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2.3 Motif, Family & Specialized Databases — Test 1
Q1. PROSITE, often cited as the first secondary database, is a database of protein:✓ Patterns and motifs (signatures)
Q2. Pfam is a database of protein families that are represented using:✓ Hidden Markov model (HMM) profiles
Q3. InterPro is best described as a database that:✓ Integrates several member databases (PROSITE, Pfam, PRINTS, etc.) into one resource
Q4. The Gene Ontology (GO) provides a controlled vocabulary organised into three domains, one of which is:✓ Molecular function
Q5. KEGG is a specialized database resource focused on:✓ Metabolic pathways and enzymes
Q6. STRING is a specialized database that stores information on:✓ Protein-protein interactions
Q7. PubChem is a specialized database that holds:✓ Chemical structures and bioactivity data
Q8. GEO (Gene Expression Omnibus) is a repository for:✓ Gene-expression and functional genomics data
Q9. SAGE, in the context of expression databases, refers to a method/data type based on:✓ Counting short sequence tags to quantify gene expression
Q10. ProDom is a database of protein:✓ Domains, generated automatically from sequence data
Q11. PRINTS is a secondary database based on protein:✓ Fingerprints (groups of conserved motifs)
Q12. The three domains of the Gene Ontology are molecular function, cellular component and:✓ Biological process
Q13. A key advantage of an integrated resource like InterPro is that it:✓ Lets users search many family/motif databases at once for consistent annotation
Q14. Sequence-motif and family databases (PROSITE, Pfam, PRINTS) are classed as secondary databases because they are:✓ Derived by analysing data from primary databases
Q15. The KEGG ENZYME database specifically organises information about:✓ Enzymes and the reactions they catalyse
Q16. Gene Ontology annotations are valuable mainly because they:✓ Provide standardised, computer-readable descriptions of gene-product roles
Q17. Databases such as SCOP and CATH are used to classify proteins by their:✓ Structural relationships (fold and family)
Q18. A PROSITE pattern is often expressed as a:✓ Regular expression describing conserved residues
Q19. Specialized databases like KEGG, STRING and GEO are important because they:✓ Organise particular types of biological data for focused analysis
Q20. Match each specialized database with its content and select the correct option.✓ A-iii, B-i, C-iv, D-ii