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.
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==Chapter 7==
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<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>
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Bidirectional replication is much more efficient for large genomes, because as both the leading strands and lagging strands are replicated at the same time<b> (and in both directions)</b>, it does not take quite as long.  Replicating one strand and then the other in large genomes would take an unnecessarily long time.  However, rolling circle replication is ideal for small, circular genomes, such as plasmids and bacteriophage genomes, because in these cases, large numbers of copies need to be made quickly <b>(in large numbers, using simpler enzymes, perhaps more error-prone)</b>.  Bacteriophages, of course, need to produce as many copies of their genomes as possible in order to either destroy the host cell or incorporate themselves into the cell's DNA.  As plasmids may contain genes that are advantageous under certain conditions--conferring antibiotic resistance, for example--it is important that each daughter cell receives these genes; much of the time, large numbers of copies of plasmids are needed, and rolling circle replication is the most efficient way to produce them.
==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>
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<b>2. What kinds of mutant phenotypes reveal aspect of the mechanism of DNA replication and cell division?  Explain two specific examples.</b>
<b><i>Aeromonas hydrophila</i></b>
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<b><i>Anabaena</i> sp.</b>
In the Caulobacter
 mutant that lacks the XerD protein, the bacterial cells filament (keep getting longer instead of dividing). The nucleoids failed to separate, even though the DNA has replicated. In DNA replication and cell division, the cell must segregate in order to form new copies. This is seen when the cell DNA is labeled with GFP. The Bowman article showed other mutants, such as the PopZ mutant that kept filamenting because PopZ is needed for polar localization of DNA. Other mutants lead to minicells, such as the FDSZ protein mutant. DNA replication mutants display repeated sectored colonies. These mutants have mutations in cell division and repair apparatus’ that do not allow the cells to separate.
 
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<b>3. Explain how it's possible for the replisome to replicate the leading and lagging strands simultaneously.</b>
<b><i>Aquifex</i> sp.</b>
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<b><i>Bacillus anthracis</i></b>
Each complex contains 2 DNA Pol III enzymes, which together form the replisome.  One copy of the enzyme synthesizes the leading strand, while the other does the lagging strand.  The synthesis of the lagging strand goes away from the replication fork.  A new RNA primer is synthesized about every thousand bases, meaning it is synthesized in pieces, called Okazaki fragments.  The DNA Pol III then uses the primer to synthesize a complementary DNA strand until it bumps into the beginning of the previous fragment.  RNase cleaves the RNA primers to allow DNA Poly I to synthesize DNA patches using the 3’ OH end of the preexisting fragment as a primer.  The pieces are joined by DNA ligase.<br>
<b>Yes, that sounds right.</b>
 
<br><br>
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<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>Bacillus subtilis</i></b>
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<b><i>Bacillus thuringiensis</i></b>
A major mutation in either the XerC or XerD proteins, which recognize the <i>dif</i> site on each DNA molecule and catalyze a series of cutting and rejoining steps that result in catenane resolution, would cause a major mutation affecting the entire genome.  A mutation in either of these proteins would cause the two replicated DNA genomes to not separate and thus the cells would filament, nucleoids would fail to separate, and the cell would not properly replicate.  The mutation could also possibly lead to one double-length genome that contains the entire genome twice, or it could lead to the wrong ends in the Holiday junction being joined, and thus may result in two genomes that are quite different from the original. This type of mutation could possibly be prevented by employing multiple proofreading steps for the replicated genome, particularly in the sequences which encode XerC and XerD.  By preventing this mutation, you would prevent improper cell replication, which would could possibly lead to further mutated replication or even cell death.
 
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<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>Bacteroides thetaiotaomicron</i></b>
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<b><i>Borrelia burgdorferi</i></b>
Once DNA replication has started, the process of cell division has to finish.  If the replication complex is physically blocked, the DNA will not be able to replicate, but the cell will start to divide into 2 daughter cells anyway.  As the septum forms, it will kill both daughter cells since the DNA will not be separated. 
 
