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Genetics 321

Genetics 321. From Mendel to Genomes. 10 Weeks. Jeff Young, Botanist young@biol.wwu.edu x3638 Office: BI412. Arabidopsis thaliana Genome-based study of plant physiology and environmental responses. Office Hours M,W,F: 12:30 - 1:30 pm …by appointment.

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Genetics 321

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  1. Genetics 321 From Mendel to Genomes 10 Weeks

  2. Jeff Young, Botanistyoung@biol.wwu.edux3638Office: BI412 Arabidopsis thaliana Genome-based study of plant physiology and environmental responses. Office Hours M,W,F: 12:30 - 1:30 pm …by appointment.

  3. ...via Biology Department Home Page -> Courses -> Jeff Young’s Courses -> Genetics. Class Business • Bulletin Board outside of BI463, • Answer Keys, • etc. • Graded exams and quizzes, • outside of BI412, • Online Materials... http://fire.biol.wwu.edu/young/321g07.html

  4. Itinerary • M W F, 10 - 11:20, 5 minute break (~10:45). • M & F, Usually, questions and answers after break, • W, (without exception) quiz 11:05 - 11:20, • All midterms in class, 10:00 - 11:20, • Final 10:30 - 12:30, Tuesday, December 11

  5. Genetics 321 From Mendel to Genomes 10 Weeks

  6. Essential Genetics: A Genomics Perspectiveby Hartl and Jones, 4th ed. • ISBN: 0-7637-3527-2 • Text Assignments: • Unless amended in class, all reading assignments listed on the syllabus are required, • Additional reading assignments will be made, • You will be responsible for ‘in class’ additions and changes made to the syllabus.

  7. Grades • Three hourly exams plus final exam (450 pts), • You will have the full session time to complete each exam, • You will be allowed one 11” x 8.5” crib sheet, one side, for each exam, • Exams - 150 points each, Final Exam cumulative. • Quizzes will be givenevery Wednesday (total 100 pts), • will cover the basics of the assigned reading (including that day's assignment), • quizzes 12.5 points each, ~15 minutes, • quizzes may be taken in teams of two (except Q #1 and #2), • No Make-up Quizzes, absolutely no exceptions, • can drop two (2) lowest quiz scores (except Q #1 and #2). • Total course points - 550

  8. Extra Credit • e-mail me a synopsis of a news story concerning Genetics, in the body of the email, 1 per email, • 1 point each for up to 15 points, • maximum, 2 per week, • journal, date, byline, who, where, what and the significance, • in English sentences, • not an automatic point, • must be well presented.

  9. Extra Credit Sources • paper newspapers, • online newspapers, • do not just cut and paste, • I reserve the right to be the final judge and arbiter of valid extra credit contributions, • you will receive automatic notification(within 24 hours) that your email got to me. This is not automatic approval. • if I suspect that liberties are being taken, your extra credit account will be tallied to zero permanently, • I’ll let you know if I have a problem with your entry. • no professional journals.

  10. Nature Lake Genomicston Geneticsville Hard Mountains Get behind Don’t work problems Don’t Listen Don’t read material Rt 321 Skip Class Map Young Pass Unhappyham You are here...

  11. Genetics...the study of heredity and variation. The most powerful tool in the biologists toolbox. • Not just for biologists, • societal, • personal.

  12. Genes Genomes Classical Geneticseucaryotic ...the transmission of the primary hereditary material, Chromosomes DNA

  13. DNA Nucleotides“Bases”

  14. Hydrogen Bonds Double Helix ChromosomesLong Polymers Phosphodiester Bonds Backbone

  15. chromosome ~ 5 - 150 Mb long Genomes ... haploid chromosome component of an organism, • human (23), 3 Gb, • fruit fly (4), 120 Mb, • nematode (5), 100 Mb, • mustard (5), 120 Mb, • yeast (16), 12 Mb, • bacteria, (1), ~5-15 Mb.

  16. Genome gene DNA (kb long) promoter: controls expression structural: codes for a protein Units of HeredityClassical Genetics chromosome: DNA (Mb long) proteins

  17. Transmission of Hereditary Materials(meiosis/sex) ...Meiosis: the process of two consecutive cell divisions in the diploid progenitors of sex cells.

  18. Cell Biology ...the mechanism, timing and steps of cell division, …how a cell divides, …growth and repair. Genetics …a major result of cell division is the partitioning of DNA, …transmission of genomes, …via the transmission of chromosomes. Meiosis

  19. Chromosomes…self-replicating genetic structures. • two copies of each chromosome are present at some stage of an eukaryotic organism’s life cycle, • haploid: cells carrying one full set of chromosomes, • diploid: cells carrying two full sets of chromosomes, • n = number of haploid chromosomes. • 2n = number of chromosomes in a diploid organism.

  20. homologous chromosomes Haploid (sex cells) n = 2 homologous chromosomes Chromosome I Chromosome II Diploid (somatic cells) Chromosome I Chromosome II 2n = 4

  21. Homologous Chromosomes …a pair of chromosomes containing the samelinear gene sequence, each derived from one parent, • homologous chromosomes carry the same complement of genes, • the DNA sequence of the genes on homologous chromosomes may differ, • alleles: genes at the same location (locus) on homologous chromosomes, but that have different DNA sequences.

  22. Alternative forms of the same gene. A- a- Heterozygous B- b- C- C- Homozygous Alleles Alleles occur at the same locations (loci) on homologous chromosomes.

