lws protein
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What’s Left in LB145? Last Class: – Course Evaluations – Take up Exam – Begin Evolution Unit Today: – Finish Evolution Unit Tuesday Apr 23rd: – Bonus survey – Traditional review (?) Don’t Forget… Friday April 19th: View Exams 1, 2, 3 in C4 from 1-3pm. OR Office hours. Weds/Thurs April 24th/25th: Lab Projects Due. Thursday April 25th: – Question-based review (?) Friday April 26th: 3-5pm in C-3 Last-Gasp Tutorial (email me to reserve a place) Evolution Write it Down: What is evolution? Evolution Write it Down: Why is evolution controversial? Social-Political-Religious Pressures Source: Gallop Poll 2007 Why is Evolution treated differently from other theories? 1. Social-PoliticalReligious Pressures 2. It’s presented as belief construct 1. It is complicated and is not often taught/learned very well Other Academic Theories Big Bang Theory, Cell Theory, Germ Theory, Molecular Theory, the Kinetic Theory of Gasses, Molecular Orbital Theory, Variance Bond Theory, Transition State Theory, Marchs Theory, DebyeHuckel Theory, Thermodynamic Theory of Polymer Elasticity, Density Functional Theory, Baeyer Strain Theory, Climate Change Theory, Macroeconomic Theory, Microeconomic Theory, Constructivist Theory, Critical Pedagogy Theory, Multiple Intelligence Theory, Circuit Theory, Control Theory, Systems Theory, Film Theory, Theory of Plate Tectonics, Literary Theory, Approximation Theory, Coding Theory, Intersection Theory, Matrix Theory, Model Theory, Ring Theory, Music Theory, Proof Theory, Theory of Truth, Acoustic Theory, Atomic Theory, Perturbation Theory, Theory of Relativity, Theory of the Mind, Cognitive Dissonance Theory, Attachment Theory, Theory of Self Fulfilling Prophecy, Sociological Theory, Critical Theory, Extreme Value Theory, Performance Theory…. Evolution Write it Down: How would you explain evolution to a nonscientist? Evolution through natural selection… Mouse Fur Color MC1R protein is stimulated and facilitates cAMP production. cAMP is used to regulate gene expression. c(tyr) Tyrp1 Tyrp2 p Evolution Evolution through natural selection… Pea Seed Taste Definitions of Evolution… Evolution – the simplest of definitions: Evolution – the simplest of definitions: Descent with modification. Descent with modification of… - Nucleotides (mutations!) Alleles Genes (deletion/duplication) Proteins Cell function - Selectable SPhenotype Evolution – a diversity definition Biological evolution is change in the properties of populations of organisms that transcend the lifetime of a single individual. Biological evolution may be slight or substantial; it embraces everything from slight changes in the proportion of different alleles within a population to the successive alterations that led from the earliest protoorganism to snails, bees, giraffes, and dandelions. Douglas J. Futuyma Evolution is… … the process by which different kinds of living organisms developed and diversified from earlier forms during the history of the earth. Patterns of Relatedness Evolution – a populations definition “Evolution can be precisely defined as any change in the frequency of alleles within a gene pool from one generation to the next” Helena Curtis and N. Sue Barnes Darwin’s Evolution • Had no knowledge of genetics. • Connected evolution with ecology. Ecology and Evolution • Beak size in Galapagos Finches Darwin’s Evolution ? Darwin’s Finches Trait Evolution • The evolution of traits relates to the evolution of