BIOL 238 Review 2009: Difference between revisions

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This page provides review questions for [http://biology.kenyon.edu/courses/biol238/biol238syl11.html BIOL 238] (Spring 2011).  Answers may be posted by students.
This page provides review questions for [http://biology.kenyon.edu/courses/biol238/biol238syl11.html BIOL 238] (Spring 2011).  Answers may be posted by students.
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==Chapter 1==
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[Note: To answer a question in edit mode, please place your answer like this, inbetween two double-line breaks.]
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<b>1. What historical discoveries in microbiology, both medical and environmental, laid the foundation for the discovery by Rita Colwell and Anwar Huq of an inexpensive way for Bangladeshi villagers to prevent cholera?</b>
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<b>2. The Colwell interview depicts three different ways of visualizing microbes.  What are the capabilities and limitations of each method?  Which method(s) would have been available before Leeuwenhoek?  By Leeuwenhoek?  For Peter Mitchell and Jennifer Moyle?</b>
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==Species to know==
<b>3. Compare the "family tree" of life as drawn by Herbert Copeland, Robert Whittaker, Lynn Margulis, and Carl Woese.  How were they similar, and how did they differ?  How did their differences relate to different tools available for study?</b>
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<b>For each species of bacteria or archaea, state one or two broader categories of organism (such as gram-positive endospore-forming bacteria), the type of genome, type(s) of metabolism, habitat, and disease caused (if any).</b>
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<b>4. Outline the different contributions to medical microbiology and immunnology of Louis Pasteur, Robert Koch, and Florence Nightingale.  What methods and assumptions did they have in common, and how did they differ?</b>
<b><i>Aeromonas hydrophila</i></b>
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<b><i>Anabaena</i> sp.</b>
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<b>5. Does the human immune system react similarly to both attenuated pathogens and more active pathogens?</b>
<b><i>Aquifex</i> sp.</b>
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<b><i>Bacillus anthracis</i></b>
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<b>6. Outline the different contributions to environmental microbiology of Sergei Winogradsky and Martinus Beijerinck.  Why did it take longer for the significance of environmental microbiology to be recognized, as compared with pure-culture microbiology?</b>
<b><i>Bacillus subtilis</i></b>
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<b><i>Bacillus thuringiensis</i></b>
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<b>7. It is always necessary to prepare a tissue culture to study viruses, as they can't grow without a host cell. Do certain bacteria need tissue in their cultures?</b>
<b><i>Bacteroides thetaiotaomicron</i></b>
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<b><i>Borrelia burgdorferi</i></b>
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<b>8. How did Alexander Fleming's cultured plate of <i>Staphylococcus</i> become moldy with <i>Penicillium notatum</i>? Is it common for petri dishes to become moldy if left in the open air for too long?</b>
<b><i>Chlamydia</i> sp.</b>
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<b><i>Clostridium botulinum</i></b>
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==Chapter 2==
<b><i>Chloroflexus</i> sp.</b>
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<b>1. Explain what features of bacteria you can study by: light microscopy; fluorescence microscopy; scanning EM; transmission EM.</b>
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<b><i>Corynebacterium diphtheriae</i></b>
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<b>2. Explain the difference between detection and resolution.  Explain how resolution is increased by magnification; why can't the details be resolved by your unaided eye?  Explain why magnification reaches a limit; why can it not go on resolving greater detail?</b>
<b><i>Deinococcus radiodurans</i></b>
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<b><i>Enterococcus </i>sp.</b>
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<b>3. How does refraction enable magnification?</b>
<b><i>Escherichia coli</i></b>
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<b><i>Geobacter metallireducens</i></b>
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<b>4. Explain why artifacts appear, even with the best lenses.  Explain how you can tell the difference between an optical artifact and an actual feature of an image.</b>
<b><i>Halobacterium</i> sp.</b>
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<b><i>Helicobacter pylori</i></b>
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<b>5. How can "detection without resolution" be useful in microscopy?  Explain specific examples of dark-field observation, and of fluorescence microscopy.</b>
<b><i>Lactobacillus</i> sp.</b>
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<b><i>Lactococcus</i> sp.</b>
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<b>6. Explain how the Gram stain works.  What are its capabilities and limitations?  How does the Gram stain relate to bacterial phylogeny?</b>
<b><i>Leptospira</i> sp.</b>
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<b><i>Methanococcus</i> sp.</b>
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<b>7. If shapes of bacteria are common to many taxonomic groups, including spirochetes which cause Lyme disease as well as others, how accurately can different bacteria be identified just based on shape?</b>
<b><i>Mycobacterium tuberculosis</i></b>
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<b><i>Mycoplasma pneumoniae</i> sp.</b>
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<b>8. Why should we believe scanning probe microscopy (SPM) is accurate? If scientists should be concerned by possible artifacts in EM why wouldn‘t they be concerned about artifacts or even further complications in SPM?</b>
<b><i>Nitrospira</i> sp.</b>
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<b><i>Prochlorococcus</i> sp.</b>
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<b>9. When would you use TEM over SEM, or vice versa?</b>
<b><i>Pseudomonas aeruginosa</i></b>
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<b><i>Pyrococcus furiosus</i></b>
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<b><i>Pyrodictium occultum</i></b>
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<b><i>Rhodobacter</i> sp.</b>
==Chapter 3==
