1. Molecular Genetics & Gene Function NEW CORE CURRICULUM: FOUNDATIONS OF THE SCIENTIFIC PROCESS

2. Concepts We Already Know: Chromosomes Genome Genes Central Dogma of Molecular Biology DNA, RNA, proteins Hershey-Chase experiment Mendel’s laws of heredity Alleles Heterozygous vs. Homozygous

3. Transcription: DNA  mRNA Translation: mRNA  protein Regulation: DNA switched on

5. . Human Genome 100% transcribed transcribed, both strands Messenger RNAs ~ 2% Mattick, J., Human Molecular Genetics, 2006, Vol. 15, Review Issue 1

6. The structure of DNA: Meaning of a genetic code Proteins variable sequence (string) built of 20 amino acids (building blocks) strings of amino acids fold up into particular shape Shape governs the Function (Meaning)

7. 1) DNA encodes RNA 2) RNA encodes Proteins 3) Proteins encode shape / function Genetic information (the MEANING) is encoded in the SEQUENCE of basis along the DNA strand; DNA is not a direct template for protein synthesis; The Central Dogma of Molecular Biology: DNA  RNA  Protein

8. The Codon Code Triplets of RNA bases translate to particular amino acids. Triples are called Codons.

9. Codons are three-base strings, so the number of possible codons are theoretically 4·4·4 = 64 What is the biological significance of the extensive redundancy of the genetic code ??? There are 20 amino acids This includes the 1 START codon (Methionine)‏ The 3 STOP codons don't code for amino acids

10. The Central Dogma of Molecular Biology... AAAGCTTTTTATGCGTTCAAG...... AAAGCUUUUUAUGCGUUCAAG...

11. LysAlaPheAlaPhe Lys Tyr

12. Essential amino acids: Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan Valine.

13. Real Genes: Globin find the start site atttgcttctgacacaactgtgttcactagcaacctcaaacagacacc atggtgcatctgactcctgaggagaagtctgccgttactgccctgtgg ggcaaggtgaacgtggatgaagttggtggtgaggccctgggcaggctg ctggtggtctacccttggacccagaggttctttgagtcctttggggat ctgtccactcctgatgctgttatgggcaaccctaaggtgaaggctcat ggcaagaaagtgctcggtgcctttagtgatggcctggctcacctggac aacctcaagggcacctttgccacactgagtgagctgcactgtgacaag ctgcacgtggatcctgagaacttcaggctcctgggcaacgtgctggtc tgtgtgctggcccatcactttggcaaagaattcaccccaccagtgcag gctgcctatcagaaagtggtggctggtgtggctaatgccctggcccac aagtatcactaagctcgctttcttgctgtccaatttctattaaaggtt cctttgttccctaagtccaactactaaactgggggatattatgaaggg ccttgagcatctggattctgcctaataaaaaacatttattttcattgc

14. Real Genes: Globin now find the stop codon atttgcttctgacacaactgtgttcactagcaacctcaaacagacacc ATGgtgcatctgactcctgaggagaagtctgccgttactgccctgtgg ggcaaggtgaacgtggatgaagttggtggtgaggccctgggcaggctg ctggtggtctacccttggacccagaggttctttgagtcctttggggat ctgtccactcctgatgctgttatgggcaaccctaaggtgaaggctcat ggcaagaaagtgctcggtgcctttagtgatggcctggctcacctggac aacctcaagggcacctttgccacactgagtgagctgcactgtgacaag ctgcacgtggatcctgagaacttcaggctcctgggcaacgtgctggtc tgtgtgctggcccatcactttggcaaagaattcaccccaccagtgcag gctgcctatcagaaagtggtggctggtgtggctaatgccctggcccac aagtatcactaagctcgctttcttgctgtccaatttctattaaaggtt cctttgttccctaagtccaactactaaactgggggatattatgaaggg ccttgagcatctggattctgcctaataaaaaacatttattttcattgc START of globin

