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Seeing Red Molecules that respond to light and an introduction to pedigrees What is Color? 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 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 ABSORBANCE: Is when the photon particle is trapped somehow. REFLECTANCE: Is when the photon is either bounced back or scattered about. 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. 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. Photons with corresponding wavelengths between 400 and 700 nm are recognized by us as light. The nitty gritty… 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 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… If you have one gene for making a protein, what’s the easiest way to get a slightly different protein? 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 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? 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 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?) Similar to how we interpreted the optical illusions shown prior. In all truth, we all saw them differently in one way or another. Illustration Interesting illustration of some types of color blindness. Think with me a little 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 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 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 Go to “page two” as the clever heading indicates. Color by polarity: gray is phobic/greasy; purple is philic/charged what’s up with that? Why? Note: “Show position” turns on the membrane Launch “Opsinize” 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 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? 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 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. 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? 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… 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 Up to the board with you! Who gets the sex linked dominant? PTC and Parentage Who can taste this? Separate into haves, have-nots Each: if trait is dominant, what can you deduce about your parents? If trait is recessive? Don’t worry, it’s harmless 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 How to set up let alone read a pedigree. Sex linked is shown on next slide. 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? How could you get an affected daughter? Some things to think about 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… 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 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? More on homework 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: Pediducer due before 10:00 pm on 10/21 Keep thinking about that Dicty paper and slime mold, you will be writing a proposal about it soon. Anything late or messed up, now would be the time to come and talk to me about it.