Mastering Concepts 16.1 1. What are two domains that contain prokaryotes? Bacteria and Archaea are the two domains that include prokaryotes. 2. List several ways that prokaryotes have influenced evolution. Prokaryotes have influenced evolution by contributing O2 to the atmosphere, helping to create the ozone layer, and becoming incorporated into eukaryotic cells as mitochondria and chloroplasts. 3. In what habitats do bacteria and archaea live? Prokaryotes live in every conceivable habitat. 4. Why is the term prokaryote controversial? The term prokaryote is controversial because it encompasses both bacteria and archaea and implies that they share close evolutionary relationships, when evidence shows a closer relationship between the archaea and the eukaryotes. 16.2 1. What are the three most common cell shapes among microbes? The three most common shapes are spherical (coccus), rod (bacillus), and spiral (spirillum). 2. What are plasmids, and how are they important? Plasmids are small loops of DNA that are not part of the prokaryotic chromosome. They are important because they are easily transmitted from one cell to another, so that prokaryotes can rapidly acquire new traits from their neighbors. They are also important because they help biologists ferry genes from one prokaryotic cell to another. 3. What does the Gram stain reveal about a cell? The basis of Gram staining is differences in the structure of the cell wall. In particular, Gram positive bacteria have a thicker cell wall that retains more crystal violet stain than the cell wall of Gram negative bacteria. 4. What are the functions of a glycocalyx, pili, flagella, and endospores? The glycocalyx helps in attachment to a surface, keeps the cell from drying out, and protects it from immune system cells. Attachment pili allow bacteria to attach to surfaces, while sex pili allow transfer of DNA from cell to cell. Flagella help the cell to move toward or away from a stimulus. The thick dormant endospores allow germination of new bacteria even after exposure to harsh conditions. 5. What terms do microbiologists use to describe carbon sources, energy sources, and oxygen requirements? Carbon: autotrophs (get carbon from inorganic sources) and heterotrophs (get carbon by eating other organisms). Energy: phototrophs (energy comes from the sun) and chemotrophs (energy comes from chemical sources). Oxygen: obligate aerobes (dependent on oxygen for respiration); obligate anaerobes (unable to exist in an oxygen environment); and facultative aerobes (able to use or not use oxygen). 6. How are molecular data changing microbial taxonomy? Molecular taxonomy has led to the creation of the three domain system and has revealed many new microbial species. However, much work remains to be done before a phylogenetic tree can be constructed with confidence. 16.3 1. What are the events of binary fission? The events of binary fission are: - DNA attaches to the cell membrane and then replicates; - newly synthesized DNA attaches to the cell membrane; - cell membrane grows between the two attachment points and moves the DNA molecules apart; - new cell wall grows in space between the two DNA molecules; - two cells separate. 2. What is the difference between vertical and horizontal gene transfer? In vertical gene transfer DNA is passed down from an original cell to daughter cells, but in horizontal gene transfer bacteria receive DNA from cells that are not their ancestors. 3. What are the sources of genetic variation in bacteria and archaea? Sources of genetic variation include mutation, transformation, transduction, and conjugation. 16.4 1. In what ways are bacteria and archaea similar and different? The cells of both bacteria and archaea are prokaryotic and small. Both have a circular chromosome, some members of each domain can fix nitrogen, and some members of each domain can grow at temperatures above 80oC. The two groups have cell walls made of different substances, bacteria use chlorophyll in photosynthesis whereas archaea do not, some archaea generate methane while no bacteria do this, no archaea are sensitive to streptomycin while bacteria are, and archaea have introns while bacteria do not. 2. What are some examples of phyla within domain Bacteria? Examples of phyla within domain Bacteria include: - Proteobacteria – purple sulfur bacteria; - Spirochaetes-organisms that cause Lyme disease and syphilis; - Cyanobacteria – photosynthesizing bacteria. 3. What are the three phyla in Archaea? Euryarchaeota-- stagnant or salty water and animal intestinal tracts. Crenarchaeota-- acidic hot springs or thermal vents. Korarchaeota— thermophiles closely related to Crenarchaeota. 16.5 1. In what ways are bacteria and archaea essential to eukaryotic life? Microbes are decomposers, photosynthetic organisms, food sources, and nitrogen fixers. 2. How are the microbes that colonize your body beneficial? The microbes that colonize the human body help defend it from attack by pathogenic bacteria. 