Q&A Hero

Q: Ignicoccus has several unique structural features that have lead scientists to propose that it may be the modern descendent of the ancestral cell type that gave rise to the origin of eukaryotic cells. What are the unique features of Ignicoccus and why do they support this hypothesis?

Q: Hyperthermophilic Archaea have been found to contain dibiphytanyl tetraether lipids. Why are these lipids different from lipids present in non-hyperthermophiles? What special properties and structures do they confer?

Q: Why does Archaeoglobus represent a metabolically transitional type of organism that bridges the energy-generating processes of H2S production and methanogenesis?

Q: Explain why the presence of many Archaea has been confirmed only by community sampling of rRNA genes and not by culture in the laboratory. How has metagenomics helped to solve this problem?

Q: Describe two mechanisms that Archaea use to avoid their DNA melting at temperatures above 100C.

Q: What makes the lifestyle and genome of Nanoarchaeum equitans unique?

Q: The amino acid composition of thermostable proteins is not particularly unusual, except for a bias for increased levels of amino acids that form α-helices.

Q: While many Archaea are bacilli or cocci, unusual morphologies such as square, flattened and irregular discs have also been identified in certain species.

Q: Archaeal histones assist in maintaining the DNA in a double-stranded form at very high temperatures in species of Euryarchaeota.

Q: When retinal in bacteriorhodopsin becomes excited, it directly catalyzes the formation of ATP.

Q: A small, heat-stable DNA-binding protein present in the cells of some Archaea, called Sac7d, binds to the minor groove of DNA in a very specific manner and increases its melting temperature by 40C.

Q: With few exceptions, hyperthermophilic crenarchaeotes are obligate aerobes.

Q: Some crenarchaeotes have growth optima above the boiling point of water (at atmospheric pressure).

Q: Archaeoglobus is a true sulfate reducer that forms a phylogenetically distinct lineage within the Euryarchaeota.

Q: The cytoplasmic membrane of Picrophilus is extremely acid impermeable at very low pH.

Q: Thermoplasma contains an extremely small genome complexed with a highly basic DNA-binding protein.

Q: Thermoplasma grows either aerobically or anaerobically by sulfur respiration.

Q: Halophilic Archaea are the only inhabitants of highly saline environments.

Q: Thermoplasma metabolizes organic compounds leached from hot coal refuse.

Q: Methanogenesis is coupled with proton motive force formation and ATP synthesis through the activity of ATPases.

Q: Though the known diversity of acetotrophic methanogens is low, they are ecologically significant in nature.

Q: Despite GC pairs having an additional hydrogen bond than AT pairs, hyperthermophilic Archaea generally have a lower GC ratio in their genomes when compared to other heat-sensitive prokaryotes.

Q: Pseudopeptidoglycan (pseudomurein) is part of the cell wall of some methanogens.

Q: The light-stimulated proton pump of Halobacterium salinarum indirectly functions to pump sodium out of the cell by the activity of a Na+/H+ antiport system.

Q: Many halophiles require a high ionic environment for survival.

Q: Replacing sodium with potassium can satisfy the requirement for sodium in the halobacteria.

Q: Most halobacteria are motile by means of lophotrichous flagella.

Q: Thus far, only Archaea have been found in the salt lakes, while Bacteria and Eukarya are noticeably absent.

Q: In chemolithotrophic Archaea, H2 is a common electron donor.

Q: There are many genes in archaealgenomes that have no known function.

Q: Some Archaea are chemoorganotrophs and use organic compounds as electron donors for energy metabolism.

Q: Although the domain Archaea contains many acidophilic organisms, there are still many others within the domain that grow well in environments with a neutral pH.

Q: Most of the Archaea are phenotypically quite similar.

Q: In general, the cold-dwelling thaumarchaeotes are evolving more slowly than the hyperthermophilic crenarchaeotes.

Q: Many hyperthermophiles are chemolithoautotrophs.

Q: Archaea is divided into three phyla.

