Glossary
-cidal
An agent that kills its target.
-lytic
Compounds that cause the lysis of bacteria.
-static
Treatments that do not kill the target organism, but prevent its growth
16s rrna
Ribosomal RNA. One RNA that is part of the ribosome. The 16 S refers to 16 Svedberg units - a measure of how fast the molecule sediments in a centrifuge.
acidophilic
acidophilic describes microbes that thrive in acidic conditions (pH below 5.0).
activation energy
Activation energy is the initial energy required to get a reaction to occur.
activator
An activator is a regulatory protein that when bound to DNA, recruits RNA polymerase to a promoter and increases the rate of transcription.
active transport
Active transport is a mechanism that uses energy to move molecules across a membrane.
adaptive immune systems
The adaptive immune system is that part of the immune system that becomes stronger when exposed to an antigen.
adeleteme
Somthing I want to delete later
adenosine triphosphate (atp)
ATP is a major energy source in the cell and one of the four nucleotides used in DNA and RNA.
adventitious root
A root that arises out of the shoot tissue, not from a parent root. They usually originate from the stem.
aeciospores
Aeciospores are a type of spore produced by rusts, a pathogenic Basidiomycota.
aerotaxis
Aerotaxis is movement toward oxygen or air.
aerotolerant anaerobes
Aerotolerant anaerobes are able to grow in the presence of air, but do not use oxygen in their catabolism.
Aerotolerant anaerobes
Microbes that can survive in air, but do not utilize oxygen in their metabolism. The most common group of microbes that fit this description are the lactic acid bacteria.
agarose gel
An agarose gel is a method for separating DNA fragments. Agarose is a long polysaccaride that when cooled below 40 °C will form a gel. This gel has a range of pore sizes that is dependent upon the concentration of agarose in the solution. If DNA is placed in an agarose gel and subjected to an electric field, it will migrate toward the positive electrode. Its rate of migration is inversely proportional to its molecular weight. Thus DNA fragments of different sizes can be resolved, with small fragments running further than large fragments.
aldehyde
An aldehyde is a organic compound with a terminal carbonyl group.
alkalophiles
Alkalophiles is a term that describes microbes that thrive in alkaline conditions (pH above 8.0).
alkylating agents
Alkylating agents are mutagenic chemicals that react with DNA and modify it by adding alkyl groups.
allosteric protein
An allosteric protein is an enzyme with two sites, the active site and an allosteric site. Binding of the allosteric site causes a change in the activity of the enzyme.
amastigotes
Amastigotes refer to cells of Trypanosoma cruzi in one stage of the protozoan's life cycle.
ames test
The Ames test is an assay to determine if a chemical can mutagenized bacteria. An auxotrophic bacteria strain of Salmonella, with a known mutation in a gene for histidine biosynthesis, is spread onto an agar plate without histidine. Colonies only appear where the original mutation has been reverted. If the addition of a chemical to the plat causes the appearance of more colonies, then that chemical is a mutagen.
amino acids
Small organic molecules with a central carbon (the α-carbon) bonded to four distinct groups. The groups are a hydrogen, an amine group, a carboxyl group and finally some type of organic molecule. The fourth group can be anything from a hydrogen, to a more complex aromatic group. Proteins are made of 20 amino acids that vary only in the fourth group.
aminoacyl-trna synthetases
Aminoacyl-tRNA synthetases are the proteins that attach amino acids to tRNAs. There is one synthetase for each amino acid, which means that many of these recognize multiple tRNAs.
amphipathic
Amphipathic molecules contain both hydrophilic and hydrophobic sections. Lipids are amphipathic.
anabolism
Anabolism consists of the enzymatic reactions of the cell that build cell structures. For example, the reactions that make amino acids or peptidoglycan.
anaerobic
Anaerobic is a state where there is an absence of oxygen
anaerobic respiration
Anaerobic respiration is a type of energy generation using an electron transport system that does not use oxygen as a terminal electron acceptor.
anamorph
Anamorph refers to the non-sexual phase of a fungus
anaphylactic hypersensitivity
Anaphylactic hypersensitivity is an allergic reaction that occurs upon second exposure to an allergin. The reaction results in the release of histamines
angstrom
The angstrom is a unit of measure. 1 angstrom is 1 x 10-10m
anoxygenic photosynthesis
Anoxygenic photosynthesis is photosynthesis that does not generate oxygen
antibiotics
Antibiotics are lower molecular weight natural substances produced by on microorganism that inhibit the growth of other microorganisms.
antibody
Antibodies are a class of proteins made by B cells (also called B lymphocytes) that reaction with antigens.
anticodon
An anticodon is a set of three bases that lie at one end of the folded structure of tRNAs. These bases interact with the codons of mRNAs by base-pairing.
antigen
Antigens are molecules that the immune system reacts to.
antigen presenting cells
Antigen presenting cells are cells that present antigens to the immune system. These include macrophages, monocytes and dendritic cells.
antigenic
A macromolecule, often a protein, that causes an immune response in a host.
antigens
Antigens are molecules that the immune system reacts to.
antiseptics
Antiseptics are compounds that inhibit or kill microorganisms and are safe to use on the skin and mucous membranes, but are normally not taken internally
apoenzyme
An apoenzyme is an enzyme without its cofactor.
ascocarp
The ascocarp is the macroscopic fruiting body of Ascomycota.
ascospore
An ascospore is the sexual spore produced by Ascomycota.
ascus
The ascus is a fruiting structure produced by Ascomycota.
attenuation (two meanings)
Attenuation is the treatment of a pathogen in such a way that it loses much of its virulence. Such a strain is said to be attenuated.
attenuator
The DNA sequence at which transcriptional attenuation occurs.
autoinduction
Autoinduction is the process in which a cell makes a low level of a compound, but the presence of more of that compound leads to higher production. When there is a population of cell that are all producing that compound, the concentration in the environment goes up and is sensed by all the cells, which then respond by increasing production even more.
autotroph, autotrophic
An autotroph obtains its cell carbon from carbon dioxide.
auxotroph
An auxotroph is a strain that requires one or more organic factors for growth, in addition to a carbon source. The term is typically used for mutants that require more additions than does the wild type.
avirulent
A property of a microbe such that it does not cause disease in a specific host.
axial filament
Flagella-like appendages anchored to the ends of the cells and pointing inwards. Rotation of the axial filament causes the cell to twitch or rotate. During rotation the cells will drill through the surrounding medium; even very viscous liquids or tissues.
b cells (b lymphocytes)
B-lymphocytes are cells that are part of the immune system that produce antibodies when activated by antigen
bacteria
A large group of unicellular organisms that lack a nucleus. Typically they are small <10 µm in diameter and can be rods, cocci, and many other shapes. This is also the name of a phylogenetic group (the Bacteria) that refers to one of the major domains of organisms that contains many of the commonly know microbes. The other domains are Archaea and Eukarya
bactericidal
An agent that kills bacteria.
bacteriochlorophyll (bchl)
Bacteriochlorophyll is a photopigment molecule containing a magnesium ion that collects light for photosynthesis. A special pair of BChl make up the active site in the reaction center in photosynthetic complexes of bacteria.
bacteriocins
Bacteriocins are toxic peptides made by lactic acids bacteria, including those that are part of the normal flora and those used in certain food fermentations
bacteriophage
A bacteriophage is a virus that infects bacteria
bacteriopheophytin
Bacteriopheophytin is a photopigment found in cyanobacteria. It is a bacteriochlorophyll molecule minus magnesium. These photopigments are often found in the light harvesting and reaction center proteins of photosynthetic microbes.
bacteriostatic
An agent that inhibits the growth of a bacteria, but does not kill it.
base
A base refers to specific purines and pyrimidines that are connected to sugar phosphates to form the monomers of DNA or RNA. There are four bases in DNA: adenine, guanine, cytosine and thymine. In RNA, uracil takes the place of thymine.
base analog mutagens
Base analog mutagens look sufficiently like normal nucleotides that they are added to DNA during replication in place of the normal nucleotides. Because these are not identical to the normal nucleotides, they often lead to errors in replication that create mutations.
base excision repair
Base excision repair is a cellular process for removing an aberrant base from DNA. It involves cutting out the entire base and sugar and then replacing it with the appropriate nucleotide.
base pair (bp)
A base pair is the pairing of two bases, a purine with a pyrimidine, in the double helix of a DNA molecule that bind together through hydrogen bonds.
base pairing
Base-pairing is interaction between two bases of nucleic acid through hydrogen bonding between the amino and carboxyl groups on their edges.
base stacking
Base stacking is the interaction between two bases that are adjacent to each other on a strand of DNA or RNA. This involves the electron density above and below the planes of the aromatic rings.
base substitution (mutation)
A base substitution (mutation)is a change in the DNA sequence such that one base pair is replaced by a different one.
