MicroBio Exam 4
Black smokers (also called hot vents) release _______ at temperatures around _______ °C.
Sulfides/350
Which metabolic strategy is most common in chemolithotrophic mats?
Sulfur oxidation
What is the name given to a process where different microbial taxa work in cooperation to degrade a compound that neither can degrade entirely on their own?
Syntrophy
Which of the following antimicrobial treatments is affective only on exposed surfaces?
Ultravioletrays
What is the fate of H2 produced within a rumen?
Used in methanogenesis
Biofilm
colonies of microbial cells encased in a porous organic matrix and attached to a surface
Antenna pigments
light-harvesting chlorophylls or bacteriochlorophylls in photocomplexes that funnel energy to the reaction center
The above figure illustrates the results for a broth dilution test for a particular antibiotic for a particular bacterium. As is standard, the growth is at 24 hr. What is the MIC?
1 mg/L (solution becomes clear)
11. Describe the structure of a typical endotoxin. How does endotoxin induce fever? What microorganisms produce endotoxin (Section 27.11)?
11. The typical endotoxin is a lipopolysaccharide found in the outer membrane of the gram-negative bacterial cell wall. Fever occurs because the endotoxin (the lipid A component of the LPS) stimulates host cells to release cytokines that act as endogenous pyrogens, which affect the temperature-controlling center of the brain. Endotoxins produced by enteric gram-negative bacteria most commonly affect human health.
11. Identify the targets that allow selective toxicity of antifungal agents (Section 26.11).
11. Unlike other eukaryotes, the cell membranes of fungi contain ergosterol. Drugs designed to disrupt ergosterol or inhibit its synthesis will be selectively toxic. Fungal cell walls contain the polysaccharide chitin. Therefore, drugs that interfere specifically with chitin synthesis will be selectively toxic to fungi.
1. Compare and contrast the carbon, sulfur, and nitrogen cycles in terms of the physiologies of the organisms that participate in the cycle. Which physiologies are part of one cycle but not another?
1. All living organisms contribute to the carbon, nitrogen, and sulfur cycles. Carbon is cycled between organic and inorganic forms by heterotrophs and autotrophs⎯the former oxidizing organic carbon to CO2 and the latter being responsible for CO2 fixation to organic forms. The sulfur and nitrogen cycles are intimately linked to the carbon cycle. Sulfur-chemolithotrophs and many anoxygenic phototrophs (the vast majority being autotrophic) are able to oxidize reduced sulfur compounds to S0 and SO42-, while sulfate- and sulfur-reducing prokaryotes reduce these compounds to sulfide using both heterotrophic and autotrophic mechanisms. Nitrogen cycling is catalyzed by nitrifiers, which oxidize reduced nitrogen compounds to NO3-, and denitrifiers, which reduce NO3- to gaseous forms (e.g., N2, NO, and N2O) and NH3. Nitrogen-cycling prokaryotes also include a diversity of both heterotrophs and autotrophs.
1. What is the origin of the phagocytes and lymphocytes active in the immune response? Track the maturation of B cells and T cells (Section 28.1).
1. All immune cells, blood, and lymph components have a common origin in bone marrow stem cells. Maturation of B cells occurs in the bone marrow in mammals; they are then dispersed throughout the body and reside in the lymph nodes, spleen, or mucosa-associated lymphoid tissue (MALT). T cells mature in the thymus and then are dispersed throughout the body like B cells.
1. Why is the decimal reduction time (D) important in heat sterilization? How would the presence of bacterial endospores affect D (Section 26.1)?
1. Decimal reduction time (D) is the time required for a ten-fold reduction in the viability of a microbial population at a given temperature. Because the relationship between D and temperature is essentially logarithmic, the slope of the line obtained by graphing this relationship provides a measure of sensitivity and can be used to calculate times required to achieve sterilization. The presence of bacterial endospores would affect the slope of the line. D for a population of endospores would be considerably longer that D for a population of vegetative cells.
1. Imagine that you have discovered a new animal that consumes only grass in its diet. You suspect it to be a ruminant and have available a specimen for anatomical inspection. If this animal is a ruminant,
1. If the animal is a ruminant, the digestive tract will consist of the rumen, reticulum, omasum, abomasum, and the intestines. The reticulo-rumen will be positioned before the stomach in the alimentary canal. If the herbivore is not a ruminant, it might have a large cecum positioned between the small and large intestines, as in the horse or the rabbit. Signature microorganisms that could be expected to be present in a ruminant would include Bacteroides succinogenes, Selenomonas ruminantium, Peptostreptococcus elsdenii, and Methanobacterium ruminantium. Key substances that would be present in the rumen contents include gaseous fermentation products, such as CO2 and CH4, and volatile fatty acids.
1. Compare and contrast the absorption spectrum of chlorophyll a and bacteriochlorophyll a. Which wavelengths are preferentially absorbed by each pigment, and how do the absorption properties of these molecules compare with the regions of the spectrum visi- ble to our eye? Why are most plants green?
1. Plant color is a function of the wavelength of light not absorbed by the pigments. Therefore, a green plant containing chlorophyll a and b absorbs red and blue light, but reflects the green range of the visible spectrum. Therefore, plants generally appear green. Chlorophyll a absorption peaks are at 680 and 430 nm, whereas bacteriochlorophyll a absorbs light most strongly at 870, 805, 590, and 360 nm. Except for the 590 nm wavelength, none of these bacteriochlorophyll a absorption peaks is detectable by the human eye. Because the bacteriochlorophyll a reflection range is from about 625 to 725 nm, the bacterium has a purplish hue.
1. Why can it be said that the carbon and nitrogen cycles are "coupled" (Section 24.1)?
1. The coupling of the carbon and nitrogen cycles is due in part because rates of primary production are dependent upon the availability of fixed nitrogen. For example, when ammonia or nitrate is available, rates of primary production are increased. In addition, higher concentrations of organic carbon stimulate N2-fixation while low concentrations of organic carbon suppress N2-fixation.
1. List some of the key resources and conditions that microorganisms need to thrive in their habitats (Sections 23.1-23.3).
1. The growth of microorganisms in nature is dependent upon the availability of key resources (macro- and micronutrients) and growth conditions. Examples of key resources and conditions are listed in Table 23.1.
1. What are the major differences between oxygenic and anoxygenic phototrophs (Sections 13.1-13.5)?
1. The major differences between oxygenic and anoxygenic phototrophs lies in their reaction center photosystems and electron donor used for photosynthesis. Anoxygenic phototrophs use electron donors other than water (e.g., sulfide and other reduced substances from their environment) and contain a single photosystem for generation of ATP and reducing power. Oxygenic phototrophs use water as an electron donor and thus evolve O2, and have two photosystems: PS II for ATP synthesis and PS I for reducing power.
1. Imagine a sewage plant that is releasing sewage containing high levels of ammonia and phosphate and very low levels of organic carbon. Which types of microbial blooms might be triggered by this sewage? How would the graphs of oxygen near and beyond the plant's release point differ from the graph shown in Figure 23.16a?
1. The release of high levels of ammonia and phosphate (but little organic carbon) from a sewage treatment plant would trigger the growth of algae, cyanobacteria, and nitrifying bacteria that will oxidize NH4+ to NO3-. The oxygen profile shown in Figure 23.16a would differ in that one would not see the decrease near the outflow because with little organic carbon present, aerobically respiring organisms would not consume it at a comparable rate. In addition, blooms of algae and cyanobacteria would contribute to increased levels of dissolved oxygen near the sewage release point due to oxygenic photosynthesis.
1. Describe the steps in the development of root nodules on a legumi- nous plant. What is the nature of the recognition between plant and bacterium and how do nod factors help control this? How does this compare with recognition in the Agrobacterium-plant system (Sections 25.3 and 25.4)?
