Q&A Hero

Q: Organisms grown with CO2 as its sole carbon source must have energy in the form of ATP as well as reducing power.

Q: RubisCO converts ribulose bisphosphate and CO2 into two molecules of 3-phosphoglyceric acid (PGA).

Q: Photosystem I is responsible for splitting a water molecule in the first step of oxygenic electron flow.

Q: Chemolithotrophs that obtain electrons from donors such as sulfide use the same electron transport chains to obtain energy as chemoorganotrophs.

Q: Despite being called the reverse citric acid cycle, it is currently identified as the most ancient autotrophic pathway.

Q: Phototrophic purple bacteria such as Rhodobacter species grow ONLY by photosynthesis, using bacteriochlorophylls to harvest light.

Q: A bacterium that uses CO2 as an electron source but CANNOT use it as a carbon source is considered a mixotroph.

Q: The Calvin cycle provides autotrophs the ability to convert inorganic carbon into biomass and generate energy during this process.

Q: Photooxidation reactions can lead to the production of toxic forms of oxygen and the destruction of the photosynthetic apparatus.

Q: Each chlorophyll and bacteriochlorophyll type is distinguished by its absorption spectrum.

Q: Carotenoids are hydrophobic accessory pigments and vary widely in the color they can absorb.

Q: Chlorosomes are present in purple bacteria but absent in green sulfur and nonsulfur bacteria.

Q: Reaction centers ONLY indirectly receive photon energy via light-harvesting molecules.

Q: The light-harvesting pigments in Bacteria are classified as bacteriochlorophylls.

Q: The conversion of light into chemical energy is called photoautotrophy.

Q: What metabolism would be favored when there is a lack of electron acceptors? A) anaerobic fermentation B) anoxygenic photosynthesis C) anoxic ammonia oxidation D) acetogenesis

Q: Which of the following is NOT a potential reason anoxic methane-oxidizing Archaea have not also acquired the ability to reduce sulfate? A) An individual electron acceptor such as sulfate is not always present where methane is. B) Minimizing the metabolic requirements of the archaeon's genome size provides flexibility to interact with other reducing bacteria, such as nitrate reducers. C) The archaeon-bacterium relationship yields more energy from methane oxidation/sulfate reduction when performed together than separately. D) The methane-oxidizing Archaea will not easily acquire this metabolic capability from the bacterial partner.

Q: Organisms that aerobically catabolize methane use the intermediate ________ for biosynthesis and produce ________ when oxidizing the substrate for energy.A) CH2O (formaldehyde) / COB) CH2O (formaldehyde) / CO2C) HCOO (formate) / COD) HCOO (formate) / CO2

Q: What products would be expected to form during anoxic degradation of the seven-carbon compound benzoate following reduction and cleavage of the aromatic ring? A) 1 three-carbon compound and 1 four-carbon compound B) 1 three-carbon compound and 2 two-carbon compounds C) 2 three-carbon compounds and CO2 D) 3 two-carbon compounds and CO2

Q: The serine pathway and ribulose monophosphate pathway can both be used by ________ as a way to incorporate carbon into biomass. A) acetogens B) anoxygenic hydrocarbon fermenters C) methanogens D) methylotrophs

Q: Methanogens that use methyl-CoM for biosynthesis use ________ as a substrate. A) acetate B) carbon monoxide C) methane D) methanol

Q: A researcher lacked the necessary equipment to measure methane production so instead monitored CO2 concentration as the unknown archaeon grew and produced methane. Why might CO2 NOT decrease but methane still increase? A) An alternative carbon source such as methanol was used. B) CO2 is not a carbon source used by methanogens. C) CO2 was used an electron donor but not as a carbon substrate. D) Methanogenic Archaea containing carboxysomes likely made measuring small losses of CO2 difficult to conclude.

Q: How is ATP made by an acetogen during CO2 fixation? A) Electrons from metal cofactors energize the electron transport chain and drive the proton motive force to activate ATP synthase. B) Substrate-level phosphorylation of ADP occurs when coenzyme A is removed from acetyl-CoA. C) It is made by substrate-level phosphorylation and a Na+-translocating ATPase. D) The energized CO-CH3 complex during thioesterification drives a Na+-translocating ATPase.

