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← Theoretical A

Q6 — Ramachandran Plot and Peptide Bond Geometry

Theoretical A Real exam question — full text reproduced under IBO's CC BY-NC-SA 4.0 license
Protein Structure, Folding & Function

The bonds between the central carbon atom and attached groups in peptides can rotate freely. The rotation angles of the N-Cα and Cα-C bonds are called φ (phi) and ψ (psi) angles, respectively. To measure the φ angle, first draw the Cα-C bond horizontally so that the N group is at 0 degrees (in the same plane as the Cα-C bond). Then rotate the distal N group around the Cα-C bond until the structure matches the structure that you aim to measure as shown in Figure 1C. For the ψ angle, place the N-Cα bond horizontally and rotate the distal C group. The Ramachandran plot visually represents the combinations of φ and ψ angles in a peptide backbone (Figure 1B).

Panel A: a peptide backbone segment with the φ and ψ angles labeled. Panel B: a Ramachandran plot for rabbit pyruvate kinase (excluding glycine) with three labeled favored regions. Panel C: a diagram illustrating how the φ angle is defined by bond rotation. Panel D: three amino-acid residue structures (a, b, c) whose φ/ψ angles must be identified and placed on the plot. Figure 1. A Part of the peptide with shown φ and ψ angles. B The Ramachandran plot with the values of φ and ψ angles for all the amino acid residues except Gly in the rabbit’s pyruvate kinase. C The φ angle values are created by the rotation. D Three structures of amino acids’ residues.

On your answer sheet, indicate “T” for true statements and “F” for false ones.

A. The structure (a) in Figure 1D is located in Region 2 in Figure 1B.
B. The structure (b) in Figure 1D is located in Region 3 in Figure 1B.
C. The structure (c) in Figure 1D is uncommon in rabbit's pyruvate kinase.
D. Amino acids, other than glycine, with 0 degrees of both φ and ψ angles do not occur in rabbit's pyruvate kinase.
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Question reproduced from IBO 2024, Theoretical Exam Part A, licensed under CC BY-NC-SA 4.0 — attributed to the International Biology Olympiad. Open the full exam PDF · Community solutions (unofficial)