Lecture 2 Flashcards
Which of the following best describes the α-carbon in an amino acid? A. It has the same group attached twice, making it non-chiral.
B. It is the carbon with a double bond to the oxygen.
C. It is the central carbon to which an amino group, a carboxyl group, a side chain, and a hydrogen are attached.
D. It is the carbon found only in the D-configuration in natural proteins.
Correct Answer: C
Explanation: The α-carbon is always attached to four different groups (amino, carboxyl, side chain, hydrogen), making it chiral (except in glycine).
Why are most naturally occurring amino acids in proteins classified as L-amino acids? A. Because the D-form is less stable at room temperature.
B. Because cells evolved molecular machinery that specifically recognizes and uses the L-form.
C. Because the L-form has no chiral center.
D. Because the D-form does not exist at all in nature.
Correct Answer: B
Explanation: Life on Earth evolved to incorporate and synthesize the L-form of amino acids, and all protein-building enzymes are adapted to the L-configuration.
Which of the following statements correctly describes the primary structure of a protein? A. It is the overall 3D shape of the protein.
B. It is the linear sequence of amino acids linked by peptide bonds.
C. It is the arrangement of multiple polypeptide subunits.
D. It is the pattern of hydrogen bonds forming α-helices or β-sheets.
Answer: B
Explanation: The primary structure is defined as the linear sequence of amino acids.
What occurs during the formation of a peptide bond? A. A phosphate group is released.
B. A hydrogen bond is formed.
C. A water molecule is released in a condensation reaction.
D. A sulfur-sulfur bond is formed.
Answer: C
Explanation: Peptide bonds form via condensation, releasing a molecule of water.
Why does the peptide bond in proteins have restricted rotation? A. Because it is purely a single bond.
B. Because of resonance that creates partial double-bond character.
C. Because the nitrogen has no electrons to share.
D. Because the oxygen cannot form hydrogen bonds.
Correct Answer: B
Explanation: Resonance between the nitrogen and carbonyl group leads to partial double-bond character, restricting rotation.
Which statement correctly describes the resonance in a peptide bond? A. The electrons are localized only on the nitrogen atom.
B. The carbonyl oxygen and the α-carbon share electrons.
C. The nitrogen’s lone pair and the carbonyl (C=O) can delocalize, making the C—N bond partly double.
D. There is no resonance; the bond is always single.
Correct Answer: C
Explanation: Resonance involves delocalization of the nitrogen’s lone pair with the carbonyl group, creating partial double-bond character in the C—N bond.
Which statement correctly describes a nonpolar (hydrophobic) amino acid side chain?
A. It contains mostly hydrocarbon groups and does not interact well with water.
B. It carries a net negative charge at physiological pH.
C. It has a net positive charge at physiological pH.
D. It always contains a hydroxyl (—OH) group.
Correct Answer: A
Explanation: Nonpolar side chains are typically hydrocarbon-rich (like CH₃, CH₂) and avoid water.
Which of the following amino acids is negatively charged at physiological pH?
A. Lysine (Lys)
B. Arginine (Arg)
C. Aspartic acid (Asp)
D. Histidine (His)
Correct Answer: C
Explanation: Aspartic acid (Asp) and Glutamic acid (Glu) have carboxyl groups that are deprotonated and negatively charged at around pH 7.
Which statement correctly describes why the peptide bond is rigid and planar? A. It is a single bond that freely rotates.
B. It has partial double-bond character due to resonance.
C. The α-carbon is chiral.
D. It forms hydrogen bonds in all directions.
Correct Answer: B
Explanation: Resonance delocalizes electrons between the carbonyl group and the nitrogen, creating a partial double bond that restricts rotation.
Why are most peptide bonds in the trans configuration rather than the cis configuration?
A. Trans allows for more resonance structures.
B. Trans reduces steric clashes between side chains.
C. Cis forms stronger hydrogen bonds.
D. Cis is more stable due to partial double-bond character.
Correct Answer: B
Explanation: In the trans arrangement, bulky side chains are positioned farther apart, minimizing steric hindrance.
Which amino acid is known to have a higher-than-usual probability of adopting the cis configuration in its peptide bonds?
