BIOL 238 Study 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 with that drawn by Carl Woese. 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 other cell types 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?

Species to know

For each species of bacteria or archaea, state:
> Broad category or phylum
> Cell shape and structure
> Metabolism and behavior
> Disease or habitat

Aeromonas hydrophila

Agrobacterium tumefaciens

Aliivibrio fischeri

Anabaena sp.

Aquifex sp.

Bacillus anthracis

Bacillus subtilis

Bacillus thuringiensis

Bacteroides thetaiotaomicron

Borrelia burgdorferi

Chlamydia sp.

Clostridium botulinum
> Broad category: Proteobacteria
> Cell shape and structure: Rod structure, motile and spore-forming
> Metabolism and behavior: Obligate anaerobe (oxygen is poisonous)
> Disease/Habitat: neurotoxin formed during sporulation in only anaerobic conditions causes foodbourne illness and eventually paralytic illness known as botulism.
Chloroflexus sp.

Corynebacterium diphtheriae

Deinococcus radiodurans
>Phylum: Deinococcus-Thermus
>Cell shape and structure: Relatively large and spherical, typically forms tetrads. Gram-positive cell envelope.
>Metabolism and behavior: Obligate aerobic chemoorganoheterotroph (uses oxygen to derive energy from organic compounds in environment). Does not form endospores and is nonmotile.
>Habitat: Extremophilic bacterium extremely resistant to radiation, UV light, desiccation, and oxidizing agents. Typically found in habitats rich with organic materials (e.g. soil, feces, meat); however, its extreme resilience allows for a diversity of habitats.

Enterococcus sp.

Escherichia coli
> Broad category: Proteobacteria.
> Cell Shape and structure: Gram negative, rod shaped bacteria with one chromosomal DNA and one plasmid.
> Metabolism and behavior: nonsporulating,facultative anaerobic organism. Possess peritrichous flagella.
> Habitat: Found in the environment, food, and the intestine of human and animals.

Geobacter metallireducens

*Halobacterium sp.
> Broad category: Haloarchaea, related to methanogens
> Cell shape and structure: Rod structure with pseudopeptidoglycan; flagella for motility
> Metabolism and behavior: Aerobic Photoheterotrophy--Heterotrophs, supplemented by bacteriorhodopsin light pump. Light taxis (swim toward light)
> Habitat: Brine, concentrated salt lakes

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.
> Phylum: Cyanobacteria
> Cell structure: Very small (0.5 µm) oval cocci. Thylakoid membranes encircle interior.
> Metabolism: Oxygenic photosynthesis. Require heterotrophic symbionts to consume oxygen.
> Habitat: Open ocean, upper littoral zone.

Pseudomonas aeruginosa
> Broad category or phylum: Proteobacteria
> Cell shape and structure: Coccobacillus (in between sphere and rod shape) with flagella. Gram negative
> Metabolism and behavior: Facultative anaerobe
> Disease or habitat: Found in soil, water, skin flora, and man-made environments. Also thrives in hypoxic atmostpheres. Found on medical equipment like catheters, used to break down oil from oil spills, colonizes in body organs causing inflammation and sepsis

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
> Phylum: Proteobacteria (Gamma-proteobacteria)
> Cell shape: Curved rod, with peptidoglycan, Gram-negative outer membrane
> Metabolism and behavior: Heterotrophy
> Disease or habitat: Causes human disease cholera; cholera toxin induces intestinal water release. In ocean, symbiont of copepods; feeds on chitin, releasing copepod eggs.