15. Real Genes: Globin atttgcttctgacacaactgtgttcactagcaacctcaaacagacacc ATGgtgcatctgactcctgaggagaagtctgccgttactgccctgtgg ggcaaggtgaacgtggatgaagttggtggtgaggccctgggcaggctg ctggtggtctacccttggacccagaggttctttgagtcctttggggat ctgtccactcctgatgctgttatgggcaaccctaaggtgaaggctcat ggcaagaaagtgctcggtgcctttagtgatggcctggctcacctggac aacctcaagggcacctttgccacactgagtgagctgcactgtgacaag ctgcacgtggatcctgagaacttcaggctcctgggcaacgtgctggtc tgtgtgctggcccatcactttggcaaagaattcaccccaccagtgcag gctgcctatcagaaagtggtggctggtgtggctaatgccctggcccac aagtatcacTAAgctcgctttcttgctgtccaatttctattaaaggtt cctttgttccctaagtccaactactaaactgggggatattatgaaggg ccttgagcatctggattctgcctaataaaaaacatttattttcattgc STOP of globin

16. atttgcttctgacacaactgtgttcactagcaacctcaaacagacacc ATGgtgcatctgactcctgaggagaagtctgccgttactgccctgtgg ggcaaggtgaacgtggatgaagttggtggtgaggccctgggcaggctg ctggtggtctacccttggacccagaggttctttgagtcctttggggat ctgtccactcctgatgctgttatgggcaaccctaaggtgaaggctcat ggcaagaaagtgctcggtgcctttagtgatggcctggctcacctggac aacctcaagggcacctttgccacactgagtgagctgcactgtgacaag ctgcacgtggatcctgagaacttcaggctcctgggcaacgtgctggtc tgtgtgctggcccatcactttggcaaagaattcaccccaccagtgcag gctgcctatcagaaagtggtggctggtgtggctaatgccctggcccac aagtatcacTAAgctcgctttcttgctgtccaatttctattaaaggtt cctttgttccctaagtccaactactaaactgggggatattatgaaggg ccttgagcatctggattctgcctaataaaaaacatttattttcattgc

17. Activity: Sickle cell anemia

18. DNA-based life is Chemical & Meaningful Chemical: Molecules that encode hereditary information are complex, yet built out of the same atomic set: in particular C, H, O, N, P, and S. Meaningful: Sequences or strings of bases encode meaningful information (govern structure & function of proteins).

19. DNA-based life is Improbable & Historical Improbable: Likelihood of 2 DNA sequences being equal by chance is exceedingly small. Historical: If you took at two people and compare a small stretch of their DNA, the chance that that small stretch agrees in all but one base pair is extraordinarily tiny if due to pure chance. It is far more likely that the correct explanation should be that all humans are related by some sort of process of inheritance. Inheritance implies ancestry, which in turn implies history. Humans share ~99.8 % of DNA with one another, ~98% of DNA with chimpanzees (our closest living relatives), and some fraction of DNA with all life on Earth.

20. DNA-based life is Improbable & Historical

21. Probability: one way of quantifying what outcomes are liable to be observed Probability P = (number of outcomes of interest) / (number of possible outcomes) Always a number between zero and one P(A OR B OR C) = P(A) + P(B) + P(C) P(A AND B AND C) = P(A) x P(B) x P(C)

22. What is a virus? DNA or RNA molecule carrying virus’ genetic code Encapsulated into protective protein shell (capsid) Viruses generally cannot self-replicate So they hijack the cell’s machinery New Central Dogma of Molecular Biology: Ex: HIV is a strand of RNA capable of transferring its information “backwards” into the cell’s DNA. DNA  RNA  Protein

23. Vaccines against Viral Infections Potential Problem: The vaccine version of the virus reverts to a virulent form. QUESTION: Suppose the chance of a base mutating is 20%, and chance to mutate back to original base is 1/3. What is the chance that base in a modified virus will revert back to what it was originally? QUESTION: Some poliovirus vaccines involves 5 effective mutations that weaken the virus. Imagine that the vaccine is administered to 5,000,000 people. How many people are liable to be infected by harmful polio that originates from a reversion of the vaccine?

