MCAT Organic Chemistry

The Robinson annulation reaction is a widely used, multistep process for generating cyclic a, B-unsaturated ketones. The first step (known as a Michael reaction) involves conjugate addition of an enol or enolate to an o. B-unsaturated carbonyl (Molecule1). The reaction then proceeds with ring closure and loss of water (cyclodehydration) to give a cyclic a,B-unsaturated ketone (Molecule 8).
Scientists have found a way to catalyze the Robinson annulation by using artificial enzymes made from antibodies (Zhong, et. al, (Am. Chem. Soc. 1997, 119, 8131). As shown in Figure 1, these catalytic antibodies speed up the reaction by using a lysine side chain to form an imine with Molecule 3. The imine more readily undergoes tautomerization and cyclodehydration to give Molecule 7, which is easily hydrolyzed to Molecule 8.
An important result is that Molecule 8 is produced as a single

enantiomer.

MCAT General Chemistry

The extent to which a salt dissolves in water can be quantified by its solubility product constant, (K_sp) which is defined, for a hypothetical salt X_a Y_b as shown in Equation 2. The greater the value of K_sp. the more soluble the compound. The K_sp of a salt is related to the free energy of dissolution by the equationΔG^°_diss = – RT In(K_sp). Table 1 lists the K_sp values for some insoluble salts.

When a solid completely dissolves, solute particles are separated and encapsulated by solvent molecules. This process requires several steps:

1) breaking all solute-solute interactions,

2) disrupting some solvent-solvent interactions, and

3) forming new solute-solvent interactions.

The combination of these processes determines the overall enthalpy change for the dissolution, which can be either exothermic or endothermic regardless of the solubility of the salt. Table 2 shows the enthalpies of dissolution for several soluble salts.

MCAT Biochemistry

The complexity of hemoglobin’s function is exemplified by its chemical structure. Multiple factors are believed to affect the kinetics of oxygen binding to the molecule’s active sites.

It has been proposed that the binding of oxygen (Figure 1) reduces strain on the heme protein superstructure by counterbalancing the pull of the proximal imidazole. Similarly, increasing basicity of the proximal imidazole (e.g., through loss of a hydrogen atom) is believed to exert additional strain on the heme protein in the deoxygenated state by inducing a dome-shaped molecular structure. Because the binding of oxygen relieves this strain, increasing basicity of the proximal imidazole increases the affinity of the heme for oxygen. The hydrophobic pocket created by hydrocarbon-like residues from adjacent heme proteins are also believed to facilitate oxygenation, though it has been proposed steric hindrance may provide an antagonistic effect. The distal imidazole shown below may inhibit dissociation by stabilizing the oxygen molecule in place.

The net effect of these and other factors affecting oxygen dissociation from hemoglobin can be expressed kinetically:

Equation 1

A single heme molecule will associate with O₂ to form a heme-O₂ complex with rate constant 𝑘’ in a reverse reaction, oxygen will dissociate from the heme-O₂ complex with rate constant k. One/study examined the kinetics of association of oxygen at different oxygen-bound states as well as the
implied equilibrium constants (K₀₂) for each stage of oxygen association (Table 1).

Another study examined the thermodynamics of the association of hemoglobin dimers (𝛼𝛽) to form the tetrameric hemoglobin protein.

Figure 2 Free energy coupling for dimer-tetramer association in deoxygenated and oxygenated hemoglobin
Extrapolating from the respective linear models depieted in Figure 2, specific data for free energy as well as enthalpy and entropy at body temperature (310 K) are shown in Table 2.

Adapted from Chang, C. K., and Traylor, I. G. Kinetics of oxygen and carbon monoxide binding to synthetic analogs of the myoglobin and hemoglobin active sies: Sp. S. H. C. and Ackers, G. K. Thermodynamic studies on subunit assembly in human hemoglobin.

