This Document Contains Chapters 22 to 24 CHAPTER 22: SYSTEMATICS, PHYLOGENIES, AND COMPARATIVE BIOLOGY WHERE DOES IT ALL FIT IN? Chapter 22 expounds on Chapters 20 and 21 by relating evolutionary principles to the ways biologists categorize biodiversity. It is important to briefly summarize the principles of biodiversity before approaching this chapter. Chapter 22 is essential to explain the categories of organisms covered later in the textbook. SYNOPSIS A peculiar characteristic of humans beginning with the early Greeks to present-day is to pigeonhole organisms into groups based on traits, first by looking at physical traits, then only recently by including physiological, genetic and behavior traits. Classification systems have existed for thousands of years; however, Carolus Linneaus in the mid-1700s created the system in use today. Taxonomy as a science is a necessary part of biology in that it provides reference points for further discussion of various organisms, their habitats, interactions, genetic relationships, biochemistry, behavior and more. Without it scientists would never be sure whether they were examining the same type of individual or group of organisms. The most widely accepted classification scheme is hierarchal with each subunit encompassing a smaller but more similar group of organisms. The arrangement from the most inclusive to the least inclusive is: domain-kingdom–phylum–class–order–family–genus–species. The binomial nomenclature system created by Linnaeus further enhanced taxonomy by providing convenience and precision in standardizing names for all organisms. On the surface, defining a species seems simple, but the criteria are not always absolute. The biological species concept states that organisms capable of producing fertile offspring are the same species. This concept, when expanded over evolutionary time, states that a species is a single linage and maintains its distinctive identity from other lineages within a population. To understand evolutionary relationships among populations of lineages through time, scientists use systematics and cladistics. Systematics studies evolutionary relationships by looking at similarities and differences between species by constructing an evolutionary tree or phylogeny. Cladistics through cladogram construction focuses on certain key characteristics of a group that are shared being inherited from a common ancestor as well as shared derived traits in which similarities arose within the group. Cladograms do not identify ancestors, but are useful hypotheses in understanding evolutionary relationships in providing insights for how, when and what rate traits evolved through adaptation, selective pressure or some other means. The proposed ancestors in traditional phylogenies are indicated at the nodes between branches. The comparisons in cladistics are objective and based on so many characters with assigned importance values that computers are required to make the assessments. The diversity of all living things is astounding! All organisms with characteristics of organization, response to stimuli, growth, development, reproduction, regulation and homeostasis are classified into three domains (a taxonomic level higher than the kingdom) Archaea, Bacteria, and Eukarya; and, the six-kingdom system proposed by Carl Woese that further separates the domains into kingdoms of: archaebacteria, bacteria, protista, fungi, plantae, and animalia. The Domain Archaea includes the kingdom archaebacteria that seem to have diverged from the bacteria and are more similar to eukarya than bacteria. Archaebacteria include the prokaryotic methanogens, the extremophiles (halophiles, thermophiles, pressure-tolerant archaebacteria) and the nonextreme archaebacteria that inhabit the same environments as bacteria. Domain Bacteria includes the prokaryotic kingdom bacteria whose members are the most abundant organisms on earth and are so tiny they cannot be seen with the naked eye. They play a critical role in the earth’s ecology as decomposers and recyclers of carbon, nitrogen, and sulfur. Still others are pathogenic and cause many diseases. Domain Eukarya include the four eukaryotic kingdoms of protista, fungi, plantae, and animalia. Analysis of the two major metabolic organelles, mitochondria and chloroplasts, indicates an origin associated with bacteria. The endosymbiosis hypothesis states that early in the history of eukaryotes, some bacteria became endosymbionts and eventually became the mitochondria and chloroplast organelles found in eukaryotic cells. All Domain Eukarya members, even though extraordinary diverse, share three characteristics not found in prokaryotes: compartmentalization, multicellularity in some, and sexuality. All Eukarya kingdoms have discrete compartments providing for specialization within the cell. Kingdom protista is primarily unicellular, while the other three Eukarya kingdoms exhibit multicellularity (with the exception of yeast in kingdom fungi). Another key characteristic of eukaryotes is sexuality. The genetic exchange that occurs in bacteria is not a predictable event. In kingdom protista the process of sexual reproduction occurs only occasionally, but in the Eukarya kingdoms of fungi, plantae and animalia sexuality is regular with predictable results and often includes an alternation between syngamy and meiosis. It is important to note that viruses are not placed in any of the six kingdoms. They are not living organisms as they do not exhibit all of the characteristics of organization, response to stimuli, growth, development, reproduction, regulation, and homeostasis and are not, therefore, properly classified as organisms. Viruses are fragments of eukaryotic or prokaryotic genomes or intracellular parasitic chemicals capable of replication only in connection with a prokaryote or eukaryote host cell. There are problems with the six-kingdom subjective approach in attempting to classify all living organisms. Proposals have been suggested to increase the number of kingdoms to reflect the diversity found within the established kingdoms. For example, kingdom protista with over 200,000 members is the weakest of the six-kingdom classification system, as it is not grouped based on evolutionary relationships. This kingdom is often used as a catchall kingdom for any eukaryotic organism that is not a plant, fungus, or animal. Many systematists are proposing a new kingdom called Virdiplantae, green plant kingdom. Phylogenies are hypothesis and subjected to change as a result of new discoveries of phylogenetic relationships. Additional phylogenetic problems include the relationships between water/land plants, segmentation among animals, flight among animals, and differences in mammals to name a few. LEARNING OUTCOMES 22.1 Systematics Reconstructs Evolutionary Relationships 1. Recognize what a phylogeny represents. 2. Explain why phenotypic similarity does not necessarily indicate close evolutionary relationship. 22.2 Cladistics Focuses on Traits Derived from a Common Ancestor 1. Differentiate between ancestral and derived characters. 2. Contrast informative shared, derived characters from noninformative ones. 3. Discuss the drawbacks of molecular clocks for timing evolutionary events. 22.3 Classification Is a Labeling Process, Not an Evolutionary Reconstruction 1. Differentiate among monophyletic, paraphyletic, and polyphyletic groups. 2. Discuss the phylogenetic species concept and its drawbacks. 22.4 Taxonomy Attempts to Classify Organisms in an Evolutionary Context 1. Explain how taxonomists name and group organisms. 