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<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>Chlamydia</i> sp.</b>
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<b><i>Clostridium botulinum</i></b>
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<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>Chloroflexus</i> sp.</b>
 
The sites at which the restriction enzymes cleave the DNA, also known as the restriction sites, are palindromic: the top and bottom strands are read the same in a 5' to 3' direction.  For example, TAACGT would pair with AATGCT.<br>
<b>A good idea, but there are far more "ends" than there are different restriction sites; so how would these tell you how to line up all the genomic pieces correctly?</b>
 
All fragments of DNA can be clones so that there are overlapping fragments (this is known as “shotgun” cloning).  Each fragment can then be sequenced using dideoxy sequencing.  The overlapping areas can be matched using a computer until the genome is reconstructed.  <br>
<b>Yes, that will do it.</b>
 
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<b><i>Corynebacterium diphtheriae</i></b>
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<b><i>Deinococcus radiodurans</i></b>
==Chapter 8==
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<b>1. Explain how a biochemical experiment can demonstrate the specific protein targeted by a new antibiotic that impairs transcription.</b>
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<b><i>Enterococcus </i>sp.</b>
This can be done in cell free systems.  The parts <b>(subunits)</b> from a RNA polymerase from a sensitive strain and a resistant strain are separated.  The RNA polymerase is then reassembled using all parts from the sensitive strain, but one, which comes from the resistant strain.  If RNA transcription proceeds in the presence of the antibiotic then the subunit from the resistant strain is targeted by the antibiotic. 
<b>Yes, that's how it works.</b>
 
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<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>Escherichia coli</i></b>
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Mycoplasma genitalium lost its genes to produce amino acids through degenerate evolution and now gain those amino acids through from the host. The M. genitalium would most likely have protein channels to let amino acids inside the cell since  it does not contain any amino acids and channels are the easiest way to transport molecules that are not permeable to the membrane. The first M. genitalium could have gotten its protein channels from the host. The host could have synthesized the protein channels for the M. genitalium.
 
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<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>Geobacter metallireducens</i></b>
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<b><i>Halobacterium</i> sp.</b>
Ordinary bases of the tRNA are modified by specific enzymes, and are turned into rarer RNA bases such as wybutosine.  It seems unlikely that such a diverse set of modified bases would arise simply to add functionality and extended half-life to tRNA molecules.  These unusual bases were probably very prevalent a long time ago, where the variety of different bases could allow a wide range of catalytic RNAs that had a larger significance in cell function.  This would be before the "rise" of amino acid proteins.<br>
<b>Yes, that's our best current view.  Who knows what happened 4-billion years ago--never trust a geologist. ;)</b>
 
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<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>Helicobacter pylori</i></b>
 
There are many possibilities.  A pharmaceutical could be designed that binds to the -35 and -10 promoters, thereby preventing RNA polymerase from binding there, in an effect similar to repressors.  Other antibiotics could simply change the shape of or otherwise denature RNA polymerase, so that it cannot bind to the promoters.
A third possible pharmaceutical agent could somehow bind to the sigma factor, preventing this protein from recognizing the promoter sequences.<br>
<b>Good ideas.</b>
 
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<b><i>Lactobacillus</i> sp.</b>
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<b>5. Why do you think bacterial cells absorb protein and nucleic acids that are exported by other bacteria?</b>
<b><i>Lactococcus</i> sp.</b>
 
Some proteins often prove useful to these other bacteria.  The proteins might be able to digest certain food sources, for example.  Also, genetic material might be exported by bacteria, genetic material that might contain resistance to viruses or antibiotics.  Naturally, any bacteria that absorbed this material would have a distinct advantage over any bacteria that did not.
<br><b>The genetic information might be useful. What else about protein and DNA molecules might be useful to a heterotroph?</b>
 
Proteins and DNA taken in by bacterial cells can get degraded into simple structures (ribose, amino acids, inorganic phosphate, etc...). These molecules then can feed directly into metabolic pathways to produce harnessed energy for the cell.
 
