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3.3 Scoring Matrices & Gap Penalties — Test 1
Q1. A substitution (scoring) matrix is used in alignment to:✓ Assign scores for aligning one residue with another
Q2. The PAM series of matrices was developed by:✓ Margaret Dayhoff (from observed point mutations)
Q3. The BLOSUM series of matrices is derived from:✓ Conserved blocks of aligned protein sequences
Q4. For BLOSUM matrices, a LOWER number (e.g. BLOSUM45 vs BLOSUM80) is designed for:✓ More distantly related sequences
Q5. For PAM matrices, a HIGHER number (e.g. PAM250 vs PAM30) is appropriate for:✓ More distantly related sequences
Q6. BLOSUM62, a commonly used default matrix, is suited to:✓ Moderately related protein sequences
Q7. In a scoring matrix, a positive score for a pair of residues indicates that the substitution is:✓ Favourable / commonly observed in related proteins
Q8. A gap penalty in alignment scoring is applied to:✓ Discourage the insertion of gaps
Q9. With affine gap penalties, the cost of opening a gap is usually:✓ Greater than the cost of extending it
Q10. Choosing an appropriate scoring matrix matters because the matrix should match the:✓ Evolutionary distance between the sequences
Q11. The diagonal of a substitution matrix (a residue aligned with itself) generally has:✓ The highest (most positive) scores
Q12. For DNA alignments, a simple scoring scheme often uses:✓ A fixed reward for a match and penalty for a mismatch
Q13. PAM and BLOSUM matrices differ in their construction in that BLOSUM is based on:✓ Directly observed substitutions in conserved blocks
Q14. A scoring matrix gives a conservative substitution (e.g. Leu↔Ile) a score that is:✓ Positive (because such swaps are common and well tolerated)
Q15. Using too low a gap penalty in an alignment tends to produce:✓ Many gaps, possibly creating an artificial alignment
Q16. The overall purpose of a scoring scheme (matrix plus gap penalties) is to:✓ Quantify alignment quality so the best alignment can be chosen
Q17. For comparing two very closely related proteins, the most appropriate matrix would be:✓ A low-divergence matrix (e.g. BLOSUM80 or PAM30)
Q18. In DNA scoring, distinguishing transitions from transversions can be useful because transitions:✓ Occur more frequently and may be penalised less
Q19. The reason scoring matrices are essential to BLAST and alignment tools is that they:✓ Provide the biological basis for ranking matches
Q20. Match each scoring concept with its description and select the correct option.✓ A-iv, B-iii, C-i, D-ii