amino acids - 2025 ACF Fall

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 This algorithm superseded FASTA (“fast A”) and allows users to compare a query to a database of sequences.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


Berkeley Boss Bandit	Berkeley Mighty Miner	10	10	0	20
Stanford B	Berkeley Archer Queen	10	10	10	30
Berkeley Little Prince	Stanford A	10	10	0	20
Berkeley Skeleton King	UCSC	10	10	0	20
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
Carleton B	Carleton A	10	10	0	20
McGill A	McGill B	10	10	0	20
McGill C	Ottawa B	10	10	0	20
McGill E	Ottawa C	10	10	0	20
Ottawa D	Ottawa A	10	10	0	20
Toronto F	Queen's A	10	10	0	20
McMaster B	Toronto E	10	10	0	20
McMaster C	Toronto I	10	10	0	20
McMaster A	Toronto B	10	10	10	30
Toronto G	Guelph A	0	10	0	10
Toronto H	Brock A	0	0	0	0
Waterloo A	Toronto D	10	10	0	20
Waterloo B	Waterloo C	0	10	0	10
Toronto C	Toronto A	0	10	0	10
Florida A	Florida B	0	10	0	10
ERAU Daytona A	Florida Tech B	0	10	0	10
South Florida A	Florida State A	0	10	0	10
UCF A	Florida Tech A	0	10	0	10
CWRU B	Louisville A	10	10	10	30
Michigan A	CWRU A	10	10	0	20
Louisville D	Kentucky	10	10	0	20
Michigan State A	Michigan B	10	10	0	20
Louisville B	Michigan C	0	10	0	10
Ohio State A	Michigan State B	10	10	0	20
CWRU C	Ohio State C	10	10	0	20
Ohio State D	Louisville C	10	0	0	10
Pittsburgh	Michigan D	0	10	0	10
Michigan State C	WVU A	0	10	0	10
WVU B	Michigan State D	10	10	10	30
CWRU D	Ohio State B	10	10	0	20
Liberty A	Duke A	0	10	0	10
Liberty B	JMU B	10	10	0	20
NCSU B	Liberty C	0	10	0	10
UNC A	NCSU A	10	10	10	30
Virginia Tech C	UNC C	0	10	10	20
VCU A	UNC B	10	10	10	30
Virginia A	William & Mary A	10	10	10	30
Virginia Tech A	Virginia Tech B	10	10	10	30
William & Mary B	William & Mary C	10	10	10	30
George Mason A	Maryland A	0	10	0	10
Rutgers A	Maryland C	0	0	0	0
Iowa A	Chicago A	10	10	0	20
Illinois Urbana	Chicago B	0	10	0	10
Purdue C	Purdue A	0	10	0	10
Purdue B	Iowa B	10	10	10	30
Rose-Hulman A	William Woods University A	10	0	0	10
Indiana B	WashU Grizzlers	0	10	0	10
WashU Grolars	Purdue D	0	10	0	10
Illinois Blue	Illinois Champaign	10	10	10	30
Iowa State	Macalester	10	10	0	20
Michigan Tech	Wisconsin B	0	0	0	0
St. Thomas	Wisconsin A	0	10	0	10
Wisconsin C	Minnesota	10	10	0	20
Illinois Canada	Indiana A	10	10	10	30
Brown A	Amherst A	0	10	0	10
Dartmouth B	Brown B	0	10	0	10
Vermont B	Dartmouth A	0	10	0	10
Williams C	Harvard	0	0	0	0
Brandeis Beethoven	MIT B	10	10	0	20
Tufts B	UConn A	10	10	0	20
Brandeis Mozart	Williams B	0	10	0	10
Amherst B	Tufts C	10	10	10	30
MIT A	Boston College A	10	10	10	30
Boston University A	Brandeis Bach	0	10	0	10
Alberta A	Washington Steelhead	10	10	0	20
Arizona State B	Washington Coho	0	10	0	10
Washington Masu	Boise State	0	10	0	10
British Columbia A	Texas	0	10	0	10
British Columbia B	Washington Atlantic	10	0	0	10
Washington Chum	British Columbia C	10	10	0	20
Washington Pink	Washington Sockeye	10	10	0	20
Washington State	Arizona State A	10	10	0	20
Kansas State A	Central Oklahoma B	10	0	0	10
Kansas State B	Rose State	0	0	0	0
Murray State College B	Nebraska C	0	10	10	20
Nebraska B	Central Oklahoma A	0	10	10	20
Oklahoma	Murray State College A	0	10	0	10
Tulsa A	Nebraska A	10	10	10	30
Tulsa B	Harding	0	10	0	10
Auburn B	Auburn A	0	10	10	20
Chipola College	Alabama A	0	10	0	10
Clemson B	Clemson C	10	10	0	20
Georgia A	Tennessee Tech	10	10	0	20
Georgia Tech F	Georgia Tech B	10	10	0	20
Georgia Tech C	Clemson A	0	10	0	10
Georgia Tech D	Montevallo	0	0	0	0
Emory A	Georgia Tech E	10	10	0	20
South Carolina A	Vanderbilt A	10	10	10	30
Georgia Tech A	Tennessee A	10	10	0	20
Tennessee B	Sewanne	0	0	0	0
Vanderbilt C	Vanderbilt B	0	10	0	10
Auburn C	Mississippi State A	10	10	0	20
Edinburgh B	Durham D	0	10	0	10
Durham B	Sheffield A	0	0	0	0
York	Edinburgh D	0	10	0	10
Durham A	Edinburgh A	10	0	0	10
Edinburgh C	Durham C	10	10	0	20
Birmingham	Southampton	0	10	0	10
Cambridge D	Bristol	10	10	10	30
Imperial B	Cambridge C	10	10	0	20
Cambridge B	Cardiff	10	10	0	20
Warwick	Imperial A	10	10	0	20
Imperial C	LSE	0	10	0	10
Cambridge E	Imperial D	10	10	0	20
Cambridge A	Oxford	10	10	10	30
Cornell B	Binghamton C	0	10	0	10
Cornell A	ESF	10	0	0	10
Cornell D	RIT B	10	10	10	30
Cornell C	RIT A	0	10	0	10
Binghamton B	Rochester	0	10	0	10