BIOL 238 Review 2009: Difference between revisions

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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>
<br>


==Chapter 7==
<br>
<b>1. What are the relative advantages and limitations of bidirectional replication versus rolling circle replication?  What kind of genetic entities are likely to favor one over the other?</b>
<br><br>


<br><br>
==Species to know==
<b>2. What kinds of mutant phenotypes reveal aspect of the mechanism of DNA replication and cell division?  Explain two specific examples.</b>
<br><br>


<b>For each species of bacteria or archaea, state one or two broader categories of organism (such as gram-positive endospore-forming bacteria), the type of genome, type(s) of metabolism, habitat, and disease caused (if any).</b>
<br><br>
<br><br>
<b>3. Explain how it's possible for the replisome to replicate the leading and lagging strands simultaneously.</b>
<b><i>Aeromonas hydrophila</i></b>
<br><br>
<br><br>
 
<b><i>Anabaena</i> sp.</b>
<br><br>
<br><br>
<b>4. During resolution of a catenane, how might a major mutation occur affecting the entire genome?  How do you think this mutation is prevented?</b>
<b><i>Aquifex</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Bacillus anthracis</i></b>
<br><br>
<br><br>
<b>5. During rapid growth, why would a bacterial cell die if the antibiotic drug “forms a physical barrier in front of the DNA replication complex.”?</b>
<b><i>Bacillus subtilis</i></b>
<br><br>
<br><br>
 
<b><i>Bacillus thuringiensis</i></b>
<br><br>
<br><br>
<b>6. What are the relative advantages and limitations of bidirectional versus rolling-circle replication of DNA?  Explain in terms of different genome sizes, types, and cell situation when replication occurs.</b>
<b><i>Bacteroides thetaiotaomicron</i></b>
<br><br>
<br><br>
 
<b><i>Borrelia burgdorferi</i></b>
<br><br>
<br><br>
<b>7. When you sequence a genome, how do you know where the base pairs in the genome are located since the DNA used to sequence the genome is in fragments?</b>
<b><i>Chlamydia</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Clostridium botulinum</i></b>
<br><br>
<br><br>
 
<b><i>Chloroflexus</i> sp.</b>
==Chapter 8==
<br>
<b>1. Explain how a biochemical experiment can demonstrate the specific protein targeted by a new antibiotic that impairs transcription.</b>
<br><br>
<br><br>
 
<b><i>Corynebacterium diphtheriae</i></b>
<br><br>
<br><br>
<b>2. If <i>Mycoplasma genitalium</i> cannot synthesize its own amino acids, does it have extensive/multiple protein channels (ABC pumps) to let amino acids pass its membrane? If proteins are made of amino acids, though, how did the first M. genitalium’s protein channels come into existence? </b>
<b><i>Deinococcus radiodurans</i></b>
<br><br>
<br><br>
 
<b><i>Enterococcus </i>sp.</b>
<br><br>
<br><br>
<b>3. In tRNA, there are "unusual" bases not found in mRNA  How are these bases generated?  Do you think they arise from a recently-evolved aspect of tRNA, or do you think they are an ancient phenomenon of the original RNA world?  Explain.</b>
<b><i>Escherichia coli</i></b>
<br><br>
<br><br>
 
<b><i>Geobacter metallireducens</i></b>
<br><br>
<br><br>
<b>4. What kinds of pharmaceutical agents could you design to act on gene promoters?  Explain using protein and/or RNA molecules.</b>
<b><i>Halobacterium</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Helicobacter pylori</i></b>
<br><br>
<br><br>
<b>5. Why do you think bacterial cells absorb protein and nucleic acids that are exported by other bacteria?</b>
<b><i>Lactobacillus</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Lactococcus</i> sp.</b>
<br><br>
<br><br>
<b>6. How could you sequence the genome of an unculturable microbe?</b>
<b><i>Leptospira</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Methanococcus</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Mycobacterium tuberculosis</i></b>
==Chapter 9 and 10==
<br>
<b>1. In the process of conjugation, how are genes moved? Are genes moved individually or in groups?  Could part of a gene be moved? </b>
<br><br>
<br><br>
 
