Term
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Definition
• Bacteria—prokaryotes
• Archaea—prokaryotes
• Eukarya—eukaryotes |
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Term
| Members of all the domains |
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Definition
*Conduct glycolysis
*Replicate DNA conservatively
*Have DNA that encodes peptides
*Produce peptides by transcription and *translation using the same genetic code
*Have plasma membranes and ribosomes |
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Term
| Prokaryotic cells differ from eukaryotic cells. |
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Definition
Prokaryotes lack a cytoskeleton
divide by binary fission.
DNA is not in a membrane-enclosed nucleus
DNA is a single, circular molecule.
Prokaryotes have no membrane-enclosed organelles |
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Term
| The common ancestor of all three domains had |
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Definition
DNA
and its machinery for transcription and translation produced RNA and proteins
the chromosome was probably circular |
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Term
| Ancestor of archaea & eukarya |
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Definition
| Archaea and Eukarya share a more recent common ancestor with each other than with Bacteria |
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Term
| The three domains & years of evolution |
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Definition
All three domains are the result of billions of years of evolution
and are well adapted to present-day environments.
None is “primitive”
The earliest prokaryote fossils date back at least 3.5 billion years, and even then there was considerable diversity |
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Term
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Definition
Prokaryotes are the most successful organisms on Earth in terms of number of individuals.
The number of prokaryotes in the ocean is perhaps 100 million times as great as the number of stars in the visible universe.
They are found in every type of habitat on Earth. |
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Term
| Among the Bacteria, three shapes are common |
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Definition
Sphere or coccus (plural cocci)
(occur singly or in plates,
blocks, or clusters)
Rod—bacillus (plural bacilli)
Helical
note: Rods and helical shapes may form chains or clusters. |
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Term
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Definition
Nearly all prokaryotes are unicellular.
In chains or clusters, each individual cell is fully viable and independent.
Associations arise when cells adhere to each other after binary fission.
Chains are called filaments
-which may be branching
-or enclosed in a tubular sheath |
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Term
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Definition
Prokaryotes usually live in communities of different species, including microscopic eukaryotes.
Microscopic organisms are sometimes referred to as microbes.
Many microbial communities perform beneficial services,
(e.g., digestion of our food,
breakdown of municipal wastes). |
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Term
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Definition
| Many microbial communities form biofilms that are formed when cells contact a solid surface and excrete a gel-like polysaccharide matrix that traps other cells. |
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Term
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Definition
It is difficult to kill cells in a biofilm (e.g., the film may be impenetrable to antibiotics).
Biofilms form in many places: contact lenses, artificial joint replacements, dental plaque, water pipes, etc.
Fossil stromatolites are layers of biofilm and calcium carbonate |
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Term
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Definition
Bacteria in biofilms communicate with
chemical signals.
Biologists are investigating ways to block the signals that lead to formation of the matrix, to prevent biofilms from forming.
New technology uses a chip with “microchemostats” to study very small populations of bacterial cells. |
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Term
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Definition
Most prokaryotes have a thick cell wall, different in structure from plant, algal, and fungal cell walls.
Bacterial cell walls contain peptidoglycan, a polymer of amino sugars.
Archaea do not have peptidoglycan, although some have a similar molecule called pseudopeptidoglycan. |
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Term
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Definition
The gram stain method reveals the complexity of bacterial cell walls.
The method uses two different stains—one violet and one red.
Gram-positive bacteria retain the violet dye. Gram-negative bacteria retain the red dye.
Differences are due to the structure of the cell wall. |
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Term
Gram-positive
Gram-negative |
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Definition
Gram-positive bacteria have a thick layer of peptidoglycan outside the plasma membrane.
Gram-negative bacteria have a thin layer of peptidoglycan between the plasma membrane and another distinct outer membrane, in the periplasmic space |
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Term
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Definition
Bacterial cell walls are often the target of drugs against pathogenic bacteria.
Antibiotics such as penicillin interfere with the synthesis of the cell walls, but don’t affect eukaryote cells. |
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Term
| Some prokaryotes are motile. |
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Definition
Helical bacteria,such as spirochetes,
-have a corkscrew-like motion
-using modified flagella
-called axial filaments
Some have gliding and rolling mechanisms.
Some cyanobacteria can move up and down in the water by adjusting the amount of gas in gas vesicles. |
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Term
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Definition
-consist of a single fibril of flagellin
-plus a hook and a basal body responsible for motion.
The flagellum rotates around its base. |
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Term
| Prokaryotes communicate with chemical signals. |
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Definition
Quorum sensing:
Bacteria can monitor the size of the population by sensing the amount of chemical signal present.