22.5 The Largest Taxons Are Domains 1. List examples showing that the three domains of life are monophyletic, but the six kingdoms are not. 2. List the distinctive characteristics of bacteria. 3. Distinguish between bacteria and archaea. 4. Distinguish between prokaryotes and eukaryotes. COMMON STUDENT MISCONCEPTIONS There is ample evidence in the educational literature that student misconceptions of information will inhibit the learning of concepts related to the misinformation. The following concepts covered in Chapter 22 are commonly the subject of student misconceptions. This information on “bioliteracy” was collected from faculty and the science education literature. • Students believe that classification is determined by appearance of the organism • Students are unfamiliar with molecular strategies of classification and phylogeny • Students believe that unrelated organisms can mate to produce hybrid creatures • Students believe that only the observable phenotype is subject to selection • Students believe that DNA variation between different organisms if always very high • Students are unfamiliar with the degree of conserved genes between unrelated organisms • Students believe that acquired traits are inherited • Student believe evolution is driven to make “better” organisms • Students believe that organisms adapt to change rather than being selected • Students do not take into account mutation in determining population genetics • Students believe “fitness” is an absolute set of characteristics • Students believe that species are genetically distinct and fixed INSTRUCTIONAL STRATEGY PRESENTATION ASSISTANCE Don’t present classification as mere memorization of names and relationships. Relate various evolutionary adaptations, primitive versus specialized characteristics, similarities versus differences, and so forth. Don’t introduce new phyla without contrasting them in some way to those already presented. Many mnemonics exist to remember kingdom, phylum, etc., although it is probably better to have students make up their own. It will help foster their creativity and they will be more likely to remember the mnemonic better since it will utilize their own language and style. Always relate this information in this chapter with information in chapter 1 which discusses the characteristics of life. Try not to get too detailed with kingdom characteristics as details will be discussed in later chapters. But do discuss evolutionary relationships between the kingdoms by discussing molecular, phylogenetic, and cladistic evidence. HIGHER LEVEL ASSESSMENT Higher level assessment measures a student’s ability to use terms and concepts learned from the lecture and the textbook. A complete understanding of biology content provides students with the tools to synthesize new hypotheses and knowledge using the facts they have learned. The following table provides examples of assessing a student’s ability to apply, analyze, synthesize, and evaluate information from Chapter 22. Application • Have students explain the factors leading to the evolution of HIV. • Have students describe how endosymbionts contribute to an organism’s evolution. • Ask students to explain how the duplication of a gene can lead to speciation. Analysis • Have students explain the role of agriculture in the evolution of new human diseases. • Ask students to compare the phylogenetic similarities and differences between animals and plants. • Ask students to hypothesize about classification of an organism that has characteristics that equally overlap those of worms and arthropods. Synthesis • Ask students to describe how molecular biology could contribute to identifying if a similarity seen between two organisms is due to homoplasy. • Have students develop a cladistic diagram relating the similarities of a box of assorted screws and bolts. • Ask students to explain the medical importance of phylogenetics. Evaluation • Ask students to compare the strengths and weaknesses of using anatomical features versus molecular characteristics to determine phylogenetic relationships. • Ask students to explain why complex changes in a species are gradual compared to simple changes over time. • Ask students to evaluate the possible consequences of producing field crops that have genes from other organisms inserted into their DNA. VISUAL RESOURCES Use photos to illustrate your presentation. Show various closely related organisms. Start at the species level and work upward through the hierarchy. Hierarchy is readily described by Venn diagrams (mathematical subset diagrams). One could begin by presenting various shapes or objects on the overhead and arranging them via some representative classification scheme. You could show various arrangements of objects to indicate the differences between traditional and cladistic taxonomic schemes in biology. A presentation of dichotomous keys is also helpful at this point and should be incorporated into the discussion or laboratory session if there isn’t time in lecture. The American Museum of Natural History has a wonderful exhibition on evolution and cladistics. The highlights are on their website at: http://www.amnh.org/exhibitions /hall_hilites/fossil_halls/perm.html. IN-CLASS CONCEPTUAL DEMONSTRATIONS A. Virtual Fossil Introduction The basics of classification can be demonstrated to students using an interactive website of the modern classification scheme. Students can be shown photographs of organisms representing different taxonomic groups. Materials • Computer with live access to Internet • LCD projector attached to computer • Web browser bookmarked to Fossil Museum at http://www.fossilmuseum.net/TreeOfLife.htm Procedure & Inquiry 1. Review the principles of classification with the class. 2. Tell students they will be viewing a contemporary classification scheme. 3. Load up the Fossil Museum website. 4. Review the three domains and click on the Domains link to show students the classification schema of the three domains. Have students explain the diagram on the website. 5. Click on the three domains to view classification schemes and images. 6. Have the students describe the characteristics of the fossils they see. 7. Then go through each kingdom and ask the students how the organisms shown representing each phylum are characteristic of that group and not another group. 8. Summarizing by explaining how the fossil record is important to classification and phyologeny LABORATORY IDEAS Field collection of fossils is still a common way to study and revise current classification and phylogenetic information. Students can get the experience of collecting field data using 3-dimensional models of representative fossils. a. Students should be provided with the following materials to perform this open-ended experiment. a. Computers with web access b. Web browser bookmarked to 3D virtual Fossil at http://www.3dmuseum.org/ c. Notebook to record field notes about each taxon d. Preserved specimens of: i. Cnidaria ii. Brachiopods iii. Mollusks iv. Arthropods v. Echinoderms vi. Chordates b. Have the students investigate the representative fossils for each taxon c. Then they should be asked to compare the similarities and differences of the fossils to modern examples. d. Have them comment if they agree or disagree with the classification category of the fossil. LEARNING THROUGH SERVICE Service learning is a strategy of teaching, learning and reflective assessment that merges the academic curriculum with meaningful community service. As a teaching methodology, it falls under the category of experiential education. It is a way students can carry out volunteer projects in the community for public agencies, nonprofit agencies, civic groups, charitable organizations, and governmental organizations. It encourages critical thinking and reinforces many of the concepts learned in a course. 