<b><i>Mycoplasma pneumoniae</i> sp.</b>
<br><br>
<br><br>
<b>2. How are microbial species defined?  What is the role of vertical phylogeny; and the role of horizontal gene exchange? Explain why species definition is a problem.</b>
<b><i>Nitrospira</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Prochlorococcus</i> sp.</b>
<br><br>
<br><br>
<b>3. Why is competence factor exported out of the cell to bind to ComD externally in transformation of Streptococcus? Why doesn't the molecule bind internally? Doesn't exporting CF waste energy? </b>
<b><i>Pseudomonas aeruginosa</i></b>
<br><br>
<br><br>
 
<b><i>Pyrococcus furiosus</i></b>
<br><br>
<br><br>
<b>4. If a spontaneous mutation occurs to form an apurinic site, transcription and replication are hindered, but what actually happens when the replisome gets to the hole where the base should be? </b>
<b><i>Pyrodictium occultum</i></b>
<br><br>
<br><br>
 
<b><i>Rhodobacter</i> sp.</b>
<br><br>
<br><br>
<b>5. Explain how a DNA sequence inverts during phase variation.  Would you expect it to revert at the same rate?  Why or why not?</b>
<b><i>Rhodopseudomonas</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Rhodospirillum rubrum</i></b>
<br><br>
<br><br>
<b>6. Explain the different propagation strategies available to a replicative transposon.  What are various ways the transposon could spread within a cell? Among organisms?</b>
<b><i>Rickettsia</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Salmonella enterica</i></b>
<br><br>
<br><br>
<b>7. Explain how the <i>ara</i> operon works, and how it differs from the lac operon.</b>
<b><i>Serratia marcescens</i></b>
<br><br>
<br><br>
 
<b><i>Sinorhizobium meliloti</i></b>
<br><br>
<br><br>
<b>8. Explain how different mechanisms acting at different levels on DNA and RNA can modulate gene expression over a range of time scales, from multiple generations to within a few seconds.</b>
<b><i>Staphylococcus epidermidis</i></b>
<br><br>
<br><br>
 
<b><i>Staphylococcus aureus</i></b>
<br><br>
<br><br>
<b>9. Explain the roles of thermodynamic and kinetic effects in attenuation control of the <i>trp</i> operon.</b>
<b><i>Streptomyces</i> sp.</b>
<br><br>
<br><br>
 
<b><i>Vibrio cholerae</i></b>
<br><br>
<br><br>
 
<b><i>Vibrio fischeri</i></b>
==Wozniak lecture on Biofilms==
<br>
<b>1. What do bacterial biofilms have in common with multicellular organisms?  How do they differ?</b>
<br><br>
 
<br><br>
<b>2. What are the advantages to bacteria of biofilm formation?  What properties do biofilms confer?</b>
<br><br>
 
<br><br>
<b>3. Where in the body do biofilms form infections?  Why?</b>
<br><br>
 
<br><br>
<b>4. Explain the basis of "twitching motility."  Compare and contrast twitching with flagellar motility.  How does twitching motility promote biofilm development?</b>
<br><br>
<br><br>


<br><br>
<b>5. How does the ara promoter work (pBAD)?  How was pBAD used to test the role of the <i>psl</i> operon in bioflim development?</b>
<br><br>
<br><br>
<b>6. How was it proved that <i>psl</i> encodes PSL polysaccharide?  How does PSL compare in structure with alginate?</b>
<br><br>
<br><br>
==Chapter 13==
==Chapter 13==
<br>
<br>
Line 201: Line 166:
<br><br>
<br><br>
<b>3. What forms of nitrogen are available to microbes for assimilation?  When fertilizer is spread on farmland to nourish crops, what problem is caused by microbes?</b>
<b>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>
<br><br>
<b>What are the other oxidized forms that bacteria and plants take up and reduce to ammonia and ammonium ion?
 
