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GENE DUPLICATION: SOMETIMES MUTATIONS ARE A GOOD THING – TEACHER HANDOUT GRADE LEVEL: • High-school biology OBJECTIVES: THE STUDENTS WILL: • • • • • • • • Become familiar with the concepts of gene duplication and translocation. Understand that gene duplication is an important source of new genes. Reconstruct the genetic history of human eye-pigments. Use a phylogenetic tree of the orders of fish to speculate on the number of times fish antifreeze evolved. Outline the steps of how fish antifreeze probably evolved. Form a hypothesis about the adaptive advantage of snake venom. Become familiar with the evolution of snake venom, including examples of nonvenomous proteins that became integral parts of snake venom. Use a phylogenetic tree of the major groups of snakes to speculate on the number of times venom evolved. BACKGROUND INFORMATION: THE STUDENTS SHOULD ALREADY BE FAMILIAR WITH THE FOLLOWING TOPICS: • • • • • • Phylogenetic trees DNA structure, transcription, and translation Chromosomes and meiosis DNA and chromosomal mutations Basic protein structure The steps of acquiring adaptations (natural selection) TIME REQUIREMENT: (Includes time for a review of DNA, transcription, translation, an overview of gene duplication and translocation, and a follow-up discussion) • Two 70-minute blocks or three 45-minute class periods TEACHER PREPARATION: • Make copies of the handouts. MATERIALS (ONE PER STUDENT): • Student handout - “Gene Duplication: Sometimes Mutations are a Good Thing” EVALUATION: • • Answers on student handout, even if technically incorrect, should be defensible. Check for understanding during classroom discussion. Gene Duplication Page 1 GENE DUPLICATION: SOMETIMES MUTATIONS ARE A GOOD THING – TEACHER HANDOUT Background Refresher: 1. Through the processes of transcription and translation, cells make _proteins_______, which are made up of folded strings of _amino acids_. 2. There are two basic categories of proteins. Name them and briefly describe what they do. a. Structural proteins – building materials of organisms b. Functional proteins – these proteins do things (e.g. enzymes) 3. A segment of DNA that codes for a protein or a trait is called a _gene__________. 4. If almost all of the cells in a human body contain the exact same sequence of DNA, how is it possible to have different types of cells that have very different jobs (e.g. nerve cells, muscle cells, liver cells, eye cells, etc.)? In other words, what do the cells do differently from each other in order to perform their different jobs? They use (transcribe and translate) different genes. 5. We know that one gene can have many forms (alleles). For example, the gene for flower color may have red, white, or yellow alleles. What is the name of the process that caused these different alleles to be formed in the first place? Mutation 6. This process is very important because it is what causes individuals to be different. Explain how this individual variation is important regarding the formation of adaptations. Variation is necessary for adaptations to evolve. Without every individual is equally able to survive and reproduce. Therefore, the species will not change over time. Gene Duplication Sometimes, a gene (which codes for a protein) is duplicated and both copies are kept in the DNA. If both copies of the gene work, then both can be transcribed and translated to make extra amount of the protein. 7. One way that genes are duplicated is from unequal crossing over. You should remember what normal (or equal) crossing over is. What is it and when does it occur? Crossing over is the process by which chromosomes exchange segments. I occurs during metaphase I of meiosis. Gametes Figure 1. Unequal crossing over occurs when one chromosome of a homologous pair keeps more DNA than it gives to the other chromosome. Gene Duplication This chromosome has two copies of the original gene. Page 2 Figure 2. Genes can move from one chromosome of a homologous pair to another chromosome of a different homologous pair. This is called translocation. Notice how one of the extra copies of the gene moved from the larger chromosome to the smaller one. Gametes This gamete has two copies of the gene, but they are on different chromosomes When an organism has two copies of a gene, the first copy usually stays the same (and does its important job), but the second copy may change (mutate). If the mutated gene helps the organism survive better than before the duplication, then it is an adaptation. This is sometimes called “Duplicate and Diverge.” The gene duplicates and then their functions diverge (by mutating). It turns out that 38% percent of human DNA exists as a result of gene duplication (Zhang, 2003)! Case Study #1 – Eye pigments Pigments are proteins that are sensitive to