MCAT Biochemistry Flashcards
Why are triacylglycerols used in the human body for energy storage?
A) They are highly hydrated, and therefore can store lots of energy.
B) They always have short fatty acid chains, for easy access by metabolic enzymes.
C) The carbon atoms of the fatty acid chains are highly reduced, and therefore yield more energy upon oxidation.
D) Polysaccharides, which would actually be a better energy storage form, would dissolve in the body.
C
Triacylglycerols are highly hydrophobic and therefore not highly hydrated (which would add extra weight from the water of hydration, taking away from the energy density of these molecules). The fatty acid chains produce twice as much energy as polysaccharides during oxidation because they are highly reduced. The fatty acid chains vary in length and saturation.
After a brief period of intense exercise, the activity of muscle pyruvate dehydrogenase is greatly increased. This increased activity is most likely due to:
A) Decreased ADP
B) Increased acetyl-CoA
C) Increased NADH/NAD+ ratio
D) Increased pyruvate concentration
D
In most biochemical pathways, only a few enzymatic reactions are under regulatory control. These often occur either at the beginning of pathways or at pathway branch points. The pyruvate dehydrogenase (PDH) complex controls the link between glycolysis and the citric acid cycle, and decarboxylates pyruvate (the end product of glycolysis) with production of NADH and acetyl-CoA (the substrate for the citric acid cycle). After intense exercise, one would expect PDH to be highly active to generate ATP. ADP levels should be high because ATP was just burned by the muscle. Acetyl-CoA is an inhibitor of PDH, causing a shift of pyruvate into the gluconeogenesis pathway. A high NADH/NAD+ ratio would imply that the cell is already energetically satisfied and not in need of energy, which would not be expected in intensely exercising muscle.
Enzyme X creates peptide bonds between amino acids leucine and valine, as well as peptide bonds between leucine molecules and between valine molecules. If enzyme X catalyzed the production of leu2val2, how many different linear tetrapeptides would be possible?
A) 4
B) 6
C) 8
D) 16
B
Keeping in mind that a tetrapeptide (i.e. an oligopeptide or even if it were a protein) has an amino end and a carboxyl end, it means that LLVV would be different to VVLL where L = leucine and V = valine. Thus there are 6 possibilities:
LLVV VLLV VVLL LVLV LVVL VLVL Basic stats is only required for the 2015 MCAT. If that is what you are considering then you should describe this problem as 4 choose 2 or: 4!/(2!)(2!) = 4*3*2*1/2*2 = 24/4 = 6.
Enzymes are one of the key proteins in cells and facilitate chemical reactions. How does a typical enzyme catalyze a chemical reaction?
A) It eliminates the activation energy of a chemical reaction
B) It reduces the activation energy of a chemical reaction
C) It provides additional energy to the chemical reaction
D) It contains a covalently bound substrate, which is needed for the chemical reaction
B
Enzymes reduce the activation energy of chemical reactions by binding substrate(s) into energetically favorable orientations. They greatly reduce the activation energy, but do not eliminate it completely. Enzymes are completely reusable—they do not participate in the reaction as a substrate. Even when cofactors are needed for the successful action of the enzyme and though they may be tightly bound, they are not covalently bound to the enzyme. Enzymes do not add additional energy to chemical reactions as heat would, for example.
What is the most correct definition of competitive inhibition?
A) Another enzyme completes the same reaction and uses the available reactant
B) An inhibitor binds directly to the active site and prevents the reactant from binding
C) A metal cofactor prevents the binding of the reactant by binding at the active site
D) An inhibitor binds to the enzyme at a binding site, and prevents the enzyme from catalyzing the reaction
B
The correct answer is B. Metal cofactors and ATP are often used to help boost enzyme activity, and are not competitive inhibitors. Non-competitive inhibition (D) occurs when an inhibitor is able to prevent the enzyme from binding with the reactant by binding to the enzyme at a site away from the active site, and change the enzyme’s conformation so it cannot bind to the reactant. Competitive inhibition occurs when the inhibitor competes directly with the reactant at the active site, and this substrate takes the place of the reactant and prevents the reaction from occurring.
At what enzymatic step in the citric acid cycle (Krebs cycle) does substrate level phosphorylation occur?