When numbers are large enough, activities such as biofilm formation can begin. |
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Term
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Definition
Some bacteria emit light by bioluminescence.
Often the bacteria only emit light when a quorum has been sensed.
Example: Vibrio colonies emit light to attract fish to eat them—they thrive best in the guts of fish.
Vibrio in the Indian Ocean can be visible from space. |
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Term
Prokaryote
metabolic pathways
intro |
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Definition
Prokaryotes utilize a diversity of metabolic pathways.
Eukaryotes use much fewer metabolic mechanisms. Much of their energy metabolism is done in mitochondria and chloroplasts that are descended from bacteria.
The long evolutionary history of prokaryotes has resulted in a variety of metabolic “lifestyles.” |
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Term
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Definition
Anaerobes do not use oxygen as an electron acceptor in respiration.
Oxygen-sensitive prokaryotes are obligate anaerobes—molecular oxygen will kill them.
Facultative anaerobes can shift their metabolism between aerobic and anaerobic modes, such as fermentation |
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Term
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Definition
Aerotolerant anaerobes do not conduct cellular respiration, but are not damaged by oxygen if it is present.
Obligate aerobes cannot survive in the absence of oxygen. |
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Term
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Definition
Prokaryotes are represented in all four categories of nutrition.
Photoautotrophs perform photosynthesis.
Cyanobacteria use chlorophyll a, and O2 is a byproduct |
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Term
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Definition
Other bacteria use bacteriochlorophyll, and don’t release O2.
Some use H2S instead of H2O as the electron donor, and produce particles of pure sulfur.
Bacteriochlorophyll absorbs longer wavelengths than chlorophyll; these bacteria can live underneath dense layers of algae. |
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Term
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Definition
Photoheterotrophs use light as an energy source, but get carbon from compounds made by other organisms.
Example: purple nonsulfur bacteria
Sunlight provides ATP through photophosphorylation. |
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Term
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Definition
Chemolithotrophs (chemoautotrophs) get energy by oxidizing inorganic compounds:
Ammonia or nitrite ions to form nitrate ions, H2, H2S, S, and others.
Many archaea are chemolithotrophs. |
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Term
| Deep-sea hydrothermal vent ecosystems |
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Definition
Deep-sea hydrothermal vent ecosystems are based on
chemolithotrophs that oxidize H2S and other compounds released from volcanic vents.
The ecosystems include large communities of crabs, mollusks, and giant tube worms, at depths of 2,500 m |
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Term
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Definition
Chemoheterotrophs obtain both energy and carbon from organic compounds—
most known bacteria and archaea, all animals, all fungi, and many protists |
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Term
| use inorganic ions such as nitrate, nitrite, or sulfate |
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Definition
Some bacteria use inorganic ions such as nitrate, nitrite, or sulfate as electron acceptors in respiratory electron transport.
Denitrifiers use NO3– as an electron acceptor if kept under anaerobic conditions, and release nitrogen to the atmosphere as N2.
Species of Bacillus and Pseudomonas. |
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Term
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Definition
Nitrogen fixers convert N2 gas into ammonia.
This vital process is carried out by many archaea and bacteria, including cyanobacteria. |
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Term
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Definition
Nitrifiers are chemolithotrophic bacteria that oxidize ammonia to nitrate.
Nitrosomonas and Nitrosococcus convert ammonia to nitrite.
Nitrobacter converts nitrite to nitrate.
Electrons from the oxidation are passed through an electron transport chain |
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Term
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Definition
Taxonomy of prokaryotes has been based on
shape, color, motility, nutrition, antibiotic sensitivity, and gram stain reaction.
The study of evolutionary relationships is hampered by their small size. |
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Term
| Nucleotide sequencing of ribosomal RNA is useful in evolutionary studies: |
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Definition
Nucleotide sequencing of ribosomal RNA is useful in evolutionary studies:
-rRNA is evolutionarily ancient
-All living organisms have rRNA
-rRNA has the same role in
translation in all organisms
-rRNA has evolved slowly
so that
-sequence similarities are easily found |
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Term
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Definition
Lateral gene transfer occurs when genes from one species become incorporated into the genome of another species.
.
Mechanisms: transfer by plasmids or virus, and uptake of DNA by transformation
Transfer can occur between the domains |
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Term
| In phylogenies, presence of transferred genes |
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Definition
In phylogenies, presence of transferred genes can result in mistaken inferences about evolutionary relationships.
It is unclear how much gene transfer complicates efforts to resolve the prokaryote tree of life.