Q: The rRNA gene sequences of hyperthermophilic Archaea and Bacteria have diverged ________ over time, likely due to ________. A) relatively little / strong constraints on sequence changes at higher temperatures B) substantially / higher mutation rates at higher temperatures C) relatively little / low mutation rates in these ancient organisms D) substantially / DNA damage at higher temperatures

Q: Nitrifying Archaea such as Nitrosopumilus maritimus use ________ as a sole carbon source and are capable of obtaining sufficient energy by aerobically oxidizing ________. A) CO2 / NO B) sugars / NH3 C) CO2 / NH3 D) organic acids / NO

Q: The bioenergetics of anaerobic respiring Archaea such as those of the Crenarchaeota involve ________ from which ________ is synthesized. A) proton translocation / ATP B) substrate level phosphorylation / ATP C) sodium translocation / ATP D) substrate level phosphorylation / GTP

Q: Nitrifying Thaumarchaeota outcompete nitrifying bacteria in many aquatic and terrestrial environments becauseThaumarchaeota A) are well-adapted to high salinity and extreme UV irradiation. B) are well-adapted to temperature extremes. C) are well-adapted to very low nutrient and electron donor concentrations. D) have very resistant specialized cells that survive long periods of dehydration and nutrient starvation.

Q: It is difficult to estimate when cyanobacteria appeared on Earth using evidence from the oxidation state of the Earth's crust, because A) several abiotic reactions could have formed Fe3+. B) there are multiple forms of anoxygenic photosynthesis. C) there are multiple groups of oxygenic photosynthetic bacteria. D) several ancient anaerobic metabolisms form Fe3+.

Q: Cyclic 2,3-diphosphoglycerate (cDPG) is present in molar quantities in the cytoplasm of many hyperthermophilic methanogens. The function of this compound is to A) prevent rRNA misfolding. B) prevent chemical damage to DNA at high temperatures. C) counteract the effects of high osmotic environments. D) activate hydrogen gas.

Q: The topoisomerase ________ introduces positive supercoils in DNA, which stabilizes DNA and prevents the DNA helix from denaturing at high temperatures. A) reverse ligase B) ligase C) DNA gyrase D) reverse DNA gyrase

Q: Proteins known as ________ function to refold partially denatured proteins. A) histones B) chaperonins C) HU proteins D) histones and chaperonins

Q: Hot sulfur-rich environments associated with terrestrial sulfur-rich springs are called A) acid-mine drainage. B) hydrothermal vents. C) solfataras. D) terrestrial volcanoes.

Q: Crenarchaeotes whose optimal growth temperature is over 80C are called A) hyperthermophiles. B) thermophiles. C) extreme halophiles. D) halophiles.

Q: The cytoplasmic membrane of Thermoplasma contains a lipopolysaccharide-like material called lipoglycan which A) behaves like peptidoglycan and creates a strong cell wall. B) forms a monolayer that stabilizes the cytoplasmic membrane. C) contains ether linkages. D) contains ether linkages and forms a monolayer that stabilizes the cytoplasmic membrane.

Q: The ribosomes of Halobacterium require high ________ levels for stability and activity. A) KCl B) NaCl C) NaSO4 D) acidic amino acids

Q: Compatible solutes counteract the tendency of a cell to become A) buoyant in high ionic strength environments. B) hyperosmotic in low ionic strength environments. C) dehydrated in high ionic strength environments. D) viscous in low ionic strength environments.

Q: Extremely halophilic Archaea often form ________ in order to access ________. A) stalks / nutrients B) intracellular inclusions / elemental sulfur C) gas vesicles / oxygen D) intracellular membranes / sunlight

Q: The most common electron donor among hyperthermophilic Archaea is A) Fe+3. B) H2. C) SO4. D) So.

Q: What is thought to be the maximum temperature for life to exist? A) 125C B) 150C C) 250C D) 500C

Q: Thermostable proteins tend to have additional features that improve thermostability. Which of the following is NOT one of these features? A) increased ionic interactions on the protein surfaces B) highly hydrophilic cores C) decreased tendency of the protein to unfold D) highly hydrophobic cores

Q: Laboratory isolation of Nanoarchaeum equitans requires the presence of A) fatty acids. B) oxygen. C) Ignicoccus. D) sunlight.

Q: Halobacterium salinarum and certain other extreme halophiles carry out light-driven synthesis of ATP under what condition? A) low oxygen concentrations B) low light C) high oxygen concentrations D) high carbon dioxide concentrations

Q: Cellular integrity and cell wall stabilization of the Halobacterium are aided by A) potassium ions. B) chloride ions. C) magnesium ions. D) sodium ions.