1. The steps in nodule formation are not identical in all legumes but may be summarized in the following major stages: (1) recognition and attachment—plant lectin and extracellular polysaccharide provide a signal permitting successful communication between symbiont and host; (2) excretion of nod factors by the bacterium; (3) invasion of the root hair by the bacterial formation of an infection thread; (4) travel to the main root via the infection thread; (5) formation of bacteroids within the plant cells and the development of the nitrogen-fixing state; and (6) continued plant and bacterial division and the formation of the mature root nodule. Bacterial attachment to the plant cells is facilitated by the adhesion protein rhicadhesin and lectins. Signal recognition between plant and bacteria is likely similar in the Agrobacterium-plant system. However, in the development of crown-gall disease, Agrobacterium must first attach to a wound site on the plant, and a region of the DNA (not the bacterium) enters the cell and is incorporated into the host genome.
1. What are some potential drawbacks to the use of radiation in food preservation? Do you think these drawbacks could be manifested as health hazards? Why or why not? How would you distinguish between radiation-damaged and radiation-contaminated food?
1. decontamination since UV rays do not penetrate tissue surfaces very deeply. The equipment for using ionizing radiation is more expensive. Also, such equipment is more difficult to operate, and there is greater danger of an accident, which may contaminate the environment if a radioisotope is used as the radiation source. Finally, there is concern that the food might become radioactively contaminated, or that undesirable mutations might occur in microorganisms that survive the irradiation. These could be health hazards, although current research indicates that the risks are minimal. Radiation-damaged food would likely show visible signs of such damage, and one could use common devices to determine if food is radiation contaminated.
Which is an example of acquisition of natural passive immunity?
A fetus protected from disease by its mother's antibodies
10. Why can it be said that despite the chemistry of its environment, Acidithiobacillus ferrooxidans does not get an energetic "free lunch" (Section 13.9)?
10. Acidithiobacillus ferrooxidans is an iron-oxidizing bacterium that lives in acidic environments (pH 1-2) and thus is "bathed" in a natural proton gradient. The natural PMF in this acidic environment is exploited to move protons across the membrane for ATP synthesis. However, to avoid acidification of the cytoplasm, which must remain at pH 5.5-6, proton movement into the cell limited by the availability of electrons from the oxidation of Fe2+, with which protons combine in the reduction of O2 to H2O.
10. Distinguish between AB toxins, cytotoxins, and superantigens. Give an example of each category of toxin. How does each toxin category promote disease (Section 27.10)?
10. Cytolytic toxins (e.g., Clostridium perfringens) work by enzymatically attacking cell constituents, causing lysis of host cells. The AB toxins (e.g., Corynebacterium diphtheriae) consist of two covalently bonded subunits, A and B. The B component generally binds to the cell-surface receptor, allowing the transfer of the A subunit across the cell membrane. The A toxin then damages the cell by a variety of mechanisms, including inhibiting protein synthesis or disrupting the function of motor neurons (a neurotoxin). The superantigen toxins (e.g., Staphylococcus aureus) stimulate large numbers of immune response cells (T helper cells), resulting in massive, even systemic, inflammatory reactions.
10. List some major prokaryotes found in the open oceans and describe how they make ATP (Section 23.10).
10. Examples of major prokaryotes found in the open oceans and their route of ATP production include the following: (1) Prochlorophytes (e.g., Prochlorococcus) generate ATP via photophosphorylation by oxygenic photosynthesis; (2) Trichodesmium, a nitrogen-fixing marine cyanobacterium, generates ATP via photosynthetic electron transport; (3) Pelagibacter, an oligotrophic bacterium that generates ATP from both aerobic oxidation of organic compounds and from light-driven proton pumping via proteorhodopsin; (4) Ostreococcus is a tiny green alga that produces ATP via photophosphorylation; and (5) aerobic anoxygenic phototrophs are obligate heterotrophs that generate ATP via aerobic respiration and by oxygen-dependent anoxygenic photosynthesis.
10. How do the microbial communities of guts of higher and lower termites differ in composition and degradation of cellulose (Section 25.10)?
10. The hindgut of higher termites contains mostly anaerobic bacteria that carry out cellulolytic reactions. By contrast, in addition to anaerobic bacteria, lower termite hindguts are populated with cellulolytic protists that are primarily responsible for breaking down cellulose.
10. Why do antiviral drugs generally exhibit host toxicity (Section 26.10)?
10. Viruses depend largely on host cell machinery to perform their metabolic functions. Because of this commonality, it is a considerable challenge to design antiviral drugs that are not also toxic to the host.
10. Describe the general mechanism used by superantigens to activate T cells. How does superantigen activation differ from T cell activa- tion by conventional antigens (Section 28.10)?
10. Whereas conventional antigens bind to an antigen-specific site on T cell receptors (TCRs), superantigens bind to all TCRs that have common conformational structure outside of the antigen-binding site, resulting in activation of more than the normal number of T cells. Because superantigens bind outside the variable region of the TCR, 5-25% of all T cells become activated, in contrast to less than 0.01% activation by conventional antigens.
What is an average concentration of prokaryotic cells along the surface of pelagic water?
10^6 cells/mL
11. Contrast classical nitrification with anammox in terms of oxygen requirements, organisms involved, and the need for monooxyge- nases (Sections 13.10 and 13.11).
11. Classical nitrification is characterized by the aerobic oxidation of ammonia and nitrite by chemolithotrophic bacteria. Species of Nitrosomonas oxidize ammonia to nitrite, and species of Nitrobacter oxidize nitrite to nitrate. Ammonia-oxidizing bacteria oxidize NH3 via ammonia monooxygenase, while the oxidation of NO2- is catalyzed by nitrite oxidoreductase. The anammox reaction occurs under anoxic conditions, and thus does not involve monooxygenase activity. In this reaction, ammonia is oxidized with nitrite to yield gaseous dinitrogen. The process is carried out by an unusual bacterium belonging to the phylum Planctomycetes: Brocadia anammoxidans. The reaction occurs within a unit membrane structure (an organelle!) called the anammoxosome, and the nitrite used as the electron acceptor in the reaction likely comes from ammonia oxidation by aerobic nitrifying bacteria. Thus, these organisms operate in microenvironments where aerobic and anaerobic conditions coexist (e.g., sewage and wastewaters).
11. What is the difference between piezotolerant and piezophilic bacteria? Between these two groups and extreme piezophiles? What properties do piezotolerant, piezophilic, and extremely piezophilic microorganisms have in common (Section 23.11)?
11. Piezotolerant bacteria are able to tolerate high pressures but do not grow optimally in such conditions. In contrast, piezophilic bacteria grow optimally under high pressures but are still able to grow at 1 atm. Extreme piezophiles are dependent upon very high pressures (e.g., 600-1000 atm) for growth and maintaining viability. Regardless of classification, all cells growing under high pressure must possess adaptations for such conditions. These may include membranes containing elevated amounts of unsaturated fatty acids and the expression of proteins specific for high-pressure growth.
11. How is the correct bacterial symbiont selected in the squid-Aliivibrio symbiosis (Section 25.11)?
11. Selection of V. fischeri by the squid, with the exclusion of all other bioluminescent bacteria, is accomplished by general and specific recognition events. The general response is the secretion of mucus from the developing light organ upon contact with bacterial peptidoglycan. The mucus is also the first layer of specificity in the symbiosis, as it causes gram-negative, but not gram-positive, cells to aggregate. For reasons that may be related to its resistance to nitric oxide produced by the squid, V. fischeri is able to outcompete other bacteria and form a monoculture within the light organ.
12. Identify six mechanisms responsible for antibiotic resistance (Section 26.12).
12. Bacterial antibiotic resistance mechanisms are summarized here (see also Table 26.8): (1) the organism may lack the target structure that the antibiotic inhibits; (2) the organism may be impermeable to the antibiotic; (3) the organism may be able to alter the antibiotic to an inactive form; (4) random mutation may modify the target of the antibiotic; (5) an alteration that circumvents the metabolic pathway that an antibiotic affects may develop or be acquired by the target organism; and (6) the organism may be able to remove the antibiotic by active transport as soon as it enters the cell (i.e., an efflux pump system).
12. Identify common factors that lead to host compromise. Indicate which factors are controllable by the host. Indicate which factors are not controllable by the host (Section 27.12).
