Biochemistry Quiz: Peptide Bonds And Primary Structure
20 questions · exam conditions
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Peptide Bonds And Primary StructureQuestion 1 of 20

Context: Primary structure determines where side chains appear along the backbone. How do peptide bonds influence the function of a protein?

They fix the residue sequence, positioning side chains that contribute to binding or catalysis.
They directly form the binding pocket by creating cross-links between nonadjacent residues.
They determine function by converting side chains into identical chemical groups.
They determine function by serving as the primary sites of oxidation and reduction.
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Biochemistry Quiz

Biochemistry Quiz: Peptide Bonds And Primary Structure

Practice Peptide Bonds And Primary Structure in Biochemistry with focused quiz questions that help you check what you know, review explanations, and build confidence with test-style prompts.

What this quiz covers

This quiz focuses on Peptide Bonds And Primary Structure, giving you a quick way to practice the rules, question types, and explanations that matter most for Biochemistry.

How to use this quiz

Try each quiz question before looking at the correct answer. Use the explanations to review missed ideas, then come back to similar questions until the pattern feels familiar.

All questions

Question 1

Context: Primary structure determines where side chains appear along the backbone. How do peptide bonds influence the function of a protein?

  1. They fix the residue sequence, positioning side chains that contribute to binding or catalysis. (correct answer)
  2. They directly form the binding pocket by creating cross-links between nonadjacent residues.
  3. They determine function by converting side chains into identical chemical groups.
  4. They determine function by serving as the primary sites of oxidation and reduction.
Explanation: This question tests understanding of peptide bonds and their role in primary protein structure. Peptide bonds are covalent bonds formed between the carboxyl group of one amino acid and the amino group of another, playing a crucial role in the chain formation of polypeptides. In the provided context, side-chain positioning depends on primary structure. The correct choice, A, is accurate because it links sequence to functional positioning. A common misconception addressed by distractor B is that peptide bonds form binding pockets directly. To help students, instructors should relate structure to activity. Case studies of proteins like hemoglobin can demonstrate this.

Question 2

Context: The sequence of residues defines primary structure; peptide bonds form the backbone. How does the sequence of amino acids affect the primary structure of a protein?

  1. It determines the exact order of residues connected by peptide bonds along the backbone. (correct answer)
  2. It determines which peptide bonds become hydrogen bonds, fixing repeating patterns.
  3. It has little effect because peptide bonds are identical regardless of residue identity.
  4. It determines how many disulfide bridges form, which defines the primary structure.
Explanation: This question tests understanding of peptide bonds and their role in primary protein structure. Peptide bonds are covalent bonds formed between the carboxyl group of one amino acid and the amino group of another, playing a crucial role in the chain formation of polypeptides. In the provided context, the residue sequence defines primary structure via the peptide backbone. The correct choice, A, is accurate because it shows how sequence determines residue order along the backbone. A common misconception addressed by distractor B is linking peptide bonds to hydrogen bonding in secondary structures. To help students, instructors should emphasize sequence specificity in primary structure. Using examples of sequence mutations can illustrate impacts on structure.

Question 3

Context: Primary structure is written from N-terminus to C-terminus. In the context of protein synthesis, what is the significance of peptide bonds?

  1. They provide reversible links that allow rapid shuffling of amino-acid order.
  2. They covalently connect amino acids, preserving the N→C sequence information. (correct answer)
  3. They are noncovalent forces that primarily determine amino-acid side-chain chemistry.
  4. They form only between identical amino acids, ensuring uniform segments in proteins.
Explanation: This question tests understanding of peptide bonds and their role in primary protein structure. Peptide bonds are covalent bonds formed between the carboxyl group of one amino acid and the amino group of another, playing a crucial role in the chain formation of polypeptides. In the provided context, the N-to-C sequence directionality is preserved by peptide bonds. The correct choice, B, is accurate because it emphasizes the covalent preservation of sequence. A common misconception addressed by distractor A is that peptide bonds are reversible for shuffling. To help students, instructors should stress the stability of covalent peptide bonds. Exercises on writing sequences from N- to C-terminus can reinforce this.

Question 4

Context: Dehydration synthesis links amino acids; the peptide bond is an amide linkage. Which of the following statements accurately describes peptide bond formation?