Q: Anaerobic fermentation often provides CO2, which can be used by ________ as an electron acceptor for energy. A) acetogens B) methanotrophs C) methanogens D) acetogens and methanogens

Q: In Bacteria, the MOST common oxidized form of nitrogen is ________ and of sulfur is ________. A) nitrate / sulfate B) nitrate / sulfite C) nitrite / sulfate D) nitrite / sulfite

Q: Obligate anaerobes can often use ________ electropositive redox couples than facultative anaerobes, and ________ metabolism is most common in this group as well. A) lower / assimilative B) lower / dissimilative C) higher / assimilative D) higher / dissimilative

Q: Which metabolic strategy's existence suggests rapid growth is NOT always the best strategy to survive in the environment? A) anaerobic fermentation B) disproportionation C) methylotrophy D) syntrophy

Q: A bacterium that catabolizes a compound by linking ion pumps to establish a proton or sodium motive force for energy A) can circumvent substrate-level and oxidative phosphorylation. B) makes insufficient energy to grow but enough for cellular maintenance to survive. C) requires a second bacterium to cooperatively drive the gradient. D) still requires another carbon substrate to provide a carbon source.

Q: The foul-smelling putrescine byproduct suggests activity of A) amino acid fermentation by clostridia. B) secondary fermentation. C) sulfur-oxidizing bacteria. D) syntrophic carbohydrate metabolism.

Q: Glucose fermentation by Clostridium spp. produce ATP only when acetate and butyrate are produced. Why do these organisms produce acetone and butanol after strong initial activity of generating ATP with acetate and butyrate byproducts? A) Acetate and butyrate accumulation creates a deadly acidic environment, which acetone and butanol do not. B) Acetate and butyrate are no longer needed for biosynthetic pathways. C) Acetone and butanol serve as better sources for NAD(P)+ reduction. D) Acetone and butanol production is favored for stability to store intracellular carbon sources for potential nutrient poor conditions.

Q: Which of the following reactions is classified as a heterofermentation? A) hexose 2 lactate + 2 H+ B) HCOOH H2 + CO2 C) glucose lactate + ethanol + CO2 + H+ D) fructose 3 acetate + 3 H+

Q: What would likely occur if an anammox bacterium was unable to use ladderane lipids? A) Ammonium rather than ammonia would be used due to ammonia toxicity to other cellular processes. B) It would require a different source for carbon assimilation. C) Rates of anammox would be considerably slower due to a lack of localized metabolism. D) Reactive nitrogen species would kill the cell.

Q: Anammox is an anaerobic process that generates energy from ________ and forms N2. A) ammonia B) ammonium C) ammonia and nitrate D) ammonia and nitrite

Q: Which of the following are NOT found within the photosynthetic gene cluster of Rhodobacter (a purple phototrophic bacterium)? A) genes encoding reaction center and light-harvesting photocomplexes B) genes encoding proteins involved in phycobiliprotein biosynthesis C) genes encoding proteins involved in bacteriochlorophyll biosynthesis D) genes encoding proteins involved in carotenoid biosynthesis

Q: The only organisms that perform photosynthesis are ones that produce some form of A) chlorophyll or bacteriochlorophyll. B) carotenoids. C) phycoerythrin. D) phycocyanin.

Q: A cell that lacks sulfite oxidase but can still oxidize sulfur for energy could be identified by A) adenosine phosphosulfate reductase coupled with substrate-level phosphorylation. B) electrons being transferred to cytochrome c prior to shuttling them into the electron transport chain. C) identifying an alternative quinone, flavoprotein, or cytochrome. D) quantifying the release of sulfate byproduct.

Q: What metabolic advantage do cells have in storing the elemental sulfur byproduct from sulfide oxidation? A) The cells avoid producing transport energy waste to secrete the sulfur. B) The byproduct serves as an electron reserve for subsequent oxidation. C) Sulfur decreases the intracellular acidification for non-acid-tolerant sulfide oxidizers. D) The byproduct can be used for other biosynthetic pathways that use sulfur, such as Rieske Fe-S proteins.

Q: What type of methods are used in microbial systematics? Why are multiple methods used to characterize and classify microbial species? Be sure to define the methods and describe the general strengths and weaknesses of each type.

Q: Draw a graph of relative fitness and number of mutations of an evolving strain versus the ancestral strain over 20,000 generations under the same growth conditions. Explain the change in fitness and mutations over time using evolutionary concepts and terms.

Q: Can gene frequencies change in the absence of selection? Why or why not?

Q: Explain the strengths and limitations of using 16S rRNA for phylogenetic analyses.

Q: How does the Black Queen Hypothesis explain the effect of gene deletions on bacterial evolution?

Q: Life is believed to have originated at hydrothermal springs on the ocean floor rather than on near the surface of Earth. What conditions made the hydrothermal springs the likely place for the beginning of life? Relate the conditions of the early oceans to the likely metabolism of the first cells.

