A program of ITEST (Information Technology Experiences for Students and Teachers) funded by the National Science Foundation Background Session #3 DNA &

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A program of ITEST (Information Technology Experiences for Students and Teachers) funded by the National Science Foundation Background Session #3 DNA & Protein Sequences May 17, 2008 Henrik Kibak Associate Professor of Biology California State University, Monterey Bay

May 17th Workshop2 Background for homework… Cytochrome c is a peripheral membrane protein that “floats” on the inner mitochondrial membrane, shuttling electrons from Complex III to Complex IV of the Electron Transport Chain.

May 17th Workshop3 Background for homework…

May 17th Workshop4 Background for homework… Using the amino acid single letter code, write the primary structure of the Cytochrome c found in your organism. >gi| |sp|P99999|CYC_HUMAN Cytochrome c MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLE NPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE t=fasta&dispmax=5&sendto=&from=begin&to=end&extrafeatpresent=1&ef_CDD=8&ef_MGC=16&ef_HPRD=32 &ef_STS=64&ef_tRNA=128&ef_microRNA=256&ef_Exon=512

May 17th Workshop5 Background for homework… Molecular weight = Residues = 105 ResidueNumberMole% A = Ala C = Cys D = Asp E = Glu F = Phe G = Gly H = His I = Ile K = Lys L = Leu M = Met N = Asn P = Pro Q = Gln R = Arg S = Ser T = Thr V = Val W = Trp Y = Tyr PropertyResiduesNumberMole% Non-polar(A+C+F+G+I+L+M+P+V+W+Y) Polar(D+E+H+K+N+Q+R+S+T) In humans there are about 52% hydrophobic amino acids in Cytochrome c. How many in your organism???

May 17th Workshop6 Background for homework… protein&dopt=GenPept&WebEnv=0HG83JukV9Q2uqf0xv_Qxhcv- KIa_I1CBqM3hBlgCpS3cE2lNXj-FwEEdz- %40D E0E590_2646SID&WebEnvRq=1&term=&tool=query&qty =1

May 17th Workshop7 Background for homework… You may use the NCBI website to obtain DNA and Protein sequence data. However, Cytochrome c is such a well-studied protein, that there is a vast number of other websites with good information.

May 17th Workshop8 Background for homework…

May 17th Workshop9 Background for homework… Protein Sequence DNA Sequence

May 17th Workshop10 Background for homework… Working with sequences can be a nightmare or a pleasure… depending upon whether you follow these rules: 1.Always work with single letter code and in Courier font!!! 2.Don’t make your sequence alignments too wide… 50 characters across is enough. 3.Color your sequences by species before you begin your multiple alignments… trust us! Organism #1 ATGGGT GATGTTGAGAAAGGCAAGAAGATTT Organism #2 ATGGGTATTCCTGCGGGTGATCCAGAAAAAGGAAAAAAGATTT Organism #3 ATGTGAATTCAGGCCGGTTATCCTAAGAAAGGTGCTACACTTT