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8.3 and 15.3 notes C-value Paradox.docx

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Western University
Biology 1001A
Tom Haffie

i) go online to learn about the "C-value Paradox" (more recently renamed the "C-value Enigma"). ii) learn about genome projects in Section 15.3b in Biology: Exploring the Diversity of Life. Have a good look at the trends in Table 15.1. iii) learn about "ploidy" in Section 8.3a in Biology: Exploring the Diversity of Life. C-value Paradox - 15.3 Genome Analysis - The Human Genome Project (HGP) The complete sequencing of the 3billion base-pair human genome 15.3a DNA-Sequencing Techniques Are Based on DNA Replication Sanger Method - Based on properties of nucleotides known as dideoxyribonucleotides Dideoxyribonucleotides  Single –H bound to the 3’ carbon of the deoxy sugar instead of the –OH normally at this position in the deoxyribonucleotides  DNA polymerases, the replication enzymes, recognize the dideoxyribonucleotides and place them in the DNA just as they do normal deoxyribonucleotides  However, because a dideoxyribonucleotide has no 3’-OH group abailable for addition of the next base, replication of a nucleotide chain stops when one of these nucleotides is added to a growing nucleotide chain  (Rmb: 3’-OH group must be present at the growing end of a nucleotide chain for the next nucleotide to be added during DNA replication) 15.3b Genome Sequence Determination and Annotation Involves Obtaining and Analyzing the Squences of Complete Genomes Whole-genome shotgun method - Developed by J. Craig Venter - Many organisms have been sequenced  E.coli  Various archaean Species  Eukaryotes: Yeast, the protist, round worm, plants, fruit flies, chicken, dog, mouse 1) Entire genome is broken into thousands/millions of random overlapping fragments 2) Each fragment is cloned and sequenced 3) By computer the genome sequence is assembled 4) Annotation  Identification of genes and other sequences of importance Bioinformatics  Combining biology and math and computer science and applying sophisticated algorithms for gene research  Predicts the structure and function of gene products Protein Coding Genes - Researchers identify possible protein-coding genes by searching for open reading frames (ORFs) by using computer analysis - This process is easy for prokaryotic genomes because the genes have no introns - In eukaryotic protein-coding genes (which typically have no introns) more sophisticated algorithms are used to try to identify the junctions between the exons and introns in scanning for ORFs Opening Reading Frames (ORFs)  A start codon (ATG, at the DNA level) separated by a multiple of 3 nucleotides from one of the stop codons (TAG, TAA, or TGA at the DNA level) Genome Sizes - Members of the domain Bacteria have genomes that vary widely in size - Archaean genomes also vary widely in size - For both Bacteria and Archaea, genes are densely packed in the genomes, with little space between them (thus, larger genomes of organisms in these 2 domains tend to have increased gene number) - In domain, Eukarya, their genomes show great differences in size  Yeast have a v
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