A) Pyruvate to acetyl coenzyme A
B) Succinyl coenzyme A to succinate
C) Malate to oxaloacetate
D) Pyruvate to oxaloacetate
B
There is only one step in the citric acid cycle that causes substrate level phosphorylation: the conversion of succinyl coenzyme A to succinate. GDP and inorganic phosphate combine to form GTP, which is roughly equivalent to the formation of one molecule of ATP. All others do not produce ATP. Oxaloacetate may be formed from pyruvate though it requires the dephosphorylation of one molecule of ATP. Moreover, this reaction is not considered one of the classic reactions in the citric acid cycle. In the conversion of malate to oxaloacetate, NAD+ loses a proton to form NADH.
The conversion of threonine to isoleucine is a five-step enzymatic pathway. The end product, isoleucine, fits into the allosteric site of the enzyme at step 1, preventing its normal function. This is an example of:
A) Enzyme specificity
B) Competitive inhibition
C) Enzyme enhancement
D) Feedback inhibition
D
When the product of an enzymatic pathway inhibits any of the previous steps in the pathway, this is referred to as feedback inhibition. Enzyme specificity refers to the conditions appropriate for an enzyme to work. Competitive inhibition occurs when a substance occupies the active site that normally binds to the substrate involved in the reaction. The question states that isoleucine fits into the allosteric site.
In a neutral solution, most amino acids exist as:
A) Positively charged compounds
B) Zwitterions
C) Negatively charged compounds
D) Hydrophobic molecules
B
Most amino acids (except for acidic and basic amino acids) have two sites for protonation; the carboxylic acid and the amine. At neutral pH, the carboxylic acid will be deprotonated (-COOH^-) and the amine will remain protonated (-NH3^+). This dipolar ion is a zwitterion.
At pH 7, the charge on a glutamic acid molecule is:
A) –2
B) –1
C) 0
D) 1
B
Glutamic acid is an acidic amino acid because it has an extra carboxyl group. At neutral pH, both carboxyl groups are deprotonated and thus negatively charged. The amino group has a positive charge because it remains protonated at pH 7. Overall, therefore, glutamic acid has a net charge of -1. Notice that you do not even need to know the pI values to solve this equation; as an acidic amino acid, glutamic acid must have a pI below 7.
Which of the following statements is most likely to be true of nonpolar R groups in aqueous solution?
A) They are hydrophilic and found buried within proteins
B) They are hydrophilic and found on protein surfaces
C) They are hydrophobic and found buried within proteins
D) They are hydrophobic and found on protein surfaces
C
Nonpolar groups are not capable of forming dipoles or hydrogen bonds; this makes them hydrophobic. Burying hydrophobic R groups inside proteins means they don’t have to interact with water, which is polar. Choices A and B are incorrect because nonpolar molecules are hydrophobic; not hydrophilic. Choice D is incorrect because they are not generally found on protein surfaces; rather they are found within proteins.
Which of these statements concerning peptide bonds is FALSE?
A) Their formation involves a reaction between an amino group and a carboxyl group
B) They are the primary bonds that hold amino acids together
C) They have partial double bond character
D) Their formation involves hydration reactions
D
Peptide bonds are the primary covalent bond between the amino acids that make up proteins. They involve a condensation reaction between the amino group of one amino acid and the carboxyl group of an adjacent amino acid. The peptide bond has a partial double bond character because the double bond can resonate between C=O and C=N. Thus, the peptide bond has a partial double bond character and exhibits limited rotation. Formation of the peptide bond is a condensation reaction - specifically a dehydration reaction involving the loss of water - not a hydration reaction involving the addition of water.
How many distinct tripeptides can be formed from one valine molecule, one alanine molecule, and one leucine molecule?
A) 1
B) 3
C) 6
D) 27
C
There are three choices for the first amino acid, leaving two choices for the second, and one choice for the third. Multiplying those numbers gives us a total of 3 x 2 x 1 = 6 distinct tripeptides. (Using the one-letter code for valine (V), alanine (A), and leucine (L), those six tripeptides are VAL, VLA, ALV, AVL, LVA, and LAV.)
Which of these is most likely to be preserved when a protein is denatured?
A) Primary structure
B) Secondary structure
C) Tertiary structure
D) Quaternary structure
A
Denaturing a protein results in the loss of three-dimensional structure and function. Because the denaturation process does not normally result in breaking the peptide chain, the primary structure should be conserved. All of the other levels of structure can be disrupted.
