BIOL 238 Review 2009: Difference between revisions

From MicrobeWiki, the student-edited microbiology resource
No edit summary
 
(25 intermediate revisions by one other user not shown)
Line 1: Line 1:
This page provides review questions for [http://biology.kenyon.edu/courses/biol238/biol238syl09.html BIOL 238] (Spring 2009).  Answers may be posted by students.
This page provides review questions for [http://biology.kenyon.edu/courses/biol238/biol238syl11.html BIOL 238] (Spring 2011).  Answers may be posted by students.
<br>
<br>
==Chapter 1==
 
 
==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>
<br><br>
<br><br>
[Note: To answer a question in edit mode, please place your answer like this, inbetween two double-line breaks.]
<b><i>Aeromonas hydrophila</i></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>
<b><i>Anabaena</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Aquifex</i> sp.</b>
<br><br>
<b><i>Bacillus anthracis</i></b>
<br><br>
<b><i>Bacillus subtilis</i></b>
<br><br>
<b><i>Bacillus thuringiensis</i></b>
<br><br>
<b><i>Bacteroides thetaiotaomicron</i></b>
<br><br>
<b><i>Borrelia burgdorferi</i></b>
<br><br>
<br><br>
<b>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?</b>
<b><i>Chlamydia</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Clostridium botulinum</i></b>
<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><i>Chloroflexus</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Corynebacterium diphtheriae</i></b>
<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><i>Deinococcus radiodurans</i></b>
<br><br>
<br><br>
 
<b><i>Enterococcus </i>sp.</b>
<br><br>
<br><br>
<b>5. Does the human immune system react similarly to both attenuated pathogens and more active pathogens?</b>
<b><i>Escherichia coli</i></b>
<br><br>
<br><br>
 
<b><i>Geobacter metallireducens</i></b>
<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><i>Halobacterium</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Helicobacter pylori</i></b>
<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><i>Lactobacillus</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Lactococcus</i> sp.</b>
<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><i>Leptospira</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Methanococcus</i> sp.</b>
<br><br>
<br><br>
==Chapter 2==
<b><i>Mycobacterium tuberculosis</i></b>
<br>
<b>1. Explain what features of bacteria you can study by: light microscopy; fluorescence microscopy; scanning EM; transmission EM.</b>
<br><br>
<br><br>
 
<b><i>Mycoplasma pneumoniae</i> sp.</b>
<br><br>
<br><br>
<b>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?</b>
<b><i>Nitrospira</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Prochlorococcus</i> sp.</b>
<br><br>
<br><br>
<b>3. How does refraction enable magnification?</b>
<b><i>Pseudomonas aeruginosa</i></b>
<br><br>
<br><br>
 
<b><i>Pyrococcus furiosus</i></b>
<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><i>Pyrodictium occultum</i></b>
<br><br>
<br><br>
 
<b><i>Rhodobacter</i> sp.</b>
<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><i>Rhodopseudomonas</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Rhodospirillum rubrum</i></b>
<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><i>Rickettsia</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Salmonella enterica</i></b>
<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><i>Serratia marcescens</i></b>
<br><br>
<br><br>
 
<b><i>Sinorhizobium meliloti</i></b>
<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>
<b><i>Staphylococcus epidermidis</i></b>
<br><br>
<br><br>
 
<b><i>Staphylococcus aureus</i></b>
<br><br>
<br><br>
<b>9. When would you use TEM over SEM, or vice versa?</b>
<b><i>Streptomyces</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Vibrio cholerae</i></b>
<br><br>
<br><br>
 
<b><i>Vibrio fischeri</i></b>
<br><br>
<br><br>


==Chapter 3==
==Chapter 13==
<br>
<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>
<b>1. ATP and NADH are both energy carriers: What are the advantages of using one over the other?</b>
<br><br>
<br><br>


<br><br>
<br><br>
<b>2. Compare and contrast the structure and functions of the cell and the S-layer.</b>
<b>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? </b>
<br><br>
<br><br>