3. What adaptations enable pathogenic bacteria to enter the body and cause disease? Pathogenic bacteria enter the body with insect or tick bites, sexual activity, in food, air, or water, or by direct contact with cut or abraded skin surfaces. Once inside the body, pili help the bacteria to attach to host cells, and bacterial enzymes attack host tissues. Bacterial toxins can disable the host’s circulatory, digestive, or nervous system. 4. What are some practical uses of bacteria and archaea? There are many practical uses of bacteria and archaea: food production, producing useful chemicals, producing human proteins, water and waste treatment. 16.6 1. How did Musser’s team use their data set to help answer two different questions? Musser’s team assembled their genetic data into a tree and looked at the pattern of resistant strains. They then looked to see if all the resistant strains were contained within one branch or scattered across the branches. 2. Propose a change to figure 16.14 that would support the hypothesis that all strains associated with toxic shock syndrome arose from one “superpathogen.” Change figure 16.14 to show all the blue TSS strains grouped together on one branch, by either moving or eliminating MSA2335 and MSA2754. Write It Out 1. Give five examples that illustrate how bacteria and archaea are important to other types of organisms. Prokaryotes play a vital role in global nutrient cycles by decomposing organic matter in soil and water; they carry out photosynthesis, providing food and O2 for countless organisms; they cause diseases in many other organisms; they fix nitrogen, which makes this element available to other organisms in ecosystems; they produce a variety of commercial products. 2. How can the polymerase chain reaction (PCR; see chapter 8) be useful in studying microbes that do not survive in laboratory culture? PCR can make large numbers of copies of DNA from just a few cells, so that it is not necessary to grow the bacteria in culture. 3. If you were developing a new “broad-spectrum” antibiotic to a kill wide variety of bacteria, which cell structures and pathways would you target? Which of those targets also occur in eukaryotic cells, and why is that important? How would your strategy change if you were designing a new “narrow-spectrum” antibiotic active against only a few types of bacteria? You could target bacterial ribosomes, production of peptidoglycan for the cell wall, the production of the cell membrane, or even metabolic enzymes. As long as you target enzymes not also found in a host cell then none of these methods would harm the eukaryotic cell. If you are designing a narrow-spectrum antibiotic you could focus in on specific things that differentiate bacteria like the photosynthetic pathway or glycocalyx production. 4. Distinguish between the following pairs of terms: (a) a phototroph and a chemotroph; (b) a gram-negative and a gram-positive bacterium; (c) an autotroph and a heterotroph; (d) an obligate anaerobe and a facultative anaerobe; and (e) transformation and transduction. (a) Phototroph – organism that derives energy from the sun. Chemotroph - organism that derives energy by oxidizing inorganic or organic chemicals. (b) Gram negative bacterium – bacterium with a thin layer of peptidoglycan in the cell wall. Gram positive bacterium – bacterium with a thick layer of peptidoglycan in the cell wall. (c) Autotroph - organism that acquires carbon from inorganic sources such as carbon dioxide (CO2). Heterotroph - organism that acquires carbon from organic molecules produced by other organisms. (d) Obligate anaerobe - organism that cannot tolerate the presence of O2. Facultative anaerobe organism that can live with or without O2. (e) Transformation – acquisition of naked DNA from the environment without cell-to-cell contact. Transduction – transfer of DNA from one cell to another via a bacteriophage or other virus. 5. Scientists are studying bacteria discovered on the seafloor. In the absence of light, these bacteria can use organic molecules to generate electricity. NASA hopes they may one day be useful in producing some of the electricity on spacecraft, using human waste as fuel. What mode of nutrition do these bacteria probably use? These bacteria are chemoheterotrophs. 6. How do prokaryotes reproduce, and what are three ways they can acquire genes other than by vertical gene transfer? Prokaryotes reproduce by binary fission, an asexual process that replicates DNA and distributes it and other cell parts into two daughter cells. Through horizontal gene transfer, a cell receives DNA from another cell that is not its ancestor. Horizontal gene transfer has three forms: transformation, transduction and conjugation. 7. List the ways that binary fission is similar to and different from mitosis. Like mitosis binary fission first replicates the DNA and produces a cloned cell through asexual reproduction. However, binary fission does not involve microtubules or the stages of prophase to telophase. Also unlike mitosis, in binary fission the DNA anchors to the cell membrane. 