Ch. 17-19 - Final HW

With respect to O2 requirements, most methanogens are which of the following?

strict anaerobes Methanogens gain energy through redox reactions that generate methane from substrates such as CO2 and H2, formate, and acetate. They require association with bacterial species that generate the needed substrates. All types of methanogenesis are poisoned by molecular oxygen and therefore require strict anaerobic conditions for growth.

Which of the following protozoans is not an example of a parasitic apicomplexan?

Trypanosoma brucei Unlike the apicomplexans T. gondii, P. falciparum, and C. parvum, which are nonmotile, T. brucei is a obligate parasite of the group Euglenida and possesses flagella. It causes the disease African sleeping sickness, which is transmitted by the tsetse fly.

Which of the following conditions would increase the accuracy of a molecular clock?

- Average mutation rates are constant across generations and between organisms. - Organisms have similar generation times - Gene sequences are orthologous (same function) Accurate resolution of phylogenies depends on the appropriate choice of a molecular clock (genetic sequence). The underlying premise is that any observed sequence changes are the result of random mutations that accumulate over time. For this reason, the molecular clock sequences should have the same function (not be subject to different selective pressures) and have constant mutation rates across generations and within the organisms under study. Ideally, the organisms should also have similar generation times so that the number of generations per unit time (and therefore opportunities for mutation) are as close as possible. The gene sequences in question should also be essential for cellular function and transmitted vertically from parent to daughter cells instead of being acquired by horizontal gene transfer.

Cellular structures shared by ALL eukaryotes and prokaryotes include which of the following?

- cytoplasm - cell membrane - DNA - ribosomes Genetic material that stores the information to make a cell's protein; ribosomes that provide the platform for protein synthesis; a selectively permeable cell membrane for transport of molecules in and out of a cell; and cytoplasm, which is composed mainly of water, salts, and proteins make up the most basic components of cells. Other structures such as a cell wall, chloroplasts, and other membrane-bound organelles are not found in prokaryotic cells, although they are found in some eukaryotes.

Which of the following are considered requirements for the emergence of life?

- essential elements for org molecules - water (l) - continual source of energy Life as we know it requires essential elements for creating organic molecules, a favorable temperature range for liquid water (the required solvent for biochemical reactions), and energy (sunlight) to build and maintain biological order. However, RNA (not DNA) was probably the first informational molecule, and early life forms did not respire oxygen. In fact, oxygenation of the atmosphere did not occur until after the appearance of the cyanobacteria.

The two major genera of Gram-positive bacteria include the _______________ , which contains the endospore-forming genera (e.g., Bacillus and Clostridium), and the _______________, which contains some filamentous forms (e.g., Streptomyces) that produce exospores.

- low GC Firmicutes - high GC Actinobacteria The two major phyla of Gram-positive bacteria are distinguished primarily on the basis of their GC genomic content. Evidence from sequencing data suggests that endospore-formation was an ancestral trait of Firmicutes that was subsequently lost during evolution of such genera as Lactobacillus, Streptococcus, Staphylococcus, etc. Similarly, only some groups within the Actinobacteria, (including the largest genus, Streptomyces) produce exospores on aerial mycelia.

Which of the following traits of bacterial cells differ significantly from the other domains of life?

- peptidoglycan in cell envelope - translation elongation factors - type of RNA polymerase Cells in all domains of life have DNA as their genetic material and share the same basic genetic code (3-bp codons that specify amino acids). Only bacteria, however, contain peptidoglycan in their cell walls, and thus, this molecule is an excellent target for antibiotics. Most components of the bacterial transcription and translation machinery (e.g., RNA polymerase, rRNA, translation elongation factors) have also significantly diverged from the other domains and are good targets for antibiotics. However, very few antimicrobial agents target bacterial plasma membranes. This is because the phospholipid membranes of bacteria and eukaryotes are very much alike (although quite different from archaea).

Halophilic Euryarchaeota that inhabit thalassic lakes adapt to high external_____ concentrations by maintaining a high intracellular concentration of _____

- sodium chloride - potassium chloride Extremely halophilic archaea, members of the class Haloarchaea, require at least 1.5 M NaCl or an equivalent ionic strength in their external environment. Haloarchaea adapt to this high external NaCl by maintaining a high intracellular concentration of potassium chloride (about 4 M KCl).

