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63 Cards in this Set
- Front
- Back
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anaerobic:
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a general term that refers to any organism, environment, or cellular process that lacks or does not require oxygen and can even be poisoned by it
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bioremediation
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utilizing various bacteria for the cleansing of toxins in the environment
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carbon fixers:
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organisms that use the simplest form of carbon, carbon dioxide, for energy and as a precursor for anabolic reactions.
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Cyanobacteria:
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blue-green algae that are capable of nitrogen fixation.
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facultative anaerobe:
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an organism that can alternate their oxygen requirement.
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legume:
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plants like peas, alfalfa, and soybeans, which house nitrogen fixing bacteria in their root nodules.
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nitrogen cycle:
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Nitrogen gas is converted to ammonia (NH3) by nitrogen-fixing bacteria. The fixed nitrogen is then used by plants (and other soil or aquatic dwelling microorganisms) in various anabolic pathways leading to the synthesis of proteins, nucleic acids, and other nitrogenous molecules. These plants are digested by other organisms, and eventually the nitrogen makes its way either back into the atmosphere or back into the soil, through the help of saprobes.
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nitrogen fixation
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a process through which nitrogen is transformed into a biologically usable state (i.e., "fixed") by certain nitrogen-fixing bacteria
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nodule:
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structure on legume roots in which rhizobia are present.
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obligate aerobe
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organisms which require oxygen
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obligate anaerobe
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have no need for oxygen and may even be poisoned by it.
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rhizobia:
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applies to several species of bacteria that participate in nitrogen-fixing symbioses with plants
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saprobe:
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those organisms that live on dead and decaying matter
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What are the normal ways bacteria acquire carbon? What are some of the more unique ways certain bacteria can acquire carbon? Why and how do you think these abilities came about?
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Most prokaryotes use sugars (monosaccharides and disaccharides) and complex carbohydrates (e.g., starch). Some other prokaryotes utilize the simplest form of carbon, carbon dioxide, from the atmosphere. However, very unusual forms of carbon can also be used by some prokaryotes. Some prokaryotes can feed on oil. Some bacteria are also capable of using such exotic carbon compounds as TNT and polychlorinated biphenols (PCBs). Mutations in metabolic genes probably enabled some “mutant” bacteria to process these more “unusual” forms of carbon; if these “mutant” bacteria were located in an environment with an abundance of these “unusual” carbon forms, then they would have reproduced to high numbers and eventually evolved enough to become a new species.
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How are bacteria that process “unusual” forms of carbon used by humans? What is the general term for this type of use called?
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Humanity has exploited this evolved diversity by utilizing various bacteria for the cleansing of toxins in the environment, in a process known as bioremediation. Oil-eating bacteria have been used to help clean oil spills. Bacteria which utilize TNT and PCBs render such compounds non-toxic. There is an emerging field of civil engineering that utilizes bacteria for the purpose of cleaning contaminated soils, wells, and river sediments.
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Why is nitrogen important? Where is it most abundant? If nitrogen is so abundant, why is it difficult for most organisms to procure?
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Nitrogen is found in all proteins and nucleic acids and hence, it is essential to all forms of life. This atom is abundant in the air around us in the form of atmospheric nitrogen. However, nitrogen availability is a problem because nitrogen, in its elemental form (N2 gas), is not usable by most organisms. Nitrogen can only be transformed into a biologically usable state (i.e., "fixed") by certain nitrogen-fixing bacteria, in a process termed nitrogen fixation.
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How does nitrogen become available for most organisms?
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Through nitrogen-fixing bacteria. "Nitrogen-fixers" live in the aquatic environment, the soil, and in or around the roots and stems of certain species of plants. When other organisms live in symbioses with nitrogen-fixing bacteria, decompose those organisms, or eat plants which absorbed nitrogen fixing bacteria (or animals which have eaten those plants), they benefit from the “fixed” nitrogen.
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What is nitrogen fixation, and what are the forms of nitrogen involved?
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Nitrogen fixation is the process of converting unusable forms of nitrogen (such as N2) into biologically usable forms of nitrogen (such as ammonia (NH3)). The cycle “starts” with unusable forms of nitrogen, and turn it into biologically useful forms.
Plants, the primary energy producers in the terrestrial environment, are a major repository for fixed nitrogen in the terrestrial biosphere. When a plant is eaten, the herbivore obtains nitrogen in the form of proteins and nucleic acids (which are broken down during digestion and used by the herbivore for the production of its own nitrogen products). When a plant dies, a variety of saprobes (those organisms that live on dead and decaying matter) also obtain nitrogen from the nitrogenous compounds previously made by the plant. Finally, fixed nitrogen can be reconverted by soil bacteria back into atmospheric nitrogen. Your browser may not support display of this image. |
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What type of symbiosis is the relationship between nitrogen-fixing bacteria and plants? How are the bacteria and plants affected?