certain wavelengths (colors) of light. Your retina contains four different light-sensitive pigments (rhodopsin, blue, red, and green pigments). The gene that codes for rhodopsin is the original eye-pigment gene. It is found on chromosome #4. All the other eyepigment genes were duplicated from this original one. This pigment is found in the rods of the retina, is sensitive to the middle wavelengths of visible light, and only works in dimly lit situations. The gene that codes for the blue-sensitive pigment (and lets you see the color blue) is found on chromosome #7. The genes that code for the red and green-sensitive pigments are both on the X-chromosome (Offner, 1994). Figure 3. This figure shows the wavelengths of light each eye pigment absorbs. BLUE PIGMENT GREEN PIGMENT RHODOPSIN RED PIGMENT 8. Fill in the following Table1 which compares the genes for eye-pigments. Table 1. Location and functions of the eye-pigment genes Eye-pigment Chromosome where gene is located Wavelength of light that it absorbs best Rhodopsin 4 498 nm Blue 7 420 nm Red X 564 nm Green X 534 nm Gene Duplication Page 3 Use the information provided to fill in the phylogenetic tree (Figure 4) that shows how the eye pigments are related to each other. There are two equally good answers. Table 2. This table shows the percent DIFFERENCES in amino acids among the eyepigment proteins (Offner, 1994). Rhodopsin 9. Blue Pigment Red Pigment Green Pigment Figure 4. Phylogenetic Tree of eye pigments Rhodopsin --- 60% 60% 60% Blue Blue Pigment --- --- 60% 60% Red or Green Red Pigment --- --- --- 4% Green Pigment --- --- --- --- RHODOPSIN Green or Red 10. Use what you know about how genes duplicate and move (translocate) to fill in the chart below. a. Fill in the names of the pigments and which chromosomes they are found on. b. In the boxes above or below each of the arrows fill in the mechanisms that probably made and/or moved the new gene. • GD = “gene duplication” • T = “transposition” There are two equally good answers. Gene:Rhodopsin G D T Gene: Chromosome #: Chromosome #: 4 G D T Gene: G D Chromosome #: Gene: Chromosome #: 11. What is an adaptation? An adaptation is a trait that helps an organism survive and/or reproduce. 12. Explain how these new eye-pigment genes are adaptations. Answers may vary It enables the animal to see colors which may be important for detecting poisonous plants and animals, ripe fruit, etc. Gene Duplication Page 4 Fill in the Table 3 to explain how a new eye-pigment adaptation could be formed. Table 3. Steps to developing new eye pigments. Steps to getting an adaptation How humans developed new eyepigments 1. More offspring are produced than can survive and reproduce. Humans produce more offspring than can survive and reproduce. 2. Because of gene duplication and further mutation (divergence), members of a population may have different genes. Because of eye-pigment duplication and further mutation, some members of a population are able to detect different colors. 3. Selective pressures are present. Selective pressure may include detecting poisons or ripe fruit (or other) 4. Individuals with the genes that give them the most favorable traits are more likely to survive and pass those genes on to their offspring. Individuals with the new eye-pigment gene are more likely to survive (avoiding toxins, finding high-calorie foods), reproduce, and pass the new gene on to offspring. 13. It turns out that some people have two working copies of the green eye-pigment gene (the green eye-pigment gene has duplicated again!). Over time, what do you think might happen to this second copy of the gene? Answers will vary. Case Study #2: Antifreeze in Fish Sometimes a gene duplication results in a protein that can do something totally new (this is called a novel function). Arctic cod (Boreodadus saida) live in the freezing cold waters of the arctic. The average temperature of this water would freeze most fish (because they are ectothermic or “coldblooded”). This would kill them because, when animals freeze, ice crystals grow inside of their bodies. These ice crystals slice cells and tissues apart. However, the arctic cod makes an antifreeze protein that prevents ice crystals from growing. The antifreeze protein is made in the cod’s liver and is released into its bloodstream. Just how did the arctic cod develop such a nifty adaptation? Well, it turns out that the gene that codes for the antifreeze protein is very similar to a gene that is used to make a digestive enzyme in the pancreas. Researchers figured out that the gene for the digestive enzyme duplicated and that the second gene mutated into one that produced the antifreeze protein. The newer antifreeze protein is made in the liver and released into the bloodstream (Cheng and Chen, 1999). 