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<b>1. Look up a pathogen of interest. Explain the type of cell membrane, cell wall, and outer membrane if any.  Explain how any particular components of the membrane and envelope contribute to pathogenesis.</b>
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<b><i>Rhodopseudomonas</i> sp.</b>
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<b>2. Compare and contrast the structure and functions of the cell and the S-layer.</b>
<b><i>Rhodospirillum rubrum</i></b>
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<b><i>Rickettsia</i> sp.</b>
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<b>3. The antibiotic linezolid prevents the 50S ribosome subunit from binding the 30S subunit.  If you isolate ribosomes by ultracentrifugation, how might the results in the tube look different with linezolid present?</b>
<b><i>Salmonella enterica</i></b>
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<b><i>Serratia marcescens</i></b>
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<b>4. In the laboratory, what selective pressure may cause loss of S-layers over several generations of subculturing?  Similarly, why would subcultured bacteria lose flagella?</b>
<b><i>Sinorhizobium meliloti</i></b>
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<b><i>Staphylococcus epidermidis</i></b>
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<b>5. For one of your card pathogens, explain what specialized structures it has, such as pili or storage granules.  Explain how they might contribute to pathogenesis.</b>
<b><i>Staphylococcus aureus</i></b>
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<b><i>Streptomyces</i> sp.</b>
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<b>6. Why might a human cell have a protein complex that imports a bacterial toxin?  How might such a situation evolve?</b>
<b><i>Vibrio cholerae</i></b>
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<b><i>Vibrio fischeri</i></b>
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<b>7. What aspects of the outer membrane prevent phagocytosis, and how?</b>
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<b>8. If the peptidoglycan cell wall is a single molecule, how does the cell expand and come apart to form two daughter cells?</b>
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<b>9. Explain two different ways that an aquatic phototroph might remain close to the light, or that an aerobe might remain close to the air surface.</b>
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==Chapter 4==
==Chapter 13==
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<b>1. Suppose in Yellowstone Park, Mammoth Spring, a thermophilic bacterium (<i>Bacillus steareothermophilus</i> increases its population size by ten-fold in 40 minutes.  What is the generation time, or doubling time?  Why might these bacteria grow faster than <i>Bacillus megaterium</i>, in our laboratory at Kenyon?</b>
<b>1. ATP and NADH are both energy carriers: What are the advantages of using one over the other?</b>
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<b>2. <i>Mycobacterium tuberculosis</i>, the cause of tuberculosis (TB), has a generation time of 18 hours.  How many days will it take to grow a colony containing a million cells?  What is the consequence for research on TB?</b>
<b>2. When cells need to make glucose (gluconeogenesis), they "reverse glycolysis" because most steps are reversible.  However, there are a couple of steps that are not reversible.  How do you think they get reversed for gluconeogenesis? </b>
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<b>3. Explain the different mechanisms that membrane protein complexes can use to transport nutrients: ABC transporters, group translocation, and ion cotransport (symport and antiport). Discuss the advantages and limitations of each mechanism.</b>
<b>3. There are 3 main pathways to form pyruvate- EMP, ED and PPS. How and why might a cell switch among these?</b>
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<b>4. Under what growth conditions do bacteria eat the contents of other bacteria?  How do they manage do do this?  What is the significance for medical research?</b>
<b>4. Explain why most soil bacteria grow using energy-yielding reactions with very small delta-G.</b>
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<b>5. In the laboratory, why is it important to grow isolated colonies?  What can occur in colonies that we might not noticeWhat research problems cannot be addressed with isolated colonies?</b>
<b>5. Why are glucose catabolism pathways ubiquitous, despite the fact that most bacterial habitats never provide glucoseExplain several reasons.</b>
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<b>6. Compare and contrast the advantages and limitations of different responses to starvation: stationary phase; sporulation; and fruiting body formation.</b>
<b>6. In glycolysis, explain why bacteria have to return the hydrogens from NADH back onto pyruvate to make fermentation products. Why can't NAD+ serve as a terminal electron acceptor, like O<sub>2</sub>?</b>
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<b>7. How do these growth curves of actual microbes (from the BIOL 239 lab) differ from the textbook "standard"? What might be the cause of the differences, and the relative advantages and limitations?</b>
<b>7. Why do environmental factors regulate catabolism? Give examples.  Why are amino acids decarboxylated at low pH, and under anaerobiosis?</b>
[[Image:growth.jpg|thumb|600px|center| Growth curves of different microbial species growing in a pitcher plant.]]
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<b>8. <i>Borrelia burgdorferi</i>, the cause of Lyme disease, has a doubling time of 15 hours. If you inoculate a tube of medium with 1 bacterium, how many days will it take to grow a million bacteria?</b>
<b>8. Why does catabolism of benzene derivatives yield less energy than sugar catabolism?  Why is benzene-derivative catabolism nevertheless widespread among soil bacteria?</b>
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<b>9. An imaginary “Andromeda strain” has a doubling time of 2 minutes. If you start with one particle, how many will there be after an hour?  Why do you think Hollywood is more likely to show a story about an Andromeda strain than about <i>Borrelia</i>?</b>
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==Chapter 14==
<b>10. In the depths of a South African gold mine, researchers bore into the rock and test the growth rate of microbes by injecting radiolabeled thymidine deoxynucleotides. After one month, DNA is isolated from the rock and found to contain 0.058% (0.00058) radiolabeled thymidine.
What is the approximate growth rate (doubling rate) of the microbes? (BTW the result approximates actual estimates of growth rate for deep subsurface bacteria.)
What objections might be made to this experiment; what followup tests might be done?</b>
 