1. Have students work with a local environmental group on biodiversity issues. 2. Have students tutor high school students covering evolution in a biology class. 3. Have students prepare an up to date literature review on biodiversity books and websites for a local library. 4. Have students do a biodiversity presentation at a school science program. ETYMOLOGY OF KEY TERMS apo- away from; formed from (from the Greek apo- away from or off) bi- two (from the Latin bi- two) clade group of taxa (from the Greek klados- branch) -gen that which produces (from the Greek genes- born or produced) mono- one; single; alone (from the Greek monos- alone) morph- form (from the Greek morphe- the shape of a thing) nomenclature name; the act of naming (from the Latin nomenclator- a slave who reminded his master of names) para- beside; next to (from the Greek para- beside) phylo- tribe; race; phylum (from the Greek phyle- tribe, clan) plesi- close; near (from the Greek pelas- near) poly- many (from the Greek polys- many) sym/syn- with; together (from the Greek syn- together) CHAPTER 23: PROKARYOTES AND VIRUSES WHERE DOES IT ALL FIT IN? Chapter 23 begins a series of chapters highlighting biodiversity. Students should be encouraged to recall the principles of genetics and evolution behind the particular features of prokaryotes and viruses. The information in chapter 23 does not stand alone. Students should know that prokaryotes and viruses are highly dependent on other organisms and originated from a common ancestor of all living creatures on Earth. SYNOPSIS • Prokaryotic organisms represent the oldest forms of life. Prokaryotic organisms are extremely adaptable to changing environments, found in a variety of land and aquatic habitats, involved in photosynthesis, decomposition and nitrogen fixation processes, commercially important in the production of food and chemicals and have applications in genetic engineering Prokaryotic organisms differ from eukaryotic organisms in the following way: unicellular, cell size, chromosomes organization, cell division and genetic recombination, internal compartmentalization, flagella structure, and metabolic diversity. Bacteria are single-celled organisms, but can exist singularly, in colonies or in filamentous organizations. There are few integrated activities between prokaryotic cells and no true specialization of cells as found in even the most primitive multicellular organisms. Bacteria do not possess chromosomes like eukaryotes as their genes are contained in a single, double-stranded ring of DNA found in the nucleoid region of the cell. They lack internal compartmentalization and do not have any membrane-bound organelles. Internally, they have a complex membrane system formed from invaginations of the plasma membrane. Photosynthetic and/or respiratory enzymes may be associated with these membranes. Like eukaryotes, they have ribosomes, but they are distinctly different in protein and RNA content. Prokaryotic organisms are divided into two major groups: the archaebacteria (or Archaea) and bacteria. Archaebacteria are distinctly different from the bacteria. They have a unique cell wall composition and different kinds of lipids in their membranes. Their gene translation machinery is more like that of eukaryotes than the bacteria and they have some genes with introns, something completely lacking in bacteria. Early classification schemes used form, habitat, and differential stains in classifying prokaryotic organisms, particularly the bacteria. Two major types of bacteria can be classified as being Gram negative (red stain) or Gram positive (purple stain) based on their outer membrane construction. Morphologically, most bacteria appear either spherical (cocci), rod-shaped (bacilli), or spirally coiled (spirilla). As there are few structural differences among bacteria groups, they therefore are further classified by their metabolic processes. Photo autrotrophs carry out photosynthesis in sunlight and build organic molecules from carbon dioxide. Chemo autrophs oxidize inorganic compounds, including ammonia, nitrates, sulfur, and hydrogen gas. Photoheterotrophs, exemplified by the purple non-sulfur bacteria, use light but obtain their carbon from carbohydrates or alcohols. Chemoheterotrophs obtain both carbon and energy from organic molecules and include decomposers and pathogenic bacteria. In addition, each species of bacteria utilizes the components of specially defined media on which it is grown in a certain characteristic manner. They may utilize only certain carbohydrates or other carbon sources, produce various fermentative gases and pigments, or produce pH changes. • Bacterial structure, although simple, is no less complex compared to eukaryotic organisms. Bacteria cell walls are composed of peptidoglycan. They may possess rigid, helical flagella, or hair-like pili. Some bacteria form thick-walled endospores that are extremely resistant to heat. Internal structures include: internal membranes for photosynthesis or respiration, a nucleoid region that contains the single double-stranded DNA ring, and ribosomes involved in protein synthesis. Genetic variation in bacteria results from exchange of DNA fragments or by mutation. A high rate of mutation coupled with a very short generation time can rapidly change the characteristics of a bacterial population. • Bacteria are serious plant and human pathogens. Most plant pathogens are rod-shaped pseudomonads, while animal pathogens are extremely diverse. In addition, bacteria cause a wide variety of human diseases including anthrax, botulism, Chlamydia, cholera, dental caries, diphtheria, gonorrhea, leprosy, lyme disease, peptic ulcers, plague, pneumonia, tuberculosis, typhoid fever, and typhus. Tuberculosis has been around for thousands of years with millions of new cases reported worldwide each year. Dental caries are caused by a wide variety of bacteria, exacerbated by high sugar diets. The many sexually transmitted diseases (STDs) are causing widespread problems throughout society with many becoming resistant to antibiotic treatment. • Viruses are non-living, intracellular parasitic particles, made of nucleic acid, either DNA or RNA, but not both. A protein coat called a capsid surrounds the nucleic core. Still another coating, a lipid-rich envelope encloses many viruses. Viruses are able to replicate only by using the host cell’s DNA and machinery that leads to the production of more viruses. Replication is slightly different for a virus with DNA rather than a virus with RNA genome. They vary greatly in appearance and size and most are so small they can only be viewed through electron microscopy. Viruses infect nearly all forms of life and cause numerous plant, fungal, and animal diseases. Bacteriophages are large, double-stranded DNA viruses that infect bacteria. They are composed of proteins that make up the head, capsid, tail, base plate, and tail fibers. Great diversity exists among the phages with some belonging to a T-series and others given different names. These bacterial viruses exhibit two types of reproductive cycles: the lytic cycle and the lysogenic cycle. The lytic cycle occurs when the virus immediately kills the infected host cell in which it is replicating. The virus injects its head, mostly