Glossary of Key Terms
The following is a compilation of key terms that may be helpful when accessing this database.
Aldehyde dehydrogenase- enzyme that catalyzes the oxidation of aldehydes
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Betaine lipids- glycerolipids that contain an ether-linked betaine, which is a specific type of zwitterion
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Biofilm- colony of microorganisms in which microbial cells adhere to each other and a stationary surface
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Biotin- water soluble vitamin B
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Carapace- dorsal section of the exoskeleton or shell in a turtle, crustacean, or arachnid
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Catechols- colorless, organic compound with the molecular formula C₆H₄(OH)₂
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Chaperone- proteins that help with the folding or assembly of other macromolecular structures
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Chelate- a compound containing a ligand bonded to a metal atom at two or more points
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Chemotaxis- movement of an organism along a gradient of increasing or decreasing concentration of a substance
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Cyclohydrolase- an enzyme which catalyzes the reversible cyclization or the ring opening of a purine ring
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Cytochrome- proteins that contain the heme prosthetic group
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Enolase- key glycolytic enzyme
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Enteric- relating to the intestines
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Exogenous- caused or produced from outside an organism
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Ferredoxin- iron–sulfur proteins that mediate electron transfer
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Fe/S proteins- proteins containing iron-sulfur clusters that are versatile cofactors of proteins related to catalysis, electron transport, and sensing of environment
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Flagellar rotation- mechanism of bacterial movement involving the rotation of whip-like appendage that protrudes from bacteria
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Flavodoxin- bacterial electron-transfer protein that contains flavin mononucleotide
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Flavoprotein- oxidizing enzymes containing flavins
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Folate- B-vitamin needed to make DNA, RNA, red blood cells, and to convert carbohydrates to energy
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Frustule- hard and porous, silicified cell wall of a diatom
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Gram-positive- bacteria that have a thicker peptidoglycan cell wall
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Halophilic- extremophiles that live in high salt concentrations
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Heme- ring-shaped organic molecule that holds an iron molecule
Heterocystous- specialized differentiated nitrogen-fixing cells formed during nitrogen starvation by some filamentous cyanobacteria in aerobic conditions
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Isoform- proteins that are similar to each other and perform similar roles within cells
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Lipoic acid- organosulfur compound derived from caprylic acid that is needed for aerobic respiration
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Macronutrients- C, H, O, N, P, and S; these elements are essential for all life (see About page for further explanation)
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Major cation- K, Mg, Ca; cations that have significant roles in the functions of cells
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Metalloregulator- protein that regulates biochemical interactions with metals through binding
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Pectin- structural starch contained in the cell walls of terrestrial plants
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Phenazines- organic compound with the formula (C₆H₄)₂N₂
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Phycobilisome- light-harvesting apparatus of photosystem 2 in cyanobacteria and red algae; anchored to thylakoid membrane
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Phycocyanins- blue photosynthetic protein-pigment complex in cyanobacteria
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Planktonic- free-living bacteria
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Plastid- membrane-bound organelle located in the cells of photosynthetic organisms
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Plastocyanin- a blue copper protein that catalyzes the transfer of electrons from the Cyt b6f complex to PS I during photosynthesis.
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Pyruvate decarboxylase- enzyme that catalyzes the non-oxidative decarboxylation of pyruvate to acetaldehyde and CO2
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Quorum sensing- bacterial cell–cell communication process that is dependent on density and causes changes in behavior when a population reaches a certain density
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Rare earth elements- includes fifteen lanthanides, as well as scandium and yttrium
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Redox- chemical reaction that involves a transfer of electrons between two chemical species, with one species undergoing oxidation and the other undergoing reduction
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RNR- Ribonucleotide reductase; crucial enzyme that mediates synthesis of deoxyribonucleotides
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Secondary metabolite- organic compounds produced by bacteria, plants, or fungi that are not required for the growth or reproduction of the organism but confer a selective advantage to the organism
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Siderophore- small, high-affinity iron-chelating compounds secreted by microbes, primarily to transport iron into the cell
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Stationary phase- stage of bacterial growth in which the size of the population remains constant, although individual bacteria are reproducing and dying
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Stomata- pore in plants that facilitates gas exchange
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Sulfolipids- lipids that contain a functional group with a sulfur
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Symbiont- an organism living in a symbiotic relationship with another organism
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Syntrophy- one species living off the product of another species
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Thiols- an organic compound containing the group —SH
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Thylakoid- membrane-bound compartments within chloroplasts and cyanobacteria where the light-dependent reactions of photosynthesis take place
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Turgor- force within the cell that pushes the plasma membrane against the cell wall so that the cell remains rigid
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Urease- enzyme that catalyzes the hydrolysis of urea, making ammonia and CO2
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Zinc finger proteins- small protein structural motif that is identified by the coordination of one or more zinc ions for stabilization
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Glossary of Species
The following is a compilation of species names that may be helpful when accessing this database.