12. Host compromise (i.e., a deficiency in host resistance mechanisms) can result from many factors, including stress, smoking, excessive alcohol consumption, drug use, sleep deprivation, poor nutrition, and certain genetic conditions. With the exception of genetic conditions, the host can usually control each of these factors. Host compromise can also occur from diseases causing immunodeficiency, primarily AIDS.
12. Why are chemolithotrophic bacteria so prevalent at hydrothermal vents (Section 23.12)?
12. Hydrothermal vents are natural habitats for chemolithotrophs because vent fluids contain large amounts of dissolved inorganic chemicals that support chemolithotrophic growth, such as HS-, S0, S2O32-, H2, NH4+, Fe2+, Mn2+, CO, and CH4. In addition, because dissolved organic carbon is present in only trace amounts in such systems, the capacity for autotrophic growth that most chemolithotrophs share is an obvious advantage in ecosystems that are devoid of sunlight.
12. What two enzymes are unique to the Calvin cycle? What reactions do these enzymes carry out? What would be the consequences if a mutant arose that lacked either of these enzymes (Section 13.12)?
12. The unique enzymes of the Calvin cycle (enzymes that may be used as markers for possessing the cycle) are (1) ribulose bisphosphate carboxylase (RubisCO) and (2) phosphoribulokinase. The reactions catalyzed by these enzymes are 1. CO2 + ribulose 1,5-bisphosphate + H2O → 2 phosphoglyceric acid 2. ribulose 5-phosphate + ATP → ribulose bisphosphate + ADP The absence of either of these enzyme activities would prevent autotrophic growth via the Calvin cycle.
12. How does a tube worm obtain nutrients if it lacks a mouth, gut, and anus (Section 25.12)?
12. Tube worms contain huge numbers of endosymbiotic sulfur-oxidizing chemolithotrophs in a large internal organ called the trophosome that constitutes about one-half of the organism's weight. The bacteria carry out CO2 fixation and provide organic carbon to the worm. The worm therefore does not need to ingest food as a source of carbon and energy.
13. Which organisms employ the hydroxypropionate or reverse citric acid cycles as autotrophic pathways (Section 13.13)?
13. Among phototrophs, Chloroflexus uses the hydroxypropionate pathway for autotrophic growth. Chlorobium, Sulfolobus, Thermoproteus, and Aquifex are known to employ the reverse citric acid cycle.
13. In which body locations might pH values differ from standard body conditions? Which organisms might benefit or be inhibited by differences in body pH (Section 27.13)?
13. Every bacterial species has an optimum pH for growth. The skin, stomach, anterior small intestine, and vagina of adult females provide environments that are acidic to varying degrees. This selects for acidophilic and/or acid-tolerant microorganisms but inhibits the growth of neutrophilic microorganisms.
13. Compare the microbial communities in the medicinal leech crop, intestinum, and bladder (Section 25.13).
13. The crop of the medicinal leeches contains a relatively simple microbial community dominated by Aeromonas veronii and a Rikenella-like member of the Bacteroidetes. The intestinum is more complex and contains Alpha- and Gammaproteobacteria, Bacteroidetes, and Firmicutes. Epithelial cells lining the bladder lumen are colonized by species of Ochrobactrum, while the biofilm coating the bladder wall is colonized by two species each of Bacteroidetes and Betaproteobacteria.
13. Explain how application of antisense RNA methods can extend traditional natural product selection methods for antibiotic discovery (Section 26.13).
13. The identification of target-specific antibiotics can be accomplished by using antisense RNA to weaken particular bacterial strains and increase their sensitivity to low concentrations of natural antibiotics. The method, though time-consuming, is applicable to any target for which the gene sequence is known. See the examples cited in the text on the isolation of platensimycin from soil Streptomyces (Section 26.13).
14. How does the body plan of corals influence their ability to symbiotically associate with Symbiodinium (Section 25.14)?
14. The morphology and composition of coral skeletons allow for enhanced absorption of light, which is obviously beneficial to the phototrophic symbionts. In addition, cnidarian corals have a simple two-tissue body plan (ectoderm and gastroderm), and dinoflagellates are housed within the gastroderm in cells that contain specialized vacuoles called symbiosomes.
14. Write out the reaction catalyzed by the enzyme nitrogenase. How many electrons are required in this reaction? How many are actu- ally used? Explain (Section 13.14).
14. The nitrogenase enzyme complex catalyzes the following reaction: N2 + 8 e- + 8 H+ + 16-24 ATP → 2 NH3 + H2 + 16-24 ADP + 16-24 Pi Although this reaction involves 8 electrons, only 6 electrons are used to reduce one mole of N2 to 2 moles of NH3. The remaining 2 electrons reduce 2 H+ to H2, the latter being a nonspecific and nonproductive (but for unknown reasons necessary) byproduct of the reaction.
15. How does the Streptomyces thermoautotrophicus nitrogenase differ from that of Azotobacter (Section 13.14)?
15. The nitrogenase of Streptomyces thermoautotrophicus is an interesting enzyme complex that functions by a different mechanism than all other nitrogenases, including those of Azotobacter. While the three dinitrogenase (Str1) polypeptides of S. thermoautotrophicus show similarity to their counterparts in other diazotrophs, the dinitrogenase reductase analog (Str2) shows high sequence identity to manganese-containing superoxide dismutases (see Section 5.18). In addition, Str2 is insensitive to oxygen and actually requires it in that it oxidizes superoxide (O2-) to supply electrons to Str1 for N2 fixation (the O2- for this reaction is derived from CO dehydrogenase activity in this organism). The nitrogenase in S. thermoautotrophicus requires less than half of the ATP energy consumed by classical nitrogenases.
16. How is nitrogenase synthesis and activity controlled by NH3 and O2 (Section 13.15)?
16. High levels of ammonia in cells represses the synthesis of nitrogenase. Ammonia "switch-off" is the regulation of the activity of already synthesized nitrogenase enzyme, and it occurs via ADP-ribosylation of dinitrogenase reductase. NifL protein, a negative regulator of nitrogenase synthesis, prevents expression of nif genes in the presence of O2.
The above table lists some of the results for a population analysis profile for a particular antibiotic for a particular bacterium. Given the colony counts shown, what is the frequency of colony forming units (CFUs) per mL in the original overnight culture that can grow on 16 mg/L of the antibiotic?
1:10^4
2. Review the data of Figure 23.21. Keeping in mind that the open- ocean waters are highly oxic, predict the possible metabolic lifestyles of open-ocean Archaea and Bacteria. Why might pro- teorhodopsin be more abundant in one group of organisms than in the other?
2. As the data in Figure 23.21 show, Bacteria tend to predominate in oceanic surface waters (<1,000 m), and the numbers of Archaea and Bacteria are about equal in lower waters. The metabolic strategy providing the greatest advantage for Bacteria in these nutrient-deficient environments is likely phototrophy. Some Archaea found within the photic zone may also have a capacity for phototrophy using the proton pump bacteriorhodopsin, but the majority of these organisms are likely chemoorganotrophs that consume dissolved organic carbon excreted by photosynthetic bacteria and algae. Archaea found in deeper waters are almost exclusively species of Crenarchaeota, many of which probably rely on chemolithotrophic metabolisms. Proteorhodopsin is found in Bacteria but not in Archaea because the latter also contain rhodopsins (e.g., bacteriorhodopsin). Both systems function in generating light-dependent ATP synthesis, which serves as a supplement to energy generated from chemotrophic metabolism.
2. How can organisms such as Syntrophobacter and Syntrophomonas grow when their metabolism is based on thermodynamically unfavorable reactions? How does coculture of these syntrophs with certain other bacteria allow them to grow (Section 24.2)?
