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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-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 17, 18==
-<b>1. Compare and contrast the major divisions of bacteria.  State an example of a species of each major division.</b>
+==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>
+<b><i>Aeromonas hydrophila</i></b>
+<br><br>
+<b><i>Anabaena</i> sp.</b>
+<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>
-There are 7 major categories of bacteria:<br>
+<b><i>Bacillus thuringiensis</i></b>
-) Thermophiles live at very high temperatures and are some of the fastest growing cells on the planet. <i>Deinococcus radiophilus</i> is an example of a thermophile that is not only adapted to high temperatures but is also extremely resistant to radiation and has a very rapid rate of DNA repair. <br>
-<b>These thermophile groups are "deep branching," that is, several branched off earlier than any of the other main groups known.  Of course, we are always discovering new deep-branching groups.</b><br><br>
-) Cyanobacteria, such as <i>Anabaena flos-aquae</i>, are oxygenic and nitrogen-fixing microbes. They contain many subcellular structures, including thylakoids, and can form spores. <br>
-<b>What kind of spores?  Cyanobacteria form particular kinds of spores called akinetes and baeocytes.</b><br>
-) The gram-positive bacteria, like <i>Staphylococcus aureus</i>, possess a variety of attributes, ranging from no outer membrane to acid-fast cell walls to the ability to form spores and pahtogenicity. <br>
-) Proteobacteria is a large category that can be further subdivided. <i>Clostridium tetani</i> and <i>Helicobacter pylori</i> are two examples of proteobacteria. Many use some form of litho- or phototrophy and some are pathogenic. <br>
-<b><i>Helicobacter pylori</i> is a good example of a Gram-negative proteobacteria.  However, what group contains <i>Clostridium tetani</i>?</b><br>
-) Bacteroidetes (i.e. <i>B. thetaiomicron</i>) are obligate anaerobes and major colonizers of the gut. <br>
-) Spirochetes like <i>Borrelia burgdorferi</i> are also spiral in shape and have 2 flagella, one at either end, which are fully encased by the periplasm. <br>
-<b>What kind of spiral form is typical of  Spirochetes? How does it differ from "spirillum"?</b>
-)Chlamydiae (<i>C. trachomatis</i>) are obligate intracellular parasites. <br>
 <br><br>
-<b>2. Explain an example of a major division of bacteria whose species show nearly uniform metabolism but differ widely in form.  Explaine a different example of a division showing a common, distinctive form, but variety of metabolism.</b>
+<b><i>Bacteroides thetaiotaomicron</i></b>
-Cyanobacteria and chlorobia are both phototrophs, obtaining energy from inorganic sources, although cyanobacteria alone produce oxygen.  In addition, cyanobacteria typically use water as an electron donor, whereas chlorobia use H<sub>2</sub>S.  Cyanobacteria also have subcellular structures: thylakoids (where photosynthesis occurs), carboxysomes, and gas vesicles (from which oxygen escapes), and they may grow as filaments, as well as forming specialized spore cells called akinetes.
-<br><b>Yes, that sounds good.  What do cyanobacteria release from the water, and how? Besides filaments, what cell and colony forms are found among cyanobacteria?</b>
-<br>Chlorobia have no subcellular structures and do not grow as filaments or form akinetes.
-<br>
-Nitrospirae and spirochetes are both Gram-negative, free-living, spiral-shaped bacteria.  However, nitrospirae are chemolithoautotrophs which oxidize nitrite to nitrate and take up inorganic carbon.
-<br><b>What is the difference between the spiral forms of nitrospirae and spirochetes?</b><br>  Spirochetes are chemoheterotrophs which take up organic molecules like glucose for carbon.
 <br><br>
+<b><i>Borrelia burgdorferi</i></b>
 <br><br>
-<b>3. Compare and contrast three different types of phototrophy found in bacteria.</b>
+<b><i>Chlamydia</i> sp.</b>
 <br><br>
+<b><i>Clostridium botulinum</i></b>
 <br><br>
-<b>4. Explain the pathology of three different gram-positive pathogens.</b>
+<b><i>Chloroflexus</i> sp.</b>
 <br><br>
-<i>Clostridium tetani</i> is a gram-positive bacteria that causes tetanus. It is contracted through contact of <i>C. tetani</i> spores with an open wound. If the environment of the wound is anaerobic, the spores will germinate and release a toxin that blocks the release of neurotransmitters from inhibitory interneurons, resulting in lockjaw and muscle contraction of primarily the neck. If left untreated, respiratory failure and death will soon follow.<br>
+<b><i>Corynebacterium diphtheriae</i></b>
-<br><i>Listeria</i> are intracellular pathogens that can survive a relatively wide range of temperatures. They are absorbed into the blood stream from the GI tract. From there they enter the nervous system where they polymerize actin, resulting in conditions such as meningitis and septicemia, among others. These bacteria can even infect macrophages.<br>
-<br><i>Mycobacterium tuberculosis</i>, yet another gram-positive bacteria, follows a different route of pathogenesis. TB is spread via coughing and the release of infected droplets by the patient into the air, where they become dispersed and contact another victim. The particles then lie dormant in the lungs of the infected individual until enough bacteria accumulate to instigate an immune response. The bacteria infect the attacking macrophages. The bacteria continue to grow and divide within the macrophage and are spread to other macrophages when these immune cells aggregate in the deeper lung tissues. The  infected macrophages develop into granulomas that wall off the infection. TB can be either active or dormant. If inactive, the bacteria remain within the granuloma. If active, the bacteria escape and cause lesions within the lungs.
-<br><b>Yes, the above mechanisms sound right.</b><br>
-<b>5. Explain two different examples of bacterial-host mutualism.</b>
 <br><br>
-<i>Oscillatoria</i> and <i>Synechocystis</i> are both cyanobacteria that are in mutualistic relationships with sponges. They supply up to 80% of the nutrional needs for the sponge and receive nutrients for themselves.
+<b><i>Deinococcus radiodurans</i></b>
-<i>Lactobacillus acidophilus</i> lives in the human intestine. It receives required nutrients and helps human health by inhibiting growth of pathogens.
