Transcript Color and Light

Seeing Red
Molecules that respond to light and
an introduction to pedigrees
What is Color?
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Color is really the brain’s interpretation of
the eye’s report of a narrow bit of the
electromagnetic spectrum.
We are going to use the word photon here,
but for our purposes is simply a descriptive
term for it’s properties as the carrier of
electromagnetic radiation of all
wavelengths, including, ultraviolet light,
visible light, and infrared light, among
others.
The Electromagnetic Spectrum
Wavelengths (nm)
Gamma
UltraX-rays
rays
violet
Shorter
wavelength
Higher
energ
Infrare
d
Visible
light
Microwaves
Radio
waves
Longer
wavelength
nm
Lower
energ
A photon has a fate depending on two things
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Energy level
(inversely
proportional to
wavelength)
The gap in
energy between
an electron’s
current orbital
and available
higher energy
orbitals
So which color
has the longest
wavelength?
Which has the
shortest?
Now what does
this mean?
Light has three potential fates
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ABSORBANCE: Is when the photon particle
is trapped somehow.
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REFLECTANCE: Is when the photon is
either bounced back or scattered about.
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TRANSMITTANCE: Is when the photon
passes right on through.
COLOR happens when EITHER:
ALL other wavelengths of visible light are absorbed.
ROY BIV
Props to C. Gibson
OR:
The wavelength of the COMPLEMENTARY color is
absorbed strongly.
RED
Props to C. Gibson
So why do we wear lighter colors in
hot arid climates?
It’s VERY hot in India and Pakistan in the summer…
ROYGBIV
E
Two examples of
reflection and
absorbance, and
why you wear
white in the desert.
E lost as heat
ROYGBIV
E
Props to C. Gibson
Now that we know a little bit about
color lets talk vision.
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If you want to use light, you must start with a
receptor molecule (presumably in the eye)
whose structure allows it to interact with and
absorb light of a given wavelength.
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Photons with corresponding wavelengths
between 400 and 700 nm are recognized by us
as light.
The nitty gritty…
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We use molecules called Retinal attached to a
protein known as opsin.
Thus, our “visual helpers” consist of a protein
plus a helper partnership.
You employ three opsins for color vision.
And there is more
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Each of the three opsins tune the retinal to
respond to a different part of the light
spectrum.
One is most responsive to blue light, one to red
and one to green.
We will be focusing on the red and green, as
their receptor proteins are remarkably similar
in amino acid sequence.
Red-green opsin similarity
webvision.med.utah.edu/Color.html
So…
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If you have one gene for making a protein,
what’s the easiest way to get a slightly
different protein?
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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
Copy the original. Twiddle.
Why should we bother
with how we see?
http://www.ritsumei.ac.jp/~akitaoka/rotsnakee.html
Not entirely relevant but fun
nonetheless.
Sometimes it’s OK to have fun
Optical illusions and
eye trickery.
Clearly, the eye is the connecting link
between objective reality and visual
perception so of course it plays an important
part in optical illusions.
In fact, at times it is solely responsible for
the optical illusion. The process of vision
can be divided into several steps such as (1)
the lighting, color, character, and disposition
of objects; (2) the mechanism by which the
image is formed upon the retina; (3) various
optical defects of this mechanism; (4) the
sensitiveness of the parts of the retina to
light and color; (5) the structure of the
retina; (6) the parts played by monocular
and binocular vision; and (7) the various
events which follow the formation of the
image upon the retina.
www.freegifthome.co.uk/blog/
Next trickery, then back to business
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What to see
You will see the silhouette of a spinning figurine.
Does she spin clockwise or opposite?
What to do
After you have decided which way she spins,
mentally try to make her spin the other way. Yes, this
is possible. But difficult. It may help to blink, or to
look a special features. People differ largely here.
While it may be very difficult to voluntarily flip the
direction, it may also occur spontaneously.
Note: Silhouettes are ambiguous! She could turn
either way and it would look exactly the same.
Our lady
Website of the original author, Nobuyuki
Kayahara
Did you see?
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Don’t distress yourself if you don’t see the
effect described, even if trying carefully. For
many illusions, there is a small percentage of
people with perfectly normal vision who just
don’t see it, for reasons currently unknown.
Where were we? Ah, vision & color
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Zen moment (deep thoughts): Lots of images show
us the differences a colorblind person can perceive,
but we really have no idea what they see (or vice
versa)--color is an interpretation; no reason to
believe that one person’s sensation spectrum is
different from another’s (this is a 2-part process-perception & interpretation right?)
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Similar to how we interpreted the optical illusions
shown prior. In all truth, we all saw them
differently in one way or another.
Illustration
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Interesting illustration of
some types of color
blindness.
Think with me a little
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Imagine a single kind of light receptor that
receives best at yellow wavelengths, and
less well otherwise.
Could you perceive ‘color’?
What can you deduce about the fact that you
can perceive color.
Bad pic but it gets the point across
Wavelengths (nm)
Gamma
UltraX-rays
rays
violet
Shorter
wavelength
Infrare
d
Visible light
Microwaves
Radio
waves
Longer
wavelength
nm
Higher
energy
Lower
energy
 What’s this all
about?
 Do the stacks
of membranebound sections
look familiar to
anyone?
 What do
membranes do
again?