MCAT Biology

Protein synthesis involves a number of complex steps, from transcription of the gene through to translation and post-translational modification. After mRNA is transcribed in eukaryotes, it must be processed (capped, poly-A tailed, and spliced) before it can be translated. Prokaryotes do not need to process their mRNA.

Due to the exonuclease activity of DNA polymerase, DNA replication is generally a high-fidelity process. Random errors occasionally occur and these mutations are classified as frameshift mutations (insertions or deletions in the base sequence) or point mutations (a single base pair change). Any mutation is subject to natural selection, with advantageous mutations preserved and the most deleterious mutations eliminated quickly. Thus, areas of the genome that appear to evolve very slowly (i.e., have a slower rate of mutation than other areas) do not actually have a slower rate; rather, that area is highly critical to normal functioning of the organism involved.

Point mutations can be further classified by their final effect on the mature protein. Because of the redundancy of the genetic code, some mutations do not alter the final amino acid sequence of the protein and are referred to as silent mutations. However, it was discovered that all redundant codons are not equal; some are used preferentially to enhance the speed or accuracy of protein translation. tRNAs corresponding to redundant codons are not found equally in the cell, some tRNAs are more common than others. Silent mutations can cause phenotypic changes by altering mRNA stem-and-loop folding, half-life, and splicing sites. Thus, mutations formerly considered “silent” have now been implicated in a number of different disorders, such as Marfan syndrome, phenylketonuria, Seckel syndrome, and increased pain sensitivity.

Figure 1 The Genetic Code

MCAT Physic & Math

Figure 1 shows a thin-walled, cylindrical metal container fitted with a tight-fitting but freely movable lightweight plastic piston and containing 0.25 mol of helium at 0°C and a pressure of
1 atm.

The volume, pressure, and temperature of the gas can be changed by various processes, such as by adding weights to the top of the piston or by heating the cylinder with a flame.
The heat exchanged between the confined helium gas and the surroundings will be denoted by Q, where a positive value of 𝒬 indicates that the heat has been transferred into the gas; if O is negative, heat has been transferred out of the gas. The work done on the gas will be denoted by W, where a positive value of W indicates that the gas does work on its surroundings; if W is negative, this means that the surroundings do work on the gas. The change in the internal energy of the gas is given by the equation.

𝚫E = 𝒬- W
Equation 1

A student conducts the following series of experiments in a chemistry lab.

Experiment 1
The student measures the volume of the gas in the cylinder, places a known mass m on top of the piston, and then increases the temperature of the gas at constant pressure to 273°C.

Experiment 2
After the gas is allowed to cool back to 0°C at 1 atm pressure the student locks the piston in place, and then increases the temperature of the gas to 273°C.

Experiment 3
After Experiment 2 is completed, the student unlocks the piston and a computer-controlled heat source maintains the temperature at a constant 273°

Experiment 4
After Experiment 2 is completed, the cylinder is completely wrapped in insulation before the piston is unlocked.

MCAT Psychology & Sociology

Recent research has explored the neurophysiological correlates of various therapies to assess their efficacy. Reduced cortical mass in areas associated with negative emotions are interpreted as indications of effective therapeutic intervention. Also, researchers looked at the mass of various regions associated with emotional regulation, such that increased mass in these regions also suggested that the therapies had helped patients improve their ability to modulate emotional experience.

Study 1: Cognitive Behavioral Therapy
A team of researchers conducted an fMRI study that looked at activation levels in a cohort of 20 patients who were given a
10-week treatment protocol, meeting with a psychologist for 45 minutes in each session. During sessions, participants explored maladaptive thought patterns and created a plan for more effective coping mechanisms that was encouraged by positive secondary reinforcement by the therapist at the next session.
To track thoughts while subjects were alone during the week, participants were told to keep a journal. Pretest and posttest measures of cortical activity were measured and compared.

