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.