DNA, into the host cell’s cytoplasm, which turns on the host cell’s replicating machinery, allowing the virus to multiply within infected host cells. Newly produced viruses are released when the host cells lyses. The lysogenic cycle does not immediately kill the infected host cells. Lysogeny occurs when the viral head is injected into the host cell’s cytoplasm and combines with the host cell’s DNA producing a prophase. The expression of the prophase genome may not immediately be expressed, but is replicated during normal mitotic division. However, at a later time, the prophase may initiate viral replication. Viruses may infect cells with damaging effects, transforming benign bacteria into disease-causing forms as in cholera. The human immunodeficiency virus (HIV) is an example of a complex animal retrovirus containing a single-stranded RNA and reverse transcriptase, an enzyme needed to convert viral RNA into viral DNA. HIV infects and kills CD4+ cells, T cells that are important components in the human immune system. Clinical symptoms of acquired immunodeficiency syndrome (AIDS) develop only after a long period of latency during which the immune system suppresses the ongoing HIV infection. First, each HIV particle possesses a glycoprotein on its surface that fits into a receptor on the CD4 cell’s surface and undergoes a conformational change and binds to CCR5. The virus then enters the cell via endocytosis. Viral RNA is synthesized into a double strand of viral DNA where in it combines with the host cell’s DNA, directing the host cell machinery to produce more HIV copies. Rupturing and killing the T cells now release the replicated viruses. The decrease in T cells debilitates the body’s immune system and the patient generally succumbs to otherwise nonfatal infections and cancers. New kinds of combination drug therapies, such as AZT other nucleoside analogs, and protease inhibitors are promising in the fight against AIDS. Discovery of HIV-infected patients with defective genes have helped discover new ways to fight the HIV infection. Chemicals called chemokines appear to inhibit HIV infection and the search for HIV-inhibiting chemokines is intense. Still others possessing a mutation in the gene that codes for the CCR5 receptor appears to block HIV infection. Viruses are nonliving infectious agents that infect all living organisms, including bacteria, protists, fungus, plants, and animals. Some human viruses include influenza, smallpox, infectious hepatitis, yellow fever, polio, rabies, AIDS, cancers, leukemias. They cause major losses in agriculture, forestry and productivity of natural ecosystems. Emerging viruses are ones that originate in one species and transfer to a different species. HIV is an example, as are influenza and the Ebola virus. Epidemiological studies link a number of viruses with certain forms of cancer and are now estimated to contribute to fifteen percent of human cancers. LEARNING OUTCOMES 23.1 Prokaryotes Are the Most Ancient Organisms 1. Describe the basic features of archaea and bacteria. 2. Differentiate between prokaryotes and eukaryotes. 3. Compare and contrast archaea and bacteria. 23.2 Prokaryotes Have an Organized but Simple Structure 1. Describe the three basic shapes of prokaryotes. 2. Explain the difference between gram-positive and gram-negative bacterial cells. 3. Characterize the internal structure of prokaryotic cells. 4. Explain the methods used to classify prokaryotes. 23.3 The Genetics of Prokaryotes Focuses on DNA Transfer 1. Describe how conjugation may be used to map the genes of bacteria. 2. Describe how transduction may be used to map the genes of bacteria. 3. Describe how transformation may be used to map the genes of bacteria. 23.4 Prokaryotic Metabolism Is Quite Diverse 1. Compare the different ways that prokaryotes acquire carbon and energy. 2. Illustrate where emerging viruses come from. 23.5 Bacteria Cause Important Human Diseases 1. Describe several important human diseases caused by bacteria. 23.6 Viruses are not organisms 1. Describe the different structural forms of viruses. 23.7 Bacterial Viruses Infect by DNA Injection 1. Distinguish between the lytic and lysogenic cycles in bacteriophage. 23.8 Animal Viruses Infect by Endocytosis 1. Describe how the HIV virus infects human cells. 2. Explain why new influenza strains arise periodically. COMMON STUDENT MISCONCEPTIONS There is ample evidence in the educational literature that student misconceptions of information will inhibit the learning of concepts related to the misinformation. The following concepts covered in Chapter 27 are commonly the subject of student misconceptions. This information on “bioliteracy” was collected from faculty and the science education literature. • Students believe that all only DNA can be the genetic information • Students believe that prokaryotes have organelles • Students believe that all bacteria cause disease • Students believe that prokaryotic DNA does not differ from eukaryotic DNA • Students believe that prokaryotic DNA lacks introns • Students believe that prokaryotes evolved from viruses • Students believe that all bacteria have cell walls • Students believe that bacterial cell walls are made of cellulose • Student believe that genetically modified bacteria are inherently dangerous • Students believe that viruses are unrelated to any other organism • Students believe that DNA is needed to carry out metabolism • Students do not understand that genes are conserved in distantly related organisms • Students believe that DNA variation between different organisms if always very high • Students believe that all evolutionary changes are gradual • Students believe that organic evolution could not have taken place on Earth • Students believe that the origins of life started out as random atoms coming together to form molecules • Students believe the early atmosphere contained oxygen • Students believe that species are genetically distinct and fixed INSTRUCTIONAL STRATEGY PRESENTATION ASSISTANCE Be certain to stress that prokaryotic organisms are now divided up into two groups: Archaea and bacteria. (Note: eubacteria are referred to as bacteria.) Identify the differences between Archaea and bacteria. Then discuss the differences between the bacteria groups. Stress that although the initial classification of bacteria was related to structure (shape, flagella, morphology, Gram reaction, endospores), today’s classification is based on metabolic differences. It is difficult to maintain bacteria so that they exhibit their characteristic metabolic traits since they mutate so readily. The American Type Culture Collection (ATCC) characterizes bacteria to ensure their proper metabolic identity for biological research. One can periodically compare the biochemical tests of a laboratory strain against the ATCC standard. • Researchers at the University of Georgia have developed a cheap and effective way to kill bacteria on food and utensils—electrolyzed water. The water is prepared by running an electrical current through a dilute saltwater solution. The antimicrobial effect may be a result of the chlorine that is produced. The water is also highly acidic and contains substantially less oxygen than normal water. • Iceminus pseudomonas has been genetically engineered to prevent frost formation in the citrus industry. Other pseudomonads have caused problems in the hot tub industry as they thrive in warm water that may not be sufficiently chlorinated. Still others cause havoc with the refrigeration of meat and dairy products as they continue to multiply