Identify the general characteristics found in the archaeal cell membrane versus those observed in bacteria.

ARCHAEA - L-glycerol - side chains composed of isoprenoid units - membrane fluidity maintained by covalent cross linking of side chains or cyclopentane rings - ether linkages between glycerol and side chains BACTERIA - D-glycerol - side chains composed of fatty acids - ester linkages between glycerol and side chains - membrane fluidity maintained by side chain saturation

Which of the following statements regarding algae is incorrect?

Algae are important in the degradation of dead plants and animals. Algae are CO2 fixing producers in all ecosystems, most crucially freshwater and marine habitats. In freshwater and marine ecology, the algae, together with photosynthetic bacteria, are known as phytoplankton.

An example of a Gram-positive, anaerobic, spore-forming microbe is

Clostridium

The members of which phylum can be found living in the widest range of temperatures?

Crenarchaeta The Crenarchaeota are found living in a wide variety of temperatures and include hyperthermophiles and psychrophiles. Little is known about the cold-adapted species; they are found in the Antarctic and probably the Arctic as well. The high-temperature species occur in solfataras and hydrothermal vents naturally, as well as in man-made habitats such as the effluent from geothermal power stations.

Which of the following most closely resembles the pseudopods used by leukocytes?

Lamellar pseudopods, as seen in dinoflagellates Leukocytes use lamellar pseudopods similar to those seen in dinoflagellates.

Which of the following metabolic processes is unique to archaea?

Methanogenesis Only some archaeans are methanogenic (they use hydrogen to reduce CO2 to methane). Organisms in all three domains perform some form of glycolysis. Both plants and cyanobacteria can perform oxygenic photosynthesis. Many bacteria can perform anaerobic respiration.

Numerous methanogenic archaea, as well as plants and algae, are autotrophs that use CO2 in their reactions. How do the reactions of these organisms differ?

Methanogens reduce CO2 to generate ATP. In methanogens that use CO2, CO2 and H2 react to produce methane. This produces an electrochemical gradient across the cell membrane that generates ATP through chemiosmosis. Phototrophs such as plants, algae, and cyanobacteria, however, use sunlight to synthesize foods from carbon dioxide and water.

Which of the following is true of all archaeans discovered to date?

None of them are human pathogens. So far no known human pathogens are archaean. While many archaeans are extremophiles, some are not. Phylogenetically, archaeans are more closely related to eukaryotes.

The production of _____ by cyanobacteria is believed to have resulted in one of Earth's earliest mass extinctions.

O2 Earth's early atmosphere was anaerobic, and the first phototrophs used light-driven proton pumps (e.g., bacteriorhodopsin) or conducted bacteriochlorophyll-based photosynthesis using substances such as H2S and H2 as electron donors. In contrast, cyanobacteria evolved the capacity to use water as an electron donor, thereby generating oxygen as a by-product of photosynthesis. Rising levels of oxygen produced by cyanobacterial photosynthesis (sometimes referred to as the "Great Oxygenation Event") would have resulted in mass die-offs of anaerobic organisms that were poisoned by this gas. Eventually, however, detoxifying enzymes such as catalase and super oxide dismutase evolved along with the capacity for aerobic metabolism. Cyanobacteria thus set the stage for the appearance of eukaryotes and multicellular life.

Single-celled heterotrophs demonstrating motility are classified as which of the following?

Protozoa Protozoa are defined as a diverse group of unicellular eukaryotic organisms. They include nonphotosynthetic protists demonstrating motility, such as the ciliates, amebas, and flagellates.

Which of the following is NOT a disease caused by spirochetes?

Rocky Mountain spotted fever Although not a general trait, certain spirochetes do cause important diseases in animals and humans. For example, leptospirosis is caused by spirochetes in the genus Leptospira. These infections of the kidneys, liver, and lungs are acquired by contact with the urine from an infected animal or person. The sexually transmitted disease syphilis is caused by Treponema pallidum, while ticks transmit Lyme disease and relapsing fever (caused by Borrelia burgdorferi and Borrelia recurrentis, respectively). Ticks also transmit Rocky Mountain spotted fever, but the causative agent of this disease is Rickettsia rickettsii, a member of the Alphaproteobacteria.