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<b>6. How could you sequence the genome of an unculturable microbe?</b>
<b><i>Leptospira</i> sp.</b>
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<b><i>Methanococcus</i> sp.</b>
Bioinformatics allows us to predict a cell’s physiology and evolutionary development by comparing known genomes of other cells.  Computer analysis can be used to find all possible protein sequences that could be formed in all reading frames.  These can then be compared to see if the protein predicted resembles other proteins in databases or proteins of known functions.<br>
<b>Bioinformatics implies you have sequence data already. How do you get the sequence data for a microbe that you cannot grow in culture?</b>
 
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<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>
 
The genes moved in conjugation are located on the F plasmid, what is commonly known as the "fertility factor".  This plasmid is transferred by pilus from bacterium to bacterium; it is nicked at the 5' end and unwound.  As this strand moves to the recipient bacterium, the remaining strand in the donor bacterium is replicated.  Whether genes are moved individually or in groups depends on how many genes are on this plasmid.  Part of a gene could be moved if the plasmid in the donor bacterium is nicked in the wrong place, or if not all is transferred to the recipient bacterium.
 
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<b>How is the strand "moved"?  If the plasmid has twenty genes, will they all be moved?</b>
<b><i>Mycoplasma pneumoniae</i> sp.</b>
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<b><i>Nitrospira</i> sp.</b>
The strand is "moved" into another cell through a translocasome (homologous to the protein used in transformation). Single-stranded binding proteins accompany the exposed, single strand of DNA.
 
<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>
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Currently, microbial species are defined as having a) 70% or greater DNA sequence relatedness and b) 97% or greater small ribosomal subunit similarity. This takes into account vertical phylogeny (the formation of daughter cells from a parent cell) while still leaving room for the horizontal transfer of genes that takes place via transformation, conjugation and transduction.
<b><i>Prochlorococcus</i> sp.</b>
 
Arriving at this definition has been a challenging process since biologists traditionally defined species based on the ability of its members to interbreed with each other. This was fine for eukaryotes, but clearly the horizontal transfer of genetic material makes this definition insufficient in the case of microbes. Another problem with species definition is the requirement that a microbe be isolated in a pure culture before it can be accepted as a distinct species. Because some species have not yet been able to be cultured, this precludes their definition as a legitimate species.
 
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<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>
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<b><i>Pyrococcus furiosus</i></b>
Each cell in the population exports CF until the concentration increased to a level high enough to induce formation of the translocasome in all the cells.  In order for the population to be induced together all the cells must be able to sense the CF, which means that it must be exported. 
 
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<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>
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<b><i>Rhodobacter</i> sp.</b>
If one base is missing and the phosphate-sugar backbone is intact the replisome will fill in a base opposite the apurinic site. However, this could be any base, not necessarily the correct one. 
 
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<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>
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<b><i>Rhodospirillum rubrum</i></b>
A phase variation may arise from a hairpin structure in the DNA that occurs from unstable DNA. Instead of returning to its starting position, however, the DNA resolves in the opposite direction (inversion). This may change the direction of a promoter in order to express different genes in different environments. I would expect it to revert at a slower rate until it reaches an environment where the reverse phase variation is favored.
 
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<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>
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<b><i>Salmonella enterica</i></b>
Nonreplicative transposons jumps from one DNA site to another without replicating. Attachment of the element onto the protruding ends of the staggered cut produces duplicated sequences at either end of the new insertion. Every time the transposable element “jumps”, a new duplication is created in the target DNA. Replicative transposons copy to a new site, while the original copy remains at the old site. The target sequence is also duplicated and flanks the replicative transposon. Transposons spread within a cell via replicative transposition. Transposons spread among organisms if the transposon is found in a plasmid, and that plasmid is spread to a neighboring microorganism via horiztonal transfer.
 
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<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>
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<b><i>Sinorhizobium meliloti</i></b>
The ara operon can repress or activate gene expression.  In the presence of arabinose, AraC binds araI1 and araI2 and interacts with RNA polymerase to permit transcription of araBCD.  In the absence of arabinose, AraC becomes elongated and binds aria and araO2 causing the DNA to form a loop so that it cannot interact with RNA polymerase stopping transcription of araBCD.  The lac operon is different in that it is only repressed by glucose because glucose inhibits cAMP production.  When glucose levels are low and lactose is present, lactose is rearranged to form allolactose, which binds the repressor and releases the operator. 
 