What about N from reduced organic compounds?</b>
<br><br>
<br><br>
<b>4. How are the pathways of amino acid biosynthesis organized?  What common routes flow from which core pathways?</b>
<b>4. How are the pathways of amino acid biosynthesis organized?  What common routes flow from which core pathways?</b>
Line 214: Line 180:
<b>6. How can we manipulate bacterial secondary product formation to develop new pharmaceutical agents?</b>
<b>6. How can we manipulate bacterial secondary product formation to develop new pharmaceutical agents?</b>
<br><br>
<br><br>
<br><br>
==Nitrogen fixation and nodulation==
<br><br>
<br><br>
==Chapter 17==
==Chapter 17==
<b>1. Explain why the first kinds of metabolism on Earth involved electron donors from the sediment reacting with electron receptors from above.  What geolotical and outer-space processed generated these electron donors and electron acceptors?</b>
<br><br>
<br><br>
==Species to know for Test==
 
<br><br>
<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>
<br><br>
<b><i>Aeromonas hydrophila</i></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><i>Anabaena</i> sp.</b>
 
<br><br>
<br><br>
<b><i>Aspergillus</i> sp.</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><i>Bacillus anthracis</i></b>
<br><br>
<br><br>
<b><i>Bacillus subtilis</i></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><i>Bacillus thuringiensis</i></b>
<br><br>
<br><br>
<b><i>Bacteroides thetaiotaomicron</i></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>
<b><i>Borrelia burgdorferi</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>
<br><br>
<b><i>Chlamydia</i> sp.</b>
 
<br><br>
<br><br>
<b><i>Clostridium botulinum</i></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><i>Escherichia coli</i></b>
 
<br><br>
<br><br>
<b><i>Geobacter metallireducens</i></b>
<b>3. Compare and contrast three different types of phototrophy found in bacteria.</b>
<br><br>
<br><br>
<b><i>Pseudomonas aeruginosa</i></b>
 
<br><br>
<br><br>
<b><i>Halobacterium</i> sp.</b>
<b>4. Explain the pathology of three different gram-positive pathogens.</b>
<br><br>
<br><br>
<b><i>Lactococcus</i> sp.</b>
 
<br><br>
<br><br>
<b><i>Methanococcus</i> sp.</b>
<b>5. Explain two different examples of bacterial-host mutualism.</b>
<br><br>
<br><br>
<b><i>Mycoplasma pneumoniae</i> sp.</b>
 
<br><br>
<br><br>
<b><i>Paramecium</i> sp.</b>
 
<br><br>
<br><br>
<b><i>Plasmodium falciparum</i></b>
<b>6. Identify these kinds of bacteria based on their descriptions:</b>
 
<br>a. This bacteria is irregularly shaped with peptidoglycan cell walls and a cytoskeleton containing tubulin (previously thought to only be present in Eukaryotes). They are heterotrophs living in variable environments that are usually low in salt, and most are oligotrophs.
<br>b. This bacteria has a nucleus similar to that of a eukaryotic organism.  It is most notable for its unique membrane structure.  It has multiple internal membranes, with a double membrane functioning to surround the nucleoid.  What am I?!
<br>c. Bacteria in this group are filamentous photoheterotrophs.  In the presence of oxygen they conduct nonphotosynthetic heterotrophy.  They can be found in microbial mats together with thermophilic cyanobacteria.  Some species contain chlorosomes.  They are also known as green nonsulfur bacteria.
<br>d. These bacteria are photolithotrophs that deposit sulfur on the cell surface.  They use H<sub>2</sub>S as an electron donor and are known as green sulfur bacteria.  These bacteria also live in strictly anaerobic conditions below the water surface.
<br>e. This bacterium is gram positive but has permanently lost its cell wall and S-layer due to reductive/degenerative evolution.  It also has the smallest genome(580 kbp) and it is parasitic.
<br>f. This bacterial species ferments complex carbohydrates and serves as one of the major mutualists of the human gut.  Has a Gram-negative structure and is an obligate anaerobe.
<br>g. These bacteria are deep branching and come in a multitude of forms.  They can be found living independently or in colonies. Often times, these different forms allow them to fix nitrogen.  While these organisms can be found in both aquatic and terrestrial habitats, many species contain gas vesicles to maintain a favorable position in the water column.
 
