BIOL 238 Study 2015

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Study questions and microbial names for BIOL 238, 2015

Chapter 1



1. How do Earth's microbes contribute to human health? Include contributions of microbes within our bodies, as well as those distant from us.



2. In Richard Lenski's evolution experiment, some of the minimal glucose-evolved Escherichia coli isolates had cells three times larger than those of the ancestral strain. Do you think the recent E. coli isolates should be considered a new species? Why or why not? What information might be relevant?



3. Compare the "family tree" of life as drawn by Lynn Margulis (Fig. 1.27) with that drawn by Carl Woese (Fig. 1.29). How are they similar, and how do they differ? Are they both consistent with each other?



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?



5. Does the human immune system react similarly to both attenuated pathogens and more active pathogens?



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?



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?



8. How did Alexander Fleming's cultured plate of Staphylococcus become moldy with Penicillium notatum? Is it common for petri dishes to become moldy if left in the open air for too long?



9. Table 1.2 lists six main phases of history in which distinctive discoveries were made about or related to microbes. For each phase, state two examples of discoveries, and discoverer if known (without looking at the table).



Chapter 2


1. Explain what features of bacteria you can study by: light microscopy; fluorescence microscopy; scanning EM; transmission EM.



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?



3. How does refraction enable magnification?



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.



5. How can "detection without resolution" be useful in microscopy? Explain specific examples of dark-field observation, and of fluorescence microscopy.



6. Explain how the Gram stain works. What are its capabilities and limitations? How does the Gram stain relate to bacterial phylogeny?



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?



8. On page 69, there are four electron micrographs, one of which probably represents an artifact (an object that was not living microbes or microbial parts). Without the legends, how might you tell which image looks questionable? What further tests might you perform on the source of the specimen, to determine whether it contains microbes, and whether the micrograph shows them?



9. When would you use TEM over SEM, or vice versa?





Chapter 3


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.



2. Compare and contrast the structure and functions of the cell and the S-layer.



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?



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?



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.



6. Why might a human cell have a protein complex that imports a bacterial toxin? How might such a situation evolve?



7. What aspects of the outer membrane prevent phagocytosis, and how?



8. If the peptidoglycan cell wall is a single molecule, how does the cell expand and come apart to form two daughter cells?



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.



Chapter 4


1. Suppose in Yellowstone Park, Mammoth Spring, a thermophilic bacterium (Bacillus steareothermophilus 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 Bacillus megaterium, in our laboratory at Kenyon?



2. Mycobacterium tuberculosis, 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?



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.



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?



5. In the laboratory, why is it important to grow isolated colonies? What can occur in colonies that we might not notice? What research problems cannot be addressed with isolated colonies?



6. Compare and contrast the advantages and limitations of different responses to starvation: stationary phase; sporulation; and fruiting body formation.



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?

Growth curves of different microbial species growing in a pitcher plant.





8. Borrelia burgdorferi, 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?



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 Borrelia?



Chapter 5


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.



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?



3. Explain which extreme environmental conditions select for membrane unsaturation. What is the advantage of unsaturated membranes for these conditions?



4. Explain how protein structure is modified during evolutionary adaptation to high temperatures, or to high pressure.



5. Suppose it takes a heat treatment 3 minutes to halve the population of bacteria in the food. How long will it take to decrease the bacteria content by 2D-values? Would you want to eat the food at this point? Explain.



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.



7. What is the mechanism of killing of organisms by ionizing radiation? Why is ionizing radiation less effective on frozen foods?

Chapter 7


1. What are the relative advantages and limitations of bidirectional replication versus rolling circle replication? What kind of genetic entities are likely to favor one over the other?



2. Explain how it's possible for the replisome to replicate the leading and lagging strands simultaneously.



3. During resolution of a catenane, how might a major mutation occur affecting the entire genome? How do you think this mutation is prevented?



4. During rapid growth, why would a bacterial cell die if the antibiotic drug “forms a physical barrier in front of the DNA replication complex.”?

Chapter 13


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



2. Which steps of glycolysis, fermentation, and TCA cycle are driven primarily by entropy change? Which steps are driven primarily by electron rearrangement?



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. What are the natural and human-made sources of aromatic substrates for catabolism? What kinds of microbes catabolize aromatic molecules? What are the major features of aromatic catabolic pathways?



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?



8. Compare and contrast the ETS/ATPase of E. coli aerobic respiration, and the ETS/ATPase of planctomycete anammox lithotrophy.

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 geological 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. What kinds of archaea metabolize ammonia? How do they contribute to ecosystems?



5. What might be the advantages of flagellar motility for a hyperthermophile living in a thermal spring or in a black smoker vent? What would be the advantages of growth in a biofilm?

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)
  • Type of genome
  • Metabolism and habitat
  • Disease caused (if any)
  • Cell shape


Aeromonas hydrophila

Agrobacterium tumefaciens

Aliivibrio fischeri

*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.

*Methanosaeta sp.

*Mycobacterium tuberculosis

Mycobacterium leprae

Mycoplasma pneumoniae

*Myxococcus xanthus

Nitrospira sp.

Nitrosopumilus

*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.

*Sulfolobus sp.

*Verrucomicrobium

*Vibrio cholerae