==Chapter 5==
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<b>1. Look through a grocery store, inspecting the labels of packaged foods.  What chemical preservatives do you recognize, and what is their mechanism for killing bacteria or inhibiting growth?  For example, propionate and sorbate are membrane-permeant acids that depress cytoplasmic pH.</b>  
<b>1. Explain how bacteria and archaea switch among various electron acceptors depending on environmental conditions.</b>
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<b>2. Explain the major difference between the effects of general sterilization and disinfectants, versus antibiotics such as penicillin or streptomycin. Why do antibiotics rapidly select for resistant strains, whereas disinfectants and sterilizing agents do not?</b>
<b>2. Explain how cell processes such as ATP synthesis can be powered by either the transmembrane pH difference or by the charge difference across the membrane.  Which form of energy is likely to be used at low external pH? At high external pH?</b>
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<b>3. Explain which extreme environmental conditions select for membrane unsaturation.  What is the advantage of unsaturated membranes for these conditions?</b>
<b>3. For phototrophy, discuss the relative advantages and limitations of using PS I versus PS II.</b>
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<b>4. Explain how protein structure is modified during evolutionary adaptation to high temperatures, or to high pressure.</b>
<b>4. What environments favor oxygenic photosynthesis, versus sulfur phototrophy and photoorganotrophy? Explain.</b>
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<b>5. Suppose it takes a heat treatment 3 minutes to halve the population of bacteria in the foodHow long will it take to decrease the bacteria content by 2D-values? Would you want to eat the food at this point? Explain.</b>
<b>5. Explain why certain lithotrophs acidify their environments, to more extreme levels than fermentationWhat are some practical consequences for human industry?</b>
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<b>6. What kind of habitats will show halophiles? What is the difference between moderate halophiles, extreme halophiles, and halotolerant organisms?  Describe what will happen to halophile populations in a pool under the hot sun.</b>
<b>6. Is it surprising that an organism may switch between lithotrophy and organotrophy? What enzymes would have to be replaced, and what enzymes could be used in common for both kinds of metabolism?</b>
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<b>7. What is the mechanism of killing of organisms by ionizing radiation?  Why is ionizing radiation less effective on frozen foods?</b>
<b>7. What kind of environments favor methanogenesis?  Why are methanogens widespread, despite the low delta-G of their energy-yielding metabolism?</b>
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==Chapters 6 and 11==
==Chapter 15==
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<b>1. Discuss the different functions of different structural proteins of a virion, such as capsid, nucleocapsid, tegument and envelope proteins.  How do these functions compare and contrast with functions of cellular proteins?</b>
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<b>2. Explain how viruses are cultured, and how a pure isolate of a virus can be obtained.  How do the procedures differ from that of pure culturing bacteriaWhat special difficulty arises when defining genetically pure isolates of RNA viruses such as herpes and HIV?</b>
<b>1. Why does biosynthesis need both ATP and NADPHWhy couldn't biosynthetic pathways use just ATP, or just NADPH?</b>
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<b>3. How can strongly oncogenic viruses be assayed in culture, if they don't produce plaques?</b>
<b>2. Compare and contrast fatty acid biosynthesis and amino acid biosynthesis.  Which pathway requires more reduction?  Which requires a greater number of different enzymes?  Why?</b>
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<b>4. What are the relative advantages of the virulent phage life cycle of phage T4; the lysis-lysogeny options of phage lambda; and the slow-release life cycle of phage M13Under what conditions might each strategy be favored over the others?</b>
<b>3. What forms of nitrogen are available to microbes for assimilationWhen fertilizer is spread on farmland to nourish crops, what problem is caused by microbes?</b>
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<b>What are the other oxidized forms that bacteria and plants take up and reduce to ammonia and ammonium ion?
 