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It is a mutualistic relationship. The plant gets fixed nitrogen from the bacteria while the bacteria get carbon from the plant
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Are rhizobia the only type of organism that can fix nitrogen? If not, what is an example of another organism than can fix nitrogen? Is it also involved in a symbiotic relationship?
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No. Cyanobacteria can as well. Anabaena is a Cyanobacterium genus that colonizes on the leaves of an aquatic fern that grows in rice paddies; the symbiosis supplies nitrogen to the pond, where it subsequently is taken up and used by rice plants. About 75% of all rice is cultivated in flooded fields and this symbiosis has allowed rice farmers to maintain high levels of productivity without the need for expensive chemical fertilizers.
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In the present world, how is oxygen (in its O2 form) most commonly utilized by organisms? In what processes is O2 utilized?
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O2 is most commonly utilized by organisms for metabolic purposes. O2 is integral in the process of cell respiration.
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Bacteria survive and flourish in many different environments. How are bacteria classified based on the different ways they handle and live in oxygen environments?
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Today, prokaryotes (and other life forms) exhibit various metabolic relationships with oxygen. Obligate aerobes require oxygen, whereas obligate anaerobes have no need for oxygen and may even be poisoned by it. Facultative anaerobes can alternate their oxygen requirement. They can use oxygen if it is present, but they also can function in an anaerobic environment.
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What does it mean to obligate to a certain environment? What would happen to an obligate organism if it was put into a different environment?
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An organism which is “obligate” to a certain environment can only live in that environment (i.e. “obligated” to live in that environment). Oftentimes, if an organism “obligate” to one environment was placed into another, the new environment would be toxic to it.
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What are cyanobacteria? What can they do that makes them unique from other bacteria? How did they cause a global catastrophe for the other species on earth at that time?
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The cyanobacteria, originating between 2.5 and 3.4 billion years ago, were the first photosynthetic bacteria to use water (H2O) as an electron source. They released oxygen as a waste product. These photosynthetic organisms thrived wherever there was sufficient light and a body of water. After several hundred million years, free oxygen began to accumulate in the atmosphere and this marks the change from a reducing to an oxidizing atmosphere. Initially, the high levels of free oxygen were toxic to life.
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Archaea:
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a prokaryotic domain that has some features that are more eukaryotic than prokaryotic (i.e., although they lack a nucleus, their genetic organization is more like a eukaryote
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asexual reproduction
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reproduction that does not require the union of two reproductive cells, and produces offspring that are genetically identical to the parent cell
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Bacteria:
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a prokaryotic domain in which organisms have a more primitive genetic organization, unlike Eukarya and Archaea.
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bacillus (pl. bacilli)
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refers to the shape of a rod-shaped prokaryote
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binary fission:
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cell division in which a prokaryotic chromosome replicates and the mother cell pinches in half to form two new daughter cells
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chemoautotroph
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: describes a prokaryote which derives energy from a high-energy molecule (i.e. “chemo”) and carbon dioxide is used as the carbon source (i.e. “auto”).
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chemoheterotroph
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describes a prokaryote which derives energy from a high energy molecule (i.e. “chemo”) and a more complex form of carbon is used as the carbon source (i.e. heterotroph)
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coccus (pl. cocci)
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refers to the shape of a spherical prokaryote
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conjugation:
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two living prokaryotic cells physically join with one another to exchange genetic information
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eukaryote:
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organisms with membrane-bound nuclei and organelles
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extremophile:
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organisms inhabiting extreme environments, such as salt ponds, hot springs, Arctic ice, etc.
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F factor
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fertility factor plasmid. A prokaryote must have this factor to be able to form a pilius for conjugation.
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genome:
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all of the genetic material within an organism
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nucleoid
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where the DNA in prokaryotes is concentrated
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pathogenic
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harmful. Prokaryotes become subjectively pathogenic when they are harmful to other organisms.
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phage:
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virus that infects bacteria
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photoautotroph:
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describes a prokaryote which derives energy from light (i.e. “photo”) and carbon dioxide is used as the carbon source (i.e. “auto”).
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photoheterotroph
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: describes a prokaryote which derives energy from light (i.e. “photo”) and a more complex form of carbon is used as the carbon source (i.e. heterotroph)
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pilus (pili):
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he appendage with which the “male” bacterium attaches to another bacterium during conjugation.