More about Opsin
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Off, off to the computers & gather round
Go to Lab 6 folder; double-click
“GoOpsin.html”
Note how retinal eats the photon and
changes shape
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local environment (= surrounding amino acids)
influences wavelengths that trigger change
Work through the page to see what’s where
and assemble all of opsin + retinal
Page two
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Go to “page two” as the clever heading
indicates.
Color by polarity: gray is phobic/greasy;
purple is philic/charged
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what’s up with that? Why?
Note: “Show position” turns on the
membrane
Launch “Opsinize”
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You’re starting with a green-tuned opsin
(531 nm)
Your target: move towards a more red tuned
one (559 nm)
Your tool: mutating codon sequences
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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
Lessons from this?
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What are the effects of mutation?
How does the location in mRNA correlate
with a 3D location in a protein?
What are the consequences of changing a
codon in mRNA?
How could evolution derive a red-sensitive
option if it had a green-sensitive one?
Human rods and cones
www.phys.ufl.edu/.../vision/retina_schema.jpg
Advanced: Nightvision
•Note that your rods (dotted lines)
absorb strongly in the green
•Looking at the graph, what
wavelength(s) of light could you
use that would be detected by one
or more CONES without ‘wearing
out’ your RODS?
How we see:
Purves 45-20
If you don’t already know
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Your retina contains two types of (light)
photoreceptors. These are called rods and
cones. The rods are way more numerous,
around 120 million and are more sensitive than
the cones. However, they are not sensitive to
color. The 6 to 7 million cones provide the
eye's color sensitivity and they are much more
concentrated in the central yellow spot known
as the macula.
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Note that your
rods (dotted lines)
absorb strongly in
the green
Looking at the
graph, what
wavelength(s) of
light could you
use that would be
detected by one or
more CONES
without ‘wearing
out’ your RODS?
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Shown are the only the positions with a different
amino acid between red and green opsins
How similar do you think their DNA sequences are?
Remind me--what happens in meiosis when the
maternal and paternal chromosomes pair?
Think anything might ever go wrong?
Short end of the stick
•
Evolution leaves footprints
• The ‘green’ opsin is right next to the ‘red’ one on
chromosome X
•
It’s a bad idea, for the reason above--but it’s still there b/c it’s
better to risk recombination than not to be able to distinguish
red from green, never ever ever…
Details, details…
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?
Sex linked, oh my…
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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
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recall, XA, Xa, Y
Up to the board with you! Who gets the sex
linked dominant?
PTC and Parentage
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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?
Don’t worry, it’s harmless
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Phenylthiocarbamide
also known as PTC, or
phenylthiourea, is an
organic compound that
either tastes very bitter,
or is virtually tasteless,
depending on the
genetic makeup of the
taster. The ability to
taste PTC is a
dominant genetic trait.
Boys and girls
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How to set up let
alone read a
pedigree.
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Sex linked is
shown on next
slide.
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Pedigree of an
X-linked carrier
of a disease Colorblindness
About 5–8 percent of males, but less than 1 percent of females,
are color blind in some way or another, whether it be one color, a
color combination, or another mutation.
The reason males are at a greater risk of inheriting an X linked
mutation is because males only have one X chromosome (XY,
with the Y chromosome being significantly shorter than the X
chromosome), and females have two (XX); if a woman inherits a
normal X chromosome in addition to the one which carries the
mutation, she will not display the mutation. Men do not have a
second X chromosome to override the chromosome which
carries the mutation. If 5% of variants of a given gene are
defective, the probability of a single copy being defective is 5%,
but the probability that two copies are both defective is 0.05 ×
0.05 = 0.0025, or just 0.25%.
Color blindness is not the swapping of colors in the observer's eyes. Grass
is never red, and stop signs are never green. The color impaired do not learn
to call red "green" and vice versa. However, dichromats often confuse red
and green items. For example, they may find it difficult to distinguish a
Braeburn from a Granny Smith and in some cases, the red and green of a
traffic light without other clues (e.g., shape or location). This is
demonstrated in this simulation of the two types of apple as viewed by a
trichromat or by a dichromat.
A colorblind family pedigree let’s write out the genotypes!
Outsider rule:
Hemizygous,
recessive
C. Gibson
Color Deficient Dichromat
Color normal
Hmm, opportunity to dig on my
sister…
So if X-linked
color blindness is
indeed a sex
derived X-linked
trait, can girls get it
too?
Boy, I wonder
if I could be
colorblind, I
trip a lot
Broken foot
So can girls get it too?
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How could
you get an
affected
daughter?
Some things to think about
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About 1:12 men and 1:200 women are redgreen colorblind in the United States.
micro.magnet.fsu.edu/.../humanvisionfigure7.jpg
What’s it like to be color blind
So What’s it like? A little…
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Seeing a little differently
Homework: Pediducer
Rules and conventions:
Assume rare genetic disease allele
what would you assume about a randomly
selected, healthy individual?
Do so for this exercise
Two phases of the game
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Phase I: Assign genotypes; justify
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?
More on homework
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Remember the outsider rule! Any outside
“mater” in a pedigree is called just that.
These pedigrees are not that hard, I know you
are all traumatized from evil butterflies.
So don’t panic, start early and read the
instructions.
Also remember if a child expresses a
phenotype, it had to come from mom or pop!
Stuff that is due:
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Pediducer due before 10:00 pm on 10/21
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Keep thinking about that Dicty paper and
slime mold, you will be writing a proposal
about it soon.
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Anything late or messed up, now would be the
time to come and talk to me about it.