14. List two ways the new gene is different from the original one. a. It is active in a different part of the body (liver instead of pancreas). b. It makes a different protein (antifreeze instead of digestion enzyme) Gene Duplication Page 5 15. Fill in Table 3 to explain how the arctic cod could have developed such a cool adaptation. Be specific with regards to how the genetic variation arose. Table 3. Steps to developing antifreeze proteins. Steps to getting an How the arctic cod adaptation developed antifreeze proteins 1. More offspring are produced than can survive and reproduce. Cod produce more offspring than can survive and reproduce. 2. Because of gene duplication and further mutation (divergence), members of a population may have different genes. Because of gene duplication and divergence, some members of the population have “antifreeze” genes 3. Selective pressures are present. Surviving in freezing cold water is the selective pressure. 4. Individuals with the genes that give them the most favorable traits are more likely to survive and pass those genes on to their offspring. Individuals that have the “antifreeze” genes are more likely to survive in the cold waters, reproduce and pass the genes on to their offspring. Figure 6. A phylogenetic tree of the orders of fish (Preikshot, 2005) Well, it turns out that arctic cod are not the only fish to have developed an antifreeze gene. A group of fish, called the Notothenoids, that live on the other side of the planet (around Antarctica) have also developed an antifreeze gene. Not only that, but their gene also resulted from the replication of a digestive enzyme gene (Chen et. al., 1997). Figure 5. Distribution of arctic cod and the notothenoids. Arctic cod (Boreogadus saida) Notothenoid species http://ww© The Exploratorium, www.exploratorium.edu Table 4. Classification of Arctic Cod and Notothenoids Arctic Cod Notothenoids Kingdom Animalia Animalia Phylum Chordata Chordata Class Actinopterygii Actinopterygii Order Gadiformes Perciformes 16. Look at the phylogenetic tree of the orders of fish (Figure 6) and the classification of the arctic cod and notothenoids (Table 4). Use them to explain whether you think fish antifreeze formed only one time or more than one time in the history of these organisms. Hint: highlight the orders of fish that make antifreeze. It seems to have evolved at least twice. If it had evolved only once, then one would expect to find it in other (closely related) orders. Gene Duplication Page 6 Case Study #3: Snake Venom Snakes are a group of reptiles that are closely related to lizards. Unlike most lizards, snakes do not have legs. Furthermore, they are strictly carnivorous and must swallow their prey whole (they cannot rip their food apart or chew it). As you can imagine, catching a live animal without being able to use arms/legs can be quite dangerous for any predator. 17. Primitive or early forms of snakes, like boas and pythons, do not produce venom. How do you think they kill or subdue their prey? Constriction 18. Many modern groups of snakes produce venom, which contains toxic proteins that kill and/or subdue their prey. Explain how this is an adaptation. It enables them to eat animals that they could not constrict (because they are too large/dangerous). Originally, scientists assumed that these venomous proteins were ones that were already in the saliva. Over time, these proteins were thought to have become more toxic as the snakes were relying on them more and more to subdue their prey. Researchers have only recently started to study the genes that code for the venomous proteins, and the explanation is not quite that simple. So far, they have identified 24 different toxic proteins in the venom. Of these proteins, only two were originally produced in the salivary glands (which then developed into venom glands) and became more toxic because of selective pressures. The remaining 22 proteins were products of gene duplication. In other words, the original proteins have other jobs in the snakes’ bodies. The genes that code for these proteins duplicated. These duplicated genes then accumulated mutations that enabled them to be made in the salivary (venom) glands (Fry, 2005 and Zimmer, 2005). These particular proteins do things that make them quite dangerous if injected directly into one’s blood stream. Figure 8. Garter snake eating a toxic newt (Brodie, 2005). Figure 7. Venom Gland (CPCS, 2000). Figure 9. Location of where some of the venomous proteins originated (Zimmer, 2005). URETERS TESTES KIDNEYS LARGE INTESTINE SMALL INTESTINE SPERM DUCT Gene Duplication SPLEEN GALLBLADDER STOMACH PANCREAS Page 7 HEART LIVER LUNG TRACHEA THYROID GLAND BRAIN VENOM GLAND ESOPHAGUS 19. Look at Table 5. It gives the name of some of the original proteins and what they do. Fill in the missing explanations of how these proteins would help kill or subdue prey if