in large numbers in cool, refrigerated environments. • • Many companies are taking advantage of the public’s fear of microorganisms causing health problems. Under normal household circumstances there is absolutely no need to use antibacterial soaps! Soap and hot water are sufficient to deal with the kinds of bacteria present in homes. Overuse of such antibacterial products may result in the same kind of resistance now experienced with antibiotics taken to combat disease. Stress the importance of viruses as tools in genetic engineering. Viral proteins and nucleic acids change very rapidly, continually producing new strains. Again the environment does not create these changes, but causes selection of those changes that improve the survivability of the virus in its host. Remember that a “good” pathogen or parasite does not kill its host as it would destroy its own ability to reproduce. A computer program is indeed a good analog of a virus, especially with the proliferation of virus programs that infect host programs much in the same way organic viruses infect host cells. The more destructive computer viruses are latent rather than virulent viruses. They insert into other programs and wait until the operator performs certain tasks a specific number of times before they crash the program. Scientists are hard at work developing a vaccine for Ebola. Vaccinated macaque monkeys were completely protected from the ravages of the disease for over six months. To develop a stronger immune response, the monkeys were injected with a three-strain Ebola virus vaccine followed by a weakened adenovirus containing a protein from the Zaire strain of the virus. Human tests are still far in the future. A new strain of influenza virus has developed in China. A type A virus that previously infected only birds (type A subtype H5N1) has caused the flu in a few humans. This virus has caused huge epidemics in birds, notably the Pennsylvania outbreak of 1983. Countries like China are the breeding ground for many new strains because of the climate and because certain animals live together in close proximity. Ducks are thought to be the mutation vessels. Pigs help transfer the virus to humans since they can possess both avian and human viruses. Thus far, only a few had been infected with what could become a more deadly epidemic than the one of 1918. This virus is exceptional in that it cannot be cultured in chicken eggs, normally the route used to produce flu vaccines – it kills the embryo. Fortunately, as of yet, there is no proof that the virus can be passed directly from one human to another! Several CJD patients in Kentucky have symptoms reminiscent of the mad-cow patients in England. The source of the prion proteins may be squirrels rather than cows. Mad cow disease has become very problematic in Europe. To reduce the likelihood of similar difficulties in the U.S., importation of meat products from certain areas is prohibited. The transfer of medical products like blood may soon be restricted as well. HIGHER LEVEL ASSESSMENT Higher level assessment measures a student’s ability to use terms and concepts learned from the lecture and the textbook. A complete understanding of biology content provides students with the tools to synthesize new hypotheses and knowledge using the facts they have learned. The following table provides examples of assessing a student’s ability to apply, analyze, synthesize, and evaluate information from Chapter 23. Application • Have students explain if antibiotics that prevent cell wall formation would be effective against all bacteria. • Have students describe relative survivability of spore forming bacteria and non-spore forming bacteria after washing hands with antibacterial soaps. • Ask students to explain if DNA is essential for viral replication. Analysis • Have students compare and contrast viruses and bacteria. • Have students explain a belief that insects and plants may be able to share the same viruses. • Ask students to explain why viruses may have evolved from numerous unrelated ancestral organisms. • Ask students discuss if it is possible to develop a drug the stops viral replication without harming the host. Synthesis • Ask students to explain why certain people do not develop immune system failure when affected by HIV. • Have the students develop a detailed hypothesis about the chance of a dog virus becoming a serious disease of humans • Ask the students to describe the role viruses may play in horizontal gene transfer between unrelated organisms. • Have the students hypothesize some feasible and realistic ways of using bacteria to produce energy. Evaluation • Ask students evaluate the pros and cons for vaccinating children against the human papilloma virus which is associated with cervical cancer. • Ask students to evaluate the effectiveness of a drug that blocks viral receptor binding as a way of controlling viral diseases. • Ask students to determine the feasibility of using bacteriophages as a treatment to cure bacterial diseases. • Ask students evaluate the pros and cons giving a person an antibiotic that kills all bacteria on the body. • Ask students to evaluate the issues of placing harmless bacteria on foods on a way of preventing the growth of disease–causing bacteria. VISUAL RESOURCES • Electron micrographs of bacteria are much more impressive than light micrographs. In addition, bring in samples of live bacteria in Petri dishes. There are a wide variety of colorful organisms available. Many biological supply companies sell already prepared plates; others sell “instant” media in the form of culture impregnated cellulose pads or a gel that is activated simply by adding sterile water. If you have your students prepare random inoculations by exposure to the air, coughing on plates, and so forth, make sure the plates stay sealed for safety! As an example, collect various soil samples and dilute them with water. Using a sterile Q-tip, dip it in the soil/water sample, and inoculate the Petri dish. Put it in a warm environment, and in about a day, you’ll see many types of bacteria colonies. • Bring in samples of virus-infected plant leaves or petri dishes with bacteriophage plaques. The latter can be observed on an overhead projector especially well if specially prepared media is used. Electron micrographs are necessary to visualize individual viruses. Construct a typical T4 bacteriophage from balls and wire in a size large enough for your classroom. IN-CLASS CONCEPTUAL DEMONSTRATIONS A. Building a Prokaryote Introduction Student directed modeling is a fun and effective way to review the structural and chemical characteristics of organisms. This quick activity has students review the structure and metabolism of different prokaryotes. Materials • Cell Structure ○ Modeling clay ○ Toothpicks ○ Large self-sealing plastic bag ○ Cardboard box large enough to hold the self-sealing bag filled with water ○ Aluminum foil ○ Water ○ Plastic wrist band ○ Large plastic beads or buttons ○ Tennis ball • Metabolism ○ Lamp or light bulb ○ Bottle of household ammonia ○ Large rock ○ Dead plant ○ Stuffed animal ○ Small vacuum cleaner Procedure & Inquiry 1. Tell students that you want to have the class review the characteristics of prokaryotes. 2. Review shape and colony size by rolling the clay into shapes resembling cocci, bacilli, spirilla. Have the students name the shape. 3. Then use the toothpicks to for the cocci or bacilli into various colonies. Have the students name the colony shape. 