Study 2: Psychoanalytic Psychotherapy
An increase in cortical mass in areas associated with self-awareness and the top-down regulation of emotion was measured through the use of positron emission tomography (PET). At the end of the 3-month program, researchers saw changes in the mass of regions of the prefrontal cortex, amygdala, and hippocampal projections to the sensory cortices. Researchers conducted the study on 10 male and female participants who had grown up in single-parent homes, based on the premise that the absence of a parent made them good candidates for psychoanalytic therapy. Researchers hypothesized that awareness and analysis of repressed thoughts, and not emotional regulation, would mediate the effectiveness of therapy and improve clinical outcomes.

Study 3: Behavioral Therapy
A reinforcement schedule was paired with aversion therapy, which was used to rewire the reward circuit in individuals with various types of addiction. 18 male and female undergraduate students who had been diagnosed with alcohol and drug addiction were given treatment. The treatment involved exposure to alcohol or the drug and nasal inhalation of an aversive agent meant to induce mild nausea. Application of the aversive treatment was potentially dangerous, so it was done in a supervised clinical environment twice a week according to a schedule. Researchers also checked in once a week at random times to see if patients had successfully avoided drug or alcohol use and gave points that could be used towards various prizes if they had. Afterward, dopaminergic circuits and the density of regions associated with impulse control were assessed.

MCAT Critical Analysis & Reasoning Skills
Passage 2

It is not easy to define Benjamin Franklin’s religious and moral beliefs; yet it is important to do so, because they are representative of a large body of men of his time, whose worldly success certainly derived from their beliefs. D. H. Lawrence, who was angered by all success, treats Franklin as a hypocrite who found the rules which lead to success and turned them into a religion. This analysis is certainly false, but even if it were true, it would not take us far enough. For it would not tell us what made Franklin respected by men as different as his American friends, his English enemies, and his French admirers. There was something in Franklin’s beliefs which had a symbolic quality for them all.

The charge that Franklin was a hypocrite can be presented simply. He advocated many virtues at a time when he undoubtedly lapsed into some vices. He began his marriage in 1730 by bringing an illegitimate son into the house. Indeed, he may never have been very vigorous in resisting the temptations of the flesh. These lapses from the conventions of family life would not have outraged D. H. Lawrence if they had not been coupled with a certain priggishness in many of the household maxims which Franklin popularized.

In 1732, Franklin began publishing Poor Richard’s Almanac, which was by far the most successful work that he wrote, and in some ways the most influential. Like other almanacs, this is stuffed with those plums of wisdom which most people like to taste and few to digest-_”hunger never saw bad bread,” and “well done is better than well said.” It is these crystallized plums, so eminently homely and homemade, which have made Franklin’s beliefs seem commonplace. But this criticism confuses the manner in which Franklin expressed himself and expressed himself at all times with the content of his thought. Franklin had a special gift for putting a thought into a simple and earthy sentence. This is a gift of expression: a rare gift, but Franklin had it to perfection.

The gift has a drawback, however. In this form, Franklin’s isolated thoughts do indeed wear a simple and sometimes a commonplace air. But it is a crude error to suppose therefore that the totality of Franklin’s thoughts, the system into which the isolated thoughts lock and combine, is commonplace.
In this respect, the simplicity of Franklin’s sentences is as deceptive as the simplicity of Bertrand Russell’s, and the outlook which they make up all together is equally complex.

The informality with which Franklin wrote and spoke is, however, just to his thought in one respect: he was opposed to formality and rigidity of belief. It is not merely that he did not care for the fine points of dogma; he thought it wrong in principle to wish to formulate religion in fine points. He did not acknowledge any sectarian monopoly of truth. For example, when, at the age of 83, he stated his belief in God, he coupled it with another belief, “that the most acceptable service we render Him is doing good to His other children.”
At bottom, it is this tolerance in Franklin’s make-up which we must understand. He was tolerant of others because he recognized in them the same humanity that he knew in himself.

He never hid his motives from himself, but neither did he belittle the motives of others. We should recognize him as honest because he judges others exactly as he judges himself, with a realistic and generous sense of what can be expected of human beings. Sustained by humanity, he could gain the respect of those as religiously diverse as the anticlerical Tom Paine and the evangelist George Whitfield.

