Ap Chapter 21

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AP Chapter 21 Genomics

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  • Ap Chapter 21

    1. 1. GENOMICS AP Biology Chap 21
    2. 2. <ul><li>Genomes – set of genes and their interactions </li></ul><ul><li>Bioinformatics – computational methods of gene analysis </li></ul><ul><li>- NCBI National Center Biotechnology </li></ul><ul><li>Information – database of DNA </li></ul><ul><li>sequences and proteins (proteomes) </li></ul>NCBI HomePage
    3. 3. <ul><li>The most ambitious mapping project to date has been the sequencing of the human genome </li></ul><ul><li>Officially begun as the Human Genome Project in 1990, the sequencing was largely completed by 2003 </li></ul><ul><li>The project had three stages: </li></ul><ul><ul><li>Genetic (or linkage) mapping </li></ul></ul><ul><ul><li>Physical mapping </li></ul></ul><ul><ul><li>DNA sequencing </li></ul></ul>
    4. 4. Fig. 21-2-4 Cytogenetic map Genes located by FISH Chromosome bands Linkage mapping 1 2 3 Genetic markers Physical mapping Overlapping fragments DNA sequencing Fluorescence In Situ Hybridization
    5. 5. <ul><li>A linkage map (genetic map) maps the location of several thousand genetic markers on each chromosome </li></ul><ul><li>A genetic marker is a gene or other identifiable DNA sequence </li></ul><ul><li>Recombination frequencies are used to determine the order and relative distances between genetic markers </li></ul>
    6. 6. Fig. 21-3-3 Cut the DNA into overlapping fragments short enough for sequencing 1 2 3 4 Clone the fragments in plasmid or phage vectors. Sequence each fragment. Order the sequences into one overall sequence with computer software.
    7. 7. <ul><li>A complete haploid set of human chromosomes consists of 3.2 billion base pairs </li></ul>
    8. 8. By summer 2007, genomes had been sequenced for 500 bacteria, 45 archaea, and 65 eukaryotes including vertebrates, invertebrates, and plants
    9. 9. What do we know? <ul><li>Humans have 20,488 genes </li></ul><ul><li>With alternate gene splicing, we can make 75,000 polypeptides </li></ul><ul><li>Genomes of most bacteria and archaea range from 1 to 6 million base pairs (Mb); genomes of eukaryotes are usually larger </li></ul>
    10. 10. <ul><li>Free-living bacteria and archaea have 1,500 to 7,500 genes </li></ul><ul><li>Unicellular fungi have from about 5,000 genes and multicellular eukaryotes from 40,000 genes </li></ul><ul><li>Number of genes is not correlated to genome size </li></ul><ul><li>Humans and other mammals have the lowest gene density , or number of genes, in a given length of DNA </li></ul>
    11. 11. Table 21-1
    12. 12. About the human genome… <ul><li>Only 1.5% codes for proteins, rRNA and tRNA </li></ul><ul><li>The rest is used for </li></ul><ul><li>regulatory sequences and introns 24% </li></ul><ul><li>pseudogenes (nonfunctioning genes) 15% </li></ul><ul><li>repetitive DNA 59% </li></ul>
    13. 13. Fig. 21-7 Exons (regions of genes coding for protein or giving rise to rRNA or tRNA) (1.5%) Repetitive DNA that includes transposable elements and related sequences (44%) Introns and regulatory sequences (24%) Unique noncoding DNA (15%) Repetitive DNA unrelated to transposable elements (15%) L1 sequences (17%) Alu elements (10%) Simple sequence DNA (3%) Large-segment duplications (5–6%)
    14. 14. Repetitive DNA <ul><li>44% transposable elements (jumping genes) </li></ul><ul><li>- Transposons - cut and paste (ex Alu in primates) </li></ul><ul><li>- Most of these are retrotransposons – cut, copy to RNA, RT to DNA, and paste (ex Line1 or L1) </li></ul><ul><li>15% – large segment and simple sequence DNA </li></ul><ul><li>- small ones STR - Short Tandem Repeats often used in centromeres and telomeres </li></ul>
    15. 15. Fig. 21-9 Transposon New copy of transposon Insertion Transposon is copied Mobile transposon DNA of genome (a) Transposon movement (“copy-and-paste” mechanism) Retrotransposon New copy of retrotransposon Insertion Reverse transcriptase RNA (b) Retrotransposon movement Animation Quiz 5 - Transposons : Shifting Segments of the Genome
    16. 16. “ Jumping Genes” <ul><li>The first evidence for wandering DNA segments came from geneticist Barbara McClintock’s breeding experiments with Indian corn </li></ul>
    17. 17. Fig. 21-8
    18. 18. Genes <ul><li>Many eukaryotic genes are present in one copy per haploid set of chromosomes </li></ul><ul><li>More than ½ occur in multigene families – such as for RNA products and hemoglobin </li></ul>
    19. 19. Fig. 21-10 DNA RNA transcripts Nontranscribed spacer Transcription unit 18S 28S 5.8S 28S 5.8S rRNA 18S DNA (a) Part of the ribosomal RNA gene family Heme Hemoglobin  -Globin  -Globin  -Globin gene family  -Globin gene family Chromosome 16 Chromosome 11      2   1  2  1    G  A      Adult Fetus Embryo Fetus and adult Embryo (b) The human  -globin and  -globin gene families
    20. 20. Genomic Evolution <ul><li>Duplication of chromosome sets (polyploidy) </li></ul><ul><li>Chromosome alteration – duplications, inversions </li></ul><ul><li>Exon shuffling </li></ul><ul><li>Transposons </li></ul>
    21. 21. <ul><li>Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairs </li></ul><ul><li>Following the divergence of humans and chimpanzees from a common ancestor, two ancestral chromosomes fused in the human line </li></ul>Why we Are Smarter!
    22. 22. <ul><li>The rate of duplications and inversions seems to have accelerated about 100 million years ago </li></ul><ul><li>This coincides with when large dinosaurs went extinct and mammals diversified </li></ul>
    23. 23. How transposons affect genomes <ul><li>Multiple copies may facilitate crossing-over </li></ul><ul><li>Insertion may block protein sequence </li></ul><ul><li>Insertion may affect promoters </li></ul><ul><li>Insertion may carry new genes to an area </li></ul><ul><li>May create new sites for alternative splicing in RNA </li></ul>
    24. 24. Fig. 21-12 Transposable element Gene Nonsister chromatids Crossover Incorrect pairing of two homologs during meiosis and
    25. 25. Comparing evolutionary developmental processes “evo-devo” <ul><li>Homeobox – 180 nucleotides that regulate gene expression during development </li></ul><ul><li>Found in many organisms, both inverts and verts </li></ul><ul><li>Called “hox genes” in mammals </li></ul><ul><li>You should read “Our Inner Fish”! </li></ul>
    26. 27. Fig. 21-17 Adult fruit fly Fruit fly embryo (10 hours) Fly chromosome Mouse chromosomes Mouse embryo (12 days) Adult mouse
    27. 28. <ul><li>Sometimes small changes in regulatory sequences of certain genes lead to major changes in body form. </li></ul><ul><li>For example, variation in Hox gene expression controls variation in leg-bearing segments of crustaceans and insects </li></ul>
    28. 29. for example, flies with feet in place of antennae.

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