amino acids - Southern California

Question

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 This algorithm superseded FASTA (“fast A”) and allows users to compare a query to a database of sequences.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>

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Summary


Northern California	Main	Y	4	22.50	100%	100%	25%
Southern California	Main	Y	6	21.67	83%	83%	50%
Eastern Canada (1)	Main	Y	5	20.00	100%	100%	0%
Eastern Canada (2)	Main	Y	9	15.56	89%	56%	11%
Florida	Main	Y	4	10.00	100%	0%	0%
Great Lakes	Main	Y	12	18.33	92%	75%	17%
Lower Mid-Atlantic	Main	Y	9	23.33	100%	67%	67%
Upper Mid-Atlantic	Main	Y	2	5.00	50%	0%	0%
Midwest	Main	Y	9	17.78	89%	56%	33%
North	Main	Y	4	12.50	75%	50%	0%
Northeast	Main	Y	10	15.00	90%	40%	20%
Pacific	Main	Y	8	15.00	88%	63%	0%
South Central	Main	Y	7	14.29	71%	29%	43%
Southeast	Main	Y	13	15.38	85%	54%	15%
UK (North)	UK	Y	5	10.00	60%	40%	0%
UK (South)	UK	Y	8	20.00	100%	75%	25%
Upstate NY	Main	Y	5	14.00	80%	40%	20%

Data


Claremont B	Claremont A	10	10	0	20
UCSD A	UC Santa Barbara	10	10	10	30
USC A	UCLA A	0	0	0	0
UCLA B	UCLA D	10	10	0	20
UCLA C	UCSD B	10	10	10	30
UC Irvine	UCLA F	10	10	10	30