Study Microbes

Students ask these questions about microbes, based on Microbiology: An Evolving Science

Chapter 1

[Note: To answer a question in edit mode, please place your answer like this, inbetween two double-line breaks.]

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?

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?

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?

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?

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. 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?

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

Chapter 3

1. For one of your card pathogens, 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.

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?

Chapters 6 and 11

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?

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 bacteria? What special difficulty arises when defining genetically pure isolates of RNA viruses such as herpes and HIV?

3. How can strongly oncogenic viruses be assayed in culture, if they don't produce plaques?

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 M13? Under what conditions might each strategy be favored over the others?

5. Compare and contrast the life cycles of Herpes virus and HIV (AIDS). What do they have in common, and how do they differ?

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?

7. Discuss the role of host-modulating viral proteins in in herpes viruses. What various kinds of functions do these proteins serve for the virus; and what are their effects on the host?

Chapter 7

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.

2. What kinds of mutant phenotypes reveal aspect of the mechanism of DNA replication and cell division? Explain two specific examples.

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

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

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.”?

6. When you sequence a genome, how do you know where the base pairs in the genome are located since the DNA used to sequence the genome is in fragments?

Chapter 8

1. Explain how a biochemical experiment can demonstrate the specific protein targeted by a new antibiotic that impairs transcription.

2. If Mycoplasma genitalium 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?

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.

4. What kinds of pharmaceutical agents could you design to act on gene promoters? Explain using protein and/or RNA molecules.

5. Why do you think bacterial cells absorb protein and nucleic acids that are exported by other bacteria?

6. How could you sequence the genome of an unculturable microbe?

7. What are the different ways of starting or stopping transcription of a gene?

8. 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. 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?

5. Explain how a DNA sequence inverts during phase variation. Would you expect it to revert at the same rate? Why or why not?

6. Explain the different propagation strategies available to a replicative transposon. What are various ways the transposon could spread within a cell? Among organisms?

7. Explain how the ara operon works, and how it differs from the lac operon.

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.

9. Explain the roles of thermodynamic and kinetic effects in attenuation control of the trp operon.

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.

Chapter 20

1. Compare and contrast the major divisions of eukaryotic microbes. Which groups include primary-symbiont algae? Secondary-symbiont algal protists? Single flagellum versus paired flagella? Motility (widespread) versus limited motility?.

2. Describe examples of eukaryotic microbes that have shells or plates of silicate or calcium carbonate.

3. Explain mixotrophy. Why are so many marine protists mixotrophs?

4. Why do eukaryotes show such as wide range of cell size? What selective forces favor large cell size, and what favors small cell size?

Chapter 21

1. Explain what is meant by symbiosis, mutualism, and parasitism. Show with specific examples how mutualism and parasitism have a lot in common, and how there are inbetween cases.

2. Compare and contrast the roles of microbes in the marine and soil ecosystems.

3. How does oxygen availability determine the community structure of the soil habitat? Of the aquatic (freshwater) sediment habitat?

4. Outline the metabolic processes of the bovine rumen microbial ecosystem.

Chapter 22

1. What are the common gases besides CO2 that contribute to global warming? What is the chemical basis for how these gases trap solar radiation as heat?

2. In the last fifty years, most of the wetlands off the coast of Louisiana have been destroyed. Is this destruction responsible for the increased run-off and pollutants in the Gulf of Mexico, as well as the notorious dead zone there Can dead zones ever be fully revived? What are the methods that used that cause the price of restoration to be $1 billion dollars per year?

3. It is interesting that the ocean's microbial communities could be responsible for over half of the biological uptake of atmospheric carbon. How soluble is CO2 is in water? Is it more soluble than oxygen gas in water?

4. How exactly is ammonium nitrate addition related to higher CO2 efflux in wetlands?

5. Iron is limiting in oceans because the iron in the benthos, where it’s abundant, is inaccessible because it’s far away. In the benthic environment then, is iron not limiting because the microbes can access the sediment? What is typically limiting instead?

7. What is the microbial process in which nitrous oxide gas builds up?

Chapter 23

1. What's the point of breeding a gnotobiotic animal?

3. How do defensins tell the difference between “good” bacteria and pathogens?

4. What are the benefits of an acidic skin? Of an acidic vaginal tract?

5. How are mast cells involved in immune response other than being differentiated with other immune cells?

6. Why do you think gnotobiotic animals have a lower cardiac output?

7. Why does an infection site heat up during vasodilation?

8. How do interferons work? How do they connect with the adaptive immune system?

9. Explain the difference between the innate and adaptive immune systems--and explain how they interconnect.

Chapter 24

1. Now that you know more about adaptive immunity, explain some examples of how the innate and adaptive immune systems interconnect. For instance, how does an innate system receiving a signal activate the adaptive immune system? How does an adaptive response to a pathogen activate an innate response component?

2. Explain the difference between the B-cell and T-cell immune systems--and explain how they interconnect.

3. Explain an example of an antigen-presenting cell within the adaptive immune response.

Species to know

For each species, 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.

Aspergillus sp.

Bacillus anthracis

Bacillus subtilis

Bacillus thuringiensis

Bacteroides thetaiotaomicron

Borrelia burgdorferi

Chlamydia sp.

Clostridium botulinum

Chloroflexus sp.

Corynebacterium diphtheriae

Escherichia coli

Geobacter metallireducens

Pseudomonas aeruginosa

Halobacterium sp.

Helicobacter pylori

Lactobacillus sp.

Lactococcus sp.

Leptospira

Methanococcus sp.

Mycobacterium tuberculosis

Mycoplasma pneumoniae sp.

Nitrospira sp.

Paramecium sp.

Plasmodium falciparum

Prochlorococcus sp.

Rhodobacter sp.

Rhodopseudomonas sp.

Rhodospirillum rubrum Rickettsia sp.

Saccharomyces cerevesiae

Salmonella enterica

Serratia marcescens

Sinorhizobium meliloti

Staphylococcus epidermidis

Staphylococcus aureus

Streptomyces sp.

Vibrio cholerae

Vibrio fischeri