1. Non-nuclear DNA is found in the mitochondria (and also in plastids, but the MCAT does not test plants). This mitochondrial DNA is in no way associated with nuclear DNA. There is no exchange of DNA between nucleus and mitochondria. Mitochondrial DNA has a different lineage: it is haploid, having a maternal copy only, compared to nuclear DNA, which is diploid (one maternal copy and one paternal copy). Mitochondrial DNA also differs structurally; it is circular rather than linear. Both nuclear and mitochondrial DNA are helical, but nuclear DNA is linear, with open ends, while in mitochondrial DNA the ends are joined to form a circle, as shown below.

FIGURE 1

2. Below is a labeled diagram of a mitochondrion. Notice that the DNA is circular (like

prokaryotes)—appropriate to the endosymbiotic theory of mitochondrial evolution.

FIGURE 2

3. The pH of the intermembrane space is approximately 1.4 pH units lower than that of the matrix. The pH of the matrix is about 7.8. You do NOT need to know these values, only that the intermembrane space will be more acidic (lower pH) because of the hydrogen ion gradient across the inner mitochondrial membrane.

4. If hydrogen ion channels were inserted in the inner mitochondrial membrane, this would present an alternate pathway for their passageway back into the matrix (down their concentration and charge gradient) other than through the ATP synthase. This would decrease the production of ATP. Although not required knowledge, thermogenin might appear on the MCAT as part of a passage. Thermogenin is a protein channel in the inner membrane that allows the passage of protons just as we have described with the concomitant production of heat. Thermogenin is found in most mammals, especially young mammals and in animals that hibernate. Human infants have high levels of thermogenin in “brown fat”—a fat present at birth that declines with age. If a similar proton channel were to be opened up in the outer mitochondrial membrane this could also negatively impact ATP production due to loss of the proton gradient as protons leak out into the cytosol.

5. Tubulin is a globular protein that polymerizes to form microtubules. Microtubules are one of three primary contributors to the cytoskeleton of the cell, microfilaments (actin polymers) and intermediate filaments being the other two. Two types of tubulin, α-tubulin and β-tubulin, form a heterodimer that is then assembled into long chains called protofilaments. Thirteen (13) protofilaments surrounding a hollow core make up one microtubule. Some students confuse the “9+2” arrangement by thinking that microtubules themselves follow this format. This is incorrect. The 9+2 arrangement is found only in eukaryotic cilia and flagella. The “9” and “2” refer to nine doublets (two microtubules each) surrounding a center doublet (2 microtubules) in a wheel-like design. That would be a total of 20 microtubules—each one of those twenty microtubules being the hollow tube of 13 protofilaments just described. The cytoskeleton is a scaffolding-like network of microfilaments, microtubules, and intermediate filaments that provides structure to the cell and creates a highway of sorts for intracellular transport. The spindle apparatus is the array of microtubules that grows outward from the centrioles during mitosis to bind with the centromere of the chromosomes at the metaphase plate. This assembly effect division of a pair of sister chromatids into two separate chromosomes (i.e., disjunction). Actin is a protein monomer that polymerizes to form microfilaments. In addition to their role in the cytoskeleton, microfilaments form the “thin filament” portion of the sarcomere. The thin filaments act as tracks along which the thick filaments (which are made of myosin motor proteins) move during contraction. An intermediate filament is a general class of several proteins that polymerize to form filaments that are intermediate in diameter between microfilaments (the smallest) and microtubules (the largest). We include this question about myosin being a microfilament because we have seen a surprising number of students who incorrectly think that actin and myosin are both examples of microfilaments. Microfilaments are made up of actin subunits. Myosin is a motor protein, not a microfilament. The 9+2 arrangement found in eukaryotic cilia and flagella is shown in the following diagram.

FIGURE 3

NOTE TO TUTORS: The biology lessons present a unique challenge that is worth discussing. Most of the Altius lessons include very few vocabulary terms, but in the biology lessons students will be presented with nearly one hundred vocabulary terms they must know for the MCAT. If they have been serious students in their prerequisite work, 90% of these terms should be at least familiar to them, and they may already have a solid mastery of a good portion of them. We do NOT want students to take a memorization-only approach to these biology vocabulary terms. Encourage your students to study each term until they have a clear understanding of the structure or process described, where it is located and/or occurs in the body, and can visualize its actual function and/or interrelation with other familiar structures or processes. The guiding principles for ensuring this kind of non-memorization knowledge are the four conceptual questions introduced in the Intro, Strategy & Math Lesson. For every topic in the lessons, including biology terms, students should not feel they have completed their studies until they can confidently answer the Four Conceptual Questions: 1) Can I visualize it? 2) Can I draw a picture, graph, or diagram of it? 3) Can I explain it to someone else in layman’s terms? 4) Can I think of real-life examples?

6. Flagella are whip-like projections from the cell body used for locomotion. In humans, sperm cells are the only cells that have flagella. Cilia are similar protrusions found on the lumen-facing side of many epithelial cells lining various cavities in the body. Cilia are NOT used for locomotion of the cell itself. The cell is fixed in place and the cilia create a beating pattern that moves fluid and or other extracellular materials past the cell. Examples include the ependymal cells that line the ventricles of the brain and the hollow center of the spinal cord (move cerebrospinal fluid), the epithelial cells that line the respiratory track (move mucus and debris), and the cells that line the fallopian tubes (move the egg toward the uterus). Eukaryotic cilia and flagella exhibit the 9+2 arrangement of microtubules while prokaryotic flagella are polymers of the protein flagellin. [NOTE: Make sure students do not confuse cilia with the microvilli in the intestines or with the hair cells found in the inner ear].

7. Correct answers could be anything related to the function of microtubules. Specifically, all cells would have weakened cytoskeletons in which microtubules would have lost the ability to function as pathways for intracellular transport of organelles and other materials. All cells would be unable to successfully complete mitosis or meiosis without the ability to form the spindle apparatus. All ciliated epithelial cells would lose their function. Infertility could result from

immobile sperm. In a female the incidence of extra-uterine pregnancy could increase because the ciliated cells that line the fallopian tubes and normally sweep the egg toward the uterus would be dysfunctional.

