MCAT Biochemistry Review
Chapter 1: Amino Acids, Peptides, and Proteins
1. In a neutral solution, most amino acids exist as:
1. positively charged compounds.
3. negatively charged compounds.
4. hydrophobic molecules.
2. At pH 7, the charge on a glutamic acid molecule is:
3. Which of the following statements is most likely to be true of nonpolar R groups in aqueous solution?
1. They are hydrophilic and found buried within proteins.
2. They are hydrophilic and found on protein surfaces.
3. They are hydrophobic and found buried within proteins.
4. They are hydrophobic and found on protein surfaces.
4. Which of these statements concerning peptide bonds is FALSE?
1. Their formation involves a reaction between an amino group and a carboxyl group.
2. They are the primary bonds that hold amino acids together.
3. They have partial double bond character.
4. Their formation involves hydration reactions.
5. How many distinct tripeptides can be formed from one valine molecule, one alanine molecule, and one leucine molecule?
6. Which of these is most likely to be preserved when a protein is denatured?
1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure
7. An α-helix is most likely to be held together by:
1. disulfide bonds.
2. hydrophobic effects.
3. hydrogen bonds.
4. ionic attractions between side chains.
8. Which of the following is least likely to cause denaturation of proteins?
1. Heating the protein to 100°C
2. Adding 8 M urea
3. Moving it to a more hypotonic environment
4. Adding a detergent such as sodium dodecyl sulfate
9. 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?
10.Which of these amino acids has a chiral carbon in its side chain?
1. I only
2. II only
3. II and III only
4. I, II, and III
11.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?
1. Enzyme activity, once lost, cannot be recovered.
2. The base can cleave peptide residues.
3. Adding a base catalyzes protein polymerization.
4. Adding a base tends to deprotonate amino acids on the surface of proteins.
12.Which of these amino acids has a side chain that can become ionized in cells?
13.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:
14.Which of the following is a reason for conjugating proteins?
1. To direct their delivery to a particular organelle
2. To direct their delivery to the cell membrane
3. To add a cofactor needed for their activity
1. I only
2. II only
3. II and III only
4. I, II, and III
15.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?
Answers and Explanations
Most amino acids (except the acidic and basic amino acids) have two sites for protonation: the carboxylic acid and the amine group. At neutral pH, the carboxylic acid will be deprotonated (–COO–), and the amine group will remain protonated (–NH3+). This dipolar ion is a zwitterion, so choice(B) is the correct answer.
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, and choice (B) is correct. Notice that you do not even need to know the pI values to solve this question; as an acidic amino acid, glutamic acid must have a pI below 7.
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. This makes choice (C) correct. 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.
Peptide bonds are the primary covalent bond between the amino acids that make up proteins, making choice (B) incorrect. They involve a condensation reaction between the amino group of one amino acid and the carboxyl group of an adjacent amino acid, eliminating choice (A). 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, eliminating choice (C). By process of elimination, choice (D) is false: 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.
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 × 2 × 1 = 6 distinct tripeptides. (Using the one-letter codes for valine (V), alanine (A), and leucine (L), those six tripeptides are VAL, VLA, ALV, AVL, LVA, and LAV.)
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.
The α-helix is held together primarily by hydrogen bonds between the carboxyl groups and amino groups of amino acids. Disulfide bridges, choice (A), and hydrophobic effects, choice (B), 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.
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.
An amino acid likely to be found in a transmembrane portion of an α-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 choice (C), phenylalanine. The other choices are all polar or charged.
Every amino acid except glycine has a chiral α-carbon, but only two of the 20 amino acids—threonine and isoleucine— also have a chiral carbon in their side chains as well. Thus, the correct answer is choice (C). Just as only one configuration is normally seen at the α carbon, only one configuration is seen in the side chain chiral carbon.
Bases can catalyze peptide bond hydrolysis. Choice (A) is incorrect: enzyme activity can be recovered in at least some cases. Choice (D) is a true statement, but fails to explain the loss of enzyme activity.
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.
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, which is closest to choice (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. Thus, choice (D) is the correct answer.
Because collagen has a triple helix, the carbon backbones are very close together. Thus, steric hindrance is a potential problem. To reduce that hindrance, we need small side chains; glycine has the smallest side chain of all: a hydrogen atom.