  1. It involves cleavage of H2O\text{H}_2\text{O} to generate free radicals that couple residues.
  2. It links the amino nitrogen to the carboxyl carbon, releasing one H2O\text{H}_2\text{O}. (correct answer)
  3. It links two amino acids by forming a disulfide bridge between cysteine residues.
  4. It occurs when the peptide bond breaks water molecules apart to power chain growth.
Explanation: This question tests understanding of peptide bonds and their role in primary protein structure. Peptide bonds are covalent bonds formed between the carboxyl group of one amino acid and the amino group of another, playing a crucial role in the chain formation of polypeptides. In the provided context, dehydration synthesis and the amide linkage are key to peptide bond formation. The correct choice, B, is accurate because it correctly identifies the linkage and water release. A common misconception addressed by distractor C is confusing peptide bonds with disulfide bridges. To help students, instructors should focus on the specifics of dehydration synthesis. Comparing peptide bonds to other covalent links like disulfides can aid understanding.

Question 5

Context: Peptide bonds are amide linkages; each new bond extends the chain by one residue. In the context of protein synthesis, what is the significance of peptide bonds?

  1. They are the covalent links that polymerize amino acids into polypeptides with defined sequences. (correct answer)
  2. They are reversible links that allow amino acids to swap positions after polymerization.
  3. They are side-chain bonds that create branching patterns essential for all proteins.
  4. They are weak interactions that mainly control how proteins dissolve in water.
Explanation: This question tests understanding of peptide bonds and their role in primary protein structure. Peptide bonds are covalent bonds formed between the carboxyl group of one amino acid and the amino group of another, playing a crucial role in the chain formation of polypeptides. In the provided context, each bond extends the chain during synthesis. The correct choice, A, is accurate because it describes polymerization into defined sequences. A common misconception addressed by distractor B is reversibility for swapping. To help students, instructors should explain ribosomal synthesis. Emphasizing irreversibility under normal conditions is important.

Question 6

Context: Primary structure refers to the linear sequence of amino acids. What is the role of peptide bonds in forming the primary structure of proteins?

  1. They covalently join amino acids into a single chain, creating the polypeptide backbone. (correct answer)
  2. They stabilize the chain by forming ionic bridges between charged side chains.
  3. They determine the final shape by forming repeating hydrogen-bonded turns.
  4. They create covalent cross-links between chains, producing multi-subunit complexes.
Explanation: This question tests understanding of peptide bonds and their role in primary protein structure. Peptide bonds are covalent bonds formed between the carboxyl group of one amino acid and the amino group of another, playing a crucial role in the chain formation of polypeptides. In the provided context, primary structure is the linear amino acid sequence. The correct choice, A, is accurate because it highlights the covalent joining into a backbone. A common misconception addressed by distractor D is confusing peptide bonds with cross-links in quaternary structure. To help students, instructors should focus on levels of protein structure. Visual models of polypeptide chains can aid comprehension.

Question 7

Context: A polypeptide has an N-terminus and C-terminus defined by its peptide-bonded backbone. In the context of protein synthesis, what is the significance of peptide bonds?

  1. They create the directional backbone that allows amino-acid sequences to be read N→C. (correct answer)
  2. They provide temporary links that are routinely broken to rearrange residue order.
  3. They connect only hydrophobic residues, producing nonpolar stretches in every protein.
  4. They are primarily responsible for catalytic activity by acting as reactive sites.
Explanation: This question tests understanding of peptide bonds and their role in primary protein structure. Peptide bonds are covalent bonds formed between the carboxyl group of one amino acid and the amino group of another, playing a crucial role in the chain formation of polypeptides. In the provided context, the N- and C-termini define the directional backbone. The correct choice, A, is accurate because it describes the directional sequence reading. A common misconception addressed by distractor B is that peptide bonds are temporary. To help students, instructors should explain polarity in polypeptides. Practice with sequence notation can solidify the concept.

Question 8

Scenario—Formation Process: A peptide bond is an amide linkage written –CO–NH– in the backbone. Which of the following statements accurately describes peptide bond formation?