8. Phospholipids are lipid molecules with non-polar tail regions and a polar phosphate heads. This polarity is pivotal to their function in membranes. Students will need to be able to visualize and draw a phospholipid at the molecular level. This includes the understanding that they are formed by combining a glycerol molecule with two fatty acids and one phosphate. They will need to be able to draw out a phospholipid in line-bond form, understanding all functional groups and connections. For example, the MCAT has asked about the functional groups present before and after a fatty acid reacts to become part of a phospholipid. To answer such a question, the student would have had to know that the fatty acid is a long carboxylic acid chain and that one of the alcohol groups on glycerol attacks the carbonyl carbon, splitting off water and forming a new ester group. Integral proteins are proteins that have one or more moieties (i.e., segments) embedded within the phospholipid bilayer. This is in contrast to surface proteins (a.k.a. peripheral proteins) which do not enter into the hydrophobic core, but are contained entirely on the polar surface of the membrane. Transport proteins are integral proteins that span the entire width of the bi-layer membrane (i.e., transmembrane proteins) creating tunnels for the passage of ions, proteins, or other substances through the hydrophobic core. A membrane receptor is any protein that specifically binds a signaling molecule (i.e., ligand) that initiates a cellular response. Steroid- hormone receptors are located inside the cell, often in the nucleus, as steroids can diffuse through the hydrophobic membrane core, while receptors for all polar ligands are located on the external surface of the membrane. Cholesterol is an amphipathic molecule with a steroid region and a polar region. It is inserted between phospholipids at very high concentrations in eukaryotic cells. It serves a dual purpose, both adding rigidity and fluidity to the membrane. At higher temperatures, around normal

physiological conditions (37°C), the non-polar region of cholesterol interacts with the hydrophobic tails of the phospholipids helping to hold them in place and thereby adding rigidity to the membrane. The polar region of cholesterol also interacts with the polar phosphate heads. However, at lower temperatures, when the interactions between the non-polar tails could cause crystallization, the presence of the rigid steroid portion of cholesterol disrupts Van der Waals forces between fatty acid tails maintaining a minimum level of fluidity. The fluid mosaic model simply refers to the dual-layer model of a phospholipid membrane with which students are likely familiar—specifically that there are two opposite-facing leaflets with the polar tails of the phospholipids directed toward the center of the bi-layer and the polar heads directed outward—creating both a cytosolic and an extracellular face. The “fluid” term refers to the fact that phospholipids are mobile—they can exchange positions with each other and move laterally across their leaflet of the membrane. Exocytosis is the process by which a vesicle on the inside of the plasma membrane fuses with the plasma membrane, dumping its contents into the extracellular environment. Endocytosis is the process by which a cell takes up small particles by invagination of the plasma membrane to form a vesicle called an endosome. Phagocytosis is a type of endocytosis specifically referring to the engulfing of very large particles, bacteria, etc., and only occurs in some cells. Pinocytosis is the non-specific endocytosis of extracellular fluid and very small particles and occurs it occurs in all cells. The key differentiator is that pinocytosis is non-specific. This is in contrast to receptor-mediated endocytosis in which the cell binds a specific target for uptake. Phagocytosis is always receptor-mediated.

NOTE TO TUTORS: It is very, very tempting for students to memorize these biology terms. It is your responsibility to make sure they actually understand them. For all of these processes they should be able to draw a diagram of their own illustrating the process, outlining the structure, and so forth. Help them recognize that a question asking for a definition has approximately ZERO chance of showing up on their exam. The questions they will face will be conceptual questions that require a working knowledge. For example, they won’t be asked to define exocytosis, but they might be asked how exocytosis will affect the total mass of the plasma membrane over time in the absence of endocytosis. That is a question that requires them to know the terminology, but also visualize the actual processes involved.

9. Hypertonic solutions are more concentrated than the cell, driving water to leave the cell. Hypotonic solutions are less concentrated than the cell, driving water to enter the cell (and potentially burst). Isotonic solutions have an equal concentration as the cell and there is no net flow of water in either direction.

10. Tight Junctions are found in the epidermis of the skin (although the many layers of dead, keratinized cells also provide a barrier function) and, in “tight epithelium” such as the lining of the bladder, the linings that form the blood-brain barrier, the distal convoluted tubule, and collecting duct of the kidney, etc. Gap Junctions occur between adjacent cells in many different tissues throughout the body. A few classic examples that allow electrical or chemical coupling between cells include: 1) the junctions between cardiac muscle cells, or between smooth muscle cells, which allow for rapid passage of an electrical potential between cells, 2) direct neuron-neuron coupling found in certain parts of the brain and in the retina of the eye. Adherens junctions are found in epithelium and between cardiac muscle cells. Desmosomes occur in tissues subject to shear stress such as the epidermis. They are particularly common in stratified epithelium. An autoimmune disease that produces antibodies against the desmosome protein (desmoglein) leads to separation of skin layers and large, painful blisters.

11. Epithelial Tissues cover the body or line its cavities. Epithelium is a general term, and some specific types are the epidermis of the skin, the endothelium of blood and lymph vessels, and the mesothelium that lines thoracic and abdominal cavities. There is some disagreement as to whether endothelium and mesothelium should be classified as epithelium as they originate from different germ layers. For the MCAT, if it is lining a cavity or separating the body from the external environment, you can consider it to be epithelial tissue. Nervous Tissues include—obviously—the neurons of the central and peripheral nervous systems. However, students often forget that glial cells—astrocytes, microglia, Schwann cells, oligodendrocytes, and ependymal cells—are also considered nervous tissue. Ependymal cells are unique because you could clearly argue that they are both epithelial and nervous. That sounds like a classic MCAT question: “Which of the following cells could potentially be classified as an example of both nervous tissue and epithelial tissue?” Connective Tissues include bone, cartilage, blood, lymphatic tissue, fat, etc. It would be fairly safe to assume that if a cell is not clearly part of one of the other three classes it is most likely connective. There are a few connective tissues students tend not to recognize as such. These include blood, lymph, tendons, ligaments, adipose tissue, the non-epithelial wrappings, coverings, and support tissue found around muscles and organs, and so forth. Most organs, for example, have a considerable amount of connective tissue interspersed with muscle tissue, nerve tissue, and epithelial linings. Muscle tissue is easy to classify: it is skeletal, cardiac, or smooth. The dermis of the skin is a connective tissue. Adipose tissue, composed of adipocytes, is a type of connective tissue.