MCAT Critical Analysis & Reasoning Skills
Passage 1

Basketball, a game of constant movement and a thousand
actions, is a difficult game to remember; Leonard Koppett makes this and other excellent points in All About Basketball.

Football is a series of set plays, as clear in our minds as moves in chess; and the high drama of a baseball game is often distilled in a single pitch, catch, throw, or hit. We remember baseball and football actions as though the players were etched upon our minds like figures on a distant green. In basketball, by contrast, we remember movement, style, flair, but only occasionally a single play. Perhaps we recall the seventh game of the Lakers-Knicks playoff on May 8, 1970, after the Lakers had pounded the Knicks in the sixth game. Willis Reed was injured and out, it seemed, for the season; and we may remember Reed walking stiffly to the floor for that final game just minutes before warm-ups were concluded; remember the sustained ovation; remember his stilt jumps as he put the hirst two shots of the game through and then had to leave the game in pain; remember that the Knicks, lifted high by his courage, went on to win game seven, bringing to New York basketball a new perspective. But it is hardly ever, even here, an individual plus one remembers. A basketball game plays past like a river,like a song In basketball as in no other sport, Koppett also notes, the referee is part of the drama. Decisions of the scorer and the timer are critical and affect the outcomes of countless games every year.

But the referee is an agent, an actor; he affects the changing tissue of the drama every instant. He cannot call every infraction, but he must control the game. He needs to gain the players’ and the crowds’ attention, respect, and emotional cohesion. Thus, referees like Pat Kennedy, Sid Borgia, and Mendy Rudolph in the NBA became better known than many of the players. Each blew the whistle in a range of different tones and styles; each had a repertoire of operatic gestures; each had an energy and physical exuberance that added to the total drama. All won respect for coolness under withering emotion.
Basketball players are visible in every action, Koppett notes, and easily singled out by the spectators as football players are not. They handle the ball scores of times and are physically involved in every moment of offense and defense, as baseball players are not. They are subject to many more flukes than baseball or football players, for they pass and run at high speed constantly, forcing dozens of errors, breaks, and opportunities. “Don’t shoot!” the coach screams in despair, his voice trailing off to “Nice shot” as he sits down.

Teams move in patterns, in rhythms, at high velocity; one must watch the game abstractly, not focusing on any single individual alone, but upon, as it were, the blurred and intricate designs woven by the paths through which all five together
cast a spell upon an opposition. The eye watches five men at once, delighting in their unity, groaning at their lapses of concentration. Yet basketball moves so rapidly and so depends on the versatility of each individual in escaping from the defense intended to contain him that the game cannot be choreographed in advance. Twelve men are constantly in movement (counting two referees), the rebounds of the ball are unpredictable, the occasions for passing or dribbling or shooting must be decided instantaneously; basketball players must be improvisers. They have a score, a melody; each team has its own appropriate tempo, a style of game best suited to its talents; but within and around that general score, each individual is free to elaborate as the spirit moves him.
Basketball is jazz: improvisatory, free, individualistic, corporate, sweaty, fast, exulting, screeching, torrid, explosive, exquisitely designed for letting first the trumpet, then the sax, then the drummer, then the trombonist soar away in virtuosic excellence.

The point to stress is the mythic line of basketball: a game of fake and feint and false intention; a game of run, run, run; a game of feet, of swift decision, instantaneous reversal, catlike “moves”, cool accuracy, spring and jump. The pace is hot. The rhythm of the game beats with the seconds: a three-second rule, a ten-second rule, a rule to shoot in twenty-four seconds. Only when the ball goes out of bounds, or a point is scored, or a foul is called does the clock stop; the play flows on. Teams do not move by timeless innings as in baseball, nor by set, formal, single plays as in football. Even when a play is called or a pattern is established, the game flows on until a whistle blows, moving relentlessly as lungs heavy and legs weary. It is like jazz.