  1. It forms an amide bond (–CO–NH–) between adjacent amino acids. (correct answer)
  2. It forms an ionic bond between carboxylate and ammonium side chains.
  3. It forms a disulfide bond between two cysteine residues.
  4. It forms a hydrogen bond between backbone carbonyl and amide groups.
Explanation: This question tests understanding of peptide bonds and their role in primary protein structure. Peptide bonds are covalent bonds formed between the carboxyl group of one amino acid and the amino group of another, playing a crucial role in the chain formation of polypeptides. In the provided scenario, the amide linkage –CO–NH– in the backbone is described, emphasizing the specific bond type. The correct choice A is accurate because it reflects the formation of an amide bond between adjacent amino acids. A common misconception addressed by distractor D is confusing it with hydrogen bonds, which are for secondary structure. To help students, instructors should differentiate bond types clearly. Using molecular models can illustrate the amide linkage.

Question 9

Scenario—Formation Process: Primary structure is written from N-terminus to C-terminus. How does the sequence of amino acids affect the primary structure of a protein?

  1. It defines the N→C order of residues connected by peptide bonds. (correct answer)
  2. It defines only the number of peptide bonds, not residue identity.
  3. It defines only the pH at which peptide bonds form.
  4. It defines only which residues can form disulfide cross-links.
Explanation: This question tests understanding of peptide bonds and their role in primary protein structure. Peptide bonds are covalent bonds formed between the carboxyl group of one amino acid and the amino group of another, playing a crucial role in the chain formation of polypeptides. In the provided scenario, primary structure written from N to C terminus is described, emphasizing sequence definition of residue order. The correct choice A is accurate because it reflects defining N→C order by sequence. A common misconception addressed by distractor B is that it only defines bond number, ignoring residue identity. To help students, instructors should teach sequence notation. Writing sequences from N to C can practice this.

Question 10

Scenario—Formation Process: A dipeptide forms when amino acids react: –COOH + –NH2 → –CO–NH– + H2O\mathrm{H_2O}. Which statement accurately describes peptide bond formation?

  1. The peptide bond forms by dehydration between carboxyl and amino groups. (correct answer)
  2. The peptide bond forms by dehydration between two amino groups.
  3. The peptide bond forms by dehydration between two carboxyl groups.
  4. The peptide bond forms by hydrolysis between carboxyl and amino groups.
Explanation: This question tests understanding of peptide bonds and their role in primary protein structure. Peptide bonds are covalent bonds formed between the carboxyl group of one amino acid and the amino group of another, playing a crucial role in the chain formation of polypeptides. In the provided scenario, the reaction –COOH + –NH2 → –CO–NH– + H2O is described, emphasizing dehydration between correct groups. The correct choice A is accurate because it reflects dehydration between carboxyl and amino groups. A common misconception addressed by distractor D is that it's hydrolysis, which is the opposite reaction. To help students, instructors should emphasize group involvement. Reaction arrows can help visualize the process.

Question 11

Scenario—Formation Process: Consider H2N ⁣− ⁣CHR ⁣− ⁣COOH+H2N ⁣− ⁣CHR′ ⁣− ⁣COOH→H2N ⁣− ⁣CHR ⁣− ⁣CO ⁣− ⁣NH ⁣− ⁣CHR′ ⁣− ⁣COOH+H2O\mathrm{H_2N\! -\!CHR\! -\!COOH + H_2N\! -\!CHR'\! -\!COOH \rightarrow H_2N\! -\!CHR\! -\!CO\! -\!NH\! -\!CHR'\! -\!COOH + H_2O}. Which statement accurately describes peptide bond formation?

  1. The bond forms between the amino nitrogen and carboxyl carbon, releasing H2O\mathrm{H_2O}. (correct answer)
  2. The bond forms between carboxyl oxygens of both amino acids, releasing H2O\mathrm{H_2O}.
  3. The bond forms between side chains, producing CO2\mathrm{CO_2} as a byproduct.
  4. The bond forms by hydrolysis, consuming H2O\mathrm{H_2O} to join residues.
Explanation: This question tests understanding of peptide bonds and their role in primary protein structure. Peptide bonds are covalent bonds formed between the carboxyl group of one amino acid and the amino group of another, playing a crucial role in the chain formation of polypeptides. In the provided scenario, the chemical equation illustrates peptide bond formation through dehydration synthesis, emphasizing the release of water and the linkage between amino nitrogen and carboxyl carbon. The correct choice A is accurate because it reflects the precise chemical groups involved and the byproduct released. A common misconception addressed by distractor D is that the bond forms by hydrolysis consuming water, which is the reverse process for breaking bonds. To help students, instructors should emphasize the dehydration reaction and use chemical equations for visualization. Practicing identification of groups in amino acid structures will reinforce correct bond formation understanding.