Sequences of entire genomes are predicted to provide a stable core of genes that have not undergone lateral transfer. |
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Term
| Many prokaryote species, and perhaps whole clades, have not been described by biologists. |
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Definition
Many prokaryote species, and perhaps whole clades, have not been described by biologists.
Many have resisted efforts to grow them in pure culture.
Biologists now examine gene sequences collected from random samples of the environment. Many new sequences imply there are thousands more prokaryotic species. |
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Term
| The most important source of genetic variation in prokaryotes |
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Definition
The most important source of genetic variation in prokaryotes is mutation and genetic drift.
Prokaryotes are haploid, mutations can have immediate consequences.
Beneficial mutant alleles spread rapidly through a population. |
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Term
| what has led to an incredible diversity among the prokaryotes. |
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Definition
-Rapid generation time,
-combined with mutation
-natural selection
-genetic drift and
-lateral gene transfer
have led to an incredible diversity among the prokaryotes. |
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Term
| Over 12 clades of bacteria have been proposed under a currently accepted classification scheme. We will focus on six clades. |
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Definition
1. Spirochetes
2. Chlamydias
3. High-GC Gram-positives
4. Cyanobacteria
5. Low-GC Gram-positives
6. Proteobacteria |
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Term
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Definition
-Gram-negative
-motile
-chemoheterotrophic
they have unique axial filaments (modified flagella) that rotate.
Many are human parasites, some are pathogens (syphilis, Lyme disease), others are free living. |
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Term
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Definition
Extremely small, gram-negative cocci, live only as parasites within cells of other organisms.
Can take up ATP from host cell with translocase.
Complex life cycle with two forms—elementary bodies and reticulate bodies.
Some are pathogens—trachoma, sexually transmitted diseases, some pneumonia. |
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Term
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Definition
High-GC Gram-positives (actinobacteria)
High G+C/A+T ratio in DNA
Form elaborately branching filaments
Some reproduce by forming chains of spores at the tips of the filaments.
Most antibiotics are from this group, also includes Mycobacterium tuberculosis. |
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Term
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Definition
Photoautotrophs with chlorophyll a; many species fix nitrogen
Contain an internal membrane system—photosynthetic lamellae or thylakoids.
Eukaryote chloroplasts are derived from endosymbiotic cyanobacteria |
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Term
| Colonies of Cyanobacteria |
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Definition
Colonies of cyanobacteria range from
-flat sheets to
-filiaments to
-spherical balls of cells
Some colonies differentiate into
-vegetative cells,
-spores, and
-heterocysts
Heterocysts are specialized for nitrogen fixation. |
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Term
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Definition
Low-GC Gram-positives (firmicutes)
Low G+C/A+T; but some are gram-negative.
Some produce endospores
-heat-resistant resting structure
-tough cell wall and spore coat
-can survive harsh conditions
-because it is dormant.
Endospore becomes active and divides when conditions improve. |
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Term
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Definition
Bacillus anthracis (anthrax)
endospores germinate when they
sense a presence of macrophages.
Closteridium and Bacillus form endospores.
C. botulinum toxins are some of most poisonous ever discovered. |
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Term
|
Definition
-have no cell wall
-are extremely small
-have very small genome
May be the minimum amount of DNA needed for a living cell. |
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Term
| Proteobacteria (purple bacteria) |
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Definition
-Largest group of bacteria
—high diversity of metabolic
phenotypes.
-Common ancestor was
photoautotrophic
Includes some nitrogen-fixing genera such as Rhizobium. |
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Term
Examples of proteobacteria
pathogens in humans & plants |
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Definition
Proteobacteria that are human pathogens:
-Yersinia pestis (plague)
-Vibrio cholerae (cholera)
-Salmonella typhimurium
(gastrointestinal disease).
Crown gall in plants is caused by Agrobacterium tumefaciens; it has a plasmid used in recombinant DNA technology. |
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Term
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Definition
Archaea are divided into two main groups,
Euryarcheota &
Crenarcheota,
and two recently discovered groups,
-Korarchaeota &
-Nanoarchaeota
Little is known about the Archaea; research is in early stages.
All archaea
-lack peptidoglycan in the cell
walls
- have distinct lipids in the cell
membranes |
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Term
| differences in lipid to glycerol linkages between bacteria/eukaryote & archaea |
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Definition
Most bacterial and eukaryotic cell membranes have lipids with fatty acids connected to glycerol by ester linkages
Archaea cell membranes have lipids with fatty acids linked to glycerol by ether linkages. |
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Term
lipid monolayers & bilayers
in archaea |
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Definition
The long-chain hydrocarbons in Archaea are unbranched.
