1. Semester Projects Rubric for the final report is posted now (worth 10% of your lab grade) Report is due Nov. 26/28 by 10 pm Optional outline is due Nov. 5/7 by 10 pm In class time for these is becoming scarce. You will possibly have time in class to work on them the week of Oct. 22, Nov. 05, and/or Nov. 12 but this is not guaranteed If you need supplies you don’t think you can get at a grocery store, you should ask for them very soon It may be necessary to plan a time to get together with your group outside of class to carry out your experiments There is a possibility that the labs will be open on Tuesday, Nov. 20 for final follow-up experiments, but DO NOT wait to START until then

2. D2L Submissions From now on, if you submit a file to the D2L drop box and it does not have your last name + the name of the assignment in the file name, I will not grade it and you will receive a ZERO on the assignment

3. “… And please let Mom, Dad, Rex, Ginger, Tucker, me and all the rest of the family see color”

4. Interested in Being a Preceptor? Reinforce your understanding of Bio182 topics Help peers navigate 182L Help make the course better Learn teaching techniques while earning 3 credits

5. Interested in Being a Preceptor? Work with TAs to teach and develop labs Travel to exotic locations (okay, not that) Contact Kevin Baker (kbaker2@email.arizona.edu) for more info (link on Bio182L homepage)

7. In a Family Way

8. What is “color”? And how do we ‘see’ it? Why is it usually men who are color blind?

9. Goals for Today: Understand properties of light and molecules and how this gives rise to ‘seeing in color’ Dark side of recombination (what goes wrong and is it always a bad thing?) Develop skill at deducing genotype by observation of phenotype and inheritance patterns

10. Higher energy Wavelengths (nm) Gamma rays X-rays Ultra- violet Infrare d Micro- waves Radio waves Shorter wavelength Visible light Longer wavelength Lower energy nm

11. Looking in at looking out http://www.bio.miami.edu/dana/pix/retina.jpg

12. Rods A Cone http://www.sciencephoto.com/media/121458/enlarge

13. Looking Deeper Where are we?

15. The difference between 2 and 3 receptors… Or, the beautiful colors of fall Can ~10 million American males be wrong?

16. http://www.rgblind.com/

19. What IS ‘color’? The brain’s interpretation of the eye’s report of (three) samplings of a narrow bit of the electromagnetic spectrum Higher energy Wavelengths (nm) Gamma rays X-rays Ultra- violet Infrare d Micro- waves Radio waves Shorter wavelength Visible light Longer wavelength Lower energy nm

20. Think Triangulation Hypothesis B: Far & Loud Hypothesis A: Near & Faint You are allowed to make one additional auditory observation http://www.faqs.org/photo-dict/phrase/1715/ear.html http://www.mediabistro.com/baynewser/bay_area_radio//

22. Higher energy Wavelengths (nm) Gamma rays X-rays Ultra- violet Infrared Micro- waves Radio waves Shorter wavelength Visible light Longer wavelength Lower energy nm If the light is red (680 nm), which receptor do you expect to ‘hear’ it more loudly? ‘green’ receptor ‘red’ receptor

23. How do you get a ‘new’ receptor? Fashioning a new gene using a hammer

24. What’s in an Opsin Week 9 calendar: click on ‘Opsin’ link Retinal eats the photon -> changes shape –Retinal shape change causes a shape (conformational) change in Opsin Work through the page, “see” and assemble opsin and retinal

25. Launch ‘Opsinize’ Starting with a‘red-tuned (559 nm) Goal is to make it “green-tuned” Opsin (531 nm) Your tool: mutating codon sequences From each menu you can mutate the codon (which reflects changes in DNA)

26. 3-Letter Code Ala: Alanine Arg: Arginine Asn: Asparagine Asp: Aspartic Acid Cys: Cysteine Gln: Glutamine Glu: Glutamic Acid Gly: Glycine His: Histidine Ile: Isoleucine Leu: Leucine Lys: Lysine Met: Methionine Phe: Phenylalanine Pro: Proline Ser: Serine Thr: Threonine Trp: Tryptophan Tyr: Tyrosine Val: Valine

27. Thinking it through… Shown: only the amino acid differences between red and green opsins DNA sequences would be… how similar? What happens in meiosis when the maternal and paternal chromosomes pair? Think anything might ever go wrong?

