MCAT – Diagnostic Test – Biology Section

The poly-A tail is important for the nuclear export, translation, and stability of mRNA. The tail is shortened over time, and, when it is short enough, the mRNA is enzymatically degraded.

We are looking for the step in which the DNA-coupled antibodies are released. Paragraph 2 outlines each step of the procedure shown in Figure 1. Beginning with step A, DNA oligonucleotides are hybridized to the oligonucleotides in the mixture. In step B, agarose beads are used to capture the biotinylated capture oligonucleotides, both in the form of conjugates and free oligonucleotides. In step C, the unconjugated antibodies are removed by washes. In step D, the MlyI enzyme is used to cleave the captured oligonucleotide hybrids, allowing both conjugates and oligonucleotides to be eluted from the solid support. Thus, step D is our answer.

The lipid-soluble vitamins are A, D, E, and K. The water-soluble vitamins are B and C. Greater amounts of subcutaneous fat sequester more of the lipid-soluble vitamins and lower their release into the circulation. Thus, excess fat increases the initial dose of vitamin required to achieve a particular effect.

Content Foundations: Vitamins, Minerals, Cofactors, and Coenzymes

An enzyme (a biological catalyst) may require another chemical compound to be present in order for it to carry out its biological functionality. In general, such “helper” molecules are known as cofactors. Cofactors can be either inorganic (with some common examples including metal ions such as Mg²⁺, Zn²⁺, and Cu⁺) or organic, and organic cofactors are sometimes known as coenzymes.

Many coenzymes are vitamins or derivatives of vitamins, and they often contribute to the function of enzymes by carrying certain functional groups from one place to another in a reaction. Perhaps the most well-known example of this is coenzyme A, which transfers acyl groups from one place to another. Coenzymes that are tightly (or even covalently) bonded to their enzyme are known as prosthetic groups. A famous example of an organometallic prosthetic group is heme, which contains an iron ion in the center of a porphyrin ring, and is attached to oxygen-transport proteins such as hemoglobin and myoglobin.

Vitamins are non-macronutrient compounds that are vital for healthy functioning and cannot be synthesized in adequate quantities by the body, meaning that they must be obtained from external sources. The B vitamins and vitamin C are coenzymes used for various important reactions, and are water-soluble. Vitamins A, D, E, and K are lipid-soluble. Vitamin A plays a key role in vision, vitamin D in calcium and phosphate absorption from the gastrointestinal tract, vitamin E is an antioxidant, and vitamin K promotes coagulation. Like vitamins, minerals contribute to essential roles in the body and must be obtained from the diet, but unlike vitamins, minerals are inorganic. The most important minerals in the body are calcium, phosphorus, magnesium, sodium, and potassium.

Content Foundations: Bicarbonate Buffering

Acid-base buffers confer resistance to a change in the pH of a solution when hydrogen ions or hydroxide ions are added or removed to solution. An acid-base buffer typically consists of a weak acid and its conjugate base. The most important buffer to know for the MCAT is the bicarbonate buffer system, which is shown below.

H₂O(aq) + CO₂(g) ↔ H₂CO₃(aq) ↔ H⁺(aq) + HCO₃^–(aq)

Carbonic acid (H₂CO₃) has the conjugate base of HCO₃^–. Buffers work because the concentrations of the weak acid and its salt are large compared to the number of protons or hydroxide ions added or removed. When protons are added to the solution from an external source, some of the bicarbonate in the buffer is converted to carbonic acid, using up the protons added; when hydroxide ions are added to the solution, protons are dissociated from some of the carbonic acid in the buffer, converting it to bicarbonate and replacing the protons lost.

Buffers resist pH changes best when the pH values are at or near the pK_a value for the acid/base used, because that is when the conjugate acid and base have equal concentrations. Optimal buffering occurs when the pH is within approximately 1 pH unit from the pK_a value of the system. The pH of a buffer solution can be calculated using the Henderson-Hasselbalch equation: pH = pK_a + log [conjugate base] / [acid].