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<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>
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The four types of control for gene expression are alterations of DNA sequence, control of transcription and mRNA stability, translational control and posttranslational control. Alterations of DNA sequence is when microbes program mutation, one way this happens is through phase variation or flipping of a DNA segment to turn off or on a gene. This method is the most irreversible and is the slowest to revert. Control of Transcription includes proteins binding DNA and inhibiting RNA polymerase or bending DNA at the promoter. This type of control  is more reversible and takes less time than DNA segment but not as fast as translational and post translational. Translational method occurs when the ribosome is inhibited, for example attenuation. Post translational is the fastest where the made proteins are modified. 
 
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<b>9. Explain the roles of thermodynamic and kinetic effects in attenuation control of the <i>trp</i> operon.</b>
<b><i>Staphylococcus aureus</i></b>
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<b><i>Streptomyces</i> sp.</b>
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<b><i>Vibrio cholerae</i></b>
==Wozniak lecture on Biofilms==
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<b>1. What do bacterial biofilms have in common with multicellular organisms?  How do they differ?</b>
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<b><i>Vibrio fischeri</i></b>
Bacterial biofilms display cell differentiation and specialization, as do multicellular organisms. Biofilms can also display resistance to antibiotics, which multicellular organisms do as well. Biofilms and muticellular organisms differ because most multicellular organisms are more specialized, forming organelles and organs. Biofilms are specialized and can form channels and columns, but are not as specialized as mutlicellular organisms.
 
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<b>2. What are the advantages to bacteria of biofilm formation?  What properties do biofilms confer?</b>
 
Biofilms confer resistance to antibiotics, predatorial cells, and harmful chemicals.  Bacteria in close contact with each other in biofilms are more likely to survive these stresses, because they are easily able to transfer genetic material to each other.
<br><b>This is a good start.  How do biofilms confer resistance to each thing?  Genetics?  Physiology and form of the biofilm?  Secreted molecules?</b><br>
 
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<b>3. Where in the body do biofilms form infections?  Why?</b>
 
The most common location on the body for biofilms that people think of is your teeth. Dark, hard to reach places are ideal for biofilms, as they are hard to clean and clear. The body has a strong immune system- cells attack infections within the body and the surface of the body is effective in keeping bacteria out. So, biofilms first need something to latch on to so they can grow, and dark holes in the body are the best opportunities. The ears, nose, throat, sweat glands, gaps around the teeth and gums, hair follicles, lungs, and tonsils are just a few examples of prime biofilm locations. Once biofilms establish themselves and build up into large enough groups protected by thick slime, they survive a better chance against the immune system and in the bloodstream, where they can spread the infection.
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<b>4. Explain the basis of "twitching motility."  Compare and contrast twitching with flagellar motility.  How does twitching motility promote biofilm development?</b>
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Twitching motility is a form of solid surface translocation of a biofilm. Individual microbes in a biofilm move by retracting their type IV fimbriae (the pilus). Twitching motility does not involve flagellum. Twitching motility is required to colonize new surfaces, and required for biofilm development. It is required for biofilm development because the movement of the microorganisms in the biofilm allows for the formation of columns and complex structures seen in many types of biofilms. Flagellar motility uses flagella as helical propellers that drive the cell forward like the motor of a boat. Twitching motility uses the “grappling hook model”, moving across a surface through retraction of a pilus. The flagellum are rotated by means of a motor driven by the cell’s transmembrane proton current. Twitching motility is ATP driven, not driven by the cell’s transmembrane proton current.
 
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<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>
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<b>6. How was it proved that <i>psl</i> encodes PSL polysaccharide?  How does PSL compare in structure with alginate?</b>
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<b>1. ATP and NADH are both energy carriers: What are the advantages of using one over the other?</b>
<b>1. ATP and NADH are both energy carriers: What are the advantages of using one over the other?</b>
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NADH carries 2 or 3 times as much energy as ATP, depending on cell conditions. In high-energy reactions, NADH is used. NAD+/NADH accept and donate electrons, therefore if a cell needs to balance its electrons NADH is used in the reaction. NADH is also useful when a substrate needs to be reduced. ATP is used when less energy than NADH is required to fuel the reaction. ATP is formed when a reaction can provide enough energy to form ATP from ADP, but not enough energy to form NADH. Some reactions need a redox change. Always need to balance the redox levels in a cell. Also, ATP is better for long-term usage, because it is more stable - NADH needs to be oxidized soon after formation.  ATP has added functionality in catabolism/anabolism because phosphate groups are cleaved and bind to the substrate, thereby activating the substrate for further processing (like in glycolysis).