<br><br>
<br><br>
<b><i>Prochlorococcus</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>
<br><br>
<br><br>
<b><i>Pseudomonas aeruginosa</i></b>
<br><br>
<br><br>
<b><i>Rhodobacter</i> sp.</b>
<b>2. Explain how archaea growing in extreme environments require specialized equipment for study.</b>
<br><br>
<br><br>
<b><i>Rhodospirillum rubrum</i></b>
 
<br><br>
<br><br>
<b><i>Rickettsia</i> sp.</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><i>Saccharomyces cerevesiae</i></b>
 
<br><br>
<b><i>Salmonella enterica</i></b>
<br><br>
<b><i>Serratia marcescens</i></b>
<br><br>
<b><i>Sinorhizobium meliloti</i></b>
<br><br>
<b><i>Staphylococcus epidermidis</i></b>
<br><br>
<b><i>Staphylococcus aureus</i></b>
<br><br>
<b><i>Streptococcus </i>sp.</b>
<br><br>
<b><i>Streptomyces</i> sp.</b>
<br><br>
<b><i>Vibrio cholerae</i></b>
<br><br>
<br><br>
<b><i>Vibrio fischeri</i></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>
<br><br>
[[Category:Pages edited by students of Joan Slonczewski at Kenyon College]]

Latest revision as of 14:53, 23 July 2011

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


Species to know

For each species of bacteria or archaea, state one or two broader categories of organism (such as gram-positive endospore-forming bacteria), the type of genome, type(s) of metabolism, habitat, and disease caused (if any).

Aeromonas hydrophila

Anabaena sp.

Aquifex sp.

Bacillus anthracis

Bacillus subtilis

Bacillus thuringiensis

Bacteroides thetaiotaomicron

Borrelia burgdorferi

Chlamydia sp.

Clostridium botulinum

Chloroflexus sp.

Corynebacterium diphtheriae

Deinococcus radiodurans

Enterococcus sp.

Escherichia coli

Geobacter metallireducens

Halobacterium sp.

Helicobacter pylori

Lactobacillus sp.

Lactococcus sp.

Leptospira sp.

Methanococcus sp.

Mycobacterium tuberculosis

Mycoplasma pneumoniae sp.

Nitrospira sp.

Prochlorococcus sp.

Pseudomonas aeruginosa

Pyrococcus furiosus

Pyrodictium occultum

Rhodobacter sp.

Rhodopseudomonas sp.

Rhodospirillum rubrum

Rickettsia sp.

Salmonella enterica

Serratia marcescens

Sinorhizobium meliloti

Staphylococcus epidermidis

Staphylococcus aureus

Streptomyces sp.

Vibrio cholerae

Vibrio fischeri

Chapter 13


1. ATP and NADH are both energy carriers: What are the advantages of using one over the other?



2. When cells need to make glucose (gluconeogenesis), they "reverse glycolysis" because most steps are reversible. However, there are a couple of steps that are not reversible. How do you think they get reversed for gluconeogenesis?



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



4. Explain why most soil bacteria grow using energy-yielding reactions with very small delta-G.



5. Why are glucose catabolism pathways ubiquitous, despite the fact that most bacterial habitats never provide glucose? Explain several reasons.



6. In glycolysis, explain why bacteria have to return the hydrogens from NADH back onto pyruvate to make fermentation products. Why can't NAD+ serve as a terminal electron acceptor, like O2?



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



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



Chapter 14


1. Explain how bacteria and archaea switch among various electron acceptors depending on environmental conditions.



2. Explain how cell processes such as ATP synthesis can be powered by either the transmembrane pH difference or by the charge difference across the membrane. Which form of energy is likely to be used at low external pH? At high external pH?



3. For phototrophy, discuss the relative advantages and limitations of using PS I versus PS II.



4. What environments favor oxygenic photosynthesis, versus sulfur phototrophy and photoorganotrophy? Explain.



5. Explain why certain lithotrophs acidify their environments, to more extreme levels than fermentation. What are some practical consequences for human industry?



6. Is it surprising that an organism may switch between lithotrophy and organotrophy? What enzymes would have to be replaced, and what enzymes could be used in common for both kinds of metabolism?



