BIOL 238 Review 2009: Difference between revisions

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.

BIOL 238 Review 2009: Difference between revisions

Latest revision as of 14:53, 23 July 2011

Contents

Species to know

Chapter 13

Chapter 14

Chapter 15

Chapter 17

Chapter 18

Chapter 19

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@@ 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>
-==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>
-[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>
-<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>
+<b><i>Aquifex</i> sp.</b>
-Rita Colwell and Anwar Huq performed research on Vibrio cholerae and discovered that it was associated with environmental zooplankton (ie. the copepod). Because copepods are large (200 micrometers), they figured that these copepods could be filtered out of the water and thus reduce the incidence of cholera. They took this to Bangladesh where they taught women to filter their water through their saris, which greatly eliminated the presence of copepods from the water.
 <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>Bacillus anthracis</i></b>
 <br><br>
+<b><i>Bacillus subtilis</i></b>
-The three methods of microbe visualization that are mentioned in the Colwell interview are scanning electron microscopy (SEM), light microscopy, and naked eye visualization. SEM is able to resolve microbes at a very detailed level and appears to give the microbes a 3-D appearance. The only shortcomings with SEM is that the microbe is killed in the process.  Light microscopy is useful in that it is not necessary to kill the microbe. However, visualizing very small microbes is near impossible and it is hard to get much resolution.  The naked eye visualization is not very helpful in that you can't see much of anything unless the microbes are cultured. Before Leeuwenhoek, only the naked eye visualization method was possible, as he was the first to observe unicellular microbes under a microscope. Leeuwekhoek would have been able to visualize the copeland zooplankton via light microscopy, but the SEM would not yet have been possible. For Peter Mitchell and Jennifer Moyle, they would have had the ability to use all three types of microbe visualization. Because they didn't develop their chemiosmotic hypothesis until 1961, and the modern electron microscope was developed in 1950, they would not have had the same limitations as Leeuwenhoek.
 <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>Bacillus thuringiensis</i></b>
 <br><br>
+<b><i>Bacteroides thetaiotaomicron</i></b>
-Herbert Copeland first proposed a classification system that divided the monera kingdom into two groups: eukaryotic protists and prokaryotic bacteria. This was an addition to the original 3 kingdom classification system by Ernst Haeckel which included animals, plants and monera. Robert Whittaker later added fungi onto Copeland's  4 kingdom hypothesis to make a 5th kingdom (bacteria, protists, fungi, multicellular plants, and multicellular animals). Neither Copeland or Whittaker had access to DNA information, which caused their classification system to be based solely on observation of cellular structure, biochemistry and behavior.
-Margulis modified this system by suggesting the endosymbiosis theory, in which eukaryotes evolved by merging with bacteria by the idea that one cell internalized another.  This was equated to the mitochondria (for example) in eukaryotic cells. This theory also suggested that these organisms had multiple ancestry of living species (polyphyletic), rather than having evolved from a common ancestor (monophyletic).  DNA sequencing was later able to confirm this hypothesis.
-Carl Woese utilized gene sequencing to determine the evolutionary origins of living things. His discoveries (mainly with archaea) suggested the need for a broader taxonomic classification than the kingdom. He named this taxa the domain, of which there are three: Bacteria, Eukarya, and Archaea. This differentiation was important because the archaea domain was shown to have genetic sequences which diverge equally from those of bacteria and eukaryotes.
 <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>Borrelia burgdorferi</i></b>
 <br><br>
+<b><i>Chlamydia</i> sp.</b>
-Nightingale used medical statistics to show that the mortality of soldiers increased with septic conditions in the summer months.  Pasteur's finding that yeast can produce alcohol in the absence of oxygen led him to assume that Spallanzani's failure to find spontaneous generation was not due to a lack of oxygen.  By using an unsealed flask with a "swan neck," which admitted air while keeping the boiled contents microbe-free, he found that the growth medium within the flask remained microbe-free for years.  However, by tilting the flask and allowing the growth medium to contact the broth with dust containing microbes, growth occurred.  Finally, Koch was responsible for developing the causative linke between a pathogen and a disease.  Nightingale used statistical analysis to elucidate the causes of disease and found a positive correlation between a septic environment and disease frequency.  