What about N from reduced organic compounds?</b>
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<b>5. Compare and contrast the life cycles of Herpes virus and HIV (AIDS). What do they have in common, and how do they differ?</b>
<b>4. How are the pathways of amino acid biosynthesis organized? What common routes flow from which core pathways?</b>
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<b>6. RNA viruses and DNA viruses represent fundamentally different reproductive strategies. What are the relative advantages and limitations of each?  How do their different strategies impact the immune response, and the development of antiviral agents?</b>
<b>5. How and why do bacteria make "secondary products"? What are their functions?</b>
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<b>7. Discuss how Papillomavirus proteins interact with host cell proteins.  What various kinds of functions do these proteins serve for the virus; and what are their effects on the host?</b>
<b>6. How can we manipulate bacterial secondary product formation to develop new pharmaceutical agents?</b>
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==Chapter 7==
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<b>1. What are the relative advantages and limitations of bidirectional replication versus rolling circle replication? Explain in terms of different types of genome, genome sizes, and cell situation when replication occurs.</b>
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<b>2. What kinds of mutant phenotypes reveal aspect of the mechanism of DNA replication and cell division? Explain two specific examples.</b>
==Chapter 17==
<b>1. Explain why the first kinds of metabolism on Earth involved electron donors from the sediment reacting with electron receptors from above.  What geolotical and outer-space processed generated these electron donors and electron acceptors?</b>
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<b>3. Explain how it's possible for the replisome to replicate the leading and lagging strands simultaneously.</b>
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<b>2. What evidence supports the "RNA world" aspect of the origin of lifeWhat are evolutionary and medical implications of the RNA world model?</b>
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<b>4. During resolution of a catenane, how might a major mutation occur affecting the entire genomeHow do you think this mutation is prevented?</b>
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<b>5. During rapid growth, why would a bacterial cell die if the antibiotic drug “forms a physical barrier in front of the DNA replication complex.”?</b>
<b>3. What is our modern definition of a microbial species?  Explain the strengths and limitations of defining microbial species based on common ancestry of DNA sequence.</b>
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<b>6. When you sequence a bacterial genome, how can you figure out the significance of all the base pairs? How do you know where genes are, and what they might be encoding? (Hint: See the handout of figures from the MRSA paper. You don't need to read the whole paper, just recall our discussion of the handout.)</b>
<b>4. Explain the evolutionary origins of mitochondria and chloroplasts. What evidence do we see in the structures of modern microbes?</b>
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==Chapter 8==
<b>5. What is a virulence gene?  How do virulence genes evolve?  How can we analyze the relationship between virulent and nonvirulent strains of a bacterium?</b>
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<b>1. Explain how a biochemical experiment can demonstrate the specific protein targeted by a new antibiotic that impairs transcription.</b>
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==Chapter 18==
<b>2. If <i>Mycoplasma genitalium</i> cannot synthesize its own amino acids, does it have extensive/multiple protein channels (ABC pumps) to let amino acids pass its membrane? If proteins are made of amino acids, though, how did the first M. genitalium’s protein channels come into existence? </b>
<b>1. Compare and contrast the major divisions of bacteria.  State an example of a species of each major division.</b>
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<b>3. In tRNA, there are "unusual" bases not found in mRNA How are these bases generated?  Do you think they arise from a recently-evolved aspect of tRNA, or do you think they are an ancient phenomenon of the original RNA world?  Explain.</b>
<b>2. Explain an example of a major division of bacteria whose species show nearly uniform metabolism but differ widely in form. Explain a different example of a division showing a common, distinctive form, but variety of metabolism.</b>
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<b>4. What kinds of pharmaceutical agents could you design to act on gene promoters?  Explain using protein and/or RNA molecules.</b>
<b>3. Compare and contrast three different types of phototrophy found in bacteria.</b>
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<b>5. Why do you think bacterial cells absorb protein and nucleic acids that are exported by other bacteria?</b>
<b>4. Explain the pathology of three different gram-positive pathogens.</b>
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<b>6. How could you sequence the genome of an unculturable microbe?</b>
<b>5. Explain two different examples of bacterial-host mutualism.</b>
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<b>7. What are the different ways of starting or stopping transcription of a gene?</b>
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<b>6. Identify these kinds of bacteria based on their descriptions:</b>


