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Questions and Answers of Biology

Why are OMZs of harm to macrobiological marine life?
Many pelagic prokaryotes can use light energy but are not considered “phototrophs” in the same sense as cyanobacteria or purple bacteria. Explain.
What is the difference between piezotolerant and piezophilic bacteria? Between these two groups and extreme piezophiles? What properties do piezotolerant, piezophilic, and extremely piezophilic
Why are chemolithotrophic bacteria so prevalent at hydrothermal vents?
In what forms does potential energy enter a microbial ecosystem? Which energy classes of microorganisms can exploit each?
Explain why both obligately anaerobic and obligately aerobic bacteria can often be isolated from the same soil sample.
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?
How are nutrients for microbial growth replenished in the deep subsurface as opposed to the near subsurface?
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
Keeping in mind that the open-ocean waters are highly oxic, predict the possible metabolic lifestyles of open-ocean Archaea and Bacteria. Why might rhodopsin-like pigments be more abundant in one
Global warming has been suggested to result in reduced transfer of oxygen to deeper waters in the ocean. How might global warming also result in reduced nutrient availability to planktonic species in
Why can it be said that the carbon and nitrogen cycles are “coupled”?
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
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
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
Why are most iron-oxidizing chemolithotrophs obligate aerobes and why are the better-studied iron oxidizers acidophilic?
In what ways are Ca and Si cycling in ocean waters similar, and in what ways do they differ? How do the calcium and silica cycles couple to the carbon cycle?
How are Hg2+ and CH3Hg+ detoxified by the mer system?
What negative effects on the oceans do rising CO2 levels have?
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?
Carbon can be sequestered in the ocean in a variety of forms. Discuss the different forms, their biological sources, and how global warming will influence them.
Why is the presence or absence of sulfate (SO42−) so important in the extent of metal corrosion? Why is the presence or absence of sulfate (SO42−) so important in the extent of metal corrosion?
What types of structures are subject to crown corrosion? Why is sulfate important here as well as in metal corrosion?
Which Bacteria and Archaea play a major role in acid mine drainage? Why do they carry out the reactions that they do? Why is air necessary for this process?
Describe a strategy for bio remediating a site that contains buried nuclear weapons that are leaking uranium. What could thwart your bioremediation efforts?
What physical and chemical conditions are necessary for the rapid microbial degradation of oil in aquatic environments? Design an experiment that would allow you to test which conditions optimized
What are xenobiotic compounds and why might microorganisms have difficulty catabolizing them?
Trace the treatment of wastewater in a typical plant from incoming water to release. What is the overall reduction in the BOD fortypical household wastewater? What is the overall reduction in the BOD
Why is advanced wastewater treatment desirable from an environmental point of view?
Identify (stepwise) the process of purifying drinking water. What important contaminants are targeted by each step in the process?
Discuss the microbial habitats that develop within drinking water distribution and premise plumbing systems. How do microorganisms persist in the presence of chlorine? What features of the
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
Why is reduction of BOD in wastewater a primary goal of wastewater treatment? What are the consequences of releasing wastewater with a high BOD into local water sources such as lakes or streams?
Discuss the microbial ecology contributing to crown corrosion of concrete sewer lines. In consideration of this ecology, what intervention strategies might be useful in reducing or eliminating
Describe the similarities and differences between the lichen and coral symbioses.
How is it possible for aphids to feed only on the carbohydrate- rich but nutrient- poor sap of phloem vessels in plants?
How is the correct bacterial symbiont selected in the squid– Aliivibrio symbiosis?
How does a tube worm obtain nutrients if it lacks a mouth, gut, and anus?
Compare the microbial communities in the medicinal leech crop, intestinum, and bladder.
How does the body plan of corals influence their ability to symbiotically associate with Symbiodinium?
In the “ Chlorochromatium” symbiosis, how does each partner benefit?
Describe the steps in the development of root nodules on a leguminous plant. What is the nature of the recognition between plant and bacterium and how do Nod factors help control this? How does this
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?
How do mycorrhizae improve the growth of trees? In what way(s) are the root nodule and mycorrhizal symbioses similar?
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
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?
What is a possible mechanism by which the microbial community of the human gut increases energy recovery, thereby contributing to obesity?
Why was Escherichia coli long thought to be a dominant member of the human gut microbial community?
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
Identify organs in the human body that are normally colonized by microorganisms. Which organs are normally devoid of microorganisms? What do the organs in each set have in common?
Identify the structural features, origins, and major effects of endotoxins.
Identify at least four mechanisms by which a healthy host resists infection.
Identify common factors that can lead to host compromise. Which factors are controllable by the host? Which factors are not controllable by the host?
Describe the microenvironments in the oral cavity. How can anaerobic bacteria survive in the mouth?
How do pH and oxygen affect the microbial communities that grow in each different region of the gastrointestinal tract?
Describe the relationship between Lactobacillus acidophilus and glycogen in the vagina. What factors influence the differences between the normal vaginal flora of adult females as compared to that of
Define virulence and identify parameters to distinguish between highly virulent and moderately virulent pathogens.