Question 12

Context: Peptide bonds are covalent and form the polypeptide backbone. What is the role of peptide bonds in forming the primary structure of proteins?

  1. They covalently connect amino acids into a continuous chain that defines primary structure. (correct answer)
  2. They create covalent bridges between distant residues, defining sequence-independent stability.
  3. They form between polar side chains to establish the chain's residue order.
  4. They are weak forces that can be rearranged without breaking covalent bonds.
Explanation: This question tests understanding of peptide bonds and their role in primary protein structure. Peptide bonds are covalent bonds formed between the carboxyl group of one amino acid and the amino group of another, playing a crucial role in the chain formation of polypeptides. In the provided context, peptide bonds form the covalent backbone. The correct choice, A, is accurate because it describes covalent chain formation. A common misconception addressed by distractor B is confusing with disulfide bridges. To help students, instructors should focus on backbone linkages. Comparing to other covalent bonds in proteins helps.

Question 13

Scenario—Formation Process: Each peptide bond formation releases one water molecule. Which of the following statements accurately describes peptide bond formation?

  1. One H2O\mathrm{H_2O} is released when a new –CO–NH– bond forms. (correct answer)
  2. One H2O\mathrm{H_2O} is consumed when a new –CO–NH– bond forms.
  3. One CO2\mathrm{CO_2} is released when a new –CO–NH– bond forms.
  4. One O2\mathrm{O_2} is released when a new –CO–NH– bond forms.
Explanation: This question tests understanding of peptide bonds and their role in primary protein structure. Peptide bonds are covalent bonds formed between the carboxyl group of one amino acid and the amino group of another, playing a crucial role in the chain formation of polypeptides. In the provided scenario, the release of one water molecule per bond is highlighted, emphasizing the dehydration process. The correct choice A is accurate because it reflects water release upon –CO–NH– formation. A common misconception addressed by distractor B is that water is consumed, mixing with hydrolysis. To help students, instructors should use balanced equations. Practicing byproduct identification can reinforce learning.

Question 14

A pentapeptide has the sequence Gly-Cys-Pro-Asp-Lys. If this peptide is treated with trypsin under standard conditions, followed by complete acid hydrolysis, how many different amino acids will be recovered from the hydrolysis products?

  1. 3 amino acids, because trypsin cleaves after Lys, producing Gly-Cys-Pro-Asp and Lys as separate products
  2. 4 amino acids, because trypsin cleaves after Lys but Pro blocks the cleavage, leaving the pentapeptide intact
  3. 5 amino acids, because acid hydrolysis breaks all peptide bonds regardless of prior trypsin treatment (correct answer)
  4. 6 amino acids, because trypsin creates an additional Lys residue at the new C-terminus during cleavage
Explanation: The correct answer is C. Acid hydrolysis completely hydrolyzes all peptide bonds, breaking the peptide into individual amino acids regardless of any prior enzymatic treatment. The original pentapeptide contains 5 different amino acids (Gly, Cys, Pro, Asp, Lys), and complete acid hydrolysis will recover all 5. Trypsin treatment beforehand is irrelevant to the final outcome since acid hydrolysis is more aggressive and breaks all remaining bonds. Choice A incorrectly focuses only on trypsin products. Choice B incorrectly suggests Pro blocks trypsin cleavage (Pro affects cleavage efficiency but doesn't completely prevent it, and this is irrelevant anyway). Choice D incorrectly suggests trypsin creates new amino acids.

Question 15

A synthetic hexapeptide contains alternating hydrophobic and charged residues. When this peptide is dissolved in aqueous buffer at pH 7.0, it spontaneously forms β-sheet structures. If the same peptide sequence is synthesized with D-amino acids instead of L-amino acids, what is the most likely structural outcome?