<b>8. As a peptide is synthesized, what problems may need to be solved in order to complete a protein and enable its function?</b>
<br>a. This bacteria is irregularly shaped with peptidoglycan cell walls and a cytoskeleton containing tubulin (previously thought to only be present in Eukaryotes). They are heterotrophs living in variable environments that are usually low in salt, and most are oligotrophs.
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<br>b. This bacteria has a nucleus similar to that of a eukaryotic organism.  It is most notable for its unique membrane structure.  It has multiple internal membranes, with a double membrane functioning to surround the nucleoid.  What am I?!
<br>c. Bacteria in this group are filamentous photoheterotrophs.  In the presence of oxygen they conduct nonphotosynthetic heterotrophy.  They can be found in microbial mats together with thermophilic cyanobacteria.  Some species contain chlorosomes.  They are also known as green nonsulfur bacteria.
<br>d. These bacteria are photolithotrophs that deposit sulfur on the cell surface.  They use H<sub>2</sub>S as an electron donor and are known as green sulfur bacteria.  These bacteria also live in strictly anaerobic conditions below the water surface.
<br>e. This bacterium is gram positive but has permanently lost its cell wall and S-layer due to reductive/degenerative evolution.  It also has the smallest genome(580 kbp) and it is parasitic.
<br>f. This bacterial species ferments complex carbohydrates and serves as one of the major mutualists of the human gut.  Has a Gram-negative structure and is an obligate anaerobe.
<br>g. These bacteria are deep branching and come in a multitude of forms.  They can be found living independently or in colonies. Often times, these different forms allow them to fix nitrogen.  While these organisms can be found in both aquatic and terrestrial habitats, many species contain gas vesicles to maintain a favorable position in the water column.