4. They use the following materials to “build” a typical prokaryote: a. Cell membrane - self-sealing plastic bag b. Cell wall – cardboard box c. Slime layer or capsule - aluminum foil d. Cytoplasm - water e. DNA - plastic wrist band f. Ribosome - plastic beads or buttons g. Endospore - tennis ball 5. Have the students name what is needed for the cell. 6. Build the cell in cooperation with the student comments. 7. Ask the students about the nature of the structures including the cell wall and its Gram staining features 8. Then use the metabolism props to review the types of bacterial feeding characteristics: a. Photoautotrophs and photoheterotrophs - Lamp or light bulb b. Chemoautotrophs - bottle of household ammonia c. Chemoautotrophs - large rock d. Chemoheterotrophs (decomposers) - dead plant e. Chemoheterotrophs (parasites or pathogens) - stuffed animal f. Anaerobes – small vacuum cleaner 9. Summarize the events with the class when the demonstration is completed. B. Virtual Virus Introduction Animations are fun ways to reinforce the principles of viral life cycles. This animation provided by the Howard Hughes Medical Institute is a good resource for demonstrating the study of viral life cycles. Materials • Computer with live access to Internet • LCD projector attached to computer • Web browser bookmarked to Howard Hughes Medical Institutes website at http://www.hhmi.org/biointeractive/animations/infection/inf_middle_frames.htm Procedure & Inquiry 10. Review the structure of viruses 11. Tell the class they are going to see how viral life cycles are studied. 12. Play the video and pause after the viruses are placed on a Petri plate of cells. 13. Then ask the students why viruses must be studied that way. 14. Then continue the video and ask questions about the various steps as the video pauses. 15. Summarize the events with the class when the demonstration is completed. LABORATORY IDEAS This activity provided by the University of Utah engages students in building a model to understand how viruses target host cells. Stress to students that models are important ways to represent abstract ideas in tangible ways. a. Tell students that they will be investigating the variation in a variety of specimens. b. Obtain the Teacher’s Guide that can be downloaded from: http://learn.genetics.utah.edu/units/genetherapy/print-and-go/Viruses%20Recognize%20Target%20Cell.pdf c. Students should be provided with the following materials mentioned in the Teacher’s Guide to perform this open-ended inquiry. a. Student pages S-1 to S-6 b. Scissors c. 2 - 4-inch smooth polystyrene balls, d. 2 - 1.5-inch smooth polystyrene balls e. Snap tape, VELCRO® hook and loop fasteners d. Instruct the students to go through the activity. e. Have students use what they learned in the activity to answer questions about viral specificity and techniques for controlling the spread of viruses. This activity provides some interesting insight into the prevalence of bacteria on everyday items such as paper currency. Students are asked to hypothesize about their findings from culturing bacteria from dollars. a. Tell students that they will be investigating the feasibility of obtaining bacterial infections by handling money. b. Provide students with the following materials a. Nutrient agar plates b. Blood agar plates c. Sterile swabs d. Antibiotic discs i. Penicillin ii. Tetracycline iii. Vancomycin c. Instruct students to design an experiment to test the potential for money to spread bacterial infections. d. Instruct them how to make swab plates on the nutrient agar and blood agar media. e. Have the collect bacteria from paper money, coins, or even credit cards that they carry with them. f. Also ask them to determine if it is possible that these bacteria are insensitive to antibiotic treatments. g. Have the students research the different antibiotics and antibiotic resistance. LEARNING THROUGH SERVICE Service learning is a strategy of teaching, learning and reflective assessment that merges the academic curriculum with meaningful community service. As a teaching methodology, it falls under the category of experiential education. It is a way students can carry out volunteer projects in the community for public agencies, nonprofit agencies, civic groups, charitable organizations, and governmental organizations. It encourages critical thinking and reinforces many of the concepts learned in a course. 1. Have students do a lesson on proper hand washing for preventing the spread of viruses to experiment to elementary school students. 2. Have students work with an AIDS education center. 3. Have students produce literature on viral diseases for a local health fair. 4. Have students produce a virus display at a local school or library. CHAPTER 24: PROTISTS WHERE DOES IT ALL FIT IN? Chapter 24 follows the tactic of Chapters 22 and 23 and highlights the diversity of protists. Students should be encouraged to recall the principles of eukaryotic cell structure and evolution associated with the particular features of eukaryotic cells. The information in chapter 24 does not stand alone. Students should know that protists and other organisms are interrelated and originated from a common ancestor of all living creatures on Earth. SYNOPSIS Prokaryotic organisms existed for over 2 billion years before the existence of something bigger. The first eukaryotic organisms most likely arose through the process of endosymbiosis. The endosymbiosis theory states that early eukaryotes probably engulfed symbiotic, aerobic bacteria similar to today’s no sulfur purple bacteria that then performed functions of energy making organelles. Mitochondria possess two membranes, the outer one derived from the host’s endoplasmic reticulum. Chloroplasts are another result of endosymbiosis, but with photosynthetic bacteria as the source. As there are three distinct classes of chloroplasts, they may have evolved through different symbiotic events. Any organism that is not a fungus, or plant or animal is classified as a protist. Therefore, this makes the kingdom protista the most diverse kingdom of living organisms. Historically, some groups have been placed in the plant, animal, or fungal kingdoms based on morphology and switches have been made into and out of kingdom protista upon new molecular data analysis. Still yet, another problem is understanding the evolutionary relationship among protists as much of it is in flux. Today, molecular methods are providing important insights into relationships and using these techniques has helped to divide protists into six supergroups: Excavata, Chromalveolata, Archaeplastida, Rhizaria, Amoebozoans, and Ophisthokonts. All but the Chromalveolata are monophyletic. The general biology of protists is quite extensive. Some protists are single celled, while others are multicellular. Some are microscopic and others are large. Some protists are surrounded by only a plasma membrane; others form glassy shells of silica around themselves. Many have flagella or cilia, others move by pseudopodia. Some protists form cysts to survive inhospitable conditions. Many are phototrophic making their own food through photosynthesis. Heterotrophs obtain energy from organic sources and are classified as phagotrophs or osmotrophs. Most protists reproduce regularly by asexual processes, utilizing sexual reproduction only in times of stress The Excavata include the diplomonads, parabasalids, and euglenozoans and are grouped based on cytoskeletal and DNA sequence similarities. Many have a groove on the side of their bodies that are used for feeding, giving rise to the name excavate. Diplomonads are unicellular organisms with