Proposals! Key points about proposals that should be taken into consideration NOW for experimentation and final reports. Reports are due the week after thanksgiving break, take advantage of the time we do have at the end of labs from now on or you may lose good opportunities to work on projects. Long labs to come 1

2 From whence things come Opsin & Information How?Why?

3 Goals for today Review: how information becomes action: DNA, mutation, translation, function How does new information come into being? Where does some of your information come from? Why were your ancestors not able to distinguish red from green and we can (well most of us)?

4 Seeing your seer Blind spot?

5 A rod, a cone

6 Deeper...

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

8 Our rods ‘n cones

9 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 FYI: these are REAL mutations Effects are the REAL effects Based on data

10 ‘New’ information via mutation Fashioning a new gene using a hammer

11 What’s in an opsin Week 9 on the calendar: click ‘Opsin’ link Opsin is the protein containing retinal Retinal eats the photon; changes shape Change there is directly transmitted to change in opsin, which is holding retinal – see how this change in opsin can be altered to sense different colors Work through the page to see what’s where and assemble all of opsin + retinal

12 Launch Opsinize You’re starting with ‘red-tuned’ opsin (559 nm) Your target: as close to ‘green tuned’ as possible (actual: 531 nm) Your tool: mutating codon sequences From each menu, you can mutate the codon (of course, mRNA reflects changes to DNA) You’ll be shown current and new amino acids After choosing, new absorbance will be displayed Logical steps here – go through ALL mutations first, figure out codon change and amino acid change  put all amino acids back to original (first on list) and mutate from there

13 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

14 Nature’s way If you have one gene for making a protein, what’s the easiest way to get a slightly different protein? Background: you already have something that performs a similar task. Start with a random stretch of DNA and randomly mutate random positions until it happens to come to match the other one Whoops! Copied the original. Whoops! Twiddling...

15 The naughty side of recombination Sometimes, it’s not as homologous as you would like to think

16 Thinking it through Shown: the only 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?

17 Where to recombine? 1 2 3

18 Oooops... 2

19 Short end of the stick

20 Consider... Given the way evolution works, it’s inevitable that a ‘new’ gene will have high similarity to pre-existing one If you wanted to them ‘safe’ from recombination, where would you NEVER put the second copy?

21 Putting the X in sex Why most colorblind folks are male

22 Blinding you with science Autosome: one of the chromosomes that is not an X or a Y Sex chromosome X or Y (named b/c of where each is joined together during meiosis) Symbolism--normally, we don’t care what chromosome a given allele is on; in sex, it matters On the X, we designate thusly: X A, X a On the Y, generally designate: Y How come no A or a? Terminology: X A Y is hemizygous--neither homo no hetero, but half

23 Sexing you up Consider two alleles, A and a How many genotypes are there for females? males? How many possible crosses are there (by genotype)? Each group Punnett one up recall, X A, X a, Y Also consider the corresponding non-sex-linked cross What is the equivalent of Y in a ‘regular’ (autosomal) trait?

24 Family secrets Knowing your parents by knowing yourself

25 Boys & Girls

Chalking up a family Pair up, decide who’s the adult consenting male & who the similarly conscientious female You’re both heterozygotes (recall: ‘different-pairing’) Diseased or not? Make the babies—hold an allele in each hand, partner picks How to determine the sex of the baby? Flip a coin

27 Pediducer Deductions from Pedigrees

28 Rules & Conventions Assume rare genetic disease allele what would you assume about a randomly selected, healthy individual? Do so for this exercise--the specific justification is ‘outsider’ One key aspect of this exercise: reasons must be sufficient & necessary

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?)

30 Two phases Phase I: Assign genotypes; justify Phase II: Rule model ‘viable’ or ‘out’ How many contradictions does it take to rule out a model? How many non-contradictions required to justify ‘viable as far as I can tell?’ “No amount of experimentation can prove me right; a single experiment can prove me wrong. —Albert Einstein

31 Round the Fourth Say hello to my li’l assay

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

33 Reagents for glucose 1% glucose 0.2% glucose Water (control) why?

34 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.)

35 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

36 Pediducer: THREE complete pedigrees solved to the plausible/ruled out point for each of three hypotheses *Research report due week after Thanksgiving break