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Lesson 5 Biology Explore Part 1: Gag Gene Amino Acid Comparison Chart Viruses contain what is known as the Gag gene. The Gag gene provides the virus with its basic physical structure. By comparing the amino acid sequence of species’ genes, scientists can determine how closely they are related on a molecular level and if they may share a common ancestor. Below is the partial 66 amino acid sequence of the Gag gene of HIV (human immunodeficiency virus), SIV (simian immunodeficiency virus found in the green monkey), and VLV (sheep visna virus). The 66 sequence is divided into two columns. Analyze the amino acid sequences of the three viruses and determine how many amino acids each virus has in common. Adapted from Visna Sequences by K. Shirriff, 2000. www.righto.com/theories/ visna_seq.html. HIV-1 Gag gene Asn Thr Glu Thr Glu Ser Ala Thr Ala Leu Glu Gln Trp Glu Asp Gln Arg Ile Val Gly His Trp Pro Met Val His Thr Ala Asn ly Asn Pro Pro Ile Pro Ala Ile Pro Pro Gly Val Gln Gly Met Glu Arg Ile Glu Tyr Pro Lys Asp Asp Gly Trp Ser Ile Asp Ile Ile Leu Ala Gly Gly Leu © 2013 Region 4 Education Service Center SIV Gag gene Asn Thr Glu Thr Glu Ser Ala Thr Ala Val Gln Gln Trp Glu Asp Gln Ile Leu Ala Glu His Trp Pro Ile Pro Tyr Pro Thr Ala Ala Gly Asn Pro Pro Leu Arg Pro Val Ala Asp Gly Val Gln Gly Leu Ala Arg Ile Asp Tyr Pro Arg Arg Arg Gly Trp Ser Ile Asp Ile Ile Leu Ala Gly Gly Leu VLV Gag gene Asn Ser Glu Gln Glu Ala Ala Asn Glu Met Arg Asp Trp Gln Val Arg Gln Asn Pro Pro Gly Pro Asn Val Leu Thr Val Asp Ala Gln Arg Ile Gln Met Ile Gly Cys Val Leu Gly Gln Gln Trp Thr Val Asn Ile Gln Thr Gln Ala Ala Leu STAAR™ Achievement Series for Science Lesson 5 Biology Questions 1. Which two viruses share the greatest number of amino acids in the Gag gene? 2. Which two viruses share the least number of amino acids in the Gag gene? 3. What conclusion can be drawn about the relationship between the viruses based on your evaluation of the amino acid sequence? 4. In the viruses that share the least number of amino acids, does this evidence suggest they may still be related? STAAR™ Achievement Series for Science © 2013 Region 4 Education Service Center Lesson 5 Biology Explore Part 2: Primate and Virus Distribution Map African primates carry a virus that is very similar to the HIV that affects humans. The virus is known as SIV (simian immunodeficiency virus). Each primate carries its own variation of the virus, and it is believed SIV was able to jump species to infect humans around the 1930s. Scientists use a variety of techniques to compare the viruses including looking at geography to find a link between species. If we look at the geographical location of some primate species and the emergence of HIV, some insight could be provided on the origin. The following figures show the geographical location of chimpanzees and sooty mangabey monkeys along with a table showing the types of HIV1 and HIV2 and the location of infection. Evaluate the location of primates and the emergence of HIV1 and HIV2 and see if you are able to determine a connection between the primate locations and the origin of the viruses. Questions 1. Do you think that there is a relationship between the location of infection and the specific type of primate in that area? 2. Were you able to conclude what species of primate could be responsible for HIV1? 3. Were you able to conclude what species of primate could be responsible for HIV2? STAAR™ Achievement Series for Science © 2013 Region 4 Education Service Center Lesson 5 Biology Explore Part 2: Primate and Virus Distribution Map Chimpanzee habitat Sooty mangabey habitat Location HIV1 Subtype M HIV1 Subtype N HIV2 Southeastern Cameroon Rare—only found in south central Cameroon Infections limited to Senegal, Liberia, Ghana, and Cote D’ Ivoire Adapted from “Origin of HIV-1 in Chimpanzee Pan troglodytes” by F. Gao et al, 1999, Nature 397: pp. 436–441. Adapted from “Simian Immunodeficiency Virus Infection in Free-ranging Sooty Mangabeys (Cercocebus atys atys) from the Tai Forest, Cote d’ Ivoire: Implications for the Origin of Epidemic Human Immunodeficiency Virus Type 2” by M. L. Santiago et al, 2005, Journal of Virology, 79(19): pp.12515–12527. © 2013 Region 4 Education Service Center STAAR™ Achievement Series for Science Lesson 5 Biology Explain: Evolution—Molecular Homology and Biogeography Molecular Homology In modern evolutionary biology, molecular homology has become an important concept to test the relationships