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
Betaine lipids- glycerolipids that contain an ether-linked betaine, which is a specific type of zwitterion
Biofilm- colony of microorganisms in which microbial cells adhere to each other and a stationary surface
Biotin- water soluble vitamin B
Carapace- dorsal section of the exoskeleton or shell in a turtle, crustacean, or arachnid
Catechols- colorless, organic compound with the molecular formula C₆H₄(OH)₂
Chaperone- proteins that help with the folding or assembly of other macromolecular structures
Chelate- a compound containing a ligand bonded to a metal atom at two or more points
Chemotaxis- movement of an organism along a gradient of increasing or decreasing concentration of a substance
Cyclohydrolase- an enzyme which catalyzes the reversible cyclization or the ring opening of a purine ring
Cytochrome- proteins that contain the heme prosthetic group
Enolase- key glycolytic enzyme
Enteric- relating to the intestines
Exogenous- caused or produced from outside an organism
Ferredoxin- iron–sulfur proteins that mediate electron transfer
Fe/S proteins- proteins containing iron-sulfur clusters that are versatile cofactors of proteins related to catalysis, electron transport, and sensing of environment
Flagellar rotation- mechanism of bacterial movement involving the rotation of whip-like appendage that protrudes from bacteria
Flavodoxin- bacterial electron-transfer protein that contains flavin mononucleotide
Flavoprotein- oxidizing enzymes containing flavins
Folate- B-vitamin needed to make DNA, RNA, red blood cells, and to convert carbohydrates to energy
Frustule- hard and porous, silicified cell wall of a diatom
Gram-positive- bacteria that have a thicker peptidoglycan cell wall
Halophilic- extremophiles that live in high salt concentrations
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
Isoform- proteins that are similar to each other and perform similar roles within cells
Lipoic acid- organosulfur compound derived from caprylic acid that is needed for aerobic respiration
Macronutrients- C, H, O, N, P, and S; these elements are essential for all life (see About page for further explanation)
Major cation- K, Mg, Ca; cations that have significant roles in the functions of cells
Metalloregulator- protein that regulates biochemical interactions with metals through binding
Pectin- structural starch contained in the cell walls of terrestrial plants
Phenazines- organic compound with the formula (C₆H₄)₂N₂
Phycobilisome- light-harvesting apparatus of photosystem 2 in cyanobacteria and red algae; anchored to thylakoid membrane
Phycocyanins- blue photosynthetic protein-pigment complex in cyanobacteria
Planktonic- free-living bacteria
Plastid- membrane-bound organelle located in the cells of photosynthetic organisms
Plastocyanin- a blue copper protein that catalyzes the transfer of electrons from the Cyt b6f complex to PS I during photosynthesis.
Pyruvate decarboxylase- enzyme that catalyzes the non-oxidative decarboxylation of pyruvate to acetaldehyde and CO2
Quorum sensing- bacterial cell–cell communication process that is dependent on density and causes changes in behavior when a population reaches a certain density
Rare earth elements- includes fifteen lanthanides, as well as scandium and yttrium
Redox- chemical reaction that involves a transfer of electrons between two chemical species, with one species undergoing oxidation and the other undergoing reduction
RNR- Ribonucleotide reductase; crucial enzyme that mediates synthesis of deoxyribonucleotides
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
Siderophore- small, high-affinity iron-chelating compounds secreted by microbes, primarily to transport iron into the cell
Stationary phase- stage of bacterial growth in which the size of the population remains constant, although individual bacteria are reproducing and dying
Stomata- pore in plants that facilitates gas exchange
Sulfolipids- lipids that contain a functional group with a sulfur
Symbiont- an organism living in a symbiotic relationship with another organism
Syntrophy- one species living off the product of another species
Thiols- an organic compound containing the group —SH
Thylakoid- membrane-bound compartments within chloroplasts and cyanobacteria where the light-dependent reactions of photosynthesis take place
Turgor- force within the cell that pushes the plasma membrane against the cell wall so that the cell remains rigid
Urease- enzyme that catalyzes the hydrolysis of urea, making ammonia and CO2
Zinc finger proteins- small protein structural motif that is identified by the coordination of one or more zinc ions for stabilization