12. Researchers know a lot about G-proteins. Keep it simple here and focus on the basic story of a

generalized G-protein response. First, a hormone or signal molecule binds to an integral protein on one of its extracellular domains—this protein is called a G-protein-coupled receptor or GPCR. This causes a conformational change that activates a cytosolic domain of that same integral protein. Near the GPCR, or at least along the cytosolic face of the membrane, is a G protein made up of an alpha, beta, and gamma subunit. The alpha subunit binds both GTP and GDP. When GDP is bound, the protein is “off” and when GTP is bound it is “on.” Usually, but not always, the activated receptor protein acts as a catalyst for the replacement of GDP by GTP, activating the alpha subunit of the G protein. The activated alpha subunit then separates from the beta and gamma subunits. The activated alpha subunit acts as an agonist for another enzyme, often adenylyl cyclase. Adenylyl cyclase is an enzyme that catalyzes the conversion of

ATP to cAMP plus two molecules of inorganic phosphate (ATP cAMP + 2Pi). Cyclic AMP just happens to be an agonist for Protein Kinase A, which phosphorylates proteins—usually enzymes. Many enzymes are turned on or off through being phosphorylated or dephosphorylated. The cascade can be shut down in various ways. Often the beta and gamma subunits re-bind with the alpha subunit, deactivating them. In other cases GPCR is phosphorylated one or more times, which deactivates it. DO NOT MEMORIZE THIS. The MCAT will not test you on names or other specifics. However, it does illustrate how cascades work and having a general familiarity with G protein signaling pathways will be a tremendous help on any passages or questions about G proteins, which have been fairly common.

13. The image below does a good job of representing the traditional cycle phases plus interphase. Interphase is the entire period outside of mitosis. Mitosis is often called “M Phase.” G1 is the first growth phase. This is the phase in which most active cells live and function. The cell grows in size considerably during G1. Cells that enter the G0 phase become “non-proliferative,” meaning they are not actively dividing and may not divide in the future. This is sometimes called “rest phase.” Many fully differentiated eukaryotic neurons remain in this phase indefinitely. During S phase the DNA is replicated. The G2 phase follows S phase and features continued cell growth and high metabolic activity, especially the production of microtubules in preparation for mitosis.

FIGURE 4

14. The G0 phase is of interest to MCAT examinees because fully differentiated neurons and cardiac muscle cells are frozen in G0 and do not divide. Multi-nucleated skeletal muscle cells can also be considered to be in the G0 phase. You may hear this state referred to as “quiescent”, which means stable, not changing, and unlikely to change.

15. a) 46; b) 46; c) 46; d) 46; e) 46; f) 46; g) 23; In a human diploid cell, prior to S phase, there are 46 unreplicated chromosomes, 23 of which originated from the father and 23 of which originated from the mother. These unreplicated chromosomes do not contain sister chromosomes. Let’s define these unreplicated chromosomes as having a mass of m. After replication, there are 46 dyads, or duplicated chromosomes. A dyad features two identical sister chromatids attached to the same centromere. The mass of a dyad would be 2m. Therefore, during DNA synthesis the mass changes from m to 2m, but the number of chromosomes does NOT change. In a human diploid cell, the chromosome number will always be 2n, but the mass could be m or 2m depending on whether or not S-phase has occurred. A tetrad is the set of two dyads aligned at the metaphase plate during Meiosis I, which are physically adjoined to one another by at least one DNA crossover. A human gamete, which is haploid, would have a mass of 0.5m. The figure below should help you visually each type of chromosome and how mass changes. The take-home point is that the chromosome number does NOT change when DNA is replicated, you just end up with twice as much DNA per chromosome. The only time the chromosome number changes is during Meiosis I, or after the fusion of gametes in the production of a zygote.

FIGURE 5

16. Histones are the proteins around which the DNA helix is wrapped during the first step of DNA condensation to form a chromosome. A nucleosome is a set of eight histone proteins in a cube shape with DNA coiled around it much like thread wound around a spool. There is further coiling and supercoiling of the nucleosomes to create the final condensed chromosome. Chromatin is a general term for DNA and protein. Therefore, chromosomes are made up of chromatin. A diploid cell has 2n chromosomes and a haploid cell has n chromosomes. The value of n varies among species, for humans it is 23, therefore all human diploid cells, being 2n, have 46 chromosomes. Diploid cells have two copies of each chromosome, one from mom and one from dad, while haploid cells have only one. Homologues are two related but non-identical chromosomes—one originating from each parent. Sister chromatids are the two strands of DNA

in a duplicated chromosome attached by a centromere. Assuming no mutations or errors in replication, they are identical as long as crossing over has not yet occurred. The centromere is the region of the chromosome that joins the two sister chromatids. The term kinetochore is often used synonymously with centromere, but they are not identical. The centromere is a region on the chromosome and the kinetochore is a specialized group of proteins to which the spindle fibers attach directly during mitosis/meiosis.

17. Nuclear DNA is found in the nucleus and never leaves the nucleus. However, mitochondria also contain DNA, although it is their own unique-lineage circular DNA, NOT nuclear DNA.

18. During prophase, the nuclear membrane degenerates and the chromosomes condense. Metaphase is indicated by the chromosomes lining up at the metaphase plate and formation of the spindle apparatus. Anaphase is indicated by separation of the chromosomes and migration toward the opposite poles of the cell. Telophase is indicated by the nuclear membranes beginning to re-form and the chromosomes unwinding. Many diagrams will also show the beginning of cytokinesis. Some diagrams will also show a single cell with a well-defined nuclear membrane and uncoiled chromosomes. This would indicate interphase. Diagrams used on the MCAT are usually highly schematic and designed so that the distinguishing features are as clear as possible. There is no change in chromosome number during mitosis. Although the splitting of the centromere will separate a tetrad into two dyads, the total number has not changed.