24. BLASTING DNA Group Activity http://serc.carleton.edu/microbelife/k12/bioinformatics/index.html ACTIVITY: BIOINFORMATICS

27. Mammals that have been sequenced (cont) OrganismTypeGenome size Number of genes predicted Year of completion Ailuropoda melanoleuca Giant panda2.4Gb [104] [104] 19,300 Bos primigenius taurus Cow2.92 GbGb21,000 [105] [105] 2009 [106] [106] Callithrix jacchusMarmoset2.78 Gb21,200 [107] [107] 2010 Canis lupus familiaris Dog2.4 Gb [108] [108] 19,300 [108] [108] 2005 [108] [108] Cavia porcellusGuinea Pig2.72 Gb18,650 Equus ferus caballus Horse2.1 Gb20,436 [109] [109] 2007 [110] [110] Felis silvestris catus Cat3 Gb20,2852007 [111] [111] Gorilla gorillaGorilla3.04 Gb20,803 [112] [112] 2008,2010 Source: wikipedia.org

28. Mammals that have been sequenced (cont) OrganismTypeGenome size Number of genes predicted Year of completion Homo sapiensHuman3.2 Gb [113] [113] 20,251 (UniProt) Draft 2001 [114][115] Complete 2006 [116] [114][115] [116] Loxodonta africana African Elephant3.2 Gb20,0002009 [117] [117] Macaca mulattaRhesus Macaque3.09 Gb21,800 [118] [118] 2007 [119] [119] Monodelphis domestica Gray Short-tailed Opossum 3.5 Gb19,400 [120] [120] 2007 [121] [121] Mus musculus Mus musculus Strain: C57BL/6JC57BL/6 Mouse2.5 Gb22,700 [122] [122] 2002 [124] [124] Myotis lucifugusLittle Brown Bat1.96 Gb13,6592010 [125] [125] Source: wikipedia.org

29. Mammals that have been sequenced (cont) OrganismTypeGenome size Number of genes predicted Year of completion Ornithorhynchus anatinus Platypus1.9 Gb18.600 [126] [126] 2007 [126] [126] Oryctolagus cuniculus Rabbit2.7 Gb19,000 [128] [128] 2010 Pan troglodytesChimpanzee3.35 Gb19,700 [129] [129] 2005 [130] [130] Pongo pygmaeusPongo pygmaeus/Pongo abeliiPongo abelii Orangutan (Borneo/Sumatra) 3.08 Gb20,100 [131] [131] 2011 [132] [132] Rattus norvegicusRat2.8 Gb23,000 [133] [133] 2004 [134] [134] Source: wikipedia.org

30. Other Vertebrates That have been Sequenced OrganismTypeGenome size Number of genes predicted Year of completion Anolis carolinensisGreen anole lizard1.74 Gb [135] [135][136] 2007 (6.3/6.8x) Callorhinchus miliiElephant shark0.9 Gb15,000 [138] [138] 2007 (survey 1.4x) Danio rerioZebrafish1.4 Gb24,200 [139] [139] 2007 Gadus morhuaAtlantic cod608 Mb20,095 [140] [140] 2011 Gallus gallusChicken1.08 Gb17,000 [141] [141] 2004 [142] [142] Gasterosteus aculeatus Three-spined stickleback 460 Mb [143] [143] 20,800 [143] [143] 2006 Meleagris gallopavo Wild turkey1.04 Gb [144] [144] 17,500 [144] [144] 2011 Source: wikipedia.org

31. Other Vertebrates That have been Sequenced OrganismTypeGenome size Number of genes predicted Year of completion Taeniopygia guttataZebra finch1.2 Gb18,447 [148] [148] 2010 Takifugu rubripesPuffer fish390 Mb22–29,000 [145] [145] 2002 [147] [147] Tetraodon nigroviridis Puffer fish340 Mb [149] [149] 22,400 (orig.), [149] 27,823 (UniProt) [149] 2004 [149] [149] Xenopus tropicalis Western clawed frog 1.7 Gb28,000 [150] [150] 2005 Source: wikipedia.org