2. Data in the literature used for thermodynamic calculations are based on standard conditions (1 molar solute, 25°C, pH 7, and 1 atm), which are not usually found in natural systems. Thus, the positive free-energy value (∆G0′) calculated under standard conditions is not an accurate assessment of in situ conditions, in which low H2 concentrations result from consumption of this electron donor by methanogens and sulfate-reducing bacteria. The secondary fermentation products generated by Syntrophobacter are utilized by methanogens. For example, in the presence of partnering methanogens, the oxidation of propionate (+ 3 H2O) to acetate, HCO3-, and H2 by Syntrophobacter wolinii changes the ∆G0′ of this reaction from +76.2 to -5.5 kJ/mol, thus supporting slow growth of the syntroph. In the laboratory, this organism can be grown in coculture with an appropriate H2-consuming partner.
2. Describe the effects of a lethal dose of ionizing radiation at the molecular level (Section 26.2).
2. Ionizing radiation can produce electrons, hydroxyl radicals, and hydride radicals, all of which can degrade and/or permanently alter macromolecules.
2. Filtration is an acceptable means of pasteurization for some liquids. Design a filtration system for pasteurization of a heat- sensitive liquid. For a liquid of your choice, identify the advantages and disadvantages of a filtration system over a heat pasteurization system. Explain in terms of product quality, shelf life, and price.
2. One could use a large membrane filter and design equipment to pull the liquid through the filter. Sterilization would not be necessary because for pasteurization, it is sufficient to simply remove a percentage of microorganisms present in a liquid. Filtration may be desirable when the liquid contains a heat-labile compound, or when the flavor of the liquid suffers from the process of heating. The product quality would likely be excellent using a filtration system for pasteurization, but the cost of the item may increase due to equipment costs for production of the consumable item.
2. Identify the cells that express pattern recognition receptors (PRRs). How do PRRs associate with pathogen-associated molecular patterns (PAMPs) to promote innate immunity (Section 28.2)?
2. Phagocytes (e.g., macrophages and neutrophils) interact directly with pathogen-associated molecular patterns (PAMPs) displayed by pathogens via their preformed pattern recognition receptors (PRRs). PRRs promote innate immunity in that a single PRR can recognize a PAMP shared by a number of related pathogens.
2. Explain why both obligately anaerobic and obligately aerobic bacteria can often be isolated from the same soil sample (Section 23.3).
2. Soil is not a homogenous system and contains numerous microenvironments, some of which are aerobic and some of which are anaerobic (see Figures 23.3 and 23.11). These microenvironments provide a suitable habitat for bacteria of diverse physiological properties.
2. 14C-labeled cellulose is added to a vial containing a small amount of sewage sludge and sealed under anoxic conditions. A few hours later, 14CH4 appears in the vial. Discuss what has happened to yield such a result.
2. The 14C-cellulose is initially degraded by a cellulolytic population that forms monomeric sugars. These sugars are then metabolized by anaerobes to fermentation products, which include 14CO2 and H2. Methanogens then use these substrates to produce 14CH4.
2. What are the functions of light-harvesting and reaction center chlorophylls? Why would a mutant incapable of making light- harvesting chlorophylls (such mutants can be readily isolated in the laboratory) probably not be a successful competitor in nature (Section 13.2)?
2. The light-harvesting sites serve as the antenna for capturing light energy, which will be transferred to the RC and converted into chemical energy. Mutants defective in the light-harvesting chlorophyll would be deficient in trapping light quanta and therefore less competitive in nature for their energy source.
2. Compare and contrast the production of a plant tumor by Agrobacterium tumefaciens and a root nodule by a Rhizobium species. In what ways are these structures similar? In what ways are they different? Of what importance are plasmids to the devel- opment of both structures (Sections 25.3 and 25.4)?
2. Trait //PlantTumors// RootNodules// Microbe A. tumefaciens// Rhizobium spp. Enters host// Plasmid DNA only// Bacterium Mode of entry Tissue lesion Infection thread Hypertrophy Yes Yes Phytohormones Yes Yes Tumorigenesis Yes No Permanent genetic change Yes No Opines produced Yes No
2. The growth rate of the phototrophic purple bacterium Rhodo- bacter is about twice as fast when the organism is grown phototrophically in a medium containing malate as the carbon source as when it is grown with CO2 as the carbon source (with H2 as the electron donor). Discuss the reasons why this is true, and list the nutritional class in which we would place Rhodobacter when growing under each of the two different conditions.
2. When Rhodobacter is growing with malate, a citric acid cycle intermediate, as the carbon source, all of the ATP formed from cyclic photophosphorylation is used for processes required for growth (i.e., the reduction of CO2 to cell material is unnecessary because malate is available), and growth rates are accelerated. The organism is therefore growing as a photoheterotroph. When CO2 and H2 are present and malate is absent, the organism is growing photoautotrophically. Even though ATP is not required to generate reducing power via reverse electron flow (H2 has a sufficiently negative reduction potential [-0.42 V] to make reverse electron flow unnecessary), ATP is required for CO2 fixation, which significantly reduces the cellular growth rate.
3. The surface of a rock in a flowing stream will often contain a biofilm. What advantages could be conferred on bacteria growing in a biofilm compared with growth within the flowing stream (Section 23.4)?
3. A free-swimming lifestyle can be challenging for bacteria because nutrient availability is generally poor and can fluctuate dramatically. Bacteria may preferentially attach to surfaces because nutrients are often trapped there. Once a population of cells is established on a surface, many bacteria are capable of forming biofilms, which are microcolonies of bacterial cells encased in a polysaccharide matrix produced by the cells themselves. Biofilms can serve to trap nutrients, prevent the detachment of cells on a flowing surface, aid in self-preservation by preventing phagocytosis and exposure to toxins, and facilitate cell-to-cell communication and genetic exchange.
3. Acid mine drainage is in part a chemical process and in part a biological process. Discuss the chemistry and microbiology that lead up to acid mine drainage and point out the key reactions that are biological. What ways can you think of to prevent acid mine drainage?
3. Acid mine drainage is a combination of chemical and biological processes. Bacterial oxidation of sulfide minerals (e.g., pyrite, FeS2) produces soluble ferrous iron (Fe2+) and sulfuric acid, thereby lowering the pH of the environment. The pyrite is first exposed in the mining operation to O2, and then a slow chemical reaction occurs (initiator reaction), resulting in the oxidation of sulfide to sulfate and the development of acidic conditions that stabilize Fe2+. Next, the biological oxidation of ferrous iron to ferric iron by A. ferrooxidans occurs. Under acidic conditions, Fe3+ is soluble and reacts with more pyrite, oxidizing it to sulfuric acid and Fe2+, and the cycle goes on.
3. Although growth factor analogs may inhibit microbial metabolism, only a few of these agents are useful in practice. Many growth fac- tor analogs, including some in wide use, such as azidothymidine, exhibit significant host cell toxicity. Describe a growth factor ana- log that is effective and has low toxicity for host cells. Why is the toxicity low for the agent you chose? Also describe a growth factor analog that is effective against an infectious disease, but exhibits toxicity for host cells. Why might a toxic agent such as AZT still be used in certain situations to treat infectious diseases? What pre- cautions would you take to limit the toxic effects of such a drug while maximizing the therapeutic activity? Explain your answer.
3. Although considerable research is being done regarding the use of irradiation in foods, there are some potential drawbacks. First, the method can be expensive. While ultraviolet irradiation of food is relatively inexpensive, it only accomplishes surface
4. Describe the procedure for obtaining the minimum inhibitory concentration (MIC) for a chemical that is bacteriocidal for E. coli (Section 26.4).
4. A series of broth tubes is prepared. The series should contain increasing concentrations of the antibiotic; the concentrations should run from none to considerably above the concentration causing complete inhibition of growth. All tubes are inoculated with a uniform quantity of the chosen Escherichia coli strain. After incubation, often overnight, the series is examined for growth. The minimum inhibitory concentration (MIC) is the antibiotic concentration in the tube containing the lowest concentration of antibiotic that shows no growth of the organism, as determined by the turbidity of the culture.
3. Although physiologically distinct, chemolithotrophs and chemo- organotrophs share a number of features with respect to the production of ATP. Discuss these common features along with rea- sons why the growth yield (grams of cells per mole of substrate) of a chemoorganotroph respiring glucose is so much higher than for a chemolithotroph respiring sulfur.