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==Chapter 9 and 10==
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<b>1. In the process of conjugation, how are genes moved? Are genes moved individually or in groups?  Could part of a gene be moved? </b>
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==Chapter 19==
<b>1. Compare and contrast the different major groups of archaea.  Which ones grow in extreme heat or cold?  Extreme salt?  Produce methane?</b>
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<b>2. How are microbial species defined?  What is the role of vertical phylogeny; and the role of horizontal gene exchange? Explain why species definition is a problem.</b>
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<b>2. Explain how archaea growing in extreme environments require specialized equipment for study.</b>
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<b>3. Why is competence factor exported out of the cell to bind to ComD externally in transformation of Streptococcus? Why doesn't the molecule bind internally? Doesn't exporting CF waste energy? </b>
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<b>4. If a spontaneous mutation occurs to form an apurinic site, transcription and replication are hindered, but what actually happens when the replisome gets to the hole where the base should be? </b>
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<b>5. Explain how a DNA sequence inverts during phase variation.  Would you expect it to revert at the same rate?  Why or why not?</b>
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<b>6. Explain the different propagation strategies available to a replicative transposon.  What are various ways the transposon could spread within a cell? Among organisms?</b>
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<b>7. Explain how the <i>ara</i> operon works, and how it differs from the lac operon.</b>
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<b>8. Explain how different mechanisms acting at different levels on DNA and RNA can modulate gene expression over a range of time scales, from multiple generations to within a few seconds.</b>
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<b>9. Explain the roles of thermodynamic and kinetic effects in attenuation control of the <i>trp</i> operon.</b>
<b>3. What kinds of archaea grow in "average" environment such as the soil? Or an animal digestive tract?</b>
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<b>4. Archaea identification: What is it?</b>
==Species to know==
<br>These archaea were once thought to be extremophiles, but it turns out they are the most abundant archaea in the ocean. Nonetheless, the thermophiles responsible for giving this false impression are found at temperatures of 113degrees. Others are found living in sulfuring springs. When gram stained, these archaea appear gram-negative.
 
<b>For each species of bacteria or archaea, state one or two broader categories of organism (such as gram-positive endospore-forming bacteria), the type of genome, type(s) of metabolism, habitat, and disease caused (if any).</b>
<br><br>
<b><i>Aeromonas hydrophila</i></b>
<br><br>
<b><i>Anabaena</i> sp.</b>
<br><br>
<b><i>Aquifex</i> sp.</b>
<br><br>
<b><i>Bacillus anthracis</i></b>
<br><br>
<b><i>Bacillus subtilis</i></b>
<br><br>
<b><i>Bacillus thuringiensis</i></b>
<br><br>
<b><i>Bacteroides thetaiotaomicron</i></b>
<br><br>
<b><i>Borrelia burgdorferi</i></b>
<br><br>
<b><i>Chlamydia</i> sp.</b>
<br><br>
<b><i>Clostridium botulinum</i></b>
<br><br>
<b><i>Chloroflexus</i> sp.</b>
<br><br>
<b><i>Corynebacterium diphtheriae</i></b>
<br><br>
<b><i>Deinococcus radiodurans</i></b>
<br><br>
<b><i>Escherichia coli</i></b>
<br><br>
<b><i>Geobacter metallireducens</i></b>
<br><br>
<b><i>Halobacterium</i> sp.</b>
<br><br>
<b><i>Helicobacter pylori</i></b>
<br><br>
<b><i>Lactobacillus</i> sp.</b>
<br><br>
<b><i>Lactococcus</i> sp.</b>
<br><br>
<b><i>Leptospira</i> sp.</b>
<br><br>
<b><i>Methanococcus</i> sp.</b>
<br><br>
<b><i>Mycobacterium tuberculosis</i></b>
<br><br>
<b><i>Mycoplasma pneumoniae</i> sp.</b>
<br><br>
<b><i>Nitrospira</i> sp.</b>
<br><br>
<b><i>Paramecium</i> sp.</b>
<br><br>
<b><i>Plasmodium falciparum</i></b>
<br><br>
<b><i>Prochlorococcus</i> sp.</b>
<br><br>
<b><i>Pseudomonas aeruginosa</i></b>
<br><br>
<b><i>Pyrococcus furiosus</i></b>
<br><br>
<b><i>Pyrodictium occultum</i></b>
<br><br>
<b><i>Rhodobacter</i> sp.</b>
<br><br>
<b><i>Rhodopseudomonas</i> sp.</b>
<br><br>
<b><i>Rhodospirillum rubrum</i></b>
<br><br>
<b><i>Rickettsia</i> sp.</b>
<br><br>
<b><i>Saccharomyces cerevesiae</i></b>
<br><br>
<b><i>Salmonella enterica</i></b>
<br><br>
<b><i>Serratia marcescens</i></b>
<br><br>
<b><i>Sinorhizobium meliloti</i></b>
<br><br>
<b><i>Staphylococcus epidermidis</i></b>
<br><br>
<b><i>Staphylococcus aureus</i></b>
<br><br>
<b><i>Streptomyces</i> sp.</b>
<br><br>
<b><i>Vibrio cholerae</i></b>
<br><br>
<b><i>Vibrio fischeri</i></b>
<br><br>
<br><br>
[[Category:Pages edited by students of Joan Slonczewski at Kenyon College]]