multiple flagella. They lack mitochondria but have two nuclei. Parabasalids have undulating membranes that assist in locomotion. Like diplomonads, parabasalids also use flagella and lack mitochondria. Some are in symbiotic relationships with bacteria inside the guts of termites. Euglenozoa (euglenoids, kinetoplastids) are most likely the earliest free-living aerobic and parasitic protists that move with flagella. Euglenoids are small, mostly freshwater organisms with a thin, flexible pellicle and characteristic eyespot. They are probably the sole reason this kingdom was established as they have characteristics of both animals and plants. About 1/3 of the 40 genera are photoautotrophs possessing chloroplasts, while the rest ingest their food and are heterotrophic. Those that have chloroplasts possess chlorophylls a and b with some carotenoids, similar to green algae and plants. It is recognized that the euglenoids most likely have multiple origins. The kinetoplastids have a unique single mitochondrion with two types of DNA. Many genera within this phyla are parasitic organisms (trypanosomes) causing human diseases such as African sleeping sickness, East Coast fever, leishmaniasis and Chagas disease. The Chromalveolates constitutes a supergroup that arose by one or more secondary endosymbiosis events and include the Alveolata and Stramenopila. Alveolata (dinoflagellates, apicomplexes, and ciliates) all share a common trait of a space or alveoli below their plasma membrane. Dinoflagellates have a distinctive biochemistry and protective plates composed of cellulose-like material, often encrusted with silica. Most have chlorophyll a and c, and carotenoids. Some species of dinoflagellates produce neurotoxins that cause respiratory failure in vertebrates in a phenomon called “red tides,” named so from the red pigments that colors the water. Apicomplexes, non-motile spore-forming animal parasites, are named so by the unique arrangement of fibrils, microtubules, vacuoles and cell organelles found at one end of the cell. They produce thick-walled cysts that enable them to survive in very inhospitable environments. Apicomplexes have extremely complex life cycles that alternate between sexual and asexual phases. Many members of this phylum cause diseases, most notably Plasmodium, which causes malaria. Ciliates are unicellular, heterotrophic and readily characterized by their hairlike cilia. They have a tough outer pellicle and possess specialized vacuoles involved in food ingestion and water regulation. Members of this group have specialized organelle systems with a complexity rivaling that of multicellular organisms. The classic ciliate is Paramecium. Some strains of Paramecium can undergo both sexual (conjunction) and asexual reproduction. The Stramenopila include brown algae, diatoms, and oomycetes (water molds). Brown algae or seaweeds are unique in that they undergo an alternation of generations between a sporophyte and gametophyte stage. The most common known brown algae is kelp. Diatoms belong to the phylum Chrysophyta are photosynthetic, unicellular with double shells made of silica. The pigments are chlorophyll a and c as well as carotenoids. Oomycetes are parasitic or saprobe and produce motile spores. Most species of oomycetes are found in water, but a few are found in terrestrial habits. Phytophthora infestans is causes blight on potatoes and was responsible for the Irish potato famine of 1845 and 1847. Archaeplastids acquired their chloroplasts through primary endosymbiosis, unlike the brown algae, which experienced secondary endosymbiosis. Comparison of brown, red, and green algal DNA sequences are consistent with closer evolutionary relationship between reds and greens. Brown algae are place in the Chromalveolates. The Rhodophytas include red algae. Red algae possess chloroplasts with chlorophyll a, carotenoids, and phycobilins (phycoerythrin, phycocyanin, allophycocyanin) that are distinctly related to cyanobacteria. They are important commercially producing polysaccharides that are used to thicken ice cream and cosmetics. The Chlorophytes and Charophytes are green algae. Chlorophytes have unusual diversity from unicellular Chlamydomonas reinhardtii to colonial members such as Volvox. Charophytes are closely related to land plants biochemically and contain chlorophylls a, b and carotenoids. Rhizaria use pseudopods for locomotion but are distinct from the supergroup Amoebozoans. Within the Rhizaria are three distinct monophyletic groups have been identified. Radiolarians have silica exoskeletons. Foraminifera are heterotrophic marine protists with pore-studded shells made of organic materials, which can give the shells very different appearances. Thin cytoplasmic projections called podia that emerge through openings in the shells. Cercozoa are a diverse group of primarily soil protists. Some have flagella but others extend pseudopods. Some have silica-based shells. A cercozoan is in a endosymbiotic relationship with an ingested green alga. Amoebozoa are amoebas that move about by a pseudopodia, a process called cytoplasmic streaming. These large, blunt cytoplasmic projections are involved in locomotion and obtaining food. They contain microfilaments actin and myosin, similar to those fibers found in the muscles of animals. Slime molds are more closely related to amoebas. The plasmodial slime molds consist of a streaming plasmodium that engulfs bacteria and organic matter. They form distinctive sporangia under adverse conditions and exposure to light. The cellular slime molds have a distinct life cycle that makes them ideal for studying differentiation. Fungi, animals, and choanoflagellates share a common ancestor and are grouped as Opisthokonta. The choanoflagellates most likely gave rise to the sponges and all animals. They possess traits found in sponges such as single emergent flagellum, a funnel shaped, contractile color, a surface receptor. LEARNING OUTCOMES 24.1 Protists, the First Eukaryotes Arose by Endosymbiosis 1. Describe the earliest evidence of eukaryotes. 2. Illustrate how endosymbiosis relates to the evolution of mitochondria. 3. Explain the origin of chloroplasts. 4. Explain why mitosis is not believed to have evolved all at once 24.2 Biologically, Protists Are a Very Diverse Group 1. Describe the feature that distinguishes protists from other eukaryotes. 24.3 The Rough Outlines of Protist Phylogeny Are Becoming Clearer 1. Describe how the 15 major phyla of protists are related. 24.4 Excavata Are Flagellated Protists Lacking Mitochondria 1. List the main features of diplomonads, and give an example. 2. List the main features of parabasalids, and give an example. 3. Describe the distinguishing feature of euglenoids and kinetoplastids. 24.5 Chromalveolata Seem to Have Originated by Secondary Symbiosis 1. Describe the distinguishing feature of dinoflagellates, apicomplexans, and ciliates. 2. Describe the distinguishing feature of brown algae, diatoms, and water molds. Explain why charophytes are considered the closest relatives of land plants. 24.6 Rhizaria Have Silicon Exoskeletons or Limestone Shells 1. Describe the pseudopodia of radiolarians. 2. Describe the exterior features of foraminifera, and give an example. 3. Explain how you would identify a Cercozoan. 24.7 Archaeplastida Are Descended from a single Endosymbiosis Event 1. List the major characteristics of red algae. 2. List the major characteristics of green algae. 3. Explain why charophytes are considered the closest relatives of plants. 