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BIO153 Ch 28 Notes.pdf

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Department
Biology
Course
BIO153H5
Professor
Christoph Richter
Semester
Winter

Description
Freeman,Biological Science, 4e, Chapter 28 Chapter 28 - Bacteria and Archaea Learning Objectives: Students should be able to ... • Defend the statement that bacteria and archaea are the most important, diverse, and abundant organisms on the planet. • Explain the six "feeding strategies" that bacteria and archaea use to produce ATP and obtain carbon building blocks. • Give several examples of the importance of bacteria in human health, in bioremediation, and in ecosystems. Lecture Outline • Bacteria, Archaea, and Eukarya are the three largest branches on the tree of life. (Fig. 28.1) • Bacteria and archaea may look similar at first glance, but they are very different. (Table 28.1) o Similarities: All bacteria and archaea are prokaryotic and unicellular. o Fundament al differences: ƒ Bacteria have cell walls made of peptidoglycan. ƒ Archaea have unique phospholipids in the cell membranes. ƒ Bacteria and archaea have different ribosome and RNA polymerase structures. ƒ Archaea are more closely related to Eukarya than to Bacteria. I. Why Do Biologists Study Bacteria and Archaea? A. Biological impact 1. Bacteria and archaea are amazingly abundant. a. Most cells in the human body are actually bacteria and archaea (living on the skin and in the gut). b. The Group I marine archaea are so abundant that a teaspoon of seawater contains a population equivalent to that of a large human city. c. If lined up end to end, all the bacteria and archaea alive today would make a chain longer than the Milky Way galaxy. 2. They are found in every possible environment. 3. They are very diverse, and we are still discovering entire new phyla. B. Medical importance 1. Some bacteria are pathogenic, meaning that they cause disease. (Table 28.2) 2. Koch's postulates: Koch proposed that four criteria had to be met to prove that a specific microbe causes a certain disease. a. The microbe must be present in individuals suffering from the disease and absent in healthy individuals. b. The microbe must be isolated and grown in pure culture. © 2011 Pearson Education, Inc. Freeman,Biological Science, 4e, Chapter 28 c. Injection of the microbe (from the pure culture) into a healthy animal should cause the disease symptoms to appear. d. The microbe should be isolatable again from the diseased animal and shown to be identical in size, shape, and color to the original microbe. e. Koch demonstrated that all four postulates were true for anthrax. 3. The germ theory of disease a. The germ theory is based on Koch’s postulates. b. The germ theory states that infectious diseases are caused by microbes (microscopic organisms). c. The germ theory's immediate impact was in improving sanitation, greatly reducing mortality due to infectious disease. (Fig. 28.2) 4. What makes some bacterial cells pathogenic? a. Virulence, or the ability to cause disease, is a heritable trait that varies among individuals in a population. b. Current research is identifying the genes responsible for virulence in a wide variety of bacteria. 5. Antibiotics are molecules that kill bacteria. a. Since their development in the late 1920s, antibiotics have been very useful in combating infectious disease. b. Unfortunately, many pathogens are evolving resistance to antibiotics. C. Role in bioremediation 1. Some of the most serious pollutants are hydrophobic compounds that accumulate in sediment and in the bodies of living organisms. 2. Bioremediation strategies use bacteria to break down these compounds. a. Fertilization of contaminated sites encourages the growth of whatever existing bacteria are already on site. These bacteria often degrade the toxic compounds. (Fig. 28.3) b. “Seeding” adds specific bacteria that are known to use that pollutant as a food source, producing a nontoxic by-product. D. Extremophiles 1. Extremophiles are bacteria that live in unusual environments. a. For example, there are bacteria that live at 121°C, at a pH less than 1.0, in seawater deeper than 2500 m, and in salt-saturated seawater with no oxygen. 2. Studying extremophiles may help us understand the origin of life, since life probably evolved in a high-temperature, anoxic environment. 3. Astrobiologists use extremophiles as model organisms in the search for extraterrestrial life. 4. Extremophiles are useful in certain commercial and research applications. a. For example, the heat-tolerant enzyme that is necessary for PCR (the DNA-copying technique fundamental to most genetic research) © 2011 Pearson Education, Inc. Freeman,Biological Science, 4e, Chapter 28 is from an extremophile found in hot springs in Yellowstone National Park. II. How Do Biologists Study Bacteria and Archaea? A. Using enrichment cultures 1. Enrichment cultures provide a specific set of living conditions (food, temperature, etc.) and can grow large populations of certain bacteria and archaea. 