An α-helix is most likely to be held together by:
A) Disulfide bonds
B) Hydrophobic effects
C) Hydrogen bonds
D) Ionic attractions between side chains
C
The ɑ-helix is held together primarily by hydrogen bonds between the carboxyl groups and amino groups of amino acids. Disulfide bridges and hydrophobic effects are primarily involved in tertiary structures, not secondary. Even if they were charged, the side chains of amino acids are too far apart to participate in strong interactions in secondary structure.
Which of the following is least likely to cause denaturation of proteins?
A) Heating the protein to 100°C
B) Adding 8 M urea
C) Moving it to a more hypotonic environment
D) Adding a detergent such as sodium dodecyl sulfate
C
High salt concentrations and detergents can denature a protein, as can high temperatures. But moving a protein to a hypotonic environment - that is, a lower solute concentration - should not lead to denaturation.
A particular α-helix is known to cross the cell membrane. Which of these amino acids is most likely to be found in the transmembrane portion of the helix?
A) Glutamate
B) Lysine
C) Phenylalanine
D) Aspartate
C
An amino acid likely to be found in a transmembrane portion of an ɑ-helix will be exposed to a hydrophobic environment, so we need an amino acid with a hydrophobic side chain. The only choice that has a hydrophobic side chain is phenylalanine. The other choices are all polar or charged.
Which of these amino acids has a chiral carbon in its side chain?
I. Serine
II. Threonine
III. Isoleucine
A) I only
B) II only
C) II and III only
D) I, II, and III
C
Every amino acid except glycine has a chiral ɑ-carbon, but only two of the 20 amino acids - threonine and isoleucine - also have a chiral carbon in their side chains as well. Just as only one configuration is normally seen at the ɑ-carbon, only one configuration is seen in the side chain chiral carbon.
Adding concentrated strong base to a solution containing an enzyme often reduces enzyme activity to zero. In addition to causing protein denaturation, which of the following is another plausible reason for the loss of enzyme activity?
A) Enzyme activity, once lost, cannot be recovered
B) The base can cleave peptide residues
C) Adding a base catalyzes protein polymerization
D) Adding a base tends to deprotonate amino acids on the surface of proteins
B
Bases can catalyze peptide bond hydrolysis. Enzyme activity can be recovered in a least some cases. Choice D is a true statement, but fails to explain the loss of enzyme activity.
Which of these amino acids has a side chain that can become ionized in cells?
A) Histidine
B) Leucine
C) Proline
D) Threonine
A
Histidine has an ionizable side chain; its imidazole ring has a nitrogen atom that can be protonated. None of the remaining answers have ionizable atoms in their side chains.
In lysine, the pKa of the side chain is about 10.5. Assuming that the pKa of the carboxyl and amino groups are 2 and 9, respectively, the pI of lysine is closest to:
A) 5.5
B) 6.2
C) 7.4
D) 9.8
D
Because lysine has a basic side chain, we ignore the pKa of the carboxyl group, and average the pKa of the side chain and the amino group; the average of 9 and 10.5 is 9.75 or 9.8.
Which of the following is a reason for conjugating proteins?
I. To direct their delivery to a particular organelle
II. To direct their delivery to the cell membrane
III. To add a cofactor needed for their activity
A) I only
B) II only
C) II and III only
D) I, II, and III
D
Conjugated proteins can have lipid or carbohydrate “tags” added to them. These tags can indicate that these proteins should be directed to the cell membrane (especially lipid tags) or to specific organelles (such as the lysosome). They can also provide the activity of the protein; for example, the heme group in hemoglobin is needed for it to bind oxygen.
Collagen consists of three helices with carbon backbones that are tightly wrapped around one another in a “triple helix.” Which of these amino acids is most likely to be found in the highest concentration in collagen?
A) Proline
B) Glycine
C) Threonine
D) Cysteine
B
Because collagen has a triple helix, the carbon backbones are very close together. Thus, steric hinderance is a potential problem. To reduce that hinderance, we need small side chains; glycine has the smallest side chain of all: a hydrogen atom.
Consider a biochemical reaction A → B, which is catalyzed by A–B dehydrogenase. Which of the following statements is true?
