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 the pathogens on our microbe list, 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?
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 8
1. What kinds of pharmaceutical agents could you design to act on gene promoters? Explain using protein and/or RNA molecules.
2. Why do you think bacterial cells absorb protein and nucleic acids that are exported by other bacteria?
3. How could you sequence the genome of an unculturable microbe?
4. What are the different ways of starting or stopping transcription of a gene?
5. As a peptide is synthesized, what problems may need to be solved in order to complete a protein and enable its function?
Chapter 9 and 10
1. In the process of conjugation, how are genes moved? Are genes moved individually or in groups? Could part of a gene be moved?
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.
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?
4. Explain how a DNA sequence inverts during phase variation. Would you expect it to revert at the same rate? Why or why not?
5. Explain the different propagation strategies available to a replicative transposon. What are various ways the transposon could spread within a cell? Among organisms?
6. Explain how the ara operon works, and how it differs from the lac operon.
7. 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.
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
>Broad category or phylum: Proteobacteria
>Cell shape and structure: straight rod-shaped with rounded ends, Gram-negative, contains flagella, which helps it travel through the blood stream of its victim to the nearest organ. It is pathogenic to unhealthy individuals
>Metabolism and behavior: The bacteria digest materials such as gelatin and hemoglobin, the pathogenic nature of this bacteria is mediated by extracellular proteins such as gelatinase and amylase. The actual mechanism is unknown, however, a recent proposal type-III secretion system has been linked.
>Disease or habitat: it can survive in aerobic and anaerobic environments and at temperatures as low a 4 celsius. Bacteria can cause gastroenteritis, which occurs mostly in young people with compromised immune systems. It can also cause eczema and myonecrosis
*Agrobacterium tumefaciens
> Broad category or phylum: Proteobacteria
> Cell shape and structure: helical rod, Gram-negative, contains flagella which helps to swim through the soil and find plant host, makes T-pilus to transfer genetic material to host.
> Metabolism and behavior: Part of the nitrogen-fixing legume symbionts but is pathogenic and doesn’t benefit the plant.
> Disease or habitat: Unique since it has a mix of linear and circular chromosomes. Causes crown gall disease (formation of tumors in eudicots) by inserting small segment of DNA from a plasmid into the plant cell.
Aliivibrio fischeri
>Broad category or phylum: Proteobacteria
>Cell shape and structure: gram-negative, rod shaped, bioluminescent properties.
>Metabolism and behavior: These bacteria subsist on organic matter in the water.
>Disease or habitat: Found mostly in marine habitats, specifically found in higher concentrations in symbiosis with deep sea life.
*Anabaena sp.
> Broad category or phylum: Cyanobacteria
> Cell shape and structure: Long filaments of vegetative cells where 1 in 10 cells differentiates into a heterocyst.
> Metabolism and behavior: Photoautotrophic, perform oxygenic photosynthesis
> Disease or habitat: Fix atmospheric N →NH3 in heterocysts which have limited oxygen and allow nitrogen fixation. Form symbiotic relationships with certain plants and produce neurotoxins which can protect the plant from grazing pressure.
Aquifex sp.
*Bacillus anthracis
>Phylum: Firmicutes
>Cell shape and structure: Rod shaped, Gram-positive, generally 3-5µm in length, synthesizes protein capsule
>Metabolism and behavior: Highly resilient, and are able to survive in extreme temperatures, low-nutrient environments
>Disease or habitat: etiologic agent of anthrax, a common disease of livestock and sometimes humans
*Bacillus subtilis
>Phylum: Firmicutes
>Cell shape and structure: Rod shaped, able to form a protective endospore, and are Gram-positive
>Metabolism and behavior: Able to withstand extreme temperatures and desiccation due to endospore, also they are facultative aerobe and obligate aerobe as well
>Disease or Habitat: Found in the upper layers of soil as well as in the normal human digestive tract
*Bacillus thuringiensis
>Phylum: Firmicutes
>Cell shape and structure: This is a Gram-positive, is rod shaped and is approximately 5 µm long
>Metabolism and Behavior: This bacteria is used as a biological pesticide from the crystal proteins it produces
>Disease and Habitat: This bacteria lives in the soil, and in the guts of caterpillars, moths and butterflies and in insect rich environments
Bacteroides thetaiotaomicron
*Borrelia burgdorferi
> Phylum: Spirochaetes
> Cell shape and structure: spirochete; double membrane (neither gram -or+)
> Metabolism and behavior: prefers micro-aerobic conditions (very little oxygen) but is effectively anaerobic
> Disease/Habitat: typically found in ticks and can be transferred by their bites. Once transferred by the tick, the bacteria invade the skin and tissue of the host causing a "Bulls-Eye" rash and ultimately Lyme disease. The exact method of pathology is not well understood.
*Caulobacter crescentus sp.
>Phylum: Proteobacteria
>Cell shape and structure: This bacteria is a curbed rod shaped, and is Gram-negative with a dimorphic life cycle
>Metabolism and behavior: Ideal growth conditions require oxygen and organic nutrients in aquatic environments
>Disease/ Habitat: These bacteria are found in fresh water, soil and sea water, and is important in the carbon cycle because they recycle organic nutrients
Chlamydia sp.
*Clostridium botulinum
> Broad category: Firmicutes
> 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.