species. Evolution facilitates speciation. How does speciation occur? Speciation occurs… • When two populations become different enough from each other. Species Concepts • Biological Species – a set of interbreeding populations. • Genetic Species – based on similarity of DNA. • Ecological Species – a set of organisms that occupy the same niche. • Phylogenetic Species – a group of organisms that share an ancestor and maintains its integrity through time and space. • Other: – Typological Species, Cohesion Species, Evolutionary Species, Morphological Species, Phenetic Species, Recognition Species, Mate-Recognition Species. Backing Up One Step… What Makes a Species Unique? One way to look at it: One species can be differentiated from another based on a differing set of traits. Traits: a functional unit of evolution • If you can describe how a trait evolved and why a trait is selected for then you can describe evolution. Evolution of Traits One More Case: • Color Vision Evolution in Monkeys What is colorblindness? Reduced ability to interpret light as color. 1 in 12 males are colorblind. < 1 in 100 females are colorblind. Are You Colorblind? A) No (Female) A) Yes (Female) A) No (Male) A) Yes, very (Male) A) Yes, somewhat (Male) Agree or Disagree: It is nearly always advantageous to have trichromatic vision. (i.e. compared to dichromatic vision) A. B. C. D. E. Strongly Agree Agree Neutral Disagree Strongly Disagree Agree or Disagree: Some humans probably have tetrachromatic vision. A. B. C. D. E. Strongly Agree Agree Neutral Disagree Strongly Disagree Do you think YOU have tetrachromatic vision? A. B. C. D. E. Yes (female) No (female) I have no idea Yes (male) No (male) Monkeys of the World TRICHROMATS DICHROMATS NEW WORLD OLD WORLD How Does Color Vision Work? Cell Biology: How Does Color Vision Work? Three types of Cone Cell • Different kinds of opsin proteins embedded in the membrane of cone cells. • Central Dogma of Molecular Biology: DNA RNA Protein Genes code for…. proteins Proteins are responsible for cell function Opsin Image modified from Scientific American, April 09 3.2a 11-cis-retinal Opsin • To produce the signal for color vision, retinal must stimulate the opsin protein but this cannot occur while the retinal molecule is in its cis- formation. Opsin Image modified from Scientific American, April 09 3.2b 11-cis-retinal Opsin • When 11-cis-retinal absorbs a photon (a basic unit of light), it changes from 11-cis-retinal to All-trans-retinal. Opsin Image modified from Scientific American, April 09 3.2c All-trans-retinal Opsin • All-trans-retinal stimulates the opsin in the membrane of the cone cell. Opsin Image modified from Scientific American, April 09 3.2d All-trans-retinal Opsin • The cone cell sends a signal to the brain that is interpreted as colored light. 3.3 The Role of Opsins SWS MWS LWS There are three types of opsins: Short Wave Sensitive (SWS) Medium Wave Sensitive (MWS) Long Wave Sensitive (LWS) An individual who produces only SWS and MWS opsin proteins will have dichromatic vision. An individual who produces SWS, MWS and LWS opsin proteins will have trichromatic vision. Cone Cell Response to Light Image from www.answers.com/topic/photopsin MWS Opsin vs. LWS Opsin What’s the difference? 4.2 Location of Opsin Genes The gene coding for the SWS opsin protein is located on chromosome #7. The gene coding for the MWS and LWS opsins are located on the X-chromosome. 