basidia
A basidia is a structure produced by fungi of the Basidiomycota that holds the spores of the dikaryotic fruiting body. In mushrooms, one example of a fruiting body, the basidia are on the gills underneath the cap of the mushroom.
basidiospores
Basidiospores are spores of the Basidiomycota that are produced during sexual reproduction. Contained in basidia.
basophils
Basophils are a type of leukocyte that is part of the immune system. Basophiils are involved in allergic reactions and fighting parasitic infections.
batch culture
A batch culture involves culturing microorganisms in a system to which media is not continuously added or removed. Examples include broth medium in a flask or tube.
binary fission
Binary fission is a method of bacterial cell division where the parental cell divides equally into two sibling cells.
biocontrol
Biocontrol is the use of microbes to mitigate the effects of harmful organisms.
bioconversion
Bioconversion is the use of microorganisms to perform certain complex chemical reactions. This process entails growing a microorganism in the presence the substrate to be transformed.
biofilm
A biofilm is a population of microorganisms that grow on a surface and encase themselves in excreted layers of polysaccharide. Dental plaque is an example of a biofilm.
biofuels
Hydrocarbon based compounds that can be burned for energy that are extraced from organisms.
bioinformatics
Bioinfomatics is the analysis of genetic sequence data by computer. A database of properties has been built that matches biochemical data from known proteins to their gene sequence. This can then be used to develop testable hypotheses about the properties and functions of proteins whose DNA sequences match that of known ones.
biological oxygen demand (bod)
Biological oxygen demand is a measure of the amount of dissolved oxygen consumed by microbes growing on the organic and inorganic compounds present in wastewater
bioluminescence
Bioluminescence is the production of light by living organisms. Typically this involves an enzymatic reaction by the enzyme luciferase.
biomass
Biomass is the total mass of living material within a given volume.
bioremediation
Bioremediation is the process of removing a pollutant from an area by the use of microorganisms who degrade the pollutant to harmless end products
biosphere
The biosphere is that part of the earth and its atmosphere that supports living things.
bradyzoites
Bradyzoites are slowly multiplying encysted from of the protozoan parasite Toxoplasma gondii
Brownian motion
The movement due to bombardment of submicrosopic particles in the liquid, where the cells (alive or dead) appear to remain in one position but shake somewhat
budding division
Budding division is the form of division where a parental cell creates a morphologically distinguishable sibling cells, that eventually separates from the parental cell.
butanediol fermentation
Butanediol fermentation is a type of fermentation by certain members of the Enterobacteriaceae that produces butanediol as one of its products
cap
The cap is the top lid of a mushroom. Underneath the cap are the gills, which contain the basidiospores. The cap is supported by a stile.
capsid
A capsid is the primary proteinaceous covering of a virus.
capsule
A capsule is a network of polysaccharide or protein containing material extending outside of the cell that is not easily washed off.
carbohydrate
A carbohydrate is an organic compound containing carbon, hydrogen and oxygen in a ratio of about 1:2:1. Sugars and polysaccharides are examples of carbohydrates.
carbona cycle
The Calvin cycle is one pathway that converts carbon into various forms in the environment
carbonate reduction
Carbonate reductions is the process of using CO2 as a terminal electron acceptor. Often performed by methanogens.
carboxylation
Carboxylation is the addition of a carboxyl group to a molecule. For example, ribulose-1,5-bisphosphate undergoes a carboxylation during the Calvin cycle
carboxysomes
Carboxysomes are polyhedral structures that look very much like phage heads and are composed of 5-6 proteins that form a shell around ribulose bisphosphate carboxylase. It is thought that the carboxysomes serve to concentrate CO2 inside the structure and thus increase the efficiency of ribulose bisphosphate carboxylase.
carotenoids
Carotenoids are photopigments found in light harvesting proteins of photosynthetic bacteria. They are also found in many other cells and tissues, such as fish and carrots. They serve a protective role, detoxifying reactive by-products of light exposure.
carrier
An animal or individual showing no outward signs of illness that harbors an infectious disease and is capable of transmitting it to others.
catabolism
A termed used to refer to the reactions of the cell that breakdown compounds into component parts and typically generate energy.
catabolite repression
Repression of gene expression in the presence of glucose. Genes for alternative carbon and energy sources are often regulated by catabolite repression
cell
The smallest unit of an organism that is capable of independent functioning. For microorganisms, this encompasses their entire structures
cell-mediated (delayed) hypersensitivity
An allergic reaction where the reacting is dependent upon the action of T cells. These become sensitized to an allergen and after a delay (about 2 weeks) they produce welts on the skin. The tuberculin test is a cell-mediated hypersensitivity to antigens from Mycobacterium tuberculosis.
cell-mediated immunity
Immunity in animals that involves the activation T cells.
central dogma
The hypothesis that biological information moves from DNA to RNA and then results in protein.
centromere
The most condense part of a chromosome to which the spindle fiber is attached during cell division.
centrosome
A structure near the nucleus that contains centrioles and is involved in pulling chromosomes apart during cell division.
chaperones
Proteins that help nascent proteins fold correctly and also repair mis-folded proteins.
chemically defined media
Media where the chemical nature of all of the ingredients and their amounts are known.
chemically defined medium
A growth medium where all the components of a medium are known both qualitatively and quantitatively.
chemiosmotic theory
An idea explaining the method of ATP synthesis that involves proton motive force and ATP synthase.
chemoautolithotroph or chemoautotrophic lithotroph
A nutritional classification where the microbe gets its energy from chemicals, its carbon from CO2 and its electrons from inorganic sources
chemoheteroorganotroph
A nutritional classification where the microbe gets its energy from chemicals and its electrons and carbon from organic compounds
chemoheterotroph
An organism that gets it energy from chemicals and uses organic compounds as its source of carbon. Microbes that fall into this class are also often organotrophs, obtaining their electrons from organic compounds.
chemoheterotrophic organotroph
A nutritional classification where the microbe gets its energy from chemicals and its electrons and carbon from organic compounds.
chemoorganotroph
An organism that gets it energy from chemicals and uses organic compounds as its source of electrons. Microbes that fall into this class are also often heterotrophs, obtaining their carbon from organic compounds.
chemostat
A vessel for the continuous culture of microbes. Fresh medium is continuously added and waste products are removed. Microbes can be grown in chemostats indefinitely.
chemotaxis
Movement toward or away from a chemical.
chemotherapeutic agents
A chemical that has some type of utility in the treatment of a disease. Antibiotics are one type of chemotherapeutic agent.
chemotroph
An organism that generates its energy by the oxidation of chemicals.
chlorophyll
Chlorophyll is a photopigment molecule containing a magnesium ion that collects light for photosynthesis. A special pair of chlorophyll make up the active site in the reaction center in photosynthetic complexes of cyanobacteria and plants
chloroplast
The organelle inside eukaryotic cells where photosynthesis takes place
chromosome
A part of the genome (DNA) of an organism that contains essential functions.
circulatory system
System of arteries, capillaries and heart that circulates blood throughout the body.
clathrin
A protein involved in the endocytosis of particles that bind to the surface of eukaryotic cells
cloning (two meanings)
1. The amplification and isolation of specific regions of DNA in vitro. This typically involves the creation of plasmids or phage with the desired region. It can also be accomplished by PCR amplification.
co-repressor
A small molecule that binds to a repressor protein and causes a conformational change that allows the repressor to bind a DNA sequence and block transcription.
codon
Three consecutive bases on an mRNA that are read simultaneously by the ribosome and signal the incorporation of a specific amino acid in translation.
coenzyme
An organic chemical that is part a enzyme and assists in the reaction that it carries out.
cofactor
A general term for any part of a protein that is not part of its peptides chain, yet is important in its function. Cofactors can be coenzymes or prosthetic groups
colonies
A mound of microorganisms growing on a plate
color indicator
A chemical added to a growth medium or other solution that changes when specific conditions change. For example, a pH decrease causes the color indicator bromcresol purple to change from purple to yellow.
combinatorial chemistry
A chemical reaction in which multiple different chemical components are allowed to react randomly to crate novel compounds. Typically this involves the polymerization of polymers from different monomers.
commensal
A symbiotic relationship where the host is neither harmed nor helped by the presence of a microbe
compatible solutes
Solutes that are compatible with the physiology of a cell and are accumulated to deal with osmotic stress.
competitiveness
A measure of how well a microbe is above to grow in a given environment. The term is often used when comparing the ability of different strains to grow on various hosts.
complement
Complement is an enzymatic system in the blood containing nine proteins (termed C1-C9). These proteins are produced in macrophages, in liver cells and by epithelial cells in the gastrointestinal mucosa. They circulate in the bloodstream and when activated, attack foreign cells.
complex media
Medium in which the ingredients and their concentration is not known. Complex medium often contains extracts of plants, animals and yeast and will support the growth of many microorganisms.