Acinetobacter baumannii- Gram-negative, aerobic bacillus and human pathogen that causes infections in hospitalized patients
Actinomycetes- Gram-positive mycelial bacterium
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Aspergillus sydowii- pathogenic fungus that causes several diseases in humans and kills corals
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Arabidopsis- genus of small flowering plants related to cabbage and mustard; contains thale cress, a model organism
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Azotobacter vinelandii- Gram-negative diazotroph that is capable of fixing nitrogen in an aerobic environment
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Bacillus arseniciselenatis- spore-forming, rod-shaped, alkaphilic anaerobe that is capable of respiring selenium
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Bacillus selenitireducens- spore-forming, rod-shaped, alkaphilic anaerobe that is capable of respiring selenium
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Bacillus subtilis- Gram-positive, spore-forming, rod-shaped facultative aerobe; model organism
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Borrelia burgdorferi- Gram-negative spirochete that causes Lyme disease
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Calothrix- genus of cyanobacteria that is typically found in freshwater
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Chlamydomonas reinhardtii- single-cell green algae; model organism
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Chlorophyte alga- taxon of green algae
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Commelina communis- herbaceous annual plant in the dayflower family that blooms once every day
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Crocosphaera watsonii- unicellular, diazotrophic marine cyanobacteria
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Cryptomonad- group of unicellular algae that often contain plastids and can be found in freshwater, marine, and brackish habits
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Daphnia manga- small planktonic freshwater crustacean
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Diazotroph- microorganisms that are capable of fixing atmospheric nitrogen into forms that can be utilized by plants
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Deinococcus radiodurans- extremophilic bacterium that can withstand intense radiation and other extreme conditions
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Desulfovibrio alaskensis- Gram-negative, mesophilic sulfate-reducing bacterium
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Diatom- single-celled alga possessing a cell wall made of silica
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Eschericia coli- Gram-negative, rod-shaped facultative anaerobe that is generally found in intestines; model organism
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Emiliania huxleyi- prominent marine coccolithophore
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Fremyella diplosiphon- cyanobacterium capable of chromatic adaptation
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Helicobacter mustelae- Gram-negative rod-shoped bacterium commonly found in the digestive system of ferrets
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Lactobacilli- Gram-positive, non-spore-forming, rod-shaped aerotolerant anaerobe that converts sugars to lactic acid
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Listeria- pathogenic facultative anaerobe that causes the infection listeriosis when people eat contaminated food
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Marinobacter- Marine Proteobacteria, many of which can degrade hydrocarbons
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Marinococcus- Gram positive, halophilic, aerobic, non-spore-forming chemolithoautotroph
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Methanococcus maripaludis- Gram-negative, non-spore-forming, mesophilic, anaerobic methanogen
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Methanogen- microbes that produce methane as a byproduct to methanogenesis, a process in which the microbe metabolizes H2 and CO2
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Methanosarcina acetivorans- methane-producing archaea found in a variety of environments
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Methanotroph- prokaryotes that metabolize methane as their source of carbon and energy
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Methylobacterium extorquens- Gram-negative bacterium that can use methanol and methylamine as well as C2, C3 and C4 compounds to grow
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Methylotroph- microbes that utilize reduced one-carbon compounds, like methanol or methane, as the carbon source for growth
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Mycobacterium tuberculosis- pathogenic, rod-shaped, aerobic bacterium that causes tuberculosis
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Prochlorococcus- small abundant marine cyanobacterium; most abundant marine phototroph
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Pseudomonas aeruginosa- Gram-negative, rod-shaped, aerobic, encapsulated bacterial pathogen that causes disease in plants and animals
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Pseudomonas putida- Gram-negative, rod-shaped, saprotrophic soil bacterium
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Rhizobia- diazotrophic soil bacterium found in the root nodules of legumes
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Saccharomyces cerevisiae- fungal pathogen commonly called Brewer's yeast; model organism
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Salmonella- Gram-negative, rod-shaped pathogenic bacterium that causes infection when humans consume contaminated food or water
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Staphylococcus spp- Gram-positive, spherical facultative anaerobic bacterium that causes Staph infections in humans
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Streptococcus spp- Gram-positive, spherical, pathogenic bacterium that causes infections in humans
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Streptomyces cattleya- Gram-positive bacterium that produces a fluorinase enzyme
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Streptomyces coelicolor- Gram-positive, filamentous soil bacterium
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Streptomyces griseus- Gram-positive, filamentous soil bacterium
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Streptomyces spp- aerobic, Gram-positive, filamentous bacteria that produce vegetative hyphae
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Sulfurospirillum barnesii- vibrio-shaped bacterium
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Synechococcus- unicellular marine cyanobacterium
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Synechocystis- unicellular freshwater cyanobacterium that is capable of both oxygenic photosynthesis and heterotrophic growth during dark periods
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Thalassiosira weissflogii- planktonic centric diatom found in marine and inland waters
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Thermococcus- genus of extreme, heterotrophic thermophiles