What do eukaryotes and archaea have in common that is lacking from bacteria?

Splicing machinery for introns Bacteria lack introns in their DNA. Both archaea and bacteria are prokaryotes and all three domains possess ribosomes. Only the archaeal membrane lipids have unique ether links.

Which of the following is true of rhizobia?

They can colonize specific plant hosts and fix nitrogen. Rhizobia form highly specific mutualistic associations with plants in which the bacteria fix nitrogen for the plants. Rhizobia can also be free living and are in a different phylum from the Gram-positive actinobacteria Frankia.

Why is it so difficult to arrive at a simple species definition for prokaryotes?

They engage in extensive horizontal gene transfer. Traditionally, eukaryotic species are defined based on distinguishing morphological characteristics and the principle of reproductive exclusion (only members of the same species can interbreed). Prokaryotes, however, may participate in extensive horizontal gene exchange with other taxa. Some prokaryotes are known to be particularly "recombinogenic" (that is, prone to frequent gene acquisition and rearrangements).

What do the phyla Bacteroidetes, Chlorobi, Fusobacteria, and Acidobacteria have in common?

They stain Gram-negative. Bacteroidetes, Chlorobi, Fusobacteria, Acidobacteria, and Nitrospirae are all deeply branching phyla that stain Gram-negative. Nitrospira and Nitrobacter (a genus of alphaproteobacteria) are primarily responsible for environmental oxidation of nitrite to nitrate. Bacteroidetes and Chlorobi are obligate anaerobes, but inhabit different niches. Bacteroides spp. make up the major component of the human gut microbiome, while Chlorobi (e.g., Chlorobium) conduct anoxygenic photosynthesis. The phylum Fusobacteria contains human-pathogenic species, while Acidobacteria is a newly discovered phylum whose member species are widespread in soil but underrepresented in culture.

The gamma class of the Proteobacteria includes many medically important genera in the families Enterobacteriaceae and Pseudomonadaceae. Which of the following characteristics allows differentiation between these two groups?

ability to grow anaerobically As the name suggests, the Enterobacteriaceae are common inhabitants of the mammalian gut. Some are commensal (e.g., E. coli strains that colonize the mucous of the gut lumen), while others (e.g., Salmonella and Shigella) are serious pathogens. As facultative anaerobes, the "enteric bacteria" are adapted for movement between their host and environmental niches, and identification of enteric isolates is accomplished primarily by their differential fermentation of various carbon sources. Pseudomonads, which include Pseudomonas aeruginosa, are obligate aerobes and thus are easily distinguished from the Enterobacteriaceae by their inability to ferment sugars. Members of both families are Gram-negative heterotrophic rods that grow well as biofilms.

Symbioses are

any relationships between two unrelated species. Symbioses occur when two unrelated species associate. Mutualisms and parasitisms are both considered symbioses. Endosymbioses are a subset of these relationships.

The lactic acid bacteria

are important in the food industry The lactic acid bacteria of firmicutes are used heavily in the food industry for their fermentation pathway products. Other firmicutes can be used for these other applications.

The brine pools shown below are colored red due to __________ produced by __________.

bacterioruberin; haloarchaea Most haloarchaea, which require high-salt environments to grow, are colored red by bacterioruberin, which protects the cells from light damage. This coloration can color the habitat that the haloarchaea inhabit.

Which of the following does not represent a mechanism of horizontal gene transfer among prokaryotes?

binary fission Binary fission is the normal process of prokaryotic cell division by which the genes of the parent are "vertically" transmitted to their progeny. But bacteria may also acquire new genes via transposable elements, conjugation, transduction (via bacteriophage) and transformation (free uptake of DNA).

Thaumarchaeota are important for the global nitrogen cycle because they

can oxidize ammonia for redox energy. Ammonia is a byproduct of many organisms' protein metabolism, and these organisms allow its recycling.

What takes place inside of cyanobacterial carboxysomes?

carbon fixation Carboxysomes are microcompartments bounded by a crystalline protein shell. They function to concentrate CO2 (which would diffuse across a lipid membrane) in proximity to the major Calvin cycle enzyme, RuBisCO. Only the initial stage of carbon fixation occurs here; the reductive and regenerative phases occur in the cytoplasm.