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



Chapter 15



1. Why does biosynthesis need both ATP and NADPH? Why couldn't biosynthetic pathways use just ATP, or just NADPH?



2. Compare and contrast fatty acid biosynthesis and amino acid biosynthesis. Which pathway requires more reduction? Which requires a greater number of different enzymes? Why?



3. What forms of nitrogen are available to microbes for assimilation? When fertilizer is spread on farmland to nourish crops, what problem is caused by microbes? What are the other oxidized forms that bacteria and plants take up and reduce to ammonia and ammonium ion? What about N from reduced organic compounds?



4. How are the pathways of amino acid biosynthesis organized? What common routes flow from which core pathways?



5. How and why do bacteria make "secondary products"? What are their functions?



6. How can we manipulate bacterial secondary product formation to develop new pharmaceutical agents?



Chapter 17

1. Explain why the first kinds of metabolism on Earth involved electron donors from the sediment reacting with electron receptors from above. What geolotical and outer-space processed generated these electron donors and electron acceptors?





2. What evidence supports the "RNA world" aspect of the origin of life? What are evolutionary and medical implications of the RNA world model?



3. What is our modern definition of a microbial species? Explain the strengths and limitations of defining microbial species based on common ancestry of DNA sequence.



4. Explain the evolutionary origins of mitochondria and chloroplasts. What evidence do we see in the structures of modern microbes?



5. What is a virulence gene? How do virulence genes evolve? How can we analyze the relationship between virulent and nonvirulent strains of a bacterium?

Chapter 18

1. Compare and contrast the major divisions of bacteria. State an example of a species of each major division.



2. Explain an example of a major division of bacteria whose species show nearly uniform metabolism but differ widely in form. Explain a different example of a division showing a common, distinctive form, but variety of metabolism.



3. Compare and contrast three different types of phototrophy found in bacteria.



4. Explain the pathology of three different gram-positive pathogens.



5. Explain two different examples of bacterial-host mutualism.





6. Identify these kinds of bacteria based on their descriptions:


a. This bacteria is irregularly shaped with peptidoglycan cell walls and a cytoskeleton containing tubulin (previously thought to only be present in Eukaryotes). They are heterotrophs living in variable environments that are usually low in salt, and most are oligotrophs.
b. This bacteria has a nucleus similar to that of a eukaryotic organism. It is most notable for its unique membrane structure. It has multiple internal membranes, with a double membrane functioning to surround the nucleoid. What am I?!
c. Bacteria in this group are filamentous photoheterotrophs. In the presence of oxygen they conduct nonphotosynthetic heterotrophy. They can be found in microbial mats together with thermophilic cyanobacteria. Some species contain chlorosomes. They are also known as green nonsulfur bacteria.
d. These bacteria are photolithotrophs that deposit sulfur on the cell surface. They use H2S as an electron donor and are known as green sulfur bacteria. These bacteria also live in strictly anaerobic conditions below the water surface.
e. This bacterium is gram positive but has permanently lost its cell wall and S-layer due to reductive/degenerative evolution. It also has the smallest genome(580 kbp) and it is parasitic.
f. This bacterial species ferments complex carbohydrates and serves as one of the major mutualists of the human gut. Has a Gram-negative structure and is an obligate anaerobe.
g. These bacteria are deep branching and come in a multitude of forms. They can be found living independently or in colonies. Often times, these different forms allow them to fix nitrogen. While these organisms can be found in both aquatic and terrestrial habitats, many species contain gas vesicles to maintain a favorable position in the water column.



Chapter 19

1. Compare and contrast the different major groups of archaea. Which ones grow in extreme heat or cold? Extreme salt? Produce methane?



2. Explain how archaea growing in extreme environments require specialized equipment for study.



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



4. Archaea identification: What is it?
These archaea were once thought to be extremophiles, but it turns out they are the most abundant archaea in the ocean. Nonetheless, the thermophiles responsible for giving this false impression are found at temperatures of 113degrees. Others are found living in sulfuring springs. When gram stained, these archaea appear gram-negative.