Download Semester Projects

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
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
“… And please let Mom, Dad, Rex, Ginger, Tucker,
me and all the rest of the family see color”
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
Interested in Being a Preceptor?
• Work with TAs to teach and develop labs
• Travel to exotic locations (okay, not that)
• Contact Kevin Baker ([email protected])
for more info (link on Bio182L homepage)
In a Family Way
What is “color”?
And how do we ‘see’ it?
Why is it usually men
who are color blind?
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
Wavelengths (nm)
Gamma X-rays Ultrarays
violet
Shorter
wavelength
Infrare
d
Visible light
Microwaves
Radio
waves
Longer
wavelength
nm
Higher
energy
Lower
energy
Looking in at looking out
http://www.bio.miami.edu/dana/pix/retina.jpg
• Rods
• A Cone
http://www.sciencephoto.com/media/121458/enlarge
Looking Deeper
Where are we?
The difference between
2 and 3 receptors…
Or, the beautiful colors of fall
Can ~10 million American males be wrong?
http://www.rgblind.com/
http://www.rgblind.com/
http://www.rgblind.com/
What IS ‘color’?
Wavelengths (nm)
Gamma X-rays Ultrarays
violet
Shorter
wavelength
Infrare
d
Visible light
Microwaves
Radio
waves
Longer
wavelength
nm
Higher
energy
Lower
energy
The brain’s
interpretation of
the eye’s report
of (three)
samplings of a
narrow bit of the
electromagnetic
spectrum
Think Triangulation
Hypothesis A:
Near & Faint
Hypothesis B:
Far & Loud
You are allowed to make one additional
auditory observation
http://www.mediabistro.com/baynewser/bay_area_radio/
http://www.faqs.org/photo-dict/phrase/1715/ear.html
Wavelengths (nm)
Gamma
rays
Shorter
wavelength
X-rays Ultraviolet
Infrared
Visible light
Microwaves
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
How do you get a ‘new’
receptor?
Fashioning a new gene using a hammer
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
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)
3-Letter Code
• Leu: Leucine
• Ala: Alanine
• Arg: Arginine
• Lys: Lysine
• Asn: Asparagine
• Met: Methionine
• Asp: Aspartic Acid
• Phe: Phenylalanine
• Cys: Cysteine
• Pro: Proline
• Gln: Glutamine
• Ser: Serine
• Glu: Glutamic Acid
• Thr: Threonine
• Gly: Glycine
• Trp: Tryptophan
• His: Histidine
• Tyr: Tyrosine
• Ile: Isoleucine
• Val: Valine
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?
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’
Remember Recombination?
Things don’t always go smoothly
Where to Recombine?
Unequal Crossing Over
How do the restriction
enzymes ‘know’ where
to cut and recombine?
R
R
R
R
But….
Remember: Unequal Crossing
Over
R
R
This one
So what if
this gamete
‘fertilized’ with...
R
R
R
Mutations are ‘bad’?
R
R
G
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?
-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
“New” Genes
• Green -> “Red” Opsin
• Myoglobin -> Hemoglobin
• Adult vs. Fetal Hemoglobin
What’s seX got to do with it?
• The “X” is big
• The “Y” not so
much
• What does this
mean?
What’s seX 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 : XA, Xa
– On the Y, generally designate. How come no A or a?
• Hemizygous
What’s seX 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
It sucks to be XY
•
•
•
•
R/G Colorblind
Hemophilia
Different anemias
Duchenne Muscular Dystrophy
How is this useful?
Pedigrees!
Boys
vs
Girls
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)
Pediducer
Deductions from Pedigrees
Pediducer
Rules and Conventions
• What assumption about randomly
selected, ‘healthy’ individual?
• Justification is “Outsider”
• REASON must be sufficient &
necessary
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”
Two Phases
• Phase I: Assign genotypes and justify
• Phase II: Rule model “plausible” or
“out”
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?)
NO POINTS!!!!!
If you don’t rule models in/out
Round the Fourth
Preparing for next week
ReDox Reactions
Let 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?
Reagents for glucose
• 1% glucose
• 0.2% glucose
• water
Capturing CO2
H2O + CO2 -> H2CO3
H2CO3 -> HCO3– -> CO32–
CO32– + Ba2+ ->BaCO3 (white ppt.)
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
59
Homework
If you don’t rule models in/out
Pedid
comp
pedig
solve
plaus
out fo
three
hypot