Q: Compare and contrast the human pathogens and non-pathogens in Clostridium. Propose a reason for why this differentiation is challenging to assay in the laboratory (NOT on living eukaryotic animal models).

Q: Select a group within Bacteria that has a rare structural morphology observable with a microscope. Describe the appearance, the group that it corresponds to, and another group that would certainly be ruled out when observing such a morphology.

Q: Considering the evolution of Bacteria, the criteria used for taxonomy, and the genetic requirements for individual metabolic pathways, explain how it is unlikely to observe three genera of the same family where one genus has strict anaerobes that degrade only small aromatics, another genus degrades large molecular weight sugars aerobically, and a third is a photoautotroph.

Q: Describe the stages chlamydia cells go through during infection of human cells and the significance for the key steps in the cycle.

Q: Which group of bacteria is most famous for their diversity of antibiotics produced? Hypothesize an ecological role production of these antibiotics might have in such environments where they are not produced at high enough levels to kill bacteria.

Q: Even to a well-trained microbiologist, isolates of Streptomyces when grown on a nutrient agar plate can appear as though they are fungi. Describe key similarities of how these two unrelated groups can so easily be mistaken for each other, and then propose methods to conclusively distinguish between them.

Q: Cytophaga columnaris causes columnaris (or "cottonmouth") disease in fish such as salmon. Based on the taxonomic group this species is a part of, predict some of the activities this bacterium has during infection of fish. Also mention a related taxon that likely has some of the same functions and another taxon that does not.

Q: Explain how the enteric bacteria can be differentiated by the type and proportion of fermentation products produced by the anaerobic fermentation of glucose.

Q: Proteobacteria members thrive in soils and occur at high concentrations as well. Other bacterial taxa are considered much less diverse in terms of their metabolic capabilities. Due to the role isolation has in discovering metabolic pathways, consider how obtaining hundreds of new isolates from a less studied phylum might change our views on metabolic diversity. Predict how the results of discovering another highly metabolically diverse group might be handled in terms of taxonomic assignment.

Q: During stationary phase, group members of Serratia produce prodigiosins that contain pyrrole. Considering its structural relatedness to other pyrrole-containing molecules of known function (e.g., chlorophylls, bacteriochlorophylls, porphyrins), propose a potential ecological role for these compounds in soil where they are involved in something other than photosynthesis.

Q: Antibiotics that disrupt or halt cell wall biosynthesis are actually ineffective at harming growth of mycoplasmas.

Q: Some species in the genus Acidobacteria are classified in Bacteria while others are considered Archaea.

Q: Deinococcus radiodurans is capable of withstanding especially high levels of radiation, and the carotenoids they produce enhance this resistance.

Q: The hypothesis that H2 was a key electron donor for energy metabolism in primitive organisms is supported by it being such a common trophic strategy in Aquificae.

Q: Thermotoga are hyperthermophiles and appear relatively closely related to Archaea in comparison to other bacteria such as Salmonella.

Q: When looking under a transmission electron microscope, you observe anammoxosomes in one bacterium and pirellulosome in another bacterium. BOTH taxa are likely a part of Planctomycetes.

Q: Chlamydiae are MOST commonly transmitted throughout environments by insects.

Q: Some Streptomyces spp. can biosynthesize several chemically unrelated structures that act as different antibiotics.

Q: Except that they are not produced in the cytoplasm, conidia produced by Streptomyces spp. are chemically quite similar in composition to endospores produced by Bacillus spp.

Q: Due to the slow and varied growth rates, mycobacteria are commonly grouped into either slow growing or very slow growing, which has consequences on the growth medium selected for culturing.

Q: Simple staining and microscopy could easily distinguish the different taxa intermixed within a community of Sarcina, Staphylococcus, and coryneform bacteria.

Q: Many Listeria spp. grow well at cold temperatures, so although refrigeration is excellent at preventing growth of most other pathogens, it is not very useful at minimizing growth of contaminated foods.

Q: To subgroup the lactic acid bacteria, which are incapable of aerobic degradation and only do fermentation, identifying products formed is a useful way to distinguish homofermentative versus heterofermentative lactic acid bacteria.

Q: Sulfur metabolism is a common trait in Deltaproteobacteria.