  23. S: synthesis of DNA, chromosomes are replicated. Meiosis Haploid Cell Diploid Cell

  24. A- -A a- -a B- -B b- -b represents gene A, from one parent. represents the same gene from the other parent, codes for the ~same protein, may have a slightly different DNA sequence. Homologous Chromosomes Synthesis

  25. sister chromatids centromere: region of the chromosome where chromatids attach. sister chromatids Chromosome Structure(cartoons) M phase

  26. M: meiosis ( two divisions) after one synthesis. S: synthesis of DNA, chromosomes are replicated. Meiosis Haploid Cell Diploid Cell

  27. A A a a B B b b Meiosis Prophase I … Synapsis: the highly specific parallel alignment of homologouschomosomes during the first division of meiosis, …tetrad: the two homologous chromosomes become attached along their length in a structure termed a tetrad.

  28. Chiasmata

  29. Meiosis Prophase I cont. A A a A a a B B b b Crossing Over: rearranges the genes from each parent.

  30. A A a A a a B B b b A A a A a a B B b b Meiosis Metaphase I -- Telophase I

  31. a A A a B B b b Meiosis Prophase II -- Telophase II Aa a A no DNA synthesis bb BB

  32. Meiosis is critical for sexual reproduction in all diploid organisms ...meiosis leads to the formation of gametes, • gametes (one from each parent) conjugate to form a zygote, ...meiosis is the basis for extensive variation among members of a population.

  33. Genetic Recombination I Crossing over.

  34. I-A I-A I-a I-a I-a II-b II-b II-B II-B II-B I-A II-b Genetic Recombination II 2n combinations of chromosomes, n = haploid number of chromosomes. Random Assortment of Chromosomes.

  35. 2n combinations of chromosomesn = number of chromosomes • n = 1, 2n = 2 • n = 2, 2n = 4 • n = 3, 2n = 8 • n = 5, 2n = 32 Arabidopsis • n = 23, 2n = 8,388,608 H. sapiens • n = 39, 2n = yip! dog

  36. Mendelian Genetics • Gregor Mendel (1822-1884), • Augustinian monk, • Botanist, • Pisum sativa, • Garden pea, • 1st “Model System”.

  37. Model Systems • Modern Biology depends largely on the ability to study simple organisms, and then apply the resulting principles to more complex systems, • i.e., ask simple questions about immensely complex processes, • the answers are often simple, though not obvious.

  38. Model Organisms • Ease of cultivation, • Rapid Reproduction, • Small size, • Fecund (large brood size), • Mutants are available and easy to identify, • Broad literature and experimental background available.

  39. o r g a n i s m a ka # g e n es 25,000- 40,000? 25,000-40,000? Model Organisms n E . c o l i b a cter i a N A 4, 3 7 7 5,770 S. c e rev i i s ae y e as t 1 6 C. e le g an s r o u n d w or m 5 1 9, 0 0 0 D ro s o p h i la fr u i t f l y 4 1 3 3 7 9 A rab i d o p s i s d i c o t p l an t 5 2 5, 4 9 8 M. mu sc u l u s m o u s e 4 0 1 0 0 ,0 0 0 H. s a pi e n s hu m an 2 3 1 0 0 ,0 0 0 P . s a t i v u m p ea 7 ~ 2 6,0 , 0 0 0 20,000- 25,000?

  40. General Cell Function ECOCYC

  41. Cell Cycle ~400 of 6022 Saccharomyces cerevisiae genes are active in conjunction with the cell cycle.

  42. o r g a n i s m a ka Model Organisms # DNA bases n 4,639,675 E . c o l i b a cter i a N A 12,495,682 S. c e rev i i s ae y e as t 1 6 100 Mb C. e le g an s r o u n d w or m 5 100 Mb D ro s o p h i la fr u i t f l y 4 120 Mb A rab i d o p s i s d i c o t p l an t 5 120 Mb M. mu sc u l u s m o u s e 4 0 3 Gb H. s a pi e n s hu m an 2 3 ?Mb P . s a t i v u m p ea 7 Genome Sizes

  43. GenomicsDNA:Reagent for the 21st Century “Biology is in the midst of an intellectual and experimental sea change.... ...essentially the discipline is moving from being largely a data-poor science to becoming a data-rich science. ” Vukmirovic and Tilghman, Nature 405, 820-822 (2000)

  44. > 145 Gb (Aug, 2006) • > 165,000 organisms

  45. 2007 Complete Genomic SequencesDNA Sequence:Reagent for the 21st Century 2001 9 ARCHAEAL 36 BACTERIAL 6 EUKARYAL 2007  • 345 Eukaryotic Genome Sequencing Projects • Complete - 26, • Assembly - 130, • In Progress - 189 • 477 Complete Microbial Genomes 2007: ~ 1,793 Viral Genomes, >547 Organelles, others…

  46. Genomics • The systematic study of genomes that begins with large scale DNA sequencing (Structural Genomics), • Functional genomics: how particular DNA sequences facilitate biological functions, • Comparative Genomics: differences between individuals, differences between species, etc. • Bioinformatics: computational discipline that has evolved to handle modern biological data...

  47. Gene Therapy Post Genomics Era Genetic Testing Drug Discovery

  48. Fundamental Research • Baxter, IR, Young, JC, Armstrong, G, Fosters, N, Bogenschutz, N, Cordova, T, Peer, WA, Hazen, SP, Murphy, A, Harper, JF. (2005) A plasma membrane H+-ATPase is required for the formation of proanthocyanidins in the seed coat endothelium of Arabidopsis thaliana. PNAS, 102 (7): 2649–2654 • - Robertson WR, Clark K, Young JC, Sussman MR. (2004) An Arabidopsis thaliana Plasma Membrane Proton Pump Is Essential for Pollen Development. Genetics. 168(3):1677-87 More Genomics

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