4.3 Origin of the LWS Opsin Gene The LWS gene arose through gene duplication and gene mutation of the MWS gene on the Xchromosome. GENE DUPLICATION GENE MUTATION 4.4 Gene Duplication 4.5 Unequal Crossing Over (Meiosis, Prophase 1) XP XM XP XM Interphase S XP XM Prophase I …Telophase II 4.3 Origin of the LWS Opsin Gene The LWS gene arose through gene duplication and gene mutation of the MWS gene on the Xchromosome. GENE DUPLICATION GENE MUTATION 3.4 Chromatic Vision: Opsins 3D Visualization 2D Visualization The opsin protein is composed of a string of amino acids. Each green dot in the 2D visualization represents one amino acid. MWS PROTEIN maqqwslqrl ifvviasvft lghpmcvleg avwtappifg qvwlairava plmaalpaff vspa agrhpqdsye nglvlaatmk ytvslcgitg wsrywphglk kqqkesestq aksatiynpv dstqssifty fkklrhplnw lwslaiiswe tscgpdvfsg kaekevtrmv iyvfmnrqfr tnsnstrgpf ilvnlavadl rwmvvckpfg ssypgvqsym vvmvlafcfc ncilqlfgkk egpnyhiapr aetviastis nvrfdaklai ivlmvtccit wgpyaffacf vddgselssa wvyhltsvwm vvnqvygyfv vgiafswiwa plsiivlcyl aaanpgypfh sktevssvss LWS PROTEIN MWS Opsin vs. LWS Opsin maqqwslqrl ifvvtasvft lghpmcvleg avwtappifg qvwlairava plmaalpayf vspa agrhpqdsye nglvlaatmk ytvslcgitg wsrywphglk kqqkesestq aksatiynpv dstqssifty fkklrhplnw lwslaiiswe tscgpdvfsg kaekevtrmv iyvfmnrqfr tnsnstrgpf ilvnlavadl rwlvvckpfg ssypgvqsym vvmifaycvc ncilqlfgkk egpnyhiapr aetviastis nvrfdaklai ivlmvtccii wgpytffacf vddgselssa wvyhltsvwm ivnqvsgyfv vgiafswiws plaiimlcyl aaanpgyafh sktevssvss http://www.ncbi.nlm.nih.gov/genbank/ MWS PROTEIN maqqwslqrl ifvviasvft lghpmcvleg avwtappifg qvwlairava plmaalpaff vspa agrhpqdsye nglvlaatmk ytvslcgitg wsrywphglk kqqkesestq aksatiynpv dstqssifty fkklrhplnw lwslaiiswe tscgpdvfsg kaekevtrmv iyvfmnrqfr tnsnstrgpf ilvnlavadl rwmvvckpfg ssypgvqsym vvmvlafcfc ncilqlfgkk egpnyhiapr aetviastis nvrfdaklai ivlmvtccit wgpyaffacf vddgselssa wvyhltsvwm vvnqvygyfv vgiafswiwa plsiivlcyl aaanpgypfh sktevssvss LWS PROTEIN There are 15 differences between the proteins: maqqwslqrl ifvvtasvft lghpmcvleg avwtappifg qvwlairava plmaalpayf vspa agrhpqdsye nglvlaatmk ytvslcgitg wsrywphglk kqqkesestq aksatiynpv dstqssifty fkklrhplnw lwslaiiswe tscgpdvfsg kaekevtrmv iyvfmnrqfr tnsnstrgpf ilvnlavadl rwlvvckpfg ssypgvqsym vvmifaycvc ncilqlfgkk egpnyhiapr aetviastis nvrfdaklai ivlmvtccii wgpytffacf vddgselssa wvyhltsvwm ivnqvsgyfv vgiafswiws plaiimlcyl aaanpgyafh sktevssvss MWS PROTEIN maqqwslqrl ifvviasvft lghpmcvleg avwtappifg qvwlairava plmaalpaff vspa agrhpqdsye nglvlaatmk ytvslcgitg wsrywphglk kqqkesestq aksatiynpv dstqssifty fkklrhplnw lwslaiiswe tscgpdvfsg kaekevtrmv iyvfmnrqfr tnsnstrgpf ilvnlavadl rwmvvckpfg ssypgvqsym vvmvlafcfc ncilqlfgkk egpnyhiapr aetviastis nvrfdaklai ivlmvtccit wgpyaffacf vddgselssa wvyhltsvwm vvnqvygyfv vgiafswiwa plsiivlcyl aaanpgypfh sktevssvss LWS PROTEIN Seven of these differences results in changes to opsin absorbance capacity. maqqwslqrl ifvvtasvft lghpmcvleg avwtappifg qvwlairava plmaalpayf vspa agrhpqdsye nglvlaatmk ytvslcgitg wsrywphglk kqqkesestq aksatiynpv dstqssifty fkklrhplnw lwslaiiswe tscgpdvfsg kaekevtrmv iyvfmnrqfr tnsnstrgpf ilvnlavadl rwlvvckpfg ssypgvqsym vvmifaycvc ncilqlfgkk egpnyhiapr aetviastis nvrfdaklai ivlmvtccii wgpytffacf vddgselssa wvyhltsvwm ivnqvsgyfv vgiafswiws plaiimlcyl aaanpgyafh sktevssvss MWS PROTEIN maqqwslqrl ifvviasvft lghpmcvleg avwtappifg qvwlairava plmaalpaff vspa agrhpqdsye nglvlaatmk ytvslcgitg wsrywphglk kqqkesestq aksatiynpv dstqssifty fkklrhplnw lwslaiiswe tscgpdvfsg kaekevtrmv iyvfmnrqfr tnsnstrgpf ilvnlavadl rwmvvckpfg ssypgvqsym vvmvlafcfc ncilqlfgkk egpnyhiapr