Complex medium
A medium that contains extracts of plants or animals where the exact quantity of each chemical is unknown and often varies from lot to lot.
component vaccines
Solutions containing only parts of pathogens (typically major antigens) that raise a protective immune response.
concatamer
The physical linkage of many identical pieces of nucleic acid in an end-to-end arrangement.
conidia
An asexual spore produced by various fungi.
conidiophores
Structures that hold conidia
conjugation
Transfer of pieces of DNA from one cell to another through cell-to-cell contact that is mediated by a number of protein factors.
consensus sequence
A composite sequence of nucleic acid or protein monomers that represents the statistical average of a number of naturally occurring sequences of the same type. In other words, all known natural sequences are compared in a monomer by monomer way and the most common monomer at each position defines that position in the consensus.
constant regions(fc)
The conserved region of antibodies that interacts with the immune system.
continuous culture
A culture that grows indefinitely. These are typically maintained inside chemostates
core polysaccharide
A highly conserved polysaccharide that is part of the lipopolysaccharide of the Gram negative cell wall.
corrinoid
Coenzymes (such as vitamins B12) that contain cobalt and have a porphyrin-like structure
covalent modification
A type of post-translational regulation of enzymes that involves the covalent attachment of a modifying group to the enzyme
Cyanobacteria
Photosynthetic bacteria found in many aquatic environments. Their photosynthetic apparatus is very similar to that used by plants.
cysts
A type of resting cell that contains a thicker cell wall.
cytokines
Small peptides produced by cells of the body that act as intracellular signals, especially between cells of the immune system.
cytoplasm
The part of the cell inside the cell membrane, but not including any organelles
cytotoxic hypersensitivity
An allergic reaction that involves the destruction of whole cells
deamination
The removal of an amine group from a molecule
death phase
In batch culture, the part of the growth curve where cells are dying
decimal reduction times
The length of time it takes for the viable population of a microbial culture to decrease 10 fold at a given temperature. This is a measure of the heat sensitivity of a microbe.
deletion
A mutation in which two or more contiguous base pairs are eliminated from the sequence.
denitrification
A respiratory process where NO3- serves as the terminal electron source and is reduced to N2 gas.
dental carries
Cavities in the teeth, Caused by the growth of microorganisms
deoxynucleotide triphosphate (dntp)
A general term used to refer to all four nucleotide triphosphates: dNTP is dATP, dCTP, dTTP and cGTP.
depth filters
A type of filter containing overlapping layers of fibrous sheets of paper, asbestos or glass fibers
depurination
The removal of purine from DNA.
dichotomous key
A flowchart or other diagram that deliniates a set of organisms based upon a set of properties. In the key, a serious of questions is asked and depending upon the answer for a particlular test orgnaisms, the path through the key is determined. At the end of the key, the exact species is often determined.
diffusion
The spontaneous mixing of particles caused by thermal motion
diglycerides
A glycerol unit that contains two fatty acids attached to it by ester linkages.
disinfectants
These are compounds that kill microorganisms and may or may not kill spores, but are not safe to apply to living tissues
dissimilatory nitrate reduction
The reduction of nitrate and its use as a terminal electron accepter.
DNA
A polymer of nucleic acd that serves as the hereditary material for all organisms. It is capable of self-replication and synthesis of RNA in the cell. DNA consists of two long chains of nucleotides twisted into a double helix and joined by hydrogen bonds. Hydrogen bonds form between cytosine and guanine or adenosine and thymine, the bases that make up DNA.
domain (two meanings)
1. With reference to proteins, a domain is a portion of the protein that forms a single structural region or, occasionally, a single function region.
duplications
Genetic mutations that involve the addition of a duplicate copy of a region of DNA elsewhere in the genome. Typically it is immediately adjacent to the original copy and oriented in the same direction, where it is termed a tandem duplication.
early phase
The initial events in the viral infection of a cell.
effector
A small molecule that signals something, typically by binding to a protein. The most typical case is where a protein binds DNA and activates transcription only after binding an effector molecule.
egestion
The expulsion of microbial material from a phagocyte after it has dealt with an invading microbe.
electron
A stable negatively-charged subatomic particle that is part of all atoms and molecules. Electrons can flow through respiratory chains and between molecules in the processes of metabolism.
electron microscopes
A type of microscope that uses electrons instead of light for visualizing samples.
electron transport level phosphorylation
A membrane bound process where the movement of electrons down a electron transport chain results in the pumping of protons across a membrane. This ensuing proton motive force is used to drive ATP synthesis using ATP synthase.
endocytosis
An uptake process that eukaryotic cells use to take in particles in which the plasma membrane infolds and surround the particle.
endoplasmic reticulum
A finely divided system of interconnected membranes, consisting of tubules and vesicles that loop through the cell and are contiguous with the nuclear membrane. It functions in the synthesis of membranes and membrane proteins and is also involved in protein secretion.
endosome
The term that describes a membrane-lined particle in a cell that has been taken up by endocytosis
endospores
A resting strucure produced by Bacillus, Clostridium and other species that is extremely resistant to heat, chemicals, radiation and drying
endosymbiosis
A symbiosis between two organisms in which one lives in the cytoplasm of the other.
endotoxin
Lipopolysaccharide. Part of the gram-negative cell wall that when released from a pathogen has systemic toxic effects
enrichment medium
Medium formulated to encourage the growth of a desired microbe, while inhibiting the growth of other microbes
enthalpy
The sum of the internal energy of a system. The heat of a system.
entropy
A measure of the disorder or randomness of a closed system.
envelope
A term used to described the outer membrane of a virus
environmental microbiology
Environmental microbiology is the study of the numbers and species present in the various environments of the earth and their physiology.
eosinophils
A type of leukocyte that is part of the immune system. They are important in regulating the immune system, in combating large parasites.
epidemiology
The branch of medicine that deals with the transmission, incidence and control of disease through public health campaigns.
epimastigote
A stage in the life cycle of protozoan of the Trypanosome genus.
erythrocytes
Red blood cells
eukarya
The domain of organisms that contain a membrane-bound nucleus
eukaryotic
Containing a membrane-bound nucleus
eutrophic
Waters rich in mineral and organic material and capable of supporting abundant growth on microorganisms
exons
A sequence of DNA in eukaryotes that codes for mRNA and protein
exotoxins
Highly poisonous protein toxins produced by some pathogens
exponential phase
In batch culture, the period in a microbe's growth curve where the population is increasing.
expression vector
A plasmid that has been designed so that genes can readily be cloned downstream from a strong promoter, allowing high levels of expression from the cloned genes.
extreme halophiles
Microorganisms that are able to grow in the presence of very high concentrations of salt (>2 M NaCl)
extreme thermophiles
Microorganisms that grow at very high temperatures (>85 °C)
extremophiles
Microorganisms that can grow at extremes of temperature, pH, pressure or salt concetration.
f factor
A specific set of genes that typically exist as plasmids in enteric bacteria. These genes encode the functions necessary for conjugation, which can result in movement of the plasmid to another cell. If the plasmid has integrated into the chromosome, then the entire chromosome is capable of being transferred.
fab
The variable region of an antibody that reacts with antigen.
facilitated diffusion
Specific transport of a molecule across a membrane facilitated by a protein. No energy is required, but the molecule is not concentrated against a gradient.
facultative anaerobes
A microbe that can grow using oxidative respiration when in oxygen, but is still capable of fermentation under anaerobic conditions
facultative anaerobes
Microbes that can grow in the presence of oxygen or in its absence. They use oxygen in their metabolism when it is present, but grow by fermentation in its absence.
fats
An ester of glycerol that contains one, two or three fatty acids.
feedback inhibition
A type of regulation of enzyme activity where the end product of a pathway inhibits the first enzyme that is unique to that pathway
fermentation
a catabolic process whereby organic molecules serve as both electron donors and electron acceptors. Because the process does not employ a very oxidizing compound such as O2, the substrates are not fully oxidized.
fermentor
A vessel to grow microorganisms in. Despite its name, fermentors can be grown aerobically or anaerobically
filamentous growth
A mode of growth where a microbe lengthens its initial tubular shape as one long filament. At certain intervals the tube will branch in some species and eventually expand in a number of directions. As the microbe grows, copies of the genome are made and laid down along the filament. Cross walls may be laid down between genomes, but this is not always true. Filamentous growth is found in the fungi and actinomycetes
fimbriae
Tubular structures that project from the outer surface of a microbe into the environment. They are involved in attachment Fimbriae are made one or a few proteins that polymerize in a helical fashion.
flagella
Tubular structures that project from the outer surface and function in motility. Flagella acts as propellers, when spun counterclockwise they push the cell forward
flavins
Tricyclic compounds involved in electron transport
formylmethionine
A special amino acid that starts all proteins in prokaryotes.