between species and to analyze, at a molecular level, the process behind evolution. Advances in technology have allowed scientists to examine DNA sequences, amino acid sequence in proteins, and also homologous protein folds of species. Contained in every species’ DNA and the proteins that the DNA codes for is the species’ evolutionary history. Homologous structures are traits derived from a common ancestor. If a species shares a DNA base sequence and the protein created from the sequence, they likely share a common ancestor. Once the species separate, they are subject to mutations and develop slight differences in the trait. These mutations can assist scientists in determining how closely related species are and in estimating the time since the separation occurred. All living things share basic similarities at the cellular and molecular levels. They use the same nucleotides within their DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Biogeography Biogeography is the study of the distribution patterns of species in geographical areas. Species are distributed largely by their genetic relationship to each other, with some exceptions. Many of the exceptions can be explained by continental drift. Biogeography can help in determining the relationship of species, but should also be confirmed with additional information. Coevolution Coevolution is when two or more species affect each other’s evolution. Coevolution is likely to happen in situations where different species have close ecological interactions. This includes predator/prey, parasite/host, and competitive and mutualistic relationships between species. Questions 1. Can scientists look at one aspect of evolution (e.g., biogeography) and predict with certainty a species’ evolution? 2. Based on the reading, explain why many primate species are able to live with SIV and never be harmed by the virus. STAAR™ Achievement Series for Science © 2013 Region 4 Education Service Center Lesson 5 Biology Elaborate: Who Is Related? There are many species of African primates infected with a version of SIV. The version of SIV is specific to that species of primates. For example, SIVgor infects gorillas, SIVdrl infects drill monkeys, SIVcpz infects chimpanzees, and SIVsm infects sooty mangabey monkeys. In many cases, it is believed that primates are cross-infected, creating a new strain; for instance, sooty mangabey monkeys have cross-infected some species of macaque monkeys in Northern Africa. Unlike HIV, the primate virus, SIV, rarely harms its host, which suggests they have been associated for a long period of time. This is further supported in the cross-contamination of the macaques. The macaques display AIDS-like symptoms when infected. Scientists believe that at some time around the 1930s, SIV was able to jump species and infect humans, leading to what is known as HIV. In order to understand the virus and its evolution, researchers study multiple versions of SIV and look for common traits among its DNA. Understanding the virus in which HIV originated may provide insight into the behavior of the virus along with how it can be effectively treated. Student Instructions Take the role of a molecular biologist trying to link a particular SIV to HIV. Analyze the 103 amino acid sequence of the Pol gene in three versions of SIV: SIVcpz (chimpanzee), SIVsm (sooty mangabey), and SIVdrl (drill monkey) and the two human HIV types: HIV1 and HIV2. Develop a logical argument that each HIV is linked or not linked to a version of primate SIV. In your science notebook, record all data and answer the questions below. Questions 1. Which SIV has the most amino acids in common with HIV1? What percentage of amino acids do they share? 2. Which SIV has the most amino acids in common with HIV2? What percentage of amino acids do they share? 3. What percentage of amino acids do HIV1 and HIV2 commonly share in the Pol gene? 4. Compare the results to the biogeography of chimpanzee and sooty mangabey monkeys and the onset of both HIVs. Do the results support one another? © 2013 Region 4 Education Service Center STAAR™ Achievement Series for Science Lesson 5 Biology Elaborate: SIV and HIV Pol Gene Amino Acid Sequence Chart SIVdrl Pol protein Asp Thr Lys Gly Val Ala Thr Asp His Asp Ala Thr Ser Val Val Ile Leu Gln Val Gly Pro Gly Thr Ile Pro Glu Val Leu Asn Thr Ile Gly Ile Lys Gly Arg Asn Trp Val Lys Leu Pro Cys Gln Lys Val Leu Ile Gly Gly Ala Gly Thr Ile Leu Gly Asn Gly Phe Cys Pro Ile Val His Val Lys Ser Gln Lys Tyr Val Phe Glu Asn Pro Cys