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<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>
<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>
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The steps are reversed for gluconeogensis by incorporating a different catabolic enzyme.  The irreversible steps are points of regulation along the pathway that maintains a consistent level of intermediates.  The reversal of a step must be catalyzed by an entirely different enzyme.  In this way the forward and reverse direction is like an on/off switch, where one enzyme is inhibited and the other is activated and vice versa usually by allosteric regulation by key intermediates, such as ADP and ATP.


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<b>3. There are 3 main pathways to form pyruvate- EMP, ED and PPS. How and why might a cell switch among these?</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>
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A cell may switch among these 3 pathways depending on the type of substrate that needs to be catabolized and on whether intermediates are needed to be redirected toward anabolism and biosynthesis.  If glucose is available, the Embden-Meyerhof-Parnas (EMP) pathway, glucose 6-phosphate isomerizes to fructose 6-phosphate, eventually yielding 2 moc. of pyruvate.  Net gain of Energy= 2NADH + 2ATP.  The Entner-Doudoroff (ED)pathway offers a new way to catabolize sugars, especially sugar acids, which can be phosphorylated to 6-phosphogluconate.  Th 6C substrate is split into 2 3C products, one of which is glyceraldehyde 3-phosphate and can enter the 2nd part of glycolysis.  This pathway allows enteric bacteria to be able to colonize the intestinal epithelium, since gluconate is the sugar acid in intestinal mucus.  The net gain of Energy= 1NADH + 1NADPH + 1ATP.  Finally the pentose phosphate shunt is a way for glucose or sugar acids to eventually form ribulose 5-phosphate via the 6-phosphogluconate intermediate.  The PPS is able to generate complex series of intermediates that can be shunted toward biosynthesis, where pairs of sugars can exchange short carbon chains to yield various sugar phosphates differing in lengths.  The net gain of Energy= 2NADPH + 1ATP. 


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<b>4. Explain why most soil bacteria grow using energy-yielding reactions with very small delta-G.</b>
<b>4. Explain why most soil bacteria grow using energy-yielding reactions with very small delta-G.</b>
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There are large quantities of starting materials in the soil (ex: landfill and methanogenesis) so rxn proceeds even though delta G is near zero. Polymers such as lignin exist in the soil, which take a long time to break down. Breaking down lignin has a small delta G b/c lignin is a stable, aromatic molecule. A lot of energy is required to break it down, so not much energy is produced at the end of the reaction, yielding a small delta G.


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<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>
<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>
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Bacteria have to transfer the hydrogens from NADH + H+ back onto pyruvate because the NADH must be recycled.  During fermentation, no oxygen is available to accept electrons, and NAD+ cannot serve as the terminal electron acceptor in place of oxygen, because there would be no way for reforming NAD+ so that it can act as the electron acceptor in another metabolic cycle. 


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<b>7. Why do environmental factors regulate catabolism?  Give examples.  Why are amino acids decarboxylated at low pH, and under anaerobiosis?</b>
<b>7. Why do environmental factors regulate catabolism?  Give examples.  Why are amino acids decarboxylated at low pH, and under anaerobiosis?</b>
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In complex environments, organisms can choose the preferred substrates depending on availability and the efficiency of Energy production.  This can occur through regulating gene expression.  An example is the sugar lactose in E. coli, which induces transcription of genes encoding beta-galactosidase  and lactose permease.  Glucose is a preferred carbon source, and its presence inhibits lac transcription.  Amino acid catabolism can occur by two routes: (1) deamination or (2) decarboxylation.  In a very acidic environment (low pH) decarboxylation is favored because the ammonia product is an amine that can buffer against the rising acidity level.  This is essential for anaerobic soil or animal digestive tracts that undergo fermentation that many times results in acid production through lactic acid formation. 