A. Glycine
B. Proline
C. Lysine
D. Valine
Correct Answer: B
Explanation: Proline’s side chain connects back to its nitrogen, making the cis form more feasible than for other amino acids (though trans is still more common overall).
Which of the following best describes a β-strand in a protein? A. A tightly coiled helix stabilized by hydrogen bonds.
B. An extended polypeptide conformation with about 2.0 residues per turn.
C. A random coil lacking any repeating pattern.
D. A chain forming only ionic bonds with neighboring chains.
Correct Answer: B
Explanation: A β-strand is an extended structure with a zig-zag backbone, sometimes described as having 2.0 residues per repeating unit.
What primarily stabilizes adjacent β-strands in a β-sheet? A. Covalent bonds between side chains.
B. Hydrogen bonds between backbone carbonyls and amide hydrogens.
C. Salt bridges between positively and negatively charged side chains.
D. Van der Waals forces between α-carbons.
Correct Answer: B
Explanation: β-sheets are formed and stabilized by hydrogen bonds between backbone groups on neighboring strands.
Which of the following describes the hydrogen-bonding pattern in a typical α-helix? A. Between residue n and residue n+2
B. Between residue n and residue n+3
C. Between residue n and residue n+4
D. Between residue n and residue n+5
Correct Answer: C
Explanation: In an α-helix, each carbonyl oxygen forms a hydrogen bond with the amide hydrogen four residues ahead in the sequence (n+4).
Which statement correctly characterizes the 3₁₀-helix in proteins? A. It has more than 5 residues per turn.
B. It is the same as an α-helix but with shorter side chains.
C. It is a tighter spiral with hydrogen bonds between n and n+3.
D. It has no hydrogen bonds in the backbone.
Correct Answer: C
Explanation: A 3₁₀-helix has three residues per turn and hydrogen bonds from residue n to residue n+3, making it tighter than an α-helix.
Which statement best describes the Ramachandran plot? A. It shows the possible angles for the peptide bond itself.
B. It plots the allowed combinations of Φ (phi) and Ψ (psi) torsion angles in polypeptides.
C. It shows the distribution of side-chain (R-group) rotations.
D. It only applies to non-biological polymers.
Correct Answer: B
Explanation: The Ramachandran plot displays the allowed Φ and Ψ angles for the protein backbone.
Where on the Ramachandran plot are right-handed α-helices typically found? A. Top-right region
B. Top-left region
C. Bottom-left region
D. Bottom-right region
Correct Answer: C
Explanation: Right-handed α-helices typically cluster in the bottom-left region (Φ ≈ –60°, Ψ ≈ –40°) of the Ramachandran plot.
Which of the following best describes the primary structure of a protein?
A. The local folding into α-helices or β-sheets
B. The linear sequence of amino acids in the polypeptide chain
C. The three-dimensional arrangement of multiple polypeptide subunits
D. The distribution of amino acid side chains in a folded protein
Correct Answer: B
Explanation: Primary structure is the linear order of amino acids, written from N-terminus to C-terminus.
What primarily stabilizes the secondary structure of a protein?
A. Hydrogen bonds between backbone groups
B. Disulfide bonds between cysteine side chains
C. Ionic interactions between charged side chains
D. Covalent linkages of the peptide backbone
Correct Answer: A
Explanation: Secondary structures like α-helices and β-sheets rely mainly on hydrogen bonds formed between the carbonyl (C=O) and amide (N–H) groups of the polypeptide backbone.
Which of the following forces does not typically stabilize tertiary protein structure?
A. Hydrogen bonding
B. Hydrophobic interactions
C. Disulfide bonds
D. Peptide bonds between side chains
Correct Answer: D
Explanation: Peptide bonds link amino acids in the main chain (primary structure), not between side chains. Tertiary structure is mainly stabilized by noncovalent interactions and sometimes disulfide bridges between side chains.
Why do globular proteins generally have a hydrophobic interior and a hydrophilic exterior?
A. Hydrogen bonding only occurs on the inside of a protein.
B. Nonpolar side chains avoid water, so they cluster inside, while polar side chains interact with water on the outside.
C. Disulfide bonds form exclusively on the outside.
D. The polypeptide chain has no control over folding.
Correct Answer: B
Explanation: Hydrophobic (nonpolar) side chains tend to sequester themselves away from water, leading to a hydrophobic core. Polar or charged side chains stay on the surface where they can interact with water.