3. Chemolithotrophs use an inorganic compound as an electron donor and energy source, whereas chemoorganotrophs use organic compounds. However, in both types of organisms, ATP can be produced using membrane-bound electron transport chains that generate a proton motive force for oxidative phosphorylation. A major reason why chemoor-ganotrophs respiring glucose have a dramatically higher growth yield than a chemolithotroph respiring sulfur is a function of the reduction potential of the electron donor/acceptor couples employed in each metabolism. For glucose-respiring prokaryotic chemoorganotrophs, the net free-energy differential yields about 38 ATPs per mole of glucose. Moreover, glucose can also serve as a reduced carbon source for biosynthesis. Most sulfur-chemolithotrophs obtain their cellular carbon autotrophically from CO2 fixation via the Calvin cycle. This is energetically expensive and consumes about 3 ATPs per mole of CO2 reduced, which drops the net ATP yield compared with chemoorganotrophs, resulting in an overall lower growth yield.
3. What are the principal advantages of membrane filters? Of depth filters? Of nucleopore filters (Section 26.3)?
3. Membrane filters are high tensile strength, open structures with about 80-85% of the filter occupied by pores. This openness provides the membrane filter with a much faster flow rate than would be obtained with a depth filter. Depth filters are composed of randomly overlapping fibers, and they are excellent for filtering gases or liquid suspensions because they resist clogging. Nucleopore filters are a type of membrane filter that contains uniform pores; these filters are excellent for isolating bacterial specimens within a single plane for microscopic viewing.
3. How do mycorrhizae improve the growth of trees? How do they promote plant diversity (Section 25.5)?
3. Mycorrhizae is a term describing the mutualistic association between plant roots and fungi. In this symbiosis, the extensive surface area of the fungal mycelium enhances nutrient absorption by plant roots in nutrient-poor soils. Plant diversity is supported in areas where a diversity of mycorrhizal fungi is abundantly present.
3. Compare and contrast the processes of nitrification and denitrification in terms of the organisms involved, the environmental conditions that favor each process, and the changes in nutrient availability that accompany each process (Section 24.3).
3. Nitrification is an oxidative process requiring a high pO2, while denitrification is a process usually accompanied by a low pO2. Although there are intermediate compounds common to both pathways, the fate of nitrogen in the two processes is different. In nitrification, NH3 is oxidized ultimately to NO3-, which is either used by other organisms or is lost from the system by leaching into groundwater. Because the reductive process leads to gaseous products that may be lost (N2, NO, N2O), denitrification can lead to major nitrogen deficiencies in some habitats, including agricultural crop fields. There is a diversity of denitrifiers in nature; however, nitrification among bacteria is quite restricted by comparison.
3. Identify the lymphocytes and the antigen-specific receptors involved in cell-mediated adaptive immunity (Section 28.3).
3. The cell-mediated adaptive immune response is initiated following contact of T lymphocytes with antigens on infected cells (i.e., host cells displaying MHC I proteins, with APCs also displaying MHC II proteins). This adaptive response requires that specific T cell receptors (TCR) recognize and make contact with MHC I and II proteins that are presenting a corresponding antigen. This stimulates the proliferation of T-cytotoxic cells, which secrete perforins and granzymes that kill antigen-bearing infected cells. This response is also indirectly mediated by two functionally distinct T-helper cell subsets: TH1 cells, which release cytokines to initiate the inflammatory response, and TH2 cells, which secrete cytokines to stimulate antigen-reactive B cells to differentiate into plasma cells and produce antibodies.
3. Where are the photosynthetic pigments located in a phototrophic purple bacterium? A cyanobacterium? A green alga? Considering the function of chlorophyll pigments, why are they not located elsewhere in the cell, for example, in the cytoplasm or in the cell wall (Section 13.2)?
3. The photosynthetic pigments of purple bacteria are located in intracellular membrane systems composed of lamellar stacks or vesicular chromatophores. In cyanobacteria, pigments occur in thylakoid membranes with attached phycobilisomes. In green algae, chlorophylls are found in the lamellae of chloroplasts. Pigment-containing RCs must be in close proximity to a membrane-associated electron transport system to facilitate the conversion of light energy to chemical energy. Therefore, the generation of ATP and NAD(P)H requires that the RC also be membrane bound.
4. Identify the lymphocytes and the antigen-specific receptors involved in antibody-mediated adaptive immunity (Section 28.4).
4. Antibody-mediated immunity involves both T cells and B cells. The T cell receptors have specificity for a specific antigen, and upon contact with that antigen, the T cell undergoes rapid growth to produce clones of those cells. A subset of the T cell population, T-helper cells (TH2 subclass), stimulate B cells to produce antibodies (immunoglobulins) specific for the stimulating antigen.
4. Employing biotechnology, you would like to genetically engineer corn (maize) to fix nitrogen. Discuss what type of nitrogenase you would try to engineer into the corn plant and why this would be the most suitable enzyme for the purpose.
4. Because plants are oxygenic phototrophs, one would logically want to genetically engineer an oxygen-insensitive nitrogenase into corn, such as the nitrogenase from Streptomyces thermoautotrophicus.
4. How can biofilms complicate treatment of infectious diseases (Section 23.4)?
4. Biofilms complicate the treatment of infectious diseases by protecting the pathogen population from the host immune system and by preventing exposure to antibiotics and other antimicrobial agents.
4. What accessory pigments are present in phototrophs, and what are their functions (Section 13.3)?
4. Carotenoids and phycobilins function as accessory pigments in that they extend the usable spectrum of light energy that can be absorbed and transferred to the RC. Carotenoids in particular protect against harmful photooxidation reactions that produce toxic oxygen species, whereas the phycobilins function primarily in light harvesting.
4. Which group of bacteria cycle sulfur compounds under anoxic conditions? If sulfur chemolithotrophs had never evolved, would there be a problem in the microbial cycling of sulfur compounds? Which organic sulfur compounds are most abundant in nature (Section 24.4)?
4. The anaerobic cycling of sulfur compounds is due to the combined activities of desulfurylation, dissimilatory and assimilatory sulfate reduction, and the oxidation of reduced sulfur compounds by phototrophs and denitrifiers (e.g., Thiobacillus denitrificans). If sulfur chemolithotrophs had not evolved, there would have been an accumulation of H2S with the only provision for its oxidation to sulfate being certain anoxygenic phototrophs. A deficiency of sulfate would seriously hinder the growth of organisms that assimilate sulfate as a source of sulfur. Organic sulfur compounds of the greatest abundance in nature are dimethyl sulfide, methanethiol, carbon disulfide, dimethyl disulfide, and dimethylsulfoxide.
4. What is a rumen and how do the digestive processes operate in the ruminant digestive tract? What are the major benefits and the disadvantages of a rumen system? How does a cecal animal compare with a ruminant (Section 25.7)?
4. The structure of the digestive tract of animals determines the fate of the nutrients and the retention time of ingested materials. In the ruminant, the stomach is modified into four compartments such that a large fermentation chamber, the rumen, accommodates the activities of a dense community of anaerobic microflora. The major advantage of this architecture is the capacity to utilize readily available plant fodder (primarily plant cellulose, hemicellulose, and pectin) as a source of volatile fatty acids oxidized by the ruminant as its main energy source. Disadvantages include problems associated with eliminating the major waste product methane by eructation that fails in the presence of plant saponins. Ruminants include cattle, goats, buffalo, deer, and elk. Analogous fermentation reactions occur in cecal fermenters (e.g., horse, rabbit). However, the cecum is located between the small and large intestines instead of before the stomach, as is the case for the rumen. Therefore, materials that enter the cecum cannot be regurgitated and further broken down by additional mastication.
5. Contrast the action of disinfectants and antiseptics. Disinfectants normally cannot be used on living tissue; why not (Section 26.5)?
5. Disinfectants are bacteriocidal (or fungicidal/viricidal) agents used on inanimate objects; antiseptics kill or inhibit the growth of microorganisms on living tissue. Because of their caustic/toxic nature, disinfectants would cause damage to living tissues; antiseptics are formulated to minimize these toxic effects.