<br><br>
<br><br>
<b>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?</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. 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>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. 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.</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. Why might a human cell have a protein complex that imports a bacterial toxin? How might such a situation evolve?</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. What aspects of the outer membrane prevent phagocytosis, and how?</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. If the peptidoglycan cell wall is a single molecule, how does the cell expand and come apart to form two daughter cells?</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>
<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>
 
==Chapter 14==
<br>
<b>1. Explain how bacteria and archaea switch among various electron acceptors depending on environmental conditions.</b>
<br><br>
<br><br>


<br><br>
<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 membrane.  Which form of energy is likely to be used at low external pH?  At high external pH?</b>
<br><br>
<br><br>


==Chapter 4==
<br><br>
<br>
<b>3. For phototrophy, discuss the relative advantages and limitations of using PS I versus PS II.</b>
<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 time?  Why might these bacteria grow faster than <i>Bacillus megaterium, in our laboratory at Kenyon?</i></b>
<br><br>
<br><br>


<br><br>
<br><br>
<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>4. What environments favor oxygenic photosynthesis, versus sulfur phototrophy and photoorganotrophy? Explain.</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>5. Explain why certain lithotrophs acidify their environments, to more extreme levels than fermentationWhat are some practical consequences for human industry?</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>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>5. In the laboratory, why is it important to grow isolated colonies?  What can occur in colonies that we might not noticeWhat research problems cannot be addressed with isolated colonies?</b>
<b>7. What kind of environments favor methanogenesisWhy are methanogens widespread, despite the low delta-G of their energy-yielding metabolism?</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>
==Chapter 15==
<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>
<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 5==
<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>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 growthFor example, propionate and sorbate are membrane-permeant acids that depress cytoplasmic pH.</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>
<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>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?</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>3. Explain which extreme environmental conditions select for membrane unsaturation.  What is the advantage of unsaturated membranes for these conditions?</b>
<b>6. How can we manipulate bacterial secondary product formation to develop new pharmaceutical agents?</b>
<br><br>
<br><br>
==Chapter 17==
<b>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?</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>
<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>
<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 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>
<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>
<b>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?</b>
<br><br>
<br><br>


==Chapter 18==
<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>
<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>
 
<br><br>
<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>7. What is the mechanism of killing of organisms by ionizing radiation?  Why is ionizing radiation less effective on frozen foods?</b>
<b>3. Compare and contrast three different types of phototrophy found in bacteria.</b>
<br><br>
<br><br>


<br><br>
<br><br>
==Chapters 6 and 11==
<b>4. Explain the pathology of three different gram-positive pathogens.</b>
<br>
<b>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?</b>
<br><br>
<br><br>


<br><br>
<br><br>
<b>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?</b>
<b>5. Explain two different examples of bacterial-host mutualism.</b>
<br><br>
<br><br>


<br><br>
<br><br>
<b>3. How can strongly oncogenic viruses be assayed in culture, if they don't produce plaques?</b>
 
<br><br>
<br><br>
<b>6. Identify these kinds of bacteria based on their descriptions:</b>
<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.
<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>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 bacteria.  These 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>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 M13Under what conditions might each strategy be favored over the others?</b>
 
==Chapter 19==
<b>1. Compare and contrast the different major groups of archaea.  Which ones grow in extreme heat or coldExtreme salt?  Produce methane?</b>
<br><br>
<br><br>
<br><br>
<br><br>
<b>5. Compare and contrast the life cycles of Herpes virus and HIV (AIDS). What do they have in common, and how do they differ?</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>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?</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>7. Discuss the role of host-modulating viral proteins in in herpes virusesWhat various kinds of functions do these proteins serve for the virus; and what are their effects on the host?</b>
<b>4. Archaea identification: What is it?</b>
<br>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 springsWhen gram stained, these archaea appear gram-negative.
<br><br>
<br><br>
[[Category:Pages edited by students of Joan Slonczewski at Kenyon College]]

Latest revision as of 14:53, 23 July 2011

This page provides review questions for BIOL 238 (Spring 2011). Answers may be posted by students.


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

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.

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.

Vibrio cholerae

Vibrio fischeri

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.