frameshift mutations
Genetics mutations where one or two contiguous base pairs are added or removed from the wild-type sequence.
frameshifts
A short-hand names for frameshift mutations.
free energy
The energy available to do work. In biology, this usually refers to the energy release from a chemical reaction.
fruiting bodies
Spore-bearing structures made when starving by molds, slime molds and some bacteria..
fungi
A class of eukaryotic microbes that grow by absorption of nutrients, typically from dead organisms.
fungicidal
An agent that kills fungi
fungistatic
An agent then inhibits the growth of fungi, but does not kill them.
fusions
Genetic rearrangements, typically created in vitro, in which two distinct regions are deliberately placed next to each other. This might be a case where a promoter from one gene is placed upstream of another gene, especially where the product of the latter gene is easily assayed. In that case, the activity of the gene product indicates the functionality of the promoter. Alternatively, portions of two different genes can be fused to create a protein that is a chimera with portions of both of the original gene products.
gamontocyst
A cyst formed around a number of gamonts that eventually fuse and then divide to form gametes
gamonts
Sexually reproductive cells produced by Apicomplexa
gas vesicles
Protein-lined chambers that are capable of trapping gas inside them and serve as little flotation devices that allow the microbes maintain their position in the water column
gastrointestinal
Referring to the digestive tract.
gene arrays
Patterns of small amounts of genes or portions of genes on solid surfaces that represent most or all of those present in the organism. Nucleic acids that are labeled in some way are then hybridized to the array and the genes to which
gene transfer systems
Any mechanism for moving DNA from one cell to another, including conjugation, transduction and transformation.
generalized transduction
The movement of host DNA from one cell to another by page. It results from the accidental packaging of host DNA into phage heads during their assembly. This DNA is subsequently injected into recipient cells in the manner typical for phage infection.
genetic engineering
The manipulation of genetic material in vitro.
genomes
The total genetic information within a given cell.
genomics
The analysis of sequence information to make predictions and conclusions of biological significance.
genotype
The precise genetic make-up of a strain. This can be defined as its DNA sequence.
geosmins
Geosmins are a class of volatile low molecular weight compounds produced by streptomycetes. The odor of soil is due to the production of geosmins.
gills
A part of the mushroom underneath the cap that holds the basidia.
gliding motility
A method of motility where bacterial move across a solid surface.
glycocalyx
A general term for any network of polysaccharide or protein containing material extending outside of the cell.
glycolipids
Lipids with covalently attached sugars.
glycolysis
the breakdown of simple sugars into pyruvate. Often refers to the Embden-Meyerhoff-Parnas pathway.
glycoprotein
Proteins with covalently attached sugars.
glycosylation enzymes
Proteins that add sugars to other proteins or lipids
golgi apparatus
An organelle containing a double membrane that is mainly devoted to the processing of proteins, by proteolysis and glycosylation, synthesized in the endoplasmic reticulum
gram
This either refers to the staining procedure developed by Hans Christian Gram that stains bacteria differentially based upon their cell wall structure or is a unit of mass in the metric system equal to one one-thousandth of a kilogram.
growth factors
Organic molecules that are necessary for growth, yet a microbe is unable to synthesize. Often these are vitamins, nucleic acids and amino acids.
halophiles
Microbes that require high salt concentrations in order to grow.
halotolerant
Microbe that can tolerate high salt concentrations, but grow better at low salt concentrations.
haploid
Having a single set of chromosomes.
heat-shock proteins
Proteins that are transiently expressed at a higher level after an increase in temperature. Many of these are molecular chaperones or proteases
helicase
A protein that imparts super-helical twists to the DNA helix.
helper virus
A wild-type virus that is required for a defective virus to grow.
hemes
Pophyrlin rings containing a iron as the chelated atom. Important in many electron carriers
heterocysts
Rounded structures distributed at regular intervals along a string of vegetative cells in some filamentous cyanobacteria.
heterotroph
A heterotroph obtains its cell carbon from organic compounds.
high frequency of recombination (hfr)
An Hfr strain is one that conjugates its chromosome to other cells frequently. The critical feature of these is that they have an F factor integrated into the chromosome.
holoenzyme
A complete and active protein containing all it protein subunits and any necessary cofactors.
horizontal transfer
The inheritance of DNA by one cell from another cell to which it is not closely related. Horizontal transfer is typically by conjugation or transduction.
hormone
Small peptides made by cells that regulate the activity of other cells.
humoral immunity
Immunity in animals that involves the production of antibodies
hybridization
The process where two complementary single-stranded DNA sequences come together and form a double-stranded DNA sequence.
hydrothermal vents
Cracks in the ocean floor where tectonic plates meet. In these areas, water seeps into the molten rock below the ocean surface and become superheated. At this high temperature, it also absorbs large amounts of reduced ions. Due to it higher temperature, the water now rises, and blasts into the open ocean. Much of the ions precipiate out and form deposits around the ejection area for the water.
hyperthermophiles
Microorganisms that grow at very high temperatures (>85 °C)
hypha (plura hyphae)
Thread-like, tubular filaments formed when growing. Commonly found in fungi and actinomycetes
hypnozoites
dormant stage of Plasmodium vivax and P. ovale that is present in liver cells. It can reemerge later to cause delayed malaria and malarial relapses.
icosahedron
A 20-sided roughly spherical structure. Icosahedrons are a common capsid structure for viruses
immune complex-mediated hypersensitivity
Allergic reactions cause by
immunity
Being resistant to disease or infection by a specific pathogen.
immunoglobulins
Another name for antibodies. A class of proteins made by B cells (also called B lymphocytes) that reaction with antigens.
in vitro
in the test tube, away from the microbe.
in vivo
in the microorganism
inducer
A small molecule signal that elicits a response. Typically it refers to the specific case of a small molecule that binds to a repressor protein and causes that protein to cease its interference with transcription.
infectious
An agent that is capable of being transmitted throughout a population. For microorganisms, this normally is applied to disease-causing organisms.
inflammation
A localized protective of tissue to damage or infection that results in pain, redness and swelling.
informational suppressors
Mutations that suppress the phenotype of another mutations by altering the way the information of the original mutation is processed into a product. Informational suppressors therefore alter transcription or, more typically, translation machinery so that the mutant information is inappropriately processed, but with the result that more functional product is made.
initiation factors
Proteins that monitor the initiation of translation by ribosomes on mRNA. Their role is to prevent inappropriate translation.
initiator trna
The tRNA that inserts formyl methionine and the first codon of genes.
innate immune systems
General mechanisms in a healthy animal that prevent colonization by microorganisms and antagonize or kill those that do enter the host Innate immunity is always present and the strength of its reaction does not increase upon repeated exposure to an antigen.
inoculation
The process of adding culture to a broth to begin growth of a culture. In immunity and health it can also mean the introduction of an antigenic substance into the body to create an immune response..
insertion sequences
Bits of selfish DNA that move from place to place in the genomes of prokaryotes and eukaryotes. More formally, they are pieces of DNA the move by a transposition mechanism, which involves a bit of new DNA synthesis, and that carry genes only related to transposition.
intracytoplasmic membranes (icm)
Invaginations of the cell membrane with the goal to increase the surface area. This is often used to provide room for membrane proteins.
introns
Regions of eukaryotic DNA that that is transcribed into mRNA but then processed out of the mRNA before translation.
inverse genetics
An approach to genetic manipulation in which specific mutations are created in vitro and then used to replace the normal region in the cell.
kb
kilobase pairs. Typically used to refer to the length of DNA
ketone
A carbonyl group in the middle of an alkyl chain
kinetochores
Region of the chromosome where microtubes attach during cell division
korarchaeota
A division of Archaea
lag phase
The first phase of growth after inoculation of a culture, where no population increase is observed.
lateral transfer
Another term for horizontal transfer: The inheritance of DNA by one cell from another cell to which it is not closely related. Horizontal transfer is typically by conjugation or transduction.
leader peptides
A very small, non-functional peptide involved in regulation by attenuation
leaky (mutant phenotype)
A leaky mutant phenotype is one that is difficult to distinguish from the wild-type phenotype. A mutation with a distinct mutant phenotype is termed tight.
lesion
An alteration in DNA that might become a mutation. A lesion necessarily has chemical features that are unlike normal base pairs, so lesions are often recognized and corrected by repair systems.
lethal
A mutation that kills the cell under some condition. Typically they are temperatur-sensitive that only kill above or below some temperature.
ligate
A biochemical reaction by which chemical bonds are formed in the backbone between two adjacent nucleotides. This is typically performed by a ligase.
lipid a
A highly conserved region of lipopolysaccharide consisting of a phosphorylated N-acetylglucosamine (NAG) dimer with six or seven fatty acids attached.