19. The characteristics that define prophase, metaphase, anaphase and telophase are approximately the same for mitosis and meiosis I and are IDENTICAL (with one exception) for mitosis and meiosis II. In some diagrams, the chromosomes will be schematically represented in a way that will allow you to count them. The chromosome number may be defined as a low hypothetical number to facilitate this counting. This would be the only way to distinguish mitosis from meiosis II. Cells in mitosis would have 2n chromosomes and cells in meiosis II would have only n chromosomes. In other words, unless you can count the chromosomes (the one exception mentioned above), diagrams of mitosis and meiosis II are indistinguishable. To distinguish between mitosis and meiosis I, there a couple of items to look for. First, if there are tetrads depicted (two pairs of sisters; four chromatids forming a single unit during crossing over), then the cell must be in meiosis I. During mitosis, the chromosomes would be condensed, but you would see only dyads. There would be no tetrads. Tetrads never form during mitosis. The next key difference occurs during metaphase. During metaphase of mitosis the replicated chromosomes (dyads) line up single-file at the metaphase plate. By contrast, during metaphase of meiosis I the chromosomes are NOT lined up single-file, they line up side-by-side as pairs of homologues, or tetrads. Seeing tetrads is a dead giveaway that you are looking at a depiction of meiosis I. It can also be helpful to consider the centromeres. When looking at metaphase of mitosis you should see a single-file line of centromeres aligned along the metaphase plate. When looking at meiosis I, you should see two side-by-side centromeres, one centromere for each of the two chromosomes forming the tetrad. During anaphase, the centromeres split. In mitosis, the sister chromatids are separated to opposite poles, but in meiosis I the two homologues that make up the tetrad are separated to opposite poles. Thus, during anaphase of mitosis you should see single chromatids being pulled to opposite poles of the cell, but in meiosis I you should see dyads being pulled to opposite poles of the cell. All of the points we have discussed are visible in the following figure.

FIGURE 6

20. Nondisjunction occurs when the chromosomes fail to separate properly during anaphase. This could be during meiosis I or II, or mitosis, although the scenario most commonly discussed is usually nondisjunction during meiosis I. Nondisjunction results in an unequal number of chromosomes in the daughter cells. When the daughter cell has an extra chromosome, this is an example of trisomy; when the daughter cell has just one chromosome, the condition is referred to as monosomy. Most cases of nondisjunction are fatal to the affected individual, but in a few instances nondisjunction can result in a viable offspring. For example, Turner’s Syndrome is the result of monosomy of the X chromosome. The most common trisomic condition is trisomy of chromosome 21, known as Down Syndrome

21. Crossing over occurs during prophase of meiosis I. Two homologous dyads pair up with one another and exchange segments of DNA. Crossover events occur at a high rate. In fact, crossing over happens to such an extent that two genes must be very close to one another on the chromosome to avoid the nearly inevitable likelihood that a crossover event will separate them. This is why genes located on the same chromosome can still assort independently, as do genes on separate chromosomes. Genes close enough to each other on the chromosome that being separated by a crossover is less likely are said to be linked. If crossing over did not exist, we would say that all of the genes on one chromosome are linked.

22. Below is a diagram of an adenine nucleotide. Notice that free nucleotides often exist as triphosphates. Notice the phosphodiester bonds between phosphate moieties and between the initial phosphate and the 5’ carbon of the ribose sugar. In a polymer chain, the third phosphate would also be bound to the 3’ carbon of the previous ribose sugar.

FIGURE 7

23. DNA and RNA are nucleotide polymers. Other common nucleotides include cAMP, NADH, FADH2, FMN, Coenzyme A, ATP, GTP, UTP, etc.

24. Below is a diagram of an adenine nucleotide. The base shown happens to be adenine.

FIGURE 7 (repeated)

25. On the following page is a diagram of a section of a DNA helix. Be sure students can visualize and easily draw all bond-to-bond connectivity—especially the phosphate bond between the 3’ hydroxyl group and the 5’ carbon, and the hydrogen bonds between bases. A common mistake students make when drawing these structures is to have too many bonds to the phosphate, too few, or the incorrect charge on the phosphate. Also make sure they have drawn the ribose WITHOUT a 2’ hydroxyl group. It is NOT required knowledge to be able to draw each base (A,T,C,G,U) from memory, but general familiarity is helpful. Drawing a helix a few times will solidify the concept of how hydrogen bonds form between these bases. The AAMC has frequently required knowledge of the actual bond-to-bond connectivity, and/or the functional groups involved in the DNA helix. Therefore, it is imperative that students can precisely draw the polymerized nucleotides that make up a section of DNA.

FIGURE 8

26. Adenine and guanine are purines, cytosine and thymine are pyrimidines. Later in this lesson we will discuss uracil, which is also a pyrimidine.

27. The origin of replication is the location on the chromosome where replication begins. For human chromosomes there are multiple origins. Bidirectional refers to the fact that replication proceeds in both directions simultaneously from the origin. Semi-conservative refers to the fact that each of the newly formed daughter helices consists of one original strand paired with one newly-replicated strand. Semi-discontinuous replication refers to the fact that one strand (the leading strand) is synthesized continuously and the other strand (the lagging strand) is synthesized in Okazaki fragments (i.e., discontinuous).

28. DNA replication begins at an origin of replication. Helicase unzips the double-helix. Immediately, single-strand binding proteins coat the individual strands and prevent them from re-annealing. Next, both strands are simultaneously fed through a replication complex that contains all of the proteins necessary for replication. Because DNA polymerase can only add to an existing 3’ OH group, primase (an RNA polymerase) first constructs short RNA primers on both strands. Two DNA polymerase molecules then begin building new complementary DNA strands. In doing so, they must “read” (i.e., move along the strand) in the 3’ to 5’ direction, building the new strands in the 5’ to 3’ direction. The sliding clamp is a protein that helps keep the DNA polymerase tightly associated with the strand. Because both enzymes must move along the strand in the 3’ to 5’ direction, they move in opposite directions. If this continued indefinitely, the two enzymes would move farther and farther apart. Instead, all enzymes and proteins remain closely associated with the replication fork in what is often called the “replication complex.” As a result, the enzyme working on the lagging strand must copy short segments downstream, release from the strand, move upstream, and copy another short segment downstream, and then repeat. This also means that while the leading strand requires only a single primer, the lagging strand requires multiple primers, one for each of these short segments called Okasaki fragments. After this initial replication step, the enzyme RNase H removes all RNA primers. DNA polymerase then

fills in the gaps. However, remember that DNA polymerase can only add nucleotides to existing 3’ OH functional groups. Therefore, although it can add a nucleotide to fill the last missing base pair in a gap, it cannot connect that last nucleotide to its downstream neighbor. This functionality is performed by DNA ligase. DNA ligase creates the last necessary phosphodiester bond, completing the strand.