 <br><br>
+<b><i>Enterococcus </i>sp.</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>
-Archaea which grow in extreme heat or cold are found in both phyla: Crenarchaeota and Euryarchaeota.  Desulfurococcales and Sulfolobales are both groups of Crenarchaeota that grow at high temperatres and gain energy by reducing sulfur.  Neither of these groups has a cell wall, and each has an S-layer present.  Other thermophiles among the Crenarcheota are Thermoproteales, which also reduce sulfur, and Caldisphaerales, which either respire anaerobically or ferment.  Yet there are certain Crenarchaeotes which live at psychrophilic temperatures: Cenararchaeum, which grows on deep-water sponges in Antarctic seawater, is a good example.  Thermophiles among the eukaryotes include Thermococcales, anaerobic archaea which use sulfur as an electron acceptor, and Archaeoglobales, which reduce sulfate to sulfide and oxidize acetate to carbon dioxide.  Thermoplasmatales are similar to Desulfurococcales and Sulfolobales: they have no cell wall.  They have no S-layer either, and an amorphous shape.
-Methanogens, archaea which produce methane by transferring electrons from H<sub>2</sub> to CO<sub>2</sub>, are all <b>Euryarchaeota</b> which live in anaerobic environments such as landfills, rumen, flooded soil, and the human gut.  Halophiles are <b>Euryarchaeota</b> which grow in extreme salt; in fact, they grow best at 4.3 M NaCl, at a pH of 7 or higher.  The high GC content in their DNA prevents denaturation in high salt, and most are photoheterotrophs, with rhodopsins which capture light energy by a proton-motive force.
-<br><b>Be careful, "Euryarchaeota," not Eukaryotes.</b><br>
 <br><br>
-<b>2. Explain how archaea growing in extreme environments require specialized equipment for study.</b>
+<b><i>Escherichia coli</i></b>
-<br>These extreme environments near extremely hot vents are challenging to explore because they are a threat to the scientists survival.  To take sample of these archae special submersive devices with robotic arms are used.  An advanced  version of this device can process the organisms DNA.  This is very important because the organisms can not survive without their specialized enironment.<br>
 <br><br>
-<b>3. What kinds of archaea grow in "average" environment such as the soil? Or an animal digestive tract?</b>
+<b><i>Geobacter metallireducens</i></b>
 <br><br>
-Methanogens are found commonly in the soil, landfills and animal digestive tracts.  In humans, they constitute about 10% of anaerobes in our gut and might increase the amount of calories we gain from our food.  In cattle however, they results in decreasing efficiency of meat production.  Methane gas produced in landfills from methanogens is sometimes diverted to be used to produce energy.  Methanogens must associate with bacteria to obtain the substrates required for methanogenesis.
+<b><i>Halobacterium</i> sp.</b>
-In addition, crenarchaeota include archaea in "average" environments.  There are many uncharacterized species that are associated with plant roots or live in the soil.  Marine pelagic plankton in the open ocean include archaea as well.
 <br><br>
+<b><i>Helicobacter pylori</i></b>
-==Chapter 20==
-<b>1. Compare and contrast the major divisions of eukaryotic microbes.  Which groups include primary-symbiont algae?  Secondary-symbiont algal protists?  Single flagellum versus paired flagella?  Motility (widespread) versus limited motility?.</b>
 <br><br>
+<b><i>Lactobacillus</i> sp.</b>
-. Opisthokonta: singal basal flagellum on reproductive cells. Not protists, share deletion in key genes
-<br>
-. Viridiplantae: include plants and algae, chloroplasts from primary endosymbiont. Includes Chlorophyta, of which the unicellular species have paired flagella.
-<br>
-. Amoebozoa or Lobosea: lobe-shapes pseudopods, move by sol-gel transition of actin filaments. Includes slime molds.
-<br>
-. Cercozoa: Filament-shaped pseudopods, some have a shell of inorganic material.
-<br>
-. Alveolata: cortex contians flattened vesicles, Ciliophora reproduce by conjugation. Dinoflagellata are secondary or tertiary endosymbiont algae.
-<br>
-. Heterokonta: pair of asymmetrical flagella, one shorter than the other, include sencondary-endosymbiont algae.
-<br>
-. Euglenozoa or Discicristata: include Euglenida, which are free-living flagellate some of which contain a secondary endosymbiotic chloroplast
-<br>
-. Excavata:flagellates that have lost mitochondria and Golgi apparatus through degenerative evolution.
 <br><br>
-<b>2. Describe examples of eukaryotic microbes that have shells or plates of silicate or calcium carbonate.</b>
+<b><i>Lactococcus</i> sp.</b>
 <br><br>
-Examples of eukaryotic microbes with shells include the Cercozoa, specifically radiolarians: shells make of silica with holes through which pseudopods radiate in all directions, and foraminiferans: generate shells of calcium carbonate laid down in helical succession, pseudopods extend from one opening. Diatoms are heterokonts that grow a bipartite shell called a frustule, which is composed of silica.
+<b><i>Leptospira</i> sp.</b>
 <br><br>
-<b>3. Explain mixotrophy.  Why are so many marine protists mixotrophs?</b>
+<b><i>Methanococcus</i> sp.</b>
 <br><br>
-Secondary endosymbiotic algae are often mixotrophic, meaning they use both phototrophy and heterotrophy. This allows them to live in a broader range of habitat: in deeper water light is not as available for photosynthesis, by using heterotrophy as well, they are able to obtain nutrients for a longer time span, at greater depths, and with a variety of environmental resources.
