Peptide Bonds and Protein Primary Structure (1A) - Bio & Biochem

1. What is the most common configuration of the peptide bond in proteins?

   Trans configuration. Minimizes steric hindrance between side chains, making it energetically favorable in most peptide bonds except near proline.

2. Which amino acid most commonly increases cis peptide bond occurrence in proteins?

   Proline. Its cyclic side chain reduces the energy difference between cis and trans, allowing cis configurations more frequently.

3. What is the name of a peptide consisting of two amino acid residues?

   Dipeptide. Consists of exactly two amino acids joined by one peptide bond, representing the smallest polypeptide unit.

4. Which bond is cleaved during proteolysis to break a polypeptide into smaller peptides?

   Peptide (amide) bond hydrolysis. Enzymatic cleavage adds water across the amide bond, reversing condensation to degrade proteins into smaller fragments.

5. What is the net number of water molecules released when $n$ amino acids form one linear peptide?

   $n-1$ molecules of $H_2O$. Each peptide bond formation eliminates one water molecule, so for $n$ amino acids, $n-1$ bonds release that many waters.

6. What partial-bond character makes the peptide bond rigid and planar?

   Partial double-bond character from resonance. Arises from electron delocalization between the carbonyl and nitrogen, restricting rotation and enforcing planarity.

7. What reaction forms a peptide bond between two amino acids?

   Condensation (dehydration) reaction releasing $H_2O$. Involves the loss of a water molecule as the carboxyl group of one amino acid reacts with the amino group of another to form the amide linkage.

8. Which atoms define the peptide bond linkage in the backbone?

   Carbonyl carbon ($C=O$) bonded to amide nitrogen ($N$). Constitutes the amide linkage where the carbonyl carbon from one residue covalently attaches to the nitrogen of the next.

9. Which terminus of a polypeptide has the free carboxyl group under physiological conditions?

   $C$-terminus (typically $COO^-$). Marks the end of the chain where the last amino acid's carboxyl group remains unlinked and deprotonated at physiological pH.

10. What is the name for amino acids after they have been incorporated into a polypeptide chain?

    Amino acid residues. Refers to amino acids that have lost water during peptide bond formation and are now integral parts of the chain.

11. Which terminus of a polypeptide has the free amino group under physiological conditions?

    $N$-terminus (typically $NH_3^+$). Represents the starting point of the chain where the first amino acid's amino group remains unlinked and protonated at physiological pH.

12. Identify the repeating backbone unit of a polypeptide (excluding side chains).

    ...$N$C_$C$... or ...$N$-C_-$C$... pattern. Reflects the polypeptide backbone's repeating motif where nitrogen bonds to alpha carbon, which bonds to carbonyl carbon.

13. What is the definition of a protein's primary structure?

    Linear amino acid sequence linked by peptide bonds. Determines the unique identity and function of the protein, as it specifies the order of residues that dictates higher-order folding.

14. What is the name of a peptide consisting of three amino acid residues?

    Tripeptide. Comprises three amino acids connected by two peptide bonds, serving as a basic model for studying peptide properties.

15. How many peptide bonds are present in a linear peptide containing $n$ amino acid residues?

    $n-1$ peptide bonds. In a chain of $n$ residues, each internal linkage is a peptide bond, totaling one less than the number of residues.

16. What is the name for a short chain of amino acids, typically fewer than about $50$ residues?

    Oligopeptide (short peptide). Describes peptides with a limited number of residues, often functioning as signaling molecules or hormones in biology.

17. Which backbone bond rotation is restricted by peptide bond resonance?

    Rotation about the $C-N$ peptide bond. Resonance stabilization imparts partial double-bond nature, limiting free rotation and contributing to backbone rigidity.

18. Find the number of peptide bonds and released waters when $7$ amino acids form one linear peptide.

    $6$ peptide bonds and $6$ molecules of $H_2O$. For 7 residues, 6 internal linkages form, each releasing one water molecule during condensation synthesis.

19. Which functional groups directly react to form a peptide bond in proteins?

    Carboxyl group of one amino acid and amino group of the next. These groups undergo dehydration synthesis, eliminating water to establish the covalent amide bond in the protein chain.

20. Which backbone bonds primarily provide conformational flexibility in polypeptides?

    Rotation about N-C_ ($$) and $C_-C$ ($$) bonds. These single bonds allow torsional flexibility, enabling diverse conformations in the protein's secondary and tertiary structures.

21. Which option correctly lists termini for the sequence $NH_3^+$-Ala-Gly-Ser-$COO^-$$?

    $N$-terminus = Ala end; $C$-terminus = Ser end. The sequence starts with alanine's free amino group at the N-end and ends with serine's free carboxyl at the C-end.

22. What is the correct direction for writing a protein primary structure sequence?

    $N$-terminus to $C$-terminus. Convention dictates starting from the amino end to the carboxyl end, reflecting the direction of protein synthesis in ribosomes.

23. What type of covalent bond links amino acids together in a polypeptide chain?

    Peptide (amide) bond between the $$-carboxyl and $$-amino groups. Forms via condensation between the carboxyl group of one amino acid and the amino group of another, creating a rigid linkage in the polypeptide backbone.

24. What is the name of the covalent linkage formed between a carbonyl carbon and an amide nitrogen?

    Amide bond (peptide bond in proteins). Results from nucleophilic attack by the amino nitrogen on the carbonyl carbon, forming a stable covalent connection in peptides.

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