Identify the role of the capsule and the fimbriae of bacteria in microbial adherence.
Explain the role of the availability of nutritional factors in infection by microorganisms in the body.
Distinguish between the mechanism of cytotoxins and AB toxins. Provide at least one example of each.
Mucous membranes are barriers against colonization and growth of microorganisms. However, mucous membranes, for example in the mouth and gut, are colonized with a variety of different microorganisms,
Coagulase is a virulence factor for Staphylococcus aureus that acts by causing clot formation at the site of S. aureus growth. Streptokinase is a virulence factor for Streptococcus pyogenes that acts
Although mutants incapable of producing exotoxins are relatively easy to isolate, mutants incapable of producing endotoxins are much harder to isolate. From what you know of the structure and
What is the origin of the phagocytes and lymphocytes active in the immune response? Track the maturation of B cells and T cells.
Describe the general mechanism used by superantigens to activate T cells. How does superantigen activation differ from T cell activation by conventional antigens?
Identify the cells that express pattern recognition receptors (PRRs). How do PRRs associate with pathogen-associated molecular patterns (PAMPs) to promote innate immunity?
Identify the lymphocytes and the antigen-specific receptors involved in cell-mediated adaptive immunity.
Identify the lymphocytes and the antigen-specific receptors involved in antibody-mediated adaptive immunity.
Identify the cells that initiate inflammation and the cells that are activated by inflammatory signals.
The acellular pertussis vaccine uses a biotechnology-based immunization strategy that has been adapted for this approved vaccine. What advantages does the biotechnology-based vaccine have over a
Define the differences between immediate and delayed-type hypersensitivity in terms of immune effectors, target tissues, antigens, and clinical outcome.
Describe the relative importance of innate immunity compared to adaptive immunity. Is one more important than the other? Can we survive in a normal environment without immunity?
Inflammation is the hallmark of an active immune response. Explain how inflammation is triggered by both innate and adaptive immune mechanisms. Are the inflammatory cells the same for both methods of
Are superantigen reactions desirable for the host? Do they confer protection for the host or do they benefit the pathogen?
Identify some pathogen-associated molecular patterns (PAMPs) that are recognized by pattern recognition receptors (PRRs). What is the significance of the interactions between these molecules?
Describe the complement system. Is the order of protein interactions important? Why or why not? Identify the components of the mannose-binding lectin pathway for complement activation. Identify the
Explain how phagocytes engulf and kill microorganisms, with particular attention to oxygen-dependent mechanisms.
What molecules induce immune responses? What properties are necessary for a molecule to induce an immune response?
Describe the basic structure of class I and class II major histocompatibility complex (MHC) proteins. In what functional ways do they differ?
Differentiate between Tc cells and NK cells. What is the activation signal for each cell type?
How do Th cells differ from Tc cells? Differentiate between the functional roles of Th1, Th2, Th17, and Treg cells.
Identify the cell interactions in production of antibodies by B cells.
Describe the potential problems that would arise if a person had an acquired inability to phagocytose pathogens. Could the person survive in a normal environment such as a college campus? What
Specificity and tolerance are necessary qualities for an adaptive immune response. However, memory seems to be less critical, at least at first glance. Define the role of immune memory and explain
What problems would arise if a person had a hereditary deficiency that resulted in an inability to present antigens to Tc cells? What would the problems be if the person had a deficiency in
Antibodies of the IgA class are probably more prevalent than those of the IgG class. Explain this and define the benefits this may have for the host.
Do you agree with the following statement? Complement is a critical component of antibody-mediated defense. Explain your answer. What might happen to persons who lack complement component C3? C5?
What are the major cytokines and their effects in an antibody-mediated response? In a Th1-mediated response?
Define the criteria used to assign a gene and its encoded protein to the Ig gene superfamily.
Identify the major structural features of class I and class II MHC proteins.
Polymorphism implies that each different MHC protein binds a different peptide motif. For the MHC class I polymorphisms, how many different MHC proteins are expressed in an individual? By the entire
Which Ig chains are used to construct a complete antigen-binding site? Which domains? Which CDRs?
Calculate the total number of germ-line-encoded VH and VL domains that can be constructed from the available Ig genes. Compare this to the numbers of germ-line-encoded Vβ and Vα domains of the TCR.
In TCRs, diversity can be generated by recombination and reassortment events as in Igs. As is the case in Igs, additional diversity is generated with somatic events such as N nucleotide additions and
Explain positive and negative selection of T cells.
What molecular interactions are necessary for activation of uncommitted T cells? For activation of uncommitted B cells?
Identify the consequences of a genetic mutation that eliminates a PRR by predicting the outcome for the host. Do this for at least one soluble PRR and one membrane-bound PRR.
Polymorphism implies that each different MHC protein binds a different peptide motif. However, for the MHC class I proteins, only 6 peptide motifs can be recognized in an individual, whereas over
Although genetic recombination events are important for generating significant diversity in the antigen-binding site of Igs, post-recombination somatic events may be even more important in achieving
What would be the result of activation of all T cells that contact antigen? How does the multiple signal mechanism prevent this from happening?

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