Latest revision as of 14:53, 23 July 2011

This page provides review questions for BIOL 238 (Spring 2011). Answers may be posted by students.


Species to know

For each species of bacteria or archaea, state one or two broader categories of organism (such as gram-positive endospore-forming bacteria), the type of genome, type(s) of metabolism, habitat, and disease caused (if any).

Aeromonas hydrophila

Anabaena sp.

Aquifex sp.

Bacillus anthracis

Bacillus subtilis

Bacillus thuringiensis

Bacteroides thetaiotaomicron

Borrelia burgdorferi

Chlamydia sp.

Clostridium botulinum

Chloroflexus sp.

Corynebacterium diphtheriae

Deinococcus radiodurans

Enterococcus sp.

Escherichia coli

Geobacter metallireducens

Halobacterium sp.

Helicobacter pylori

Lactobacillus sp.

Lactococcus sp.

Leptospira sp.

Methanococcus sp.

Mycobacterium tuberculosis

Mycoplasma pneumoniae sp.

Nitrospira sp.

Prochlorococcus sp.

Pseudomonas aeruginosa

Pyrococcus furiosus

Pyrodictium occultum

Rhodobacter sp.

Rhodopseudomonas sp.

Rhodospirillum rubrum

Rickettsia sp.

Salmonella enterica

Serratia marcescens

Sinorhizobium meliloti

Staphylococcus epidermidis

Staphylococcus aureus

Streptomyces sp.

Vibrio cholerae

Vibrio fischeri

Chapter 13


1. ATP and NADH are both energy carriers: What are the advantages of using one over the other?



2. When cells need to make glucose (gluconeogenesis), they "reverse glycolysis" because most steps are reversible. However, there are a couple of steps that are not reversible. How do you think they get reversed for gluconeogenesis?



3. There are 3 main pathways to form pyruvate- EMP, ED and PPS. How and why might a cell switch among these?



4. Explain why most soil bacteria grow using energy-yielding reactions with very small delta-G.



5. Why are glucose catabolism pathways ubiquitous, despite the fact that most bacterial habitats never provide glucose? Explain several reasons.



6. In glycolysis, explain why bacteria have to return the hydrogens from NADH back onto pyruvate to make fermentation products. Why can't NAD+ serve as a terminal electron acceptor, like O2?



7. Why do environmental factors regulate catabolism? Give examples. Why are amino acids decarboxylated at low pH, and under anaerobiosis?



8. Why does catabolism of benzene derivatives yield less energy than sugar catabolism? Why is benzene-derivative catabolism nevertheless widespread among soil bacteria?



Chapter 14


1. Explain how bacteria and archaea switch among various electron acceptors depending on environmental conditions.



2. Explain how cell processes such as ATP synthesis can be powered by either the transmembrane pH difference or by the charge difference across the membrane. Which form of energy is likely to be used at low external pH? At high external pH?



3. For phototrophy, discuss the relative advantages and limitations of using PS I versus PS II.



4. What environments favor oxygenic photosynthesis, versus sulfur phototrophy and photoorganotrophy? Explain.



5. Explain why certain lithotrophs acidify their environments, to more extreme levels than fermentation. What are some practical consequences for human industry?



6. Is it surprising that an organism may switch between lithotrophy and organotrophy? What enzymes would have to be replaced, and what enzymes could be used in common for both kinds of metabolism?



