13Practset1answers - Practice question#1 reading frame#1...

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#1 5' ... C G T T A C C G T T C G A G A A C T T G T G C A ... 3' #2 5' ... C G A T A C C A T T T G A T A A T C T G T G T A ... 3' “reading frame #1” Could look for an initiation codon, but it might be further upstream…. “reading frame #2” #1 5' ... C G T T A C C G T T C G A G A A C T T G T G C A ... 3' #2 5' ... C G A T A C C A T T T G A T A A T C T G T G T A ... 3' “reading frame #3” So divide into possible reading frames… Practice question #1 Any potential stop codons (to exclude any frames)?? If protein- coding sequence under strong functional constraint… might expect (mostly) silent nt substitutions between #1 and #2… and conservative amino acid substitutions Leu Ile Pro Pro Phe Phe Glu Asp etc ....
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# non-syn sites = 600 x 75% = 450 What if protein Y is rich in methionine? What type of protein would have a relatively low number of non-synonymous sites ? Protein Y coding sequence = 200 x 3 = 600 nt then expect higher # non-syn sites... because any change to AUG triplet will alter amino acid encoded Note however, that number of non- synonymous
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