+<b><i>Mycobacterium tuberculosis</i></b>
 <br><br>
-<b>4. Why do eukaryotes show such as wide range of cell size?  What selective forces favor large cell size, and what favors small cell size?</b>
+<b><i>Mycoplasma pneumoniae</i> sp.</b>
 <br><br>
+<b><i>Nitrospira</i> sp.</b>
 <br><br>
+<b><i>Prochlorococcus</i> sp.</b>
-==Chapter 21==
-<b>1. Explain what is meant by symbiosis, mutualism, and parasitism.  Show with specific examples how mutualism and parasitism have a lot in common, and how there are inbetween cases.</b>
 <br><br>
+<b><i>Pseudomonas aeruginosa</i></b>
 <br><br>
-<b>2. Compare and contrast the roles of microbes in the marine and soil ecosystems.</b>
+<b><i>Pyrococcus furiosus</i></b>
 <br><br>
+<b><i>Pyrodictium occultum</i></b>
 <br><br>
-<b>3. How does oxygen availability determine the community structure of the soil habitat?  Of the aquatic (freshwater) sediment habitat?</b>
+<b><i>Rhodobacter</i> sp.</b>
-In a soil habitat, aerobic species of microbes are found in the organic horizon and the aerated horizon, among decaying and decomposed matter, because there is plenty of oxygen available in these soil layers.  Below the water table, species of anaerobes thrive, as this area is anoxic.  In the bedrock, there are lithotrophs up to three km down.  Obviously these microbes are anaerobic, and they must obtain their energy from inorganic sources, such as sulfur and hydrogen, because no organic minerals can reach the bedrock.
-In a freshwater habitat, oxygen is available in the epilimnion, but not so much in the hypolimnion or the benthos; therefore, anaerobic organisms are found in the epilimnion.  In the lower levels, anaerobic organisms are prevalent; photosynthetic sulfate reducers, in particular, are found in the hypolimnion.
 <br><br>
+<b><i>Rhodopseudomonas</i> sp.</b>
 <br><br>
-<b>4. Outline the metabolic processes of the bovine rumen microbial ecosystem.</b>
+<b><i>Rhodospirillum rubrum</i></b>
 <br><br>
+<b><i>Rickettsia</i> sp.</b>
 <br><br>
+<b><i>Salmonella enterica</i></b>
-==Chapter 22==
-<b>1. What are the common gases besides CO2 that contribute to global warming?  What is the chemical basis for how these gases trap solar radiation as heat?</b>
 <br><br>
-Nitrous oxide gas (N<sub>2</sub>) can escape as a byproduct of denitrification in the presence of excess nitrate; as a greenhouse gas it generates 200 times the warming effect of carbon dioxide. Additionally, it can react with the upper atmosphere and break down the ozone layer. Methane is another potent greenhouse gas: it is produced by methanogens, especially in wetland habitats. Large amounts of methane are crystalized around vents, the sudden release of one of these stores could have a detrimental effect on global temperatures.
+<b><i>Serratia marcescens</i></b>
 <br><br>
-<b>2. In the last fifty years, most of the wetlands off the coast of Louisiana have been destroyed.  Is this destruction responsible for the increased run-off and pollutants in the Gulf of Mexico, as well as the notorious dead zone there Can dead zones ever be fully revived?  What are the methods that used that cause the price of restoration to be $1 billion dollars per year?</b>
+<b><i>Sinorhizobium meliloti</i></b>
 <br><br>
-Nitrogenous waste from agriculture all along the Mississippi River is eventually expelled off the coast of Louisiana. The excess of nitrogen fuels algal blooms, and when the algae die their bodies are consumed by heterotrophs that use up all of the available oxygen, causing hypoxia and ultimately dead zones. Wetlands are capable of denitrifying waste from agriculture, so their absence is a large factor contributing to the dead zones and pollution in the Gulf of Mexico.
+<b><i>Staphylococcus epidermidis</i></b>
-<br>
-Restoration of the dead zone would require all of the communities along river drainage areas to eliminate nitrogenous waste before disposal. This could be done either with wastewater treatment or wetland filtration.
 <br><br>
-<b>3. It is interesting that the ocean's microbial communities could be responsible for over half of the biological uptake of atmospheric carbon.  How soluble is CO2 is in water?  Is it more soluble than oxygen gas in water? </b>
+<b><i>Staphylococcus aureus</i></b>
 <br><br>
+<b><i>Streptomyces</i> sp.</b>
 <br><br>
-<b>4. How exactly is ammonium nitrate addition related to higher CO2 efflux in wetlands? </b>
+<b><i>Vibrio cholerae</i></b>
-<br>Ammonium nitrate is a common fertilizer used for agricultural purposes. When it runs off into water systems and makes its way into wetland regions it increases the rate of CO2 efflux of the area by increasing the amount of aerobic respiration of microbes.  This then causes a positive feedback loop in the wetland with regards to CO2 production. The increased atmospheric CO2 from the microbial respiration increases the amount of CO2 available for plants to use in photosynthesis, which allows the plants to grow larger and establish more associations with microbes like micorrhizae. This results in higher CO2 output from the soil, which is one of the largest fluxes in the global carbon cycle.<br>
 <br><br>
-<b>5. Iron is limiting in oceans because the iron in the benthos, where it’s abundant, is inaccessible because it’s far away.  In the benthic environment then, is iron not limiting because the microbes can access the sediment?  What is typically limiting instead?</b>
+<b><i>Vibrio fischeri</i></b>
 <br><br>
+==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>
-<b>7. What is the microbial process in which nitrous oxide gas builds up?</b>
-<br>The process in which nitrous oxide (N2O) gas builds up is nitrate respiration during the nitrification process of the nitrogen cycle. This happens most frequently in environments where heavy fertilization increases the amount of nitrate in the soil. During nitrate respiration, N2O is produced in excess and given off into the environment where it depetes the ozone layers and acts as a greenhouse gas.It depletes the ozone layer by reacting catalytically with ozone in the upper atmosphere. <br>
-<br> N2O also builds up in marine dead zones, areas where eutrophication has resulted in the death of almost all of the organisms that lived there. Without oxygen, microbes are forced to utilize nitrate as an electron acceptor during anaerobic respiration. This process gives off a large amount of nitrate as well as N2O gas, which diffuses into the atmosphere and contributes to global warming by functioning as a greenhouse gas.<br>
 <br><br>
+<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>
-==Chapter 23==
+<br><br>
-<b>1. What's the point of breeding a gnotobiotic animal?</b>
-A gnotobiotic animal is an animal that satisfies one of two rules. It is either entirely germ-free, or all of the microbial species that colonize it are known. These animals are used to demonstrate how microbiotic organisms affect their host. They can be developed so that only particular microbiota are present and then observe any changes in the in the organism's function that may occur. In general, gnotobiotic organisms also demonstrate how microbiota are important to organisms as they show signs of poorly developed immune systems, low cardiac output, thin intestinal walls, and an increased susceptibility to pathogens.
