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This page provides review questions for [http://biology.kenyon.edu/courses/biol238/biol238syl13.html BIOL 238] (Spring 2013).
This page provides review questions for [http://biology.kenyon.edu/courses/biol238/biol238syl13.html BIOL 238] (Spring 2013).
<br>
<br>
==Chapter 1==
==Chapter 13==
<br>
<b>1. ATP and NADH are both energy carriers: What are the advantages of using one over the other?</b>
<br><br>
<br><br>


<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>
<br><br>
<br><br>
 
<b>2. When cells need to make glucose (gluconeogenesis), they "reverse glycolysis" because most steps are reversibleHowever, there are a couple of steps that are not reversible. How do you think they get reversed for gluconeogenesis? </b>
<br><br>
<b>2. The Colwell interview depicts three different ways of visualizing microbesWhat 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>
<br><br>
<br><br>


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


<br><br>
<br><br>
<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>4. Explain why most soil bacteria grow using energy-yielding reactions with very small delta-G.</b>
<br><br>
<br><br>


<br><br>
<br><br>
<b>5. Does the human immune system react similarly to both attenuated pathogens and more active pathogens?</b>
<b>5. Why are glucose catabolism pathways ubiquitous, despite the fact that most bacterial habitats never provide glucose? Explain several reasons.</b>
<br><br>
<br><br>


<br><br>
<br><br>
<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>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>
<br><br>
<br><br>


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


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


<br><br>
<br><br>


==Chapter 2==
==Chapter 14==
<br>
<br>
<b>1. Explain what features of bacteria you can study by: light microscopy; fluorescence microscopy; scanning EM; transmission EM.</b>
<b>1. Explain how bacteria and archaea switch among various electron acceptors depending on environmental conditions.</b>
<br><br>
<br><br>


<br><br>
<br><br>
<b>2. Explain the difference between detection and resolutionExplain how resolution is increased by magnification; why can't the details be resolved by your unaided eyeExplain why magnification reaches a limit; why can it not go on resolving greater detail?</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 membraneWhich form of energy is likely to be used at low external pHAt high external pH?</b>
<br><br>
<br><br>


<br><br>
<br><br>
<b>3. How does refraction enable magnification?</b>
<b>3. For phototrophy, discuss the relative advantages and limitations of using PS I versus PS II.</b>
<br><br>
<br><br>


<br><br>
<br><br>
<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>4. What environments favor oxygenic photosynthesis, versus sulfur phototrophy and photoorganotrophy? Explain.</b>
<br><br>
<br><br>


<br><br>
<br><br>
<b>5. How can "detection without resolution" be useful in microscopy?  Explain specific examples of dark-field observation, and of fluorescence microscopy.</b>
<b>5. Explain why certain lithotrophs acidify their environments, to more extreme levels than fermentation. What are some practical consequences for human industry?</b>
<br><br>
<br><br>


<br><br>
<br><br>
<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>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>
<br><br>
<br><br>


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


<br><br>
<br><br>
<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>
==Chapter 15==
<br><br>
<br><br>
 
<b>1. Why does biosynthesis need both ATP and NADPH?  Why couldn't biosynthetic pathways use just ATP, or just NADPH?</b>
<br><br>
<b>9. When would you use TEM over SEM, or vice versa?</b>
<br><br>
<br><br>


<br><br>
<br><br>
 
<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>
<br><br>
<br><br>


==Chapter 3==
<br>
<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>
<br><br>
<br><br>
 
<b>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?</b>
<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>
<br><br>
<br><br>
<b>2. Compare and contrast the structure and functions of the cell and the S-layer.</b>
<b>4. How are the pathways of amino acid biosynthesis organized?  What common routes flow from which core pathways?</b>
<br><br>
<br><br>


<br><br>
<br><br>
<b>3. The antibiotic linezolid prevents the 50S ribosome subunit from binding the 30S subunitIf you isolate ribosomes by ultracentrifugation, how might the results in the tube look different with linezolid present?</b>
<b>5. How and why do bacteria make "secondary products"? What are their functions?</b>
<br><br>
<br><br>


<br><br>
<br><br>
<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>6. How can we manipulate bacterial secondary product formation to develop new pharmaceutical agents?</b>
<br><br>
<br><br>
<br><br>
<br><br>
<b>5. For one of your card pathogens, explain what specialized structures it has, such as pili or storage granulesExplain how they might contribute to pathogenesis.</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 aboveWhat geolotical and outer-space processed generated these electron donors and electron acceptors?</b>
<br><br>
<br><br>