lipids
An amphipathic molecule containing a backbone of glycerol with two hydrophobic fatty acids attached by ester linkages and a hydrophilic group attached to the third hydroxyl of glycerol. Lipids are a major component of membranes
lipopolysaccharide
A glycolipid composed of Lipid A, core polysaccharide and O-specific antigen.
lipoteichoic acid
A phosphodiester polymer of glycerol or ribitol joined by phosphate groups and linked to a lipid.
lithotroph
A lithotroph obtains its electrons from inorganic compounds.
localized anaphylaxis
An anaphylactic allergic reaction that is localized to a specific area, such as the nose or gastrointestinal tract.
longitudinal
Moving lengthwise rather than across something.
loss-of-function (mutation)
A mutation that eliminates the function of the encoded gene product entirely.
lymph nodes
Encapsulated tissues that are major centers for immune function. They are present throughout the body and filter large volumes of liquid and cells, detecting antigens and removing microbes. Lymph nodes also interact with phagocytes to begin various immune functions that we will elucidate later
lymphocytes
Another name for white blood cells
lymphokines
Chemical signal peptides secreted by white blood cells
lyse
The disruption of the integrity of a cell, either by biological means (such as a virus) or by physical means.
lysogen
Typically this refers to a cell that carries a virus in a state of hibernation (lysogeny), but is sometimes used to refer to the virus in that state.
lysogeny
The situation in which a virus has entered into a hibernating state within a cell.
lysosomes
Membrane encased particles that contain digestive enzymes and toxic substances. Lysosomes are present in cytoplasm of eukaryotic cells and fuse with incoming phagosomes.
macroconidia
Large structures produced by some fungi that bear asexual spores.
macrogametocyte
A female gamete for the malaria parasites, Plasmodium vivax, P. falciparum, P. ovale and P. malariae
macrogamont
A precursor cell to the zygote for Cryptosporidium parvum. This cell will mate with a microgamont to form a zygote.
macronucleus
Ciliate protozoa have a two nuclei. The macronucleus is involved in the production of mRNA for protein synthesis and other cell functions. The other nucleus is called the micronucleus
macronutrients
Nutrients needed by the cell in quantities that are larger than 1% of the cells dry weight. Common macronutirents include C, N, H, O and P
macrophages
Long-lived specialized phagocytes. Macrophages are found in the brain, lungs, liver, spleen, lymph nodes, joints and peritoneum.
magnetosomes
Lipid-encased structures made of magnetite (Fe3O4), iron sulfide greisite (Fe3S4) or Fe3S4 and iron pyrites FeS2. Magnetosomes are magnetized and cause the microbe to orient itself in a magnetic field.
major histocompatibility complex (mhc)
Special surface proteins of animal cells that hold protein fragments in a groove and present them to the immune system.
mapping
The determination of where mutations or genes lie on a genome with respect to other mutations or genes. Genome sequencing is an extremely precise form of mapping.
mast cells
Immune cells located throughout the body that secrete a number of chemicals (including histamine) when activated.
mbp
Megabase pairs, 1,000,000 base pairs.
medium
A solution or solid that is used for the growth of bacteria. For example LB medium or minimal medium.
meiosporangia
A type of zoosporangium made by chytrids that is involved in sexual reproduction.
merodiploid
A cell that is partially diploid, because some region is duplicated either in the chromosome or on a plasmid. The strain is said to be merodiploid for that region.
meront
One type of cell produced during the life cycle of Cryptosporidium species
merozoites
A cell that arrises from the outgrowth of a parent sprozoan. It can have either a sexual or asexual mode of replication.
mesophiles
Microbe that grow at intermediate temperatures (15-45°C)
messenger rna (mrna)
A version of the DNA primary structure that is suitable for translation into protein
metabolism
The sum total of all the biological reactions in a cell.
metaphase
That period in the cell cycle in eukaryotes where the chromosomes condense.
methanogen
A microorganism that produces methane as a metabolic product
methanogenesis
The process of producing methane
microaerophiles
Microbes that requires oxygen for their metabolism, but cannot survive at atmospheric concentrations of oxygen.
microconidia
Smaller structures produced by some fungi that bear asexual spores
microgametocytes
A male gamete for the malaria parasites, Plasmodium vivax, P. falciparum, P. ovale and P. malariae
microgamont
A precursor cell to the zygote for Cryptosporidium parvum. This cell will mate with a macrogamont to form a zygote.
micronucleus
Ciliate protozoa have two nuclei. The micronucleus is involved in inheritance and sexual reproduction. . The other nucleus is called the macronucleus
micronutrients
Nutrients required in low concentrations (0.1-1.0% of the cells dry weight). Micronutrients include calcium, potassium, magnesium, sulfur, iron and manganese
micropipettes
Hand held tools capable of measuring very small volumes. Various micropipettes can dispense volumes ranging from 0.1 l to 5000 l.
microtubules
Hollow cylindrical structures that are 20-25 nm in diameter containing tubulin as the major structural protein. They are involved in moving items around eukaryotic cells and in the cell cytoskeleton.
minimal media
A chemically defined medium that provides the minimal number of chemicals to provide a cells nutritional requirements.
minimal medium
A growth medium that contains the minimal requirements for a species to grow. All minimal medium is chemically defined medium.
minimum inhibitory concentration (mic)
The lowest concentration of a compound that still inhibits its growth
mismatch repair system
A set of proteins in bacterial cells (though there are certainly counterparts in most other cell types) that scan the DNA for base pairs that are not normal. The abnormality might be because the two bases do not match or because of extra chemical modifications on a base. This scanning typically follows along the DNA replication fork, so it removes the base of the aberrant pair that is on the newly synthesized strands.
missense
A type of base substitution mutation that causes an amino acid to be inserted at that codon that differs from that in the wild type.
mitochondria
Eukaryotic organelles involved in energy generation through respiration.
mitosporangia
Fungal structures in the Zygomycota that produce asexual spores
mixed acid fermenters
A type of fermentation by certain members of the Enterobacteriaceae that produces acetic acid, succinic acid, formic acid, lactic acid, ethanol, CO2 and H2 as end products
mobile genetic elements
Any piece of DNA that has the ability to cause itself to be moved to another place in the genome.
mobilizable
A replicon that carries a mob site, so that it can be moved during conjugation.
modifying enzyme
An enzyme that chemically modifies another macromolecule. Typically, the substrate is another protein and the modification affects the activity of that protein.
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monocytes
Long-lived migrating phagocytic cells found in the bloodstream that eventually enter other tissues, and differentiate into macrophages.
motif
A sequence of protein that correlates with a particular biochemical activity. This might be several residues with a particular spacing between them that is found in many sites that bind ATP, for example.
mucosal associated lymphoid tissue (malt)
Tissues of the immune system associated with mucosal surfaces
mutagen
A chemical that increase the mutation rate in a specific organism.
mutant
Historically, this was a strain that is a derivative of the wild type but has a discernibly different phenotype. While this is still correct, it is now safer to say that it is a strain that is a derivative of the wild type but that has a change in its genotype.
mutation
Any change in the DNA sequence of an organism relative to that of the wild type of the species.
mutation fixation
The process by which a lesion is converted into a base pair that is different from that found in the wild type, but is otherwise a normal base pair.
mutualistic
A symbiotic relationship where both members benefit
mycelium
Mats of hyphae formed by microbes that grow filamentously.
mycorrhizae
Fungi that form symbiotic relationships with plants roots
nad
Nicotinamide adenine dinucleotide. An electron carrier involved in many oxidation reduction reactions in the cell
nanotubes
Small tubes made of carbon that form a hollow mesh just a few nanometers in diameter.
nascent polypeptide
A growing polypeptide chain that is being synthesized on a ribosome
nasopharyngeal
The upper throat behind the nose.
nasopharynx
The area in the back of the throat behind the nasal cavity.
natural killer cells
A type of immune cell present in the body that can attack foreign cells, but is not inducible
naturally transformable
The property of certain wild-type organisms by which they take up DNA from their environment and incorporate some of that into their genome.
negative regulation
Any process that has the net result of lowering the expression of function of something in the cell. This is typically a decrease in gene expression, but might be at other levels including modification of protein activity.
neutrophiles
Microbes that have optimum pH ranges from 5.0 to 8.0 for growth.
neutrophils
Short-lived phagocytic cells present in the body.
nitrogen cycle
A cycle of reactions that convert nitrogen into various forms in the environment
nitrogen fixation
The process of reducing nitrogen gas to ammonia. Microorganisms perform this reaction using nitrogenase.
nod factors
Genes involved in the process of nodulating plants
non-permissive (condition)
The growth condition under which a conditional mutation displays its mutant phenotype.
nonsense codons
A codon that signals to the ribosome that it should terminate translation.
normal flora
The typical inhabitants of a host organism that do not cause disease and in some examples are even helpful.
nucleoid
The region in bacterial cells where the chromosome is located. This region is not divided from the rest of the cell as in eukaryotes.