-<br><b>Yes, that sounds right.</b><br>
 <br><br>
-<b>3. How do defensins tell the difference between “good” bacteria and pathogens?</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>4. What are the benefits of an acidic skin?  Of an acidic vaginal tract?</b>
+<b>4. Explain why most soil bacteria grow using energy-yielding reactions with very small delta-G.</b>
 <br><br>
 <br><br>
-<b>5. How are mast cells involved in immune response other than being differentiated with other immune cells?</b>
+<b>5. Why are glucose catabolism pathways ubiquitous, despite the fact that most bacterial habitats never provide glucose?  Explain several reasons.</b>
-<br>Mast cells are involved in autoimmune and hypersensitivity responses as well as functioning to differentiate into other immune cells. One example of another function of mast cells can be seen in the acute inflammatory response. When an infection takes place in a person's tissue, bradykinin, a polypeptide that allows for extravasation, is released into the area. These molecules then bind mast cells and cause a calcium influx that triggers the mast cells to degranulate and release histamine into the area, which further increases the permeability of blood vessels. The bradykinins then attach to capillary cells, which produce prostaglandins, which stimulate nerve endings and produce a pain response. <br>
+<br><br>
-<br> Ultimately, another function of mast cells is to release inflammatory factors during particular processes.<br>
 <br><br>
-<b>6. Why do you think gnotobiotic animals have a lower cardiac output?</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>7. Why does an infection site heat up during vasodilation?</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>
-This helps create a localized fever in the region, which helps kill microbes infecting the area.
 <br><br>
-<b>8. How do interferons work?  How do they connect with the adaptive immune system?</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>Interferons are soluble proteinaceous cytokines that "interfere" with viral replication. They are often produced by eukaryotic cells in response to intracellular infections, infections by pathogens that grow within the cell. They are species specific, which means that interferons from one species won't be functional in another species, but they are nonspecific with regards to viruses. This means that they generally target different kinds of viruses. Furthermore, there are two classes of interferons:<br>
-<br>Type I interferons preventatively bind receptors on the membranes of uninfected cells, thus rendering them resistant to viral infection. It can do this by promoting the production of two classes of proteins within the cell. The first of these proteins is an RNA-activated endoribonuclease, which functions to cleave viral RNA in the cell. The second class of proteins are protein kinases, that inactivate eIF2, a eukaryotic initiation factor that is necessary for translation.<br>
-<br>Type II interferons work with the adaptive immune system by activating macrophages, natural killer T-cells, and T-cells to increase their production of major histocompatibility complex antigens they present on their cell surface. Presentation of antigens is important because many adaptive immune cells, including T-cells, need to bind MHC-presented antigens before they become activated. Once these cells are activated, they can deal with infections effectively.<br>
 <br><br>
-<b>9. Explain the difference between the innate and adaptive immune systems--and explain how they interconnect.</b>
 <br><br>
+==Chapter 14==
+<br>
+<b>1. Explain how bacteria and archaea switch among various electron acceptors depending on environmental conditions.</b>
 <br><br>
-==Chapter 24==
+<br><br>
-<b>1. Now that you know more about adaptive immunity, explain some examples of how the innate and adaptive immune systems interconnect.  For instance, how does an innate system receiving a signal activate the adaptive immune system?  How does an adaptive response to a pathogen activate an innate response component?</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>2. Explain the difference between the B-cell and T-cell immune systems--and explain how they interconnect.</b>
+<b>3. For phototrophy, discuss the relative advantages and limitations of using PS I versus PS II.</b>
 <br><br>
 <br><br>
-<b>3. Explain an example of an antigen-presenting cell within the adaptive immune response.</b>
+<b>4. What environments favor oxygenic photosynthesis, versus sulfur phototrophy and photoorganotrophy? Explain.</b>
-In the adaptive immune system, dendritic cells are a type of antigen-presenting cell. Dendritic cells begin as white blood cells, also known as monocytes. Monocytes are capable of differentiating into dendritic cells and macrophages. As its name indicates, the dentritic cell has a highly branched morphology. These cells reside in the spleen and lymph nodes and can absorb and process small antigens. Once the antigens have been properly processed, the dentritic cell can display the antigen on its surface for recognition by T-cells.
 <br><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>
 <br><br>
-==Species to know for Test 3==
+<br><br>
+<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>
-<b>For each species, state one or two broader categories of organism (such as gram-positive endospore-forming bacteria), the type of genome, type(s) of metabolism, habitat, and disease caused (if any).</b>
 <br><br>
-<b><i>Aeromonas hydrophila</i></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>
-Broader Categories: Gram-negative, anaerobic
-<br>Genome: Genes that contribute to its toxicity are cytotoxic enterotoxin gene (act), heat labile enterotoxins (Alt), and heat-stable cytotonic enterotoxins (Ast).
-<br>Metabolism: Heterotrophic, ferments glucose, digests gelatin, hemoglobin, and elastin.
-<br>Habitat: Exists in aerobic and anaerobic environments: aquatic environments, fish guts, food, human bloodstream and organs.
-<br>Disease: Causes many diseases in fish and amphibians, since it exists in aquatic environments.  Can cause disease in humans, such as septiticemia, meningitis, pneumonia, and gastroenteritis.
-<b><i>Anabaena</i> sp.</b>
 <br><br>
-<br>Broader Categories: Barrel-shaped cells.  Filamentous cyanobacteria (blue-green algae) found as plankton.
