MCAT Biology : Organic Chemistry, Biochemistry, and Metabolism

Study concepts, example questions & explanations for MCAT Biology

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Example Questions

Example Question #2 : Other Reactions

Carbonic anhydrase is a very important enzyme that is utilized by the body. The enzyme catalyzes the following reaction:

A class of drugs that inhibits this enzyme is carbonic anhydrase inhibitors (eg. acetazolamide, brinzolamide, dorzolamide). These drugs are commonly prescribed in patients with glaucoma, hypertension, heart failure, high altitude sickness and for the treatment of basic drugs overdose.   

In patients with hypertension, carbonic anhydrase inhibitors will prevent the reabsorption of sodium chloride  in the proximal tubule of the kidney. When sodium is reabsorbed back into the blood, the molecule creates an electrical force. This electrical force then pulls water along with it into the blood. As more water enters the blood, the blood volume increase. By preventing the reabsorption of sodium, water reabsorption is reduced and the blood pressure decreases. 

When mountain climbing, the atmospheric pressure is lowered as the altitude increases. As a result of less oxygen into the lungs, ventilation increases. From the equation above, hyperventilation will result in more  being expired. Based on Le Chatelier’s principle, the reaction will shift to the left. Since there is more bicarbonate than protons in the body, the blood will become more basic (respiratory alkalosis). To prevent such life threatening result, one would take a carbonic anhydrase inhibitor to prevent the reaction from shifting to the left.  

Carbonic anhydrase inhibitors are useful in patients with a drug overdose that is acidic. The lumen of the collecting tubule is nonpolar. Due to the lumen's characteristic, molecules that are also nonpolar and uncharged are able to cross the membrane and re-enter the circulatory system. Since carbonic anhydrase inhibitors alkalize the urine, acidic molecules stay in a charged state.

When a patient is not ventilating efficiently, the kidneys try to compensate by producing more bicarbonate to buffer the decreasing pH of the blood due to the buildup of . Which of the following will increase the amount of  in the blood?

I. Increase  level in the blood

II. Increase  level in the blood

III. Increase metabolism 

Possible Answers:

III only

I and III

II only

I only

I, II, and III

Correct answer:

I and III

Explanation:

To answer this question, we must understand Le Chatelier’s principle. The reaction favorites the product when there is more of the reactants. The opposite is also true in that when there is a buildup of the products, the reaction will reverse and favorite the reactants. Increasing the metabolism will produce more , which will shift the equation to the right.  

Example Question #51 : Organic Chemistry, Biochemistry, And Metabolism

Carbonic anhydrase is a very important enzyme that is utilized by the body. The enzyme catalyzes the following reaction:

A class of drugs that inhibits this enzyme is carbonic anhydrase inhibitors (eg. acetazolamide, brinzolamide, dorzolamide). These drugs are commonly prescribed in patients with glaucoma, hypertension, heart failure, high altitude sickness and for the treatment of basic drugs overdose.   

In patients with hypertension, carbonic anhydrase inhibitors will prevent the reabsorption of sodium chloride  in the proximal tubule of the kidney. When sodium is reabsorbed back into the blood, the molecule creates an electrical force. This electrical force then pulls water along with it into the blood. As more water enters the blood, the blood volume increase. By preventing the reabsorption of sodium, water reabsorption is reduced and the blood pressure decreases. 

When mountain climbing, the atmospheric pressure is lowered as the altitude increases. As a result of less oxygen into the lungs, ventilation increases. From the equation above, hyperventilation will result in more  being expired. Based on Le Chatelier’s principle, the reaction will shift to the left. Since there is more bicarbonate than protons in the body, the blood will become more basic (respiratory alkalosis). To prevent such life threatening result, one would take a carbonic anhydrase inhibitor to prevent the reaction from shifting to the left.  

Carbonic anhydrase inhibitors are useful in patients with a drug overdose that is acidic. The lumen of the collecting tubule is nonpolar. Due to the lumen's characteristic, molecules that are also nonpolar and uncharged are able to cross the membrane and re-enter the circulatory system. Since carbonic anhydrase inhibitors alkalize the urine, acidic molecules stay in a charged state.