7. What kind of environments favor methanogenesis? Why are methanogens widespread, despite the low delta-G of their energy-yielding metabolism?



Chapter 15



1. Why does biosynthesis need both ATP and NADPH? Why couldn't biosynthetic pathways use just ATP, or just NADPH?



2. Compare and contrast fatty acid biosynthesis and amino acid biosynthesis. Which pathway requires more reduction? Which requires a greater number of different enzymes? Why?



3. What forms of nitrogen are available to microbes for assimilation? When fertilizer is spread on farmland to nourish crops, what problem is caused by microbes? What are the other oxidized forms that bacteria and plants take up and reduce to ammonia and ammonium ion? What about N from reduced organic compounds?



4. How are the pathways of amino acid biosynthesis organized? What common routes flow from which core pathways?



5. How and why do bacteria make "secondary products"? What are their functions?



6. How can we manipulate bacterial secondary product formation to develop new pharmaceutical agents?



Chapter 17

1. Explain why the first kinds of metabolism on Earth involved electron donors from the sediment reacting with electron receptors from above. What geolotical and outer-space processed generated these electron donors and electron acceptors?





2. What evidence supports the "RNA world" aspect of the origin of life? What are evolutionary and medical implications of the RNA world model?



3. What is our modern definition of a microbial species? Explain the strengths and limitations of defining microbial species based on common ancestry of DNA sequence.



4. Explain the evolutionary origins of mitochondria and chloroplasts. What evidence do we see in the structures of modern microbes?



5. What is a virulence gene? How do virulence genes evolve? How can we analyze the relationship between virulent and nonvirulent strains of a bacterium?

Chapter 18

1. Compare and contrast the major divisions of bacteria. State an example of a species of each major division.



2. Explain an example of a major division of bacteria whose species show nearly uniform metabolism but differ widely in form. Explain a different example of a division showing a common, distinctive form, but variety of metabolism.



3. Compare and contrast three different types of phototrophy found in bacteria.



4. Explain the pathology of three different gram-positive pathogens.



5. Explain two different examples of bacterial-host mutualism.





6. Identify these kinds of bacteria based on their descriptions:


a. This bacteria is irregularly shaped with peptidoglycan cell walls and a cytoskeleton containing tubulin (previously thought to only be present in Eukaryotes). They are heterotrophs living in variable environments that are usually low in salt, and most are oligotrophs.
b. This bacteria has a nucleus similar to that of a eukaryotic organism. It is most notable for its unique membrane structure. It has multiple internal membranes, with a double membrane functioning to surround the nucleoid. What am I?!
c. Bacteria in this group are filamentous photoheterotrophs. In the presence of oxygen they conduct nonphotosynthetic heterotrophy. They can be found in microbial mats together with thermophilic cyanobacteria. Some species contain chlorosomes. They are also known as green nonsulfur bacteria.
d. These bacteria are photolithotrophs that deposit sulfur on the cell surface. They use H2S as an electron donor and are known as green sulfur bacteria. These bacteria also live in strictly anaerobic conditions below the water surface.
e. This bacterium is gram positive but has permanently lost its cell wall and S-layer due to reductive/degenerative evolution. It also has the smallest genome(580 kbp) and it is parasitic.
f. This bacterial species ferments complex carbohydrates and serves as one of the major mutualists of the human gut. Has a Gram-negative structure and is an obligate anaerobe.
g. These bacteria are deep branching and come in a multitude of forms. They can be found living independently or in colonies. Often times, these different forms allow them to fix nitrogen. While these organisms can be found in both aquatic and terrestrial habitats, many species contain gas vesicles to maintain a favorable position in the water column.



Chapter 19

1. Compare and contrast the different major groups of archaea. Which ones grow in extreme heat or cold? Extreme salt? Produce methane?



2. Explain how archaea growing in extreme environments require specialized equipment for study.



3. What kinds of archaea grow in "average" environment such as the soil? Or an animal digestive tract?



4. Archaea identification: What is it?
These archaea were once thought to be extremophiles, but it turns out they are the most abundant archaea in the ocean. Nonetheless, the thermophiles responsible for giving this false impression are found at temperatures of 113degrees. Others are found living in sulfuring springs. When gram stained, these archaea appear gram-negative.