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4.1 Protein Structure & Visualization — Test 1
Q1. The Protein Data Bank (PDB) is the primary repository for:✓ Experimentally determined 3D structures of biomolecules
Q2. A PDB file fundamentally contains:✓ The 3D atomic coordinates of the molecule
Q3. RasMol, Jmol and PyMOL are examples of:✓ Molecular visualisation (structure-viewing) tools
Q4. SCOP (Structural Classification of Proteins) organises proteins by their:✓ Structural and evolutionary relationships (fold, superfamily, family)
Q5. The CATH database classifies protein structures, and its name stands for:✓ Class, Architecture, Topology, Homologous superfamily
Q6. Common experimental methods for determining protein 3D structure include X-ray crystallography and:✓ NMR spectroscopy (and cryo-EM)
Q7. In a protein, common secondary-structure elements visualised in viewers are:✓ α-helices and β-sheets
Q8. A Ramachandran plot is used to assess a protein structure by showing:✓ The allowed combinations of backbone dihedral angles (phi, psi)
Q9. A protein domain is best described as a:✓ Compact, independently folding structural/functional unit
Q10. Each structure in the PDB is identified by a unique:✓ PDB ID code
Q11. The 'fold' of a protein refers to its:✓ Overall arrangement of secondary-structure elements in 3D
Q12. The fact that structure is more conserved than sequence means that two proteins can share a fold even when they:✓ Have low sequence identity
Q13. Cryo-electron microscopy (cryo-EM) has become important because it can determine structures of:✓ Large complexes that are hard to crystallise
Q14. In structure viewers, the 'cartoon' or 'ribbon' representation is used mainly to:✓ Show the overall fold and secondary structure clearly
Q15. SCOP and CATH differ in that CATH is:✓ More automated, while SCOP relied more on expert manual curation
Q16. Supersecondary structures (motifs) such as the β-hairpin are:✓ Simple combinations of a few secondary-structure elements
Q17. Knowing a protein's 3D structure is valuable because structure largely determines:✓ Function (including active sites and binding)
Q18. The hierarchy of SCOP places proteins into class, then fold, then:✓ Superfamily, then family
Q19. Structural bioinformatics relies on the PDB mainly to:✓ Provide structures for analysis, comparison and prediction
Q20. Match each structural resource/tool with its purpose and select the correct option.✓ A-ii, B-i, C-iv, D-iii