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medical sciences
biology
Brock Biology of Microorganisms 14th edition Michael Madigan, John Martinko, Kelly Bender, Daniel Buckley - Solutions
What is the endosymbiotic hypothesis for the origin of mitochondria and chloroplasts? What evidence supports this hypothesis?
What evidence supports the classification of life into three domains?
What major physiological and biochemical properties do Archaea share with Eukarya or with Bacteria?
Why are SSU rRNA genes good choices for phylogenetic studies, and what are their limitations?
Why is sequence alignment necessary prior to phylogenetic tree construction?
What is homoplasy and why does it create problems for molecular phylogenetic analyses?
Compare and contrast the physical and chemical conditions on Earth at the time life first arose with conditions today. From a physiological standpoint, discuss at least two reasons why animals could not have existed on early Earth. In what ways has microbial metabolism altered Earth’s biosphere?
For the following sequences, construct the phylogenetic tree that best depicts their evolutionary relationships. Taxon 1: ......... GTTCCCTTA Taxon 2: ......... GTTCGGTAT Taxon 3: ......... GAAAAACCCTAT Taxon 4: ......... CTTCCCTTT Taxon 5: ......... GTAAAACCCGAT
Imagine that you have discovered a new form of microbial life, one that appears to represent a fourth domain. How would you go about characterizing the new organism and determining if it actually is evolutionarily distinct from Bacteria, Archaea, and Eukarya?
What are the major differences between oxygenic and anoxygenic phototrophs?
Which inorganic electron donors are used by the organisms Ralstonia, Thiobacillus, and Acidithiobacillus?
Contrast classical nitrification with anammox in terms of oxygen requirements, organisms involved, and the need for monooxygenases.
Define the term substrate-level phosphorylation. How does it differ from oxidative phosphorylation? What compound(s) do fermentative bacteria need to synthesize in order to make ATP by substrate-level phosphorylation?
What are the major fermentation products of the following bacteria: Lactobacillus, Clostridium, Propionibacterium, Escherichia?
Give an example of a fermentation that does not employ substrate-level phosphorylation. How is energy conserved in this fermentation?
Why is syntrophy also called "interspecies H2 transfer"?
Why is NO3- a better electron acceptor for anaerobic respiration than is SO42-?
Why is the enzyme hydrogenase useful to Desulfovibrio even when it is not grown on H2 as electron donor?
Compare and contrast acetogens with methanogens in terms of (1) substrates and products of their energy metabolism, (2) ability to use organic compounds as electron donors in energy metabolism, and (3) phylogeny.
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?
Compare and contrast ferric iron reduction with reductive dechlorination in terms of (1) product of the reduction and (2) environmental significance.
How do monooxygenases differ from dioxygenases in terms of the reactions they catalyze? Why are oxygenases necessary for the aerobic catabolism of hydrocarbons?
How does a methanotroph differ from a methanogen? Which pathway for C1 assimilation found in methanotrophs is most energetically efficient and why?
How do denitrifying and sulfate-reducing bacteria degrade hydrocarbons anaerobically and without oxygenases?
What accessory pigments are present in phototrophs, and what are their functions?
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?
How is reducing power for autotrophic growth obtained in a purple bacterium? In a cyanobacterium?
How does the reduction potential (E0′) of chlorophyll a in PSI and PSII differ? Why must the reduction potential of PSII chlorophyll a be so highly electropositive?
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?
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?
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?
The growth rate of the phototrophic purple bacterium Rhodobacter 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
Although physiologically distinct, chemolithotrophs and chemoorganotrophs share a number of features with respect to the production of ATP. Discuss these common features along with reasons why the growth yield (grams of cells per mole of substrate consumed) of a chemoorganotroph respiring glucose
A fatty acid such as butyrate cannot be fermented in pure culture, although its anaerobic catabolism under other conditions occurs readily. How do these conditions differ, and why does the latter allow for butyrate catabolism? How then can butyrate be fermented in mixed culture?
When methane is made from CO2 (plus H2) or from methanol (in the absence of H2), various steps in the metabolic pathways are shared in common. Compare and contrast methanogenesis from these two substrates, highlighting the similarities and differences in the processes.
