1. 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

2. 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)

3. Lab 9: In a Family Way

4. Goals for Today: Understand properties of light and molecules Dark side of recombination Develop skill at deducing genotype by observation of phenotype and inheritance patterns

5. What is “color”? And how do we ‘see’ it?

6. 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

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

8. Looking Deeper Where are we?

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

10. http://www.rgblind.com/

13. 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

15. 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

16. How do you get a ‘new’ receptor?

17. What’s in an Opsin Week 9 calendar: click on ‘Go_Opsin’ link Retinal eats the photon -> changes shape –Change is directly transmitted to change in opsin (which is holding retinal) Work through the handout

18. Launch ‘Opsinize’ Starting with “red-tuned” opsin (559 nm) Your objective: make a ‘green-tuned’ (as close to 531) nm Your tool: mutating codon sequences From each menu you can mutate the codon (which reflects changes in DNA)

19. 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

20. Thinking it through… Shown: the only 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?

21. How do you get a ‘new’ receptor? What’s the ‘easiest’ way to get a slightly different protein? –Make a new segment of DNA that happens to be similar –Start with a random stretch of existing DNA and randomly mutate until… –Copy the original gene and ‘tweek’

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

23. Where to Recombine?

24. Oooooops 2

25. GG How do the restriction enzymes ‘know’ where to cut and recombine?

26. GG

27. But….

28. G G

29. So….. Is it easier to make a gene, or tinker with an existing one?

30. G G So what if this gamete ‘fertilized’ with... G This one

31. GG G How many colors? But what if you altered the protein to make it sensitive to a different wavelength R NOW what do you have? Red and green 98% similar. Why?

32. “New” Genes – Sound Familiar?

33. Green -> “Red” Opsin Myoglobin -> Hemoglobin Adult vs. Fetal Hemoglobin

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

35. 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: Y How come no A or a? Hemizygous

36. What’s se X got to do with it? Consider A and a How many genotypes for females? Males? How many possible crosses? –How to distribute

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

38. It sucks to be XY R/G Colorblind Hemophilia Different anemias

39. How is this useful? Pedigrees!

40. PTC and parentage WASH HANDS Who can taste this? Separate into haves, have-nots Each: if trait is dominant, what can you deduce about your parents? If trait is recessive?

41. Boys Girls vs

42. Makin’ Babies 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?

43. Pediducer Deductions from Pedigrees

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

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

46. 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”

47. 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?)

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

49. Preparing for next week

50. Let me intreduce myself RHC=O + H 2 O => RCOOH + 2H + + 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?

51. Reagents for glucose (do all three) 1% glucose 0.2% glucose water

52. 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.)

53. 53 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) Candidate solution = glucose Do the CO2 test on C-2 –Place dry ice in flasks with appropriate tubes/stopper –Why dry ice?

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