Based on the passage, which of the following statements, if true, will contradict the effectiveness of carbonic anhydrase inhibitors as a treatment? 

Possible Answers:

Basic molecules will release its proton in the basic environment of the lumen of the collecting tubule

Acidic molecules have a better ability to cross the membrane than basic molecules 

Acidic molecules will not release its proton in the basic environment of the lumen of the collecting tubule

Basic Molecules will not release its proton in the basic environment of the lumen of the collecting tubule.  

Acidic molecules will release its proton in the basic environment of the lumen of the collecting tubule

Correct answer:

Acidic molecules will not release its proton in the basic environment of the lumen of the collecting tubule

Explanation:

Carbonic anhydrase inhibitors are used to alkalinize the urine. When the urine is alkalinized, acidic molecules will lose its proton and go into a charged state. Charged molecules are unable to cross the membrane of the lumen of the collecting tubule. Without the ability to cross the membrane, the molecule is therefore unable to be reabsorbed. Therefore, if the statement "Acidic molecules will not release its proton in the basic environment of the lumen of the collecting tubule" was true, then alkalinizing the urine will have no effect.  

Example Question #1 : Substitution And Elimination Mechanisms

Which of the following reactions is the nucleophile potassium tert-butoxide often used for?

Possible Answers:

E2

SN1           

SN2

E1

Correct answer:

E2

Explanation:

Tert-butoxide is a large, sterically hindered, strong nucleophile that is often used in E2 reactions. Strong nucleophiles usually undergo the SN2 or E2 pathway, but tert-butoxide is much too large to undergo a substitution reaction.

Example Question #1 : Substitution And Elimination Mechanisms

Which of the following factors do NOT favor an SN2 reaction of an alkyl halide?

Possible Answers:

A good nucleophile 

A polar aprotic solvent

A tertiary carbocation

A primary halide

Correct answer:

A tertiary carbocation

Explanation:

The way the question is phrased, three answer choices must favor an SN2 reaction, while the "correct" answer is a factor that does not favor, or disfavors an SN2 reaction.

SN2 reactions are bimolecular, and thus their rate of reaction depends on both the substrate and the nucleophile, forming a high energy transition state in which the nucleophile will displace the substate's leaving group at an angle of 180o. The more sterically hindered the compound is, the higher in energy the transition state will be, and the slower the rate of reaction will be. Consequently, SN2 reactions are favored when the leaving group (a halogen in this case) is on a primary carbon center. Additionally, because the reaction is bimolecular, step two of the reaction will NOT occur without a good nucleophile to displace the leaving group. Finally, all SN2 reactions are favored by polar aprotic solvents.  

Because SN2 reactions proceed via a transition state, no carbocation intermediate is formed (that happens in SN1 reactions) and therefore the formation of any carbocation favors an SN1 reaction, not an SN2 reaction.

Example Question #1 : Reaction Mechanisms

Organic reactions can often be classified into two broad categories: substitution and elimination. Substitution reactions substitute one substituent for another. Elimination reactions typically form after the wholesale removal of a substituent, with no replacement. Below are examples of two types of reactions.

Reaction 1:

1

Reaction 2:

2

The reaction depicted in reaction 1 takes place in solution with a solvent. What type of solvent is most likely to be preferred for the reaction to occur as written?

Possible Answers:

This reaction requires water as a solvent

Polar, aprotic solvent

Nonpolar, aprotic solvent

Polar, protic solvent

Nonpolar, protic solvent

Correct answer:

Polar, aprotic solvent

Explanation:

Reaction 1 is an SN2 reaction. This type of substitution reaction prefers a polar, aprotic solvent. The polarity helps to solvate the nucleophile. Aprotic solvents help mediate the transition state and increase reaction rate.

Example Question #1 : Reaction Mechanisms

Organic reactions can often be classified into two broad categories: substitution and elimination. Substitution reactions substitute one substituent for another. Elimination reactions typically form after the wholesale removal of a substituent, with no replacement. Below are examples of two types of reactions.

Reaction 1:

1

Reaction 2:

2

In reaction 1, a scientist is trying to modify the reaction by using a weaker nucleophile. Which of the following is a weaker nucleophile than what is used above (hydroxide ions)?