nucleotide
The base, sugar and phosphoryl group of nucleic acid.
nucleotide excision repair
The removal and proper replacement of about a dozen bases surrounding a defective one on one strand of DNA.
nucleotide triphosphate
A nucleotide with a triphosphate - a precursor in nucleic acid synthesis.
nucleotides
The compounds that make up the building blocks of DNA and RNA. DNA is composed of adenosine, cytosine, guanine and thymine. Each of these bases is linked to a ribose sugar and a phosphate to make nucleotide monomer.
nucleus
An organelle surrounded by a membrane that houses the chromosome of eukaryotes.
nutrients
Elements or molecules needed by organisms for growth
o antigen
Part of LPS. O antigen is attached to the core antigen and consists of repeating units of three to five sugars. The sugars present in O antigen will vary greatly, even within a single species
obligate aerobes
Microbes that require oxygen form growth and use it as their terminal electron acceptor
obligate parasites
Parasites that are absolutely dependent upon their target host for replication. They cannot grow outside of their host. All viruses and some bacterial pathogens are obligate parasites.
oligotrophic
A term to describe an aquatic environment where nutrient concentrations are low..
oocyst
Resting cells of several protozoa that allow them to survive in the environment
ookinetes
One phase of the malaria parasite. These cells grow only in mosquitoes
open complex
A complex formed between RNA polymerase and DNA just before polymerase begins transcription. It is an intermediary step that follows the binding of the promoter by RNA polymerase, and refers to opening of the DNA duplex before transcription initiates.
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open reading frame
An open reading frame is a stretch of DNA that have all the appropriate signals for DNA transcription and translation into a protein. This includes a recognizable promoter, a termination signal, a start codon, a stretch of codons of significant length, and a stop codon a.
operon
One or more genes that are typically co-transcribed.
opsonins
Macromolecules, such as complement and antibodies, that bind to pathogens and help increase the efficiency of phagocytosis.
opsonization
The process of enhancing the binding of phagocytes
optical density
A measurement of the turbidity of a culture that depends upon the portion of light scattered by the culture.
orfs
A region of DNA that, based on sequence analysis, has the apparent properties of encoding a protein, such as a good start codon, stop codon and reasonable length.
organelles
Organized, membrane enclosed structures, such as mitochondria, chloroplasts and nuclei, inside eukaryotic cells that perform some function.
organotroph
An organotroph obtains its electrons from organic compounds.
oric
The site on a DNA replicon, typically the chromosome, at which bidirectional replication begins.
origin of replication
The site of where the replication of a replicon begins, which has different specific terms for different replicons.
origin of transfe
(oriT) Organism that have optimum growth in the presence of high solute concentrations. This term is typically applied to fungi.
osmosis
Diffusion of fluid through a semipermiable membrane from an area of high concentration to an area of low concetration.
oxygenic photosynthesis
Photosynthesis that generate oxygen
palindromic
A sequence in DNA that has the same sequence when read in either direction.
parasite
A organisms that lives benefits from an association with another organism and in doing so does its host harm
parasitic
Of. or relating to a parasite
parfocal
The arrangement of lenses in a microscope such that when one objective lens is in focus, all other lens are also in focus. Thus if one focuses a specimen with the 10X objective, it is also in focus when the 40X objective is brought in line. Due to the narrower focal plane, some minor adjustment may be needed when increasing magnification.
pasteurization
A heating process that raises the temperature of a substance, most often a food or beverage, to kill pathogenic microorganisms in it. Original heat treatments were for 66 °C for 30 minutes, but modern treatment are at higher temperatures for shorter time periods (72°C for 15 seconds)
pathogen
A organisms that causes disease in another organsim
pathogenicity
The degree to which an organisms can cause disease
penicillin-binding proteins (pbps)
Bacterial proteins that bind penicillin. These normally are involved in bacterial cell wall synthesis.
periodontal disease
Infection of the various supporting structures of the teeth, due to prolonged periods of plaque formation. The most common form of this disease is gingivitis, an inflammation of the gums.
periplasm
The space between the cytoplasmic and outer membranes in gram-negative bacteria or the space between the cytoplasmic membrane and the peptidoglycan in gram-positive bacteria.
permissive (condition)
The growth condition under which a conditional mutation displays a wild-type phenotype.
petri plates
Shallow glass or plastic containers about 7 cm in width with a transparent cover. The cover is a few mm wider and fits over the plate, thus protecting it from microbes in the air.
ph
A measure of the hydrogen ion concentration of a solution. The pH is equal to the negative log of the hydrogen ion concentration. pH = -log10[H+].
ph indicator
A dye or other compound that changes characteristics based upon the pH of a solution.
phage
A virus that infects prokaryotes.
phagocytes
Immune cells in the body that ingest pathogens and kill them.
phagocytosis
The process of ingesting a particle into a cell by invagination of a membrane and then digesting it by fusion with a lysosome.
phagolysosome
The vesicle that results after a phagosome fuses with a lysosome. The contents of the lysosome typically rapidly inactivate and digest everything inside the phagolysosome after fusion.
phagosome
The vesicle that develops after phagocytosis that contains the ingested particle.
phenotype
The behavior or appearance of a strain
photoautolithotroph or photoautotrophic lithotroph
A nutritional classification where the microbe gets its energy from light, its carbon from CO2 and its electrons from inorganic sources
photoheterolithotroph or photoheterotrophic lithotroph
A nutritional classification where the microbe gets its energy from light, its carbon from organic chemicals and its electrons from inorganic sources
photoheteroorganotroph or photoheterotrophic organotroph
A nutritional classification where the microbe gets its energy from light, its carbon from organic chemicals and its electrons from organic chemicals
photophosphorylation
A process of generating ATP that depends upon light.
photopigment
Photopigments are light-absorbing, unsaturated, small molecules involved in photosynthesis.
photopigments
Organic molecules produced by photosynthetic organisms that are used to absorb light and generate high-energy electrons during photosynthesis.
photorepair
A repair system that rep[airs certain forms of DNA damage caused by UV light and this requires the presence of light for its action.
phototaxis
Movement toward or away from light
phototroph
A phototroph uses light as its source of energy.
phylogenies
The evolutionary development and history of a groups organisms or a species
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pili
Proteinaceous rod-shaped, structures that protrude from the cell. Pili are used by microorganisms to attach surfaces and one method for exchanging DNA (conjugation).
pipettes
Hollow glass tubes with volume markings on them used to measure and dispense liquids. Pipettes come in sizes capable of measuring 0.1 to 25 ml.
plaque
Typically, a visible clearing in a lawn of bacteria caused by lysis by a phage, though the term can also be applies to a similar effect with certain eukaryotic cultures and their viruses.
plasma
The noncellular portion of the blood that contains the protein fibrinogen as a major constituent. Many other immune proteins are also found in plasma.
plasmid
A piece of DNA capable of autonomous replication in the cytoplasm.
point mutations
Any mutation that affects only a single base in the genome. This could be a base substitution or a frameshift mutation.
polarity
The property of a mutation that decreases the expression of genes that are downstream in the same operon. This might be because the mutation directly stops transcription by the introduction of a transcriptional termination signal or does so indirectly by creating a stop codon.
polycistronic mrna
The mRNA from a multi-gene operon.
polymerase chain reaction
An enzymatic reaction where temperature stable DNA polymerase, DNA primers, dNTPs and a DNA template are mixed together. A three step temperature cycle is used to denature, anneal primers to and then copy the DNA. The first step at near 95C causes the double stranded DNA template to denature. The second step at near 55C allows the primers to anneal to the DNA template. In the third step at 72C, DNA polymerase copies the template. This process is repeated from 25-50 times, resulting in a large amplification of the template DNA.
polymorphonuclear granulocytes
A general term given to neutrophils, eosinophils and basophils. The first half of the name describes the appearance of the nucleus that seems to be split into a number of different lobes. The rest of the name comes from the appearance of the cytoplasm, which looks speckled.
polynucleotide
Two or more nucleic acid monomers that are covalently linked.
polyphosphate granules
Granules observed in some cells that function as a phosphate reserve.
polysaccharides
Polymers of sugars
positive regulation
Any process that has the effect of increase the activity of something. Typically this is an increase in transcription of a region, but the term can also be applied to direct effects on a proteins activity.
