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MBIO Exam 3
Terms in this set (67)
What lessons have we learned from DNA sequencing of microbial genomes?
Organismal complexity is not directly correlated with genetic complexity. A large number of open reading frames encode proteins without any known function. There has been far more horizontal (lateral) gene transfer than expected between prokaryotes.
We learned organismal complexity is NOT directly correlated with genomic complexity. We also learned in DNA sequencing analysis if you have a DNA sequence that looks like a gene it is considered an open reading frame [ORF] because we assume it is a protein encoding gene, but it has not been experimentally proven; Therefore we have found that there are a large percentage of ORFs depending on the organism that has genes we assume encode for a protein but we dont know what those protein are doing in the cell, leaving a lot of the genetic capacity to be discovered
We learned about gene transfer which can give the receiving organism new genes to express and can lead the certain organism to become pathogenic.
We learned that genes that are associated with a particular phenotypic characteristic/function can be clustered together, forming genomic islands. For example, if pathogenic bacteria have a cluster of genes that contributes to its virulence factor they can be referred to as pathogenicity islands.
What does the term metagenomics refer to?
The study of genetic material recovered directly from environmental samples.
Refers to the genomic content of DNA that is found in direct environmental samples. For example, if you isolate DNA from a soil sample you will get different microbes and therefore different DNA sequences. This can be analyzed to view the population structure of the soil sample and you can view how many microbes were in the soil sample through the different DNA content.
Classical DNA sequencing
Done in pure cultures, meaning the DNA is coming from a single organism
How does the concept of species differ between prokaryotes and eukaryotes?
A prokaryotic species is a population of cells with similar characteristics. Prokaryotes do not perform cell division by sexual conjugation therefore reproduction is not always species specific. A eukaryotic species is grouped together based on ability of exchanging genes and breeding.
A prokaryotic species is a population of cells with similar characteristics; Prokaryotes do not perform cell division by sexual conjugation therefore reproduction is not always species specific
A eukaryotic species is grouped together based on ability of exchanging genes and breeding.
Historically a species was defined based upon the organisms physiology, morphology, ecology, and or medical importance.
What molecular technique is most widely used today to distinguish evolutionary lineages of microorganisms and how does it differ from more traditional methods?
Nucleic acid and protein sequencing.
What are the three domains of life?
Archea, Bacteria, Eukaryotes.
What is the most widely accepted scheme for the major lines of cell descent during the history of life on Earth?
What are stromatolites?
Hardened mats made up of various layers of filamentouscyanobacteria. Resemble rocks. They precipitate calcium out of the seawater which is what hardens them.
What distinguishes cyanobacteria from other photosynthetic prokaryotes in terms of their photosynthetic metabolism?
The possession of chlorophyll a and the use of oxygenic photosynthesis
How do some filamentous cyanobacteria carry out nitrogen fixation?
Nitrogenase takes N2 from the atmosphere and turns it into organic Nitrogen. Nitrogenase is oxygen sensitive however, so cyanobacteria have certain cells called heterocyst that lack photosynthetic apparatuses so they can perform nitrogen fixation. Sometimes cyanobacteria also do PSS during the day and nitrogen fixation at night.
What distinguishes purple and green photosynthetic bacteria from other photosynthetic prokaryotes in terms of their photosynthetic metabolism?
Purple and green - anoxygenic photosynthesis bacteriochlorophyll a-h. In lakes, cyanobacteria and algae grow closer to surface level, whereas green and purple bacteria grow lower down. This is so they're closer to sediments (that release H2S and CO2) and because their bacteriochlorophylls absorb lights at a higher frequency, which are found deeper.
What are bacteriochlorophylls?
(modified chlorophyll) Are photosynthetic pigments that occur in various phototrophic bacteria, like purple & green photosynthetic bacteria. Groups that contain bacteriochlorophyll conduct photosynthesis, but do not produce oxygen. They use shorter wavelengths of light not absorbed by plants or Cyanobacteria.
In general, where do photosynthetic microorganisms grow in stratified (meromictic) lakes?