>Category: Firmicutes
>Cell shape and structure: cocci often in pairs or short chains, gram-positive
>Metabolism and behavior: facultative anaerobe
>Disease and habitat: tolerate wide range of environmental conditions such as extreme temperature (10-45 C), pH (4.5-10), high NaCl concentrations. Exhibits gamm-hemolysis on sheep's blood agar. Causes urinary tract infection and meningitis
*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
> Broad category: Proteobacteria
> Shape and structure: Curved rod, Gram negative, has flagella.
> Metabolism and behavior: Microaerophilic (needs oxygen but at lower than atmospheric concentration). Can produce energy by oxidizing molecular hydrogen. Can form biofilms. Chemotaxis to move to less acidic areas, uses flagella to bury into stomach lining.
> Habitat/disease: found in human gastrointestinal tract and is linked to ulcers and stomach cancer.
Lactobacillus sp.
Lactococcus sp.
Leptospira sp.
Methanococcus sp.
Methanosaeta sp.
*Mycobacterium tuberculosis
> Phylum: antinobacteria
> In family myobacteriaceae
> gram-positive but doesn't hold stain
> Causative agent of tuberculosis
> Metabolism: aerobic requires high levels of oxygen, bacillus shape
> Cell structure: waxy coating, resistant to gram staining
*Mycobacterium leprae
> phylum: actinobacteria
> Structure: rod-shaped, gram-positive
> metabolism: aerobic
> cause of leprosy
Mycoplasma pneumoniae
Myxococcus xanthus
Nitrospira sp.
Nitrosopumilus
*Nostoc
>Phylum: Cyanobacteria
>Cell shape and structure: These are single celled bacteria with without nucleus or internal membrane systems, and are mostly water. They also create colonies covered in a gelatinous sheath
>Metabolism and behavior: Nostocs are photosynthetic and use cytoplasmic photosynthetic pigments
>Disease/Habitat: These bacteria are found in soil, on moist rocks and at the bottom of lakes and springs
*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. Uses nitrate as an electron acceptor; thus, reduces nitrate to nitrite, and finally N2.
> 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
>Broad category or phylum: Euryarchaeota
>Cell shape and structure: Coccus shape, roughly spherical, 0.8μ-1.5μ in diameter, has cellular envelope that is made up of glycoprotein.
>Metabolism and Behavior: Simple respiratory system that creates an electrochemical gradient across the cell membrane by reducing protons to hydrogen gas. This gradient drives ATP synthesis. Its metabolic products are hydrogen and carbon dioxide.
>Disease or habitat: Is a hyperthermophile that lives in temperatures ranging from 70°C to 103°C, although it’s optimum growth temperature is 100°C. pH ranges from 5-9. Lives in geothermally heated marine sediments.
Pyrodictium occultum
Rhodobacter sp.
Rhodopseudomonas sp.
Rhodospirillum rubrum
Rickettsia sp.
*Salmonella enterica
>Phylum: Proteobacteria
>Cell shape and structure: This is a Gram-negative, rod shaped, flagellated bacterium
>Metabolism and behavior: This bacteria is facultative, being capable of both aerobic respiration fro the production of ATP as well as fermentation in the absence of oxygen
>Disease/Habitat: These bacteria are most know for causing digestive infection in humans and animals
Serratia marcescens
Sinorhizobium meliloti
*Staphylococcus epidermidis
>Phylum: Firmicutes
>Cell shape and structure: This is a Gram-positive and coagulase-negative staphylococci. This is also cocci shaped with a very strong cell wall
>Metabolism and behavior: These bacteria are able to grow under anaerobic conditions using glucose and can produce acid under sugar conditions
>Disease/Habitat: These bacteria are part of normal human skin, and are do not normally cause infection but will cause infection in immune compromised humans
*Staphylococcus aureus
>Phylum: Firmicutes
>Cell shape and structure: Cocci shaped, Gram positive, approximately 1 µm
>Metabolism and behavior: Facultative anaerobe, being able to make ATP by aerobic respiration and fermentation
>Disease/Habitat: Found in human respiratory tract, and skin, common cause of skin infections, respiratory disease and food poisoning
*Streptococcus pneumoniae
>Phylum: Firmicutes
>Cell shape and structure: Gram-positive streptococci, with a thick cell wall.
>Metabolism and behavior: Heterotrophs, aerobic or facultatively anaerobic.
>Disease/Habitat: Cause pneumonia, particularly in patients weakened by other illness such as influenza.
*Streptomyces sp.
>Phylum: Actinobacteria
>Cell shape and structure: gram positive cells form a filamentous arrangement called a mycelium
>Metabolism and behavior: due to a large genome that codes for many transcription factors depending on different environmental stresses, streptomyces can metabolize many different molecules, including sugars, alcohols, amino acids, and aromatic compounds
>Disease/Habitat: live in soil and attack root vegetables, namely potatoes; important for their function in decomposition of organic matter (ie. compost)
*Sulfolobus sp.
>Domain: Archaea, phylum Crenarchaota
>Cell shape and structure: Irregular shaped and have flagella
>Metabolism and behavior: Grow lithoautotrophically oxidizing sulfur, or chemoheterotrophically by using sulfur to oxidize carbon compounds
>Disease/Habitat: Found in geothermal locations such as volcanoes and hot springs
*Verrucomicrobium
> Phylum: Verrucomicrobia
> Cell shape: Gram negative; has appendages called prosthecae that increase surface area for nutrient uptake.
> Metabolism/behavior: Heterotrophic, oligotrophic, facultative anaerobe, nonmotile.
> Disease/habitat: Found in ponds where there are low levels of nutrients.
*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.