28. How do you get a ‘new’ receptor? What’s the ‘easiest’ way to get a slightly different protein? (These are all possible HYPOTHESES) –Start with a random stretch of existing DNA and randomly mutate until… OR –Copy the original gene and ‘tweak’

29. Remember Recombination? Things don’t always go smoothly

30. Where to Recombine?

31. Unequal Crossing Over

32. How do the restriction enzymes ‘know’ where to cut and recombine? R R

33. RR

34. But….

35. Remember: Unequal Crossing Over

36. RR

37. So what if this gamete ‘fertilized’ with... This one RRR

38. Mutations are ‘bad’? But what if you altered the protein to make it sensitive to a different wavelength NOW what do you have? Why would red and green be so similar? R G R

39. - Genes for Green and “Red” are 98% Similar* - Red and green Opsin genes are on the same chromosome (23) What hypothesis does this support? –Start with a random stretch of existing DNA and randomly mutate until… OR –Copy the original gene and ‘tweak’ *Howard Hughes Medical Institute

40. “New” Genes Green -> “Red” Opsin Myoglobin -> Hemoglobin Adult vs. Fetal Hemoglobin

41. What’s se X got to do with it? The “X” is big The “Y” not so much What does this mean?

42. What’s se X got to do with it? Autosomal: chromosome NOT X or Y Sex chromosome: X or Y (b/c of where each is joined together during meiosis) Symbolism: normally, we don’t care what chromosome given allele is on; in sex, it matters –On the X, we designate : X A, X a –On the Y, generally designate. How come no A or a? Hemizygous

43. What’s se X got to do with it? Consider A and a How many genotypes for females? Males? How many possible crosses? Do the cross –How can you tell it’s sex-linked? –Compare sex-linked vs autosomal

44. It sucks to be XY R/G Colorblind Hemophilia Different anemias Duchenne Muscular Dystrophy

45. How is this useful? Pedigrees!

46. Boys Girls vs

47. Makin’ Babies (make your own pedigree chart) Pair up, decide who’s the adult consenting male & who the similarly conscientious female You’re both heterozygotes (recall: ‘different-pairing’) Make the babies--hold an allele in each hand, partner picks How to determine the sex of the baby? (random as well)

48. Pediducer Deductions from Pedigrees

49. Pediducer Rules and Conventions What assumption about randomly selected, ‘healthy’ individual? Justification is “Outsider” REASON must be sufficient & necessary

50. Pediducer Rules and Conventions What does affected indiv. look like? You are TESTING models –How many right for model to be right? –How many wrong... Justification “Check me”

51. Two Phases Phase I: Assign genotypes and justify Phase II: Rule model “plausible” or “out”

52. Explore Menu progression: left to right If not logged in, first menu tells you what the ‘answer’ is Third menu specifies the model you are currently considering You are seeking to prove (how much data?) or disprove model (how many internal contradictions?)

53. NO POINTS!!!!! If you don’t rule models in/out

54. Round the Fourth Preparing for next week

55. ReDox Reactions

56. Let me intreduce myself 2RHC=O + 2OH - => 2RCOOH + H 2 O + 2e - 2CU 2+ + 2e- => 2Cu + 2Cu + + 2OH - => Cu 2 O (red ppt.) + H 2 O Who is oxidized (loses electron ownership--often to oxygen)? Who is reduced?

57. Reagents for glucose 1% glucose 0.2% glucose water

58. Capturing CO2 H 2 O + CO 2 -> H 2 CO 3 H 2 CO 3 -> HCO 3 – -> CO 3 2– CO 3 2– + Ba 2+ ->BaCO 3 (white ppt.)

59. 59 Do it! Appendix C--the supplies are on your benches Do the Benedict’s test on C-1 (substituting 0.1% glucose for the 1% starch indicated) Do the CO2 test on C-2

60. If you don’t rule models in/out Homework Pediducer: Two complete pedigrees solved to the plausible/ruled out for each of three hypotheses