2. Most bacteria and archaea species were discovered when they were grown in a culture in a lab. 3. Example: discovering bacteria from the depths of Earth. (Fig. 28.4) a. Samples were taken from 860–2800 meters below Earth’s surface, where temperatures reach 85 ºC. b. Scientists hypothesized that if anything were living down there, it would produce magnetite as a by-product of cellular respiration. c. Magnetite did appear in cultures, and microscopy confirmed the presence of previously unidentified thermophiles (bacteria that grow at only high temperatures). 4. Students should be able to design an enrichment culture that will isolate species that can be used to clean up oil spills. B. Using direct sequencing 1. Direct sequencing allows biologists to name and characterize organisms that have never been seen. 2. DNA is sequenced directly from a small sample from a habitat (soil, water, etc.). The DNA sequences are then compared to known sequences to determine whether any previously undiscovered species exist in the sample. (ig. 28.5 ) 3. Direct sequencing has changed the way we think about archaea. a. Entire new lineages were discovered, showing that archaea cannot be classified into the four simple categories that had previously been used. 4. Students should be able to design a study to identify the bacterial and archaeal species present in a soil sample near the biology building on your campus. C. Evaluating molecular phylogenies (Fig. 28.6) 1. Ribosomal RNA sequences have shown that the tree of life has three major lineages: Bacteria, Archaea, and Eukarya. a. Archaea are more closely related to Eukarya than to Bacteria. 2. Further analysis has identified several monophyletic groups within each of these domains. III. What Themes Occur in the Diversification of Bacteria and Archaea? A. Morphological diversity 1. Size, shape, and motility (Fig. 28.7) a. Bacteria vary greatly in size. For example, more than a billion of the smallest bacterium could fit inside the largest bacterium. b. Bacteria may be filaments, spheres, rods, chains, or spirals. c. Many bacteria can swim or glide. 2. Cell wall composition and the Gram stain (Fig. 28.8) © 2011 Pearson Education, Inc. Freeman,Biological Science, 4e, Chapter 28 a. Gram-positive bacteria have a cell wall with abundant peptidoglycan, which stains dark purple when exposed to a Gram stain. b. Gram-negative bacteria have a cell wall with a thin layer of peptidoglycan surrounded by a phospholipid bilayer. They stain light pink. c. Gram stain analysis can predict sensitivity to certain drugs. (1) Gram-positive bacteria are often sensitive to penicillin-like drugs that disrupt peptidoglycan synthesis. (2) Gram-negative bacteria are more likely to be affected by drugs that target bacterial ribosomes. B. Metabolic diversity 1. Bacteria and archaea are astonishingly diverse in the ways they acquire energy to make ATP and the carbon compounds they can use as building blocks. 2. There are three ways to acquire energy to produce ATP: (Table 28.3) a. Phototrophs use light energy to energize electrons, producing ATP by photophosphorylation (light reactions of photosynthesis). b. Chemoorganotrophs oxidize organic molecules with high potential energy, such as sugars (cellular respiration, fermentation). c. Chemolithotrophs oxidize inorganic molecules with high potential energy, such as ammonia or methane (usually via cellular respiration). 3. There are two ways to acquire carbon: (Table 28.3) a. Autotrophs use carbon dioxide or methane to build their own carbon-containing compounds. Example: Calvin cycle. b. Heterotrophs acquire carbon-containing compounds from other organisms. 4. Overall, there are six major "feeding strategies" (the six possible combinations of three methods of acquiring energy and two methods of acquiring carbon). a. Plants, animals, fungi, and other eukaryotes use only two strategies. b. Bacteria and archaea use all six. (Table 28.4) c. Students should be able to match the six example species described in Table 28.3 to the appropriate categories in Table 28.4. 5. Producing ATP via cellular respiration: variation in electron donors and acceptors a. In cellular respiration, electrons are moved from molecules with high potential energy and gradually "stepped down" to a molecule with low potential energy, using the released energy to make ATP. (Fig. 28.9) b. Eukaryotes are chemoorganotrophs that use a sugar like glucose as the electron donor and oxygen as the final electron acceptor.
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