Possible Answers:

Correct answer:

Explanation:

Nucleophilicity increases to the left on the periodic table.  Nucleophilicity will also generally increase with charge. The only equally charged ion in the answers that is present to the right of oxygen on the periodic table is the fluoride ion.

Example Question #51 : Organic Chemistry, Biochemistry, And Metabolism

Organic reactions can often be classified into two broad categories: substitution and elimination. Substitution reactions substitute one substituent for another. Elimination reactions typically form after the wholesale removal of a substituent, with no replacement. Below are examples of two types of reactions.

Reaction 1:

1

Reaction 2:

2

Using the product of reaction 2, a scientist adds bromine gas to the reaction chamber. After the bromine and the alkene react, he finds that his product consists entirely of single bonds, with two bromine atoms on the carbon chain. What kind of reaction most likely took place?

Possible Answers:

Elimination reaction

Addition reaction

Halogenation reaction

Oxymercuration/demercuration reaction

Substitution reaction

Correct answer:

Addition reaction

Explanation:

The addition of bromine gas () to the reaction vessel would likely result in the addition of one half of the diatomic bromine to each carbon, eliminating the double bond and resulting in an alkyl halide chain.

Halogenation reactions refer to reactions between a halogen and an alkane, while addition reactions occur between a halogen and an alkene (such as the product in reaction 2).

Example Question #1 : Substitution And Elimination Mechanisms

Cyclohex

Students in an organic chemistry lab perform two E2 elimination reactions, using compounds 1 and 2. The students observe that while compound 2 undergoes elimination with reagent X (not shown), compound 1 is unreactive. What is the best explanation for this discrepancy?

Possible Answers:

Compound 1 has no hydrogen molecules anti-periplanar to the bromine leaving group

Reagent X is more selective for compound 2 than for compound 1

Compound 1 is too sterically hindered

Bromine is not a good enough leaving group

Correct answer:

Compound 1 has no hydrogen molecules anti-periplanar to the bromine leaving group

Explanation:

This question tests your understanding on E2 elimination reactions. Because E2 reactions have no carbocation intermediates, the reaction proceeds through a transition state. The bromine atom (Br) must be displaced by the bond between an adjacent carbon and hydrogen, and that hydrogen must be anti-periplanar to the bromine. Compound 2, unlike compound 1 has one hydrogen that is anti-periplanar to the bromine, and thus undergoes an E2 elimination.

If compound 2 reacts, it is unlikely the reason that compound 1 would not react is because of steric hindrance. Additionally, aside from stereochemistry, there is nothing different enough about the two compounds that would suggest any reagent would be more favorable for one over the other.

Example Question #1 : Reaction Mechanisms

Which of the following compounds could NEVER undergo an E2 reaction when treated with potassium tert-butoxide?

Possible Answers:

Bromoethane

3-methyl-3-iodopentane

Cyclopentylbromide

Cis-2-bromo-1-methylcyclohexane

Benzylbromide

Correct answer:

Benzylbromide

Explanation:

For an E2 reaction to occur, there must be a hydrogen on the carbon adjacent to the carbon with the leaving group. Benzyl bromide contains no hydrogens on the carbon next to the carbon with the bromide, and would therefore undergo only a substitution reaction.

Example Question #1 : Substitution And Elimination Mechanisms

Organic reactions can often be classified into two broad categories: substitution and elimination. Substitution reactions substitute one substituent for another. Elimination reactions typically form after the wholesale removal of a substituent, with no replacement. Below are examples of two types of reactions.

Reaction 1:

1

Reaction 2:

2

In reaction 2, which of the following describe the rate limiting step?

I. It involves the formation of carbocation

II. It is favored by the presence of substituents on the central carbon

III. It involves a transition state, but no intermediate

Possible Answers:

I and II

II and III

III, only

I, only

II, only

Correct answer:

I and II

Explanation:

Reaction 2 represents an E1 reaction. The rate limiting step of reaction 2 involves the formation of a carbocation, whose stability is favored by the presence of substituents on the carbon involved. Carbocations are considered intermediates due to their relative stability compared to transition states.

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