29. The DNA polymerases require an existing 3’ hydroxyl group to which they can add their first nucleotide—they cannot set down a nucleotide with a free 5’ end. For this reason, an RNA primer must be placed at the 5’ end of any DNA strand. Later in the process all primers are removed and the gaps are filled in by DNA polymerase and DNA ligase. At the 5’ end, however, there are still no existing 3’ hydroxyl group so DNA polymerase cannot replace that section of primer. As a result, every time a chromosome is replicated the new daughter strands will be slightly shorter than the parent strands, by an amount exactly equal to the RNA primers that were in place on both ends of the chromosome.

30. Because telomeres are shortened by each round of cell division, they provide somewhat of a “time clock” for cells. After the telomeres are gone, subsequent division will quickly damage important coding sections of the DNA. Presumably the cell could not survive very many additional divisions without being directed into apoptosis. This would act to prevent the uncontrolled cell division found in tumors. However, if the enzyme telomerase were present, the cell could replace the telomere as it was being used up—essentially removing the “clock function” of the telomeres and theoretically allowing for unlimited cell division.

31. Restriction endonucleases are enzymes that cut DNA at specific pre-determined sequences. They are used in DNA cloning to create DNA fragments with “sticky ends” that can be hybridized with vector DNA to form recombinant DNA. The “sticky ends” are so named because the endonuclease cuts the DNA in a staggered fashion that leaves one side of the helix longer than the other. The specific base sequence recognized by the endonuclease is called the recognition sequence. Because the endonuclease ONLY cuts at one sequence, any fragment cut by that same enzyme will be complementary to any other fragment—and therefore any two fragments can hybridize, or join together to form a single strand. A vector is a segment of DNA used to transfer a desired sequence into another cell. Often, the vector is a bacterial DNA sequence such as a plasmid. The target DNA sequence that researchers desire to multiply is added into the bacterial vector using restriction endonucleases. The vector can then be placed inside of bacteria and the bacteria cultured. Because bacteria reproduce exponentially, a huge number of new copies of the vector (with the target sequence included) can be created in relatively little time. Phage is an abbreviated name for a bacteriophage (a virus that infects bacteria). As an alternative to the use of a bacterial plasmid as just described, the vector can also be inserted into a bacteriophage. Bacteria are then infected with the phage. The phages take over the machinery of the bacteria they infect in order to reproduce large numbers of new phages. This also results in many copies being made of the vector and the target sequence that was inserted into it. Gel electrophoresis is a lab technique used to separate molecules by size. A mixture of molecules (usually nucleotide segments or proteins) is loaded onto a plate covered with an agarose gel. A charged field is created across the gel. Because nucleotides are negatively charged (due to the phosphate groups) they will be pulled through the gel toward the positive side of the field, which is called the anode. (IMPORTANT NOTE: The charge of the anode and cathode in gel electrophoresis is the exact OPPOSITE of the charges on the anode and cathode in galvanic cells). The gel acts like a molecular sieve, providing more resistance to the larger

molecules. As a result, the smallest of all molecules travels the farthest, with all other molecules traveling a somewhat shorter path along a continuum down to the largest molecule. When a special kind of paper is placed on top of the gel, the separated molecules attach to the paper at their respective positions. This paper can then be exposed on a film to create a map of the separated molecules.

32. To answer the second question, PCR requires that one know at the outset the specific sequence on the DNA that will be used. Primers are then synthesized that will anneal with the DNA on either side of the target sequence. Two primers are required: one that is complimentary to the 3’ end of the sense strand and one complimentary to the 3’ end of the antisense strand. The DNA is heated to about 95° C to denature the helix and the primers to denature the helix. The primers are added along with special DNA polymerases (usually Taq Polymerase) harvested from thermophilic bacteria that live in hot springs. The mixture is then cooled to a much lower

temperature to allow the primers to anneal (50-65°C). The temperature is then raised again to

the optimum temperature range for the thermophilic enzyme (around 72° for Taq Polymerase). The polymerase then copies the DNA, creating two new DNA helices. The temperature is raised again high enough to denature both helices and the entire process is repeated. The number of copies doubles for each cycle.

33. Ribosomal RNA (rRNA) is the polymer of which ribosomes are constructed. Remind students that ribosomes are assembled in the nucleolus. Ribosomes are a non-protein entity that act as enzymes in the polymerization of proteins, and are an example of a non-protein enzyme. Transfer RNA (tRNA) is the molecule that bridges the gap between mature mRNA and the assembled protein. Each tRNA has an anti-codon on one end and the other end is covalently bonded to the amino acid associated with that anti-codon (or more precisely, the codon that is complementary to the anti-codon). Messenger RNA (mRNA) is the complementary RNA strand copied from the DNA template strand. The original copy is called pre-mRNA because it contains many non-coding introns and lacks the poly-A tail and 5’ cap. After it is fully processed and ready for translation it is called mature mRNA.

34. RNA polymerase binds to the promoter region with the aid of various transcription factors. Helicase unwinds the DNA, forming the transcription bubble. RNA polymerase reads the template strand in the 3’ to 5’ direction, creating a pre-mRNA transcript that matches the coding strand with U substituted for T. Termination factors cause the release of the mRNA transcript. During post-transcriptional processing, large sections of non-coding sequences called introns are spliced out, leaving only the exons, or sequences that code for actual amino acids in the eventual protein. A poly-adenosine tail (a.k.a., “poly-A tail”) is added to the 3’ end, along with a 5’ cap. This is the mature mRNA strand that will be translated at a ribosome.

35. The coding strand is identical to the pre-mRNA except for U is substituted for T.

36. Alternative splicing refers to the fact that after introns are removed from the mRNA transcript, the exons can be assembled in any of a number of different orders—each variation resulting in a different protein. This process is often cited as an explanation for how eukaryotes produce an almost unfathomable number of antibodies from relatively few genes.

37. a) no transcription (inhibitor would be bound); b) yes, gene is transcribed; c) no transcription (inhibitor would be bound); d) no transcription (or very little; inhibitor would not be bound, but cAMP levels (the activator) will be low when glucose is present).

38. The code is said to be degenerative because given a specific amino acid it cannot be determined which codon coded for that amino acid—it could have been multiple codes, usually at least two or three. This redundancy is considered degenerative because you cannot know the codon from the amino acid. The code is considered unambiguous because given a codon, there is no ambiguity about which amino acid it will code for. Even though multiple codons may code for the same amino acid, none of those individual codons will ever code for a different amino acid.