5. Identify the cells that initiate inflammation and the cells that are activated by inflammatory signals (Section 28.5).
5. Inflammation is initiated by the release of cytokines and chemokines, primarily from leukocytes (both phagocytes and lymphocytes). Inflammation activates phagocytic macrophages, and their production and release of cytokines and chemokines recruits phagocytic neutrophils to the site of infection.
5. How does light result in ATP production in an anoxygenic phototroph? In what ways are photosynthetic and respiratory electron flow similar? In what ways do they differ (Section 13.4)?
5. Just like in respiratory metabolisms, ATP production in an anoxygenic phototroph comes from the proton motive force generated during electron transport. However, in phototrophs, electron transport is initiated by the light-induced change in reduction potential of RC pigments, allowing the RC to reduce a series of low-potential electron carriers while pumping protons outside the membrane. The return of these protons into the cytoplasm through ATP synthase provides the energy for ATP synthesis. This process is referred to as cyclic photophosphorylation. Electron transport in phototrophs uses some of the same electron carriers as those found in nonphototrophs. Unlike in respiration, however, there is no net input or consumption of electrons in cyclic photophosphorylation—the electrons simply travel in a closed loop.
5. How do microbial mats compare with biofilms in terms of dimen- sions and microbial diversity (Section 23.5)?
5. Microbial mats are larger and thicker than biofilms, and while biofilms may contain one or several species, microbial mats consist of layered communities composed of species from multiple guilds.
9. Why do symbionts that are transmitted horizontally show less genome reduction, as opposed to the significant genome reduction observed in heritable symbionts (Section 25.9)?
9. Horizontally-transmitted symbionts must be capable of maintaining a free-living lifestyle since they often exist outside of their hosts⎯a condition not experienced by heritable symbionts. Excessive genome reduction would prevent this since essential genes would likely be lost.
5. What is an example of a single microbial species contributing to herbivore health? What is an example of a single microbial species contributing to herbivore pathology (Section 25.7)?
5. Synergistes jonesii contributes to ruminant health by breaking down toxic compounds formed from the amino acid-like compound mimosine, which is present in some legumes fed to livestock as a nutritional supplement. Streptococcus bovis is a species that can rapidly grow to detrimental populations when ruminants are suddenly fed diets containing high starch and lower cellulose content, such as corn and other starchy grains.
5. Why are most iron-oxidizing chemolithotrophs obligate aerobes and why are most iron oxidizers acidophilic (Section 24.5)?
5. Under acid conditions, ferrous iron (Fe2+) is stable, and in such environments it can serve as an electron donor. At neutral or alkaline pH, Fe2+ spontaneously oxidizes in the presence of O2. The redox potential of the ferric/ferrous iron couple is high (+0.77V); thus, oxygen (1/2O2/H2O; E0′ = +0.82V) is the sole available electron acceptor from which energy could be obtained by iron oxidation. Hence, the iron-oxidizing chemolithotrophs are obligate aerobes.
6. List the diseases for which you have been immunized. List the diseases for which you may have acquired immunity naturally (Sections 28.6 and 28.7).
6. Answers will vary.
6. How is reducing power for autotrophic growth obtained in a pur- ple bacterium? In a cyanobacterium (Section 13.4)?
6. Because the E0′ of the quinone is 0 V and that of the NAD+/NADH couple is -0.32 V, reduction of NAD+ requires reverse electron flow and consumption of ATP. Reducing power during phototrophic growth in purple bacteria comes from reduced substances in their environment (e.g., H2S, S2O32-, S0), which are oxidized by c-type cytochromes and ultimately reduce NAD+ to NADH via the quinone pool. In cyanobacteria, NAD(P)+ is reduced to NAD(P)H directly from electron transport reactions from photosystem I.
6. In what ways are Ca and Si cycling in ocean waters similar, and in what ways do they differ? How do the Ca and Si cycles couple to the carbon cycle (Section 24.6)?
6. Calcium and silica are used by separate eukaryotic protists for the production of exoskeletons. Foraminifera and coccolithophores produce calcareous exoskeletons, while radiolarans and diatoms (among others) produce silica exoskeletons. The formation of CaCO3 for phytoplankton exoskeletons depletes dissolved HCO3- and increases dissolved CO2, which reduces the influx of atmospheric CO2 into surface waters. Unicellular eukaryotes having Si-based exoskeletons, such as diatoms, contribute to the biological pump of marine systems. By this mechanism, huge amounts of organic carbon are deposited into benthic ecosystems when blooms of diatoms become silica-limited, die, and sink to deep waters and sediments. Thus, the silica and calcium cycles are related in that they both influence the pH of ocean waters by affecting levels of dissolved CO2.
6. Growth factor analogs are generally distinguished from antibiotics by a single important criterion. Explain (Section 26.6).
6. Growth factor analogs are synthetic compounds that mimic a growth factor but do not perform its function, and this mimicry inhibits growth. Antibiotics are natural substances produced by certain microorganisms that inhibit other organisms.
6. In what soil horizon are microbial numbers and activities the highest, and why (Section 23.6)?
6. Microbial numbers and activities in soils are highest in the A horizon, usually within the rhizosphere. This is mainly due to the higher levels of free and adsorbed water and the availability of rich organic matter (humus).
6. What is a possible mechanism by which the microbial community of the human gut increases energy recovery, thereby contributing to obesity (Section 25.8)
6. The inheritance of human gut microflora that are composed of lower numbers of Bacteroidetes and higher numbers of Firmicutes, methanogenic Archaea, and Actinobacteria from a mother may contribute to obesity. The presence of large numbers of methanogens is believed to rapidly remove H2 produced by fermentation, thus improving fermentative efficiency and providing the individual access to a higher proportion of usable nutrients, which contributes to obesity.
6. Define virulence and identify parameters to distinguish between highly virulent and moderately virulent pathogens (Section 27.6).
6. Virulence is the ability of a pathogen to cause disease. Virulence is estimated using experiments that determine the LD50 of a pathogen for a particular host. Unlike pathogens having mild virulence, highly virulent pathogens show little difference between the number of cells needed to kill 50% of a test group and the number of cells that kill 100% of the test group. The LD50 is therefore more difficult to determine for highly virulent pathogens (see Figure 27.14).
7. How are nutrients for microbial growth replenished in the deep subsurface as opposed to the near subsurface (Section 23.7)?
7. Deep subsurface microbial communities obtain nutrients through a combination of abiotic sources (e.g., radiolysis of water, geochemical oxidations, and percolation of surface waters carrying dissolved minerals into groundwater) and nutrient cycling by autotrophic chemolithotrophs and heterotrophic chemoorganotrophs.
7. Identify the role of the capsule and the fimbriae of bacteria in microbial adherence (Section 27.7).
7. Fimbriae (and pili) are cell-surface proteins that function as adherence factors and allow attachment to epithelial surfaces. Capsules are dense polymer layers (usually polysaccharides) surrounding cells that are not covalently attached to the bacterium but function in adherence to host tissues and to other bacteria. In some cases, such as in Streptococcus pneumoniae, capsules prevent destruction of the bacterium by phagocytes and are essential for pathogenicity.
7. Identify common sources for naturally occurring antimicrobial drugs (Section 26.7).
7. Natural antibiotics are produced by a variety of bacteria and fungi, including in particular species of Streptomyces and Penicillium, respectively.
7. How does the reduction potential of chlorophyll a in PSI and PSII differ? Why must the reduction potential of PSII chlorophyll be so highly electropositive (Section 13.5)?
7. PS II (P680) must have a highly electropositive reduction potential to allow H2O to serve as the electron donor (1/2 O2/H2O = E0′ +0.82 V), a byproduct of which is O2. PS I (P700) is at a lower reduction potential than P680 and is reduced by the final electron carrier from PS II, plastocyanin. Therefore, the highly electropositive reduction potential of PS II is essential for establishing the chain of electron carriers that can result in the eventual reduction of PS I.