Cyanobacteria grow about 0-10 meters from the surface because their chlorophyll a absorbs longer wavelengths. Green & Purple photosynthetic bacteria form layers 20-25 m below the surface of the water because their bacteriochlorophylls a-h absorb shorter wavelengths
What are the unique metabolic aspects of nitrifying bacteria? What distinguishes the two different groups of these bacteria?
They are chemoliphotrophic, meaning they use chemicals as a source of energy and inorganic hydrogen donors. Nitrosomonas oxidizes ammonium to nitrite and Nitrobacteria oxidizes nitrite to nitrate.
What is a unique characteristic of some spirilla as discussed in lecture?
Spiral-shaped bacteria and usually motile by lophotrichous flagella (a tuft on either end of the cell). Microaerophilic prefer 5-10% O2, inhabit soil and aquatic environments, found in different lineages of bacteria, suggesting multiple evolutionary origins. Some are magneototatic (form chains granules made of magnetic meals like iron in the cytoplasm that act as a bar magnet). It is hypothesized that this helps them swim down towards microaerophilic environments.
What unique characteristics do Hyphomicrobium and Caulobacter possess?
Hyphomicrobium- found in fresh water environments. Form stalks called pros theca. Replicate via budding that occurs at the ends of the prostheca. Calvobacter- forms stalks-immotile in stalk form. Reproduce via binary fission in which the parent cell is anchored to a substrate and the daughter cell is called a swarmer once separated. It has a flagellum and is motile until it loses it and forms a stalk.
What is gliding motility, and what group of bacteria discussed in lecture has this characteristic?
Gliding motility allows cells to glide on surfaces. It is hypothesized that this occurs when bacteria synthesize slime and eject it out of protein nozzles to then propel themselves forward. Myxobacteria have this characteristic.
What is a unique characteristic of some members of Vibrio and Photobacterium, and what is the enzyme that is responsible for this characteristic?
These genera emits light and are considered to have bacterial bioluminescence. The enzyme that allows this is luciferase.
What is a unique aspect of motility among the spirochetes? What are two potentially deadly diseases caused by members of this group?
Spirochetes have axial filaments which are endoflagella that provide motility by rotating in a cork screw behavior. Treponema pallidum causes syphilis and Borrelia Burgdorferi causes lyme disease.
What is a fundamental, shared characteristic of the rickettsias and chlamydias? What diseases mentioned in lecture are caused by rickettsias? By chlamydias?
Both grow as obligate intracellular parasites of eukaryotic cells, both require biosynthetic precursers from their host cells, in addition they have a specific transport system that exchanges internal ADP for external ATP "energy parasites".Rickettsias cause epidemic typhus (a systematic infection), Q ("query" respiratory infection) fever, and rocky mountain spotted fever (fever and rash).Chlamydias cause psittacosis (parrot fever-respiratory infection), trachoma (eye infection) and the STD.
What distinguishes the phylum Firmicutes, Tenericutes, and Actinobacteria?
Low G+C gram positive bacteria are Firmicutes. This phyla includes lactic acid bacteria, staphylococci, and endospore formers.Tenericutes also have low G+C count and lack cell walls, meaning they have no peptidoglycan. This phyla includes mycoplasmas.High G+C count bacteria are called Actinobacteria and include coryneform bacteria, mycobacteria, actinomycetes, propionic acid bacteria, and micrococci.
What two types of fermentation patterns are observed among the lactic acid bacteria?
Homofermentation (1 glucose to 2 lactic acid) or Heterofermentation (1 glucose to 1 lactic acid, plus ethanol and CO₂)
What characteristic is used to distinguish between different types of (pathogenic) streptococci?
Hemolysis can distinguish between different types of streptococci. Alpha hemolysis is the partial lysis of red blood cells and shows a green halo around the colonies-s. pneumoniae. Beta hemolysis is the complete lysis of RBC and has a clear halo around the colony- s. pyogenes. Finally gamma hemolysis refers to no lysis of RBCs.