A(n) _____ is a group of organisms that all share a common ancestor, not shared with any other organism outside of its group.

clade A branch on a phylogenetic tree represents evolutionary descent from a common ancestor. Branch points (nodes) are used to indicate points of divergence from other taxa, and outgroups (known to be distantly related to the group under investigation) are used to root the tree. Genomic islands are acquired via horizontal gene transfer among organisms, and paralogs are genes that have evolved different functions.

The chloroplasts found in every plant cell on Earth are descended from a species of endosymbiotic _____.

cyanobacteria Cyanobacteria are the only prokaryotes that evolved the ability to use water as an electron donor during the light reactions of photosynthesis, thereby generating oxygen as a by-product. Their appearance on Earth resulted in the slow oxygenation of the atmosphere that began approximately 2.4 billion years ago and set the stage for the evolution of eukaryotes. Around 1 billion years ago, a free-living cyanobacterium was engulfed by a eukaryotic cell (which had already acquired mitochondria) and became assimilated as an organelle. This event gave rise to the algal lineage from which all plants are derived. Like mitochondria, chloroplasts retain a small circular chromosome and bacteria-like 70S ribosomes. Analysis of the 16S rRNA gene also reveals their origin within the cyanobacterial lineage.

Which form of Giardia intestinalis is involved in the transmission of disease?

cyst The life cycle of Giardia intestinalis alternates between two forms: the trophozoite and the dormant cyst. When the trophozoite experiences stress conditions (high levels of bile and high pH) in the host gut, the organism encysts. The cyst then detaches from the intestine and is expelled from the host. It remains dormant until ingested by a new host from a contaminated source. Once in the stomach, acid triggers differentiation back into the trophozoite form.

Which of the following structures is most likely to be a component of both chytrid zoospores and motile animal cells?

flagella The life cycle of a chytrid includes mycelia that are haploid (gametophye) or diploid (sporophyte). Haploid mycelia produce motile gametes that detect each other by sex-specific attractants. The gametes fuse to produce a motile zygote.

An organism's phylogeny describes what?

genetic relatedness to other species A phylogeny attempts to reconstruct the evolutionary descent and relatedness of a given species to other organisms. It is produced using DNA sequences of some type (e.g., 16S rRNA genes) which are analyzed by computer programs using a variety of criteria and assumptions.

Bacteriorhodopsin-based phototrophy is exhibited by _____.

halophiles Most Haloarchaea are photoheterotrophs, which use light energy captured by retinal-containing transmembrane proteins (bacteriorhodopsin) to supplement respiration. Respiration occurs with oxygen or anaerobically using nitrate.

Some, but not all, cyanobacteria produce differentiated cell types known as

heterocysts All cyanobacteria fix carbon. Many also fix nitrogen, but not all of these form heterocysts.

Cyanobacteria changed the atmosphere on early Earth because they led to

increased atmospheric O2 levels. Cyanobacteria are capable of oxygenic photosynthesis, using light to split water with the production of oxygen gas as a byproduct.

The underground mycelia of some mushrooms form mycorrhizae with tree roots. The mycorrhizae enhance and extend the absorptive power of the tree roots, while obtaining plant sugars for the fungus. What type of symbiotic relationship does this demonstrate?

mutualism Mutualism is the way two organisms of different species exist in a relationship in which each individual benefits from the activity of the other. This symbiotic relationship is observed with the Glomeromycota, a phylum of fungi in which all members are obligate mutualists of plants. These fungi form extensive networks of filamentous connections with plant roots in which the fungal filaments actually penetrate plant cells. This connection expands the tree's absorptive capacity as well as providing the fungi with plant sugars.

The _____ is the entire interwoven mass of one multicellular fungal organism.

mycelium The fungal mycelium is the vegetative part of a fungus, consisting of a mass of branching, thread-like hyphae. A mycelium may be microscopic, forming a colony that is too small to see, or it may be extensive and spread through acres of soil. Mycelium is vital in terrestrial and aquatic ecosystems for its role in the decomposition of plant material.

The species shown here is an example of a pathogenic species of Epsilonproteobacteria. It is able to cause disease by manipulating the _____ in its microenvironment.

pH Helicobacter pylori (not to be confused with Heliobacterium, a phototroph in the Firmicutes phylum) is a causative agent of gastritis and stomach ulcers. Its spiral shape and polar flagella are likely adaptive for penetrating the epithelial lining of the stomach. Urease production is considered a virulence factor that enables H. pylori to survive the acidic pH (~ 2-4) of the stomach. Breakdown of urea releases ammonia which raises the pH in the cell's microenvironment to tolerable levels.