  1. The D-peptide will form identical β-sheet structures because amino acid charge properties are unchanged by stereochemistry
  2. The D-peptide will form left-handed β-sheet structures instead of the typical right-handed structures formed by L-peptides
  3. The D-peptide will be unable to form regular β-sheet structures due to incompatible backbone geometry and steric clashes (correct answer)
  4. The D-peptide will form α-helical structures instead of β-sheets because D-amino acids favor helical conformations over extended conformations
Explanation: The correct answer is C. D-amino acids have opposite stereochemistry at the α-carbon compared to L-amino acids, which fundamentally alters the backbone geometry and φ/ψ angles accessible to the peptide. Regular β-sheet formation requires specific backbone conformations that are sterically accessible to L-amino acids but not to D-amino acids. The D-peptide cannot adopt the same extended conformations needed for proper β-sheet hydrogen bonding patterns. Choice A is wrong because while side chain properties are unchanged, backbone geometry is critical for secondary structure. Choice B is wrong because the issue isn't handedness but rather steric incompatibility. Choice D is wrong because D-amino acids don't preferentially favor α-helices; they face similar geometric constraints for all regular secondary structures.

Question 16

A researcher synthesizes two dipeptides: Ala-Pro and Pro-Ala. Both peptides are dissolved in water at pH 7.0 and analyzed by 1^1H NMR spectroscopy. Compared to Pro-Ala, the Ala-Pro dipeptide shows significantly broader NMR peaks for the proline residue. What is the most likely explanation for this observation?

  1. The proline residue in Ala-Pro undergoes faster chemical exchange between cis and trans conformations around the peptide bond
  2. The proline residue in Ala-Pro undergoes slower chemical exchange between cis and trans conformations around the peptide bond (correct answer)
  3. The proline residue in Ala-Pro is more highly solvated, leading to increased molecular tumbling and peak broadening
  4. The proline residue in Ala-Pro experiences stronger intramolecular hydrogen bonding, causing conformational averaging on the NMR timescale
Explanation: The correct answer is B. When proline is preceded by another amino acid (as in Ala-Pro), the peptide bond to proline exhibits restricted rotation due to the cyclic nature of proline's side chain. This creates a significant barrier to cis-trans isomerization, resulting in slower exchange between conformers. On the NMR timescale, this slow exchange causes peak broadening because the instrument detects both conformations but cannot resolve them as separate peaks. In Pro-Ala, the proline is at the N-terminus, so there's no preceding peptide bond to restrict. Choice A is incorrect because slower, not faster, exchange causes broadening. Choice C is incorrect because solvation effects wouldn't specifically affect proline differently in these two dipeptides. Choice D is incorrect because the issue is peptide bond rotation, not hydrogen bonding.

Question 17

A decapeptide is treated with cyanogen bromide (CNBr), which cleaves peptide bonds specifically after methionine residues. The treatment produces three fragments with the following compositions determined by amino acid analysis: Fragment 1 contains Met, Ala, Val; Fragment 2 contains Met, Gly, Pro, Leu; Fragment 3 contains Ser, Thr, Phe. What can be concluded about the original decapeptide?

  1. The original peptide contained exactly 2 methionine residues, with one at the C-terminus and one in the interior
  2. The original peptide contained exactly 2 methionine residues, both located in the interior of the sequence (correct answer)
  3. The original peptide contained exactly 3 methionine residues, with one at the C-terminus
  4. The original peptide contained exactly 1 methionine residue located in the interior of the sequence
Explanation: The correct answer is B. CNBr cleaves after methionine residues, and we observe 3 fragments. To produce 3 fragments from a single peptide, exactly 2 cleavages must have occurred, meaning exactly 2 methionine residues were present. Fragments 1 and 2 each contain methionine, which makes sense because CNBr cleavage leaves the methionine attached to the N-terminal side of each cleavage site. Fragment 3 contains no methionine, indicating it was the C-terminal fragment (after the last cleavage). Since Fragment 3 has no methionine, the C-terminus of the original peptide was not methionine. Choice A is wrong because if methionine were at the C-terminus, Fragment 3 would contain it. Choice C is wrong because 3 methionines would produce 4 fragments. Choice D is wrong because 1 methionine would produce only 2 fragments.

Question 18

A biochemist synthesizes a tetrapeptide with the sequence His-Cys-Met-Arg and measures its net charge at different pH values. At pH 6.0, the peptide has a net charge of +2. If the same tetrapeptide is cross-linked through disulfide bond formation between two peptide molecules, what would be the net charge of the resulting octapeptide at pH 6.0?