What potentially deadly human diseases are caused by streptococci?
Pneumonia is a potentially deadly human disease caused by streptococci.
How are endospore-forming bacteria classified into genera (i.e., Bacillus versus Clostridium)?
Endospore formers are classified into genera based on their use of oxygen. Strict aerobes or facultative anaerobes belong to Bacillus, while strict anaerobes belong to the genus Clostridium.
What natural products are made by some members of the genus Bacillus that are important to humans?
Bacillus make many medically important anti-biotics.
What natural product is made by Bacillus thuringiensis and how is it important ?
B. thuringiensis produces insecticidal delta-endotoxins that form a parasporal crystal which is sprayed on crops to kill larvae.
What potentially deadly diseases mentioned in lecture are caused by species of Bacillus and Clostridium?
Potentially deadly diseases: Bacillus antracis- Anthrax, C. tetani causes tetanus, C. botulinum causes botulism (food poisoning), C. perfringens causes another type of food poisoning and gas gangrene (wound infections).
What is a unique characteristic of the mycoplasmas (class Mollicutes)?
They lack a cell wall, have protein ribbons underneath the cell membrane that form a cytoskeleton and are thought to confer cell shape and motility. Widespread parasites of plants and animals. Cell membranes contain sterols to protect from osmotic stress.
What category of natural products are made by some actinomycetes, especially members of the genus Streptomyces, that are important to humans?
Over 500 antibiotics.
What unique or unusual characteristics distinguish the Archaea from the Bacteria?
In the cell wall, (NAM) in bacteria is replaced with (NAT) in archaea. Which means it has "pseudopeptidoglycan" which is similar to peptidoglycan but not the same. Cell membrane: archaea have ether-linked phospholipids whereas bacteria are ester linked. Transcription and Translation have eukaryotic-like features. Archaea contain a variety of unique coenzymes and metabolic pathways.
What metabolic reaction do the methanogens carry out to generate energy? Where are methanogens commonly found?
Methanogenisis (4 H₂ + CO₂ --> CH₄ +2 H₂O) They are strict anaerobes and will only be found in environments that lack O2.
What range of salt concentrations supports optimal growth of the halophilic archaea?
High salt concentrations such as those in the dead sea support halophilic archaea.
What is a unique characteristic of the metabolism of halophilic archaea when grown under anaerobic conditions in sunlight, and what is the essential pigment called?
Their metabolism allows them to convert light into energy by bacteriorhodopsin. This is a protein that correspond to purple photosynthetic pigment.
Where are hyperthermophilic archaea commonly found?
Incredibly hot areas (sea vents/between tectonic plates, hot vents)
What contributions did Dmitri Ivanovsky, Martinus Beijerinck, Friedrich Loeffler and Paul Frosch, Peyton Rous, Frederick Twort, and Felix d'Herelle make in the history of virology?
Dimitri Ivanovsky- Tobacco mosaic disease is caused by an infectious agentMartinus Beijerinck- infectious agent that causes tobacco mosaic disease is not a bacteriumFriedrich Loeffler and Paul Frosch- foot and mouth disease in animals is also caused by a virusPeyton Rous- Malignant sarcomas in chickens are caused by virus= cancer can be caused by viruses.Fredrick and Felix- discovery of the first bacterial virusus (bacteriophages)
In general terms, what techniques are used to grow viruses in the laboratory?
Cell culture techniques. Use bacteriophage plaques to see how bacteria are affected by certain viruses. Grow viruses on top of either animal or plant cells to view the plaques.
What is a plaque? What do we usually assume about the viruses in a single, isolated plaque?
A viral plaque is a clear zone formed when a cell culture, such as bacterial cultures within some nutrient medium, are affected by a virus.
What are the three basic shapes of virus particles? What is an enveloped virus?
Filamentous (tubular)-usually having a helical symmetry; e.g., tobacco mosaic virus.Polyhedral (rough spherical)-usually having an icosahedral symmetry; e.g., adenovirusComplex or combined (polyhedral head attached to a contractile tail); e.g., E.coli, bacteriophage T4Filamentous VirusesEnveloped viruses-The virus particle is surrounded by a lipid bilayer and has spikes made of protein that can recognize host cell structures.