7. List the immunizations recommended for adults in the United States (Section 28.7).
7. The recommended immunizations for adults of at least 18 years of age are shown in Figure 28.14. Familiar examples include diphtheria, tetanus, pertussis, measles, mumps, rubella, and poliovirus.
7. Why was E. coli long thought to be a dominant member of the human gut microbial community (Section 25.8)?
7. We now know from molecular surveys that Gammaproteobacteria, which includes E. coli, make up less than 1% of the human gut microflora. This is in stark contrast to analyses carried out using traditional culturing techniques, which are prone to enrichment bias. Because E. coli grows very well in laboratory culture, it was mistakenly believed to be a major component of the gut microflora.
8. Describe a biotechnology-based immunization strategy that has been adapted for an approved vaccine. Did this vaccine replace an existing vaccine? If so, what advantage does the biotechnology- based vaccine have over the conventional vaccine (Section 28.8)?
8. A biotechnology-based immunization strategy would be the use of genetically engineered vaccines or DNA vaccines to produce a suitable immunogen. The difference between these vaccines and conventional immunization strategies is that these new approaches do not employ whole organisms or toxoids, and they are therefore generally considered safer. The human papillomavirus vaccine is a recombinant-antigen vaccine that represents the only vaccine effective against a sexually transmitted disease.
8. How is it possible for aphids to feed on the carbohydrate-rich but nutrient-poor sap of phloem vessels in plants (Section 25.9)?
8. Aphid endosymbionts (e.g., Buchnera spp.) allow them to feed exclusively on carbohydrate-rich but nutrient-poor sap because metabolites produced by the symbionts account for nutrient deficiencies of the sap. For example, amino acids that are completely lacking or rare in the sap are provided to the aphid by its symbionts.
8. Explain the role of the availability of nutritional factors in infection by microorganisms in the body (Section 27.8).
8. Bacteria are limited in their ability to infect, grow, and multiply in a host by the availability of essential nutrients. Iron is particularly important, as it is a vital component of cytochromes and iron-sulfur proteins in electron transport chains. If nutrients, including trace elements, are not present in sufficient quantities in a particular part of the body, then colonization by infecting organisms cannot occur.
8. Compare and contrast the utilization of H2S by a purple phototrophic bacterium and by a colorless sulfur bacterium such as Beggiatoa. What role does H2S play in the metabolism of each organism (Sections 13.4 and 13.8)?
8. Purple phototrophs use H2S as an electron donor for photophosphorylation, and elemental sulfur may be deposited inside or outside the cell. In phototrophs, light rather than H2S is used as the energy source to generate electron transport. In the aerobic colorless sulfur bacteria (e.g., Beggiatoa), H2S serves as both the electron donor and the energy source for chemolithotrophic growth. Elemental sulfur may also be deposited inside or outside the cell, depending on the specific microorganism. Most commonly, S0 is oxidized further to SO42-.
8. Describe the mode of action that characterizes a β-lactam antibiotic. Why are these antibiotics generally more effective against gram-positive bacteria than against gram-negative bacteria (Section 26.8)?
8. The enzymes (transpeptidases) that cross-link the two glycan-linked peptide chains of peptidoglycan also bind the β-lactam ring. Thus, these proteins are known as penicillin-binding proteins (PBPs). When PBPs are bound to the β-lactam ring, they no longer catalyze the transpeptidase reaction. The cell wall continues to be formed but becomes progressively weaker as autolysins continue to remove the existing cell wall, resulting in lysis. The outer membrane of gram-negative bacteria is impermeable to naturally occurring β-lactam antibiotics, and therefore such cells are not susceptible to the effects of these antimicrobial drugs. Gram-positive bacteria have no outer membrane, and therefore β-lactam drugs can freely bind transpeptidases.
8. How and in what way does an input of organic matter, such as sewage, affect the oxygen content of a river or stream (Section 23.8)?
8. The input of large amounts of organic matter, such as sewage, into a river or stream causes a decrease in oxygen content as a result of exponential growth of aerobic chemoorganotrophs. This, of course, is deleterious to multicellular aquatic life. It also rapidly increases the activities of anaerobic bacteria, which produce foul-smelling compounds that are often toxic to higher organisms.
What percentage of terrestrial plants are colonized by arbuscular mycorrhizae?
85%
9. Identify the role of coagulase and streptokinase in the invasiveness of Staphylococcus and Streptococcus, respectively (Section 27.9).
9. Coagulase produced by Staphylococcus aureus is a clotting enzyme that induces clot formation in the host by causing fibrin particles to adhere to cells of the invading bacterium. The resulting fibrin matrix causes extremely localized colonization of S. aureus and protects the bacterium from host defense mechanisms. By contrast, Streptococcus pyogenes produces a fibrinolytic enzyme called streptokinase that prevents clot formation and increases the invasiveness of the pathogen.
9. Define the differences between immediate and delayed-type hypersensitivity in terms of immune effectors, target tissues, antigens, and clinical outcome (Section 28.9).
9. Immediate hypersensitivity (type I) involves an immediate response to antigen exposure mediated by antibodies. Although usually relatively mild (e.g., allergies), some reactions can become severe so quickly that death can result (anaphylactic shock). The primary chemical mediators are histamines and serotonin released from mast cells, the latter of which have IgE receptors on their surfaces that are stimulated upon interaction with ntigen (e.g., insect venoms, pollen, certain foods, and animal dander). Delayed-type hypersensitivity is cell mediated and involves the activities of the TH1 inflammatory cells. Symptoms begin to appear several hours after secondary exposure to antigen and maximum response is within 24-48 hours in most cases. The release of cytokines from TH1 cells attracts large numbers of macrophages to the site, and a localized inflammatory response is also observed. Examples of delayed hypersensitivity include poison ivy, mumps, and the tuberculin test.
9. Distinguish between the modes of action of at least three of the protein synthesis-inhibiting antibiotics (Section 26.9).
9. Tetracycline (as well as streptomycin, spectinomycin, and others) is a protein synthesis inhibitor that acts by binding to and inhibiting function of the 30S ribosomal subunit. Chloramphenicol and erythromycin interfere with the 50S ribosomal subunit. Mupirocin and puromycin interfere with tRNA synthesis. All have the net effect of blocking protein synthesis in bacterial cells.
9. Which inorganic electron donors are used by the organisms Ralstonia and Thiobacillus (Sections 13.6-13.8)?
9. The inorganic electron donor used by Ralstonia is hydrogen (H2), whereas species of Thiobacillus use reduced sulfur compounds (e.g., H2S, S2O32-, S0) as electron donor.
9. What organisms are the major phototrophs in the oceans (Section 23.9)?
9. The prochlorophytes, relatives of cyanobacteria that lack phycobilins, are the major phototrophs in open oceans.
Among present-day chemolithotrophs, microorganisms that derive their energy from oxidizing H2 are more common than microorganisms that derive their energy from oxidizing Fe2+. As to why the H2‒oxidzing microbes are more common, there are several plausible explanations.
A. H2 is a better electron donor than Fe2+. B. The redox pair 2H+/H2 is higher on the redox tower than Fe3+/Fe2+. 2+ C. In most habits on present-day Earth, there is not an abundant supply of Fe
the Z scheme in non-cyclic photophosphorylation
A. In plants, the electron transport components (e.g. P680, Ph, PQA, etc.) are embedded in the thylakoid membrane of chloroplasts. B. In cyanobacteria, the electron transport components are embedded in the cytoplasmic membrane. C. The electrons donated by the light-harvesting complex of photosystem II (i.e. P680) are replaced by electrons from the reaction H2O 1⁄2O2 + 2H+ + 2e‒ catalyzed by a water-splitting enzyme. E. NADPH is generated by the electron transport chain of photosystem I (starting at P700).
the process of cyclic photophosphorylation
A. The electron transport components (e.g. P870, Bchl, Bph, etc.) are embedded in a membrane. C. A proton motive force is usually generated. D. The light-harvesting complex (e.g. P870) usually contains bacteriochlorophyll.
microbially mediated processes that produce organic carbon in the form of (CH2O)n?