24.8 Amoebozoa and Opisthokonta Are Closely Related 1. Distinguish between cellular and plasmodial slime molds. 2. Describe the evolutionary significance of the Choanoflagellates. COMMON STUDENT MISCONCEPTIONS There is ample evidence in the educational literature that student misconceptions of information will inhibit the learning of concepts related to the misinformation. The following concepts covered in Chapter 24 are commonly the subject of student misconceptions. This information on “bioliteracy” was collected from faculty and the science education literature. • Students do not fully understand the link between prokaryotes and endosymbionts. • Students believe that most protists cause disease. • Students are not familiar with the ways protists are classified. • Students believe that species are genetically distinct and fixed. • Students believe that the classification of protists is rigid and fixed. • Students are unaware that protists possess organelles. • Students believe that protists are prokaryotes due to their common single-celled nature. • Students believe that all protists are single celled. • Students believe that all protists live in fresh water. • Students believe that eukaryotes evolved directly from bacteria. • Students believe that all algae are plants. • Students believe that algae do not carry out cellular respiration. • Students believe that all algae contain chlorophyll. INSTRUCTIONAL STRATEGY PRESENTATION ASSISTANCE One can determine the previous taxonomic associations of protists by examining the phylum/division suffix. “Mycota” relates to fungi, “phyta” refers to plants. Differentiate between true multicellularity and simple colonialism. Some green algae and diatoms are good examples of the latter. Stress the evolutionary diversity of the unicellular protists and the advanced multicellular forms that evolved from them. Diatomaceous earth is used to filter various liquids and is often used in swimming pool filters. Few organisms are small enough to get through the holes in the diatom shell. The shells are also very useful in determining the optical quality of the lenses of light microscopes. Discuss the significance of algae blooms and pollution, especially as related to runoff of fertilizers and phosphate detergents. Excessive growth of certain protists can deplete lakes, ponds, and rivers of large quantities of oxygen, which ultimately kills all other forms of life. HIGHER LEVEL ASSESSMENT Higher level assessment measures a student’s ability to use terms and concepts learned from the lecture and the textbook. A complete understanding of biology content provides students with the tools to synthesize new hypotheses and knowledge using the facts they have learned. The following table provides examples of assessing a student’s ability to apply, analyze, synthesize, and evaluate information from Chapter 24. Application • Have students explain why biologists perform pigment analyses to categorize new type of algae. • Have students describe the probable characteristics of a protist found on the bark of a tree. Analysis • Have students compare and contrast bacteria and protists. • Ask students to distinguish between the environmental needs of heterotrophic and autotrophic protists • Ask students to explain why the specialization of cell function is a likely evolutionary consequence of multicellularity. Synthesis • Ask students to explain a strategy for using protists as a source of food for people. • Have the students devise a general strategy for preventing the spread of malaria without harming the environment. • Ask the students to hypothesize the possible uses of protists for making commercial products. Evaluation • Ask students to evaluate the feasibility of using protists as microscopic “machines’ for delivering medicine throughout the body. • Ask students to evaluate the safety of a chemical added to bodies of water that controls certain protistan diseases by inhibiting action of the flagella. VISUAL RESOURCES Light micrographs show the various colors exhibited by protists, especially those that are photosynthetic. Electron micrographs of hard-¬walled forms (diatoms, dinoflagellates, and foraminiferans) are especially impressive. A Petri dish is an excellent example of a radially symmetrical diatom. IN-CLASS CONCEPTUAL DEMONSTRATIONS A. Protistan Locomotion Videos Introduction An understanding of locomotion strategies is important for understanding the classification of protists. This demonstration uses video clips of protists to demonstration and test locomotion methods. Materials • Computer with Internet access • LCD hooked up to computer • Web browser linked to the Protist Movies website at http://protist.i.hosei.ac.jp/Movies/htmls/indexE.html. Procedure & Inquiry 1. Introduce the importance of locomotion methods in understanding protist classification. 2. Demonstrate the movement of representative protists. 3. Ask students to describe particular features of the locomotion strategy. 4. Then ask the students to identify a type of locomotion or the category of protist by cutting off the LCD signal so students cannot see the computer screen and click on a video clip. 5. Then play the video clip with the LCD projecting the image. LABORATORY IDEAS This activity permits students to investigate protists as a tool in medical forensics. Students will use variations in protistan populations to determine the source of contaminated water. a. Tell students that they will be investigating the source of drinking water contamination. b. Explain that a camper picked up a rare virus that was discovered in their water bottle. The source of the water must be discovered to prevent further spread of the disease. However, it is impossible to try to test the nearby bodies of water for the virus. So, the students must compare the protistan populations in the water bottle to those in the three suspected bodies of water. c. Provide students with the following materials a. Microscope b. Microscope slides and coverslips c. Four droppers d. Samples for testing: i. Water bottle – Mixture of live amoeba, paramecium, euglena ii. Sample 1 – Mixture of live paramecium, euglena, chlorella iii. Sample 2 - Mixture of live amoeba, paramecium, euglena iv. Sample 3 – Mixture of live amoeba, paramecium, mixed flagellates e. Charts for identifying protists d. Instruct students to find a method to determine the source of the water using only the information from observing the protists. e. Have the students record their findings and justify the methods they used. LEARNING THROUGH SERVICE Service learning is a strategy of teaching, learning and reflective assessment that merges the academic curriculum with meaningful community service. As a teaching methodology, it falls under the category of experiential education. It is a way students can carry out volunteer projects in the community for public agencies, nonprofit agencies, civic groups, charitable organizations, and governmental organizations. It encourages critical thinking and reinforces many of the concepts learned in a course. 1. Have students do a Power Point presentation on protists using locomotion videos and images for local high school teachers. 2. Have students produce literature on protistan STDs for a local health clinic. 3. Have students raise awareness about the global impact of malaria to a local civic group. 4. Have students develop Protist Flash Cards for a local high school. Instructor Manual for Understanding Biology Kenneth Mason, George Johnson, Jonathan Losos, Susan Singer 9780073532295, 9781259592416
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