MCAT Biochemistry: Amino Acids

In a neutral solution, most amino acids exist as: A. positively charged compounds B. zwitterions C. negatively charged compounds D. hydrophobic molecules

B. zwitterions Most amino acids (except the 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 (−COO-) and the amine will remain protonated (-NH3+). This dipolar ion is a zwitterion, so (B) is the correct answer.

A polypeptide with a net positive charge at physiologic pH (~7.4) most likely contains amino acids with R groups of what type? A. Basic R groups B. Aliphatic R groups C. Acidic R groups D. Aromatic R groups

A. Basic R groups

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 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.

The amino acids in hemoglobin (or any protein) uniformly have which of the following configurations? A. L B. R C. S D. D

A. L-Configuration Configurations (either relative or absolute) in amino acids refers to the stereochemical configuration around the chiral carbon. Due to differences in the priority of different amino acid side chains, not all amino acids have the same "Absolute Configuration", which refers the R/S naming convention. Some amino acids are R, and some are S. However, all amino acids have the same "Relative Configuration", which refers to the D/L naming convention. All biologically produced amino acids are in the L configuration.

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. Primary structure 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.

At pH 7, the charge on a glutamic acid molecule is: A. -2 B. -1 C. 0 D. +1

B. -1 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 remain protonated at pH 7. Overall, therefore, glutamic acid has a net charge of -1, and (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.

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. Glycine 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

Electrophoretic separation at pH 6 of a sample of polypeptide 1 (mw 100) polypeptide 2 (mw 200) and polypeptide 3 (mw 400) would result in which of the following? (Note: the isoelectric point of each polypeptide occurs at pH 6) A. Polypeptide 1 would move the farthest B. None of the polypeptides would move C. Polypeptide 3 would move the farthest D. Polypeptide 2 would move the farthest

B. None of the polypeptides would move The isoelectric point for a polypeptide is the pH at which the molecule does not have a net charge. Electrophoretic separation depends on the existence of a negative net charge. None of the polypeptides would move at pH 6.

All hydrophobic amino acids (valine, leucine, isoleucine, etc.) share which of the following properties? A. Acidic R groups B. Nonpolar uncharged R groups C. Polar uncharged R groups D. Basic R groups

B. Nonpolar uncharged R groups Hydrophobic amino acids prefer to minimize their interactions with water molecules. Polar, acidic, and basic R groups all share partial or full charges, which interact favorably with polar water molecules. All hydrophobic amino acids share nonpolar uncharged R groups.

The unique cyclic structure of which of the following amino acids plays a central role in the formation of alpha helices and beta sheets? A. Lysine B. Proline C. Arginine D. Valine

B. Proline Alpha helices and beta sheets are two three dimensional motifs that regularly appear in local segments of amino acids. Proline has a unique cyclic structure which differentiates it from the other common amino acids. Proline plays a central role in the FORMATION of alpha helices and beta sheets. While proline's unique structure may also disrupt both alpha helixes and beta sheets, it's ability to make sharp turns facilitates the FORMATION of both structures, with proline commonly being found at the beginning of alpha helices or at the turns in beta sheets.

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. The base can cleave peptide residues Bases can catalyze peptide bond hydrolysis. (A) is incorrect: enzyme activitiy can be recovered in at least some cases. (D) is a true statement, but fails to explain the loss of enzyme activity.

The alpha helix is an example of which of the following structural properties of proteins? A. quaternary structure B. secondary structure C. tertiary structure D. primary structure

B. secondary structure Secondary structure refers to the three dimensional arrangement of small segments of amino acids in a polypeptide. The alpha helix is three dimensional arrangement of amino acids in a polypeptide, where the chain takes on a telephone-cord-like shape. The alpha helix is an example of secondary structure.

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. 6 There are three choices for the first maino 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.)

Electrophoretic separation of leucine from a protein sample would be least effective at which of the following pH values? A. 0.4 B. 1.4 C. 7.4 D. 2.4

C. 7.4 Leucine has an aliphatic side chain. At physiological pH, leucine exists as a zwitterion. Electrophoretic separation of leucine from a protein sample would be least effective at pH 7.4.

Which of the following amino acids has a net negative charge at physiologic pH (~7.4)? A. Histidine B. Asparagine C. Glutamic Acid D. Lysine

C. Glutamic Acid

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. Hydrogen bonds The alpha helix is held together primarily by hydrogen bonds between the carboxyl groups and amino groups of amino acids. Disulfide bridges, (A), and hydrophobic effects, (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.

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. II and III only Every amino acid exept glycine has a chiral alpha 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 (C). Just as only one configuration is normally seen at the alpha carbon, only one configuration is seen in the side chain chiral carbon.

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 dodium dodecyl sulfate

C. Moving it to a more hypotonic environment High salt concentration 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. Phenylalanine An amino acid likely to be found in a transmembrane portion of an alpha 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 (C), phenylalanine. The other choice are all polar or charged.

Which of the following properties of a protein is least likely to be affected by changes in pH? A. Net charge B. Tertiary structure C. Primary structure D. Secondary structure

C. Primary structure Primary structure is the amino acid sequence of a protein plus the peptide bonds joining them together. Change in pH are unlikely to alter amino acid sequence or break peptide bonds. The primary structure of a protein is least likely to be affected by changes in pH.

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. They are hydrophobic and found buried within proteins. 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 (C) correct. (A) and (B) are incorrect because nonpolar molecules are hydrophobic, not hydrophilic; (D) is incorrect because they are not generally found on protein surfaces.

Hydrogen bonding between separate subunits of DNA polymerase is an example of which of the following? A. 1 degree structure B. 2 degree structure C. 3 degree structure D. 4 degree structure

D. 4 degree structure 1 degree structure through 3 degree structure have to do with individual polypeptides. 4 degree structure refers to the global three dimensional arrangements found in multi-subunit proteins. Hydrogen bonding between separate subunits of DNA polymerase is an example of 4 degree structure.

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. 9.8 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 answer choice D.

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. I, II and III 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.

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. Their formation involves hydration reactions. Peptide bonds are the primary covalent bond between the amino acids that make up proteins, making (B) incorrect. They involve a condensaton reaction between the amino group of one amino acid and the carboxyl group of an adjacent amino acid, eliminating (A). The peptide bond has a partial double bond character because the double bond can resonate double bond character and exhibits limited rotation, eliminating between C=O and C=N. Thus, the peptide bond has a partial double bond character and exhibits limited rotaion, eliminating (C). By process of elimination, (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.