32. Insects that have been sequenced OrganismTypeGenome size Number of genes predicted Year of completion Acyrthosiphon pisumPea aphid510 Mb<30,000 [151] [151] 2010 [151] [151] Aedes aegyptiMosquito1376 Mb15,419 [152] [152] 2007 [152] [152] Anopheles gambiaeMosquito278 MbMb13,683 [153] [153] 2002 [153] [153] Apis melliferaHoney bee236 Mb10,157 [154] [154] 2006 [154] [154] Bombyx moriMothMoth(domestic silk worm) 530 Mb2004 [155] [155] Culex quinquefasciatus Mosquito? Mb18,8832010 [156] [156] Source: wikipedia.org

33. Insects that have been sequenced (cont) OrganismTypeGenome size Number of genes predicted Year of completion Drosophila melanogaster Fruit fly165 Mb13,600 [157] [157] 2000 [157] [157] Drosophila pseudoobscura Fruit fly139 Mb 11,000, [158] 15,948 (UniProt) [158] 2005 [158] [158] Pediculus humanusSucking louse108 Mb10,773 [159] [159] 2010 [159] [159] Tribolium castaneum Tribolium castaneum Strain:GA-2 Beetle204 Mb16,404 [160] [160] 200 Source: wikipedia.org

35. Announcement: Your presentations are due by email Monday night. If they aren’t in by then you will not be permitted to present and your group will get a ZERO.

36. Using DNA to our Advantage Genetic Modification Introduction of new DNA sequences into an organism to alter the genetic makeup Introduces very specific characteristics Use enzymes to manipulate DNA Recombinant DNA - new form of DNA that is introduced Gene cloning – splicing genes from a variety of species into a host cell Gene therapy – inserting, deleting or manipulating genes in order to cure or lessen the effects of genetic diseases

37. Using DNA to our Advantage Sequencing Compare nucleotide sequences from different cells Analyze for similarities and differences –PCR (polymerase chain reaction)  copying selected segments of DNA –Genetic fingerprinting –Cloning

38. Discussion Activity: GATTACA…our future?

39. It’s not so far off The case of 23andme.com 39

40. What do you think? If you had the choice would you choose to know your ‘genetic future’? 40

41. What do you think? Molecular biology scientists have developed a technique, which enables parents to select the sex of their future child. This technique simply separates the X carrying sperms from the Y carrying sperms, and then inseminating females with the preferred sex chromosomes. This procedure is currently banned in Canada except for medical reasons. Potential parents with sex-linked diseases may choose to have a girl, avoiding the possibility of having a boy with hemophilia, for example. Should sex selection for medical and non-medical reasons be available for parents in Canada or the rest of the world? 41

42. What do you think? In the movie clip, the genetic counselor tells the perspective parents: “This child is still you, it is simply the best of you”. How do we understand that statement? 42

43. What do you think? How would we as humans decide what are the best genes to pass on? 43

44. What do you think? How does nature select the best choice of genes to pass on? 44

45. What do you think? What are some of the implications of humans deciding which genes should be selected for? Does such a selection put the entire human population at a greater risk? 45

46. What do you think? In the short clip, the counselor is suggesting that one can screen for alcoholism, baldness, etc., via genetics. How far are we from this level of technology today? Is it even plausible? 46

47. What do you think? In the movie they state that Vincent will have a 60% chance of developing a neurological condition, 42% of being manic depressive, 89% of having ADD, 99% of having heart disease. How accurate are these predictions for the various disorders? 47

48. What do you think? Why won’t Insurance cover the medical bills for Vincent? Does that bring the ethical dilemma of DNA testing? 48

49. What do you think? Sperm and egg donation service agencies offer hope to infertile parents who hope to conceive their own children in the future. Sperm donation is a relatively easy process, requiring no more than an hour’s time. However, donating eggs is a rather complicated task, requiring months of hormone therapy and minor surgical procedures to retrieve the harvested eggs. In addition, drugs injected into women cause their ovaries to ovulate several eggs at once, greatly increasing the odds of developing cancer. To compensate for the ‘inconvenience’, women are given a large sum of money. Often, young, female college students are targeted for egg donations since they are considered more educated and healthier that their older female counterparts. Do you think females should be compensated for donating their eggs? Why or why not? Is it appropriate for egg donation agencies to advertise for potential egg donors on college campuses? 49