+==Chapter 15==
-<br>Genome: 1 circular chromosome with 5368 protein-coding regions and 6 plasmids (from sequenced PCC 7120 strain).
+<br><br>
-<br>Metabolism: Photoautotrophic, perform oxygenic photosynthesis.  Form heterocysts (specialized nitrogen-fixing cells that convert nitrogen to ammonia) during nitrogen starvation.
+<b>1. Why does biosynthesis need both ATP and NADPH?  Why couldn't biosynthetic pathways use just ATP, or just NADPH?</b>
-<br>Habitat: Freshwater and damp soil.  Form symbiotic relationships with certain plants.
+<br><br>
-<br>Disease: Produce neurotoxins, such as anatoxins (neuromuscular poisons), that are harmful to wildlife and farm animals.
-<b><i>Aquifex</i> sp.</b>
 <br><br>
-Broader categories: gram-negative, generally rod-shaped, thermophilic, non spore forming, aerobe.
+<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>
-Genome: Densely packed genome with overlapping genes. No introns or splicing proteins. Genome is about 1/3 the size of that of E. coli.
+<br><br>
-Metabolism: Autotrophic chemolithotrophs that fix carbon from the environment and draw energy from inorganic chemical sources. Uses oxygen as terminal electron acceptor when it oxidizes hydrogen to form water “aquifex=water forming.” They can also use sulfur or thiosulfate to produce H2S instead of water. Some aquifcales aren’t aerobic, however, and reduce nitrogen instead of oxygen. In this case the reaction ends with H2.
-Habitat: Near volcanoes or hot springs
-Diseases Caused: None
-<b><i>Aspergillus</i> sp.</b>
 <br><br>
-Broader Categories: Over 185 species of this genus
+<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>
-Genome: Largely incomplete
+<b>What are the other oxidized forms that bacteria and plants take up and reduce to ammonia and ammonium ion?
-Metabolism: Highly aerobic.  Pathogenic species obtain nutrients from host, while non-pathogenic species obtain nutrients from soil, wood, and plant detritus.
+What about N from reduced organic compounds?</b>
-Habitat: Grow as molds in oxygen-rich environments and carbon-sources.  Some species are capable of living in nutrient-depleted environments as well.
-Disease: About 20 species are  pathogenic in humans and animals.  Aspergillus fumigatus and Aspergillus flavus cause invasive pulmonary aspergillosis and is often fatal.
+<br><br>
+<b>4. How are the pathways of amino acid biosynthesis organized?  What common routes flow from which core pathways?</b>
-<b><i>Bacillus anthracis</i></b>
 <br><br>
-Broader Categories: Gram-positive, rod-shaped, form endo-spores and biofilms
-<br>Genome: 1 circular chromosome with over 5 million b.p.  2 circular plasmids: pxO1 and pxO2.  These plasmids encode main virulent factors.
-<br>Metabolism: Facultative anaerobe and must grow in medium with essential nutrients including C and N sources.  Upon nutrient deprivation, endospores form (requires oxygen to form) and can live in inhospitable envrionments for many years.  Can grow into vegetative cells in aqueous environment with adequate nutrients.
-<br>Habitat: Live in soils world-wide and is the main habitat.
-<br>Disease: Anthrax disease.  Infectious endospores harm host by germinating for vegetative growth.  During growth the bacteria produce toxins in the body of humans and animals.  The slime capsule enables it to resist phagocytosis.  3 main forms of the disease: cutaneous, pulmonary, and gastrointestinal.  Can cause death in 2-48 hours.
-<b><i>Bacillus subtilis</i></b>
 <br><br>
-Broader Categories: Gram-positive, rod-shaped, form stress-resistant endospores
+<b>5. How and why do bacteria make "secondary products"?  What are their functions?</b>
-Genome: 1 circular chromosome with 4100 genes coding for proteins.
-Metabolism: Can grow in aerobic and anaerobic conditions.  Uses fermentation and nitrate ammonification to make ATP in the absence of oxygen.
-Habitat: Soil and vegetation at mesophilic temperatures.
-Disease: Non-pathogenic.  Responsible for spoilage of food, since contamination often results in decomposition, but it rarely causes food-poisoning.
-<b><i>Bacillus thuringiensis</i></b>
 <br><br>
-Broader Categories: Gram-positive, spore-forming, rod-shaped
-Genome: 1 circular chromosome with 5.2-5.8 Megabases.  Contains many plasmids.
-Metabolism: Facultative anaerobe (makes ATP by aerobic respiration if oxygen is present, but can switch to fermentation).
-Habitat: Soil.  It is used in 90% of pesticides.  Fends off insects by producing crystal proteins (Cry proteins).
-Disease: Species-specific, non-pathogenic to humans, making it an environmentally-friendly insecticide.  Cry toxin grows and sporulates in alkaline gut o finsect, which aids in its ability to infect the insect gut.  The gut breaks down and the insect eventually dies.
-<b><i>Bacteroides thetaiotaomicron</i></b>
 <br><br>
-Broader Categories: Gram-negative, anaerobic, human-bacterial symbiosis model
+<b>6. How can we manipulate bacterial secondary product formation to develop new pharmaceutical agents?</b>
-Genome: 1 circular chromosome made of d.s. DNA, consists of 4776 proein-coding genes, 90% of which are essential in the binding and import of various polysaccharides.
-Metabolism: Starch (all 3 forms) is primary carbohydrate used as its source of C and Energy.  Polysaccharides bind to the cell surface before undergoing hydrolysis.
-Habitat: Adult intestine-allows humans to degrade plant polysaccharides
-Disease: Serious infections include intra-abdominal sepsis and bacteremia.  It is resistant to many antimicrobial agents.
-<b><i>Borrelia burgdorferi</i></b>
 <br><br>
-Broader Categories: Sprial-shaped with 2 flagella
-Genome: A linear chromosome with 910,725 b.p. with 853 genes.  17 linear and circular plasmids.
-Metabolism: Require specific nutritional requirements making it difficult to culture in vitro.
-Habitat: Live extracellularly and adapts to various host animals (tick, rodents, birds) by regulating various lipoproteins on thier surface.