39. Translation begins when the small subunit attaches to the mRNA strand at the 5’ end under the influence of various initiation factors. The small subunit scans the mRNA until it reaches the start codon, AUG. The first tRNA, which will always carry methionine and will have the anticodon 3’ UAC 5’ (to complement the start codon 5’ AUG 3’), binds to the start codon along with the large ribosomal subunit (both ribosomal subunits are made up of rRNA plus some protein). The process up to this point is considered initiation. The complete ribosome then begins moving along the mRNA strand from 5’ to 3’. There are aminoacyl (A), peptidyl (P), and exit (E) sites on the ribosome. New tRNA molecules carrying their associated amino acid enter at the A site driven by hydrogen bonding between the anticodon of the tRNA and the codon on the mRNA strand. A peptide bond then forms between the amino acid on the new tRNA and the amino acid on the previous tRNA, which sits in the adjacent P site. The new tRNA then shifts over into the P site and the previous tRNA enters the E site, dissociates from the protein, and exits the ribosome. Another new tRNA enters the A site and the process repeats. This entire process is called elongation. Finally, at some point, the ribosome reaches a codon on the mRNA such as UAG, which is a stop codon. There are no tRNAs that recognize and bind the stop codons. Instead a protein called a release factor binds to the stop codon and causes dissociation of the ribosome complex. This is referred to as termination.

40. Translation occurs in the cytoplasm on free-floating ribosomes and on the rough endoplasmic reticulum ER. Recall that many proteins bound for certain organelles, the plasma membrane, the ER membrane, the lumen, and for excretion from the cell are translated on the cytosolic side of the rough ER and translocate into the ER membrane or into the ER lumen instead of into the cytoplasm. Some translation also occurs in the mitochondria because they have their own protein-synthesis machinery.

41. A point mutation is a single base pair substitution. A missense mutation is a mutation that changes the codon so that a different amino acid will be incorporated. A silent mutation is any mutation that does NOT alter the amino acid sequence. This could be because the codon was changed from one codon that codes for an amino acid to one of the other codons that also codes for that same amino acid (i.e., degeneracy/redundancy of the code). Mutations in an intron would also be considered silent mutations. A frameshift mutation is any mutation that changes the reading frame. This would be any insertion or deletion that does not occur in multiples of three. A nonsense mutation is a mutation that changes a normal codon into a premature stop codon. A neutral mutation is any mutation that does not negatively impact the fitness of the individual. Theoretically, any of the above types of mutations could be silent, although it is reasonable to assume that most nonsense or frameshift mutations will cause too much alteration to the protein for it to remain functional.

42. The MCAT loves this concept, but fortunately it’s pretty straightforward. Germ cells are the only

cells passed on to offspring (only one of the gametes formed from a germ cell, to be precise). Therefore, ONLY those mutations that occur in germ cells are heritable. Mutations in somatic cells may harm that particular cell during its lifetime, and daughter cells derived from that cell via mitosis, but the next generation will ONLY receive the genetic information found in the sperm or egg cell they receive from each respective parent. Mutations to any or all somatic cells will not be incorporated into the offspring.

43. Malignant refers to tumors that are cancerous—meaning they are currently exhibiting uncontrolled growth and are likely to metastasize, etc. Benign refers to tumors that are still slowly growing, have not invaded other tissues, but could become cancerous later on. Metastasis is the spreading of a cancer from one tissue or organ to another. Proto-oncogenes are “good” or “normal” genes that can become oncogenes (i.e., cancer-causing genes) if mutated; proto-oncogenes usually regulate cell division, cell cycle, growth, apoptosis, etc. as their normal function. It is therefore logical to see how they could cause cancer when mutated. Tumor suppressor genes help protect the cell form uncontrolled growth. When function of such a gene is lost the cell is more easily able to become cancerous. Tumor suppressor genes require two recessive alleles to lose function. Oncogenes, however, are generally gain-of-function alleles and therefore having only one bad copy can result in the undesired cancer-promoting protein. Most cancers follow the “two-hit” or “multiple hit” hypothesis. In other words, multiple mutations must accumulate before the cell becomes cancerous. For example, a proto-oncogene could be mutated, but the cell might not become cancerous because of the action of a tumor suppressor gene. If the tumor suppressor gene lost function (the “second hit”) then the cell would become cancerous. Carcinogens are mutagenic chemicals that cause or promote cancer.

44. The P1 Generation is the first parental generation in Mendel’s experiments. Both parents in this generation were pure-breeding (i.e., homozygous) for their trait. This would tell us that one was homozygous dominant (TT) and the other homozygous recessive (tt). The F1 Generation was the offspring from the P1 Generation, which Mendel crossed with each other. Both parents in the F1 generation had to be heterozygotes (Tt). The F2 Generation was the offspring of the F1 generation. The F2 generation showed the characteristic 3:1 phenotypic ratio and 1:2:1 genotypic ratio. The former is often referred to as the Mendelian ratio. A test cross is a cross between a homozygous recessive individual and an individual with a dominant phenotype for whom the genotype is uncertain (could be TT or Tt). If the dominant individual was TT then all offspring of the test cross will have the dominant phenotype (all will be Tt). However, if the dominant individual was a heterozygote then half would have the dominant phenotype (genotype Tt) and half would have the recessive phenotype (genotype tt). Phenotype refers to the expression of the gene in terms of its visible or observable characteristics. The genotype refers to the specific alleles held by that individual. Note that individuals with different genotypes (TT and Tt) can exhibit the same phenotype (tall and tall). A gene is a segment of DNA that codes for a protein. An allele is one of various alternative forms of the same gene. For example, if hair color is determined by a single gene at a single locus, that segment of DNA would be the “hair color gene.” One version of that gene (i.e., one allele) might produce blonde hair, while another variation in the sequence at that segment (i.e., a second allele) might produce brown hair, and so forth. A locus is the specified physical location of a gene on a chromosome.

45. Hemophilia is more common in males because all X-linked recessive genetic disorders are easier for males to contract. This is seen rather simply by considering that males only need to receive a single “bad X” chromosome to be affected. This is because all males, by definition, will have a Y chromosome rather than a second X chromosome. A Y chromosome does not mask a recessive allele as would another wild-type X. In females, however, two “bad X” chromosomes are required for the female to be affected. As a result, there is no such thing as a male carrier for an X-linked condition. If a male has one copy, he IS affected, and it is impossible for any male to have two copies of an X-linked gene because, by definition, HE only has one X chromosome.

