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
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Proposals! Key points about proposals that should be taken into consideration NOW for experimentation and final reports. Reports are due the week after.
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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)?
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
1010
‘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?