injected directly into their body. Table 5. Examples of proteins are now made in the venom glands of some snakes (Fry, 2005). Name of modified protein (venom protein) Where the original protein is made What the original protein does How the modified protein (venom) helps kill or subdue prey when injected into bloodstream Acetylcholinesterase Muscles Helped control muscle contractions Disrupts nerve impulses causing heart and respiratory failure of the prey. BNP Heart Relaxes muscles around heart Blood pressure drops dramatically. L-amino oxidase Immune tissues Causes cells to burst open Kills cells Lectin Throughout body Makes blood clot Causes blood to coagulate. ADAM Sperm ducts, colon, lung, lymph node, thymus Tissue decay Kills cells Note: these are only a sample of the 24 venom proteins that have been identified. So far, studies suggest that all venomous snakes make the same toxic proteins in their venom glands. Some snakes are less poisonous than others (e.g. garter snakes). This difference is because they either make a smaller amount of the toxic proteins, or they inject less into their prey. 20. Look at Figure 10 (Phylogenetic Tree of Major Snake Groups). Does it appear that the evolution of snake venom occurred one time or more than one time? Explain your answer. (Hint: highlight all of the snake groups that can make venom.) It appears to have evolved only one time because all of the venomous snakes share a common ancestor. Figure 10. Phylogenetic Tree of Major Snake Groups (Uetz, 2002). Scolecophidia (incl. Blind snakes) NF, NV Henophidia (incl. Boas and pythons) NF, NV Viperidae (incl. Vipers and rattlesnakes) FF, V Homalopsinae (incl. Stout-bodied water snakes) some species RF and MV Colubrinae (incl. Bullsnakes, kingsnakes, brown tree snakes) some species RF and MV Natricinae (incl. Water snakes and garter snakes) NF, some species MV Xenodontinae (incl. Hognosed snake) some species RF and MV Atractaspidae (incl. Mole viper and burrowing asp) FF, V Elapidae (incl. Cobras, coral snakes, and sea snakes) FF, V Note: NF = “no fangs”, RF = “rear fangs”, FF = “front fangs” NV = “non-venomous”, MV = “mildly venomous”, V= “venomous” 21. In your own words, describe the “take-home message” of this lesson. Think about what all of these case studies have in common. Organisms can gain new adaptations through gene duplication and divergence (e.g. color-vision, antifreeze, venom). Gene Duplication Page 8 References: Brodie, S.(2005). Biology faculty web page of Edmund D. Brodie III. Indiana University. Retrieve October 23, 2005 from: http://www.bio.indiana.edu/facultyresearch/sciencepics/brodie_snake.jpg. Chen, L., A.L. DeVries, and Cheng, C.C. (1997). Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenoid fish. Proceedings of the National Academy of Sciences, 94, 3811 – 3816. Cheng, C.C. and L. Chen. (1999). Evolution of an antifreeze glycoprotein. Nature, 401, 443 – 444. CPCS. (2000). Rattlesnake Bites. California Poison Control Sytem. Retrieved October 23, 2005 from: http://www.calpoison.org/public/snake-gland.gif Fry, B. (2005). From genome to “venome”: Molecular origin and evolution of the snake venom proeome inferred from phylogenetic analysis of toxin sequences and related body proteins. Genome Research [online], 15, 403 – 420. Retrieved October 23, 2005 from: www.genome.org. Kingsley, D. (2003). Ancient worlds news – venom common, predates snake evolution. ABC Science Online. August 22. Retrieved October 23, 2005 from: http://www.abc.net.au/science/news/ancient/AncientRepublish 927762.htm Logsdon, J.M. and W.F. Doolittle. (1997). Commentary: Origin of antifreeze protein genes: a cool tale in molecular evolution. Proceedings of the National Academy of Sciences, 94, 3485 – 3487. Offner, S. (1994). Using chromosomes to teach evolution I. Conserved genes and gene families. The American Biology Teacher, 56(2), 79 – 85. Onge, D. Origins Antarctica: scientific journeys from McMurdo to the Pole. The Exploratorium, Retrieved October 23, 2005 from:http://www.exploratorium.edu/origins/antarctica/ideas/fish4.html Preikshot, D., R. Froese and D. Pauly. (2005) The orders table. FishBase. World Wide Web electronic publication, version (10/2005). Retrieved October 23, 2005 from: http://www.fishbase.org/manual/English/orders.htm Uetz, P. (2002). Phylogeny of snakes. EMBL Heidelberg. European Molecular Biology Laboratory. Retrieved October 23, 2005 from: http://www.emblheidelberg.de/~uetz/families/taxa.html#Ser Wikipedia.org. (2005). Rhodopsin. Wikipedia: Free Encyclopedia [Online]. Retrieved October 23, 2005 from: http://en.wikipedia.org/wiki/Rhodopsin Zhang, J. (2003). Evolution by gene duplication: an update. Trends in Ecology and Evolution, 18(6), 292 – 298. Zimmer, C. (2005). Open Wide: Decoding the Secrets of Venom. The New York Times, April 5. Gene Duplication Page 9