Acetogenesis Anoxygenic photosynthesis Oxygenic photosynthesi
Ferrous iron (Fe2+) oxidation generally occurs in environments with:
Acidic conditions
Acid mine drainage
Acidic water containing H2SO4 derived from the microbial oxidation of iron sulfide minerals.
Which bacterium contains a large Ti plasmid and causes crown gall disease in plants?
Agrobacterium tumefaciens
The above figure shows the results for an Etest for the antibiotic oxacillin for a strain of MRSA. The scale on the strip is in mg/L. What is the MBC?
An Etest cannot be used to determine the MBC
The life-threatening condition that may develop during a type I hypersensitivity reaction is called:
Anaphylaxis
In what environmental condition are methanogens generally most active?
Anoxic
In the adaptive immune system in vertebrates, most of the antibiodies are produced by:
B cells
The function of leghemoglobin in root nodules is to:
Bind oxygen
Which layer in a soil profile generally has the lowest microbial activity?
C horizon
A microbial guild contains populations of:
Cells that share a metabolic relation
humus
Dead organic matter
Which cell type has a nucleus?
Erythrocytes (NO) Lymphocytes (YES) Phagocyte (YES)
examples of a biofilm
Human normal flora Toiletbowlscum Organisms that colonize indwelling medical devices Dentalplaque
What adaptation do organisms have that tolerate high pressures?
Increased unsaturated fatty acids
Which iron species is produced primarily from iron smelting and rarely is produced by microbial-mediated processes?
Iron (Fe0)
For an antibacterial, typically how are the MIC and MBC related?
MBC > MIC
heat sterilization
Microbial death is more rapid at an acidic pH. High concentrations of sugars and salts influence sterilization time. The amount of water in a substance is a major factor in heat resistance.
Soils derived from rock weathering are called ________ soils.
Mineral
Two organisms that both benefit from each other are in a symbiotic relationship called:
Mutualism
Blood and lymph have the following in common
Nucleated cells Proteins
Due to the sensitivity of dinitrogenase reductase, nitrogen fixation is inhibited by:
O2
What is the most abundant prokaryote in the ocean?
Pelagibacter
The metabolic process of ammonification ________ ammonia.
Produces
The metabolic process of denitrification:
Reduces NO3
The spread of pathogens through the blood and lymph systems that results in a bloodborne systemic infection is called:
Septicemia
The specificity of certain rhizobia to infect only particular plants is in part due to the:
Rhizobial lipids that act as signaling molecules
Plant root nodules are:
Sites where nitrogen fixation occurs
The rhizosphere is the:
Soil that receives secretions from plant roots
Which metric describes the total number of species present in a community?
Species richness
How do arbuscular mycorrhizae (AM) help plants obtain more nutrients from the soil?
The AM increase the total surface area to absorb more nutrients.
Which of the following is true about the Calvin cycle?
The cycle fixes carbon. The cycle requires ATP and NAD(P)H. To produce one hexose from carbon dioxide, 6 turns of the cycle are required. RuBisCO converts ribulose bisphosphate and CO2 into two molecules of 3-phosphoglyceric acid (PGA).
What is the role of the vir genes on a Ti plasmid?
Ti-DNA transfer
Gram-positive bacteria don't produce endotoxins.
True
In plants and cyanobacteria, carbon fixation does not occur in both non-cyclic photophosphorylation and the Calvin cycle.
True
Monocytes and granulocytes are the two lineages of myeloid cells.
True
Not all phototrophs are autotrophs.
True
Relatively few microorganisms are able to use N2, yet the most stable form of nitrogen is N2.
True
Phagocyte
a cell that engulfs foreign particles, and can ingest, kill, and digest most pathogens
Growth factor analog
a chemical agent that is related to and blocks the uptake of a growth factor
Antiseptic (germicide)
a chemical agent that kills or inhibits growth of microorganisms and is sufficiently nontoxic to be applied to living tissues
Carotenoid
a hydrophobic accessory pigment present along with chlorophyll in photosynthetic membranes
Neutrophil
a leukocyte exhibiting phagocytic properties, a granular cytoplasm (granulo- cyte), and a multilobed nucleus; also called polymorphonuclear leukocyte or PMN
Chlorophyll
a light-sensitive, Mg-containing porphyrin of phototrophic organisms that initiates the process of photophosphorylation
T cell
a lymphocyte that interacts with antigens through a T cell receptor for antigen; T cells are divided into functional subsets including TC (T-cytotoxic) cells and TH (T-helper) cells. TH cells are further subdivided into TH1 (inflammatory) cells and TH2 helper cells, which aid B cells in antibody formation
B cell
a lymphocyte with immunoglobulin sur- face receptors that produces immunoglobulin and may present antigens to T cells
Chemolithotroph
a microorganism that oxidizes inorganic compounds as electron donors in energy metabolism
Leukocyte
a nucleated cell in blood; also called a white blood cell
Superantigen
a pathogen product capable of eliciting an inappropriately strong immune response by stimulating greater than normal numbers of T cells
Reaction center
a photosynthetic complex containing chlorophyll or bacteriochlorophyll and several other components, within which occurs the initial electron transfer reactions of photosynthetic electron flow
Pattern recognition receptor (PRR)
a protein in a phagocyte membrane that recognizes a pathogen-associated molecular pattern (PAMP)
Pathogen-associated molecular pattern (PAMP)
a repeating structural component of a microorganism or virus recognized by a pattern recognition receptor (PRR)
Cytokine
a soluble protein produced by a leukocyte that modulates an immune response
Chemokine
a soluble protein that modulates an immune response
Lymphocyte
a subset of nucleated cells in blood involved in the adaptive immune response
Mycorrhizae
a symbiotic association between a fungus and the roots of a plant
Root nodule
a tumorlike growth on plant roots that contains symbiotic nitrogen-fixing bacteria
Immediate hypersensitivity
an allergic response mediated by vasoactive products released from IgE-sensitized mast cells
Beta (β)-lactam antibiotic
an antibiotic, including penicillin, that contains the four- membered heterocyclic β-lactam ring
T cell receptor (TCR)
an antigen-specific receptor protein on the surface of T cells
Hydroxypropionate pathway
an autotrophic pathway found in Chloroflexus and a few Archaea
Hypersensitivity
an immune response leading to damage to host tissues
Vaccine
an inactivated or weakened pathogen or innocuous pathogen product used to stimulate protective immunity
Delayed hypersensitivity
an inflammatory aller- gic response mediated by TH1 lymphocytes
Symbiosis
an intimate relationship between two organisms, often developed through prolonged association and coevolution
Autotroph
an organism that uses CO2 as its sole carbon source
Phototroph
an organism that uses light as an energy source
The reverse citric acid cycle is used to fix:
carbon
Immunity
the ability of an organism to resist infection
Adaptive immunity
the acquired ability to recognize and destroy a particular pathogen or its products, dependent on previous expo- sure to the pathogen or its products; also called specific immunity and antigen-specific immunity
Phycobiliprotein
the antenna pigment complex in cyanobacteria that contains phycocyanin and allophycocyanin or phycoerythrin coupled to proteins
Calvin cycle
the biochemical pathway for CO2 fixation in many autotrophic organisms
Denitrification
the biological reduction of NO3- to gaseous N compounds
Syntrophy
the cooperation of two or more microorganisms to degrade anaerobically a substance neither can degrade alone
Rumen
the first vessel in the multichambered stomach of ruminant animals in which cellulose digestion occurs
Sterilization
the killing or removal of all living organisms and viruses from a growth medium
Endotoxin
the lipopolysaccharide portion of the cell envelope of most gram- negative Bacteria, which is a toxin when solubilized
Nitrification
the microbial conversion of NH3 to NO3-
Minimum inhibitory concentration (MIC)
the minimum concentration of a substance necessary to prevent microbial growth
Innate immunity
the noninducible ability to recognize and destroy an individual pathogen or its products that does not rely on previous exposure to a pathogen or its products; also called nonspecific immunity
Virulence
the relative ability of a pathogen to cause disease