A) The reaction will proceed until the enzyme concentration decreases
B) The reaction will be most favorable at 0°C
C) A component of the enzyme is transferred from A to B
D) The free energy change (ΔG) of the catalyzed reaction is the same as for the uncatalyzed reaction
D
Enzymes catalyze reactions by lowering their activation energy, and are not changed or consumed during the course of the reaction. While the activation energy is lowered, the free energy of the reaction, ∆G, remains unchanged in the presence of an enzyme. A reaction will continue to occur in the presence or absence of an enzyme; it simply runs slower without the enzyme. Most physiological reactions are optimized at body temperature, 37℃. Finally, dehydrogenases catalyze oxidation-reduction reactions, not transfer reactions.
Which of the following statements about enzyme kinetics is FALSE?
A) An increase in the substrate concentration (at constant enzyme concentration) leads to proportional increases in the rate of the reaction
B) Most enzymes operating in the human body work best at a temperature of 37°C
C) An enzyme–substrate complex can either form a product or dissociate back into the enzyme and substrate
D) Maximal activity of many human enzymes occurs around pH 7.4
A
Most enzymes in the human body operate at maximal activity around a temperature of 37℃ and a pH of 7.4, which is the pH of most body fluids. In addition, as characterized by the Michaelis-Menten equation, enzymes form an enzyme-substrate complex, which can either dissociate back into the enzyme and substrate or proceed to form a product. An increase in the substrate concentration, while maintaining a constant enzyme concentration, leads to a proportional increase in the rate of the reaction only initially. However, once most of the active sites are occupied, the reaction rate levels off, regardless of further increases in substrate concentration. At high concentrations of substrate, the reaction rate approaches its maximal velocity and is no longer changed by further increases in substrate concentration.
Some enzymes require the presence of a nonprotein molecule to behave catalytically. An enzyme devoid of this molecule is called a(n):
A) Holoenzyme
B) Apoenzyme
C) Coenzyme
D) Zymoenzyme
B
An enzyme devoid of its necessary cofactor is called an apoenzyme and is catalytically inactive.
Which of the following factors determine an enzyme’s specificity?
A) The three-dimensional shape of the active site
B) The Michaelis constant
C) The type of cofactor required for the enzyme to be active
D) The prosthetic group on the enzyme
A
An enzyme’s specificity is determined by the three dimensional shape of its active site. Regardless of which explanation for enzyme specificity we are discussing (lock and key or induced fit), the active site determines which substrate the enzyme will react with.
Enzymes increase the rate of a reaction by:
A) Decreasing the activation energy
B) Increasing the overall free energy change of the reaction
C) Increasing the activation energy
D) Decreasing the overall free energy change of the reaction
A
Enzymes increase the rate of reaction by decreasing the activation energy. They do not affect the overall free energy, ∆G, or the reaction.
In the equation below, substrate C is an allosteric inhibitor to enzyme 1. Which of the following is another mechanism necessarily caused by substrate C?
A —————-> B —————-> C
Enzyme 1 Enzyme 2
A) Competitive inhibition
B) Irreversible inhibition
C) Feedback enhancement
D) Negative feedback
D
By limiting the activity of enzyme 1, the rest of the pathway is slowed, which is the definition of negative feedback. Choice A is incorrect because there is no competition for the active site with allosteric interactions. While many products do indeed competitively inhibit an enzyme in the pathway that creates them, this is an example of an allosterically inhibited enzyme. There is not enough information for Choice B to be correct because we aren’t told whether inhibition is reversible. In general, allosteric interactions are temporary. Choice C is incorrect because it is the opposite of what occurs when enzyme 1 activity is reduced.
The activity of an enzyme is measured at several different substrate concentrations, and the data are shown in the table below.
[S] (mM) [v(mmol/sec)] 0.01 1 0.05 9.1 0.1 17 0.5 50 1 67 5 91 10 95 50 99 100 100
Km for this enzyme is approximately:
A) 0.5
B) 1
C) 10
D) 50
A
While the equations given in the text are useful, recognizing relationships is even more important. You can see that as substrate concentration increases significantly, there is only a small change in the rate. This occurs as we approach Vmax. Because the Vmax is near 100 mmol/min, Vmax/2 equals 50 mmol/min. The substrate concentration giving this rate is 0.5mM and corresponds to Km.
