Download From whence things come

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How?
Why?
From whence things
come
Opsin & Information
Goals for today
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Review: how information becomes action: DNA, mutation,
translation, function
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How does new information come into being?
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Where does some of your information come from?
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Seeing your seer
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http://www.bio.miami.edu/dana/pix/retina.jpg
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A rod,
a cone
http://www.sciencephoto.com/media/121458/enlarge
Deeper...
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Wavelengths (nm)
Gamma
UltraX-rays violet
rays
Shorter
wavelength
Infrared
Visible light
Microwaves
Radio
waves
The brain’s interpretation of
the eye’s report of (a few)
samplings of a narrow bit of
the electromagnetic
spectrum
Longer
wavelength
nm
Higher
energy
Lower
energy
What is ‘color’?
Hypothesis A:
Near & Faint
Hypothesis B:
Far & Loud
Hint: You are allowed to make one additional auditory
observation
Images:
http://www.mediabistro.com/baynewser/bay_area_radio/
http://www.faqs.org/photo-dict/phrase/1715/ear.html
Our rods ‘n cones
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Wavelengths (nm)
Gamma
UltraX-rays
rays
violet
Shorter
wavelength
Infrared
Visible light
Microwaves
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Radio
waves
Longer
wavelength
nm
Higher
energy
Lower
energy
If the light is red
(680 nm), which
receptor do you
expect to ‘hear’ it
more loudly?
‘green’ receptor
FYI: these are REAL mutations
Effects are the REAL effects
Based on data
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‘New’ information
via mutation
Fashioning a new gene using a hammer
What’s in an opsin
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Week 9 on the calendar: click ‘Opsin’ link
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retinal eats the photon; changes shape
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Change there is directly transmitted to change in opsin,
which is holding retinal
Work through the page to see what’s where and assemble all of
opsin + retinal
Launch Opsinize
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You’re starting with ‘green-tuned’ opsin (559 nm)
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Your target: as close to ‘red tuned’ as possible (actual: 531 nm)
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Your tool: mutating codon sequences
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From each menu, you can mutate the codon (of course,
mRNA reflects changes to DNA)
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You’ll be shown current and new amino acids
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After choosing, new absorbance will be displayed
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3-letter code
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Ala: Alanine
Arg: Arginine
Asn: Asparagine
Asp: Aspartic Acid
Cys: Cysteine
Gln: Glutamine
Glu: Glutamic Acid
Gly: Glycine
His: Histidine
Ile: Isoleucine
Leu: Leucine
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Lys: Lysine
Met: Methionine
Phe: Phenylalanine
Pro: Proline
Ser: Serine
Thr: Threonine
Trp: Tryptophan
Tyr: Tyrosine
Val: Valine
Nature’s way
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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.
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Start with a random stretch of DNA and randomly mutate
random positions until it happens to come to match the other
one
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Whoops! Copied the original. Whoops! Twiddling...
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The naughty side of
recombination
Sometimes, it’s not as homologous as you
would like to think
Thinking it through
Quic kTime™ and a
None dec ompres sor
are needed to see this picture.
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Shown: the only the only amino acid differences
between red and green opsins
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DNA sequences would be… how similar?
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What happens in meiosis when the maternal and
paternal chromosomes pair?
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Think anything might ever go wrong?
Where to recombine?
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Oooops...
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Short end of the stick
http://www.blackwellpublishing.com/korfgenetics/figure.asp?chap=02&fig=Fig2-3
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Consider...
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Given the way evolution works, it’s inevitable that a ‘new’ gene
will have high similarity to pre-existing one
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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
Why most colorblind folks are male
Blinding you with science
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Autosome: one of the chromosomes that is not an X or a Y
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Sex chromosome X or Y (named b/c of where each is joined
together during meiosis)
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Symbolism--normally, we don’t care what chromosome a given
allele is on; in sex, it matters
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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
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Review: x_plorer
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How did x_plorer enable you to know which crosses to do?
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How did x_plorer enable you to know when one model was
‘correct’ and one ruled out?
Sexing you up
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Consider two alleles, A and a
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How many genotypes are there for females? males?
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How many possible crosses are there (by genotype)?
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Each group Punnett one up
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recall, XA, Xa, Y
Also consider the corresponding non-sex-linked cross
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What is the equivalent of Y in a ‘regular’ (autosomal)
trait?
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Family secrets
Knowing your parents by knowing yourself
PTC and parentage
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WASH HANDS
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Who can taste this?
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Separate into haves, have-nots
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Each: if trait is dominant, what can you deduce about your
parents?
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If trait is recessive?
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Boys & Girls
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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’)
Make the babies--hold an allele in each hand, partner
picks
How to determine the sex of the baby?
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Pediducer
Deductions from Pedigrees
Rules & Conventions
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Assume rare genetic disease allele
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what would you assume about a randomly selected,
healthy individual?
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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?)
Two phases
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Phase I: Assign genotypes; justify
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Phase II: Rule model ‘viable’ or ‘out’
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How many contradictions does it take to rule
out a model?
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How many non-contradictions required to
justify ‘viable as far as I can tell?’
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“No amount of experimentation can prove
me right; a single experiment can prove me
wrong. —Albert Einstein
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Round the Fourth
Say hello to my li’l assay
Let me intreduce
myself
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2RHC=O + 2OH- => 2RCOOH + H2O + 2e-
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2CU2+ + 2e- => 2Cu+
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2Cu+ + 2OH- => Cu2O (red ppt.) + H2O
Who is oxidized (loses electron ownership--often to oxygen)?
Who is reduced?
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Reagents for
glucose
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1% glucose
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0.2% glucose
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water
Capturing CO2
H2O + CO2 => H2CO3
H2CO3 => HCO3– => CO32–
CO32– + Ba2+ => BaCO3 (white ppt.)
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Do it!
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Appendix C--the supplies are on your benches
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Do the Benedict’s test on C-1 (substituting 0.1% glucose for
the 1% starch indicated)
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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