8. Why did the discovery of archaea generate interest in searching for cells on other planets? Because many archaea have been discovered in extreme places where no life is expected, expectations are higher that life could exist on some inhospitable planet in space. 9. What adaptations in pathogenic bacteria enable them to cause disease? For bacteria to cause disease, they first must enter the body via contaminated food or water, respiratory droplets, sexual contact, injury, or vectors. Once inside the body, the bacteria produce enzymes that will attack and break down the host tissue and provoke fever, swollen lymph nodes, pain, and nausea. Bacteria also have adaptations that enable them to spread to new hosts. 10. How have humans harnessed the metabolic diversity of bacteria and archaea for industrial purposes? Disease-causing bacteria can be used as weapons. Bacteria that use fermentation to generate ATP are used in the food industry in the production of wine, cheese, olives, yogurt, and other products. Enzymes from bacteria that live in extremely warm environments are used in PCR. Heterotrophic bacteria are important in water and waste treatment facilities and in bioremediation. 11. A young child develops a very high fever and an extremely painful sore throat. Knowing that the child could have an infection with a strain of Streptococcus that could be deadly, the physician seeks a precise diagnosis. What three approaches might the doctor (or a laboratory) use to tell whether this infection is viral or bacterial and, if the latter, to identify the bacterium? If a doctor suspects that the child has a Streptococcus infection from his observations, he or she should order a throat culture; viruses will not grow in culture, but bacteria will. To identify the microorganism, a medical technologist could examine the cells under a microscope, do a gram stain, and test for sensitivity to different antibiotics. 12. Stomach ulcers, once thought to be entirely a product of spicy food or high stress, are now known to be caused by bacteria (Helicobacter pylori). How has ulcer treatment changed because of this new knowledge? Early treatments for ulcers included a special diet and less stress. The discovery that bacteria cause ulcers led to antibiotic treatments. 13. Researchers can raise mice in the complete absence of microorganisms. When these animals are subsequently exposed to pathogenic microbes, they are more likely to develop disease than are mice that have been raised in a normal (nonsterile) environment. Explain this finding. The mice raised in a non-sterile environment have developed immunity to many organisms, including pathogens. In addition, their resident microbes helped prevent colonization by the newly introduced pathogens. The mice raised in a sterile environment develop disease because they did not get a chance to develop natural immunity to the microorganism, nor did they form a protective community of beneficial microbes. 14. Botox is a toxin produced by the bacterium Clostridium botulinum. When ingested with tainted food, Botox can kill by paralyzing muscles needed for breathing and heartbeat. Physicians inject small quantities of diluted Botox into facial muscles to paralyze them and reduce the appearance of wrinkles. Some people have expressed concern about a trend in which people come together for “Botox parties” at hair salons and other nonmedical settings. What are the risks of getting injections in such a setting? The equipment may not be sterile, and needles may accidentally be reused. The location may be contaminated with microorganisms and not as clean as the doctor’s office. The person administering the injection may not be medically trained and may not know what to do if the person receiving the injection has a serious allergic reaction. The dose may be too strong and cause widespread muscle paralysis, which could make the person’s heart stop. 15. Use the Internet to learn about the goals of the Human Microbiome Project. Why is it important to study the microbes that live in and on humans? There are more bacteria than human cells in our body, and we do not understand the majority of how they affect us: our development, physiology, nutrition, or health. 16. Use the Internet to learn how the federal government investigates outbreaks of foodborne illnesses such as E. coli O157:H7 and Salmonella. What can you do to protect yourself from food poisoning? Be sure that food from animal sources is fully cooked or pasteurized, cook with a thermometer, keep raw poultry and shellfish from contaminating other foods or food preparation items, thoroughly wash hands and food preparation surfaces, wash vegetables prior to eating them, and defrost food in the refrigerator rather than at room temperature. 