Secondary structure assignment MCQs With Answer

Introduction:
Secondary structure assignment MCQs With Answer is a concise revision resource tailored for M.Pharm students studying Bioinformatics and Computational Biotechnology. This collection focuses on methods and principles used to assign protein secondary structures from three-dimensional coordinates, including widely used algorithms (DSSP, STRIDE, P-SEA), hydrogen-bond patterns, phi/psi torsion angles, and distinctions among helices, sheets, turns, and coils. Carefully designed questions probe both conceptual understanding and practical algorithmic criteria, helping students link structural assignments to applications such as homology modeling, structure validation, and structure-based drug design. Each question includes clear options and the correct answer to aid efficient exam preparation and deeper learning.

Q1. What is meant by secondary structure assignment in protein structural analysis?

• Predicting secondary structure from primary sequence using neural networks
• Assigning local backbone conformations (helix, sheet, turn) based on 3D coordinates
• Calculating tertiary folds from secondary structure elements
• Annotating functional sites on the protein surface

Correct Answer: Assigning local backbone conformations (helix, sheet, turn) based on 3D coordinates

Q2. In the DSSP algorithm, what is the commonly used hydrogen-bond energy cutoff for considering an interaction significant?

• -0.1 kcal/mol
• -0.5 kcal/mol
• -2.0 kcal/mol
• -10.0 kcal/mol

Correct Answer: -0.5 kcal/mol

Q3. Which principle distinguishes STRIDE from DSSP when assigning secondary structures?

• STRIDE uses only C-alpha positions while DSSP uses full backbone atoms
• STRIDE combines hydrogen-bond information with backbone torsion-angle statistical potentials
• STRIDE assigns secondary structure based solely on solvent accessibility
• STRIDE is sequence-based whereas DSSP is structure-based

Correct Answer: STRIDE combines hydrogen-bond information with backbone torsion-angle statistical potentials

Q4. Who are the authors associated with the original DSSP algorithm for secondary structure assignment?

• Kabsch and Sander
• Jones and Thornton
• Levinthal and Anfinsen
• Baker and Vendruscolo

Correct Answer: Kabsch and Sander

Q5. What hydrogen-bonding pattern defines a 3-10 helix?

• i → i+4 hydrogen bond
• i → i+3 hydrogen bond
• i → i+5 hydrogen bond
• No regular hydrogen bonds

Correct Answer: i → i+3 hydrogen bond

Q6. Which hydrogen-bond pattern corresponds to a pi (π) helix?

• i → i+3
• i → i+4
• i → i+5
• i → i+7

Correct Answer: i → i+5

Q7. How does a beta-bridge differ from an extended beta-strand in sheet assignment?

• Beta-bridge involves a single residue forming a short helix
• Beta-bridge is an isolated single hydrogen-bonded residue pair between strands
• Beta-bridge indicates a residue in a loop region with no hydrogen bonds
• Beta-bridge requires at least four consecutive residues with i→i+4 bonds

Correct Answer: Beta-bridge is an isolated single hydrogen-bonded residue pair between strands

Q8. Typical backbone phi/psi angles for an ideal right-handed alpha-helix cluster around which values?

• phi ≈ -60°, psi ≈ -45°
• phi ≈ -135°, psi ≈ 135°
• phi ≈ 60°, psi ≈ 45°
• phi ≈ 0°, psi ≈ 180°

Correct Answer: phi ≈ -60°, psi ≈ -45°

Q9. Which of the following methods is designed to assign secondary structure using only C-alpha atom coordinates?

• DSSP
• STRIDE
• P-SEA
• DSSP-C implemented by Kabsch & Sander

Correct Answer: P-SEA

Q10. How many residues per turn are there approximately in an alpha-helix?

• 2.7 residues per turn
• 3.6 residues per turn
• 4.4 residues per turn
• 5.0 residues per turn

Correct Answer: 3.6 residues per turn

Q11. In DSSP one-letter codes, which code denotes a 3-10 helix?

• H
• G
• I
• E

Correct Answer: G

Q12. What is the main difference between secondary structure prediction and secondary structure assignment?

• Prediction uses X-ray coordinates; assignment uses only sequence
• Prediction is performed on RNA; assignment is for proteins
• Assignment derives structure labels from experimental 3D coordinates; prediction infers labels from sequence
• There is no difference; the terms are interchangeable

Correct Answer: Assignment derives structure labels from experimental 3D coordinates; prediction infers labels from sequence

Q13. Which amino acid is most commonly considered a strong helix breaker and often terminates helices?

• Alanine
• Leucine
• Proline
• Glycine

Correct Answer: Proline

Q14. How do hydrogen bonds differ between parallel and antiparallel beta-sheets?

• Parallel sheets have linear hydrogen bonds; antiparallel have angled hydrogen bonds
• Antiparallel sheets have nearly linear hydrogen bonds; parallel sheets have slightly skewed hydrogen bonds
• There is no hydrogen bonding in parallel sheets
• Both have identical hydrogen bond geometry

Correct Answer: Antiparallel sheets have nearly linear hydrogen bonds; parallel sheets have slightly skewed hydrogen bonds

Q15. In DSSP notation which code is used for an extended strand that participates in a beta-sheet?

• B
• E
• C
• T

Correct Answer: E

Q16. In secondary structure annotation, what does the term “coil” generally refer to?

• A left-handed helix region
• A regular beta-strand with two hydrogen bonds
• Irregular or unstructured regions not assigned as helix, sheet or turn
• A region of permanent disorder in the primary sequence

Correct Answer: Irregular or unstructured regions not assigned as helix, sheet or turn

Q17. Why do different assignment algorithms (DSSP, STRIDE, P-SEA) sometimes give different secondary structure labels for the same protein?

• Because experimental coordinates are always incorrect
• Because each algorithm uses different geometric criteria, energy functions and cutoffs to define structures
• Because secondary structure is independent of atomic coordinates
• Because some algorithms use nucleotide sequences instead of amino acid sequences

Correct Answer: Because each algorithm uses different geometric criteria, energy functions and cutoffs to define structures

Q18. Which program explicitly incorporates knowledge-based torsion angle potentials into its assignment scheme?

• DSSP
• STRIDE
• PDBsum
• MolProbity

Correct Answer: STRIDE

Q19. According to common DSSP criteria, what is the minimum number of consecutive residues typically required to define an alpha-helix segment?

• 2 residues
• 3 residues
• 4 residues
• 6 residues

Correct Answer: 4 residues

Q20. Which of the following is NOT a direct application of accurate secondary structure assignment in pharmaceutical research?

• Guiding homology model building for target proteins
• Designing helix-stabilizing peptidomimetics for protein–protein interaction inhibitors
• Predicting a compound’s metabolic half-life in liver microsomes
• Refining docking constraints for structure-based ligand design

Correct Answer: Predicting a compound’s metabolic half-life in liver microsomes

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