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<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>
<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>
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<b>1. Explain how bacteria and archaea switch among various electron acceptors depending on environmental conditions.</b>
<b>1. Explain how bacteria and archaea switch among various electron acceptors depending on environmental conditions.</b>
The electron acceptors used by bacteria and archaea depend on what elements are available in the environment.  For example, if the environment is rich in oxygen and the prokaryotes can perform aerobic respiration, they will use oxygen as an electron acceptor and a less efficient NADH Dehydrogenase.  On the other hand, if the microbes live in an anaerobic environment, other electron acceptors such as nitrogen and sulfur compounds can be used, as these tend to accept electrons easily as well. 
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<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>
<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>
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Both transmembrane pH and electrical potential can be used to store energy in the proton motive force in two distinct but equivalent forms.  The transmembrane pH difference can contribute to the proton motive force even if there is no charge gradient.  This could occur if there was the same number of positive charged ions inside and outside of the membrane, but the ions differed in identity (Na+, H+, or K+); specifically, a higher concentration of H+ ions are on the outside than the inside, creating a force that tends to drive protons inward.  A charge difference results when there is a greater number of positive charge on the outside of the membrane than the inside, and the excess cations outside are something other than H+ to result in only a charge gradient with no pH gradient.  This creates a charged potential along the membrane that tends to pull positive charge in.  At low pH, the form of energy probably used is the transmembrane pH, since the concentration of H+ rises sharply to create the drive for protons to enter.  In high pH, the energy form used is likely to be the electrical potential, because there is a lack of H+ on the outside and other cations must be used to generate the electrical gradient for the proton to enter.


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<br><br>
<b>4. What environments favor oxygenic photosynthesis, versus sulfur phototrophy and photoorganotrophy? Explain.</b>
<b>4. What environments favor oxygenic photosynthesis, versus sulfur phototrophy and photoorganotrophy? Explain.</b>
Watery environments favor oxygenic photosynthesis, as water, H20, serves as the electron donor for the ETS.  Evidently this is why cyanobacteria and other microbes that perform oxygenic photosynthesis first developed underwater.
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<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>
<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>
It seems that it would be difficult for an organism to switch between lithotrophy and organotrophy unless the organism is switching between an environment where organic and inorganic materials are present.  If the organism contained both sets of enzymes that were required, then it would be necessary to use these enzymes as to avoid reductive evolution and lose the ability to use both lithotrophy and organotrophy. 


<br><br>
<br><br>
<b>7. What kind of environments favor methanogenesis?  Why are methanogens widespread, despite the low delta-G of their energy-yielding metabolism?</b>
<b>7. What kind of environments favor methanogenesis?  Why are methanogens widespread, despite the low delta-G of their energy-yielding metabolism?</b>
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<br><br>
Environments favoring methanogenesis are landfills and the digestive systems of cattle or humans.  This because methanogenesis must occur in the presence of adequate carbon dioxide and hydrogen, which are the gaseous fermentation products of bacteria undergoing anaerobic respiration that can be trapped in these habitats.  Methanogens are so widespread despite their weak electron acceptors of carbon dioxide and water and strong electron donors of hydrogen and methane due to the fact that the availability of the carbon and hydrogen substrates is so abundant.


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==Chapter 15==
==Chapter 15==
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<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>
<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>
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<br><br>
Fatty acid biosynthesis is a cyclic cycle using acetyl-CoA with rounds of the same synthesis over and over again. The cycle feeds its products back repeatedly as substrates for further synthesis, so large polymers can be made using a limited number of enzymes. This pathway requires fewer enzymes in comparison to AA biosynthesis because it is a smaller pathway. Amino acid biosynthesis substrates are derived from the glycolysis pathways and the TCA cycle. AA biosynthesis requires more reduction because there are many different pathways used to form AA’s, while there is a single pathway to form fatty acids. AA biosynthesis requires also requires a greater number of different enzymes due to the many different pathways used to form AA’s. AA’s are complex, asymmetrical molecules that require many different conversions to synthesize. Each conversion is mediated by a different enzyme, therefore AA biosynthesis requires a greater number of different enzymes in comparison to fatty acid biosynthesis.