Consider a reaction catalyzed by enzyme A with a Km value of 5 × 10^–6 M and Vmax of 20 mmol/min.
At a concentration of 5 × 10^–6 M substrate, the rate of the reaction will be:
A) 10 mmol/min
B) 20 mmol/min
C) 30 mmol/min
D) 40 mmol/min
A
Relationships are important. At a concentration of 5 × 10^–6 M, enzyme A is working at one-half its Vmax because the concentration is equal to the Km of the enzyme. Therefore, one-half of 20 mmol/min is 10 mmol/min.
Consider a reaction catalyzed by enzyme A with a Km value of 5 × 10^–6 M and Vmax of 20 mmol/min.
At a concentration of 5 × 10^–4 M substrate, the rate of the reaction will be:
A) 10 mmol/min
B) 15 mmol/min
C) 20 mmol/min
D) 30 mmol/min
C
At a concentration of 5 × 10^–4 M, there is 100 times more substrate than present at half maximal velocity. At high values (significantly larger than the value of Km), the enzyme is at or near its Vmax, which is 20 mmol/min.
The conversion of ATP to cyclic AMP and inorganic phosphate is most likely catalyzed by which class of enzyme?
A) Ligase
B) Hydrolase
C) Lyase
D) Transferase
C
Lyases are responsible for the breakdown of a single molecule into two molecules without the addition of water or the transfer of electrons. Lyases often form cyclic compounds or double bonds in the products to accommodate this. Water was not a reactant, and no cofactor was mentioned; thus lyase remains the best answer choice.
Which of the following is NOT a method by which enzymes decrease the activation energy for biological reactions?
A) Modifying the local charge environment
B) Forming transient covalent bonds
C) Acting as electron donors or receptors
D) Breaking bonds in the enzyme to provide energy
D
Enzymes are not altered by the process of catalysis. A molecule that breaks intramolecular bonds to provide activation energy would not be able to be reused.
A certain cooperative enzyme has four subunits, two of which are bound to substrate. Which of the following statements can be made?
A) The affinity of the enzyme for the substrate has just increased
B) The affinity of the enzyme for the substrate has just decreased
C) The affinity of the enzyme for the substrate is at the average for this enzyme class
D) The affinity of the enzyme for the substrate is greater than with one substrate bound
D
Cooperative enzymes demonstrate a change in affinity for the substrate depending on how many substrate molecules are bound and whether the last change was accomplished because a substrate molecule was bound or left the active site of the enzyme. Because we cannot determine whether the most recent reaction was binding or dissociation, Choices A and B are incorrect. We can make absolute comparisons though. The unbound enzyme has the lowest affinity for substrate, and the enzyme with all but one subunit bound has the highest. The increase in affinity is not linear, so Choice C is not necessarily true. An enzyme with two subunits occupied must have a higher affinity for the substrate than the same enzyme with only one subunit occupied.
Which of the following is LEAST likely to be required for a series of metabolic reactions?
A) Triglyceride acting as a coenzyme
B) Oxidoreductase enzymes
C) Magnesium acting as a cofactor
D) Transferase enzymes
A
Triglycerides are unlikely to act as coenzymes for a few reasons, including their large size, neutral charge, and ubiquity in cells. Cofactors and coenzymes tend to be small in size, such as metal ions or small organic molecules. They can usually carry a charge by ionization, protonation, or deprotonation. Finally, they are usually in low, tightly regulated concentrations within cells. Metabolic pathways would be expected to include both oxidation-reduction reactions and movement of functional groups.
How does the ideal temperature for a reaction change with and without an enzyme catalyst?
A) The ideal temperature is generally higher with a catalyst than without
B) The ideal temperature is generally lower with a catalyst than without
C) The ideal temperature is characteristic of the reaction, not the enzyme
D) No conclusion can be made without knowing the enzyme type
B
The rate of reaction increases with temperature because of the increased kinetic energy of the reactants, but reaches a peak temperature because the enzyme denatures with the disruption of hydrogen bonds at excessively high temperatures. In the absence of enzyme, this peak temperature is generally much hotter. Heating a reaction provides molecules with an increased chance of achieving the activation energy, but the enzyme catalyst would typically reduce activation energy. Keep in mind that thermodynamics and kinetics are not interchangeable, so we are not considering the impact of heat on the equilibrium position.
