that explains the malleability, conductivity, and ductility of metals. Though some proteins (like hemoglobin) rely on a metallic compound, metallic interactions do not dictate the majority of protein folding interactions.
Proteins have a non-metal backbone, and are more dependent on dipole, hydrogen, covalent, and van der Waals forces to dictate their conformation.
Example Question #6 : Protein Structure
In the crusade to create a vaccine for Poliomyelitis, Jonas Salk and Albert Sabin created two separate vaccines that proved to be successful in preventing Polio onset.
The Salk vaccine, which is given by standard injection, contained virus particles inactivated by an organic solvent. This method has the advantage of inactivating each of the three Polio strains with no bias.
Albert Sabin's vaccine, given by oral inoculation via sugar water, contained live virus particles that had been genetically attenuated. With this method, each of the three Polio strains acquired separate mutations that made them unable to infect the human host cells. Strain 2 in particular contained one single nucleotide polymorphism in the internal ribosomal entry site (IRES) that prevented successful viral replication.
The organic solvent used to inactivate the Poliovirus in the Salk vaccine significantly alters the viral capsid. For the purposes of this question, let us assume that the capsid proteins are bound together by multiple di-sulfide bonds. Given this information, which of the solvents listed below would be most effective in disrupting the Poliovirus capsid?
Ethanol
2-mercaptoethanol
Methanol
Dimethyl sulfoxide (DMSO)
2-mercaptoethanol
The answer is 2-mercaptoethanol because it contains strong reducing groups that are capable of reducing the di-sulfide bonds.
Dimethyl sulfoxide (DMSO), methanol, and ethanol do not contain reducing groups capable of breaking di-sulfide bonds, if at all.
Example Question #7 : Protein Structure
Proteins can have a maximum of four levels of structure: primary, secondary, tertiary, and quaternary. Although the proteins can spontaneously fold to a functional conformation, there are a variety of denaturing agents that can be used to disrupt the folding strategies of proteins. Mercaptoethanol is an example of a protein denaturing agent; its mechanism for dismantling proteins is to disrupt the disulfide bonds found in the protein. When urea is introduced to a protein, the hydrogen bonds holding the protein together are disrupted. Heat can also be considered a denaturing agent, which has the potential to disrupt all intermolecular interactions in a protein.
Which of the following levels of structure in a protein would not be disrupted by the introduction of mercaptoethanol?
All of the given levels will be affected
Quaternary structure
Secondary structure
Tertiary structure
Secondary structure
When discussing the secondary structure of a protein, you can assume that the only forces that are relevant are the hydrogen bonds between the carbonyl oxygen of one amino acid, and the hydrogen on the amino group of another. Because hydrogen bonds are the only intermolecular interaction involved in secondary structure, mercaptoethanol would not affect the secondary structure.
Disulfide bonds are generally integral to defining the tertiary structure of a protein; thus, mercaptoethanol would affect the tertiary structure (and subsequent quaternary structure) of a protein.
Example Question #2 : Protein Structure
Proteins can have a maximum of four levels of structure: primary, secondary, tertiary, and quaternary. Although the proteins can spontaneously fold to a functional conformation, there are a variety of denaturing agents that can be used to disrupt the folding strategies of proteins. Mercaptoethanol is an example of a protein denaturing agent; its mechanism for dismantling proteins is to disrupt the disulfide bonds found in the protein. When urea is introduced to a protein, the hydrogen bonds holding the protein together are disrupted. Heat can also be considered a denaturing agent, which has the potential to disrupt all intermolecular interactions in a protein.
Which of the following levels of structure would not be affected by urea?
Quaternary structure
All given levels would be affected
Tertiary structure
Secondary structure
All given levels would be affected
Urea is used to denature proteins by interrupting hydrogen bonds. Hydrogen bonds are found in all levels beyond the primary structure, so all of the above levels will be affected by an introduction of urea.
Hydrogen bonds are particularly important to defining secondary structure, as it is these forces that create alpha-helices and beta-pleated sheets. Without proper secondary structure, tertiary and quaternary development will also be disrupted.
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