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<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>
The only form of nitrogen that microbes can directly assimilate into biomass is ammonium ion (NH4+ protonated from NH3). While there are other forms of nitrogen available in the environment, these other forms have to be reduced to ammonia before they can be assimilated.
<b>What are the other oxidized forms that bacteria and plants take up and reduce to ammonia and ammonium ion?
<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>
What about N from reduced organic compounds?</b>
 
   
When fertilizer is spread on farmland to nourish crops, lithotrophic microbes cause a problem by oxidizing ammonia fertilizer to nitrates and nitrites. Plants can take up the nitrates and reduce them (with energy input), but a large excess runs into streams and water supplies.  These high concentrations of nitrates in water form nitrites that can combine with hemoglobin (in the blood) to create a form of hemoglobin that is not able to take up oxygen.  This is a problem for babies trying to breathe. 
 
 
 
Nitrogen sources include: organic amines (NH3→ NH4+), N2 gas from the atmosphere, and NO3- (nitrate, which is then made into ammonia). The only form of nitrogen that microbes can directly assimilate into biomass is ammonium ion (NH4+ protonated from NH3). Most bacteria can acquire nitrate (NO3-) or nitrite (NO2-) for reduction to ammonium ion, although they repress these E-expensive pathways when ammonium ion is present. While there are other forms of nitrogen available in the environment, these other forms have to be reduced to ammonia before they can be assimilated. Worldwide, factories fix enormous amts of N2 into ammonia for agricultural fertilizers. Industrial nitrogen fixation uses the Haber process, in which N gas is hydrogenated by methane under extreme heat and pressure. When nitrogen fertilizer is used, much of it is washed from the soil into streams when it rains. The streams take the nitrogen fertilizer to the oceans, where marine phytoplankton phototrophs fix the nitrogen and overgrow, causing algal blooms. The massive amounts of algal phototrophs eventually die, and sink to the bottom layers of the ocean.  They deplete the oxygen available there by decomposing, causing eutrophication, where the lower layers of a body of water are depleted of oxyen as a result of overgrowth of microbial producers. The lack of oxygen causes a “dead zone” where no other aerobic organisms can survive. This has been a really big problem because it essential eliminates marine habitats, and has killed many marine organisms.
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<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>
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<b>5. How and why do bacteria make "secondary products"?  What are their functions?</b>
<b>5. How and why do bacteria make "secondary products"?  What are their functions?</b>
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<br><br>
Bacteria can produce secondary products (many of which are antibiotics) through the biosynthesis of polyketides, a family of pharmaceuticals, that are commonly produced by actinomycetes.  The secondary products are usually generated in the stationary phase instead of growth phases.  These molecules are not essential nutrients, but enhance nutrient uptake and inhibit competitors in order to enhance competition with other bacteria.


<br><br>
<br><br>
<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>
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==Nitrogen fixation and nodulation==
<br><br>
<b>1. Explain why nitrogen fixation requires the absence of oxygen, in terms of how the nitrogenase enzyme complex workd.</b>
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<br><br>
<b>2. How do cyanobacteria manage their metabolism and cell structure so as to fix nitrogen while performing oxygenic photosynthesis?</b>
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==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>
<b>1. How do we know that humans evolved from microbes?  Explain why the evidence is so strong, despite the controversies over evidence such as microfossils.  Explain in terms of biochemistry, genetics, and physiology.</b>
<br><br>
In terms of a biochemistry point of view, humans use very similar metabolic mechanisms and pathways with respect to microbes.  The glycolysis pathway is universally conserved among all living organisms on the planet.  From a genetics standpoint, the general mechanism of DNA replication, repair, etc. (though slightly more complex) is very similar to that of microbes as well. 


<br><br>
<br><br>
<b>2. Explain how different kinds of evidence point to when different kinds of microbes and microbial metabolism evolved.</b>
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<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>
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<br><br>
<b>3. Explain why living organisms are made of carbon, nitrogen, and oxygen, and why iron is so prevalent in metabolism.</b>
Stars that are becoming supergiants are capable of synthesizing carbon, nitrogen and oxygen from hydrogen by means of the CNO Reaction.  When stars become even larger, they are able to synthesize heavier elements, specifically iron.  The theory is that carbon, nitrogen, oxygen and iron were synthesized in other stars in the universe and traveled to the early Earth via meteors.  Iron was prevalent in the core of the earth and the other three organic atoms existed on the surface of early Earth.  Eventually, organic molecules began to form and carbon, nitrogen and oxygen were present, and particularly useful in building these molecules (carbon is able to form four, stable bonds, nitrogen is key in forming amino acids, and acting as an acid/base in key reactions and oxygen is a primary electron acceptor).  Iron is a key component of many metabolic pathways based on its prevalence in early earth and its ability to stabilize negative charges.  Ultimately, these molecules are found in living organisms and metabolic pathways because they were prevalent when the Earth was being formed, but they also have important properties that allow life as we know it to occur. 