What is a capsid? A virion?
A capsid is the protein shell of a virus. Completely assembled infectious viruses-Intact virus particle.
What types of nucleic acids may be found inside different virus particles?
What are the individual structures of a virus particle such as bacteriophage T4?
Head, Tail, Whiskers, Base plate, Long tail fibers. Look at photo on phone.
What is an enveloped virus? How does an envelope help animal viruses enter a host cell?
Fusing with the cells. The spikes can also recognize host cell structures. Viruses that are enveloped lose their infectious ability if their lipids are interrupted.
What are the individual steps in the lytic growth of a virus (using phage T4 as a model?)
Attachment, Penetration, Takes over host cell's DNA replication and protein synthesis machinery to synthesize nucleic acids and proteins, Assembly and Packaging, Release (lysis)
What are the individual steps in the lysogenic growth of a virus? What is a prophage?
Virus DNA is inserted into bacterial chromosome. All virus genes are turned off except one that encodes a repressor protein to keep all other genes from being expressed. At this point of the cycle, the virus is called prophage.Prophage- the genetic material of a bacteriophage, incorporated into the genome of a bacterium and able to produce phages if specifically activated.Next the bacterial cell reproduces. Under stressful bacterial cell conditions, the virus goes through induction to pop out of the chromosome and follow the lytic cycle.
What unique enzyme do retroviruses possess, and what is the activity of this enzyme?
SS RNA to DS DNA
The RNA acts as a template for the DNA copy
What are oncogenes, and how are they associated with certain animal viruses?
Oncogenes- are signaling or cancer-causing genesThe signaling genes maintain proper growth and metabolism, but retroviruses take some of the genes and package them into the virus particles. This detaches the gene and ruins intracellular signaling pathways.
What are viroids, and how are they different from viruses? What types of diseases do viroids cause?
Viroids are small (120-463 nucleotides) circular, single-stranded RNA molecules. Largely folded into double stranded structures that are highly resistant to degradation. Infectious without a protein coat. Mostly cause plant diseases.
What are prions, and what types of diseases do they cause?
Prion, an abnormal form of a normally harmless protein found in the brain that is responsible for a variety of fatal neurodegenerative diseases of animals, including humans (particles that are infectious in the absence of nucleic acids)(ok copy=PrpC bad copy=PrpSC).Animal:Scrapie (sheep and goat), bovine spongiform encephalopathy (mad cow), transmissible mink encephalopathy (TME), Chronic wasting disease (CWD).Human:Creuzfeldt-Jakob disease, Gerstmann- staussler-scheinker disease, fatal familial insomnia, kuru.
What characteristics distinguish fungi from other eukaryotic microorganisms?
Fungi are nonphotosynthetic, obtain nutrients by absorption, chemoheterotrophs. They have cell walls made of Chitin and can either be filamentous (molds) or unicellular (yeasts). Can also be di-morphic (either unicellular or filamentous depending on environmental conditions).
What is the difference between molds and yeasts?
Molds (filamentous), Yeasts (unicellular)
What is a hypha? What is the difference between coenocytic hyphae and septate hyphae? What is a mycelium?
Hypha pertains to a single filament of a fungus (or actinomycetes) and are the branching filaments that make up the mycelium of a fungus. Mycelium=interwoven hyphae that make up the body of the individual fungal organism. In coenocytic hyphae the filament is undivided, whereas in septate hyphae- cross-awls divide the filaments into compartments.
What are some activities of fungi that make them important to humans?
They are saprophytes, meaning they feed on dead organic matter. They play an important ecological role as decomposers. Yeasts are also used to ferment alcohols.
In general, what environments are optimal for the growth of molds? Of yeasts?