One class of these lipids has glycerol at both ends, and forms a lipid monolayer.
Lipid bilayers and lipid monolayers are both found in the Archaea. |
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Term
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Definition
Most known Crenarcheota are both
thermophilic &
acidophilic
Sulfolobus lives in hot sulfur springs (70–75°C, pH 2 to 3).
One species of Ferroplasma lives at pH near 0.
They can still maintain an internal pH of near 7. |
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Term
| Euryarcheota that are methanogens |
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Definition
Some Euryarcheota are methanogens—
produce methane (CH4) by reducing
CO2—obligate anaerobes.
Methanogens release 2 billion tons of methane per year. Many live in the guts of grazing mammals.
Increased cattle farming and rice growing contributes methane to the atmosphere.
Methanopyrus lives in deep-ocean hydrothermal vents. |
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Term
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Definition
Extreme halophiles (salt lovers)
-have pink carotenoid pigments
making them easy to see.
-Have been found at pH up to 11.5.
-They live in the most salty,
most alkaline environments on
Earth
-Some have a light-absorbing molecule bacteriorhodopsin
and can form ATP by a chemiosmotic process. |
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Term
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Definition
-thermophilic and acidophilic
-has aerobic metabolism
-lives in coal deposits
Has the smallest genome of the Archaea; genome size is comparable to mycoplasmas. |
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Term
Korarchaeota
&
Nanoarchaeota |
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Definition
The Korarchaeota are known only by evidence from DNA isolated from hot springs.
-Nanoarchaeota are so called because of their small size.
-Discovered in deep sea vents off Iceland
-they live attached to cells of the crenarcheota Ignicoccus |
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Term
| How many prokaryotes are human pathogens? |
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Definition
Only a small minority of known prokaryotes are human pathogens (disease-causing organisms).
Many species play many positive roles in such diverse applications as cheese making, sewage treatment, and production of antibiotics, vitamins, and chemicals. |
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Term
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Definition
Many prokaryotes are decomposers
—they metabolize organic compounds
in dead organisms & other
organic matierials
The products such as carbon dioxide are returned to the environment, key steps in the cycling of elements. |
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Term
| How did cyanobacteria help with the development of eukaryotic life? |
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Definition
Plants depend on prokaryotes for their nutrition, for processes such as nitrogen fixation and nutrient cycling.
In the ancient past, cyanobacteria had a large impact on life when they started generating O2 as a byproduct of photosynthesis.
This led to loss of anaerobic species, but the development of cellular respiration and eukaryotic life |
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Term
Many prokaryotes live in and on other organisms.
Give examples |
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Definition
Animals harbor a variety of prokaryotes in their digestive tracts.
Bacteria in cattle produce cellulase, the enzyme that allows cattle to digest cellulose.
Bacteria in the human large intestine produce vitamins B12 and K.
The biofilm that lines human intestines facilitates uptake of nutrients, and induces immunity to the gut contents. |
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Term
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Definition
-The microorganism is always found in persons with the disease.
-It can be taken from the host and grown in pure culture.
-A sample of the culture causes the disease in a new host.
-The new host also yields a pure culture. |
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Term
Human pathogens are all in the Bacteria.
What must an organism do to become a pathogen? |
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Definition
-Arrive at the body surface of a host
-Enter the host’s body
-Evade the host’s defenses
-Multiply inside the host
-Infect a new host |
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Term
| What do consequences of bacterial infection depend on? |
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Definition
Invasiveness of the pathogen—
its ability to multiply in the host.
Toxigenicity of the pathogen—
its ability to produce toxins. |
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Term
Give two examples of
invasiveness
vs
toxigenicity |
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Definition
Corynebacterium diphtheriae (diptheria) has low invasiveness
but the toxins it produces affect
the entire body.
Bacillus anthracis (anthrax) has low toxigenicity
but very high invasiveness—
it colonizes the entire
bloodstream. |
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Term
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Definition
Endotoxins
-are released when certain gram-
negative bacteria are lysed.
-They are lipopolysaccharides from
the outer membrane.
Endotoxins are rarely fatal.
Some producers are Salmonella and Escherichia. |
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Term
|
Definition
Exotoxins are
-soluble proteins released by
living bacteria.
-Are highly toxic and often fatal.
Exotoxin-induced diseases include tetanus (Clostridium tetani)
botulism (Clostridium botulinum)cholera (Vibrio cholerae)
plague (Yersinia pestis)
anthrax (three exotoxins produced by
Bacillus anthracis). |
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Term
| What are the two types of bacterial toxins? |
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Definition
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