Val Arg Lys Ile Val Gln Thr Ile Leu Ala Lys Gly Pro Gly Met Pro SIVcpz Pol protein Asp Thr Arg Gly Lys Ala Val Asp Val Asp Gly Thr Thr Val Val Ile Leu Glu Val Gly Pro Arg Thr Ile Pro Gln Val Leu Asn Gln Ile Gly Ile Leu Gly Arg Asn Trp Ile Lys Leu Pro Thr Lys Gln Met Leu Ile Gly Gly Cys Gly Thr Ile Leu Gly Val Gly Phe Phe Pro Ile Ile Lys Val Lys Ser Gln Ser Phe Ile Asp Glu Asn Thr Val Val His Pro Ile Val Glu Lys Ile Leu Glu Lys Gly Pro Gly Met Pro - - SIVsm Pol protein Asp Thr Lys Gly Val Ala Ile Asp Lys Asp Gly Ser Thr Ile Ile Val Met Ala Thr Gly Asp Gly Thr Ile Pro Glu Ile Leu Asn Gly Ile Pro Phe Asn Gly Arg Asn Tyr Leu Thr Leu Pro Thr Lys Ala Ile Met Val Gly Gly Met Gly Ser Ile Leu Gly Asn Gly Leu Phe Pro Ile Ile Asn Thr Lys Ala Glu Lys Tyr Ile Lys Glu Asp Pro Val Ile Lys Lys Ile Ile Arg Met Val Leu Leu Lys Asn Pro Gly Lys Pro - HIV-1 Pol protein Asp Thr His Gly Lys Ala Ala Asp Ile Asp Gly Thr Thr Val Val Leu Leu Glu Val Gly Pro Glu Thr Met Pro Asn Val Leu Asn Pro Ile Gly Ile Lys Gly Arg Asn Trp Leu Lys Leu Pro Thr Lys Gln Met Ile Ile Gly Gly Cys Gly Thr Ile Leu Gly Asn Gly Phe Phe Pro Ile Ile Lys Val Arg Ser Gln Pro Tyr Ile Asp Glu Gln Thr Ile Val Leu Pro Ile Val Glu Lys Ile Leu Cys Lys Gly Pro Gly Met Pro - HIV-2 Pol protein Asp Thr Lys Gly Arg Ala Val Asp Arg Asp Ala Ser Thr Ile Ile Val Met Ala Thr Gly Asp Gly Thr Val Pro Glu Ile Leu Asn Gly Ile Ser Phe Asn Gly Arg Asn Tyr Ile Ser Leu Pro Thr Lys Ala Ile Leu Val Gly Gly Met Gly Ser Ile Leu Gly Asn Gly Leu Phe Pro Ile Val Asn Thr Lys Ala Glu Lys Tyr Ile Lys Glu Asn Pro Val Ile Glu Lys Ile Ile Arg Met Val Leu Leu Lys Asn Pro Gly Lys Pro - Adapted from “A Novel Simian Immunodeficiency Virus (SIVdrl) Pol Sequence from the Drill Monkey, Mandrillus leucophaeus,” by J. P. Clewley et al,1998, Journal of Virology, 72(12), pp.10305–10309. STAAR™ Achievement Series for Science © 2013 Region 4 Education Service Center Lesson 5 Biology Name: _____________________________________________ Date: __________ Evaluate: Evolution—Molecular and Biogeographical Evidence 1 2 3 The majority of African primates are carriers of a version of SIV, but do not normally suffer any harmful effects from the virus. This is most likely due to — A covergent evolution B coevolution C divergent evolution D speciation Molecular biology uses all of the following to determine the relationship among species except — F DNA sequences G homologous protein folds in species H carbon dating J amino acid sequence in proteins Which of the following would be the best evidence to suggest that two species share a common ancestor? A Similar features B Similar DNA sequence C Compete for the same food source D Share the same ecosystem © 2013 Region 4 Education Service Center STAAR™ Achievement Series for Science Lesson 5 Biology 4 5 During the first half of the 20th century, Guinea-Bissau in West Africa was a Portuguese colony and many of the residents used the local sooty mangabey monkey as a food source (bush meat) and as house pets. Around the same time, a war for independence erupted and changed the economic status of the region. People within the region began contracting a new type of HIV, known as HIV2 Type A, that was isolated to the GuineaBissau area. HIV2 Type A was very similar genetically to the SIVsm (sooty mangabey). As the war ended and the Portuguese soldiers returned home, some Portuguese veterans displayed symptoms of HIV and were later diagnosed with HIV2 Type A. What evolutionary evidence strongly suggests that the virus the Portuguese veterans contracted is closely related to HIV2 Type A without analyzing the DNA sequence? F Biogeography G Molecular H Speciation J Natural selection It was believed that SIV in African primates is fairly young, being only a few centuries old. This offered promise for the outlook of HIV. If SIV was able to evolve so rapidly and coexist and not harm its host, then HIV may follow the same evolution. Recently, monkeys on Bioko Island, off the coast of West Africa, were found to carry types of SIV that were similar to their species’ counterparts on the mainland of Africa. The island split off the African continent around 12,000 years ago. If no primate species has been introduced to the island, this suggests that SIV had already infected the primates that were on the island when it split. Explain what this new evidence suggests about SIV and the future of the HIV evolution? What type of evolution evidence is this an example? STAAR™ Achievement Series for Science © 2013 Region 4 Education Service Center