aetviastis nvrfdaklai ivlmvtccit wgpyaffacf vddgselssa wvyhltsvwm vvnqvygyfv vgiafswiwa plsiivlcyl aaanpgypfh sktevssvss LWS PROTEIN Differences at positions 180, 277 and 285 result in an absorbance capacity shift of 31nm. maqqwslqrl ifvvtasvft lghpmcvleg avwtappifg qvwlairava plmaalpayf vspa agrhpqdsye nglvlaatmk ytvslcgitg wsrywphglk kqqkesestq aksatiynpv dstqssifty fkklrhplnw lwslaiiswe tscgpdvfsg kaekevtrmv iyvfmnrqfr tnsnstrgpf ilvnlavadl rwlvvckpfg ssypgvqsym vvmifaycvc ncilqlfgkk egpnyhiapr aetviastis nvrfdaklai ivlmvtccii wgpytffacf vddgselssa wvyhltsvwm ivnqvsgyfv vgiafswiws plaiimlcyl aaanpgyafh sktevssvss What difference does 31nm make? MWS PROTEIN maqqwslqrl ifvviasvft lghpmcvleg avwtappifg qvwlairava plmaalpaff vspa agrhpqdsye nglvlaatmk ytvslcgitg wsrywphglk kqqkesestq aksatiynpv dstqssifty fkklrhplnw lwslaiiswe tscgpdvfsg kaekevtrmv iyvfmnrqfr tnsnstrgpf ilvnlavadl rwmvvckpfg ssypgvqsym vvmvlafcfc ncilqlfgkk egpnyhiapr aetviastis nvrfdaklai ivlmvtccit wgpyaffacf vddgselssa wvyhltsvwm vvnqvygyfv vgiafswiwa plsiivlcyl aaanpgypfh sktevssvss LWS PROTEIN Positions 116, 230, 233 and 309: smaller absorbance capacity shifts of 1-3nm. maqqwslqrl ifvvtasvft lghpmcvleg avwtappifg qvwlairava plmaalpayf vspa agrhpqdsye nglvlaatmk ytvslcgitg wsrywphglk kqqkesestq aksatiynpv dstqssifty fkklrhplnw lwslaiiswe tscgpdvfsg kaekevtrmv iyvfmnrqfr tnsnstrgpf ilvnlavadl rwlvvckpfg ssypgvqsym vvmifaycvc ncilqlfgkk egpnyhiapr aetviastis nvrfdaklai ivlmvtccii wgpytffacf vddgselssa wvyhltsvwm ivnqvsgyfv vgiafswiws plaiimlcyl aaanpgyafh sktevssvss What difference does 1-3nm make? • Different variants of the MWS and LWS opsins. • Smaller shifts are called “spectral tuning” and can result in very slight differences in color perception. 4.18 LWS GENE MWS GENE Differences at positions 65, 111, 153, 236, 274, 275, 279 & 298 do not cause changes in spectral properties maqqwslqrl ifvviasvft lghpmcvleg avwtappifg qvwlairava plmaalpaff vspa agrhpqdsye nglvlaatmk ytvslcgitg wsrywphglk kqqkesestq aksatiynpv dstqssifty fkklrhplnw lwslaiiswe tscgpdvfsg kaekevtrmv iyvfmnrqfr tnsnstrgpf ilvnlavadl rwmvvckpfg ssypgvqsym vvmvlafcfc ncilqlfgkk egpnyhiapr aetviastis nvrfdaklai ivlmvtccit wgpyaffacf vddgselssa wvyhltsvwm vvnqvygyfv vgiafswiwa plsiivlcyl aaanpgypfh sktevssvss maqqwslqrl ifvvtasvft lghpmcvleg avwtappifg qvwlairava plmaalpayf vspa agrhpqdsye nglvlaatmk ytvslcgitg wsrywphglk kqqkesestq aksatiynpv dstqssifty fkklrhplnw lwslaiiswe tscgpdvfsg kaekevtrmv iyvfmnrqfr tnsnstrgpf ilvnlavadl rwlvvckpfg ssypgvqsym vvmifaycvc ncilqlfgkk egpnyhiapr aetviastis nvrfdaklai ivlmvtccii wgpytffacf vddgselssa wvyhltsvwm ivnqvsgyfv vgiafswiws plaiimlcyl aaanpgyafh sktevssvss 4.19 Gene Mutation The LWS opsin is a mutated copy of the MWS opsin. Knowing that most of the difference in spectral sensitivity comes from two differences in amino acid structure of these two opsins), what is the likely number of nucleotide mutations needed for successful mutation from a MWS opsin to a LWS opsin? Position 277: phenylalanine to tyrosine Position 285: alanine to threonine Amino Acid Possible Codons Alanine GCU, GCC, GCA, GCG Threonine ACU, ACC, ACA, ACG Phenylalanine UUU, UUC Tyrosine UAU, UAC Can a primate with only TWO functional opsin genes (e.g. SWS & MWS) ever have trichromatic vision? A. B. C. D. E. Yes – definitely Not sure, but possibly No idea Not sure, but probably not No – definitely not Descent with modification of… - Nucleotides (mutations!) Alleles Genes (deletion/duplication) Proteins Cell function - Selectable Phenotype The Ecology of Color Vision in Monkeys 2.5 Food Selection – The Driver of Trichromacy Evolution? 