<br><br>
<br><br>
<b>6. Why might a human cell have a protein complex that imports a bacterial toxin?  How might such a situation evolve?</b>
<br><br>
<br><br>
 
<b>2. What evidence supports the "RNA world" aspect of the origin of life?  What are evolutionary and medical implications of the RNA world model?</b>
<br><br>
<b>7. What aspects of the outer membrane prevent phagocytosis, and how?</b>
<br><br>
<br><br>


<br><br>
<br><br>
<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>
<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>
<br><br>
<br><br>
<br><br>
<br><br>
<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>
<b>4. Explain the evolutionary origins of mitochondria and chloroplasts.  What evidence do we see in the structures of modern microbes?</b>
<br><br>
<br><br>
<br><br>
<br><br>
 
<b>5. What is a virulence gene? How do virulence genes evolveHow can we analyze the relationship between virulent and nonvirulent strains of a bacterium?</b>
==Chapter 4==
<br>
<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 timeWhy might these bacteria grow faster than <i>Bacillus megaterium</i>, in our laboratory at Kenyon?</b>
<br><br>
<br><br>


<br><br>
==Chapter 18==
<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>1. Compare and contrast the major divisions of bacteria.  State an example of a species of each major division.</b>
<br><br>
<br><br>


<br><br>
<br><br>
<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>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>
<br><br>
<br><br>


<br><br>
<br><br>
<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>3. Compare and contrast three different types of phototrophy found in bacteria.</b>
<br><br>
<br><br>


<br><br>
<br><br>
<b>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?</b>
<b>4. Explain the pathology of three different gram-positive pathogens.</b>
<br><br>
<br><br>


<br><br>
<br><br>
<b>6. Compare and contrast the advantages and limitations of different responses to starvation: stationary phase; sporulation; and fruiting body formation.</b>
<b>5. Explain two different examples of bacterial-host mutualism.</b>
<br><br>
<br><br>


<br><br>
<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>
[[Image:growth.jpg|thumb|500px|center| Growth curves of different microbial species growing in a pitcher plant.]]
<br><br>
<br><br>


<br><br>
<br><br>
<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>6. Identify these kinds of bacteria based on their descriptions:</b>
<br><br>
 
<br><br>
<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>
<br><br>
 
<br><br>
 
==Chapter 5==
<br>
<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>
<br><br>


<br><br>
<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.
<b>2. Explain the major difference between the effects of general sterilization and disinfectants, versus antibiotics such as penicillin or streptomycinWhy do antibiotics rapidly select for resistant strains, whereas disinfectants and sterilizing agents do not?</b>
<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><br>
<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 bacteriaThese 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.


<br><br>
<br><br>
<b>3. Explain which extreme environmental conditions select for membrane unsaturation. What is the advantage of unsaturated membranes for these conditions?</b>
==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>
<br><br>
<br><br>
<br><br>
<br><br>
<b>4. Explain how protein structure is modified during evolutionary adaptation to high temperatures, or to high pressure.</b>
<b>2. Explain how archaea growing in extreme environments require specialized equipment for study.</b>
<br><br>
<br><br>


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


<br><br>
<br><br>
<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>4. What kinds of archaea metabolize ammonia? How do they contribute to ecosystems?</b>
<br><br>
<br><br>


<br><br>
<br><br>
<b>7. What is the mechanism of killing of organisms by ionizing radiation?  Why is ionizing radiation less effective on frozen foods?</b>
<b>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?
<br><br>
<br><br>


<br><br>
==Species to know==
==Species to know==


<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>
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>
<br><br>
<b><i>Aeromonas hydrophila</i></b>
<b><i>Aeromonas hydrophila</i></b>
<br><br>
<b><i>Agrobacterium tumefaciens</i></b>
<br><br>
<br><br>
<b><i>Anabaena</i> sp.</b>
<b><i>Anabaena</i> sp.</b>
Line 275: Line 254:
<br><br>
<br><br>
<b><i>Vibrio cholerae</i></b>
<b><i>Vibrio cholerae</i></b>
<br><br>
<b><i>Vibrio fischeri</i></b>
<br><br>
<br><br>

Latest revision as of 23:17, 23 July 2021

This page provides review questions for BIOL 238 (Spring 2013).

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. 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), the type of genome, type(s) of metabolism, habitat, and disease caused (if any).

Aeromonas hydrophila

Agrobacterium tumefaciens

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.

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.

Verrucomicrobium

Vibrio cholerae