Both Pasteur and Koch used a similar approach in that they both did experiments that allowed them to factor out confounds and focus on a causative link.  After Pasteur found no growth even in the presence of oxygen, he then tilted the flask in order to establish the link between dust contanct and growth.  Koch could have easily stopped after postulate 2, but in order to establish causation instead of correlation, he needed to introduce the isolated microbe into a healthy organism to see if the same symptoms occurred and reisolate it again.  Pasteur's experiment was essentially trying extend Spallanzani's and disprove proponents claiming that non-spontaneous generation was a lack of oxygen, while Koch put Nightingale's statistics and Pasteur's theory that microbial growth requires preexisting microbes together to elucidate the chain of infection in organisms.
-<br><br>These are excellent insights.  The one point I'm not sure about is that Koch probably did not know about Nightingale's  statistics, but he knew about anecdotal evidence of disease associated with germs.  His postulates were designed to give a "yes or no" answer, rather than a statistical probability.  Koch was aware of Pasteur's work, and much of their experiments consisted of a scientific dialogue (often contentious).
 <br><br>
-<b>5. Does the human immune system react similarly to both attenuated pathogens and more active pathogens?</b>
+<b><i>Clostridium botulinum</i></b>
 <br><br>
+<b><i>Chloroflexus</i> sp.</b>
-Yes, if the weakened (attenuated) pathogens are introduced in great enough quantity.  The weakened pathogens will have the same physical presence as the more active form - human antibodies should bind to both with equal tenacity and trigger the immune response.  Furthermore, if the active form has increased resistance to phagocytosis or is capable of weakening the immune system, then human response to the attenuated type will be more favorable (for the human.
 <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>Corynebacterium diphtheriae</i></b>
-Winogradsky was one of the first to study microbes in their natural environment. He developed a model of wetland microbial ecosystems, the Winogradsky column, which could be studied within a laboratory setting. He also discovered lithotrophic bacteria and utilized selective growth media in order to sustain them in the lab. His findings demonstrated the important role of bacteria in geochemical cycling.
-Beijerinck was the first to discover the endosymbiotic relationship between nitrogen-fixing bacteria and leguminous plants.
 <br><br>
+<b><i>Deinococcus radiodurans</i></b>
 <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>Enterococcus </i>sp.</b>
 <br><br>
+<b><i>Escherichia coli</i></b>
-Yes, I believe some bacteria need tissue in their cultures.  Those that need a complex requirement of additional growth factors, such as Staphylococcus.
 <br><br>
-What kind of bacteria would need cell tissue culture to grow?
+<b><i>Geobacter metallireducens</i></b>
 <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>Halobacterium</i> sp.</b>
 <br><br>
+<b><i>Helicobacter pylori</i></b>
 <br><br>
+<b><i>Lactobacillus</i> sp.</b>
-==Chapter 2==
-<br>
-<b>1. Explain what features of bacteria you can study by: light microscopy; fluorescence microscopy; scanning EM; transmission EM.</b>
 <br><br>
+<b><i>Lactococcus</i> sp.</b>
-Light microscopy includes bright-field and dark-field. Bright-field allows you to determine the relative shape of individual microbes and how they associate with one another (chains, tetrads, etc.) Using dark-field, you can detect narrow microbial species and subparts (flagella). Fluorescence enables you to label specific parts of cells using antibody tags. It is good for the detection of microbes and subcellular structures and avoid seeing "dust" and non-living cells. Further, it is good for detection of organisms living in dilute environments. SEM enables you to examine the surface of microbes in detail and see smoothness/bulges that serve special functions such as pathogen attachment. TEM enables you to determine the intracellular structures of attachment sites and internal organelles as well as the shape of macromolecular complexes.
 <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>Leptospira</i> sp.</b>
 <br><br>
+<b><i>Methanococcus</i> sp.</b>
-Detection is the ability to perceive the presence of something, while resolution is the smallest distance between two objects at which they can be distinguished.  Therefore, resolution refers to the detail in which one sees an object.  Resolution with the human eye is limited by the distance between photoreceptors, which is about 500 times larger than the wavelengths of visible light.  For an object to be resolved, light with a wavelength equal to or smaller than the object is needed.  Magnification increases resolution in that it spreads these light rays needed to observe small objects so that they may be detected by the photoreceptors.  This appears to make an object bigger.  Magnification is limited due to interference at the focal point from converging light rays and the resulting Airy disks.  This decreases the expansion of detail that accompanies increased magnification.