In what ways are sulfur-reducing bacteria different from sulfate-reducing bacteria and in what ways are they similar?
What are some ecological strategies that aerobic sulfide-oxidizers use to compete with the chemical oxidation of H2S by atmospheric O2?
What are some ways that diazotrophs protect nitrogenase from O2?
Compare and contrast the nitrogen metabolism of nitrifiers with that of denitrifiers.
In what ways are the dissimilative iron-reducing bacteria Shewanella and Geobacter similar and in what ways are they different?
Compare and contrast the metabolism of Gallionella and Geobacter. In what habitats might you find these organisms?
Which group of dissimilative iron-oxidizers is the least diverse and in what way is this related to oxygen and pH?
Contrast the metabolic characteristics of acetic acid bacteria and acetogens. What characteristic do they share and in what ways do they differ?
Compare and contrast the life cycle of Myxococcus with that of Bdellovibrio.
Contrast the life cycle of Hyphomicrobium with that of Caulobacter.
Describe the manner in which cell density regulates light production in luminescent bacteria.
Compare and contrast the metabolism, morphology, and phylogeny of purple sulfur and purple nonsulfur bacteria.
Compare and contrast the metabolism of purple nonsulfur bacteria and aerobic anoxygenic phototrophs
In what ways is Chloracidobacterium thermophilum similar to green sulfur bacteria and in what ways is it different?
With respect to sulfate-reducing bacteria, what is the difference between complete and incomplete oxidizers?
Describe a key physiological feature of the following Bacteria that would differentiate each from the others: Acetobacter, Methylococcus, Azotobacter, Photobacterium, Desulfovibrio, and Spirillum.
Describe the metabolism for each of the following Bacteria and state whether the organism is an aerobe or an anaerobe: Thiobacillus, Nitrosomonas, Ralstonia eutropha, Methylomonas, Pseudomonas, Acetobacter, and Gallionella.
Describe a key feature that would differentiate each of the following Bacteria: Streptococcus, Planctomyces, Verrucomicrobium, and Gemmata.
Describe a key physiological feature of the following Bacteria that would differentiate each from the others: Lactobacillus, Nitrospira, and Geothrix.
Why might Deinococcus thrive in soils that have been contaminated by radioactive fallout?
What morphological and physiological features distinguish Burkholderia cepacia from Pseudomonas aeruginosa? In what common environments might these organisms be encountered?
What is the catalase test? What catalase reaction would you expect from an obligate aerobe? What reaction would you expect from an obligate anaerobe?
What key features could be used to differentiate the following genera of gram-positive bacteria: Bacillus, Mycoplasma, Staphylococcus, Propionibacterium, Streptomyces, and Mycobacterium?
What traits do the chlamydia and the rickettsias have in common? In what ways do they differ? What is the function of each of the two types of cells formed by Chlamydia?
Enteric bacteria, lactic acid bacteria, and propionic acid bacteria have distinctive metabolic traits that can be used to characterize and identify these organisms. Describe the metabolic characteristics of these organisms, name a genus that belongs to each group, and indicate in what way these
Microorganisms can have a variety of different relationships with oxygen. Describe the terms used to characterize a cell’s response to oxygen, and give an example from this chapter of an organism that can be described by each of these terms.
How can organisms such as Halobacterium survive in a high-salt environment, whereas an organism such as Escherichia coli cannot? (Section 16.1)
What is unusual about the metabolism of S0 by Acidianus?
What is reverse DNA gyrase and why is it important to hyperthermophiles?
Why might H2 metabolism have evolved as a mechanism for energy conservation in the earliest organisms on Earth?
Contrast the roles of bacteriorhodopsin, halorhodopsin, and sensory rhodopsin in Halobacterium salinarum.
What two major physiological features unify species of Thermoplasmatales? Why does this allow some of them to successfully colonize coal refuse piles?
What is physiologically unique about Methanopyrus compared with another methanogen such as Methanobacterium? What is physiologically unique about Archaeoglobus?
How is Nanoarchaeum similar to other Archaea? How does it differ?