46. When we are not told about the other mate, we always assume that they are NOT a carrier and are NOT affected. If they were, the MCAT would always give this information. This means that the mother in this case must be unaffected, with two normal X chromosomes. Because male children must get the bad X chromosome from their mother (because dad had to give them a Y in order for them to be a male in the first place) NONE of the male offspring will have hemophilia. By contrast, ALL of his daughters must be carriers because the defective X chromosome is the only one he can give to daughters. Note, however, that the daughters will be carriers, but NONE of them will be affected. For a female to be affected with an X-linked recessive condition she must have had an affected father AND a carrier or affected mother.

47. Incomplete Dominance is an expression pattern in which the phenotypes of the dominant and recessive alleles appear to be mixed or blended in the phenotype of a heterozygote. For example, RR may give red flowers, rr white flowers, but Rr gives pink flowers (rather than the normal dominant-recessive pattern wherein Rr would still produce red flowers). Co-Dominance is the case in which both phenotypes are fully-expressed at the same time in a heterozygote. In the flower example this could mean that RR gives red flowers, rr gives white flowers, and Rr gives red-and-white striped flowers. Antigens on human red blood cells are another example. A person with the genotype AB does not have a blend of the A and B antigens, they have BOTH A and B antigens. Incomplete Penetrance occurs when various individuals all have identical genotypes and yet some have the disease phenotype and others do not. Limited Expressivity is the case in which various individuals all have the same genotype AND all of them have the disease phenotype (i.e., 100% penetrance), but individuals are impacted in varying degrees. The term polygenic is used when many genes contribute to one phenotypic trait. Pleiotropy describes the situation in which one single gene contributes to multiple phenotypic traits. Mosaicism is the case in which different cells within the same individual contain non-identical genotypes (NOT different alleles for the same gene, but different genotypes. Normally, all cells have the same genotype: Tt, Rr, etc. In this case one cell line may be TT and the other Tt). Genetic Imprinting (a.k.a. Genomic Imprinting) results when one specific gene is expressed differently depending on which parent it originated from. Epigenetic refers to any heritable phenotype resulting from any process other than a change in the DNA sequence itself. You could think of this as any genetic influence that is “outside” of the DNA sequence itself just as Epi-dermis is on the “outside” of the body (The prefix epi- translates in Greek to mean above, beyond, outside, or near).

48. When we say that two genes are linked we mean that they do not assort independently. In other words, inheriting one gene changes the probability of inheriting the other. When you look at chromosomes and consider that they contain many, many genes, and yet are inherited as a single, whole chromosome, we would expect that all of the genes on a chromosome would be linked. This is not the case due to crossing over. Crossing over between chromosomes during

Prophase I of Meiosis happens so often that it is as if all of the genes were not riding together on chromosomes, but were individual little segments assorted independently each with an equal and independent probability of landing in one cell or the other. Linkage does occur, however, when two genes are very, very close to each other on the same chromosome because at certain proximity it becomes unlikely that a crossing over event will occur exactly between them.

49. The gene pool is the complete set of genes and alleles in a population. Evolution is defined as any change in the allelic frequency within a given gene pool across generations. Polymorphisms are random variations in genetic sequence among individuals. Polymorphisms are random, usually due to mutation, and may or may not be increasingly represented in future generations depending on whether or not that particular genetic variation provides an evolutionary fitness advantage. A niche is the very specific status or role an organism plays in its ecosystem. It can also refer to a specific habitat occupied by one organism within its ecological community. Survival of the fittest is a term meaning that the individual best suited to its environment will be most likely to survive and pass on its genetic information to future generations. Natural selection is the more precise term for the concept described by “Survival of the fittest.” For the MCAT you could consider them to be synonyms. A careful definition of natural selection would be something like: the process by which individuals with genetic traits that provide them with a fitness advantage produce more offspring, and therefore those advantageous traits become more prevalent in subsequent generations. Speciation simply means the formation of new species from existing ones. Adaptive radiation is the rapid formation of a variety of species from one ancestral species—usually characterized by a strong environment-species connection. An example would be: if one species of turtle immigrated to five different environments and rapidly formed five different species based on natural selection driven by the unique characteristics of each environment. An evolutionary bottleneck is a sudden decrease in the number of individuals in a population. Genetic drift is a change in the allele frequency within a population due to random, non-genetic, non-selective factors. A bottleneck would be an example of genetic drift because there is no “fitness advantage” or other factor responsible for the change in allele frequency. For example, if a meteorite struck the earth the question of who survived and who did not would not be a question of fitness, it would be a random result of who happened to be in the meteor’s path. Carrying capacity is the maximum number of individuals an ecosystem or environment can sustain.

50. Convergent evolution results when two species arrive at a point where they have similar functional forms, but they have developed those similar forms via different evolutionary pathways. For example, the last common ancestor between bats and birds did not have wings, so wings are not part of their shared evolutionary connection. Therefore, it must be convergent evolution. Divergent evolution is the process by which species develop different forms AND thereby form new species, all radiating from that common ancestor. Adaptive radiation is an example of rapid divergent evolution.

51. The most important thing for students to understand with regard to Hardy-Weinberg Equilibrium (H-W) problems is the correct definition of each term. The terms p and q NEVER refer to a number or fraction of individuals—they do NOT refer to genotypes. Rather, p and q refer to the percentage of each allele present as a fraction of all of the alleles in the population. The term p2 represents the fraction of individuals who have the homozygous dominant genotype (TT). The term q2 represents the fraction of individuals with the homozygous recessive genotype (tt). The term 2pq represents the fraction of individuals with the heterozygous

genotype (Tt). In other words, p and q represent the fractions of p and q alleles in the population. The terms q2, 2pq, and q2 all represent fractions of individuals with each possible genotype. All of the variables can be calculated simply by knowing that 90/1,000 individuals have a recessive phenotype. The fraction 90/1,000—by definition—is the term q2. Simplifying 90/1,000 we get 0.09. The square root of this is 0.3 and therefore q = 0.3. Because p + q = 1, p must equal 0.7. We can then calculate 2pg as: (2)(0.7)(0.3) = 0.42. To find p2 we simply square p: (.7)2 = 0.49. Therefore, 49% of the population have the genotype TT, 42% are Tt, and 9% are tt. From p and q we now that 70% of all alleles are p and 30% of all alleles are q.