 <br><br>
-<b>3. How does refraction enable magnification?</b>
+<b><i>Mycobacterium tuberculosis</i></b>
 <br><br>
+<b><i>Mycoplasma pneumoniae</i> sp.</b>
-The light that pass through a refractive media are shaped in a way (convex lens) that spreads its rays, thus widening the wave front. The parallel light impinging on the lens intersect at the focal point and continue to expand outward on the other side of the lens. The refractive index of the lens is higher, thus the light slows down, thus causing a change in direction.
 <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>Nitrospira</i> sp.</b>
 <br><br>
+<b><i>Prochlorococcus</i> sp.</b>
 <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>Pseudomonas aeruginosa</i></b>
 <br><br>
+<b><i>Pyrococcus furiosus</i></b>
 <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>Pyrodictium occultum</i></b>
 <br><br>
+<b><i>Rhodobacter</i> sp.</b>
 <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>Rhodopseudomonas</i> sp.</b>
 <br><br>
+<b><i>Rhodospirillum rubrum</i></b>
 <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>Rickettsia</i> sp.</b>
 <br><br>
+<b><i>Salmonella enterica</i></b>
 <br><br>
-<b>9. When would you use TEM over SEM, or vice versa?</b>
+<b><i>Serratia marcescens</i></b>
 <br><br>
+<b><i>Sinorhizobium meliloti</i></b>
-TEM would be used to view internal structures of a microorganism.  In TEM, electrons pass through the sample, and the electron density is added through the depth of the section.  For example, TEM could be used to view a cross section of a microorganism.  SEM would be used to examine the outer surface and shape of a specimen, as the electron beams move over the sample to create a three-dimensional picture.
 <br><br>
+<b><i>Staphylococcus epidermidis</i></b>
-==Chapter 3==
-<br>
-<b>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.</b>
 <br><br>
+<b><i>Staphylococcus aureus</i></b>
 <br><br>
-<b>2. Compare and contrast the structure and functions of the cell and the S-layer.</b>
+<b><i>Streptomyces</i> sp.</b>
 <br><br>
+<b><i>Vibrio cholerae</i></b>
 <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><i>Vibrio fischeri</i></b>
 <br><br>
-One would witness fractions of the 30S and 50S subunits at their appropriate levels in the sucrose gradient.  No 70S (entire ribosome complex) fraction should be seen.  If linezolid is large enough (probably not?) then it may also have its own fraction in the centrifuge tube.
+==Chapter 13==
+<br>
-<br><br>
+<b>1. ATP and NADH are both energy carriers: What are the advantages of using one over the other?</b>
-<b>4. Explain how the FtsZ and MinD proteins function in cell division.  What happens to a cell with a mutation in one of these genes?</b>
 <br><br>
 <br><br>
-<b>5. 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>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>
-Loss of the S-layer is an example of reductive evolution.  S-layers require many proteins/glycoproteins for construction, and are therefore energetically costly to maintain.  In the lab culture there is no risk of predation, so those organisms that lose their s-layers and focus their resources on proliferation are the most successful.  Loss of the flagella probably occurs because growth medium is abundant and the organisms have little need to move - the food is all around them.
 <br><br>
-<b>6. 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>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>
-<b>7. Why might a human cell have a protein complex that imports a bacterial toxin?  How might such a situation evolve?</b>
+<b>4. Explain why most soil bacteria grow using energy-yielding reactions with very small delta-G.</b>
 <br><br>
-One way in which this may happen is that the the receptor for this bacterial toxin may be present in many species, but the protein toxin is really only "toxic" to certain species.  An example of this is E. coli O157:H7, which is present in undercooked hamburger meat (thus lives in the cow naturally), however, ingestion of this strain in humans causes hemolytic uremic syndrome.  The protein may evolve perhaps because of it benefiting certain species but is detrimental to other species due to other environmental/physiological factors.
 <br><br>
-<b>8. What aspects of the outer membrane prevent phagocytosis, and how?</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>
-The LPS is the outermost covering on gram negative and gram positive cells and is essentially a slippery, mucousy capsule, which helps prevents phagocytosis by macrophages.
 <br><br>
-<b>9. If the peptidoglycan cell wall is a single molecule, how does the cell expand and come apart to form two daughter cells?</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>
-<b>10. What form of energy is used to drive the membrane-embedded ATP synthase, and the flagellar motor?  Suppose a cell only makes ATP from glucose breakdown (not from the membrane complex).  How could it use the membrane ATP synthase complex to drive flagellar rotation?</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>