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plasmid
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smaller rings of extrachromosomal DNA in prokaryotes, consisting of only a few genes
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prokaryote
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organisms without membrane-bound nuclei
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spirillum (pl. spirilla)
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refers to the shape of a helical prokaryote.
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transduction
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the exchange of DNA between prokaryotes that is made possible by phages
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transformation
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when prokaryotes acquire genes from the surrounding environment; a method of “swapping” genetic material between prokaryotes
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) Make a list of all the major characteristics of prokaryotes. What are the major differences between prokaryotic cells and eukaryotic cells?
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no membrane bound nucleus, unlike eukaryotes
- have less subcellular specialization than eukaryotes - much smaller than eukaryotes - usually single celled, but may be colonial - smaller genome and simpler morphologies than eukaryotes - replicates via binary fission, unlike eukaryotes - short generation times |
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xplain the Three Domain system of Classification as it applies to prokaryotes. Why was this system adopted?
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Classification schemes strive to show the evolutionary relationships between groups and in recent years it became apparent that the evolutionary relationships within prokaryotes are quite complex. To reconcile new findings, the taxonomic scheme of life has been revised once again. The most current scheme, proposes that life be divided into three domains. In this scheme, prokaryotic organisms can be described as either an Archaea, or as a Bacteria, while those organisms that have a nucleus comprise the third domain, known as Eukarya. Organisms that make up these three domains are sometimes referred to as the Archaebacteria, the Eubacteria, and the Eukaryotes).
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What other systems have been used to classify bacteria and life in general? What problems arose with these systems?
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Several systems have been used to classify life. One of the simplest divided life into prokaryotes and eukaryotes (i.e., those organisms without nuclei went into one group and those with nuclei went into another). Another commonly used scheme divided life into five kingdoms; Monera (i.e., prokaryotes), Protista, Plantae, Fungi, and Animalia. However, the evolutionary relationships within prokaryotes are quite complex. Both of these systems simply group all prokaryotes together—in reality, they should be divided based on their morphologies and evolutionary histories.
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What does the suffix “-phile” mean? What do the names “extremophile” and “thermophile” imply about an organism? Name some examples of environments that “extremophile” Archaea inhabit.
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“-Phile” means “to love”, so “extremophile” generally refers to organisms which are fond of “extreme” environments such as salt, Arctic ice, and hotsprings. “Thermophile” refers to organisms which are fond of living in unusually warm (or hot) temperatures.
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Research the biological technology called “PCR”. What is it? How did extremophilic bacteria contribute to the process?
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PCR is a method by which segments of genetic material are replicated many times relatively quickly. PCR uses heat to quickly break and replicate DNA molecules. Some of the enzymes necessary for the PCR process were derived from extremophilic bacteria that live in temperatures which would kill many other organisms. Because of these thermophilic bacteria evolved to have enzymes which work at high temperatures, these enzymes can also be used in the PCR process.
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What are the major distinctions between archaebacteria and eubacteria?
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Unlike eubacteria, archaea have some features that are more eukaryotic than prokaryotic (i.e., although they lack a nucleus, their genetic organization is more like a eukaryote). Also, most archaebacteria are extremophiles, whereas eubacteria are not.
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Describe how bacteria replicate. How do they do it so quickly? What factors contribute to this?
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Bacteria replicate by binary fission, which is a form of cell division in which a prokaryotic chromosome replicates and the mother cell pinches in half to form two new daughter cells. Prokaryotes have three factors which enable them to grow rapidly. First, prokaryotes have a small genome. Second, prokaryotes have simple morphologies (structural features). Third, prokaryotes replicate via binary fission. These three factors allow for a short generation time.
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Discuss the genome of prokaryotes. What is its structure, and how does the structure aid in quick replication? Without a nucleus, where is the genome stored?
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Compared to eukaryotes, prokaryotes usually have much smaller genomes. On average, a eukaryotic cell has 1000 times more DNA than a prokaryote. This means that less DNA must be replicated with each division in prokaryotes. The DNA in prokaryotes is concentrated in the nucleoid. The prokaryotic chromosome is a double-stranded DNA molecule arranged as a single large ring.
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What are plasmids? Are plasmids essential for the survival of a bacterium in a non-extreme environment? How are plasmids transmitted?
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Prokaryotes often have smaller rings of extrachromosomal DNA termed plasmids. Most plasmids consist of only a few genes. Plasmids are not required for survival in most environments, because the prokaryotic chromosome programs all of the cell's essential functions. However, plasmids may contain genes that provide resistance to antibiotics, metabolism of unusual nutrients, and other special functions. Plasmids can be transmitted from prokaryote to prokaryote through transformation and conjugation.