On Test Day, you may see the bicarbonate buffer concept tested from a chemical, biochemical, or biological perspective. For example, hyperventilation (rapid shallow breathing) results in excess CO₂ being expelled from the blood, causing the pH to rise. In response, the buffer needs to release more H⁺ to lower the pH back to physiological norms. An additional fact to be aware of is that other mechanisms in the body are also used to regulate pH, since carbonic acid works best at a pH below physiological conditions, because its pK_a1 (pK_a1 = 6.3, pK_a2 = 10.3) is much lower than the normal pH of blood (7.4).

Arginine is a basic amino acid, meaning that it is positively charged at physiological pH. Positive species interact best with negative species, and of the answers listed, only phosphate groups are negatively-charged.

Content Foundations: Biomolecules

There are four main classes of biomolecules: amino acids/proteins, lipids, carbohydrates, and nucleic acids. All of these classes except for lipids can occur as polymers, as proteins can be seen as polymers of amino acids, DNA and RNA are polymers of nucleic acids, and compounds such as starch, cellulose, and glycogen are polymers of carbohydrates.

Amino acids contain a central carbon to which –NH₂, –COOH, –H, and –R groups are added, and they combine by peptide bonds to form dipeptides, tripeptides, oligopeptides, and proteins. The key functionality of an amino acid is determined by its side chain (–R). Proteins are the building blocks of the body, and are involved in structural and signaling roles.

Lipids are nonpolar (or amphipathic, with both polar and nonpolar areas) molecules that play roles in signaling, structural functions, and energy storage. The main categories of lipids that you must know for the MCAT are fatty acids and the derivatives thereof (triacylglycerols, phospholipids, and sphingolipids), cholesterol and its derivatives (steroid hormones and vitamin D), prostaglandins, and terpenes and terpenoids.

Carbohydrates are important for energy storage and are used in metabolism. They are made up of carbon, hydrogen, and oxygen, often in the ratio C_x(H₂O)_y. Important monosaccharides include glucose, fructose, and galactose. Key disaccharides are sucrose (glucose + fructose), lactose (glucose + galactose), and maltose (glucose + glucose). Polysaccharides (starch and glycogen) are polymers of glucose that are used for energy storage in plants and animals,

respectively.

Nucleic acids are involved in the storage and transmission of biological information. They are made up of nucleotides, which have three components: a nitrogenous base, a five-carbon sugar (ribose in RNA and deoxyribose in DNA), and at least one phosphate group. RNA contains uracil (U) instead of thymine (T) and is generally single-stranded, whereas DNA is generally double-stranded. DNA is used for the long-term storage of genetic information, while RNA is used for gene expression.

he protozoa will typically be diploid, and as stated in the second paragraph, cyst formation involves a round of DNA replication, followed by nuclear replication, followed by a second round of DNA replication. This process is illustrated below, and the presence of four 4n nuclei yields a final total ploidy of 16n.

Content Foundations: Ploidy, Aneuploidy, and Nondisjunction

Ploidy refers to how many copies of each chromosome a cell has. In humans, the vast majority of cells are diploid (2n), meaning that they contain two copies of each chromosome (except for the sex chromosomes; females have two X chromosomes and males have an X and a Y chromosome). Such cells are known as somatic cells—that is, the cells of the body. In contrast, germ cells (i.e., ova and spermatozoa) are haploid (n), meaning that the only have a single copy of each chromosome.

Aneuploidy results from having too many or too few copies of a given chromosome. This results from nondisjunction in anaphase during cell division. Having only one copy of a chromosome is known as monosomy, and having three copies is known as trisomy. Aneuploidy is commonly discussed as occurring in meiosis, and indeed, this is the only way for aneuploidy to be inheritable. For this reason, nondisjunction during meiosis is the cause of aneuploidies such as Down syndrome (trisomy 21) or Turner syndrome (monosomy X). However, nondisjunction during mitosis can also occur, and this is extremely common in cancer cells.

Tight junctions are areas where the membranes of two closely-joined cells adhere tightly and form a near-impenetrable barrier. This is a hallmark of epithelial barriers and is not likely to be a property of monocytes, which are immune cells.