17. Use the Internet to learn about sexually transmitted diseases (STDs). Which of the most common STDs are caused by bacteria? Choose one STD caused by bacteria to study in more depth; describe how the pathogen spreads and its symptoms, treatment, and prevention. Syphilis, chlamydia, gonorrhea, and bacterial vaginosis are all common STDs that are caused by bacteria. [Remainder of answer will vary] 18. Impetigo, MRSA, and other bacterial skin infections spread easily among people living in close quarters such as dorms. To prevent the spread of skin infections, health experts recommend washing hands, showering after participating in sports, disinfecting surfaces, covering open wounds with bandages, not sharing personal items such as razors, and washing athletic clothing after use. How does each strategy help prevent infection? Washing hands, washing athletic clothing, and showering after sports all help decrease the number of bacteria. Disinfecting surfaces helps kill any bacteria that might be present for transmission. Not sharing personal items and covering open wounds also keeps the possibility of transmission low by shutting off transmission routes. 19. If you worked for a school confronting an outbreak of S. aureus, how would you determine whether the strains were MRSA? What measures would you recommend to control the outbreak? Culturing the bacteria and exposing it to antibiotics will determine whether the strains are MRSA. Proper personal hygiene, covering open wounds, and not sharing personal items are the best ways to control the outbreak. 20. Genome sequencing projects are complete or in progress for many prokaryotes other than E. coli. Use the Internet to choose one of these bacteria or archaea, and describe some new discoveries that have come from research on this organism. [Answers will vary] 21. Mycobacterium tuberculosis causes most cases of tuberculosis. Recently, strains of this bacterium that are resistant to all known antibiotic drugs have become increasingly common. Explain how this change occurred; use the terms mutation, DNA, and natural selection in your answer. Mutations to the Mycobacterium tuberculosis DNA resulted in resistant strains appearing. Under the influence of the antibiotic rich environment the resistant strains were favored by natural selection and greatly increased in numbers. This process would've repeated until there were strains resistant to all known drugs. 22. This book depicts the diversity of life with an evolutionary tree (see, for example, figure 16.1). Some biologists, however, are beginning to show life’s evolutionary history with a more weblike diagram that accounts for genes moving among multiple branches and does not assume a single common root. What are some arguments in favor of each approach? There are more arguments in favor of a bush of life rather than a tree of life, but some of the arguments in favor of the tree of life include: it is logical to assume that similar genes come from closely related organisms; more people use and are familiar with the tree of life; the tree of life is easier to depict. Arguments in favor of a bush of life include: not all DNA segments show vertical gene transfer; when different genes are used to draw the tree, different trees appear; horizontal gene transfer is common in the bacteria and archaea, and these two domains represent a very large percentage of life. Pull it Together 1. How are archaea different from bacteria? (See Table 16.1) Cell wall Membrane Chlorophyll Methane production Streptomycin resistance Introns Bacteria Peptidoglycan Fatty acids Some None No No Archaea Protein, pseudo-peptidoglycan Non-fatty acids None Some Yes Some 2. What are the most common cell shapes for bacteria? The three most common bacterial shapes are coccus (spheroid), bacillus (rod-shaped) and spirillum (corkscrew). 3. Add autotrophs, heterotrophs, phototrophs, and chemotrophs to this concept map. These terms could branch off of the “Metabolism” box. The autotrophs and heterotrophs refer to different ways to acquire carbon, and the phototrophs and chemotrophs refer to different ways to acquire energy. 4. Where do obligate aerobes, obligate anaerobes, and facultative anaerobes fit into this map? These terms could branch off of the “Metabolism” box. Obligate aerobes require oxygen, obligate anaerobes require the absence of oxygen, and facultative anaerobes can live with or without oxygen. 5. Which terms on this concept map refer to types of horizontal gene transfer? Conjugation, transduction and transformation are types of horizontal gene transfer. 6. Create a new concept map that includes the internal and external parts of a prokaryotic cell. The concept map should include internal parts (DNA, cytoplasm, ribosomes, plasmids) and external parts (cell wall, glycocalyx, pili, flagella) 7. What are the cell features and metabolic criteria by which biologists classify microbes? Physical features include shape; the presence or absence of a glycocalyx, pili, and flagella; and whether the cell is gram-positive or gram-negative. Metabolic features include carbon source, energy source, and the requirement for oxygen.