-Disease: Lyme disease and recurring fever.
-<b><i>Chlamydia</i> sp.</b>
 <br><br>
-Broader Categories: Gram-negative, aerobic, coccoid or rod-shaped
+==Chapter 17==
-Genome: C. trachomatis-1,042,519 b.p. with 894 protein-coding sequences (70 genes are not homologous to sequences on the C. pneumoniae genome).  C. pneumoniae- 1,230,230 b.p. (186 genes are not homologous to sequences on the C. trachomatis genome)
+<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>
-Metabolism: Cannot synthesize its own ATP, so they cannot be grown on artificial medium and require growing cells to remain viable.
-Habitat: C. trachomatis-human host cells, C. suis- swine host cells, C. muridarum- mice and hamster host cells.  Infectious elementary body form induces endocytosis upon contact with host cell.  Once inside, the elementary body germinates to vegetative form, and divides every 2-3 hrs.  It then reverts back to the elementary form and is released by the cell through exocytosis.
-Disease: C. trahomatis causes chlamydia and is the most common STD in the world.  C. pneumoniae causes pneumonia and bronchitis
-<b><i>Clostridium botulinum</i></b>
 <br><br>
-Broader Categories: Gram-positive, rod-shaped, anaerobic, spore-former
-Genome: Genome size of 4039 kbp, which is larger than most Gram-positive genomes, indicating the extra genomic requirements needed for sporulation and pathogenic toxin production
-Metabolism: Lie dormant in very adverse environments.  Spores can begin to grow in favorable conditions: non-halophilic salinity and anaerobic conditions.  Grows at mesophilic temps.
-Habitat: Soils and improperly canned food products
-Disease: A-G subtypes produce different botulin toxin- al except C and D subtypes are human pathogens.  The toxin prevents propagation of action potentials to the muscle fibers- causing paralysis by inhibiting muscle contraction.  Fatalities usually occur due to asphyxiation
-<b><i>Chloroflexus</i> sp.</b>
 <br><br>
-<b><i>Corynebacterium diphtheriae</i></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>
-<b><i>Escherichia coli</i></b>
 <br><br>
-Broader Categories: Gram-negative, rod-shaped, aerobic
-Genome: 1 circular chromosome, (4300 coding sequences) with 1800 known proteins.  Some contain circular plasmid.
-Metabolism: Facultative anaerobe.  Uses mixed-acid fermentation in anaerobic conditions.  Growth driven by aerobic or anaerobic respiration using a large variety of redox pairs: oxidation of pyruvic acid, formic acid, hydrogen, and amino acids and reduction of oxygen, nitrate, dimethyl sulfoxide, trimethylamine N-oxide.
-Habitat: Lower intestines of human and mammals, where it aids in digestion processes: vitamin K production, food breakdown and absorption
-Disease: E. coli O157:H7 (enterohemorrhagic strain) causes food poisoning- leading to bloody diarrhea and kidney failure due to its production of Shiga-like toxin.  Also can cause urinary tract infections by ascending infections of the urethra.
-<b><i>Geobacter metallireducens</i></b>
 <br><br>
-Broader Categories: Gram-negative, rod-shaped, possesses flagella, and pili
+<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>
-Genome: 1 circular chromosome encoding 3621 genes.  Plasmid encodes 13 genes, 1 of which is addiction module toxin (gives resistance to bacteria and another encoding plasmid stabilization system protein (allows bacteria to adapt to new environmental conditions)
-Metabolism: First organism with the ability to oxidize organic compounds and metals (iron, radioactive metals like Uranium, and petroleum compounds) into environmentally benign carbon dioxide while using iron oxide and other available metals an electron acceptors.
-Habitat: anaerobic conditions in soils and aquatic sediments
-Disease: Non-pathogenic
-<b><i>Pseudomonas aeruginosa</i></b>
 <br><br>
-Broader categories: Gram-negative, rod-shaped, does not produce spores. Habitat: due to its capability to synthesize arginine, P. aeruginosa proliferates in anaerobic conditions. It can be found in environments such as soil, water, humans, animals, plants, sewage, and hospitals. Metabolism: Aerobic respiration. P. aeruginosa can metabolize on hundreds of other things besides arginine, and can respire on nitrate (although it does much better on O2).Genome: a single and supercoiled circular chromosome in the cytoplasm. Disease(s) caused: Causes disease in immuno-compromised patients, such as those with cystic fibrosis, cancer, or AIDS. It further weakens the patient, allowing the patient to become more susceptible to other diseases. Usually this kills the patient. P. aeruginosa forms biofilms in the lung of cystic fibrosis patients; it is the major cause of death in these individuals.
-Broader Categories: Gram-negative, rod-shaped, and contains 1 flagella
-Genome: It contains a 5.2 to 7 million base pairs and a single, supercoiled circular chromosome in the cytoplasm with many plasmids contributing to its pathogenicity.
-Metabolism: Facultative aerobe, with its preferred metabolism being aerobic respiration by transferring electrons from glucose to oxygen.
-Habitat: Ubiquitous in that it can live in both human and inanimate environments.  This is possible mainly because of the vast array of enzymes that allow uptake of diverse forms of nutrients.
-Pathogenicity: Disease-causing agent to immuno-compromised individuals (cystic fibrosis patients) or indivuals in a trauma (burn victims).  It tends to form biofilms and cause tissue damage through its virulence factors.
-<b><i>Halobacterium</i> sp.</b>
 <br><br>
-Broader categories: rod-shaped, halophilic, candidate for life on Mars. Genome: 1 large chromosome and 2 plasmids (3 circular replicons). Metabolism: aerobic, but not glucose degradation. Habitat: highly saline lakes. Disease: non-pathogenic
+<b>4. Explain the evolutionary origins of mitochondria and chloroplasts.  What evidence do we see in the structures of modern microbes?</b>
-<b><i>Helicobacter pylori</i></b>
 <br><br>
-Broader Categories: Gram-negative, spiral-shaped, 6-8 flagella at one end
-Genome: Single circular chromosome with genes that encode urease, membrane cytotoxins, and the cag pathogenicity island.