What is the main idea behind the “protein folding problem”?
A. Proteins have no unique shape in solution.
B. The number of possible backbone conformations is huge, yet proteins fold quickly into a specific shape.
C. Protein folding always requires external energy input.
D. Only small proteins can fold spontaneously, while large proteins cannot.
Correct Answer: B
Explanation: The paradox is that proteins adopt their correct structure very fast despite having a massive number of possible conformations.
Which of the following did Christian Anfinsen’s experiment demonstrate about protein folding?
A. Folding is controlled solely by the cell membrane.
B. The information for folding is contained in the primary amino acid sequence.
C. Proteins cannot refold after being denatured.
D. Chaperones are always required for any folding to occur.
Correct Answer: B
Explanation: Anfinsen’s classic work showed that, at least for some proteins, the final folded structure is determined by the sequence itself.
Which structural feature distinguishes proline from most other amino acids?
A. It has a sulfur-containing side chain.
B. Its side chain forms a ring with the amino nitrogen, making it a secondary amine.
C. It has two carboxyl groups attached to the α-carbon.
D. Its side chain has no carbon atoms.
Correct Answer: B
Explanation: Proline’s ring fuses the side chain to the nitrogen, creating a secondary amine and restricting backbone flexibility.
Why is proline often described as a “helix breaker” in protein structures?
A. It forms extra hydrogen bonds that stabilize helices.
B. It lacks an α-carbon, preventing helix formation.
C. Its rigid ring disrupts normal helical hydrogen bonding and introduces bends.
D. It cannot be incorporated into a peptide bond.
Correct Answer: C
Explanation: The rigid five-member ring of proline constrains the backbone geometry and disrupts the typical α-helix hydrogen-bonding pattern, often causing bends or kinks.
Why can proline more easily adopt the cis conformation compared to other amino acids?
A. Proline lacks an α-carbon.
B. Its side chain forms a rigid ring with the amino nitrogen, reducing the energy gap between cis and trans.
C. Proline contains a sulfur atom that stabilizes the cis form.
D. The cis form of proline does not involve a peptide bond.
Correct Answer: B
Explanation: Proline’s ring structure makes the cis and trans forms closer in energy, so cis is less unfavorable.
What is the function of a proline isomerase (peptidyl-prolyl cis-trans isomerase)?
A. It removes proline from the polypeptide chain.
B. It catalyzes the formation of disulfide bonds.
C. It converts proline-containing peptide bonds between cis and trans forms, aiding protein folding.
D. It prevents the formation of α-helices.
Correct Answer: C
Explanation: Proline isomerases speed up the interconversion between cis and trans proline peptide bonds, facilitating proper protein folding.
What does the term pKa specifically represent for an ionizable group in an amino acid?
A. The exact pH at which the group is always deprotonated
B. The negative log of the acid dissociation constant, indicating the pH at which half of those groups are protonated and half are deprotonated
C. The net charge of the amino acid at a certain pH
D. The highest possible pH at which the amino acid can exist
Correct Answer: B
Explanation: pKa = −log₁₀(Kₐ), indicating the pH at which 50% of that group is protonated and 50% is deprotonated.
If the pH is much lower than an amino acid side chain’s pKa, that side chain is likely to be:
A. Mostly deprotonated
B. Mostly protonated
C. Always positively charged
D. Unable to form hydrogen bonds
Correct Answer: B
Explanation: At a pH well below the pKa, the environment is acidic, so the side chain remains protonated (e.g., –COOH or –NH₃⁺).
What is the main reason a protein’s net charge can change with pH?
A. Proteins only have covalent bonds that never change.
B. Proteins contain ionizable groups that can gain or lose protons depending on pH.
C. The amino acid sequence is altered by changes in pH.
D. pH has no effect on protein charge.
Correct Answer: B
Explanation: Proteins have many ionizable side chains (and terminal groups). Under acidic conditions, they gain protons; under basic conditions, they lose protons.
When the pH is lower than a protein’s isoelectric point (pI), the protein generally carries:
A. No charge at all
B. A net positive charge
C. A net negative charge
D. Equal positive and negative charges
Correct Answer: B
Explanation: Below the pI, the protein has more protonated groups, leading to a net positive charge.