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<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>
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==Species to know for Test==
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<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>
<b>4. Explain the evolutionary origins of mitochondria and chloroplasts. What evidence do we see in the structures of modern microbes?</b>
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<b><i>Aeromonas hydrophila</i></b>
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Broader Categories: Gram-negative, anaerobic
<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>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><br>
<br>Broader Categories: Barrel-shaped cells.  Filamentous cyanobacteria (blue-green algae) found as plankton.
<br>Genome: 1 circular chromosome with 5368 protein-coding regions and 6 plasmids (from sequenced PCC 7120 strain).
<br>Metabolism: Photoautotrophic, perform oxygenic photosynthesis.  Form heterocysts (specialized nitrogen-fixing cells that convert nitrogen to ammonia) during nitrogen starvation.
<br>Habitat: Freshwater and damp soil.  Form symbiotic relationships with certain plants.
<br>Disease: Produce neurotoxins, such as anatoxins (neuromuscular poisons), that are harmful to wildlife and farm animals.


<b><i>Aspergillus</i> sp.</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>
Broader Categories: Over 185 species of this genus
Genome: Largely incomplete
Metabolism: Highly aerobic.  Pathogenic species obtain nutrients from host, while non-pathogenic species obtain nutrients from soil, wood, and plant detritus.
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.


<b><i>Bacillus anthracis</i></b>
<br><br>
<br><br>
Broader Categories: Gram-positive, rod-shaped, form endo-spores and biofilms
<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>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>
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Broader Categories: Gram-positive, rod-shaped, form stress-resistant endospores
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>
<br><br>
Broader Categories: Gram-positive, spore-forming, rod-shaped
<b>3. Compare and contrast three different types of phototrophy found in bacteria.</b>
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>
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Broader Categories: Gram-negative, anaerobic, human-bacterial symbiosis model
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>
<br><br>
Broader Categories: Sprial-shaped with 2 flagella
<b>4. Explain the pathology of three different gram-positive pathogens.</b>
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>
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<br><br>
Broader Categories: Gram-negative, aerobic, coccoid or rod-shaped
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)
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>
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<br><br>
Broader Categories: Gram-positive, rod-shaped, anaerobic, spore-former
<b>5. Explain two different examples of bacterial-host mutualism.</b>
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>Escherichia coli</i></b>
<br><br>
<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>
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<br><br>
Broader Categories: Gram-negative, rod-shaped, possesses flagella, and pili
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>
<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.
<b>6. Identify these kinds of bacteria based on their descriptions:</b>


<b><i>Halobacterium</i> sp.</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: 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
<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.


<b><i>Lactococcus</i> sp.</b>
<br><br>
<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>Methanococcus</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>
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><i>Mycoplasma pneumoniae</i> sp.</b>
<br><br>
<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>2. Explain how archaea growing in extreme environments require specialized equipment for study.</b>
 
<b><i>Paramecium</i> sp.</b>
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<br><br>
<b><i>Plasmodium falciparum</i></b>
<br><br>
<b><i>Prochlorococcus</i> sp.</b>
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<b><i>Pseudomonas aeruginosa</i></b>
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<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.


<b><i>Rhodospirillum rubrum</i></b>
<br><br>
<b><i>Rickettsia</i> sp.</b>
<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>
<br><br>
<b><i>Staphylococcus aureus</i></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>
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><i>Streptococcus </i>sp.</b>
<br><br>
<br><br>
<b><i>Streptomyces</i> sp.</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.
<b><i>Vibrio cholerae</i></b>
<br><br>
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>
<br><br>
<br><br>
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]]

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.

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