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What is antibiotic resistance? Research how bacteria gain this resistance and how it spreads. How can something like antibiotic resistance increase in frequency so rapidly in a population?
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Antibiotic resistance is the ability of a bacterium to survive despite the presence of antibiotics in its environment. Bacteria can pick up plasmids with genes that confer antibiotic resistance. The process of “picking up plasmids” is called transformation. Transformation occurs when prokaryotes acquire genes from the surrounding environment. This DNA might have been left behind by other bacteria (from the same or different species) when they died. The foreign DNA is directly taken up by the cell and expressed. If the DNA contains a beneficial gene (e.g., one encoding for antibiotic resistance), then the individuals harboring that gene will have a selective advantage over their non-transformed counterparts. As long as individuals with this gene reproduce more successfully, compared to those lacking the gene, they will be more fit and the gene will increase in frequency (i.e., microevolution, via natural selection, will occur).
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How does genetic variation occur in bacteria if they asexually reproduce?
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Through the rapid proliferation of mutations. Because bacteria have such short generation times, a single mutation in an asexually-reproducing population can reach great numbers in a relatively short period of time.
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Describe the processes that occur in transformation, conjugation, and transduction. What do these processes do to the bacteria? Describe how each process can change gene frequencies in a bacterial population.
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Transformation occurs when prokaryotes acquire genes from the surrounding environment. The foreign DNA is directly taken up by the cell and expressed. If the DNA contains a beneficial gene (e.g., one encoding for antibiotic resistance), then the individuals harboring that gene will have a selective advantage over their non-transformed counterparts. As long as individuals with this gene reproduce more successfully, compared to those lacking the gene, they will be more fit and the gene will increase in frequency.
The mechanism of conjugation requires that two living prokaryotic cells physically join with one another. Typically, DNA transfer only goes one way, with the "male" using an appendage called a pilus (plural, pili). Conjugation can create genetic variation through “sexual”-like reproduction. Genetic material can also be moved between bacteria by transduction. In this event, the exchange of DNA between prokaryotes is made possible by phages (viruses that infect bacteria). Phages reproduce by injecting their genetic material inside the bacterial cell, then multiplying, and eventually bursting from the cell. In a mechanism referred to as specialized transduction, the phage DNA inserts somewhat benignly into the bacterial host chromosome. Here it can lay dormant for many generations. However, under certain conditions, the phage DNA excises itself from the bacterial chromosome (usually carrying pieces of the chromosome with it), then replicates and forms new phages that burst out of the cell. These phages can reinfect other bacteria and thereby transfer not only their own DNA, but pieces of the former host DNA into the newly infected bacterium. Transduction in some situations can be beneficial if former host DNA is incorporated into phage DNA, and the phage DNA undergoes specialized transduction (i.e. a new host will survive long enough to express the new genes). In this way, genetic variation in created. |
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What is the F factor, and in what bacterial process is it involved? How does it determine “male” and “female” bacteria?
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The F factor is a plasmid which is involved in the bacterial process of conjugation. In order to produce pili, prokaryotes must have the F factor (fertility factor) plasmid. When a cell has the F factor plasmid, it is said to be F+. This F+ condition is heritable. If an F+ cell divides, both of the resulting cells will be F+. This condition is also "contagious." After an F+ cell conjugates with a "female" cell that does not contain the F factor, the "female" cell obtains the F factor plasmid and becomes F+ (i.e., "male").
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Review the factors that contribute to increasing variation in bacteria. How do these factors contribute to adaptation and evolution? What enables bacterial populations to respond so quickly to environmental change?
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Short generation times and mutations combined with sexual events (the processes of conjugation and transduction can be considered a form of sex because genetic information is being exchanged), help prokaryotic populations achieve vast genetic variation (without the alternation of haploid/diploid states seen in many eukaryotes). Generation times are minutes to hours, and can result in a beneficial mutation being heavily favored and passed on to a great number of offspring in a very short period of time. A short generation span enables prokaryotic populations to adapt very rapidly to environmental change.
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What are nutritional modes and how are they used to describe and categorize prokaryotes? What different terms are relevant to the study of prokaryote nutritional modes, and what do they mean?
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All life can be categorized nutritionally, according to how an organism obtains its energy and from where it gets its carbon. The prefixes "chemo" and "photo" are used to describe whether the energy comes from a high energy molecule (e.g., glucose) or from light, respectively. "Auto" and "hetero" are used to describe whether carbon dioxide, or a more complex form of carbon, is used as a carbon source, respectively. The prefixes are then affixed to the suffix "troph," meaning nourishment.
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