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

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From whence things come

From whence things come

Opsin & InformationOpsin & Information

How? Why?

3Goals 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)?

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http://www.bio.miami.edu/dana/pix/retina.jpg

Seeing your seer

Blind spot?

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http://www.sciencephoto.com/media/121458/enlarge

A rod, a cone

6Deeper...

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What is ‘color’?

The brain’s interpretation of the eye’s report of (a few) samplings of a narrow bit of the electromagnetic spectrum

Higherenergy

Wavelengths (nm)

Gamma rays X-rays

Ultra-violet Infrared

Micro-waves

Radiowaves

Shorterwavelength

Visible light

Longerwavelength

Lowerenergy

nm

8Our rods ‘n cones

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Higherenergy

Wavelengths (nm)

Gamma rays X-rays

Ultra-violet Infrared

Micro-waves

Radiowaves

Shorterwavelength

Visible light

Longerwavelength

Lowerenergy

nm

If the light is red (680 nm), which receptor do you expect to ‘hear’ it more loudly?

‘gre

en’ re

cepto

r

‘red’ re

cepto

r

FYI: these are REAL mutationsEffects are the REAL effects

Based on data

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‘New’ information via mutation

‘New’ information via mutation

Fashioning a new gene using a hammer

Fashioning a new gene using a hammer

11What’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

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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

133-letter code3-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

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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...

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The naughty side of recombinationThe naughty side of recombinationSometimes, it’s not as homologous as

you would like to thinkSometimes, it’s not as homologous as

you would like to think

16Thinking 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?

17Where to recombine?

1 23

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Oooops...

2

19Short end of the stick

http://www.blackwellpublishing.com/korfgenetics/figure.asp?chap=02&fig=Fig2-3

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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?

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Putting the X in sex

Putting the X in sex

Why most colorblind folks are maleWhy most colorblind folks are male

22Blinding 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: XA, Xa

• On the Y, generally designate: Y How come no A or a?

• Terminology: XA Y is hemizygous--neither homo no hetero, but half

23Sexing 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, XA, Xa, Y

• Also consider the corresponding non-sex-linked cross

• What is the equivalent of Y in a ‘regular’ (autosomal) trait?

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Family secretsFamily secretsKnowing your parents by knowing

yourselfKnowing your parents by knowing

yourself

25Boys & Girls

Chalking up a familyPair 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

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PediducerPediducerDeductions from PedigreesDeductions from Pedigrees

28Rules & 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

ExploreMenu 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?)

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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

3131

Round the FourthRound the Fourth

Say hello to my li’l assaySay hello to my li’l assay

32Let me intreduce myself

• 2RHC=O + 2OH- => 2RCOOH + H2O + 2e-

• 2CU2+ + 2e- => 2Cu+

• 2Cu+ + 2OH- => Cu2O (red ppt.) + H2O

Who is oxidized (loses electron ownership--often to oxygen)?

Who is reduced?

33Reagents for glucose

• 1% glucose

• 0.2% glucose

• Water (control) why?

34Capturing CO2

H2O + CO2 → H2CO3

H2CO3 ↔ HCO3– ↔ CO3

2–

CO32– + Ba2+ → BaCO3 (white ppt.)

35Do 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

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Pediducer: THREE complete pedigrees solved to the plausible/ruled out point for

each of three hypotheses

Pediducer: THREE complete pedigrees solved to the plausible/ruled out point for

each of three hypotheses

*Research report due week after Thanksgiving break