Q: How did cyanobacteria, oxygen, and ozone impact the evolution of eukaryotic cells?

Q: Rhodobacter cells perform photosynthesis in the presence of light and grow heterotrophically in the dark. After being cultured in total darkness for multiple generations phenotypic and genotypic changes occur. What phenotypic changes occur and what evolutionary processes are driving them?

Q: You have isolated a microbe from an environmental sample. The microbe has the ability to perform a new metabolic reaction at a very low temperature, so you are excited that it could be a new species. What experiments should you perform to determine if your isolate is truly a new species? What process will you follow to officially name your isolate?

Q: Construct a chart to demonstrate the molecular features of the primary domains of life. Why are there overlapping or shared molecular features between all three domains? Relate the shared and unique molecular features of each domain to early evolution, the last universal common ancestor (LUCA), and the evolution of the three domains

Q: Why is the biological species concept useful for Eukarya but not meaningful for Archaea and Bacteria? How are prokaryotic species defined?

Q: Carl Woese was an important figure in microbial classification and changed our understanding of the evolution and diversity of life. What breakthrough did he make that allowed us to infer evolutionary relationships between organisms? What assumptions was his breakthrough based on?

Q: Describe the hydrogen hypothesis and why it is favored over other hypotheses.

Q: Explain the endosymbiotic theory. What is the evolutionary value of endosymbiosis?

Q: Draw a rooted phylogenetic tree containing seven organisms labeled A to G. Label your tree with the following terms: branches, extant taxa, nodes, last common ancestor, and an outgroup.

Q: Lateral gene transfer is one plausible explanation as to why organisms in Archaea, Bacteria, and Eukarya still share so many genes among such distinct domains.

Q: When exposed to UV light, oxygen gas produces ozone gas.

Q: Approximately 4 billion years ago Archaea and Bacteria diverged as being distinct from each other.

Q: All unicellular organisms belong to the same domain of life.

Q: The primary domains were founded based on comparative ribosomal RNA gene sequencing.

Q: Oxygen was a driving factor in the formation of eukaryotic cells.

Q: In taxonomy, family is a more general term than order.

Q: One phenotypic trait used for species identification and description is the analysis of the types and proportions of the fatty acids present in the cytoplasmic and outer membranes. The methodology employed is often nicknamed FAME.

Q: DNA:DNA hybridization is a sensitive method for revealing subtle genetic differences because it measures the degree of sequence similarity between two genomes.

Q: The 16S rRNA sequence is an approximately 1,500 bp linear strand of single stranded RNA.

Q: The hyperthermophilic members of the Crenarchaeota branch very close to the root of the universal tree.

Q: At present there are four phyla in the domain Bacteria.

Q: Most bacterial phyla lack strong phenotypic cohesiveness.

Q: Microbial species are difficult to define because they are often polyphyletic.

Q: The domains of life arose as barriers between gene exchange evolved between organisms.

Q: Prior to rRNA sequencing and the use of molecular phylogeny, Bacteria and Archaea were classified as in a single group of simple organisms called the Monera.

Q: Sequencing technology and molecular phylogenetic analyses have had very little impact on our understanding of the evolution and diversity of life on Earth.

Q: Two organisms containing identical GC ratios are not necessarily related.

Q: Eukaryotes originated after the rise in atmospheric oxygen.

Q: The establishment of DNA as the genome of the cell may have resulted from the need to store genetic information in a more stable form than RNA.

Q: The earliest nucleic acid was probably a simple DNA molecule.

Q: The atmosphere of primitive Earth is usually classified as an oxidizing atmosphere.

Q: Systematic analysis now commonly includes ________ to identify, characterize, and determine relationships between new strains of bacterial species. A) whole genome analysis B) microscopy C) staining D) pigments

Q: Multilocus sequence typing involves sequencing several different A) genomes. B) housekeeping genes. C) tRNA genes. D) rRNA genes.

Q: One widely used cladistic method of examining evolutionary relationships is ________, which is based on the assumption that evolution is most likely to have proceeded by the path requiring fewest changes. A) topology B) neighbor joining C) parsimony D) systematics

Q: The evolutionary history of a group of organisms is called its ________ and it is inferred from ________. A) taxonomy / phenotype B) phylogeny / nucleotide sequence data C) phylogeny / phenotype D) taxonomy / morphology

Q: The first catalytic and self-replication biological molecule was most likely A) RNA. B) DNA. C) proteins. D) ATP.

Q: ________ formed the semipermeable membrane-like surfaces for the earliest life forms. A) Proteins B) Hydrogen sulfide C) Lipid bilayers D) RNA