Why is it difficult to determine the phylogenetic placement of Nanoarchaeota and Korarchaeota?
What forms of energy metabolism are present in Crenarchaeota? What form is absent?
Using the phylogenetic tree in Figure 16.1 as a guide, discuss what indicates that bacteriorhodopsin may have been a late evolutionary invention and that anaerobic respiration with S0 as electron acceptor might have been an early evolutionary invention.
Defend or refute the following statement: The upper temperature limit to life is unrelated to the stability of proteins or nucleic acids.
If streptomycin blocks protein synthesis in organelles, what does this tell you about the organelles’ relationship to Bacteria?
What is the major difference between a mold and a yeast?
List the different types of sexual spores of fungi. Are conidia sexual or asexual spores?
How is the mating type of a yeast cell determined?
Distinguish between a primary and a secondary endosymbiosis. Which groups of protists are derived from which form of endosymbiosis?
Examine the phylogenetic tree of life in Figure 1.6b. In what ways and why does it differ from the tree in Figure 17.3?
Although both are slime molds, Dictyostelium and Physarum differ in major ways. Explain.
Explain why the process of endosymbiosis can be viewed as both an ancient event and a more recent event. What advantages could endosymbiosis give to both the endosymbiont and the host?
Summarize the evidence for endosymbiosis. How could the endosymbiotic hypothesis have originated before the era of molecular biology? How has molecular biology supported the theory?
What is the basis of the enrichment culture technique? Why is an enrichment medium usually suitable for the enrichment of only a certain group or groups of organisms?
Give an example of how environmental genomics has discovered a known metabolism in a new organism.
Why is environmental proteomics limited by natural abundance of microbial populations, whereas environmental genomics and metatranscriptomics are not so limited?
What are the major advantages of radioisotopic methods in the study of microbial ecology? What type of controls (discuss at least two) would you include in a radioisotopic experiment to show 14CO2 incorporation by phototrophic bacteria or to show 35SO42− reduction by sulfate-reducing bacteria?
How might you combine SIP and NanoSIMS to identify novel methane-consuming cells in a natural community?
What is the principle of the Winogradsky column, and what types of organisms does it serve to enrich? How might a Winogradsky column be used to enrich organisms present in an extreme environment, like a hot spring microbial mat?
Describe the principle of MPN for enumerating bacteria from a natural sample.
Why would the laser tweezers be a method superior to dilution and liquid enrichment for obtaining an organism present in a sample in low numbers?
What is the GFP? In what ways does a green fluorescing cell differ from a cell fluorescing from, for example, phylogenetic staining?
Compare and contrast the use of FISH and phylochips for enumerating microbial cells in natural environments. What advantages and limitations do each of these methods have?
Can nucleic acid probes in microbial ecology be as sensitive as culturing methods? What advantages do nucleic acid methods have compared with culture methods? What disadvantages?
How can a phylogenetic picture of a microbial community be obtained without culturing its inhabitants?
After PCR amplification of total community DNA using a specific primer set, why is it necessary to either clone or run DGGE on the products before sequencing them?
Design an experiment for measuring the activity of sulfur-oxidizing bacteria in soil. If only certain species of the sulfur oxidizers present were metabolically active, how could you tell this? How would you prove that your activity measurement was due to biological activity?
You wish to know whether Archaea exist in a lake water sample but are unsuccessful in culturing any. Using techniques described in this chapter, how could you determine whether Archaea existed in the sample, and if they did, what proportion of the cells in the lake water were Archaea?
Design an experiment to solve the following problem. Determine the rate of methanogenesis (CO2 + 4 H2 S CH4 + 2H2O) in anoxic lake sediments and whether or not it is H2-limited. Also, determine the morphology of the dominant methanogen (recall that these are Archaea, Section 16.2). Finally,
Design a SIP experiment that would allow you to determine which organisms in a lake water sample were capable of oxidizing the hydrocarbon hexane (C6H14). Assume that four different species could do this. How would you combine SIP with other molecular analyses to identify these four species?
How and in what way does an input of organic matter, such as sewage, affect the oxygen content of a river or stream?
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