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
Aspergillus sydowii- pathogenic fungus that causes several diseases in humans and kills corals
Arabidopsis- genus of small flowering plants related to cabbage and mustard; contains thale cress, a model organism
Azotobacter vinelandii- Gram-negative diazotroph that is capable of fixing nitrogen in an aerobic environment
Bacillus arseniciselenatis- spore-forming, rod-shaped, alkaphilic anaerobe that is capable of respiring selenium
Bacillus selenitireducens- spore-forming, rod-shaped, alkaphilic anaerobe that is capable of respiring selenium
Bacillus subtilis- Gram-positive, spore-forming, rod-shaped facultative aerobe; model organism
Borrelia burgdorferi- Gram-negative spirochete that causes Lyme disease
Calothrix- genus of cyanobacteria that is typically found in freshwater
Chlamydomonas reinhardtii- single-cell green algae; model organism
Chlorophyte alga- taxon of green algae
Commelina communis- herbaceous annual plant in the dayflower family that blooms once every day
Crocosphaera watsonii- unicellular, diazotrophic marine cyanobacteria
Cryptomonad- group of unicellular algae that often contain plastids and can be found in freshwater, marine, and brackish habits
Daphnia manga- small planktonic freshwater crustacean
Diazotroph- microorganisms that are capable of fixing atmospheric nitrogen into forms that can be utilized by plants
Deinococcus radiodurans- extremophilic bacterium that can withstand intense radiation and other extreme conditions
Desulfovibrio alaskensis- Gram-negative, mesophilic sulfate-reducing bacterium
Diatom- single-celled alga possessing a cell wall made of silica
Eschericia coli- Gram-negative, rod-shaped facultative anaerobe that is generally found in intestines; model organism
Emiliania huxleyi- prominent marine coccolithophore
Fremyella diplosiphon- cyanobacterium capable of chromatic adaptation
Helicobacter mustelae- Gram-negative rod-shoped bacterium commonly found in the digestive system of ferrets
Lactobacilli- Gram-positive, non-spore-forming, rod-shaped aerotolerant anaerobe that converts sugars to lactic acid
Listeria- pathogenic facultative anaerobe that causes the infection listeriosis when people eat contaminated food
Marinobacter- Marine Proteobacteria, many of which can degrade hydrocarbons
Marinococcus- Gram positive, halophilic, aerobic, non-spore-forming chemolithoautotroph
Methanococcus maripaludis- Gram-negative, non-spore-forming, mesophilic, anaerobic methanogen
Methanogen- microbes that produce methane as a byproduct to methanogenesis, a process in which the microbe metabolizes H2 and CO2
Methanosarcina acetivorans- methane-producing archaea found in a variety of environments
Methanotroph- prokaryotes that metabolize methane as their source of carbon and energy
Methylobacterium extorquens- Gram-negative bacterium that can use methanol and methylamine as well as C2, C3 and C4 compounds to grow
Methylotroph- microbes that utilize reduced one-carbon compounds, like methanol or methane, as the carbon source for growth
Mycobacterium tuberculosis- pathogenic, rod-shaped, aerobic bacterium that causes tuberculosis
Prochlorococcus- small abundant marine cyanobacterium; most abundant marine phototroph
Pseudomonas aeruginosa- Gram-negative, rod-shaped, aerobic, encapsulated bacterial pathogen that causes disease in plants and animals
Pseudomonas putida- Gram-negative, rod-shaped, saprotrophic soil bacterium
Rhizobia- diazotrophic soil bacterium found in the root nodules of legumes
Saccharomyces cerevisiae- fungal pathogen commonly called Brewer's yeast; model organism
Salmonella- Gram-negative, rod-shaped pathogenic bacterium that causes infection when humans consume contaminated food or water
Staphylococcus spp- Gram-positive, spherical facultative anaerobic bacterium that causes Staph infections in humans
Streptococcus spp- Gram-positive, spherical, pathogenic bacterium that causes infections in humans
Streptomyces cattleya- Gram-positive bacterium that produces a fluorinase enzyme
Streptomyces coelicolor- Gram-positive, filamentous soil bacterium
Streptomyces griseus- Gram-positive, filamentous soil bacterium
Streptomyces spp- aerobic, Gram-positive, filamentous bacteria that produce vegetative hyphae
Sulfurospirillum barnesii- vibrio-shaped bacterium
Synechococcus- unicellular marine cyanobacterium
Synechocystis- unicellular freshwater cyanobacterium that is capable of both oxygenic photosynthesis and heterotrophic growth during dark periods
Thalassiosira weissflogii- planktonic centric diatom found in marine and inland waters
Thermococcus- genus of extreme, heterotrophic thermophiles