Packet 9: Bonus 7
Margaret Dayhoff developed a substitution matrix called PAM (“pam”) whose 20 rows and 20 columns each represent one of these molecules. For 10 points each:
[10m] Name these molecules that may be referred to as residues. One of these molecules symbolized W has an indole group as its side chain.
ANSWER: amino acids [prompt on amines; prompt on carboxylic acids; reject “proteins” or “peptides” or “polypeptides”] (W is tryptophan.)
[10e] The PAM matrix is named for the “point accepted” form of these phenomena, the replacement of one amino acid by another. The “silent” form of these genetic alterations results in no phenotypic change.
ANSWER: mutations [accept silent mutations; accept point accepted mutations]
[10h] This algorithm developed by the National Center for Biotechnology Information uses PAM matrices for scoring. This algorithm superseded FASTA (“fast A”) and allows users to compare a query to a database of sequences.
ANSWER: BLAST [or basic local alignment search tool; prompt on basic local alignment or sequence alignment]
<Editors, Biology> | Packet I
| Editions | Heard | PPB | Easy % | Medium % | Hard % |
|---|---|---|---|---|---|
| 2 | 120 | 16.67 | 88% | 58% | 22% |
Conversion
| Team | Opponent | Part 1 | Part 2 | Part 3 | Total | Parts |
|---|---|---|---|---|---|---|
| Carleton B | Carleton A | 10 | 10 | 0 | 20 | ME |
| McGill A | McGill B | 10 | 10 | 0 | 20 | ME |
| McGill C | Ottawa B | 10 | 10 | 0 | 20 | ME |
| McGill E | Ottawa C | 10 | 10 | 0 | 20 | ME |
| Ottawa D | Ottawa A | 10 | 10 | 0 | 20 | ME |
Summary
| Tournament | Edition | Exact Match? | Heard | PPB | Easy % | Medium % | Hard % |
|---|---|---|---|---|---|---|---|
| UK (North) | UK | Y | 5 | 10.00 | 60% | 40% | 0% |
| UK (South) | UK | Y | 8 | 20.00 | 100% | 75% | 25% |
| Northern California | US | Y | 4 | 22.50 | 100% | 100% | 25% |
| Southern California | US | Y | 6 | 21.67 | 83% | 83% | 50% |
| Eastern Canada (1) | US | Y | 5 | 20.00 | 100% | 100% | 0% |
| Eastern Canada (2) | US | Y | 9 | 15.56 | 89% | 56% | 11% |
| Florida | US | Y | 4 | 10.00 | 100% | 0% | 0% |
| Great Lakes | US | Y | 12 | 18.33 | 92% | 75% | 17% |
| Lower Mid-Atlantic | US | Y | 9 | 23.33 | 100% | 67% | 67% |
| Upper Mid-Atlantic | US | Y | 2 | 5.00 | 50% | 0% | 0% |
| Midwest | US | Y | 9 | 17.78 | 89% | 56% | 33% |
| North | US | Y | 4 | 12.50 | 75% | 50% | 0% |
| Northeast | US | Y | 10 | 15.00 | 90% | 40% | 20% |
| Pacific | US | Y | 8 | 15.00 | 88% | 63% | 0% |
| South Central | US | Y | 7 | 14.29 | 71% | 29% | 43% |
| Southeast | US | Y | 13 | 15.38 | 85% | 54% | 15% |
| Upstate NY | US | Y | 5 | 14.00 | 80% | 40% | 20% |