Content Foundations: Cell Junctions

Cell junctions describe ways in which neighboring cells interact with each other to form structures. There are three main types of cell junctions that you should be aware of: anchoring junctions, gap junctions, and tight junctions.

Anchoring junctions include adherens junctions, which are associated with cadherins. The essential idea behind anchoring junctions is that they connect cytoskeletal components of the cell with other cells and/or the extracellular matrix, thereby contributing to the overall structural stability of tissues. Adherens junctions involve cadherin-mediated connections between actin filaments and other cells and the extracellular matrix. Desmosomes also involve cadherin, but in this case cadherin connects intermediate filaments to other cells. Hemidesmosomes are junctions in which integrins connect the intermediate filaments of cells to the extracellular matrix.

Gap junctions are formed by connexin proteins, which connect cells in a way such that diffusion can take place between them, enabling communication, without involving direct contact between the cytoplasmic fluids of each cell. Gap junctions are relatively less common, but they play certain crucial roles within the body. The most important example for the MCAT is in cardiac muscle, where gap junctions allow cells to contract at the same time.

Finally, tight junctions are found in epithelial cells. As the name suggests, the cells in tight junctions are linked very closely to each other, preventing solutes from being able to move freely from one tissue into another. A classic example is the blood-brain barrier, where the epithelial cells in blood vessels in the brain form very tight junctions that allow the close regulation of which substances from the bloodstream can enter the central nervous system. Some types of epithelial tissue have relatively few tight junctions; these are known as leaky epithelia. Examples include some parts of the kidney.

Monocytes are the largest type of white blood cells. Factors secreted by the epithelium help form a cascade that leads to accumulation of immune cells at the site of an injury.

Paragraph 3 states that HDAC1 regulates the production of TGFβ and acts to remove acetyl groups from lysine residues of histones. This is important to gene regulation because DNA is wrapped around histone proteins, and DNA expression is regulated by the addition and removal of acetyl groups.

The energy released by oxidative phosphorylation and used to make ATP is generated from potential energy in the form of an H⁺ gradient, which creates an electrochemical gradient across the mitochondrial membrane. If this membrane is disrupted, this gradient cannot be maintained. Without this gradient, oxidative phosphorylation cannot continue to produce ATP.

Content Foundations: Oxidative Phosphorylation

The final major process of aerobic respiration is oxidative phosphorylation, through which the majority of aerobically-derived ATP is synthesized. This process begins by passing electrons through a series of chemical reactions, known as the electron transport chain (ETC), to a final electron acceptor, oxygen. This is the only time in eukaryotic aerobic respiration where oxygen is directly required. These reactions take place in specialized proteins where the energy from NADH and FADH₂ is used up, molecular oxygen is reduced into water, and approximately 30-36 ATP are created from ADP and inorganic phosphate.

The electron transport chain (ETC) uses free oxygen as the final electron acceptor of the electrons removed from NADH and FADH₂ formed in glycolysis and the Krebs cycle (also known as the citric acid cycle). The ETC is composed of four large protein complexes (Complexes I-IV) embedded in the inner mitochondrial membrane and two small electron carriers shuttling electrons between them. Complex I is known as NADH dehydrogenase, II is known as succinate dehydrogenase, III is known as cytochrome bc or c, and IV is known as cytochrome c oxidase. Electrons are released from NADH and FADH₂ through a series of reactions.

In the ETC, the energy released from the series of electron transfers is used to pump H⁺ across the membrane. The unequal concentrations of H⁺ ions across the membrane establishes an electrochemical gradient, leading to chemiosmosis, or the passive diffusion of the protons down their concentration gradient, which is coupled to ATP synthase. This proton movement generates 90% of the ATP synthesized during oxidative phosphorylation. The electrons passing through the electron transport chain gradually lose energy until eventually they are donated to O₂, which accepts two H⁺ ions and is transformed into water. If the proton gradient is disrupted or destroyed, chemiosmosis can become uncoupled from the ETC, resulting in little to no ATP generation despite the transfer of electrons carrying on. Many poisons and toxins act by uncoupling the proton gradient from ATP synthase.