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posttranslational regulatory system
Any regulatory mechanism that modulates the activity of an enzyme directly. This might be by covalent modification of that protein or through allostery.
pre-mutational lesion
See lesion.
preservatives
Static agents that are added to food and medical supplies to inhibit microbial growth and are safe to consume.
primary metabolites
Metabolites that are formed while a microbe is actively growing.
primary structure
The sequence of monomers in a polymer. Most often applied to the sequence of amino acids in a protein.
primer
An oligonucleotide of 10-20 bp that can serve as a primer for the replication of DNA. Typically this refers to replication in vitro, by PCR, for example.
prion
A normal protein that causes disease when it changes to an abnormal conformation.
probe
A short single stranded DNA used to detect the presence of a compatible DNA sequence in a solution.
promoters
DNA sequences that serve as sites of transcription initiation.
prostaglandins
A groups of hormone-like substances produced by the body that regulate a wide range of physiological functions, including blood pressure, contraction of smooth muscle and inflammation.
prosthetic groups
Covalently attached cofactors on enzymes. These include hemes, iron-sulfur centers and chlorophylls
protein
a polymer of amino acids. Many proteins are enzymes while others form structures in living things.
proteomics
The analysis of the range and amounts of the accumulated proteins in a cell. This information provides an insight into the metabolic actions of the cell at that time.
protists
Small unicellular eukaryotes that were of the kingdom Protista and included protozoa, algae and slime molds. Protista is part of an older classification system and is no longer used by most biologists, but the general name is still in the vernacular.
protoplasm
Similar to cytoplasm. The part of the cell inside the cell membrane, but not including any organelles
prototroph
A strain whose only organic requirement is for a carbon source.
protozoa
A large group of small unicellular eukaryotes that are ubiquitous in the environment.
provirus
An intermediate in the assembly of a virus in the cell.
psychrophiles
Microbes that grow best at temperatures below 15 °C.
psycrotrophs
Another name for psychrophiles
purines
A particular set of bi-cyclic organic compounds. Adenine and guanine are the biologically significant purines.
pycnidiospores
Male spores, analogous to pollen, that are produced by some fungi, especially rust. Contact with a receptive hyphae of a different mating type will result in fertilization and the creation of a dikaryotic fungus that will continue the life cycle.
pyrimidines
A particular set of unicyclic organic compounds with uracil, thymine and cytosine being of greatest biological significance.
pyrogenic
Fever inducing.
quarantine
The isolation of contagious individuals to prevent them from spreading the disease to others
quorum-sensing
A regulatory mechanism whereby microbes are capable of sensing their population and changing gene expression because of it. Quorum-sensing mechanisms are common in mutualistic and pathogenic microbes.
reaction intermediate
A structural conformation that is unstable and halfway between a substrate and a product in a reaction.
receptor
Any molecule, though typically a protein, that specifically binds another molecule. Often this is use as part of a sensing system by the cell, but the term is also used for the targets of pathogens on the surfaces of cells.
recombinant molecules
Any molecule that is created in vitro. Typically it refers to DNA molecules created through use of restriction enzymes or PCR.
recombination repair
A repair system in all cells that corrects may form of DNA damage by borrowing a strand of the same region from an unmutated copy in the cell and using that as a template to synthesize a normal region.
reduction
A reaction that results in the addition of electrons to a chemical. A reaction where hydrogens are added or oxygen is removed from a chemical.
regulons
To or more operons that are co-regulated at the level of gene expression, typically because they are regulated by the identical transcriptional factors.
release factors
Protein factors associated with the ribosome that recognize nonsense codons and react by terminating translation.
repair systems
Any mechanism by which lesions in DNA are repaired.
replication complexes
The complex of proteins that replicates DNA (or RNA, in the case of RNA viruses).
replication fork
The specific complex of protein and DNA that exists where the replication complex is actively opening the DNA duplex and synthesizing complementary strands.
replicative form
The form of a virus involves in replication. Typically this refers to the situation in normally single-stranded DNA or RNA viruses in which they form a double-stranded form as a substrate for replication.
replicon
Any piece of nucleic acid capable of replication in a cell.
reporter
A molecule that is used to indicate the level of something in the cell. The typical case is a transcriptional reporter whereby the gene for an easily assayed protein is placed under the control of a specific promoter. the level of activity of the assayable protein in the cell is therefore an indication of promoter activity.
repressor
A protein tat, under some conditions, binds a specific DNA sequence and prevents the initiation of transcription of an adjacent gene. The term can also be used for the rare cases of proteins that bind to mRNA and inhibit their translation.
restriction enzyme
A protein in prokaryotes that cuts specific DNA sequences, as a way of blocking the invasion of the cell by foreign DNA.
restriction-modification
The combination of a restriction enzyme that cuts certain DNA sequences and a modification enzyme that masks those sequences by covalent methylation. The latter event protects the cells own DNA from the effect of the restriction enzyme.
reversion
A mutational event in a mutant strain that restores its phenotype to one that is more like that of the wild type. This might involve the recreation of the wild-type genotype, or it might be by the creation of a suppressor mutation.
revertants
A strain that has undergone a reversion event.
ribosomal rna (rrna)
One of the three RNA the form the structure of the ribosome.
ribosome
The complex of RNA and protein that is the site of translation.
rich media
Medium that contains many different nutrients and normally will support the growth of a wide array of microbes.
saccharolytic
A term describing organisms that are capable of using sugars as their growth substrate.
sanitation
The treatment and disposal of sewage and waste with a major goal being the prevention of disease spread.
satellite viruses
Viruses that cannot replicate on their own but require the presence of another virus that provides critical functions.
schizont
A multinucleated large cell that grows in the liver and is one of the first cells types present during infections with Plasmodium species that cause malaria.
screens (enrichments)
The analysis of a population of cells for those with a particular phenotype or property. In this method, all cells in the population grow, but eh experimenter uses some method to find the desired cell type in that population.
secondary metabolites
Metabolites made after active growth had ceased.
secondary structure
The folding and twisting of local polymer sequences into higher order structures. Most often referred to when describing the structure of proteins and RNA.
selections
A manipulation of a population of cells so that only those with the desired phenotype survive.
selective media
Medium that contains compounds that favor the growth of desired microbes and inhibit the growth of undesirable microbes.
selfish dna
Any sequence of DNA that manages to increase the number of copies of itself in the hosts genome. Typically this refers to transposons, but is not inappropriate for viral DNA and many plasmids.
semi-conservative
The replication of only one strand of the DNA, as is the case in conjugation.
septum (pl. septa)
In prokaryotic cell division, the new wall in the cell whose synthesis leads to the separation of the two daughter cells. In fungi it also refers to the wall that divides cells in hyphae.
serum (pl. sera)
The leftover liquid when blood is allowed to clot. Immunoglobulins are a major constituent of serum.
shine-dalgarno sequence
In prokaryotes, this is a sequence in mRNA 5' of the start codon that is important in translation initiation. The sequence functions by forming base-pairs with a complementary sequence on the 16S rRNA.
siderophores
Small molecules that bind metal atoms, typically iron, with extremely high affinity. These are synthesized and secreted from cells and then taken up after iron is bound. The siderophore is then iron apart to liberate the iron.
sigma subunit
A protein tat associates with RNA polymerase only during the act of transcription initiation. Its roles is to identify the proper region at which transcription is to begin. There are at least different sigma subunits in any cell, and each has distinct sequence preferences, though there can be some overlap.
signal molecules
Any small molecule that is recognized by cells as an indication of an environmental situation that demands a response. These molecules might be produced by the cell themselves, by other cells or simply be small molecules in the environment.
signal sequences
Sequence in nucleic acid that serve as recognition sites for regulatory or catalytic proteins.
solfatara
Hot, sulfur rich environments commonly found in areas of volcanic activity that support the growth of many extreme thermophiles.
sos repair
A desperate response of bacterial cells to a region of DNA that cannot be read by DNA polymerase. The SOS response is a novel polymerase that simply adds random nucleotides to that region until a redabale section of template DNA is reached.
spontaneous generation
A theory, that was popular since antiquity, that living things could spontaneously emerge from inanimate objects given the right conditions. Experiments by Louis Pasteur and Francesco Redi were most convincing in invalidating this hypothesis.
sporangiophores
Arial hyphae produced by fungi of the Zygomycota that bear spores.
sporangium
A spore-containing structure that is enclosed by a cell wall.
spore
A resting cell made by many different types of microorganisms that allow them to survive harsh environmental conditions
spore coat
One layer of a spore that is located outside the spore cortex. Most often used in reference to endospores.
spore cortex
A protective layer in endospores between the spore coat and spore cell wall.
sporodium
A haploid spore produced by smuts. Smuts are fungi and are part of the Basidiomycota.
sporozoites
A cell type produced by protozoa of the Apicomplexa that function as a means to transmit the microbes between hosts
stationary phase
The part of the growth curve in batch after active growth has ceased, but cells are not dying.
sterilants
Disinfectants that are powerful enough to eliminate all forms of life in a defined area.
sterilization
The process of removal of all forms of life in a defined area.
stipe
The stalk that supports the cap of a mushroom
stop codons
A three-base sequence that is read in the normal translational reading frame and signals the termination of translation and the release of the nascent polypeptide. There are three stop codons in almost all cells and organelles: UAA, UAG and UGA.