  1. The octapeptide would have a net charge of +4, representing the simple sum of two tetrapeptide charges (correct answer)
  2. The octapeptide would have a net charge of +2, because disulfide formation neutralizes positive charges
  3. The octapeptide would have a net charge of +3, because one positive charge is lost during disulfide bond formation
  4. The octapeptide would have a net charge of +6, because disulfide formation creates additional positive charges
Explanation: The correct answer is A. Disulfide bond formation between two cysteine residues involves the oxidation of their sulfur-containing side chains, creating a covalent S-S bridge. This reaction does not involve the gain or loss of protons, so it does not change the ionization state of any amino acid side chains or terminal groups. Each tetrapeptide contributes a +2 charge at pH 6.0, so two tetrapeptides linked by a disulfide bond would have a combined charge of +4. The disulfide bond formation only affects the tertiary structure through the covalent linkage, not the primary structure charge contributions. Choice B incorrectly suggests charge neutralization. Choice C incorrectly suggests charge loss. Choice D incorrectly suggests additional positive charges are created.

Question 19

A research team is studying a novel heptapeptide isolated from a marine organism. The peptide contains seven different amino acids: Ala, Cys, Glu, Lys, Pro, Trp, and Tyr. Initial characterization reveals that the peptide has unusual stability and resistance to proteolytic degradation.

The research team treats the heptapeptide with chymotrypsin under standard conditions and analyzes the products by mass spectrometry. They observe only two peaks corresponding to masses that sum to the original peptide mass plus water. If one fragment contains Trp and Pro, and the other contains Tyr and Cys, what additional information can be deduced about the peptide sequence?

  1. The peptide must have Ala, Glu, or Lys immediately following the Trp residue to allow chymotrypsin cleavage
  2. The peptide must have Pro immediately following either Trp or Tyr, preventing multiple cleavages by chymotrypsin
  3. The peptide contains exactly one chymotrypsin cleavage site, located between the fragments containing Trp and Tyr respectively (correct answer)
  4. The peptide must have both Trp and Tyr at the C-terminus of their respective fragments for chymotrypsin recognition
Explanation: The correct answer is C. Chymotrypsin cleaves peptide bonds after large aromatic amino acids (Phe, Trp, Tyr) and large hydrophobic amino acids (Leu). The observation of exactly two fragments indicates exactly one cleavage occurred. Since the peptide contains both Trp and Tyr (potential cleavage sites), but only one cleavage occurred, this suggests that only one of these residues was in a position to be cleaved by chymotrypsin. The fact that one fragment contains Trp and the other contains Tyr confirms that the cleavage occurred between these aromatic amino acids or their associated regions. Choice A is incorrect because it doesn't account for why only one cleavage occurred. Choice B is incorrect because while Pro can affect cleavage efficiency, the data shows cleavage did occur. Choice D is incorrect because chymotrypsin cleaves after (C-terminal to) aromatic residues, not necessarily at the fragment termini.

Question 20

A synthetic peptide has the sequence Asp-Pro-Gly-Phe-Leu-Ser. When this hexapeptide is subjected to automated Edman degradation, the process stops after the second cycle, yielding only two identifiable amino acids. What is the most likely explanation for the premature termination?

  1. The Gly residue at position 3 lacks a side chain, making it undetectable by the Edman chemistry
  2. The Pro residue at position 2 forms a stable cyclic intermediate that blocks further degradation (correct answer)
  3. The Phe residue at position 4 undergoes side reactions with the Edman reagents, terminating the sequence
  4. The peptide bond between Pro and Gly is unusually stable and resistant to the cyclization step
Explanation: The correct answer is B. Proline is known to cause problems in Edman degradation because its cyclic structure can lead to the formation of stable intermediates that resist the normal cyclization and cleavage steps of the Edman reaction. When proline is encountered during automated sequencing, it often causes the process to terminate prematurely or proceed with very low efficiency. The fact that two amino acids were identified (presumably Asp from cycle 1 and Pro from cycle 2) before termination is consistent with proline-induced problems. Choice A is incorrect because glycine can be detected in Edman degradation despite lacking a side chain. Choice C is incorrect because phenylalanine doesn't typically cause Edman sequencing problems. Choice D is incorrect because the issue is with the Edman chemistry itself, not peptide bond stability.