2.6 Food Selection – The Research Part I DICHROMATS TRICHROMATS Given choice of food… vs. Selected ripe fruit 53% of the time. Selected ripe fruit 37% of the time. F 1,10 = 8, p < 0.05, Smith et al., 2003 2.7 Food Selection – The Research Part II TRICHROMATS DICHROMATS Orange-colored Kix Green-colored Kix Caine and Mundy, 2000 2.8 Food Selection – The Research Part II Orange-colored Kix Green-colored Kix TRICHROMATS DICHROMATS 60% 46% 40% 54% Caine and Mundy, 2000 2.9 Food Selection – The Research Part II TRICHROMATS DICHROMATS 60% 46% 40% 54% Trichromats are more effective than dichromats selecting orange food in a green environment… … but dichromats are more effective than trichromats selecting green food in a green environment. Could there be an advantage to being dichromatic in certain environments? Caine and Mundy, 2000 Is color vision always an advantage? • http://www.evoed.com/Pages/Primates/PatchGame/PatchGame.h tml 2.12 Food Selection – The Research TRICHROMATIC VISION DICHROMATIC VISION Saito et al, 2005 2.13 The RESULTS Food Selection – The Research Part III REWARD TRICHROMATS DICHROMATS 51% 85% Saito et al, 2005 Recreate this experiment! 2.14 Food Selection – Summary Research suggests that trichromatic vision is more likely to be selected for when food is distinguished from non-food by color. Research suggests that dichromatic vision is more likely to be selected for when food is distinguished from non-food by shape. Descent with modification of… - Nucleotides (mutations!) Alleles Genes (deletion/duplication) Proteins Cell function - Selectable Phenotype - And Beyond! 1.0 Phylogenetics & Biogeography 5.1 Biogeography of Global Monkeys FULL COLOR VISION COLOR BLIND NEW WORLD OLD WORLD Gene Duplication and Mutation Color Vision Evolves! Wooly Monkey Spider Monkey Sakis Marmoset Old World Primates Owl Monkey Squirrel Monkey Capuchin Colobus Langur Mona Mangabey Baboon Rhesus Gibbon Orangutan Gorilla Chimpanzee Human Phylogenetics – Exploring Relationships Among Species 5.3 New World Primates 5.4 Geology: Plate Tectonics and Drift 225 million years ago 135 million years ago 65 million years ago today New/Old World Separated ~ 50 Million Years Ago. Image: McGraw-Hill Companies Inc. 5.5 How Old are Primates? ~70-80 Million Years Ago 5.6 When did primates first inhabit North America? Wooly Monkey Spider Monkey Sakis Marmoset Owl Monkey Squirrel Monkey Capuchin Colobus Langur Mona Mangabey Baboon Rhesus Gibbon Orangutan Gorilla Chimpanzee Human Continents Split 50 Million Years Ago Color Vision Evolves! Gene Duplication and Mutation Primates In New/Old World 55 Million Years Ago Rise of Primates 75 Million Years Ago Monkey Opsins Exam Question How would you explain evolution to a nonscientist? - Describe the evolution of a trait from the nucleotide level to the ecological level. - Nucleotides Amino Acids Protein Cell Function Phenotype Selection Population/Species Level What’s Left in LB145? Last Class: – Course Evaluations – Take up Exam – Begin Evolution Unit Today: – Finish Evolution Unit Tuesday Apr 23rd: – Bonus survey – Traditional review (?) Don’t Forget… Friday April 19th: View Exams 1, 2, 3 in C4 from 1-3pm. OR Office hours. Weds/Thurs April 24th/25th: Lab Projects Due. Thursday April 25th: – Question-based review (?) Friday April 26th: 3-5pm in C-3 Last-Gasp Tutorial (email me to reserve a place)
