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Unformatted text preview: Problem Set 2 Please make sure to show your work and calculations and state any assumptions you make in answering the following questions. Include the names of the people you worked with at the top of your problem set. Problem 1: Genome sizes and data storage (35 points total) The NIH s National Center for Biotechnology Information (NCBI) provides a huge repository and a multitude of databases for biological information. NCBI Entrez's Genome page (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome)is a good starting place for resources on genome projects. Many biology textbooks also commonly discuss genomic size and its biological basis. 1 (a) Find the approximate size of the West Nile viral genome, the microbial Escherichia coli K12 genome, the Caenorhabditis elegans haploid genome, the haploid human genome and the Amoeba dubia genome in base pairs. (1 pt each, total of 5) West Nile virus: 10,962 bp http://www.ncbi.nlm.nih.gov:80/PMGifs/Genomes/vis.html Escherichia coli K12: 4.6 Mbp http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=115 Caenorhabditis elegans: 97 Mbp http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_search?chr=celegans.inf Human: 3.2 Gbp http://www.ncbi.nlm.nih.gov/genome/seq/page.cgi?F=HsProgress.shtml&ORG= Hs Amoeba dubia: 670 Gbp http://gnn.tigr.org/articles/02_01/Sizing_genomes.shtml 1(b) Find out the estimated total number of genes in each of the above organisms. (1 pt each, total of 5) NOTE: While the size of the genome for Amoeba dubia is known, an accurate estimate of the number of genes is not. For this case of 1(b), draw your conclusions based on a comparison of the complexity of the morphology of Amoeba dubia to the other organisms relative to the number of genes. West Nile virus: 9-11 genes http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=1149761 9&dopt=GenBank http://mbe.library.arizona.edu/data/1992/0904/8watt.pdf Escherichia coli K12: 4288 genes http://www.ncbi.nlm.nih.gov/entrez/utils/qmap.cgi?uid=97426617&form=6&db=m&Dopt=r Caenorhabditis elegans: 19,000 genes http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_search?chr=celegans.inf Human: 30,000-40,000 genes http://www.nature.com/genomics/human/papers/409860a0_fs_1.html Amoeba dubia: Unknown Due to estimates that vary with different sources, any estimates that approximate the above results is an acceptable answer. Because Amoeba dubia is unknown (as indicated in the note), full credit is given for either an unknown or a number supported by a literature reference. Is the size of genome proportional to the total number of genes? Give at least one reason why this is or is not the case.(4 points) Not precisely. Higher eukaryotes generally need larger genomes to accommodate the extra genes, but this is not precise (e.g., yeast, with a genome size of 12Mb or 0.004 times the size of the human genome, would be expected to have 0.004 * 80000 human genes = 320 genes, rather than it's 6000 genes, if its ratio of gene number to genome size...
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- Fall '02