52. Humans belong to the following taxa: Kingdom: Animalia; Phylum: Chordata; Class: Mammalia; Order: Primates; Family: Hominidae; Genus: Homo; Species: Homo sapiens. Animals are multicellular, motile, heterotrophic eukaryotes. They are distinguished from plants, algae, and fungi by not having cell walls. The chordates are deuterostomes, have a notochord, dorsal hollow nerve cord, pharyngeal gill slits, and a post-anal tail at some point during development. Mammals are warm-blooded vertebrates that usually give live-birth to their young, have hair or fur, and mammary glands. Primates are essentially all of the apes, gorillas, monkeys, and humans. Common distinguishing characteristics include opposable thumbs, fingernails, and an enlarged cerebral cortex. The rest of the taxa for humans, Homonidae, Homo, and Homo sapiens are just increasingly specific classifications for human or very “human-like” creatures—such as Neanderthals, Homo erectus, etc. Distinguishing between them is a difficult exercise in minutia and therefore would never be tested on the MCAT.

53. Chemotrophs oxidize organic or inorganic compounds to harvest energy. Phototrophs can capture their own energy directly from the sun via photosynthesis. Autotrophs are capable of fixing CO2 and can therefore use CO2 as their carbon source for synthesizing organic molecules. Heterotrophs, by contrast, cannot fix CO2 and therefore must ingest organic molecules such as carbohydrates as their carbon source.

54. walls; chitin

55. Sexual reproduction is costly in terms of energy, but increases genetic diversity. Asexual reproduction is less expensive than sexual reproduction in terms of energy, but provides no genetic diversity. When fungi experience difficult survival conditions they can employ sexual reproduction so that future generations have an opportunity to adapt/evolve. When survival is easy and resources are plentiful, the fungi can simply save the energy and employ asexual reproduction because adaptation is not necessary.

56. Mutualism is a form of symbiosis where both participants benefit equally. Commensalism is symbiosis in which one participant benefits and the other participant’s experience is neutral—neither beneficial nor harmful. Parasitism is a symbiosis wherein one participant benefits at the expense of the other (i.e., the other participant is harmed).

57. A virus is extremely difficult to define in terms of living vs. non-living, and therefore we can be fairly confident that the MCAT won’t test it in those specific terms. Focus students on the fact that viruses are acellular and cannot survive, grow, or reproduce on their own. They require a host to accomplish most if not all of the functions we normally associate with “living things.”

58. Viruses always contain some form of nucleic acid (DNA or RNA, but never both) plus proteins. Bacteriophages, the viruses that infect bacteria, have very specific components. Bacteriophages always include a capsid head, a tail, and tail fibers, as shown below. Enveloped viruses, such as the cold virus and HIV, are small spherical membranes surrounding a protein capsid and the nucleic acid (as shown below). Retroviruses always contain RNA, and therefore must also contain a specific enzyme called reverse transcriptase capable of translating this RNA nucleotide sequence into DNA (because RNA could not be incorporated into the host’s genome).

FIGURE 9

59. The lytic cycle of a virus is the period during which viral genes are actively transcribed and new viruses are assembled. During this phase, infected cells eventually burst to release large numbers of new viruses. Examples would be an active cold sore (herpes virus) or AIDS. The lysogenic cycle is the dormant cycle of the virus during which time viral DNA is incorporated into the host’s genome but new viruses are not being assembled. This would be equivalent to HIV infection without AIDS symptoms, or to the presence of the herpes virus in the DNA of the host without any current cold sores or other symptoms.

60. A vaccine is an inactive virus, or portion of a virus, delivered to a person so that their immune system can develop antibodies against the virus without the host experiencing an actual viral infection. Upon exposure to the viral proteins, the immune system will create memory B-cells with antibodies that match the viral proteins. If this host is later infected with that same virus, these B-cells will differentiate into plasma cells that rapidly produce and release antibodies for the virus. Vaccines tend to lose effectiveness over time because viruses mutate at a rate that is faster than any known living thing.

61. Bacilli are rod-shaped bacteria; cocci are spherical bacteria; spirilla are spiral-shaped bacteria.

62. Mitosis is a complex process coordinated and heavily regulated by a large number of genes and involving intricate interactions between centrioles, spindle fibers (microtubules), centromeres, chromosomes, and many other cellular components. Absent any errors, mitosis delivers an exact and equal amount of DNA to each new daughter cell. Binary fission is the method employed by prokaryotes and involves none of the items listed above, except for DNA. In binary fission, the circular DNA is copied and attached to the membrane. The cell splits, pulling the two copies apart, and each daughter cell gets one copy of the chromosome. An important caveat, however, is that prokaryotes contain extrachromosomal DNA (usually circular plasmids). There is no system for segregating this DNA, so each daughter cell may or may not get certain plasmids based solely on random chance.

63. Prokaryotes have no nuclei, no membrane-bound organelles, no histones, and no chromosome structure; they do have circular DNA and 70S (30S and 50S) ribosomes. Eukaryotes have a true nucleus, complex, membrane-bound organelles, linear DNA with histones, chromosome structure, and 80S (60S & 40S) ribosomes. Explain to students that the ribosome measures do

not add up (i.e., 50S + 30S ≠ 70S) because they are not directly related to mass or volume, but are sedimentation coefficients derived from the result of centrifuging the ribosomes.

FIGURE CREDITS

1. Altius image, adapted from Wikipedia commons.

2. http://en.wikipedia.org/wiki/File:Animal_mitochondrion_diagram_en_(edit).svg

3. http://en.wikipedia.org/wiki/File:Eukaryotic_flagellum.svg

4. http://upload.wikimedia.org/wikipedia/commons/thumb/e/e0/Cell_Cycle_2-2.svg/2000px-Cell_Cycle_2-

2.svg.png

5. Altius image adapted from www.slideshare.net

6. http://www.tutorvista.com/content/biology/biology-iii/cell-reproduction/mitosis-meiosis-differences.php

7. http://cyberbridge.mcb.harvard.edu/dna_1.html

8. http://www.slvhealth.org/programs/stdHivClinic/stdHIVProgram/hivFacts.htmlHello;

9. http://wharton.nj.k12us.com/kallen/2576?rc&q=12234