110.PS3.09 - 2009 MCB 110 Problem set 3. Genomes,...

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2009 1/2 MCB 110 Problem set 3. Genomes, bioinformatics and DNA repair 1. Over a third of the human genome is made up of LINEs and SINEs. a) What is the difference between a LINE and a SINE? b) What is the evidence that many human pseudogenes arise from RNA intermediates? 2. The most commonly mutated human disease gene is APC (adenomatous polyposis coli), which is altered in 75% of colon cancers. a) Using the web (e.g. Entrez-Protein), find the sequence for the human APC protein. What are the first 5 amino acids in the protein sequence? b) Find the nucleotide sequence of the APC gene (Hint: an accession number for the gene is gi:182396) and display it with the Graphics option in Entrez Nucleotide. Design two PCR primers to amplify the segment coding for the first 55 amino acids of the protein, starting with the initiator met (ATG) and ending with Ile55 (ATT). The primers should have calculated melting temperatures of ~56 ºC, using the formula, Tm=a(GC) x 4º + b(AT) x 2º, where a(GC) and
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110.PS3.09 - 2009 MCB 110 Problem set 3. Genomes,...

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