Molds- grow best in environments that are warm, moist and acidic, pH 4-5. Like PDA plates.Yeasts- grow best in environments with a high sugar content (flowers, nectars, fruit surfaces)
What two types of asexual (reproductive) spores that are formed by fungi were discussed in lecture? What distinguishes these two different types of spores?
Sporangiospores (in molds)- hyphae grow on the surface and produce aryl hyphae that stick up into the air. Tips form enclosed incubating sacs for sporangiospores called sporangium. Sporangium breaks open when the spores are mature and they travel via wind/water.Conidiospores (in molds)- fruiting body called sterigma is formed on the tip of aryl hyphae. This time, the spores are not enclosed. The condiospores form chains and are dispensed by wind/water.
What are the four divisions of fungi? What types of sexual (reproductive) spores are formed by each group, and what distinguishes these different types of spores?
Zygomycta form zygospores and an example is Rhizomes stolonoifera or bread mold. Ascomycota form ascopspores and include ergot fungus. This fungus can infect grains and cause hallucinations-salem witch trials. Basidiomycota form basidiospore and are the common cultivated mushrooms we generally see. Deuteromycota do not form sexual spores. As far as we know they only form asexual spores.
What characteristics distinguish algae from other eukaryotic microorganisms?
Algae are photosynthetic and can be unicellular, colonial, or multicellular. Most are freshwater or marine and they have cell walls that contain cellulose.
What characteristics distinguish protozoa from other eukaryotic microorganisms?
Mostly non photosynthetic, acquire nutrients by absorption or ingestion (phagocytosis) lack a cell wall and are unicellular. Classified by type of motility.
In what environments do we commonly find algae?
Algae are found in fresh water or marine environments, but some are in terrestrial environments. Algae form mutualistic associations with fungus on rocks (lichen) or a variety of animals on coral reefs.
What mutually beneficial symbiotic relationship is formed between algae and other organisms as discussed in lecture? How does each partner benefit from the association?
Lichen: mutualistic association between an alga or cyanobacterium (or both) and a fungus-advantage to fungus: alga synthesizes organic nutrients by photosynthesis-advantage to alga: fungus helps in uptake water and inorganic nutrients; protects alga from desiccation and excessive light intensity.
In what ways are algae important to humans?
They produce a vast amount of oxygen and are primary producers. The primary and secondary consumers we eat to obtain nutrients are around because of these producers.
What is eutrophication? What sequence of steps leads to a eutrophied body of water?
Eutrophication- excessive richness of nutrients in a lake or other body of water, frequently due to agricultural runoff or sewage, which causes a dense growth of plant life and death of animal life from lack of oxygen. This process includes nutrient input that leads to algal overgrowth called a bloom. At the end of the growing season, the cells die and the water body experiences an O2 depletion that kills aquatic animals. Growth of anaerobic bacteria and production of malodorous compounds cause rotting.
In what environments do we commonly find protozoa?
Mostly aquatic environments but some are parasites or have mutualistic relationships with animals.
What sorts of mutually beneficial symbiotic relationships are formed between protozoa and other organisms as discussed in lecture?
Protozoa in the rumen of cattle and sheep are essential for digestion of plant material.Protozoa in the hind guts of termites are essential for the digestion of cellulose in wood consumed by the insects.
What is the dormant resting body that is formed by some protozoa (especially animal parasites) called?
What distinguishes the two different types of social amoebas (slime molds)?
Acellular slime molds- a plasmodium (giant mass of cytoplasm) flows in amoeboid fashion across surfaces, meaning it extends cytoplasm and pulls itself towards that cytoplasm. This occurs when nutrients run out.Cellular slime molds- individual amoeboid cells aggregate into pseudoplasmodium of multiple cells. Aggregation is triggered by cAMP.
What human diseases are caused by Plasmodium falciparum, Trypanosoma brucei, and Trypanosoma cruzi?
Plasmodium falciparum- Malaria; insect vector: anopheles mosquitoTrypanosoma brucei- African sleeping sickness; insect vector: tests flyTrypanosoma cruzi- Chagas' disease; insect vector: triatomine "kissing" bugs.
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