The eukaryotic cell membrane is composed of a phospholipid bilayer, cholesterol, and various transmembrane protein pores, channels, and gates. The largely hydrophobic nature of the lipid bilayer prevents ions and polar solutes from diffusing across the membrane, while allowing for the free movement of hydrophobic molecules. Calcium ions are charged, and so would be unable to pass through the membrane in significant amounts. Thus, calcium ions require an ion channel.

Content Foundations: Membrane Transport

The plasma membrane of eukaryotic cells is primarily composed of a lipid bilayer of amphipathic phospholipids with hydrophilic heads and hydrophobic tails. It also contains cholesterol and membrane proteins. Transmembrane proteins are membrane-spanning proteins with hydrophilic cytosolic and extracellular domains and a hydrophobic membrane-spanning domain. Additionally, peripheral proteins are only transiently attached to integral proteins or peripheral regions of the lipid bilayer, and lipid-anchored proteins are covalently bound to membrane lipids without actually contacting the membrane directly. Membrane transport is accomplished through several mechanisms.

Some molecules, like small gases, can directly diffuse through the membrane. This is known as simple diffusion, and is an example of passive transport because no energy is necessary. Osmosis is a type of simple diffusion in which water moves in or out of the cell to attempt to equalize concentrations of solute. Facilitated diffusion is another form of passive transport where no energy is necessary because molecules diffuse down their concentration gradient, but a transmembrane channel is necessary because the molecule may be too large or polar for simple diffusion. Ions are often transported through facilitated diffusion, and aquaporins are facilitated diffusion channels for water that augment osmosis.

In primary active transport, energy is used directly to move a solute against its gradient through a transmembrane channel. Secondary active transport is a more complicated system in which the energy stored in an electrochemical gradient established via primary active transport is used to facilitate the movement of a solute. An example is the sodium-calcium exchanger, which allows three Na⁺ ions to flow down their concentration gradient, which was previously established by a primary active transport mechanism, into the cell, while transporting one Ca²⁺ ion out.

Endocytosis is used to ingest larger materials. It is divided into pinocytosis and phagocytosis. In pinocytosis, cells engulf liquid substances, while in phagocytosis, they engulf solid particles. The basic pathway of endocytosis involves recognition of a target molecule at the plasma membrane, followed by invagination and the formation of a vesicle on the inside of the cell. Exocytosis can be thought of as endocytosis in reverse. It is used to release hormones, neurotransmitters, membrane proteins and lipids, and other materials.

Content Foundations: Sympathetic and Parasympathetic Nervous Systems

The autonomic nervous system, which controls involuntary responses in the body, including things like sweating, blushing, and pupil dilation, is divided into the sympathetic and parasympathetic systems. The sympathetic nervous system stimulates the body in the classic “fight or flight” response, mediated by hormones such as epinephrine and norepinephrine. If the body needs to get ready for action, it will dilate the pupils, raise the heart rate, and increase blood flow to skeletal muscles to prepare for sudden action. By contrast, the parasympathetic nervous system is the “rest and digest” system that increases blood flow to the digestive system, slows the heart rate, constricts the pupils, and generally exerts actions opposite to those of the sympathetic nervous system.

In turn, the autonomic nervous system is part of the peripheral nervous system, which describes the nervous system throughout the body and is distinguished from the central nervous system, which corresponds to the brain and spinal cord. The peripheral nervous system is also divided into the visceral nervous system, which modulates the digestive system, and the somatic nervous system, which connects to skeletal muscle to allow for voluntary movement.

To recognize the antigens on the botulinum protein, an antibody could be used. Antibodies are made to recognize and bind specific epitopes of biomolecules like proteins.

Paragraph 2 states that the dual-layered system is composed of smooth muscle. Smooth muscle is uninucleate, non-striated, and under the control of the autonomic nervous system (ANS). Its activity is also regulated by parasympathetic and sympathetic branches of the ANS.