-<b>11. 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>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>
-==Bowman <i>et al.</i>, 2008==
+==Chapter 14==
 <br>
-<b>1. Compare and contrast the mechanisms of cell division and DNA replication in <i>Caulobacter crescentus</i> and in <i>E. coli</i>.  What feature of <i>C. crescentus</i> cell division may explain the different organization of DNA replication?</b>
+<b>1. Explain how bacteria and archaea switch among various electron acceptors depending on environmental conditions.</b>
 <br><br>
 <br><br>
-<b>2. Draw a diagram showing how <i>Caulobacter</i> replicates its DNA during cell division.  Show the positions and movements of proteins MreB, FtsZ, ParB, MipZ, and PopZ.</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 membrane.  Which form of energy is likely to be used at low external pH?  At high external pH?</b>
 <br><br>
 <br><br>
-<b>3. Explain what is tested, and what the results show about cell division, in Figures 1, 2, 3, and 5.  For each figure, explain what the panels show, and what remains to be shown.</b>
+<b>3. For phototrophy, discuss the relative advantages and limitations of using PS I versus PS II.</b>
 <br><br>
+<br><br>
+<b>4. What environments favor oxygenic photosynthesis, versus sulfur phototrophy and photoorganotrophy? Explain.</b>
 <br><br>
-==Chapter 4==
+<br><br>
-<br>
+<b>5. Explain why certain lithotrophs acidify their environments, to more extreme levels than fermentation.  What are some practical consequences for human industry?</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>
-<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>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>
-<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>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>
-<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>
+==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>
-<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>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>
-<b>6. Compare and contrast the advantages and limitations of different responses to starvation: stationary phase; sporulation; and fruiting body formation.</b>
+<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>
+<b>4. How are the pathways of amino acid biosynthesis organized?  What common routes flow from which core pathways?</b>
 <br><br>
 <br><br>
-<b>7. Explain the differences between: phototrophy and chemotrophy; autotrophy and heterotrophy; literotrophy and organotrophy.  Explain examples of metabolism combining aspects of these concepts.</b>
+<b>5. How and why do bacteria make "secondary products"?  What are their functions?</b>
 <br><br>
+<br><br>
+<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>
-==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>
-<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>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>
-<b>3. Explain which extreme environmental conditions select for membrane unsaturation.  What is the advantage of unsaturated membranes for these conditions?</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 how protein structure is modified during evolutionary adaptation to high temperatures, or to high pressure.</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>
-<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>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>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>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>7. What is the mechanism of killing of organisms by ionizing radiation?  Why is ionizing radiation less effective on frozen foods?</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>
-<b>8. Explain the mechanism of action of Penecillin, and of Linezolid.  How might bacteria evolve resistance to each antibiotic?  Describe a form of resistance carried on a plasmid, and a form of resistance inherited on the genomic chromosome.</b>
+<b>3. Compare and contrast three different types of phototrophy found in bacteria.</b>
 <br><br>
 <br><br>
+<b>4. Explain the pathology of three different gram-positive pathogens.</b>
-==Chapters 6 and 11==
-<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>
-<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>
-<b>3. Explain two different ways that viruses may cause cancer (oncogenesis).  How can strongly oncogenic viruses be assayed in culture?</b>
 <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>
-<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 M13?  Under 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 cold?  Extreme salt?  Produce methane?</b>
 <br><br>
 <br><br>
-<b>5. Compare and contrast the life cycles of polio virus and influenza virus.  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>
-<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>
-<b>7. Discuss the role of host-modulating viral proteins in smallpox, in herpes, and in papillomavirus.  What 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 springs.  When gram stained, these archaea appear gram-negative.
 <br><br>
+[[Category:Pages edited by students of Joan Slonczewski at Kenyon College]]