strain development
Genetic approaches to modifying a strain to enhance a desirable property. For example, increasing antibiotic production in a strain.
strict aerobes
Organisms that require oxygen for their metabolism.
strict anaerobes
Microbes that can only grow in the absence of oxygen
substrate
The starting molecule that is modified in a chemical or enzymatic reaction.
substrate level phosphorylation (slp)
The production of ATP whereby the phosphate is obtained directly from the substrate and passed onto ATP
superantigen
An antigen that can stimulate a large number of T cells due to incorrect binding to conserved regions on MHC molecules and T cell receptors.
supercoiling
The winding or unwinding of the DNMA double helix compared to what it would be if the DNA was linear and therefore without tension. By convention, unwinding the helix is referred to as negative supercoiling and it is the typical form of most DNA in cells.
supernal
of exceptional quality or extent. This is how a glossary item looks. You can change the look of it in your books, by editing the javascript: wz_tooltip.js that comes with the package.
suppressors
Starting with a mutant strain that displays a mutant phenotype, any additional mutation that changes the phenotype to be like that of the wild-type strain is termed a suppressor (of the original mutation).
svedberg
Svedberg is a unit of measure that indicates the rate of sedimentation of a compound when spun at high speed in an ultracentrifuge. The higher the Svedberg unit is, the faster a molecule sediments. Sedimentation coefficients were a common property to determine before it was possible to easily determine the sequence of macromolecules.
symbiotic
A relationship between to organisms
systemic anaphylaxis
A potential allergic reaction where there is a system-wide reaction to an antigen and the release of large amounts of histamine by mast cells. Systemic anaphylaxis can be fatal if not dealt with quickly.
t cells
Lymphocytes that are involved in cell-mediated immunity and regulation of the immune system,
t lymphocytes
Also called T cells. Lymphocytes that are involved in cell-mediated immunity and regulation of the immune system,
tachyzoites
The repilcative for of the protozoan pathogen Toxoplasmosis gondii
tata box
A short sequence found in the promoter regions of eukaryotes.
teleomorph
A form of a fungus based upon a sexual state.
teliospores
Spores produced by rusts and smuts while in the dikaryotic state.
telomeres
The ends of linear replicons in prokaryotes and eukaryotes. These have a special and complex structure because the ends need to be replicated even though there is no DNA 5' of one strand, as is typically required by DNA polymerase.
temperature-sensitive (mutant phenotype)
A phenotype that appears more wild-type at one temperature and more mutant at another temperature. While the temperature that causes the mutant phenotype might be the higher or lower of the two, typically, this term is used when the phenotype appears mutant at the elevated temperature. The reverse is often termed cold-sensitive.
template
A piece of DNA that serves as a guide for making copies of itself.
terminal repeats
Sequences of DNA that are repeated at each end of transposons and insertion sequences. These are the regions recognized by the tranposase during transposition.
terminus of replication
The site on any circular replicon where replication ceases. Typically this is where the two replication forks, transcribing in different direction from the origin of replication, meet.
tertiary structure
The 3-dimensional structure of a single polypeptide or RNA molecule
thermoacidophiles
Microbes that have optimal growth in host acidic conditions
thermoacidophilic
Microbes that have their optimal growth under acidic conditions.
thermophiles
Microbes that have optimal growth rates at temperatures above 45°C
thymine
A pyrimidine base found only in DNA.
tight (mutant phenotype)
A tight mutant phenotype is one that is clearly distinct from the wild-type phenotype. A mutation with an indistinct mutant phenotype is termed leaky.
toxoid
An inactivated exotoxin that can still raise an immune response and is protective for the toxin.
trace elements
Nutrients required in very small amounts (<0.1%)
transcription initiation
The process by which RNA polymerase separates the strands of the DNA duplex and begins to make an RNA copy of one strand.
transcriptional termination signal
A sequence in the DNA that signals to a transcribing RNA polymerase that it should stop transcription and release the synthesized RNA.
transducing particles
The name for particles that look just like normal phage, but contain host DNA instead of viral DNA.
transduction
The process by which host DNA is moved from one cell to another by viruses. Typically this occurs in prokaryotes when a virus accidentally packages host DNA instead of its own and then injects that into another cell.
transfer rna(trna)
An RNA molecule of about 80 nucleotides that brings amino acids to the ribosome to be polymerized in the sequence defined by the mRNA. tRNA molecules have a complex structure with the anticodon at one end and the site of amino acid attachment at the other.
transformation
The process by which bare DNA is taken up by cells from the medium and retained. Some prokaryotes naturally perform this feat, while other need to be tricked into doing it by specific treatment of the cell.
transition-state complex
Another name for a reaction intermediate. A unstable structural conformation that is "halfway" between the substrates and the products in a reaction.
transport
The process of moving molecules across the cell membrane.
transposons
Bits of selfish DNA that move from place to place in the genomes of prokaryotes and eukaryotes. More formally, they are pieces of DNA the move by a transposition mechanism, which involves a bit of new DNA synthesis, and that carry genes unrelated to transposition.
triglycerides
One type of fat molecule where glycerol has three fatty acids attached to it by ester linkages.
trisaccharide
A polymer of sugar made up of three monomers.
trophozoite
A protozoan, especially of the class Sporozoa, in the active stage of its life cycle.
trypomastigotes
An active cell type observed in the life cycle of several Trypanosoma species
turbidity
The cloudiness of a solution. This is dependent upon the amount of light scattered by particles (typically bacteria) present in the solution.
two-component regulatory systems
A regulatory circuit that contains two components. A histidine kinase that senses an environmental signal and subsequently phosphorylates a response regulator. The response regulator then has its effect, often causing a change in gene expression.
tyndalization
An old method for the sterlization of medium. A liquid broth is boiled and cooled in succession, with the cooling interval being more that 3 hours. The first boiling eliminated most vegetative cells, while the second and third destroyed any endospores that may have germinated after the first boiling. This method has been superseeded in almost all modern laboratories by autoclaving.
type iii secretion and type iv secretion
Protein tubes that allow pathogens to penetrate host cells and pump toxins and other enzymes directly into them.
type iv pili
A class of pili produced by some microbes that have been found to be involved in motility among other functions.
type strain
The specific strain isolate that defines a given species. Essentially synonymous with the term "wild type."
vaccines
Antigens prepared from pathogens that can raise a protective immune response, yet do not cause illness
variable regions (fab)
The variable region of an antibody that reacts with antigen.
variolation
A practice popular before the introduction of the smallpox vaccine where the liquid from the pustules of a smallpox victim, were scratched on the skin of a healthy patient, causing mild disease and immunity to smallpox
vesicle
A membrane enclosed particle.
viable plate count.
An estimate of the total number of bacteria in a sample determined by diluting the sample and plating on appropriate solid growth medium.
villi
A minute projection from a mucous membrane, especially the numerous vacuolar projections of the small intestine.
virion
A complete viral particle
viroid
Short pieces of RNA that can replicate inside host cells. These are common in plants.
virulence
A measure of the ability of a microbe to cause disease
virulence factors
Proteins and other macromolecules made by microbe that make it able to cause disease.
virus
Particles capable of causing disease in animals, plants or bacteria that consist of nucleic acid enclosed in an outer shell made of protein, lipids or both.
viruses
Particles capable of causing disease in animals, plants or bacteria that consist of nucleic acid enclosed in an outer shell made of protein, lipids or both.
vitamins
Small organic molecules used in metabolism to catalyze reactions. These compounds are normally associated with enzymes and help them to carry out their necessary reactions.
water availability
A measurement of how much free water is available to carry out necessary reactions in a cell
wild type
When referring to an organism, it is the specific strain that was chosen as the reference strain for the species, typically the first isolate. The genotype and the phenotype of that strain are also referred to as the wild-type genotype and phenotype for the species.
wild-type
When referring to an organism, it is the specific strain that was chosen as the reference strain for the species, typically the first isolate. The genotype and the phenotype of that strain are also referred to as the wild-type genotype and phenotype for the species.
wobble hypothesis
There are fewer tRNAs in most organisms than there are codons, so Crick proposed that the interaction between bases at the third (3') position of the codon and the first (5') position of the anticodon on the tRNA followed different rules than the A-T and G-C base pairing in DNA. The suggestion was that a C in that position in the anticodon could "wobble" and pair with either a G or A in the third position of the codon, while a U in the same position could pair with either
xerophiles
Organisms that grow best in dry environments.
xylem
The vascular tissue in plants that conducts water and dissolved nutrients from the roots.
zoosporangium
A spore containing compartment found in Chytrids (a type of fungus)
zoospores
Spores that are motile by flagella. Produced by Oomycetes and Chytrids
zygospores
Spores produced by fungi of the Zygomycota
zygote
A diploid cell formed by the union of two gametes.
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