Stromatolites are the ancient fossilized remains of layered communities of what?

photoautotrophic bacteria Stromatolites are bulbous-shaped sedimentary deposits of either silica or limestone. These are formed by fossilization of successive layers of biofilms composed of primarily phototrophic bacteria. In living stromatolites, cyanobacteria grow at the surface, providing niches for anoxygenic bacterial phototrophs and sulfate reducers underneath.

Fungi were originally classified with __________ but are actually closely related to __________.

plants; animals Traditionally, fungi were placed with plants, but genetic analysis shows fungi form a monophyletic group with animals called opisthokont.

Fungi are important members of the environment because they

recycle dead, organic material to usable molecules. Fungi provide essential support for all communities of multicellular organisms. They secrete extracellular enzymes and then absorb the digested molecules from the environment, as well as recycle dead organic matter such as wood and leaves. As a result, the recycled dead plants and animals are converted into chemical nutrients such as carbon and nitrogen that are released back into the soil, air, and water.

Botox is a medical application using the toxin produced by Clostridium botulinum to

relax muscle spasms The toxin produced by C. botulinum is a paralytic agent, so it can be used to relax muscle spasms and reduce the appearance of wrinkles.

Hyperthermophiles grow at extreme temperatures and therefore possess unique enzymes to stabilize their DNA structure. Which of the following choices includes the correct enzyme and its chromosomal function found in hyperthermophiles?

reverse gyrase; positive supercoiling of DNA A distinctive feature of hyperthermophilic archaea is the reverse gyrase enzyme. This enzyme maintains positive supercoiling to stabilize their DNA. The positive superturns "overwind" the DNA, preventing the helix from melting into separate strands at high temperature.

Carl Woese _____ RNA gene sequences as a "molecular clock" to develop his three domains of classification.

ribosomal All cells contain ribosomes, and because they catalyze such a critical process (translation), they evolve very slowly. For his analyses, Woese used the small subunit (SSU) rRNAs. These are designated 16S in prokaryotes (Bacteria and Archaea) and 18S in eukaryotes (Eukarya).

The mitochondria in eukaryotic cells is most closely related to modern day _____.

rickettsias Mitochondria evolved from an ancient pre-eukaryotic cell (likely from the Archaean eon) that contained an endosymbiotic alphaproteobacterium related to modern day rickettsias. The mitochondrion still retains its own circular DNA molecule, although it has undergone significant genome reduction. Some genes were simply lost, while thousands of others (including ones that code for specific components of the electron transport system) migrated to the host's nuclear genome. The remaining genes in the mitochondrion are still expressed using bacterial-like transcription and translation machinery. Sequencing of its 16S rRNA gene allowed its phylogenetic placement as seen here.

All Proteobacteria share

same cell envelope structure All the Proteobacteria share a similar cell envelope structure and are Gram-negative. Their cell morphologies and metabolisms vary widely. Not all have hosts, and in those that do, the hosts vary.

The most deep-branching bacterial phyla that diverged earliest contain many members that are

thermophiles The most deeply branching bacterial phyla (i.e., those that appear to have diverged earliest) include thermophiles and hyperthermophiles.

Actinomycetes are important in medicine because of all but their

use in the food industry Actinomycetes include many antibiotic producers, the pathogens causing tuberculosis, leprosy, and diphtheria among others, and form symbioses with plants and animals.

A species within the genus Deinococcus is famous for its ability to:

withstand high doses of radiation and extreme dryness Deinococcus spp. belongs to the Deinococcus-Thermus phylum, which along with the phyla Aquificae, Thermotogae, and Chloroflexi make up the deep-branching thermophiles. Deinococcus radiodurans is not, however, a thermophile. Rather, they are the most radiation-resistant organism on planet Earth, able to withstand acute doses of ionizing radiation in excess of 500,000 rad with no loss in viability. These bacteria possess efficient mechanisms to protect cellular proteins and repair DNA, which may also help to explain their cross-resistance to acid, UV light, and desiccation.