-Metabolism: Glucose is the only carbohydrate used by H. pylori and is metabolized through the ED pathway.  Pyruvate is synthesized from D-amino acids, lactate, L-alanine, and L-serine, rather than glucose.  Fermentation of pyruvate yields acetate.  Urease converts urea into ammonia and bicarbonate to buffer the low pH of the stomach.
-Habitat: The lining of the stomach and duodenum, where it is well adapted to a pH of 2 or less.
-Pathogenicity: Peptic ulcers and gastritis
-<b><i>Lactobacillus</i> sp.</b>
 <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>
-<b><i>Lactococcus</i> sp.</b>
 <br><br>
-Broader categories: spherical, gram positive. Genome: 1 circular chromosome with 2, 365, 589 bp, where 86 % of the genome code for protein, 1.4 % for RNA, and 12.6 % for noncoding region. 64.2 % of the genes code for known functional proteins, and 20.1 % of the genes for known protein with unknown function. Metabolism: aerobic or anaerobic, often use lactic acid fermentation. Habitat: plant surfaces, digestive tract of cows. Disease: non-pathogenic.
-<b><i>Leptospira</i></b>
+==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>
-Broader Categories: spirochete, spiral-shaped with one or both ends usually hooked, of the family Leptospiraceae, and the genus Leptospira.  Very thin and must be observed through darkfield microscopy.
-Genome: Consists of a large chromosome and a small chromosome, with about 4768 total genes.
-Metabolism: aerobic using oxygen as the final electron acceptor.  Energy is gained primarily through long-chain fatty acids.  Carbohydrates are not used as a source of carbon, but can be synthesized through the TCA cycle.
-Habitat: Occupies diverse environments, habitats, and life cycles.  Stagnant waters are its natural environment.  Prefers slightly alkaline environment.  Prefers a temp of 28-30 degrees C bu can grow at temp. as low as 11-13 degrees C.
-Pathogenicity: Leptospirosis is potentially deadly in both humans and animals.  In humans it can cause symptoms of fever, chills, sore muscles, vomiting, jaundice, red eyes, abdominal pain, diarrhea, or rashes.  It is typically spread through contact with water, food, or urine of an infected animal.
-<b><i>Methanococcus</i> sp.</b>
 <br><br>
-Broader categories: gram-negative, cocci-shaped, archaea domain, thermophilic and mesophilic. Genome: 1 circular chromosome with 1 large extra-chromosomal element and 1 small extra-chromosomal element. Metabolism: autotrophic, anaerobic, reduces carbon dioxide with hydrogen gas to generate methane. Habitat: can grow up to pressures of 200 atm, temperature ranges between 48-94 degrees C, with optimal growth at 85 degrees C. Disease: non-pathogenic.
+<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>
-<b><i>Mycobacterium tuberculosis</i></b>
 <br><br>
-<b><i>Mycoplasma pneumoniae</i> sp.</b>
 <br><br>
-Broader categories: spherical without a cell wall, highly pathogenic--osmotic instability. Genome: 1 small circular chromosome. Metabolism: major nutrients come from mucosal epithelial cells of the host, many proposed metabolic pathways. Habitat: not found in the environment but can be cultured in medium-rich agar. Disease: highly pathogenic; parasitizes epithelial cells in the respiratory tract.
+<b>3. Compare and contrast three different types of phototrophy found in bacteria.</b>
-<b><i>Nitrospira</i> sp.</b>
 <br><br>
-<b><i>Paramecium</i> sp.</b>
 <br><br>
+<b>4. Explain the pathology of three different gram-positive pathogens.</b>
-Broader categories: Eukaryotic ciliated unicellular organisms. Genome: Linear. Metabolism: Paramecium eject trichocyts to help capture their prey. They commonly eat bacteria, yeasts, algae, and small protozoa. Paramecium are also heterotrophs.  Habitat: Aquatic environments, usually in stagnant warm water. Some Paramecium species form symbiotic relationships with green algae or bacteria. The bacteria/algae live in the cytoplasm of the Paramecium and perform photosynthesis. Disease: Non-pathogenic
-<b><i>Plasmodium falciparum</i></b>
 <br><br>
-Broader Categories: Protazoan parasite Genome: It contains a 23-megabase nuclear genome consisting of 14 chromosomes, encoding about 5,300 genes, and is the most A/T rich genome sequenced to date
-Metabolism: Uses intracellular hemoglobin as a food source.  Anaerobic glycolisis with pyruvate being converted to lactate.
-Habitat: Requires both human and mosquito hosts
-Pathogenicity: Causative agent of malaria
-<b><i>Prochlorococcus</i> sp.</b>
 <br><br>
-Broader Categories: Single-celled cyanobacteria
+<b>5. Explain two different examples of bacterial-host mutualism.</b>
-Genome: It is about 1.67 Mega-base pairs long with 1,694 predicted protein-coding regions
-Metabolism: photoautotrophic
-Habitat: Oceans
-Pathogenicity: Non-pathogenic
-<b><i>Rhodobacter</i> sp.</b>
 <br><br>
-Broader categories: quorum-sensing bacteria, flagella motility. Genome: unique complexities-2 chromosomes, 1 large and 1 small, circular chromosomes. Metabolism: photosynthesis mostly, also capable of lithotrophy, aerobic, and anaerobic respiration pathways. Habitat: aquatic and marine environments. Disease: non-pathogenic.<br><b>Which photosystem does it use?  Does it conduct phototrophy anaerobically, or in the presence of oxygen?</b>
-<b><i>Rhodopseudomonas</i> sp.</b>
 <br><br>
-<b><i>Rhodospirillum rubrum</i></b>
-<br><b>Which photosystem does it use?</b><br>
-<b><i>Rickettsia</i> sp.</b>
 <br><br>
+<b>6. Identify these kinds of bacteria based on their descriptions:</b>
-<b><i>Saccharomyces cerevesiae</i></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><br>
+<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?!
-Broader Categories: Best known as brewer's and baker's yeast, used as a model system due to its short generation time (1.5-2 hrs. at 30 degrees C), can be easily cultured, easily transformed which allows the addition or deletion of genes, and is a eukaryote so it shares much of the non-coding DNA stretches found in higher order eukaryotes
+<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.
-Genome: Single, linear, d.s. DNA, with little repeated sequences and less the 5% of the sequences have introns.
+<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.
-Metabolism: Heterotrophs that use both aerobic respiration and fermentation and obtain their energy from glucose.
+<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.
-Habitat: The natural habitat is the surface of fruits.  Industrially, it is used in baking and brewing and is considered an ale yeast, or top yeast.
+<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.
-Pathogenicity: Is used as a probiotic in humans.  However, new evidence may suggest that the use of S. cerevesiae probiotics could potentially be harmful, causing the infection of S. cerevesiae fungemia.
+<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.
-<b><i>Salmonella enterica</i></b>
 <br><br>
-Broader Categories: Gram-negative, rod-shaped, flagellated
-Genome: Circular chromosome with a one to a few plasmids (depending on the 1 of 2,000 serovars that comprise S. enterica.
-Metabolism: aerobic respiration
-Habitat: Reptile and amphibian microbiota.  It is also found in red meat, poultry, and raw egg shells Pathogenicity: Salmonella enterica serovar Typhi is the causative agent of typhoid fever.  Salmonella enterica serovar Typhimurium generally causes gastroenteritis.  Its major virulent factor is its secreted proteins, such as adhesins that help colonize the host and are involved in biofilm formation.
-<b><i>Serratia marcescens</i></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>
-Broader Categories: Gram-negative, rod-shaped, motile, of the family Enterobacteriaceae.
-Genome: Singular circular chromosome.  Few plasmids
-Metabolism: Facultative anaerobe, but uses primarily fermentation to obtain Energy.  Nitrate is usually the final electron acceptor.
-Habitat: Found in diverse environments from water and soil to plants and animals.  One of the most common contaminant on laboratory Petri dishes.
-Pathogenicity: A wide variety of diseases can result mainly in immuno-compromised individuals, such as bacteremia, meningitis,  urinary tract infections, osteomyelitis, ocular infections, and endocarditis.  It is resistant to penicillin and ampicillin, due to R-factors on plasmids encoding genes involved in antibiotic resistance and is able to produce biofilms.
-<b><i>Sinorhizobium meliloti</i></b>
 <br><br>
-<b><i>Staphylococcus epidermidis</i></b>
+<b>2. Explain how archaea growing in extreme environments require specialized equipment for study.</b>
 <br><br>
-Broader Categories: Gram positive, spherical, arrange in grape-like clusters, resistant to all penicillins and methicillin.
-Genome: The chromosome length is 2,616,530 bp and contains a few plasmids, depending on the strain.
-Metabolism: Facultative anaerobe that can grow by aerobic respiration or by fermentation.  Most strains can reduce nitrate.
-Habitat: The skin and in mucous membranes of animals.  Has the ability to produce slime and biofilms, which enable it to grow on biomedical devices.
-Pathogenicity: The primary virulence factor is its ability to form biofilms.  With the increased use of intravascular catheters, the rate of infection has increased.  It is more resistant to antibiotics that most other species.
-<b><i>Staphylococcus aureus</i></b>
 <br><br>
-Broader categories: gram positive, spherical, immobile. Genome: 1 circular genome, resistance for antibiotics are encoded by a transposon. Metabolism: EMP and Pentose-Phosphate pathways. Lactate is the end product of anaerobic glucose metabolism. Acetate and carbon dioxide are the end products of aerobic metabolism. Habitat: skin, mucous membranes of animals. Disease: skin infections, invasive diseases, toxic shock syndrome (TSS).
+<b>3. What kinds of archaea grow in "average" environment such as the soil? Or an animal digestive tract?</b>
-<b><i>Streptococcus </i>sp.</b>
 <br><br>
-Broader Categories: Gram positive, spherical, can be found in chains or in pairs, immobile. Genome: 1 circular chromosome. Metabolism: Many species of Streptococcus are facultative anaerobes, while others are obligate anaerobes. Habitat: Part of normal animal flora. Can become pathogenic and infect humans and other animals. They often imitate aspects of their host organism to avoid being detected. Disease: Can cause step throat, necrotizing fasciitis, scarlet fever, rheumatic fever, postpartum fever, and streptococcal toxic shock syndrome. Some species of Streptococcus can cause pneumonia.
-<b><i>Streptomyces</i> sp.</b>
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-<b><i>Vibrio cholerae</i></b>
+<b>4. Archaea identification: What is it?</b>
-<br><br>
+<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.
-Broader Categories: Gram-negative, bent rod shaped, one polar flagellum.  Genome:  Two circular chromosomes.  Metabolism:  Fermentative and respiratory.  Habitat:  Aquatic environments.  Disease:  Responsible for cholera in humans, which is characterized by diarrhea and vomiting leading to dehydration.  The bacteria secrete a toxin that ultimately causes an increase in cyclic AMP levels that stimulates ion transport in the cells lining the intestine.  This is followed by water leaving the intestinal cells to compensate for the change in osmolarity.
-<b><i>Vibrio fischeri</i></b>
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-Broader Categories:  Rod shaped, gram-negative.  Genome:  Two circular chromosomes with 2,284,050 bp and a plasmid.  The lux operon controls bioluminescence.  Metabolism:  Heterotrophic.  Habitat:  Found in marine environments in a symbiotic relationship or as free-living.  It can also be parasitic and saprophytic.  Often found in the Hawaiian squid, Euprymna scolopes, where the bacteria bioluminesce in the light organ.  The squid protects the bacteria from predators and provides nutrients, while the bacteria’s light eliminates the squid’s shadow, protecting it from predators.  Disease:  Other Vibrio species can cause human infections.
+[[Category:Pages edited by students of Joan Slonczewski at Kenyon College]]